Building Standards and Codes for Energy Conservation

Science.gov (United States)

Gross, James G.; Pierlert, James H.

1977-01-01

Current activity intended to lead to energy conservation measures in building codes and standards is reviewed by members of the Office of Building Standards and Codes Services of the National Bureau of Standards. For journal availability see HE 508 931. (LBH)

A Very Fast and Angular Momentum Conserving Tree Code

International Nuclear Information System (INIS)

Marcello, Dominic C.

2017-01-01

There are many methods used to compute the classical gravitational field in astrophysical simulation codes. With the exception of the typically impractical method of direct computation, none ensure conservation of angular momentum to machine precision. Under uniform time-stepping, the Cartesian fast multipole method of Dehnen (also known as the very fast tree code) conserves linear momentum to machine precision. We show that it is possible to modify this method in a way that conserves both angular and linear momenta.

A Very Fast and Angular Momentum Conserving Tree Code

Energy Technology Data Exchange (ETDEWEB)

Marcello, Dominic C., E-mail: dmarce504@gmail.com [Department of Physics and Astronomy, and Center for Computation and Technology Louisiana State University, Baton Rouge, LA 70803 (United States)

2017-09-01

There are many methods used to compute the classical gravitational field in astrophysical simulation codes. With the exception of the typically impractical method of direct computation, none ensure conservation of angular momentum to machine precision. Under uniform time-stepping, the Cartesian fast multipole method of Dehnen (also known as the very fast tree code) conserves linear momentum to machine precision. We show that it is possible to modify this method in a way that conserves both angular and linear momenta.

Non-coding RNA in Deinococcus radiodurans

International Nuclear Information System (INIS)

Chen Zhongzhong; Wang Liangyan; Lin Jun; Tian Bing; Hua Yuejin

2006-01-01

Researches on DNA damage and repair pathways of Deinococcus radiodurans show its extreme resistance to ionizing radiation, ultraviolet radiation and reactive oxygen species. Non-coding (ncRNA) RNAs are involved in a variety of processes such as transcriptional regulations, RNA processing and modification, mRNA translation, protein transportation and stability. The conserved secondary structures of intergenic regions of Deinococcus radiodurans R1 were predicted using Stochastic Context Free Grammar (SCFG) scan strategy. Results showed that 28 ncRNA families were present in the non-coding regions of the genome of Deinococcus radiodurans R1. Among these families, IRE is the largest family, followed by Histone3, tRNA, SECIS. DicF, ctRNA-pGA1 and tmRNA are one discovered in bacteria. Results from the comparison with other organisms showed that these ncRNA can be applied to the study of biological function of Deinococcus radiodurans and supply reference for the further study of DNA damage and repair mechanisms of this bacterium. (authors)

Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity

Directory of Open Access Journals (Sweden)

Ivaylo P. Ivanov

2017-06-01

Full Text Available Neurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs in its >700-nucleotide (nt 5′ leader, and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4, respectively, in controlling translation. We also found that the 5′ region upstream of the main coding sequence of the cpc-1 mRNA extends for more than 700 nucleotides without any in-frame stop codon. For 100 cpc-1 homologs from Pezizomycotina and from selected Basidiomycota, 5′ conserved extensions of the CPC1 reading frame are also observed. Multiple non-AUG near-cognate codons (NCCs in the CPC1 reading frame upstream of uORF2, some deeply conserved, could potentially initiate translation. At least four NCCs initiated translation in vitro. In vivo data were consistent with initiation at NCCs to produce N-terminally extended N. crassa CPC1 isoforms. The pivotal role played by CPC1, combined with its translational regulation by uORFs and NCC utilization, underscores the emerging significance of noncanonical initiation events in controlling gene expression.

Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT

Directory of Open Access Journals (Sweden)

Dominic eRose

2011-10-01

Full Text Available Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs. The evolutionary history of mlncRNAs is still largely uncharted territory.In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT, an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs. EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyse patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrat here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved and thermodynamic stable secondary structures.Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element.

Computational evidence for hundreds of non-conserved plant microRNAs

DEFF Research Database (Denmark)

Lindow, Morten; Krogh, Anders Stærmose

2005-01-01

Background MicroRNAs (miRNA) are small (20-25 nt) non-coding RNA molecules that regulate gene expression through interaction with mRNA in plants and metazoans. A few hundred miRNAs are known or predicted, and most of those are evolutionarily conserved. In general plant miRNA are different from...

Simulation of Plasma Disruptions for HL-2M with the DINA Code

International Nuclear Information System (INIS)

Xue Lei; Duan Xu-Ru; Zheng Guo-Yao; Yan Shi-Lei; Liu Yue-Qiang; Dokuka, V. V.; Khayrutdinov, R. R.; Lukash, V. E.

2015-01-01

Plasma disruption is often an unavoidable aspect of tokamak operations. It may cause severe damage to in-vessel components such as the vacuum vessel conductors, the first wall and the divertor target plates. Two types of disruption, the hot-plasma vertical displacement event and the major disruption with a cold-plasma vertical displacement event, are simulated by the DINA code for HL-2M. The time evolutions of the plasma current, the halo current, the magnetic axis, the minor radius, the elongation as well as the electromagnetic force and eddy currents on the vacuum vessel during the thermal quench and the current quench are investigated. By comparing the electromagnetic forces before and after the disruption, we find that the disruption causes great damage to the vacuum vessel conductors. In addition, the hot-plasma vertical displacement event is more dangerous than the major disruption with the cold-plasma vertical displacement event. (paper)

Parity-non-conserving nuclear forces

International Nuclear Information System (INIS)

Desplanques, B.

1979-01-01

Theoretical and phenomenological approaches to parity-non-conserving nuclear forces are reviewed. Recent developments in the calculation of weak meson-nucleon coupling constants, whose knowledge is necessary to determine theoretically the parity-non-conserving nucleon-nucleon potential, are described. The consistency of different measurements of parity-non-conserving effects is discussed and the information they provide is compared to theoretical predictions

Training program for energy conservation in new building construction. Volume III. Energy conservation technology for plan examiners and code administrators. Energy Conservation Technology Series 200

Energy Technology Data Exchange (ETDEWEB)

None

1977-12-01

Under the sponsorship of the United States Department of Energy, a Model Code for Energy Conservation in New Building Construction has been developed by those national organizations primarily concerned with the development and promulgation of model codes. The technical provisions are based on ASHRAE Standard 90-75 and are intended for use by state and local officials. The subject of regulation of new building construction to assure energy conservation is recognized as one in which code officials have not had previous exposure. It was also determined that application of the model code would be made at varying levels by officials with both a specific requirement for knowledge and a differing degree of prior training in the state-of-the-art. Therefore, a training program and instructional materials were developed for code officials to assist them in the implementation and enforcement of energy efficient standards and codes. The training program for Energy Conservation Tehnology for Plan Examiners and Code Administrators (ECT Series 200) is presented.

Non-Protein Coding RNAs

CERN Document Server

Walter, Nils G; Batey, Robert T

2009-01-01

This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and ot...

microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus

DEFF Research Database (Denmark)

Leucci, Eleonora; Patella, Francesca; Waage, Johannes

2013-01-01

-coding RNAs. Here we report that microRNA-9 (miR-9) regulates the expression of the Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT-1), one of the most abundant and conserved long non-coding RNAs. Intriguingly, we find that miR-9 targets AGO2-mediated regulation of MALAT1 in the nucleus. Our...

Transport and stability analyses supporting disruption prediction in high beta KSTAR plasmas

Science.gov (United States)

Ahn, J.-H.; Sabbagh, S. A.; Park, Y. S.; Berkery, J. W.; Jiang, Y.; Riquezes, J.; Lee, H. H.; Terzolo, L.; Scott, S. D.; Wang, Z.; Glasser, A. H.

2017-10-01

KSTAR plasmas have reached high stability parameters in dedicated experiments, with normalized beta βN exceeding 4.3 at relatively low plasma internal inductance li (βN/li>6). Transport and stability analyses have begun on these plasmas to best understand a disruption-free path toward the design target of βN = 5 while aiming to maximize the non-inductive fraction of these plasmas. Initial analysis using the TRANSP code indicates that the non-inductive current fraction in these plasmas has exceeded 50 percent. The advent of KSTAR kinetic equilibrium reconstructions now allows more accurate computation of the MHD stability of these plasmas. Attention is placed on code validation of mode stability using the PEST-3 and resistive DCON codes. Initial evaluation of these analyses for disruption prediction is made using the disruption event characterization and forecasting (DECAF) code. The present global mode kinetic stability model in DECAF developed for low aspect ratio plasmas is evaluated to determine modifications required for successful disruption prediction of KSTAR plasmas. Work supported by U.S. DoE under contract DE-SC0016614.

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish.

Science.gov (United States)

Chen, Wen; Zhang, Xuan; Li, Jing; Huang, Shulan; Xiang, Shuanglin; Hu, Xiang; Liu, Changning

2018-05-09

Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.

Continuous Non-malleable Codes

DEFF Research Database (Denmark)

Faust, Sebastian; Mukherjee, Pratyay; Nielsen, Jesper Buus

2014-01-01

or modify it to the encoding of a completely unrelated value. This paper introduces an extension of the standard non-malleability security notion - so-called continuous non-malleability - where we allow the adversary to tamper continuously with an encoding. This is in contrast to the standard notion of non...... is necessary to achieve continuous non-malleability in the split-state model. Moreover, we illustrate that none of the existing constructions satisfies our uniqueness property and hence is not secure in the continuous setting. We construct a split-state code satisfying continuous non-malleability. Our scheme...... is based on the inner product function, collision-resistant hashing and non-interactive zero-knowledge proofs of knowledge and requires an untamperable common reference string. We apply continuous non-malleable codes to protect arbitrary cryptographic primitives against tampering attacks. Previous...

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

DEFF Research Database (Denmark)

Lindgreen, Stinus; Gardner, Paul P; Krogh, Anders

2007-01-01

function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. AVAILABILITY: Source code available from http://mastr.binf.ku.dk/......MOTIVATION: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore......, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. RESULT: We present a novel solution to the problem of simultaneous structure prediction...

Non-binary Entanglement-assisted Stabilizer Quantum Codes

OpenAIRE

Riguang, Leng; Zhi, Ma

2011-01-01

In this paper, we show how to construct non-binary entanglement-assisted stabilizer quantum codes by using pre-shared entanglement between the sender and receiver. We also give an algorithm to determine the circuit for non-binary entanglement-assisted stabilizer quantum codes and some illustrated examples. The codes we constructed do not require the dual-containing constraint, and many non-binary classical codes, like non-binary LDPC codes, which do not satisfy the condition, can be used to c...

Applicability evaluation on the conservative metal-water reaction(MWR) model implemented into the SPACE code

International Nuclear Information System (INIS)

Lee, Suk Ho; You, Sung Chang; Kim, Han Gon

2011-01-01

The SBLOCA (Small Break Loss-of-Coolant Accident) evaluation methodology for the APR1400 (Advanced Power Reactor 1400) is under development using the SPACE code. The goal of the development of this methodology is to set up a conservative evaluation methodology in accordance with Appendix K of 10CFR50 by the end of 2012. In order to develop the Appendix K version of the SPACE code, the code modification is considered through implementation of the code on the required evaluation models. For the conservative models required in the SPACE code, the metal-water reaction (MWR) model, the critical flow model, the Critical Heat Flux (CHF) model and the post-CHF model must be implemented in the code. At present, the integration of the model to generate the Appendix K version of SPACE is in its preliminary stage. Among them, the conservative MWR model and its code applicability are introduced in this paper

Parity non-conservation in atoms

International Nuclear Information System (INIS)

Barkov, L.M.

1982-01-01

The parity non-conservation discovered in particle physics in 1959 has consequences on the behaviour of atoms illuminated by light of circular polarization. The theoretical treatments of this topic and recent experimental test of detecting the effects of parity non-conservation on atomic physics are listed, reviewed and illustrated. The main experimental results and limits are summarized. Proposed future experiments are discussed. (D.Gy.)

Long non-coding RNA expression profiling of mouse testis during postnatal development.

Directory of Open Access Journals (Sweden)

Jin Sun

Full Text Available Mammalian testis development and spermatogenesis play critical roles in male fertility and continuation of a species. Previous research into the molecular mechanisms of testis development and spermatogenesis has largely focused on the role of protein-coding genes and small non-coding RNAs, such as microRNAs and piRNAs. Recently, it has become apparent that large numbers of long (>200 nt non-coding RNAs (lncRNAs are transcribed from mammalian genomes and that lncRNAs perform important regulatory functions in various developmental processes. However, the expression of lncRNAs and their biological functions in post-natal testis development remain unknown. In this study, we employed microarray technology to examine lncRNA expression profiles of neonatal (6-day-old and adult (8-week-old mouse testes. We found that 8,265 lncRNAs were expressed above background levels during post-natal testis development, of which 3,025 were differentially expressed. Candidate lncRNAs were identified for further characterization by an integrated examination of genomic context, gene ontology (GO enrichment of their associated protein-coding genes, promoter analysis for epigenetic modification, and evolutionary conservation of elements. Many lncRNAs overlapped or were adjacent to key transcription factors and other genes involved in spermatogenesis, such as Ovol1, Ovol2, Lhx1, Sox3, Sox9, Plzf, c-Kit, Wt1, Sycp2, Prm1 and Prm2. Most differentially expressed lncRNAs exhibited epigenetic modification marks similar to protein-coding genes and tend to be expressed in a tissue-specific manner. In addition, the majority of differentially expressed lncRNAs harbored evolutionary conserved elements. Taken together, our findings represent the first systematic investigation of lncRNA expression in the mammalian testis and provide a solid foundation for further research into the molecular mechanisms of lncRNAs function in mammalian testis development and spermatogenesis.

The origins and evolutionary history of human non-coding RNA regulatory networks.

Science.gov (United States)

Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.

Science.gov (United States)

Bajaj, Deepak; Saxena, Maneesha S; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

2015-03-01

Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Improvements to Busquet's Non LTE algorithm in NRL's Hydro code

Science.gov (United States)

Klapisch, M.; Colombant, D.

1996-11-01

Implementation of the Non LTE model RADIOM (M. Busquet, Phys. Fluids B, 5, 4191 (1993)) in NRL's RAD2D Hydro code in conservative form was reported previously(M. Klapisch et al., Bull. Am. Phys. Soc., 40, 1806 (1995)).While the results were satisfactory, the algorithm was slow and not always converging. We describe here modifications that address the latter two shortcomings. This method is quicker and more stable than the original. It also gives information about the validity of the fitting. It turns out that the number and distribution of groups in the multigroup diffusion opacity tables - a basis for the computation of radiation effects in the ionization balance in RADIOM- has a large influence on the robustness of the algorithm. These modifications give insight about the algorithm, and allow to check that the obtained average charge state is the true average. In addition, code optimization resulted in greatly reduced computing time: The ratio of Non LTE to LTE computing times being now between 1.5 and 2.

Analysis of Non-binary Hybrid LDPC Codes

OpenAIRE

Sassatelli, Lucile; Declercq, David

2008-01-01

In this paper, we analyse asymptotically a new class of LDPC codes called Non-binary Hybrid LDPC codes, which has been recently introduced. We use density evolution techniques to derive a stability condition for hybrid LDPC codes, and prove their threshold behavior. We study this stability condition to conclude on asymptotic advantages of hybrid LDPC codes compared to their non-hybrid counterparts.

Non-Coding RNAs in Hodgkin Lymphoma

Directory of Open Access Journals (Sweden)

Anna Cordeiro

2017-05-01

Full Text Available MicroRNAs (miRNAs, small non-coding RNAs that regulate gene expression by binding to the 3’-UTR of their target genes, can act as oncogenes or tumor suppressors. Recently, other types of non-coding RNAs—piwiRNAs and long non-coding RNAs—have also been identified. Hodgkin lymphoma (HL is a B cell origin disease characterized by the presence of only 1% of tumor cells, known as Hodgkin and Reed-Stenberg (HRS cells, which interact with the microenvironment to evade apoptosis. Several studies have reported specific miRNA signatures that can differentiate HL lymph nodes from reactive lymph nodes, identify histologic groups within classical HL, and distinguish HRS cells from germinal center B cells. Moreover, some signatures are associated with survival or response to chemotherapy. Most of the miRNAs in the signatures regulate genes related to apoptosis, cell cycle arrest, or signaling pathways. Here we review findings on miRNAs in HL, as well as on other non-coding RNAs.

Conservation and non-conservation in general relativity

International Nuclear Information System (INIS)

Bondi, H.

1990-01-01

The difficulties of conservation laws in general relativity are discussed, with special reference to the non-tangible nature of gravitational energy and its transformation into tangible forms of energy. Inductive transfer of energy is marked out as wholly distinct from wave transfer. Slow (adiabatic) changes are utilized to make clear, in the axi-symmetric case, that the mass of an isolated body is conserved irrespective of any local changes (e.g. of shape) and that in inductive transfer the movement of energy between two bodies can readily be traced by the changes in their masses. (author)

Development of Multi-Dimensional RELAP5 with Conservative Momentum Flux

Energy Technology Data Exchange (ETDEWEB)

Jang, Hyung Wook; Lee, Sang Yong [KINGS, Ulsan (Korea, Republic of)

2016-10-15

The non-conservative form of the momentum equations are used in many codes. It tells us that using the non-conservative form in the non-porous or open body problem may not be good. In this paper, two aspects concerning the multi-dimensional codes will be discussed. Once the validity of the modified code is confirmed, it is applied to the analysis of the large break LOCA for APR-1400. One of them is the properness of the type of the momentum equations. The other discussion will be the implementation of the conservative momentum flux term in RELAP5. From the present study and former, it is shown that the RELAP5 Multi-D with conservative convective terms is applicable to LOCA analysis. And the implementation of the conservative convective terms in RELAP5 seems to be successful. Further efforts have to be made on making it more robust.

Energy conservation: policy issues and end-use scenarios of savings potential. Part V. Energy efficient buildings: the causes of litigation against energy conservation building codes

Energy Technology Data Exchange (ETDEWEB)

Benenson, P.; Codina, R.; Cornwall, B.

1978-09-01

The guidelines laid out for the five subjects investigated in this series are to take a holistic view of energy conservation policies by describing the overall system in which they are implemented; provide analytical tools and sufficiently disagregated data bases that can be adapted to answer a variety of questions by the users; identify and discuss some of the important issues behind successful energy conservation policy; and develop an energy conservation policy in depth. Three specific cases reviewed are: the California nonresidential code (1976); the California residential code (1978); and the Farmers Home Administration code (1978). Although these three suits were brought by the building industry, this report also discusses considerations relevant to architects, bankers, and building inspectors. These cases are discussed from three perspectives: (1) objections to the codes explicitly stated in court, (2) industry conditions and practices behind objections stated in court, and (3) general beliefs not stated in court. This discussion focuses on suits intended to limit those building codes which the building industry sees as too strong. However, some energy conservation industries may sue to strengthen codes which they consider too weak. An example of such a case is Polarized Corporation's current suit against the Lighting section of ASHRAE 90-75 (Los Angeles Federal District Court, see Murnane, 1978). (MCW)

SIMMER-III code-verification. Phase 1

International Nuclear Information System (INIS)

Maschek, W.

1996-05-01

SIMMER-III is a computer code to investigate core disruptive accidents in liquid metal fast reactors but should also be used to investigate safety related problems in other types of advanced reactors. The code is developed by PNC with cooperation of the European partners FZK, CEA and AEA-T. SIMMER-III is a two-dimensional, three-velocity-field, multiphase, multicomponent, Eulerian, fluid-dynamics code coupled with a space-, time-, and energy-dependent neutron dynamics model. In order to model complex flow situations in a postulated disrupting core, mass and energy conservation equations are solved for 27 density components and 16 energy components, respectively. Three velocity fields (two liquid and one vapor) are modeled to simulate the relative motion of different fluid components. An additional static field takes into account the structures available in a reactor (pins, hexans, vessel structures, internal structures etc.). The neutronics is based on the discrete ordinate method (S N method) coupled into a quasistatic dynamic model. The code assessment and verification of the fluid dynamic/thermohydraulic parts of the code is performed in several steps in a joint effort of all partners. The results of the FZK contributions to the first assessment and verification phase is reported. (orig.) [de

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence.

Science.gov (United States)

Benko, Sabina; Fantes, Judy A; Amiel, Jeanne; Kleinjan, Dirk-Jan; Thomas, Sophie; Ramsay, Jacqueline; Jamshidi, Negar; Essafi, Abdelkader; Heaney, Simon; Gordon, Christopher T; McBride, David; Golzio, Christelle; Fisher, Malcolm; Perry, Paul; Abadie, Véronique; Ayuso, Carmen; Holder-Espinasse, Muriel; Kilpatrick, Nicky; Lees, Melissa M; Picard, Arnaud; Temple, I Karen; Thomas, Paul; Vazquez, Marie-Paule; Vekemans, Michel; Roest Crollius, Hugues; Hastie, Nicholas D; Munnich, Arnold; Etchevers, Heather C; Pelet, Anna; Farlie, Peter G; Fitzpatrick, David R; Lyonnet, Stanislas

2009-03-01

Pierre Robin sequence (PRS) is an important subgroup of cleft palate. We report several lines of evidence for the existence of a 17q24 locus underlying PRS, including linkage analysis results, a clustering of translocation breakpoints 1.06-1.23 Mb upstream of SOX9, and microdeletions both approximately 1.5 Mb centromeric and approximately 1.5 Mb telomeric of SOX9. We have also identified a heterozygous point mutation in an evolutionarily conserved region of DNA with in vitro and in vivo features of a developmental enhancer. This enhancer is centromeric to the breakpoint cluster and maps within one of the microdeletion regions. The mutation abrogates the in vitro enhancer function and alters binding of the transcription factor MSX1 as compared to the wild-type sequence. In the developing mouse mandible, the 3-Mb region bounded by the microdeletions shows a regionally specific chromatin decompaction in cells expressing Sox9. Some cases of PRS may thus result from developmental misexpression of SOX9 due to disruption of very-long-range cis-regulatory elements.

Linkage disequilibrium of evolutionarily conserved regions in the human genome

Directory of Open Access Journals (Sweden)

Johnson Todd A

2006-12-01

Full Text Available Abstract Background The strong linkage disequilibrium (LD recently found in genic or exonic regions of the human genome demonstrated that LD can be increased by evolutionary mechanisms that select for functionally important loci. This suggests that LD might be stronger in regions conserved among species than in non-conserved regions, since regions exposed to natural selection tend to be conserved. To assess this hypothesis, we used genome-wide polymorphism data from the HapMap project and investigated LD within DNA sequences conserved between the human and mouse genomes. Results Unexpectedly, we observed that LD was significantly weaker in conserved regions than in non-conserved regions. To investigate why, we examined sequence features that may distort the relationship between LD and conserved regions. We found that interspersed repeats, and not other sequence features, were associated with the weak LD tendency in conserved regions. To appropriately understand the relationship between LD and conserved regions, we removed the effect of repetitive elements and found that the high degree of sequence conservation was strongly associated with strong LD in coding regions but not with that in non-coding regions. Conclusion Our work demonstrates that the degree of sequence conservation does not simply increase LD as predicted by the hypothesis. Rather, it implies that purifying selection changes the polymorphic patterns of coding sequences but has little influence on the patterns of functional units such as regulatory elements present in non-coding regions, since the former are generally restricted by the constraint of maintaining a functional protein product across multiple exons while the latter may exist more as individually isolated units.

Non-coding RNAs enter mitosis: functions, conservation and implications

OpenAIRE

Pek, Jun Wei; Kai, Toshie

2011-01-01

Abstract Nuage (or commonly known as chromatoid body in mammals) is a conserved germline-specific organelle that has been linked to the Piwi-interacting RNA (piRNA) pathway. piRNAs are a class of gonadal-specific RNAs that are ~23-29 nucleotides in length and protect genome stability by repressing the expression of deleterious retrotransposons. More recent studies in Drosophila have implicated the piRNA pathway in other functions including canalization of embryonic development, regulation of ...

Indirect Effects of Functional Communication Training on Non-Targeted Disruptive Behavior

Science.gov (United States)

Schieltz, Kelly M.; Wacker, David P.; Harding, Jay W.; Berg, Wendy K.; Lee, John F.; Padilla Dalmau, Yaniz C.; Mews, Jayme; Ibrahimovic, Muska

2011-01-01

The purpose of this study was to evaluate the effects of functional communication training (FCT) on the occurrence of non-targeted disruptive behavior. The 10 participants were preschool-aged children with developmental disabilities who engaged in both destructive (property destruction, aggression, self-injury) and disruptive (hand flapping,…

Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs.

Directory of Open Access Journals (Sweden)

Chen Xie

2012-09-01

Full Text Available Tinkering with pre-existing genes has long been known as a major way to create new genes. Recently, however, motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs. How these genes originated is not well addressed to date. Here we identified 24 hominoid-specific de novo protein-coding genes with precise origination timing in vertebrate phylogeny. Strand-specific RNA-Seq analyses were performed in five rhesus macaque tissues (liver, prefrontal cortex, skeletal muscle, adipose, and testis, which were then integrated with public transcriptome data from human, chimpanzee, and rhesus macaque. On the basis of comparing the RNA expression profiles in the three species, we found that most of the hominoid-specific de novo protein-coding genes encoded polyadenylated non-coding RNAs in rhesus macaque or chimpanzee with a similar transcript structure and correlated tissue expression profile. According to the rule of parsimony, the majority of these hominoid-specific de novo protein-coding genes appear to have acquired a regulated transcript structure and expression profile before acquiring coding potential. Interestingly, although the expression profile was largely correlated, the coding genes in human often showed higher transcriptional abundance than their non-coding counterparts in rhesus macaque. The major findings we report in this manuscript are robust and insensitive to the parameters used in the identification and analysis of de novo genes. Our results suggest that at least a portion of long non-coding RNAs, especially those with active and regulated transcription, may serve as a birth pool for protein-coding genes, which are then further optimized at the transcriptional level.

Function and Application Areas in Medicine of Non-Coding RNA

Directory of Open Access Journals (Sweden)

Figen Guzelgul

2009-06-01

Full Text Available RNA is the genetic material converting the genetic code that it gets from DNA into protein. While less than 2 % of RNA is converted into protein , more than 98 % of it can not be converted into protein and named as non-coding RNAs. 70 % of noncoding RNAs consists of introns , however, the rest part of them consists of exons. Non-coding RNAs are examined in two classes according to their size and functions. Whereas they are classified as long non-coding and small non-coding RNAs according to their size , they are grouped as housekeeping non-coding RNAs and regulating non-coding RNAs according to their function. For long years ,these non-coding RNAs have been considered as non-functional. However, today, it has been proved that these non-coding RNAs play role in regulating genes and in structural, functional and catalitic roles of RNAs converted into protein. Due to its taking a role in gene silencing mechanism, particularly in medical world , non-coding RNAs have led to significant developments. RNAi technolgy , which is used in designing drugs to be used in treatment of various diseases , is a ray of hope for medical world. [Archives Medical Review Journal 2009; 18(3.000: 141-155

Comprehensive safety analysis code system for nuclear fusion reactors II: Thermal analysis during plasma disruptions for international thermonuclear experimental reactor

International Nuclear Information System (INIS)

Honda, T.; Maki, K.; Okazaki, T.

1994-01-01

Thermal characteristics of a fusion reactor [International Thermonuclear Experimental Reactor (ITER) Conceptual Design Activity] during plasma disruptions have been analyzed by using a comprehensive safety analysis code for nuclear fusion reactors. The erosion depth due to disruptions for the armor of the first wall depends on the current quench time of disruptions occurring in normal operation. If it is possible to extend the time up to ∼50 ms, the erosion depth is considerably reduced. On the other hand, the erosion depth of the divertor is ∼570 μm for only one disruption, which is determined only by the thermal flux during the thermal quench. This means that the divertor plate should be exchanged after about nine disruptions. Counter-measures are necessary for the divertor to relieve disruption influences. As other scenarios of disruptions, beta-limit disruptions and vertical displacement events were also investigated quantitatively. 13 refs., 5 figs

Annotating pathogenic non-coding variants in genic regions.

Science.gov (United States)

Gelfman, Sahar; Wang, Quanli; McSweeney, K Melodi; Ren, Zhong; La Carpia, Francesca; Halvorsen, Matt; Schoch, Kelly; Ratzon, Fanni; Heinzen, Erin L; Boland, Michael J; Petrovski, Slavé; Goldstein, David B

2017-08-09

Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants. TraP accurately distinguishes known pathogenic and benign variants in synonymous (AUC = 0.88) and intronic (AUC = 0.83) public datasets, dismissing benign variants with exceptionally high specificity. TraP analysis of 843 exomes from epilepsy family trios identifies synonymous variants in known epilepsy genes, thus pinpointing risk factors of disease from non-coding sequence data. TraP outperforms leading methods in identifying non-coding variants that are pathogenic and is therefore a valuable tool for use in gene discovery and the interpretation of personal genomes.While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

Numerical solution of conservation equations in the transient model for the system thermal - hydraulics in the Korsar computer code

International Nuclear Information System (INIS)

Yudov, Y.V.

2001-01-01

The functional part of the KORSAR computer code is based on the computational unit for the reactor system thermal-hydraulics and other thermal power systems with water cooling. The two-phase flow dynamics of the thermal-hydraulic network is modelled by KORSAR in one-dimensional two-fluid (non-equilibrium and nonhomogeneous) approximation with the same pressure of both phases. Each phase is characterized by parameters averaged over the channel sections, and described by the conservation equations for mass, energy and momentum. The KORSAR computer code relies upon a novel approach to mathematical modelling of two-phase dispersed-annular flows. This approach allows a two-fluid model to differentiate the effects of the liquid film and droplets in the gas core on the flow characteristics. A semi-implicit numerical scheme has been chosen for deriving discrete analogs the conservation equations in KORSAR. In the semi-implicit numerical scheme, solution of finite-difference equations is reduced to the problem of determining the pressure field at a new time level. For the one-channel case, the pressure field is found from the solution of a system of linear algebraic equations by using the tri-diagonal matrix method. In the branched network calculation, the matrix of coefficients in the equations describing the pressure field is no longer tri-diagonal but has a sparseness structure. In this case, the system of linear equations for the pressure field can be solved with any of the known classical methods. Such an approach is implemented in the existing best-estimate thermal-hydraulic computer codes (TRAC, RELAP5, etc.) For the KORSAR computer code, we have developed a new non-iterative method for calculating the pressure field in the network of any topology. This method is based on the tri-diagonal matrix method and performs well when solving the thermal-hydraulic network problems. (author)

Functional long non-coding RNA transcription in Schizosaccharomyces pombe

OpenAIRE

Ard, Ryan Anthony

2016-01-01

Eukaryotic genomes are pervasively transcribed and frequently generate long noncoding RNAs (lncRNAs). However, most lncRNAs remain uncharacterized. In this work, a set of positionally conserved intergenic lncRNAs in the fission yeast Schizosaccharomyces pombe genome are selected for further analysis. Deleting one of these lncRNA genes (ncRNA.1343) exhibited a clear phenotype: increased drug sensitivity. Further analyses revealed that deleting ncRNA.1343 also disrupted a prev...

Guide to the Changes between the 2009 and 2012 International Energy Conservation Code

Energy Technology Data Exchange (ETDEWEB)

Mapes, Terry S.; Conover, David R.

2012-05-31

The International Code Council (ICC) published the 2012 International Energy Conservation Code{reg_sign} (IECC) in early 2012. The 2012 IECC is based on revisions, additions, and deletions to the 2009 IECC that were considered during the ICC code development process conducted in 2011. Solid vertical lines, arrows, or asterisks printed in the 2012 IECC indicate where revisions, deletions, or relocations of text respectively were made to 2009 IECC. Although these marginal markings indicate where changes have been made to the code, they do not provide any further guidance, leaving the reader to consult and compare the 2009 and 2012 IECC for more detail.

On Coding Non-Contiguous Letter Combinations

Directory of Open Access Journals (Sweden)

Frédéric eDandurand

2011-06-01

Full Text Available Starting from the hypothesis that printed word identification initially involves the parallel mapping of visual features onto location-specific letter identities, we analyze the type of information that would be involved in optimally mapping this location-specific orthographic code onto a location-invariant lexical code. We assume that some intermediate level of coding exists between individual letters and whole words, and that this involves the representation of letter combinations. We then investigate the nature of this intermediate level of coding given the constraints of optimality. This intermediate level of coding is expected to compress data while retaining as much information as possible about word identity. Information conveyed by letters is a function of how much they constrain word identity and how visible they are. Optimization of this coding is a combination of minimizing resources (using the most compact representations and maximizing information. We show that in a large proportion of cases, non-contiguous letter sequences contain more information than contiguous sequences, while at the same time requiring less precise coding. Moreover, we found that the best predictor of human performance in orthographic priming experiments was within-word ranking of conditional probabilities, rather than average conditional probabilities. We conclude that from an optimality perspective, readers learn to select certain contiguous and non-contiguous letter combinations as information that provides the best cue to word identity.

Constraints of a parity-conserving/time-reversal-non-conserving interaction

International Nuclear Information System (INIS)

Oers, Willem T.H. van

2002-01-01

Time-Reversal-Invariance non-conservation has for the first time been unequivocally demonstrated in a direct measurement at CPLEAR. One then can ask the question: What about tests of time-reversal-invariance in systems other than the kaon system? Tests of time-reversal-invariance can be distinguished as belonging to two classes: the first one deals with time-reversal-invariance-non-conserving (T-odd)/parity violating (P-odd) interactions, while the second one deals with T-odd/P-even interactions (assuming CPT conservation this implies C-conjugation non-conservation). Limits on a T-odd/P-odd interaction follow from measurements of the electric dipole moment of the neutron ( -26 e.cm [95% C.L.]). It provides a limit on a T-odd/P-odd pion-nucleon coupling constant which is less than 10 -4 times the weak interaction strength. Experimental limits on a T-odd/P-even interaction are much less stringent. Following the standard approach of describing the nucleon-nucleon interaction in terms of meson exchanges, it can be shown that only charged ρ-meson exchange and A 1 -meson exchange can lead to a T-odd/P-even interaction. The better constraints stem from measurements of the electric dipole moment of the neutron and from measurements of charge-symmetry breaking in neutron-proton elastic scattering. The latter experiments were executed at TRIUMF (497 and 347 MeV) and at IUCF (183 MeV). All other experiments, like detailed balance experiments, polarization - analyzing power difference determinations, and five-fold correlation experiments with polarized incident nucleons and aligned nuclear targets, have been shown to be at least an order to magnitude less sensitive. Is there room for further experimentation?

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

Science.gov (United States)

Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Calixto, Edmundo P da R; Motta, Mariana R; Ballesteros, Helkin G F; Peixoto, Barbara; de Lima, Berenice N S; Vieira, Lucas M; Walter, Maria Emilia; de Armas, Elvismary M; Entenza, Júlio O P; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

2017-12-20

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae . Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae , while the siRNAs were repressed in the presence of A. avenae . Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408-a copper-microRNA-was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5'RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

Science.gov (United States)

Grativol, Clícia; Motta, Mariana R.; Ballesteros, Helkin G. F.; Peixoto, Barbara; Vieira, Lucas M.; Walter, Maria Emilia; de Armas, Elvismary M.; Entenza, Júlio O. P.; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S.

2017-01-01

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly. PMID:29657296

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

Directory of Open Access Journals (Sweden)

Flávia Thiebaut

2017-12-01

Full Text Available Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR. Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

Non-binary Hybrid LDPC Codes: Structure, Decoding and Optimization

OpenAIRE

Sassatelli, Lucile; Declercq, David

2007-01-01

In this paper, we propose to study and optimize a very general class of LDPC codes whose variable nodes belong to finite sets with different orders. We named this class of codes Hybrid LDPC codes. Although efficient optimization techniques exist for binary LDPC codes and more recently for non-binary LDPC codes, they both exhibit drawbacks due to different reasons. Our goal is to capitalize on the advantages of both families by building codes with binary (or small finite set order) and non-bin...

Metformin-Induced Changes of the Coding Transcriptome and Non-Coding RNAs in the Livers of Non-Alcoholic Fatty Liver Disease Mice.

Science.gov (United States)

Guo, Jun; Zhou, Yuan; Cheng, Yafen; Fang, Weiwei; Hu, Gang; Wei, Jie; Lin, Yajun; Man, Yong; Guo, Lixin; Sun, Mingxiao; Cui, Qinghua; Li, Jian

2018-01-01

Recent studies have suggested that changes in non-coding mRNA play a key role in the progression of non-alcoholic fatty liver disease (NAFLD). Metformin is now recommended and effective for the treatment of NAFLD. We hope the current analyses of the non-coding mRNA transcriptome will provide a better presentation of the potential roles of mRNAs and long non-coding RNAs (lncRNAs) that underlie NAFLD and metformin intervention. The present study mainly analysed changes in the coding transcriptome and non-coding RNAs after the application of a five-week metformin intervention. Liver samples from three groups of mice were harvested for transcriptome profiling, which covered mRNA, lncRNA, microRNA (miRNA) and circular RNA (circRNA), using a microarray technique. A systematic alleviation of high-fat diet (HFD)-induced transcriptome alterations by metformin was observed. The metformin treatment largely reversed the correlations with diabetes-related pathways. Our analysis also suggested interaction networks between differentially expressed lncRNAs and known hepatic disease genes and interactions between circRNA and their disease-related miRNA partners. Eight HFD-responsive lncRNAs and three metformin-responsive lncRNAs were noted due to their widespread associations with disease genes. Moreover, seven miRNAs that interacted with multiple differentially expressed circRNAs were highlighted because they were likely to be associated with metabolic or liver diseases. The present study identified novel changes in the coding transcriptome and non-coding RNAs in the livers of NAFLD mice after metformin treatment that might shed light on the underlying mechanism by which metformin impedes the progression of NAFLD. © 2018 The Author(s). Published by S. Karger AG, Basel.

Non-Binary Protograph-Based LDPC Codes: Analysis,Enumerators and Designs

OpenAIRE

Sun, Yizeng

2013-01-01

Non-binary LDPC codes can outperform binary LDPC codes using sum-product algorithm with higher computation complexity. Non-binary LDPC codes based on protographs have the advantage of simple hardware architecture. In the first part of this thesis, we will use EXIT chart analysis to compute the thresholds of different protographs over GF(q). Based on threshold computation, some non-binary protograph-based LDPC codes are designed and their frame error rates are compared with binary LDPC codes. ...

Long non-coding RNAs: Mechanism of action and functional utility

OpenAIRE

Bhat, Shakil Ahmad; Ahmad, Syed Mudasir; Mumtaz, Peerzada Tajamul; Malik, Abrar Ahad; Dar, Mashooq Ahmad; Urwat, Uneeb; Shah, Riaz Ahmad; Ganai, Nazir Ahmad

2016-01-01

Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological ...

NALAP: an LMFBR system transient code

International Nuclear Information System (INIS)

Martin, B.A.; Agrawal, A.K.; Albright, D.C.; Epel, L.G.; Maise, G.

1975-07-01

NALAP is a LMFBR system transient code. This code, adapted from the light water reactor transient code RELAP 3B, simulates thermal-hydraulic response of sodium cooled fast breeder reactors when subjected to postulated accidents such as a massive pipe break as well as a variety of other upset conditions that do not disrupt the system geometry. Various components of the plant are represented by control volumes. These control volumes are connected by junctions some of which may be leak or fill junctions. The fluid flow equations are modeled as compressible, single-stream flow with momentum flux in one dimension. The transient response is computed by integrating the thermal-hydraulic conservation equations from user-initialized operating conditions by an implicit numerical scheme. Point kinetics approximation is used to represent the time dependent heat generation in the reactor core

Bistability in self-activating genes regulated by non-coding RNAs

International Nuclear Information System (INIS)

Miro-Bueno, Jesus

2015-01-01

Non-coding RNA molecules are able to regulate gene expression and play an essential role in cells. On the other hand, bistability is an important behaviour of genetic networks. Here, we propose and study an ODE model in order to show how non-coding RNA can produce bistability in a simple way. The model comprises a single gene with positive feedback that is repressed by non-coding RNA molecules. We show how the values of all the reaction rates involved in the model are able to control the transitions between the high and low states. This new model can be interesting to clarify the role of non-coding RNA molecules in genetic networks. As well, these results can be interesting in synthetic biology for developing new genetic memories and biomolecular devices based on non-coding RNAs

Weight Distribution for Non-binary Cluster LDPC Code Ensemble

Science.gov (United States)

Nozaki, Takayuki; Maehara, Masaki; Kasai, Kenta; Sakaniwa, Kohichi

In this paper, we derive the average weight distributions for the irregular non-binary cluster low-density parity-check (LDPC) code ensembles. Moreover, we give the exponential growth rate of the average weight distribution in the limit of large code length. We show that there exist $(2,d_c)$-regular non-binary cluster LDPC code ensembles whose normalized typical minimum distances are strictly positive.

Short-lived non-coding transcripts (SLiTs): Clues to regulatory long non-coding RNA.

Science.gov (United States)

Tani, Hidenori

2017-03-22

Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs). Although the importance of lncRNAs has been documented in previous reports, the biological and physiological functions of lncRNAs remain largely unknown. The role of lncRNAs seems an elusive problem. Here, I propose a clue to the identification of regulatory lncRNAs. The key point is RNA half-life. RNAs with a long half-life (t 1/2 > 4 h) contain a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t 1/2 regulatory ncRNAs and regulatory mRNAs. This novel class of ncRNAs with a short half-life can be categorized as Short-Lived non-coding Transcripts (SLiTs). I consider that SLiTs are likely to be rich in functionally uncharacterized regulatory RNAs. This review describes recent progress in research into SLiTs.

Binary Linear-Time Erasure Decoding for Non-Binary LDPC codes

OpenAIRE

Savin, Valentin

2009-01-01

In this paper, we first introduce the extended binary representation of non-binary codes, which corresponds to a covering graph of the bipartite graph associated with the non-binary code. Then we show that non-binary codewords correspond to binary codewords of the extended representation that further satisfy some simplex-constraint: that is, bits lying over the same symbol-node of the non-binary graph must form a codeword of a simplex code. Applied to the binary erasure channel, this descript...

Unbiased and non-supervised learning methods for disruption prediction at JET

International Nuclear Information System (INIS)

Murari, A.; Vega, J.; Ratta, G.A.; Vagliasindi, G.; Johnson, M.F.; Hong, S.H.

2009-01-01

The importance of predicting the occurrence of disruptions is going to increase significantly in the next generation of tokamak devices. The expected energy content of ITER plasmas, for example, is such that disruptions could have a significant detrimental impact on various parts of the device, ranging from erosion of plasma facing components to structural damage. Early detection of disruptions is therefore needed with evermore increasing urgency. In this paper, the results of a series of methods to predict disruptions at JET are reported. The main objective of the investigation consists of trying to determine how early before a disruption it is possible to perform acceptable predictions on the basis of the raw data, keeping to a minimum the number of 'ad hoc' hypotheses. Therefore, the chosen learning techniques have the common characteristic of requiring a minimum number of assumptions. Classification and Regression Trees (CART) is a supervised but, on the other hand, a completely unbiased and nonlinear method, since it simply constructs the best classification tree by working directly on the input data. A series of unsupervised techniques, mainly K-means and hierarchical, have also been tested, to investigate to what extent they can autonomously distinguish between disruptive and non-disruptive groups of discharges. All these independent methods indicate that, in general, prediction with a success rate above 80% can be achieved not earlier than 180 ms before the disruption. The agreement between various completely independent methods increases the confidence in the results, which are also confirmed by a visual inspection of the data performed with pseudo Grand Tour algorithms.

Linear-Time Non-Malleable Codes in the Bit-Wise Independent Tampering Model

DEFF Research Database (Denmark)

Cramer, Ronald; Damgård, Ivan Bjerre; Döttling, Nico

Non-malleable codes were introduced by Dziembowski et al. (ICS 2010) as coding schemes that protect a message against tampering attacks. Roughly speaking, a code is non-malleable if decoding an adversarially tampered encoding of a message m produces the original message m or a value m' (eventuall...... non-malleable codes of Agrawal et al. (TCC 2015) and of Cher- aghchi and Guruswami (TCC 2014) and improves the previous result in the bit-wise tampering model: it builds the first non-malleable codes with linear-time complexity and optimal-rate (i.e. rate 1 - o(1)).......Non-malleable codes were introduced by Dziembowski et al. (ICS 2010) as coding schemes that protect a message against tampering attacks. Roughly speaking, a code is non-malleable if decoding an adversarially tampered encoding of a message m produces the original message m or a value m' (eventually...... abort) completely unrelated with m. It is known that non-malleability is possible only for restricted classes of tampering functions. Since their introduction, a long line of works has established feasibility results of non-malleable codes against different families of tampering functions. However...

Municipal & Non-Governmental Organization Conservation Lands; LocCons11

Data.gov (United States)

University of Rhode Island Geospatial Extension Program — Non-State Conservation lands are real property permanently protected from future development by fee simple ownership, conservation or other restrictive easements, or...

Non-Coding RNAs in Arabidopsis

DEFF Research Database (Denmark)

van Wonterghem, Miranda

This work evolves around elucidating the mechanisms of micro RNAs (miRNAs) in Arabidopsis thaliana. I identified a new class of nuclear non-coding RNAs derived from protein coding genes. The genes are miRNA targets with extensive gene body methylation. The RNA species are nuclear localized and de...

Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva

Directory of Open Access Journals (Sweden)

Guo Xiang

2008-12-01

Full Text Available Abstract Background Parasites in the genus Theileria cause lymphoproliferative diseases in cattle, resulting in enormous socio-economic losses. The availability of the genome sequences and annotation for T. parva and T. annulata has facilitated the study of parasite biology and their relationship with host cell transformation and tropism. However, the mechanism of transcriptional regulation in this genus, which may be key to understanding fundamental aspects of its parasitology, remains poorly understood. In this study, we analyze the evolution of non-coding sequences in the Theileria genome and identify conserved sequence elements that may be involved in gene regulation of these parasitic species. Results Intergenic regions and introns in Theileria are short, and their length distributions are considerably right-skewed. Intergenic regions flanked by genes in 5'-5' orientation tend to be longer and slightly more AT-rich than those flanked by two stop codons; intergenic regions flanked by genes in 3'-5' orientation have intermediate values of length and AT composition. Intron position is negatively correlated with intron length, and positively correlated with GC content. Using stringent criteria, we identified a set of high-quality orthologous non-coding sequences between T. parva and T. annulata, and determined the distribution of selective constraints across regions, which are shown to be higher close to translation start sites. A positive correlation between constraint and length in both intergenic regions and introns suggests a tight control over length expansion of non-coding regions. Genome-wide searches for functional elements revealed several conserved motifs in intergenic regions of Theileria genomes. Two such motifs are preferentially located within the first 60 base pairs upstream of transcription start sites in T. parva, are preferentially associated with specific protein functional categories, and have significant similarity to know

Disruption modeling in support of ITER

International Nuclear Information System (INIS)

Bandyopadhyay, I.

2015-01-01

Plasma current disruptions and Vertical Displacement Events (VDEs) are one of the major concerns in any tokamak as they lead to large electromagnetic forces to tokamak first wall components and vacuum vessel. Their occurrence also means disruption to steady state operations of tokamaks. Thus future fusion reactors like ITER must ensure that disruptions and VDEs are minimized. However, since there is still finite probability of their occurrence, one must be able to characterize disruptions and VDEs and able to predict, for example, the plasma current quench time and halo current amplitude, which mainly determine the magnitude of the electromagnetic forces. There is a concerted effort globally to understand and predict plasma and halo current evolution during disruption in tokamaks through MHD simulations. Even though Disruption and VDEs are often 3D MHD perturbations in nature, presently they are mostly simulated using 2D axisymmetric MHD codes like the Tokamak Simulation Code (TSC) and DINA. These codes are also extensively benchmarked against experimental data in present day tokamaks to improve these models and their ability to predict these events in ITER. More detailed 3D models like M3D are only recently being developed, but they are yet to be benchmarked against experiments, as also they are massively computationally exhaustive

On the structure on non-local conservation laws in the two-dimensional non-linear sigma-model

International Nuclear Information System (INIS)

Zamolodchikov, Al.B.

1978-01-01

The non-local conserved charges are supposed to satisfy a special multiplicative law in the space of asymptotic states of the non-linear sigma-model. This supposition leads to factorization equations for two-particle scattering matrix elements and determines to some extent the action of these charges in the asymptotic space. Their conservation turns out to be consistent with the factorized S-matrix of the non-linear sigma-model. It is shown also that the factorized sine-Gordon S-matrix is consistent with a similar family of conservation laws

An evolutionary model for protein-coding regions with conserved RNA structure

DEFF Research Database (Denmark)

Pedersen, Jakob Skou; Forsberg, Roald; Meyer, Irmtraud Margret

2004-01-01

in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagious" context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume...... components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses......Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair...

Non conventional energy sources and energy conservation

International Nuclear Information System (INIS)

Bueno M, F.

1995-01-01

Geographically speaking, Mexico is in an enviable position. Sun, water, biomass and geothermal fields main non conventional energy sources with commercial applications, are presents and in some cases plentiful in national territory. Moreover the coastal tidal power which is in research stage in several countries. Non conventional energy sources are an alternative which allow us to reduce the consumption of hydrocarbons or any other type of primary energetic, are not by oneself choices for the energy conservation, but energy replacements. At the beginning of this year, CONAE created the Direction of Non conventional Energy Sources, which main objective is to promote and impulse programs inclined towards the application of systems based in renewable energy sources. The research centers represent a technological and consultative support for the CONAE. They have an infrastructure developed along several years of continuous work. The non conventional energy sources will be a reality at the same time that their cost be equal or lower than the cost for the traditional generating systems. CONAE (National Commission for Energy Conservation). (Author)

Code of practice for safety in laboratory - non ionising radiation

International Nuclear Information System (INIS)

Ramli Jaya; Mohd Yusof Mohd Ali; Khoo Boo Huat; Khatijah Hashim

1995-01-01

The code identifies the non-ionizing radiation encountered in laboratories and the associated hazards. The code is intended as a laboratory standard reference document for general information on safety requirements relating to the usage of non-ionizing radiations in laboratories. The nonionizing radiations cover in this code, namely, are ultraviolet radiation, visible light, radio-frequency radiation, lasers, sound waves and ultrasonic radiation. (author)

Long non-coding RNAs: Mechanism of action and functional utility

Directory of Open Access Journals (Sweden)

Shakil Ahmad Bhat

2016-10-01

Full Text Available Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA, small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs. Keywords: LncRNA, X-chromosome inactivation, Genome imprinting, Transcription regulation, Cancer, Immunity

Development of non-linear vibration analysis code for CANDU fuelling machine

International Nuclear Information System (INIS)

Murakami, Hajime; Hirai, Takeshi; Horikoshi, Kiyomi; Mizukoshi, Kaoru; Takenaka, Yasuo; Suzuki, Norio.

1988-01-01

This paper describes the development of a non-linear, dynamic analysis code for the CANDU 600 fuelling machine (F-M), which includes a number of non-linearities such as gap with or without Coulomb friction, special multi-linear spring connections, etc. The capabilities and features of the code and the mathematical treatment for the non-linearities are explained. The modeling and numerical methodology for the non-linearities employed in the code are verified experimentally. Finally, the simulation analyses for the full-scale F-M vibration testing are carried out, and the applicability of the code to such multi-degree of freedom systems as F-M is demonstrated. (author)

Non-Coding Transcript Heterogeneity in Mesothelioma: Insights from Asbestos-Exposed Mice.

Science.gov (United States)

Felley-Bosco, Emanuela; Rehrauer, Hubert

2018-04-11

Mesothelioma is an aggressive, rapidly fatal cancer and a better understanding of its molecular heterogeneity may help with making more efficient therapeutic strategies. Non-coding RNAs represent a larger part of the transcriptome but their contribution to diseases is not fully understood yet. We used recently obtained RNA-seq data from asbestos-exposed mice and performed data mining of publicly available datasets in order to evaluate how non-coding RNA contribute to mesothelioma heterogeneity. Nine non-coding RNAs are specifically elevated in mesothelioma tumors and contribute to human mesothelioma heterogeneity. Because some of them have known oncogenic properties, this study supports the concept of non-coding RNAs as cancer progenitor genes.

VDE/disruption EM analysis for ITER in-vessel components

International Nuclear Information System (INIS)

Miki, N.; Ioki, K.; Ilio, F.; Kodama, T.; Chiocchio, S.; Williamson, D.; Roccella, M.; Barabaschi, P.; Sayer, R.S.

1998-01-01

This paper summarises the results of EM analyses for ITER in-vessel components, such as blanket modules, backplate and divertor modules. In the ITER design the following two disruption scenarios are taken into account: centered or radial disruption, and vertical displacement event (VDE). Eddy currents and forces due to plasma disruption were calculated using the 3D shell element code EDDYCUFF and the 3D solid element code EMAS. The plasma motion and current decay used in the EM analysis was supplied by 2-D axisymmetric plasma equilibrium codes, TSC and MAXFEA. (authors)

Min-Max decoding for non binary LDPC codes

OpenAIRE

Savin, Valentin

2008-01-01

Iterative decoding of non-binary LDPC codes is currently performed using either the Sum-Product or the Min-Sum algorithms or slightly different versions of them. In this paper, several low-complexity quasi-optimal iterative algorithms are proposed for decoding non-binary codes. The Min-Max algorithm is one of them and it has the benefit of two possible LLR domain implementations: a standard implementation, whose complexity scales as the square of the Galois field's cardinality and a reduced c...

Non-Host Plant Volatiles Disrupt Sex Pheromone Communication in a Specialist Herbivore.

Science.gov (United States)

Wang, Fumin; Deng, Jianyu; Schal, Coby; Lou, Yonggen; Zhou, Guoxin; Ye, Bingbing; Yin, Xiaohui; Xu, Zhihong; Shen, Lize

2016-09-02

The ecological effects of plant volatiles on herbivores are manifold. Little is known, however, about the impacts of non-host plant volatiles on intersexual pheromonal communication in specialist herbivores. We tested the effects of several prominent constitutive terpenoids released by conifers and Eucalyptus trees on electrophysiological and behavioral responses of an oligophagous species, Plutella xylostella, which feeds on Brassicaceae. The non-host plant volatile terpenoids adversely affected the calling behavior (pheromone emission) of adult females, and the orientation responses of adult males to sex pheromone were also significantly inhibited by these terpenoids in a wind tunnel and in the field. We suggest that disruption of both pheromone emission and orientation to sex pheromone may explain, at least in part, an observed reduction in herbivore attack in polyculture compared with monoculture plantings. We also propose that mating disruption of both male and female moths with non-host plant volatiles may be a promising alternative pest management strategy.

Non-Host Plant Volatiles Disrupt Sex Pheromone Communication in a Specialist Herbivore

Science.gov (United States)

Wang, Fumin; Deng, Jianyu; Schal, Coby; Lou, Yonggen; Zhou, Guoxin; Ye, Bingbing; Yin, Xiaohui; Xu, Zhihong; Shen, Lize

2016-01-01

The ecological effects of plant volatiles on herbivores are manifold. Little is known, however, about the impacts of non-host plant volatiles on intersexual pheromonal communication in specialist herbivores. We tested the effects of several prominent constitutive terpenoids released by conifers and Eucalyptus trees on electrophysiological and behavioral responses of an oligophagous species, Plutella xylostella, which feeds on Brassicaceae. The non-host plant volatile terpenoids adversely affected the calling behavior (pheromone emission) of adult females, and the orientation responses of adult males to sex pheromone were also significantly inhibited by these terpenoids in a wind tunnel and in the field. We suggest that disruption of both pheromone emission and orientation to sex pheromone may explain, at least in part, an observed reduction in herbivore attack in polyculture compared with monoculture plantings. We also propose that mating disruption of both male and female moths with non-host plant volatiles may be a promising alternative pest management strategy. PMID:27585907

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

Science.gov (United States)

Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

2015-01-01

Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence.

Directory of Open Access Journals (Sweden)

Kacy L Gordon

2015-05-01

Full Text Available Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2 from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements.

Non-coding RNAs enter mitosis: functions, conservation and implications

Directory of Open Access Journals (Sweden)

Kai Toshie

2011-02-01

Full Text Available Abstract Nuage (or commonly known as chromatoid body in mammals is a conserved germline-specific organelle that has been linked to the Piwi-interacting RNA (piRNA pathway. piRNAs are a class of gonadal-specific RNAs that are ~23-29 nucleotides in length and protect genome stability by repressing the expression of deleterious retrotransposons. More recent studies in Drosophila have implicated the piRNA pathway in other functions including canalization of embryonic development, regulation of maternal gene expression and telomere protection. We have recently shown that Vasa (known as Mouse Vasa Homolog in mouse, a nuage component, plays a mitotic role in promoting chromosome condensation and segregation by facilitating robust chromosomal localization of condensin I in the Drosophila germline. Vasa functions together with Aubergine (a PIWI family protein and Spindle-E/mouse TDRD-9, two other nuage components that are involved in the piRNA pathway, therefore providing a link between the piRNA pathway and mitotic chromosome condensation. Here, we propose and discuss possible models for the role of Vasa and the piRNA pathway during mitosis. We also highlight relevant studies implicating mitotic roles for RNAs and/or nuage in other model systems and their implications for cancer development.

Diversity of antisense and other non-coding RNAs in Archaea revealed by comparative small RNA sequencing in four Pyrobaculum species

Directory of Open Access Journals (Sweden)

David L Bernick

2012-07-01

Full Text Available A great diversity of small, non-coding RNA molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs in archaea is limited. We employed RNA-seq to identify novel small RNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among four species, we were able to identify conserved RNA genes fitting into known and novel families. Among our findings, we highlight three novel cis-antisense small RNAs encoded opposite to key regulatory (ferric uptake regulator, metabolic (triose-phosphate isomerase, and core transcriptional apparatus genes (transcription factor B. We also found a large increase in the number of conserved C/D box small RNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. Furthermore, the genus-specific nature of these small RNAs indicates they are relatively recent, stable adaptations.

Major disruption process in tokamak

International Nuclear Information System (INIS)

Kurita, Gen-ichi; Azumi, Masafumi; Tuda, Takashi; Takizuka, Tomonori; Tsunematsu, Toshihide; Tokuda, Shinji; Itoh, Kimitaka; Takeda, Tatsuoki

1981-11-01

The major disruption in a cylindrical tokamak is investigated by using the multi-helicity code, and the destabilization of the 3/2 mode by the mode coupling with the 2/1 mode is confirmed. The evolution of the magnetic field topology caused by the major disruption is studied in detail. The effect of the internal disruption on the 2/1 magnetic island width is also studied. The 2/1 magnetic island is not enhanced by the flattening of the q-profile due to the internal disruption. (author)

Sideways Force Produced During Disruptions

Science.gov (United States)

Strauss, H. R.; Paccagnella, R.; Breslau, J.; Jardin, S.; Sugiyama, L.

2012-10-01

We extend previous studies [1] of vertical displacement events (VDE) which can produce disruptions. The emphasis is on the non axisymmetric ``sideways'' wall force Fx. Simulations are performed using the M3D [2] code. A VDE expels magnetic flux through the resistive wall until the last closed flux surface has q VDE is presented. The wall force depends strongly on γτw, where γ is the mode growth rate and τw is the wall resistive penetration time. The force Fx is largest when γτw is a constant of order unity, which depends on the initial conditions. For large values of γτw, the wall force asymptotes to a relatively smaller value, well below the critical value ITER is designed to withstand. The principle of disruption mitigation by massive gas injection is to cause a disruption with large γτw. [4pt] [1] H. R. Strauss, R. Paccagnella, and J. Breslau,Phys. Plasmas 17, 082505 (2010) [2] W. Park, E.V. Belova, G.Y. Fu, X. Tang, H.R. Strauss, L.E. Sugiyama, Phys. Plasmas 6, 1796 (1999).

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

KAUST Repository

Guturu, H.

2013-11-11

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and \\'through-DNA\\' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

KAUST Repository

Guturu, H.; Doxey, A. C.; Wenger, A. M.; Bejerano, G.

2013-01-01

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and 'through-DNA' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex.

Retrotransposons and non-protein coding RNAs

DEFF Research Database (Denmark)

Mourier, Tobias; Willerslev, Eske

2009-01-01

does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review...

Conserved syntenic clusters of protein coding genes are missing in birds.

Science.gov (United States)

Lovell, Peter V; Wirthlin, Morgan; Wilhelm, Larry; Minx, Patrick; Lazar, Nathan H; Carbone, Lucia; Warren, Wesley C; Mello, Claudio V

2014-01-01

Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases.

Voluntary non-monetary approaches for implementing conservation

OpenAIRE

Santangeli, Andrea; Arroyo, Beatriz; Dicks, Lynn V.; Herzon, Irina; Kukkala, Aija S.; Sutherland, William J.; Moilanen, Atte

2016-01-01

The voluntary non-monetary approach to conservation refers to actions that citizens or organizations could voluntarily implement in their area of influence without the incentive of monetary compensations. To be effectively implemented by untrained actors, actions should be clearly defined, straightforward to implement and not require specific scientific knowledge. The costs of actions should also be sufficiently affordable to be widely applied without monetary incentives. A voluntary non-mone...

R-charge Conservation and More in Factorizable and Non-Factorizable Orbifolds

CERN Document Server

Bizet, Nana Geraldine Cabo; Pena, Damian Kaloni Mayorga; Parameswaran, Susha L; Schmitz, Matthias; Zavala, Ivonne

2013-01-01

We consider the string theory origin of R-charge conservation laws in heterotic orbifold compactifications, deriving the corresponding string coupling selection rule for factorizable and non-factorizable orbifolds, with prime ordered and non-prime ordered point groups. R-charge conservation arises due to symmetries among the worldsheet instantons that can mediate the couplings. Among our results is a previously missed non-trivial contribution to the conserved R-charges from the Gamma-phases in non-prime orbifolds, which weakens the R-charge selection rule. Symmetries among the worldsheet instantons can also lead to additional selection rules for some couplings. We make a similar analysis for Rule 4 or the 'torus lattice selection rule'. Moreover, we identify a new string selection rule, that we call Rule 6 or the 'coset vector selection rule'.

Complex organisation and structure of the ghrelin antisense strand gene GHRLOS, a candidate non-coding RNA gene

Directory of Open Access Journals (Sweden)

Herington Adrian C

2008-10-01

Full Text Available Abstract Background The peptide hormone ghrelin has many important physiological and pathophysiological roles, including the stimulation of growth hormone (GH release, appetite regulation, gut motility and proliferation of cancer cells. We previously identified a gene on the opposite strand of the ghrelin gene, ghrelinOS (GHRLOS, which spans the promoter and untranslated regions of the ghrelin gene (GHRL. Here we further characterise GHRLOS. Results We have described GHRLOS mRNA isoforms that extend over 1.4 kb of the promoter region and 106 nucleotides of exon 4 of the ghrelin gene, GHRL. These GHRLOS transcripts initiate 4.8 kb downstream of the terminal exon 4 of GHRL and are present in the 3' untranslated exon of the adjacent gene TATDN2 (TatD DNase domain containing 2. Interestingly, we have also identified a putative non-coding TATDN2-GHRLOS chimaeric transcript, indicating that GHRLOS RNA biogenesis is extremely complex. Moreover, we have discovered that the 3' region of GHRLOS is also antisense, in a tail-to-tail fashion to a novel terminal exon of the neighbouring SEC13 gene, which is important in protein transport. Sequence analyses revealed that GHRLOS is riddled with stop codons, and that there is little nucleotide and amino-acid sequence conservation of the GHRLOS gene between vertebrates. The gene spans 44 kb on 3p25.3, is extensively spliced and harbours multiple variable exons. We have also investigated the expression of GHRLOS and found evidence of differential tissue expression. It is highly expressed in tissues which are emerging as major sites of non-coding RNA expression (the thymus, brain, and testis, as well as in the ovary and uterus. In contrast, very low levels were found in the stomach where sense, GHRL derived RNAs are highly expressed. Conclusion GHRLOS RNA transcripts display several distinctive features of non-coding (ncRNA genes, including 5' capping, polyadenylation, extensive splicing and short open reading

Toward understanding non-coding RNA roles in intracranial aneurysms and subarachnoid hemorrhage

Directory of Open Access Journals (Sweden)

Huang Fengzhen

2017-05-01

Full Text Available Subarachnoid hemorrhage (SAH is a common and frequently life-threatening cerebrovascular disease, which is mostly related with a ruptured intracranial aneurysm. Its complications include rebleeding, early brain injury, cerebral vasospasm, delayed cerebral ischemia, chronic hydrocephalus, and also non neurological problems. Non-coding RNAs (ncRNAs, comprising of microRNAs (miRNAs, small interfering RNAs (siRNAs and long non-coding RNAs (lncRNAs, play an important role in intracranial aneurysms and SAH. Here, we review the non-coding RNAs expression profile and their related mechanisms in intracranial aneurysms and SAH. Moreover, we suggest that these non-coding RNAs function as novel molecular biomarkers to predict intracranial aneurysms and SAH, and may yield new therapies after SAH in the future.

Energy conservation in SIMMER

International Nuclear Information System (INIS)

Arnold, L.A.; Knowles, J.B.

1983-11-01

The SIMMER code contains models of the many interacting thermo-hydraulic processes that occur during a hypothetical core disruptive accident (HCDA), to provide an overall picture from accident initiation to containment loading. In calculations of roof loadings following the HCDA, errors in computing the overall energy balance were found to be up to ten times the kinetic energy of the sodium slug which creates the loading. On this account, the results were considered to be seriously compromised. This report describes a systematic investigation into the effect, nature and origin of the energy discrepancies. Its main conclusion are that, the errors stem from a systematic rather than a random source, energy errors for individual cells can be two decades larger than the mean value provided by the code, and cellular mass and energy errors are strongly correlated and they can actually increase when the mesh is refined. A likely cause of the conservation errors is identified as the solution of the liquid phase mass and energy equations at effectively different time instants during each timestep. (author)

Non-coding RNAs in the Ovarian Follicle

Directory of Open Access Journals (Sweden)

Rosalia Battaglia

2017-05-01

Full Text Available The mammalian ovarian follicle is the complex reproductive unit comprising germ cell, somatic cells (Cumulus and Granulosa cells, and follicular fluid (FF: paracrine communication among the different cell types through FF ensures the development of a mature oocyte ready for fertilization. This paper is focused on non-coding RNAs in ovarian follicles and their predicted role in the pathways involved in oocyte growth and maturation. We determined the expression profiles of microRNAs in human oocytes and FF by high-throughput analysis and identified 267 microRNAs in FF and 176 in oocytes. Most of these were FF microRNAs, while 9 were oocyte specific. By bioinformatic analysis, independently performed on FF and oocyte microRNAs, we identified the most significant Biological Processes and the pathways regulated by their validated targets. We found many pathways shared between the two compartments and some specific for oocyte microRNAs. Moreover, we found 41 long non-coding RNAs able to interact with oocyte microRNAs and potentially involved in the regulation of folliculogenesis. These data are important in basic reproductive research and could also be useful for clinical applications. In fact, the characterization of non-coding RNAs in ovarian follicles could improve reproductive disease diagnosis, provide biomarkers of oocyte quality in Assisted Reproductive Treatment, and allow the development of therapies for infertility disorders.

Decoding the function of nuclear long non-coding RNAs.

Science.gov (United States)

Chen, Ling-Ling; Carmichael, Gordon G

2010-06-01

Long non-coding RNAs (lncRNAs) are mRNA-like, non-protein-coding RNAs that are pervasively transcribed throughout eukaryotic genomes. Rather than silently accumulating in the nucleus, many of these are now known or suspected to play important roles in nuclear architecture or in the regulation of gene expression. In this review, we highlight some recent progress in how lncRNAs regulate these important nuclear processes at the molecular level. Copyright 2010 Elsevier Ltd. All rights reserved.

About the lepton number non conservation

International Nuclear Information System (INIS)

Bernabeu, J

1989-01-01

The possibility of lepton number non conservation through the mixing of lepton flavours, as well as the IΔLI=2 lepton antilepton conversion, is discussed. The paper follows the scheme: i) Experimental Situation; ii) Relation with the Neutrino Mass problem; iii) Majorana Neutrinos?; iv) Extensions of the Standard Model; v) Lepton Flavour Violating Decays of μ and τ; vi) Z∞ Boson Decays. (Author)

Linear-time non-malleable codes in the bit-wise independent tampering model

NARCIS (Netherlands)

R.J.F. Cramer (Ronald); I.B. Damgård (Ivan); N.M. Döttling (Nico); I. Giacomelli (Irene); C. Xing (Chaoping)

2017-01-01

textabstractNon-malleable codes were introduced by Dziembowski et al. (ICS 2010) as coding schemes that protect a message against tampering attacks. Roughly speaking, a code is non-malleable if decoding an adversarially tampered encoding of a message m produces the original message m or a value m′

Cyclic and constacyclic codes over a non-chain ring

Directory of Open Access Journals (Sweden)

Ayşegül Bayram

2014-09-01

Full Text Available In this study, we consider linear and especially cyclic codes over the non-chain ring $Z_{p}[v]/\\langle v^{p}-v\\rangle$ where $p$ is a prime. This is a generalization of the case $p=3.$ Further, in this work the structure of constacyclic codes are studied as well. This study takes advantage mainly from a Gray map which preserves the distance between codes over this ring and $p$-ary codes and moreover this map enlightens the structure of these codes. Furthermore, a MacWilliams type identity is presented together with some illustrative examples.

GYSELA, a full-f global gyrokinetic Semi-Lagrangian code for ITG turbulence simulations

International Nuclear Information System (INIS)

Grandgirard, V.; Sarazin, Y.; Garbet, X.; Dif-Pradalier, G.; Ghendrih, Ph.; Crouseilles, N.; Latu, G.; Sonnendruecker, E.; Besse, N.; Bertrand, P.

2006-01-01

This work addresses non-linear global gyrokinetic simulations of ion temperature gradient (ITG) driven turbulence with the GYSELA code. The particularity of GYSELA code is to use a fixed grid with a Semi-Lagrangian (SL) scheme and this for the entire distribution function. The 4D non-linear drift-kinetic version of the code already showns the interest of such a SL method which exhibits good properties of energy conservation in non-linear regime as well as an accurate description of fine spatial scales. The code has been upgrated to run 5D simulations of toroidal ITG turbulence. Linear benchmarks and non-linear first results prove that semi-lagrangian codes can be a credible alternative for gyrokinetic simulations

Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure

DEFF Research Database (Denmark)

de Groot, Saskia; Mailund, Thomas; Hein, Jotun

2007-01-01

Motivation: Detecting genes in viral genomes is a complex task. Due to the biological necessity of them being constrained in length, RNA viruses in particular tend to code in overlapping reading frames. Since one amino acid is encoded by a triplet of nucleic acids, up to three genes may be coded...... allows for coding in unidirectional nested and overlapping reading frames, to annotate two homologous aligned viral genomes. Our method does not insist on conserved gene structure between the two sequences, thus making it applicable for the pairwise comparison of more distantly related sequences. Results...... and HIV2, as well as of two different Hepatitis Viruses, attaining results of ~87% sensitivity and ~98.5% specificity. We subsequently incorporate prior knowledge by "knowing" the gene structure of one sequence and annotating the other conditional on it. Boosting accuracy close to perfect we demonstrate...

The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species.

Science.gov (United States)

Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy

2016-01-01

Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.

Helicity non-conserving form factor of the proton

Energy Technology Data Exchange (ETDEWEB)

Voutier, E.; Furget, C.; Knox, S. [Universite Joseph Fourier, Grenoble (France)] [and others

1994-04-01

The study of the hadron structure in the high Q{sup 2} range contributes to the understanding of the mechanisms responsible for the confinement of quarks and gluons. Among the numerous experimental candidates sensitive to these mechanisms, the helicity non-conserving form factor of the proton is a privileged observable since it is controlled by non-perturbative effects. The authors investigate here the feasibility of high Q{sup 2} measurements of this form factor by means of the recoil polarization method in the context of the CEBAF 8 GeV facility. For that purpose, they discuss the development of a high energy proton polarimeter, based on the H({rvec p},pp) elastic scattering, to be placed at the focal plane of a new hadron spectrometer. It is shown that this experimental method significantly improves the knowledge of the helicity non-conserving form factor of the proton up to 10 GeV{sup 2}/c{sup 2}.

Optimal inventory policies with non-stationary supply disruptions and advance supply information

NARCIS (Netherlands)

Atasoy, B.; Güllü, R.; Tan, T.

2012-01-01

We consider the production/inventory problem of a manufacturer (or a retailer) under non-stationary and stochastic supply availability. Although supply availability is uncertain, the supplier would be able to predict her near future shortages – and hence supply disruption to (some of) her customers

Optimal inventory policies with non-stationary supply disruptions and advance supply information

NARCIS (Netherlands)

Atasoy, B.; Güllü, R.; Tan, T.

2011-01-01

We consider the production/inventory problem of a manufacturer (or a retailer) under non-stationary and stochastic supply availability. Although supply availability is uncertain, the supplier would be able to predict her near future shortages -and hence supply disruption to (some of) her customers-

Construction of local and non-local conservation laws for non-linear field equations

International Nuclear Information System (INIS)

Vladimirov, V.S.; Volovich, I.V.

1984-08-01

A method of constructing conserved currents for non-linear field equations is presented. More explicitly for non-linear equations, which can be derived from compatibility conditions of some linear system with a parameter, a procedure of obtaining explicit expressions for local and non-local currents is developed. Some examples such as the classical Heisenberg spin chain and supersymmetric Yang-Mills theory are considered. (author)

Non-coding, mRNA-like RNAs database Y2K.

Science.gov (United States)

Erdmann, V A; Szymanski, M; Hochberg, A; Groot, N; Barciszewski, J

2000-01-01

In last few years much data has accumulated on various non-translatable RNA transcripts that are synthesised in different cells. They are lacking in protein coding capacity and it seems that they work mainly or exclusively at the RNA level. All known non-coding RNA transcripts are collected in the database: http://www. man.poznan.pl/5SData/ncRNA/index.html

Conservative performance analysis of a PWR nuclear fuel rod using the FRAPCON code

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Fabio Branco Vaz de; Sabundjian, Gaiane, E-mail: fabio@ipen.br, E-mail: gdjian@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2015-07-01

In this paper, some of the preliminary results of the sensitivity and conservative analysis of a hypothetical pressurized water reactor fuel rod are presented, using the FRAPCON code as a basic and preparation tool for the future transient analysis, which will be carried out by the FRAPTRAN code. Emphasis is given to the evaluation of the cladding behavior, since it is one of the critical containment barriers of the fission products, generated during fuel irradiation. Sensitivity analyses were performed by the variation of the values of some parameters, which were mainly related with thermal cycle conditions, and taking into account an intermediate value between the realistic and conservative conditions for the linear heat generation rate parameter, given in literature. Time lengths were taken from typical nuclear power plant operational cycle, adjusted to the obtention of a chosen burnup. Curves of fuel and cladding temperatures, and also for their mechanical and oxidation behavior, as a function of the reactor operation's time, are presented for each one of the nodes considered, over the nuclear fuel rod. Analyzing the curves, it was possible to observe the influence of the thermal cycle on the fuel rod performance, in this preliminary step for the accident/transient analysis. (author)

A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

Science.gov (United States)

Zhang, Ai-bing; Feng, Jie; Ward, Robert D; Wan, Ping; Gao, Qiang; Wu, Jun; Zhao, Wei-zhong

2012-01-01

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37%) for 1094 brown algae queries, both using ITS barcodes.

A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

Directory of Open Access Journals (Sweden)

Ai-bing Zhang

Full Text Available Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish and two representing non-coding ITS barcodes (rust fungi and brown algae. Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ and Maximum likelihood (ML methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40% for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37% for 1094 brown algae queries, both using ITS barcodes.

Mutation of Rubie, a novel long non-coding RNA located upstream of Bmp4, causes vestibular malformation in mice.

Directory of Open Access Journals (Sweden)

Kristina A Roberts

Full Text Available The vestibular apparatus of the vertebrate inner ear uses three fluid-filled semicircular canals to sense angular acceleration of the head. Malformation of these canals disrupts the sense of balance and frequently causes circling behavior in mice. The Epistatic circler (Ecl is a complex mutant derived from wildtype SWR/J and C57L/J mice. Ecl circling has been shown to result from the epistatic interaction of an SWR-derived locus on chromosome 14 and a C57L-derived locus on chromosome 4, but the causative genes have not been previously identified.We developed a mouse chromosome substitution strain (CSS-14 that carries an SWR/J chromosome 14 on a C57BL/10J genetic background and, like Ecl, exhibits circling behavior due to lateral semicircular canal malformation. We utilized CSS-14 to identify the chromosome 14 Ecl gene by positional cloning. Our candidate interval is located upstream of bone morphogenetic protein 4 (Bmp4 and contains an inner ear-specific, long non-coding RNA that we have designated Rubie (RNA upstream of Bmp4 expressed in inner ear. Rubie is spliced and polyadenylated, and is expressed in developing semicircular canals. However, we discovered that the SWR/J allele of Rubie is disrupted by an intronic endogenous retrovirus that causes aberrant splicing and premature polyadenylation of the transcript. Rubie lies in the conserved gene desert upstream of Bmp4, within a region previously shown to be important for inner ear expression of Bmp4. We found that the expression patterns of Bmp4 and Rubie are nearly identical in developing inner ears.Based on these results and previous studies showing that Bmp4 is essential for proper vestibular development, we propose that Rubie is the gene mutated in Ecl mice, that it is involved in regulating inner ear expression of Bmp4, and that aberrant Bmp4 expression contributes to the Ecl phenotype.

Utilizing elements of the CSAU phenomena identification and ranking table (PIRT) to qualify a PWR non-LOCA transients system code

Energy Technology Data Exchange (ETDEWEB)

Greene, K.R.; Fletcher, C.D.; Gottula, R.C.; Lindquist, T.R.; Stitt, B.D. [Framatome ANP, Richland, WA (United States)

2001-07-01

Licensing analyses of Nuclear Regulatory Commission (NRC) Standard Review Plan (SRP) Chapter 15 non-LOCA transients are an important part of establishing operational safety limits and design limits for nuclear power plants. The applied codes and methods are generally qualified using traditional methods of benchmarking and assessment, sample problems, and demonstration of conservatism. Rigorous formal methods for developing code and methodology have been created and applied to qualify realistic methods for Large Break Loss-of-Coolant Accidents (LBLOCA's). This methodology, Code Scaling, Applicability, and Uncertainty (CSAU), is a very demanding, resource intensive, process to apply. It would be challenging to apply a comprehensive and complete CSAU level of analysis, individually, to each of the more than 30 non-LOCA transients that comprise Chapter 15 events. However, certain elements of the process can be easily adapted to improve quality of the codes and methods used to analyze non- LOCA transients. One of these elements is the Phenomena Identification and Ranking Table (PIRT). This paper presents the results of an informally constructed PIRT that applies to non-LOCA transients for Pressurized Water Reactors (PWR's) of the Westinghouse and Combustion Engineering design. A group of experts in thermal-hydraulics and safety analysis identified and ranked the phenomena. To begin the process, the PIRT was initially performed individually by each expert. Then through group interaction and discussion, a consensus was reached on both the significant phenomena and the appropriate ranking. The paper also discusses using the PIRT as an aid to qualify a 'conservative' system code and methodology. Once agreement was obtained on the phenomena and ranking, the table was divided into six functional groups, by nature of the transients, along the same lines as Chapter 15. Then, assessment and disposition of the significant phenomena was performed. The PIRT and

TSC [Tokamak Simulation Code] disruption scenarios and CIT [Compact Ignition Tokamak] vacuum vessel force evolution

International Nuclear Information System (INIS)

Sayer, R.O.; Peng, Y.K.M.; Strickler, D.J.; Jardin, S.C.

1990-01-01

The Tokamak Simulation Code and the TWIR postprocessor code have been used to develop credible plasma disruption scenarios for the Compact Ignition Tokamak (CIT) in order to predict the evolution of forces on CIT conducting structures and to provide results required for detailed structural design analysis. The extreme values of net radial and vertical vacuum vessel (VV) forces were found to be F R =-12.0 MN/rad and F Z =-3.0 MN/rad, respectively, for the CIT 2.1-m, 11-MA design. Net VV force evolution was found to be altered significantly by two mechanisms not noted previously. The first, due to poloidal VV currents arising from increased plasma paramagnetism during thermal quench, reduces the magnitude of the extreme F R by 15-50% and modifies the distribution of forces substantially. The second effect is that slower plasma current decay rates give more severe net vertical VV loads because the current decay occurs when the plasma has moved farther from midplane than is the case for faster decay rates. 7 refs., 9 figs., 1 tab

Large break LOCA uncertainty evaluation and comparison with conservative calculation

International Nuclear Information System (INIS)

Glaeser, H.G.

2004-01-01

The first formulation of the USA Code of Federal Regulations (CFR) 10CFR50 with applicable sections specific to NPP licensing requirements was released 1976. Over a decade later 10CFR 50.46 allowed the use of BE codes instead of conservative code models but uncertainties have to be identified and quantified. Guidelines were released that described interpretations developed over the intervening years that are applicable. Other countries established similar conservative procedures and acceptance criteria. Because conservative methods were used to calculate the peak values of key parameters, such as peak clad temperature (PCT), it was always acknowledged that a large margin, between the 'conservative' calculated value and the 'true' value, existed. Beside USA, regulation in other countries, like Germany, for example, allowed that the state of science and technology is applied in licensing. I.e. the increase of experimental evidence and progress in code development during time could be used. There was no requirement to apply a pure evaluation methodology with licensed assumptions and frozen codes. The thermal-hydraulic system codes became more and more best-estimate codes based on comprehensive validation. This development was and is possible because the rules and guidelines provide the necessary latitude to consider further development of safety technology. Best estimate codes are allowed to be used in licensing in combination with conservative initial and boundary conditions. However, uncertainty quantification is not required. Since some of the initial and boundary conditions are more conservative compared with those internationally used (e.g. 106% reactor power instead 102%, a single failure plus a non-availability due to preventive maintenance is assumed, etc.) it is claimed that the uncertainties of code models are covered. Since many utilities apply for power increase, calculation results come closer to some licensing criteria. The situation in German licensing

Non-Noether Conserved Quantity for Relativistic Nonholonomic System with Variable Mass

International Nuclear Information System (INIS)

Qiao Yongfen; Li Renjie; Ma Yongsheng

2005-01-01

Using form invariance under special infinitesimal transformations in which time is not variable, the non-Noether conserved quantity of the relativistic nonholonomic system with variable mass is studied. The differential equations of motion of the system are established. The definition and criterion of the form invariance of the system under infinitesimal transformations are studied. The necessary and sufficient condition under which the form invariance is a Lie symmetry is given. The condition under which the form invariance can be led to a non-Noether conserved quantity and the form of the conserved quantity are obtained. Finally, an example is given to illustrate the application of the result.

Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli

DEFF Research Database (Denmark)

Boysen, Anders; Møller-Jensen, Jakob; Kallipolitis, Birgitte H.

2010-01-01

Small non-coding RNAs (sRNA) have emerged as important elements of gene regulatory circuits. In enterobacteria such as Escherichia coli and Salmonella many of these sRNAs interact with the Hfq protein, an RNA chaperone similar to mammalian Sm-like proteins and act in the post...... that adaptation to anaerobic growth involves the action of a small regulatory RNA....... of at least one sRNA regulator. Here, we extend this view by the identification and characterization of a highly conserved, anaerobically induced small sRNA in E. coli, whose expression is strictly dependent on the anaerobic transcriptional fumarate and nitrate reductase regulator (FNR). The sRNA, named Fnr...

Extracellular vesicle associated long non-coding RNAs functionally enhance cell viability

Directory of Open Access Journals (Sweden)

Chris Hewson

2016-10-01

Full Text Available Cells communicate with one another to create microenvironments and share resources. One avenue by which cells communicate is through the action of exosomes. Exosomes are extracellular vesicles that are released by one cell and taken up by neighbouring cells. But how exosomes instigate communication between cells has remained largely unknown. We present evidence here that particular long non-coding RNA molecules are preferentially packaged into exosomes. We also find that a specific class of these exosome associated non-coding RNAs functionally modulate cell viability by direct interactions with l-lactate dehydrogenase B (LDHB, high-mobility group protein 17 (HMG-17, and CSF2RB, proteins involved in metabolism, nucleosomal architecture and cell signalling respectively. Knowledge of this endogenous cell to cell pathway, those proteins interacting with exosome associated non-coding transcripts and their interacting domains, could lead to a better understanding of not only cell to cell interactions but also the development of exosome targeted approaches in patient specific cell-based therapies. Keywords: Non-coding RNA, Extracellular RNA, Exosomes, Retroelement, Pseudogene

Progressive changes in non-coding RNA profile in leucocytes with age

Science.gov (United States)

Muñoz-Culla, Maider; Irizar, Haritz; Gorostidi, Ana; Alberro, Ainhoa; Osorio-Querejeta, Iñaki; Ruiz-Martínez, Javier; Olascoaga, Javier; de Munain, Adolfo López; Otaegui, David

2017-01-01

It has been observed that immune cell deterioration occurs in the elderly, as well as a chronic low-grade inflammation called inflammaging. These cellular changes must be driven by numerous changes in gene expression and in fact, both protein-coding and non-coding RNA expression alterations have been observed in peripheral blood mononuclear cells from elder people. In the present work we have studied the expression of small non-coding RNA (microRNA and small nucleolar RNA -snoRNA-) from healthy individuals from 24 to 79 years old. We have observed that the expression of 69 non-coding RNAs (56 microRNAs and 13 snoRNAs) changes progressively with chronological age. According to our results, the age range from 47 to 54 is critical given that it is the period when the expression trend (increasing or decreasing) of age-related small non-coding RNAs is more pronounced. Furthermore, age-related miRNAs regulate genes that are involved in immune, cell cycle and cancer-related processes, which had already been associated to human aging. Therefore, human aging could be studied as a result of progressive molecular changes, and different age ranges should be analysed to cover the whole aging process. PMID:28448962

MicroRNA-encoding long non-coding RNAs

Directory of Open Access Journals (Sweden)

Zhu Xiaopeng

2008-05-01

Full Text Available Abstract Background Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs. Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. Results A few ml-ncRNA have been shown to have genomic loci that overlap with microRNA loci, leading us to suspect that a fraction of ml-ncRNA may encode microRNAs. We therefore developed an algorithm (PriMir for specifically detecting potential microRNA-encoding transcripts in the entire set of 34,030 mouse full-length ml-ncRNAs. In combination with mouse-rat sequence conservation, this algorithm detected 97 (80 of them were novel strong miRNA-encoding candidates, and for 52 of these we obtained experimental evidence for the existence of their corresponding mature microRNA by microarray and stem-loop RT-PCR. Sequence analysis of the microRNA-encoding RNAs revealed an internal motif, whose presence correlates strongly (R2 = 0.9, P-value = 2.2 × 10-16 with the occurrence of stem-loops with characteristics of known pre-miRNAs, indicating the presence of a larger number microRNA-encoding RNAs (from 300 up to 800 in the ml-ncRNAs population. Conclusion Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.

BIRTH: a beam deposition code for non-circular tokamak plasmas

International Nuclear Information System (INIS)

Otsuka, Michio; Nagami, Masayuki; Matsuda, Toshiaki

1982-09-01

A new beam deposition code has been developed which is capable of calculating fast ion deposition profiles including the orbit correction. The code incorporates any injection geometry and a non-circular cross section plasma with a variable elongation and an outward shift of the magnetic flux surface. Typical cpu time on a DEC-10 computer is 10 - 20 seconds and 5 - 10 seconds with and without the orbit correction, respectively. This is shorter by an order of magnitude than that of other codes, e.g., Monte Carlo codes. The power deposition profile calculated by this code is in good agreement with that calculated by a Monte Carlo code. (author)

Primate-specific spliced PMCHL RNAs are non-protein coding in human and macaque tissues

Directory of Open Access Journals (Sweden)

Delerue-Audegond Audrey

2008-12-01

Full Text Available Abstract Background Brain-expressed genes that were created in primate lineage represent obvious candidates to investigate molecular mechanisms that contributed to neural reorganization and emergence of new behavioural functions in Homo sapiens. PMCHL1 arose from retroposition of a pro-melanin-concentrating hormone (PMCH antisense mRNA on the ancestral human chromosome 5p14 when platyrrhines and catarrhines diverged. Mutations before divergence of hylobatidae led to creation of new exons and finally PMCHL1 duplicated in an ancestor of hominids to generate PMCHL2 at the human chromosome 5q13. A complex pattern of spliced and unspliced PMCHL RNAs were found in human brain and testis. Results Several novel spliced PMCHL transcripts have been characterized in human testis and fetal brain, identifying an additional exon and novel splice sites. Sequencing of PMCHL genes in several non-human primates allowed to carry out phylogenetic analyses revealing that the initial retroposition event took place within an intron of the brain cadherin (CDH12 gene, soon after platyrrhine/catarrhine divergence, i.e. 30–35 Mya, and was concomitant with the insertion of an AluSg element. Sequence analysis of the spliced PMCHL transcripts identified only short ORFs of less than 300 bp, with low (VMCH-p8 and protein variants or no evolutionary conservation. Western blot analyses of human and macaque tissues expressing PMCHL RNA failed to reveal any protein corresponding to VMCH-p8 and protein variants encoded by spliced transcripts. Conclusion Our present results improve our knowledge of the gene structure and the evolutionary history of the primate-specific chimeric PMCHL genes. These genes produce multiple spliced transcripts, bearing short, non-conserved and apparently non-translated ORFs that may function as mRNA-like non-coding RNAs.

lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine.

Science.gov (United States)

Sun, Lei; Liu, Hui; Zhang, Lin; Meng, Jia

2015-01-01

Functional long non-coding RNAs (lncRNAs) have been bringing novel insight into biological study, however it is still not trivial to accurately distinguish the lncRNA transcripts (LNCTs) from the protein coding ones (PCTs). As various information and data about lncRNAs are preserved by previous studies, it is appealing to develop novel methods to identify the lncRNAs more accurately. Our method lncRScan-SVM aims at classifying PCTs and LNCTs using support vector machine (SVM). The gold-standard datasets for lncRScan-SVM model training, lncRNA prediction and method comparison were constructed according to the GENCODE gene annotations of human and mouse respectively. By integrating features derived from gene structure, transcript sequence, potential codon sequence and conservation, lncRScan-SVM outperforms other approaches, which is evaluated by several criteria such as sensitivity, specificity, accuracy, Matthews correlation coefficient (MCC) and area under curve (AUC). In addition, several known human lncRNA datasets were assessed using lncRScan-SVM. LncRScan-SVM is an efficient tool for predicting the lncRNAs, and it is quite useful for current lncRNA study.

Impact evaluation to communicate and improve conservation non-governmental organization performance: the case of Conservation International.

Science.gov (United States)

McKinnon, Madeleine C; Mascia, Michael B; Yang, Wu; Turner, Will R; Bonham, Curan

2015-11-05

The rising prominence of more rigorous approaches to measuring conservation outcomes has included greater adoption of impact evaluation by conservation non-governmental organizations (CNGOs). Within the scientific literature, however, little consideration has been given to the unique and specific roles of CNGOs in advancing impact evaluation. We explore these issues in the context of one CNGO-Conservation International (CI)-and its experiences producing, using and funding impact evaluations over the past decade. We examine the contributions of impact evaluation to CI's mission at three different stages of CI's strategy: innovation, demonstration and amplification. Furthermore, we review incentives and barriers encountered by CI in its 10+ years' experience in impact evaluation. More coordinated and strategic use of impact evaluation by CNGOs would facilitate learning and promote accountability across the conservation community. © 2015 The Author(s).

Perceptual consequences of disrupted auditory nerve activity.

Science.gov (United States)

Zeng, Fan-Gang; Kong, Ying-Yee; Michalewski, Henry J; Starr, Arnold

2005-06-01

Perceptual consequences of disrupted auditory nerve activity were systematically studied in 21 subjects who had been clinically diagnosed with auditory neuropathy (AN), a recently defined disorder characterized by normal outer hair cell function but disrupted auditory nerve function. Neurological and electrophysical evidence suggests that disrupted auditory nerve activity is due to desynchronized or reduced neural activity or both. Psychophysical measures showed that the disrupted neural activity has minimal effects on intensity-related perception, such as loudness discrimination, pitch discrimination at high frequencies, and sound localization using interaural level differences. In contrast, the disrupted neural activity significantly impairs timing related perception, such as pitch discrimination at low frequencies, temporal integration, gap detection, temporal modulation detection, backward and forward masking, signal detection in noise, binaural beats, and sound localization using interaural time differences. These perceptual consequences are the opposite of what is typically observed in cochlear-impaired subjects who have impaired intensity perception but relatively normal temporal processing after taking their impaired intensity perception into account. These differences in perceptual consequences between auditory neuropathy and cochlear damage suggest the use of different neural codes in auditory perception: a suboptimal spike count code for intensity processing, a synchronized spike code for temporal processing, and a duplex code for frequency processing. We also proposed two underlying physiological models based on desynchronized and reduced discharge in the auditory nerve to successfully account for the observed neurological and behavioral data. These methods and measures cannot differentiate between these two AN models, but future studies using electric stimulation of the auditory nerve via a cochlear implant might. These results not only show the unique

Quantitative Profiling of Peptides from RNAs classified as non-coding

Science.gov (United States)

Prabakaran, Sudhakaran; Hemberg, Martin; Chauhan, Ruchi; Winter, Dominic; Tweedie-Cullen, Ry Y.; Dittrich, Christian; Hong, Elizabeth; Gunawardena, Jeremy; Steen, Hanno; Kreiman, Gabriel; Steen, Judith A.

2014-01-01

Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences - including introns and several classes of non-coding RNAs (ncRNAs) do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here, we use computational methods to identify the products of non-canonical translation in mouse neurons by analyzing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from anti-sense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential. PMID:25403355

Effect of disruptions on plasma-facing components

International Nuclear Information System (INIS)

Gilligan, J.G.; Bourham, M.A.; Tucker, E.C.

1995-01-01

Erosion of plasma-facing components during disruptions is a limiting factor in the design of large tokamaks like ITER. During a disruption, much of the stored thermal energy of the plasma will be dumped onto divertor plates, resulting in local heat fluxes, which may exceed 100 GW/m 2 over a period of about 0.1--1.0 msec. Melted and/or vaporized material is produced which is redistributed in the divertor region. Simulation of disruption damage is summarized from code results and from experimental exposure of materials to high heat-flux plasmas in plasma guns. In the US several codes have been used to predict both melt/vaporization and heat transfer on surfaces as well as energy and momentum transport in the vapor/plasma shield produced at the surface

Non-Saccharomyces yeasts protect against epithelial cell barrier disruption induced by Salmonella enterica subsp. enterica serovar Typhimurium.

Science.gov (United States)

Smith, I M; Baker, A; Arneborg, N; Jespersen, L

2015-11-01

The human gastrointestinal epithelium makes up the largest barrier separating the body from the external environment. Whereas invasive pathogens cause epithelial barrier disruption, probiotic micro-organisms modulate tight junction regulation and improve epithelial barrier function. In addition, probiotic strains may be able to reduce epithelial barrier disruption caused by pathogenic species. The aim of this study was to explore non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Benchmarking against established probiotic strains, we evaluated the ability of four nonpathogenic yeast species to modulate transepithelial electrical resistance (TER) across a monolayer of differentiated human colonocytes (Caco-2 cells). Further, we assessed yeast modulation of a Salmonella Typhimurium-induced epithelial cell barrier function insult. Our findings demonstrate distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function. While the established probiotic yeast Saccharomyces boulardii increased TER across a Caco-2 monolayer by 30%, Kluyveromyces marxianus exhibited significantly stronger properties of TER enhancement (50% TER increase). In addition, our data demonstrate significant yeast-mediated modulation of Salmonella-induced epithelial cell barrier disruption and identify K. marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion. This study demonstrates distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Further, our data demonstrate significant yeast-mediated modulation of Salmonella Typhimurium-induced epithelial cell barrier disruption and identify Kluyveromyces marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion. This study is the first to demonstrate significant non-Saccharomyces yeast

At the intersection of non-coding transcription, DNA repair, chromatin structure, and cellular senescence

Directory of Open Access Journals (Sweden)

Ryosuke eOhsawa

2013-07-01

Full Text Available It is well accepted that non-coding RNAs play a critical role in regulating gene expression. Recent paradigm-setting studies are now revealing that non-coding RNAs, other than microRNAs, also play intriguing roles in the maintenance of chromatin structure, in the DNA damage response, and in adult human stem cell aging. In this review, we will discuss the complex inter-dependent relationships among non-coding RNA transcription, maintenance of genomic stability, chromatin structure and adult stem cell senescence. DNA damage-induced non-coding RNAs transcribed in the vicinity of the DNA break regulate recruitment of the DNA damage machinery and DNA repair efficiency. We will discuss the correlation between non-coding RNAs and DNA damage repair efficiency and the potential role of changing chromatin structures around double-strand break sites. On the other hand, induction of non-coding RNA transcription from the repetitive Alu elements occurs during human stem cell aging and hinders efficient DNA repair causing entry into senescence. We will discuss how this fine balance between transcription and genomic instability may be regulated by the dramatic changes to chromatin structure that accompany cellular senescence.

Characterization and Analysis of Whole Transcriptome of Giant Panda Spleens: Implying Critical Roles of Long Non-Coding RNAs in Immunity.

Science.gov (United States)

Peng, Rui; Liu, Yuliang; Cai, Zhigang; Shen, Fujun; Chen, Jiasong; Hou, Rong; Zou, Fangdong

2018-01-01

Giant pandas, an endangered species, are a powerful symbol of species conservation. Giant pandas may suffer from a variety of diseases. Owing to their highly specialized diet of bamboo, giant pandas are thought to have a relatively weak ability to resist diseases. The spleen is the largest organ in the lymphatic system. However, there is little known about giant panda spleen at a molecular level. Thus, clarifying the regulatory mechanisms of spleen could help us further understand the immune system of the giant panda as well as its conservation. The two giant panda spleens were from two male individuals, one newborn and one an adult, in a non-pathological condition. The whole transcriptomes of mRNA, lncRNA, miRNA, and circRNA in the two spleens were sequenced using the Illumina HiSeq platform. EBseq and IDEG6 were used to observe the differentially expressed genes (DEGs) between these two spleens. Gene Ontology and KEGG analyses were used to annotate the function of DEGs. Furthermore, networks between non-coding RNAs and protein-coding genes were constructed to investigate the relationship between non-coding RNAs and immune-associated genes. By comparative analysis of the whole transcriptomes of these two spleens, we found that one of the major roles of lncRNAs could be involved in the regulation of immune responses of giant panda spleens. In addition, our results also revealed that microRNAs and circRNAs may have evolved to regulate a large set of biological processes of giant panda spleens, and circRNAs may function as miRNA sponges. To our knowledge, this is the first report of lncRNAs and circRNAs in giant panda, which could be a useful resource for further giant panda research. Our study reveals the potential functional roles of miRNAs, lncRNAs, and circRNAs in giant panda spleen. © 2018 The Author(s). Published by S. Karger AG, Basel.

Characterization and Analysis of Whole Transcriptome of Giant Panda Spleens: Implying Critical Roles of Long Non-Coding RNAs in Immunity

Directory of Open Access Journals (Sweden)

Rui Peng

2018-04-01

Full Text Available Background/Aims: Giant pandas, an endangered species, are a powerful symbol of species conservation. Giant pandas may suffer from a variety of diseases. Owing to their highly specialized diet of bamboo, giant pandas are thought to have a relatively weak ability to resist diseases. The spleen is the largest organ in the lymphatic system. However, there is little known about giant panda spleen at a molecular level. Thus, clarifying the regulatory mechanisms of spleen could help us further understand the immune system of the giant panda as well as its conservation. Methods: The two giant panda spleens were from two male individuals, one newborn and one an adult, in a non-pathological condition. The whole transcriptomes of mRNA, lncRNA, miRNA, and circRNA in the two spleens were sequenced using the Illumina HiSeq platform. EBseq and IDEG6 were used to observe the differentially expressed genes (DEGs between these two spleens. Gene Ontology and KEGG analyses were used to annotate the function of DEGs. Furthermore, networks between non-coding RNAs and protein-coding genes were constructed to investigate the relationship between non-coding RNAs and immune-associated genes. Results: By comparative analysis of the whole transcriptomes of these two spleens, we found that one of the major roles of lncRNAs could be involved in the regulation of immune responses of giant panda spleens. In addition, our results also revealed that microRNAs and circRNAs may have evolved to regulate a large set of biological processes of giant panda spleens, and circRNAs may function as miRNA sponges. Conclusion: To our knowledge, this is the first report of lncRNAs and circRNAs in giant panda, which could be a useful resource for further giant panda research. Our study reveals the potential functional roles of miRNAs, lncRNAs, and circRNAs in giant panda spleen.

Designing non-Hermitian dynamics for conservative state evolution on the Bloch sphere

Science.gov (United States)

Yu, Sunkyu; Piao, Xianji; Park, Namkyoo

2018-03-01

An evolution on the Bloch sphere is the fundamental state transition, including optical polarization controls and qubit operations. Conventional evolution of a polarization state or qubit is implemented within a closed system that automatically satisfies energy conservation from the Hermitian formalism. Although particular forms of static non-Hermitian Hamiltonians, such as parity-time-symmetric Hamiltonians, allow conservative states in an open system, the criteria for the energy conservation in a dynamical open system have not been fully explored. Here, we derive the condition of conservative state evolution in open-system dynamics and its inverse design method, by developing the non-Hermitian modification of the Larmor precession equation. We show that the geometrically designed locus on the Bloch sphere can be realized by different forms of dynamics, leading to the isolocus family of non-Hermitian dynamics. This increased degree of freedom allows the complementary phenomena of error-robust and highly sensitive evolutions on the Bloch sphere, which could be applicable to stable polarizers, quantum gates, and optimized sensors in dynamical open systems.

On the classification of long non-coding RNAs

KAUST Repository

Ma, Lina; Bajic, Vladimir B.; Zhang, Zhang

2013-01-01

Long non-coding RNAs (lncRNAs) have been found to perform various functions in a wide variety of important biological processes. To make easier interpretation of lncRNA functionality and conduct deep mining on these transcribed sequences

Fuel disruption mechanisms determined in-pile in the ACRR

International Nuclear Information System (INIS)

Wright, S.A.; Fischer, E.A.

1984-09-01

Over thirty in-pile experiments were performed to investigate fuel disruption behavior for LMFBR loss of flow (LOF) accidents. These experiments reproduced the heating transients for a variety of accidents ranging from slow LOF accidents to rapid LOF-driven-TOP accidents. In all experiments the timing and mode of the fuel disruption were observed with a high speed camera, enabling detailed comparisons with a fuel pin code, SANDPIN. This code transient intra- and inter-granular fission gas behavior to predict the macroscopic fuel behavior, such as fission gas induced swelling and frothing, cracking and breakup of solid fuel, and fuel vapor pressure driven dispersal. This report reviews the different modes of fuel disruption as seen in the experiments and then describes the mechanism responsible for the disruption. An analysis is presented that describes a set of conditions specifying the mode of fuel disruption and the heating conditions required to produce the disruption. The heating conditions are described in terms of heating rate (K/s), temperature gradient, and fuel temperature. A fuel disruption map is presented which plots heating rate as a function of fuel temperature to illustrate the different criteria for disruption. Although this approach to describing fuel disruption oversimplifies the fission gas processes modeled by SANDPIN, it does illustrate the criteria used to determine which fuel disruption mechanism is dominant and on what major fission gas parameters it depends

The drug target genes show higher evolutionary conservation than non-target genes.

Science.gov (United States)

Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

2016-01-26

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

Non-Coding RNAs and Endometrial Cancer

Directory of Open Access Journals (Sweden)

Cristina Vallone

2018-03-01

Full Text Available Non-coding RNAs (ncRNAs are involved in the regulation of cell metabolism and neoplastic transformation. Recent studies have tried to clarify the significance of these information carriers in the genesis and progression of various cancers and their use as biomarkers for the disease; possible targets for the inhibition of growth and invasion by the neoplastic cells have been suggested. The significance of ncRNAs in lung cancer, bladder cancer, kidney cancer, and melanoma has been amply investigated with important results. Recently, the role of long non-coding RNAs (lncRNAs has also been included in cancer studies. Studies on the relation between endometrial cancer (EC and ncRNAs, such as small ncRNAs or micro RNAs (miRNAs, transfer RNAs (tRNAs, ribosomal RNAs (rRNAs, antisense RNAs (asRNAs, small nuclear RNAs (snRNAs, Piwi-interacting RNAs (piRNAs, small nucleolar RNAs (snoRNAs, competing endogenous RNAs (ceRNAs, lncRNAs, and long intergenic ncRNAs (lincRNAs have been published. The recent literature produced in the last three years was extracted from PubMed by two independent readers, which was then selected for the possible relation between ncRNAs, oncogenesis in general, and EC in particular.

Junk DNA and the long non-coding RNA twist in cancer genetics

NARCIS (Netherlands)

H. Ling (Hui); K. Vincent; M. Pichler; R. Fodde (Riccardo); I. Berindan-Neagoe (Ioana); F.J. Slack (Frank); G.A. Calin (George)

2015-01-01

textabstractThe central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs

The identification and functional annotation of RNA structures conserved in vertebrates

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus

2017-01-01

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure...... (RBPs) or (ii) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared...... expression and shared structure despite low abundance and low sequence identity. About 30k CRS regions are located near coding or long non-coding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their non-structured...

An expanding universe of the non-coding genome in cancer biology.

Science.gov (United States)

Xue, Bin; He, Lin

2014-06-01

Neoplastic transformation is caused by accumulation of genetic and epigenetic alterations that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential and invasive growth [Hanahan,D. et al. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674]. Although the majority of the cancer studies have focused on the functions of protein-coding genes, emerging evidence has started to reveal the importance of the vast non-coding genome, which constitutes more than 98% of the human genome. A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs, including small ncRNAs and long ncRNAs (lncRNAs), play an important role in cancer development by regulating protein-coding gene expression through diverse mechanisms. In addition to ncRNAs, nearly half of the mammalian genomes consist of transposable elements, particularly retrotransposons. Once depicted as selfish genomic parasites that propagate at the expense of host fitness, retrotransposon elements could also confer regulatory complexity to the host genomes during development and disease. Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor development. Taken together, the functional significance of non-coding genome in tumorigenesis has been previously underestimated, and diverse transcripts derived from the non-coding genome could act as integral functional components of the oncogene and tumor suppressor network. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Design of ACM system based on non-greedy punctured LDPC codes

Science.gov (United States)

Lu, Zijun; Jiang, Zihong; Zhou, Lin; He, Yucheng

2017-08-01

In this paper, an adaptive coded modulation (ACM) scheme based on rate-compatible LDPC (RC-LDPC) codes was designed. The RC-LDPC codes were constructed by a non-greedy puncturing method which showed good performance in high code rate region. Moreover, the incremental redundancy scheme of LDPC-based ACM system over AWGN channel was proposed. By this scheme, code rates vary from 2/3 to 5/6 and the complication of the ACM system is lowered. Simulations show that more and more obvious coding gain can be obtained by the proposed ACM system with higher throughput.

Visual in-pile fuel disruption experiments

International Nuclear Information System (INIS)

Cano, G.L.; Ostensen, R.W.; Young, M.F.

1978-01-01

In a loss-of-flow (LOF) accident in an LMFBR, the mode of disruption of fuel may determine the probability of a subsequent energetic excursion. To investigate these phenomena, in-pile disruption of fission-heated irradiated fuel pellets was recorded by high speed cinematography. Instead of fuel frothing or dust-cloud breakup (as used in the SAS code) massive and very rapid fuel swelling, not predicted by analytical models, occurred. These tests support massive fuel swelling as the initial mode of fuel disruption in a LOF accident. (author)

Chimeric cellulase matrix for investigating intramolecular synergism between non-hydrolytic disruptive functions of carbohydrate-binding modules and catalytic hydrolysis.

Science.gov (United States)

Wang, Yuguo; Tang, Rentao; Tao, Jin; Wang, Xiaonan; Zheng, Baisong; Feng, Yan

2012-08-24

The conversion of renewable cellulosic biomass is of considerable interest for the production of biofuels and materials. The bottleneck in the efficient conversion is the compactness and resistance of crystalline cellulose. Carbohydrate-binding modules (CBMs), which disrupt crystalline cellulose via non-hydrolytic mechanisms, are expected to overcome this bottleneck. However, the lack of convenient methods for quantitative analysis of the disruptive functions of CBMs have hindered systematic studies and molecular modifications. Here we established a practical and systematic platform for quantifying and comparing the non-hydrolytic disruptive activities of CBMs via the synergism of CBMs and a catalytic module within designed chimeric cellulase molecules. Bioinformatics and computational biology were also used to provide a deeper understanding. A convenient vector was constructed to serve as a cellulase matrix into which heterologous CBM sequences can be easily inserted. The resulting chimeric cellulases were suitable for studying disruptive functions, and their activities quantitatively reflected the disruptive functions of CBMs on crystalline cellulose. In addition, this cellulase matrix can be used to construct novel chimeric cellulases with high hydrolytic activities toward crystalline cellulose.

Chimeric Cellulase Matrix for Investigating Intramolecular Synergism between Non-hydrolytic Disruptive Functions of Carbohydrate-binding Modules and Catalytic Hydrolysis*

Science.gov (United States)

Wang, Yuguo; Tang, Rentao; Tao, Jin; Wang, Xiaonan; Zheng, Baisong; Feng, Yan

2012-01-01

The conversion of renewable cellulosic biomass is of considerable interest for the production of biofuels and materials. The bottleneck in the efficient conversion is the compactness and resistance of crystalline cellulose. Carbohydrate-binding modules (CBMs), which disrupt crystalline cellulose via non-hydrolytic mechanisms, are expected to overcome this bottleneck. However, the lack of convenient methods for quantitative analysis of the disruptive functions of CBMs have hindered systematic studies and molecular modifications. Here we established a practical and systematic platform for quantifying and comparing the non-hydrolytic disruptive activities of CBMs via the synergism of CBMs and a catalytic module within designed chimeric cellulase molecules. Bioinformatics and computational biology were also used to provide a deeper understanding. A convenient vector was constructed to serve as a cellulase matrix into which heterologous CBM sequences can be easily inserted. The resulting chimeric cellulases were suitable for studying disruptive functions, and their activities quantitatively reflected the disruptive functions of CBMs on crystalline cellulose. In addition, this cellulase matrix can be used to construct novel chimeric cellulases with high hydrolytic activities toward crystalline cellulose. PMID:22778256

Non-Saccharomyces yeasts protect against epithelial cell barrier disruption induced by Salmonella enterica subsp. enterica serovar Typhimurium

DEFF Research Database (Denmark)

Smith, Ida Mosbech; Baker, A; Arneborg, Nils

2015-01-01

distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function. While the established probiotic yeast Saccharomyces boulardii increased TER across a Caco-2 monolayer by 30%, Kluyveromyces marxianus exhibited significantly stronger properties of TER enhancement (50% TER increase....... In addition, probiotic strains may be able to reduce epithelial barrier disruption caused by pathogenic species. The aim of this study was to explore non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Benchmarking against established probiotic strains, we evaluated the ability......). In addition, our data demonstrate significant yeast-mediated modulation of Salmonella-induced epithelial cell barrier disruption and identify K. marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion. SIGNIFICANCE AND IMPACT...

u-Constacyclic codes over F_p+u{F}_p and their applications of constructing new non-binary quantum codes

Science.gov (United States)

Gao, Jian; Wang, Yongkang

2018-01-01

Structural properties of u-constacyclic codes over the ring F_p+u{F}_p are given, where p is an odd prime and u^2=1. Under a special Gray map from F_p+u{F}_p to F_p^2, some new non-binary quantum codes are obtained by this class of constacyclic codes.

Long non-coding RNA expression profile in cervical cancer tissues

Science.gov (United States)

Zhu, Hua; Chen, Xiangjian; Hu, Yan; Shi, Zhengzheng; Zhou, Qing; Zheng, Jingjie; Wang, Yifeng

2017-01-01

Cervical cancer (CC), one of the most common types of cancer of the female population, presents an enormous challenge in diagnosis and treatment. Long non-coding (lnc)RNAs, non-coding (nc)RNAs with length >200 nucleotides, have been identified to be associated with multiple types of cancer, including CC. This class of nc transcripts serves an important role in tumor suppression and oncogenic signaling pathways. In the present study, the microarray method was used to obtain the expression profile of lncRNAs and protein-coding mRNAs and to compare the expression of lncRNAs between CC tissues and corresponding adjacent non-cancerous tissues in order to screen potential lncRNAs for associations with CC. Overall, 3356 lncRNAs with significantly different expression pattern in CC tissues compared with adjacent non-cancerous tissues were identified, while 1,857 of them were upregulated. These differentially expressed lncRNAs were additionally classified into 5 subgroups. Reverse transcription quantitative polymerase chain reactions were performed to validate the expression pattern of 5 random selected lncRNAs, and 2lncRNAs were identified to have significantly different expression in CC samples compared with adjacent non-cancerous tissues. This finding suggests that those lncRNAs with different expression may serve important roles in the development of CC, and the expression data may provide information for additional study on the involvement of lncRNAs in CC. PMID:28789353

Non-Noether conserved quantity for differential equations of motion in the phase space

Institute of Scientific and Technical Information of China (English)

无

2002-01-01

A non-Noether conserved quantity for the differential equations of motion of mechanical systems in the phase space is studied. The differential equations of motion of the systems are established and the determining equations of Lie symmetry are given. An existence theorem of non-Noether conserved quantity is obtained. An example is given to illustrate the application of the result.

MANAGING DISRUPTIVE BEHAVIOR OF STUDENTS IN LANGUAGE CLASSROOM

Directory of Open Access Journals (Sweden)

Siti Khasinah

2017-05-01

Full Text Available This article describes students’ disruptive behaviors in language classroom that may greatly affect language teaching and learning process, especially in ESL or EFL classes. Teachers should know what disruptive behavior is to enable them to deal with problems occurred in their classroom or to take preventive actions to keep their students well-behaved during the class. This can reduce the occurrence of misbehavior of students in their classroom. To prevent disruption in the classroom, teachers should establish behavioral expectations in the first day of the semester and the expectations can be based on students attendance, arrivals and departures, class participation, full English speaking, and other appropriate conducts in the syllabus and discuss them at the outset of the term. The agreement is then assigned as a learning contract or a code of conducts with which bounds the whole class. Consequently, whenever students are misbehaved, teachers and other students will directly know and recognize that the behaviors are out of the code. There are factors reasoning students to behave badly, so teachers as trouble solvers have to find appropriate strategies that are effective in helping students keep the code. Otherwise, the disruptions will escalate quickly and the problems will increase in numbers rapidly and finally, teachers will have to work very hard to avoid teaching failure and “losing face” when they cannot manage the disruption as listed in the expectation.

78 FR 18321 - International Code Council: The Update Process for the International Codes and Standards

Science.gov (United States)

2013-03-26

... Energy Conservation Code. International Existing Building Code. International Fire Code. International... Code. International Property Maintenance Code. International Residential Code. International Swimming Pool and Spa Code International Wildland-Urban Interface Code. International Zoning Code. ICC Standards...

Strategies for measuring evolutionary conservation of RNA secondary structures

Directory of Open Access Journals (Sweden)

Hofacker Ivo L

2008-02-01

Full Text Available Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. Results We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. Conclusion Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.

Numerical investigation of disruption characteristics for the snowflake divertor configuration in HL-2M

Science.gov (United States)

Xue, L.; Duan, X. R.; Zheng, G. Y.; Liu, Y. Q.; Pan, Y. D.; Yan, S. L.; Dokuka, V. N.; Lukash, V. E.; Khayrutdinov, R. R.

2016-05-01

Cold and hot vertical displacement events (VDEs) are frequently related to the disruption of vertically-elongated tokamaks. The weak poloidal magnetic field around the null-points of a snowflake divertor configuration may influence the vertical displacement process. In this paper, the major disruption with a cold VDE and the vertical disruption in the HL-2M tokamak are investigated by the DINA code. In order to better illustrate the effect from the weak poloidal field, a double-null snowflake configuration is compared with the standard divertor (SD) configuration under the same plasma parameters. Computational results show that the weak poloidal magnetic field can be partly beneficial for mitigating the vertical instability of the plasma under small perturbations. For major disruption, the peak poloidal halo current fraction is almost the same between the snowflake and the SD configurations. However, this fraction becomes much larger for the snowflake in the event of a hot VDE. Furthermore, during the disruption for a snowflake configuration, the distribution of electromagnetic force on a vacuum vessel gets more non-uniform during the current quench.

Numerical investigation of disruption characteristics for the snowflake divertor configuration in HL-2M

International Nuclear Information System (INIS)

Xue, L; Duan, X R; Zheng, G Y; Liu, Y Q; Pan, Y D; Yan, S L; Dokuka, V N; Khayrutdinov, R R; Lukash, V E

2016-01-01

Cold and hot vertical displacement events (VDEs) are frequently related to the disruption of vertically-elongated tokamaks. The weak poloidal magnetic field around the null-points of a snowflake divertor configuration may influence the vertical displacement process. In this paper, the major disruption with a cold VDE and the vertical disruption in the HL-2M tokamak are investigated by the DINA code. In order to better illustrate the effect from the weak poloidal field, a double-null snowflake configuration is compared with the standard divertor (SD) configuration under the same plasma parameters. Computational results show that the weak poloidal magnetic field can be partly beneficial for mitigating the vertical instability of the plasma under small perturbations. For major disruption, the peak poloidal halo current fraction is almost the same between the snowflake and the SD configurations. However, this fraction becomes much larger for the snowflake in the event of a hot VDE. Furthermore, during the disruption for a snowflake configuration, the distribution of electromagnetic force on a vacuum vessel gets more non-uniform during the current quench. (paper)

An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.

Directory of Open Access Journals (Sweden)

Ru Huang

Full Text Available Imprinted macro non-protein-coding (nc RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80-118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3' end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets.

Design evaluation on sodium piping system and comparison of the design codes

International Nuclear Information System (INIS)

Lee, Dong Won; Jeong, Ji Young; Lee, Yong Bum; Lee, Hyeong Yeon

2015-01-01

A large-scale sodium test loop of STELLA-1 (Sodium integral effect test loop for safety simulation and assessment) with two main piping systems has been installed at KAERI. In this study, design evaluations on the main sodium piping systems in STELLA-1 have been conducted according to the DBR (design by rule) codes of the ASME B31.1 and RCC-MRx RB-3600. In addition, design evaluations according to the DBA (design by analysis) code of the ASME Section III Subsection NB-3200 have been conducted. The evaluation results for the present piping systems showed that results from the DBR codes were more conservative than those from the DBA code, and among the DBR codes, the non-nuclear code of the ASME B31.1 was more conservative than the French nuclear DBR code of the RCC-MRx RB-3600. The conservatism on the DBR codes of the ASME B31.1 and RCC-MRx RB-3600 was quantified based on the present sodium piping analyses.

Design evaluation on sodium piping system and comparison of the design codes

Energy Technology Data Exchange (ETDEWEB)

Lee, Dong Won; Jeong, Ji Young; Lee, Yong Bum; Lee, Hyeong Yeon [KAERI, Daejeon (Korea, Republic of)

2015-03-15

A large-scale sodium test loop of STELLA-1 (Sodium integral effect test loop for safety simulation and assessment) with two main piping systems has been installed at KAERI. In this study, design evaluations on the main sodium piping systems in STELLA-1 have been conducted according to the DBR (design by rule) codes of the ASME B31.1 and RCC-MRx RB-3600. In addition, design evaluations according to the DBA (design by analysis) code of the ASME Section III Subsection NB-3200 have been conducted. The evaluation results for the present piping systems showed that results from the DBR codes were more conservative than those from the DBA code, and among the DBR codes, the non-nuclear code of the ASME B31.1 was more conservative than the French nuclear DBR code of the RCC-MRx RB-3600. The conservatism on the DBR codes of the ASME B31.1 and RCC-MRx RB-3600 was quantified based on the present sodium piping analyses.

Development of a locally mass flux conservative computer code for calculating 3-D viscous flow in turbomachines

Science.gov (United States)

Walitt, L.

1982-01-01

The VANS successive approximation numerical method was extended to the computation of three dimensional, viscous, transonic flows in turbomachines. A cross-sectional computer code, which conserves mass flux at each point of the cross-sectional surface of computation was developed. In the VANS numerical method, the cross-sectional computation follows a blade-to-blade calculation. Numerical calculations were made for an axial annular turbine cascade and a transonic, centrifugal impeller with splitter vanes. The subsonic turbine cascade computation was generated in blade-to-blade surface to evaluate the accuracy of the blade-to-blade mode of marching. Calculated blade pressures at the hub, mid, and tip radii of the cascade agreed with corresponding measurements. The transonic impeller computation was conducted to test the newly developed locally mass flux conservative cross-sectional computer code. Both blade-to-blade and cross sectional modes of calculation were implemented for this problem. A triplet point shock structure was computed in the inducer region of the impeller. In addition, time-averaged shroud static pressures generally agreed with measured shroud pressures. It is concluded that the blade-to-blade computation produces a useful engineering flow field in regions of subsonic relative flow; and cross-sectional computation, with a locally mass flux conservative continuity equation, is required to compute the shock waves in regions of supersonic relative flow.

Parity non-conserving effects in neutron-nucleus scattering

International Nuclear Information System (INIS)

Desplanques, B.

1990-01-01

The present lecture reviews the motivations which led to study the contribution of the neutron-nucleus component to parity-non-conserving effects observed in medium-heavy nuclei and considers its present status. It is shown that it cannot account for those experimental data. The order interpretation of these effects, which cannot lead to precise statements, is schematically described

Symmetries and conservation laws in non-Hermitian field theories

Science.gov (United States)

Alexandre, Jean; Millington, Peter; Seynaeve, Dries

2017-09-01

Anti-Hermitian mass terms are considered, in addition to Hermitian ones, for P T -symmetric complex-scalar and fermionic field theories. In both cases, the Lagrangian can be written in a manifestly symmetric form in terms of the P T -conjugate variables, allowing for an unambiguous definition of the equations of motion. After discussing the resulting constraints on the consistency of the variational procedure, we show that the invariance of a non-Hermitian Lagrangian under a continuous symmetry transformation does not imply the existence of a corresponding conserved current. Conserved currents exist, but these are associated with transformations under which the Lagrangian is not invariant and which reflect the well-known interpretation of P T -symmetric theories in terms of systems with gain and loss. A formal understanding of this unusual feature of non-Hermitian theories requires a careful treatment of Noether's theorem, and we give specific examples for illustration.

Organization of cytokeratin cytoskeleton and germ plasm in the vegetal cortex of Xenopus laevis oocytes depends on coding and non-coding RNAs: Three-dimensional and ultrastructural analysis

International Nuclear Information System (INIS)

Kloc, Malgorzata; Bilinski, Szczepan; Dougherty, Matthew T.

2007-01-01

Recent studies discovered a novel structural role of RNA in maintaining the integrity of the mitotic spindle and cellular cytoskeleton. In Xenopus laevis, non-coding Xlsirts and coding VegT RNAs play a structural role in anchoring localized RNAs, maintaining the organization of the cytokeratin cytoskeleton and germinal granules in the oocyte vegetal cortex and in subsequent development of the germline in the embryo. We studied the ultrastructural effects of antisense oligonucleotide driven ablation of Xlsirts and VegT RNAs on the organization of the cytokeratin, germ plasm and other components of the vegetal cortex. We developed a novel method to immunolabel and visualize cytokeratin at the electron microscopy level, which allowed us to reconstruct the ultrastructural organization of the cytokeratin network relative to the components of the vegetal cortex in Xenopus oocytes. The removal of Xlsirts and VegT RNAs not only disrupts the cytokeratin cytoskeleton but also has a profound transcript-specific effect on the anchoring and distribution of germ plasm islands and their germinal granules and the arrangement of yolk platelets within the vegetal cortex. We suggest that the cytokeratin cytoskeleton plays a role in anchoring of germ plasm islands within the vegetal cortex and germinal granules within the germ plasm islands

Calculations for BDAS Setpoint with Non-conservative Boron Dilution Analysis

International Nuclear Information System (INIS)

Lee, Hwan Soo; Shin, Ho Cheol; Kim, Yong Bae

2014-01-01

BDAS (Boron Dilution Alarm System) utilizes the ex-core detector instrumentation signals to detect a possible inadvertent boron dilution event during operation mode 3, 4, 5, 6. For boron dilution analysis, discrepancies in the active coolant volume and the assumed linearity of the ex-core instrumentation response were identified for CE type PWR and they were reported by NASL-04-02 These discrepancies have potential to impact to determine BDAS setpoint in a non-conservative manner Therefore, in this study, the calculation of BDAS setpoint with those discrepancies condition about OPR1000 was performed and analyzed for checking the safety of BDAS. The new BDAS setpoint is calculated with conservative condition which recommended from Westinghouse Electric Company. The setpoint of BDAS using non-linear ICRR curve decrease to about 5% compared to the setpoint of that using linear ICRR curve. And this effect of the non-linearity is to slightly delay the boron dilution alarm during the inadvertence boron dilution at mode 3, 4, and 5

An uncertainty inclusive un-mixing model to identify tracer non-conservativeness

Science.gov (United States)

Sherriff, Sophie; Rowan, John; Franks, Stewart; Fenton, Owen; Jordan, Phil; hUallacháin, Daire Ó.

2015-04-01

Sediment fingerprinting is being increasingly recognised as an essential tool for catchment soil and water management. Selected physico-chemical properties (tracers) of soils and river sediments are used in a statistically-based 'un-mixing' model to apportion sediment delivered to the catchment outlet (target) to its upstream sediment sources. Development of uncertainty-inclusive approaches, taking into account uncertainties in the sampling, measurement and statistical un-mixing, are improving the robustness of results. However, methodological challenges remain including issues of particle size and organic matter selectivity and non-conservative behaviour of tracers - relating to biogeochemical transformations along the transport pathway. This study builds on our earlier uncertainty-inclusive approach (FR2000) to detect and assess the impact of tracer non-conservativeness using synthetic data before applying these lessons to new field data from Ireland. Un-mixing was conducted on 'pristine' and 'corrupted' synthetic datasets containing three to fifty tracers (in the corrupted dataset one target tracer value was manually corrupted to replicate non-conservative behaviour). Additionally, a smaller corrupted dataset was un-mixed using a permutation version of the algorithm. Field data was collected in an 11 km2 river catchment in Ireland. Source samples were collected from topsoils, subsoils, channel banks, open field drains, damaged road verges and farm tracks. Target samples were collected using time integrated suspended sediment samplers at the catchment outlet at 6-12 week intervals from July 2012 to June 2013. Samples were dried (affected whereas uncertainty was only marginally impacted by the corrupted tracer. Improvement of uncertainty resulted from increasing the number of tracers in both the perfect and corrupted datasets. FR2000 was capable of detecting non-conservative tracer behaviour within the range of mean source values, therefore, it provided a more

TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements.

Directory of Open Access Journals (Sweden)

Kamila Maliszewska-Olejniczak

2015-07-01

Full Text Available Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs. Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium

nRC: non-coding RNA Classifier based on structural features.

Science.gov (United States)

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana

Science.gov (United States)

Richardson, Dale N.; Wiehe, Thomas

Whole genome duplication (WGD) has catalyzed the formation of new species, genes with novel functions, altered expression patterns, complexified signaling pathways and has provided organisms a level of genetic robustness. We studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences (URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene pairs in Arabidopsis. Three distinct methods revealed significant evolutionary conservation between paralogous URSs and were highly correlated with microarray-based expression correlation of the respective gene pairs. Positional information on exact matches between sequences unveiled the contribution of micro-chromosomal rearrangements on expression divergence. A three-way rank analysis of URS similarity, CDS divergence and EC uncovered specific gene functional biases. Transcription factor activity was associated with gene pairs exhibiting conserved URSs and divergent CDSs, whereas a broad array of metabolic enzymes was found to be associated with gene pairs showing diverged URSs but conserved CDSs.

Long Non-Coding RNA in Cancer

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Damjan Glavač

2013-02-01

Full Text Available Long non-coding RNAs (lncRNAs are pervasively transcribed in the genome and are emerging as new players in tumorigenesis due to their various functions in transcriptional, posttranscriptional and epigenetic mechanisms of gene regulation. LncRNAs are deregulated in a number of cancers, demonstrating both oncogenic and tumor suppressive roles, thus suggesting their aberrant expression may be a substantial contributor in cancer development. In this review, we will summarize their emerging role in human cancer and discuss their perspectives in diagnostics as potential biomarkers.

75 FR 19944 - International Code Council: The Update Process for the International Codes and Standards

Science.gov (United States)

2010-04-16

... documents from ICC's Chicago District Office: International Code Council, 4051 W Flossmoor Road, Country... Energy Conservation Code. International Existing Building Code. International Fire Code. International...

A Case for Dynamic Reverse-code Generation to Debug Non-deterministic Programs

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Jooyong Yi

2013-09-01

Full Text Available Backtracking (i.e., reverse execution helps the user of a debugger to naturally think backwards along the execution path of a program, and thinking backwards makes it easy to locate the origin of a bug. So far backtracking has been implemented mostly by state saving or by checkpointing. These implementations, however, inherently do not scale. Meanwhile, a more recent backtracking method based on reverse-code generation seems promising because executing reverse code can restore the previous states of a program without state saving. In the literature, there can be found two methods that generate reverse code: (a static reverse-code generation that pre-generates reverse code through static analysis before starting a debugging session, and (b dynamic reverse-code generation that generates reverse code by applying dynamic analysis on the fly during a debugging session. In particular, we espoused the latter one in our previous work to accommodate non-determinism of a program caused by e.g., multi-threading. To demonstrate the usefulness of our dynamic reverse-code generation, this article presents a case study of various backtracking methods including ours. We compare the memory usage of various backtracking methods in a simple but nontrivial example, a bounded-buffer program. In the case of non-deterministic programs such as this bounded-buffer program, our dynamic reverse-code generation outperforms the existing backtracking methods in terms of memory efficiency.

Identification of Novel Long Non-coding and Circular RNAs in Human Papillomavirus-Mediated Cervical Cancer

Directory of Open Access Journals (Sweden)

Hongbo Wang

2017-09-01

Full Text Available Cervical cancer is the third most common cancer worldwide and the fourth leading cause of cancer-associated mortality in women. Accumulating evidence indicates that long non-coding RNAs (lncRNAs and circular RNAs (circRNAs may play key roles in the carcinogenesis of different cancers; however, little is known about the mechanisms of lncRNAs and circRNAs in the progression and metastasis of cervical cancer. In this study, we explored the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in HPV16 (human papillomavirus genotype 16 mediated cervical squamous cell carcinoma and matched adjacent non-tumor (ATN tissues from three patients with high-throughput RNA sequencing (RNA-seq. In total, we identified 19 lncRNAs, 99 circRNAs, 28 miRNAs, and 304 mRNAs that were commonly differentially expressed (DE in different patients. Among the non-coding RNAs, 3 lncRNAs and 44 circRNAs are novel to our knowledge. Functional enrichment analysis showed that DE lncRNAs, miRNAs, and mRNAs were enriched in pathways crucial to cancer as well as other gene ontology (GO terms. Furthermore, the co-expression network and function prediction suggested that all 19 DE lncRNAs could play different roles in the carcinogenesis and development of cervical cancer. The competing endogenous RNA (ceRNA network based on DE coding and non-coding RNAs showed that each miRNA targeted a number of lncRNAs and circRNAs. The link between part of the miRNAs in the network and cervical cancer has been validated in previous studies, and these miRNAs targeted the majority of the novel non-coding RNAs, thus suggesting that these novel non-coding RNAs may be involved in cervical cancer. Taken together, our study shows that DE non-coding RNAs could be further developed as diagnostic and therapeutic biomarkers of cervical cancer. The complex ceRNA network also lays the foundation for future research of the roles of coding and non-coding RNAs in cervical cancer.

Identification of Novel Long Non-coding and Circular RNAs in Human Papillomavirus-Mediated Cervical Cancer

Science.gov (United States)

Wang, Hongbo; Zhao, Yingchao; Chen, Mingyue; Cui, Jie

2017-01-01

Cervical cancer is the third most common cancer worldwide and the fourth leading cause of cancer-associated mortality in women. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) may play key roles in the carcinogenesis of different cancers; however, little is known about the mechanisms of lncRNAs and circRNAs in the progression and metastasis of cervical cancer. In this study, we explored the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in HPV16 (human papillomavirus genotype 16) mediated cervical squamous cell carcinoma and matched adjacent non-tumor (ATN) tissues from three patients with high-throughput RNA sequencing (RNA-seq). In total, we identified 19 lncRNAs, 99 circRNAs, 28 miRNAs, and 304 mRNAs that were commonly differentially expressed (DE) in different patients. Among the non-coding RNAs, 3 lncRNAs and 44 circRNAs are novel to our knowledge. Functional enrichment analysis showed that DE lncRNAs, miRNAs, and mRNAs were enriched in pathways crucial to cancer as well as other gene ontology (GO) terms. Furthermore, the co-expression network and function prediction suggested that all 19 DE lncRNAs could play different roles in the carcinogenesis and development of cervical cancer. The competing endogenous RNA (ceRNA) network based on DE coding and non-coding RNAs showed that each miRNA targeted a number of lncRNAs and circRNAs. The link between part of the miRNAs in the network and cervical cancer has been validated in previous studies, and these miRNAs targeted the majority of the novel non-coding RNAs, thus suggesting that these novel non-coding RNAs may be involved in cervical cancer. Taken together, our study shows that DE non-coding RNAs could be further developed as diagnostic and therapeutic biomarkers of cervical cancer. The complex ceRNA network also lays the foundation for future research of the roles of coding and non-coding RNAs in cervical cancer. PMID:28970820

Estradiol-Induced Transcriptional Regulation of Long Non-Coding RNA, HOTAIR.

Science.gov (United States)

Bhan, Arunoday; Mandal, Subhrangsu S

2016-01-01

HOTAIR (HOX antisense intergenic RNA) is a 2.2 kb long non-coding RNA (lncRNA), transcribed from the antisense strand of homeobox C (HOXC) gene locus in chromosome 12. HOTAIR acts as a scaffolding lncRNA. It interacts and guides various chromatin-modifying complexes such as PRC2 (polycomb-repressive complex 2) and LSD1 (lysine-specific demethylase 1) to the target gene promoters leading to their gene silencing. Various studies have demonstrated that HOTAIR overexpression is associated with breast cancer. Recent studies from our laboratory demonstrate that HOTAIR is required for viability of breast cancer cells and is transcriptionally regulated by estradiol (E2) in vitro and in vivo. This chapter describes protocols for analysis of the HOTAIR promoter, cloning, transfection and dual luciferase assays, knockdown of protein synthesis by antisense oligonucleotides, and chromatin immunoprecipitation (ChIP) assay. These protocols are useful for studying the estrogen-mediated transcriptional regulation of lncRNA HOTAIR, as well as other protein coding genes and non-coding RNAs.

Identification of long non-coding RNAs in two anthozoan species and their possible implications for coral bleaching.

Science.gov (United States)

Huang, Chen; Morlighem, Jean-Étienne R L; Cai, Jing; Liao, Qiwen; Perez, Carlos Daniel; Gomes, Paula Braga; Guo, Min; Rádis-Baptista, Gandhi; Lee, Simon Ming-Yuen

2017-07-13

Long non-coding RNAs (lncRNAs) have been shown to play regulatory roles in a diverse range of biological processes and are associated with the outcomes of various diseases. The majority of studies about lncRNAs focus on model organisms, with lessened investigation in non-model organisms to date. Herein, we have undertaken an investigation on lncRNA in two zoanthids (cnidarian): Protolpalythoa varibilis and Palythoa caribaeorum. A total of 11,206 and 13,240 lncRNAs were detected in P. variabilis and P. caribaeorum transcriptome, respectively. Comparison using NONCODE database indicated that the majority of these lncRNAs is taxonomically species-restricted with no identifiable orthologs. Even so, we found cases in which short regions of P. caribaeorum's lncRNAs were similar to vertebrate species' lncRNAs, and could be associated with lncRNA conserved regulatory functions. Consequently, some high-confidence lncRNA-mRNA interactions were predicted based on such conserved regions, therefore revealing possible involvement of lncRNAs in posttranscriptional processing and regulation in anthozoans. Moreover, investigation of differentially expressed lncRNAs, in healthy colonies and colonial individuals undergoing natural bleaching, indicated that some up-regulated lncRNAs in P. caribaeorum could posttranscriptionally regulate the mRNAs encoding proteins of Ras-mediated signal transduction pathway and components of innate immune-system, which could contribute to the molecular response of coral bleaching.

Advanced GF(32) nonbinary LDPC coded modulation with non-uniform 9-QAM outperforming star 8-QAM.

Science.gov (United States)

Liu, Tao; Lin, Changyu; Djordjevic, Ivan B

2016-06-27

In this paper, we first describe a 9-symbol non-uniform signaling scheme based on Huffman code, in which different symbols are transmitted with different probabilities. By using the Huffman procedure, prefix code is designed to approach the optimal performance. Then, we introduce an algorithm to determine the optimal signal constellation sets for our proposed non-uniform scheme with the criterion of maximizing constellation figure of merit (CFM). The proposed nonuniform polarization multiplexed signaling 9-QAM scheme has the same spectral efficiency as the conventional 8-QAM. Additionally, we propose a specially designed GF(32) nonbinary quasi-cyclic LDPC code for the coded modulation system based on the 9-QAM non-uniform scheme. Further, we study the efficiency of our proposed non-uniform 9-QAM, combined with nonbinary LDPC coding, and demonstrate by Monte Carlo simulation that the proposed GF(23) nonbinary LDPC coded 9-QAM scheme outperforms nonbinary LDPC coded uniform 8-QAM by at least 0.8dB.

Facial expression coding in children and adolescents with autism: Reduced adaptability but intact norm-based coding.

Science.gov (United States)

Rhodes, Gillian; Burton, Nichola; Jeffery, Linda; Read, Ainsley; Taylor, Libby; Ewing, Louise

2018-05-01

Individuals with autism spectrum disorder (ASD) can have difficulty recognizing emotional expressions. Here, we asked whether the underlying perceptual coding of expression is disrupted. Typical individuals code expression relative to a perceptual (average) norm that is continuously updated by experience. This adaptability of face-coding mechanisms has been linked to performance on various face tasks. We used an adaptation aftereffect paradigm to characterize expression coding in children and adolescents with autism. We asked whether face expression coding is less adaptable in autism and whether there is any fundamental disruption of norm-based coding. If expression coding is norm-based, then the face aftereffects should increase with adaptor expression strength (distance from the average expression). We observed this pattern in both autistic and typically developing participants, suggesting that norm-based coding is fundamentally intact in autism. Critically, however, expression aftereffects were reduced in the autism group, indicating that expression-coding mechanisms are less readily tuned by experience. Reduced adaptability has also been reported for coding of face identity and gaze direction. Thus, there appears to be a pervasive lack of adaptability in face-coding mechanisms in autism, which could contribute to face processing and broader social difficulties in the disorder. © 2017 The British Psychological Society.

Non-axisymmetric equilibrium reconstruction and suppression of density limit disruptions in a current-carrying stellarator

Science.gov (United States)

Ma, Xinxing; Ennis, D. A.; Hanson, J. D.; Hartwell, G. J.; Knowlton, S. F.; Maurer, D. A.

2017-10-01

Non-axisymmetric equilibrium reconstructions have been routinely performed with the V3FIT code in the Compact Toroidal Hybrid (CTH), a stellarator/tokamak hybrid. In addition to 50 external magnetic measurements, 160 SXR emissivity measurements are incorporated into V3FIT to reconstruct the magnetic flux surface geometry and infer the current distribution within the plasma. Improved reconstructions of current and q profiles provide insight into understanding the physics of density limit disruptions observed in current-carrying discharges in CTH. It is confirmed that the final scenario of the density limit of CTH plasmas is consistent with classic observations in tokamaks: current profile shrinkage leads to growing MHD instabilities (tearing modes) followed by a loss of MHD equilibrium. It is also observed that the density limit at a given current linearly increases with increasing amounts of 3D shaping fields. Consequently, plasmas with densities up to two times the Greenwald limit are attained. Equilibrium reconstructions show that addition of 3D fields effectively moves resonance surfaces towards the edge of the plasma where the current profile gradient is less, providing a stabilizing effect. This work is supported by US Department of Energy Grant No. DE-FG02-00ER54610.

Parity non-conserving effects in thermal neutron-deuteron radiative capture

International Nuclear Information System (INIS)

Desplanques, B.

1985-01-01

Predictions of parity non-conserving effects in thermal neutron-deuteron radiative capture are presented. The sensitivity of the results to models of the strong interaction as well as the validity of approximations made in previous calculations are discussed

Neural-net disruption predictor in JT-60U

International Nuclear Information System (INIS)

Yoshino, R.

2003-01-01

The prediction of major disruptions caused by the density limit, the plasma current ramp-down with high internal inductance l i , the low density locked mode and the β-limit has been investigated in JT-60U. The concept of 'stability level', newly proposed in this paper to predict the occurrence of a major disruption, is calculated from nine input parameters every 2 ms by the neural network and the start of a major disruption is predicted when the stability level decreases to a certain level, the 'alarm level'. The neural network is trained in two steps. It is first trained with 12 disruptive and six non-disruptive shots (total of 8011 data points). Second, the target output data for 12 disruptive shots are modified and the network is trained again with additional data points generated by the operator. The 'neural-net disruption predictor' obtained has been tested for 300 disruptive shots (128 945 data points) and 1008 non-disruptive shots (982 800 data points) selected from nine years of operation (1991-1999) of JT-60U. Major disruptions except for those caused by the -limit have been predicted with a prediction success rate of 97-98% at 10 ms prior to the disruption and higher than 90% at 30 ms prior to the disruption while the false alarm rate is 2.1% for non-disruptive shots. This prediction performance has been confirmed for 120 disruptive shots (56 163 data points), caused by the density limit, as well as 1032 non-disruptive shots (1004 611 data points) in the last four years of operation (1999-2002) of JT-60U. A careful selection of the input parameters supplied to the network and the newly developed two-step training of the network have reduced the false alarm rate resulting in a considerable improvement of the prediction success rate. (author)

Python Radiative Transfer Emission code (PyRaTE): non-LTE spectral lines simulations

Science.gov (United States)

Tritsis, A.; Yorke, H.; Tassis, K.

2018-05-01

We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability method. When computing the escape probability, the optical depth is calculated towards all directions with density, molecular abundance, temperature and velocity variations all taken into account. A very easy-to-use interface, capable of importing data from simulations outputs performed with all major astrophysical codes, is also developed. The code is written in PYTHON using an "embarrassingly parallel" strategy and can handle all geometries and projection angles. We benchmark the code by comparing our results with those from RADEX (van der Tak et al. 2007) and against analytical solutions and present case studies using hydrochemical simulations. The code will be released for public use.

Computation of electromagnetic effects in a tokamak due to a plasma disruption

International Nuclear Information System (INIS)

Turner, L.R.

1989-01-01

To model the consequences of a plasma disruption in a tokamak one must combine a code that computes the detailed MHD behavior of the plasma with one that treats the three-dimensional features of the conducting toroidal components around the plasma. The NET (Next European Torus) Team have undertaken a treatment of electromagnetic effects from plasma disruptions using both open loop and closed loop integration of codes. In America, workers at Oak Ridge National Laboratory, Idaho National Engineering Laboratory, and Argonne National Laboratory have looked at plasma disruption effects on the ITER blanket using the codes TSC and EDDYNET. Results show how the forces on a blanket segment depend on the number and size of the segments and on the gap between them. 9 refs., 4 figs., 1 tab

Understanding the threats posed by non-native species: public vs. conservation managers.

Directory of Open Access Journals (Sweden)

Rodolphe E Gozlan

Full Text Available Public perception is a key factor influencing current conservation policy. Therefore, it is important to determine the influence of the public, end-users and scientists on the prioritisation of conservation issues and the direct implications for policy makers. Here, we assessed public attitudes and the perception of conservation managers to five non-native species in the UK, with these supplemented by those of an ecosystem user, freshwater anglers. We found that threat perception was not influenced by the volume of scientific research or by the actual threats posed by the specific non-native species. Media interest also reflected public perception and vice versa. Anglers were most concerned with perceived threats to their recreational activities but their concerns did not correspond to the greatest demonstrated ecological threat. The perception of conservation managers was an amalgamation of public and angler opinions but was mismatched to quantified ecological risks of the species. As this suggests that invasive species management in the UK is vulnerable to a knowledge gap, researchers must consider the intrinsic characteristics of their study species to determine whether raising public perception will be effective. The case study of the topmouth gudgeon Pseudorasbora parva reveals that media pressure and political debate has greater capacity to ignite policy changes and impact studies on non-native species than scientific evidence alone.

Modeling of thermal effects on TIBER II divertor during plasma disruptions

International Nuclear Information System (INIS)

Bruhn, M.L.; Perkins, L.J.

1987-01-01

Mapping the disruption power flow from the mid-plane of the TIBER Engineering Test Reactor to its divertor and calculating the resulting thermal effects are accomplished through the modification and coupling of three presently existing computer codes. The resulting computer code TADDPAK (Thermal Analysis Divertor during Disruption PAcKage) provides three-dimensional graphic presentations of time and positional dependent thermal effects on a poloidal cross section of the double-null-divertor configured reactor. These thermal effects include incident heat flux, surface temperature, vaporization rate, total vaporization, and melting depth. The dependence of these thermal effects on material choice, disruption pulse shape, and the characteristic thickness of the plasma scrape-off layer is determined through parametric analysis with TADDPAK. This computer code is designed to be a convenient, rapid, and user-friendly modeling tool which can be easily adapted to most tokamak double-null-divertor reactor designs

Evolutionary modeling and prediction of non-coding RNAs in Drosophila.

Directory of Open Access Journals (Sweden)

Robert K Bradley

2009-08-01

Full Text Available We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3' end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Science.gov (United States)

Huang, Jingshan; Eilbeck, Karen; Smith, Barry; Blake, Judith A; Dou, Dejing; Huang, Weili; Natale, Darren A; Ruttenberg, Alan; Huan, Jun; Zimmermann, Michael T; Jiang, Guoqian; Lin, Yu; Wu, Bin; Strachan, Harrison J; He, Yongqun; Zhang, Shaojie; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming

2016-01-01

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl.

Comprehensive reconstruction andvisualization of non-coding regulatorynetworks in human

Directory of Open Access Journals (Sweden)

Vincenzo eBonnici

2014-12-01

Full Text Available Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs. Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established online repositories. The interactions involve RNA, DNA, proteins and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command line and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.

Therapeutic targeting of non-coding RNAs in cancer

Czech Academy of Sciences Publication Activity Database

Slabý, O.; Laga, Richard; Sedláček, Ondřej

2017-01-01

Roč. 474, č. 24 (2017), s. 4219-4251 ISSN 0264-6021 R&D Projects: GA MŠk(CZ) LQ1604; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 Keywords : non-coding RNA * RNA delivery * polymer carriers Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemical research methods Impact factor: 3.797, year: 2016

An atlas of human long non-coding RNAs with accurate 5′ ends

KAUST Repository

Hon, Chung-Chau

2017-02-28

Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5′ ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Incorporating genetic and expression data, we show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases. We further demonstrate that lncRNAs overlapping expression quantitative trait loci (eQTL)-associated single nucleotide polymorphisms of messenger RNAs are co-expressed with the corresponding messenger RNAs, suggesting their potential roles in transcriptional regulation. Combining these findings with conservation data, we identify 19,175 potentially functional lncRNAs in the human genome.

Avoidance of singularity and global non-conservation of energy in general relativity

International Nuclear Information System (INIS)

Verma, M.M.

2009-06-01

We show that the singularity in the General Theory of Relativity (GTR) is the expression of a non-Machian feature. It can be avoided with a scale-invariant dynamical theory, a property lacking in GTR. It is further argued that the global non-conservation of energy in GTR also results from the lack of scale-invariance, and the field formulation presented by several authors can only partly resolve the problem. Assuming the global energy conservation, we propose a negative energy density component with a positive equation of state that can drive the late-time acceleration in the universe, while the positive component confines to smaller scales. (author)

Constacyclic codes over the ring F_q+v{F}_q+v2F_q and their applications of constructing new non-binary quantum codes

Science.gov (United States)

Ma, Fanghui; Gao, Jian; Fu, Fang-Wei

2018-06-01

Let R={F}_q+v{F}_q+v2{F}_q be a finite non-chain ring, where q is an odd prime power and v^3=v. In this paper, we propose two methods of constructing quantum codes from (α +β v+γ v2)-constacyclic codes over R. The first one is obtained via the Gray map and the Calderbank-Shor-Steane construction from Euclidean dual-containing (α +β v+γ v2)-constacyclic codes over R. The second one is obtained via the Gray map and the Hermitian construction from Hermitian dual-containing (α +β v+γ v2)-constacyclic codes over R. As an application, some new non-binary quantum codes are obtained.

Accelerated electricity conservation in Juneau, Alaska: A study of household activities that reduced demand 25%

International Nuclear Information System (INIS)

Leighty, Wayne; Meier, Alan

2011-01-01

An avalanche destroyed the main hydroelectric transmission line to Juneau, Alaska in April, 2008. Diesel-generated electricity was substituted, causing electricity prices to increase 500% for 45 days. Electricity demand fell by 25% during the supply disruption. Most of the reduction occurred before the higher rates were implemented. Some conservation - about 8% of historic consumption - persisted after the transmission line was repaired and prices returned to normal. Consumers reduced energy use through a combination of new habits and technical improvements. A survey of residential consumers indicated that the average household undertook 10 conservation actions, with major changes in lighting, space heating, fuel switching, and water and appliance use. We propose a method for prioritizing conservation actions for promotion according to their impact in electricity savings (as a function of popularity, effectiveness, and persistence) and a dynamic framework for electricity use before, during, and after a supply disruption (i.e., both the magnitude and rates of change in electricity conservation). - Research highlights: → An electricity supply disruption caused prices to increase 500% for 45 days. → Electricity conservation of 25% occurred in a matter of days. → Electricity conservation of 8% persisted after the supply disruption was repaired. → Conservation occurred through behavior change and technology adoption. → The disruption induced consumers to try new behaviors that became new habits.

Redefining Secondary Forests in the Mexican Forest Code: Implications for Management, Restoration, and Conservation

Directory of Open Access Journals (Sweden)

Francisco J. Román-Dañobeytia

2014-05-01

Full Text Available The Mexican Forest Code establishes structural reference values to differentiate between secondary and old-growth forests and requires a management plan when secondary forests become old-growth and potentially harvestable forests. The implications of this regulation for forest management, restoration, and conservation were assessed in the context of the Calakmul Biosphere Reserve, which is located in the Yucatan Peninsula. The basal area and stem density thresholds currently used by the legislation to differentiate old-growth from secondary forests are 4 m2/ha and 15 trees/ha (trees with a diameter at breast height of >25 cm; however, our research indicates that these values should be increased to 20 m2/ha and 100 trees/ha, respectively. Given that a management plan is required when secondary forests become old-growth forests, many landowners avoid forest-stand development by engaging slash-and-burn agriculture or cattle grazing. We present evidence that deforestation and land degradation may prevent the natural regeneration of late-successional tree species of high ecological and economic importance. Moreover, we discuss the results of this study in the light of an ongoing debate in the Yucatan Peninsula between policy makers, non-governmental organizations (NGOs, landowners and researchers, regarding the modification of this regulation to redefine the concept of acahual (secondary forest and to facilitate forest management and restoration with valuable timber tree species.

Conservation genetics of otters: Review about the use of non-invasive samples

OpenAIRE

Aristizábal Duque, Sandra L.; Orozco-Jiménez, Luz Y.; Zapata-Escobar, Carolina; Palacio-Baena, Jaime A.

2018-01-01

Abstract: Wild population management programs require determining some fundamental aspects for conservation, including population structure, flow between populations, evolutionary history and kinship, among others. Since sample collection from wild mammals for DNA extraction is a complex task, conservation genetics has developed non-invasive sampling techniques, which allow obtaining DNA without the need to capture individuals. For the genetic characterization of otter populations, stools are...

Construction of Fixed Rate Non-Binary WOM Codes Based on Integer Programming

Science.gov (United States)

Fujino, Yoju; Wadayama, Tadashi

In this paper, we propose a construction of non-binary WOM (Write-Once-Memory) codes for WOM storages such as flash memories. The WOM codes discussed in this paper are fixed rate WOM codes where messages in a fixed alphabet of size $M$ can be sequentially written in the WOM storage at least $t^*$-times. In this paper, a WOM storage is modeled by a state transition graph. The proposed construction has the following two features. First, it includes a systematic method to determine the encoding regions in the state transition graph. Second, the proposed construction includes a labeling method for states by using integer programming. Several novel WOM codes for $q$ level flash memories with 2 cells are constructed by the proposed construction. They achieve the worst numbers of writes $t^*$ that meet the known upper bound in many cases. In addition, we constructed fixed rate non-binary WOM codes with the capability to reduce ICI (inter cell interference) of flash cells. One of the advantages of the proposed construction is its flexibility. It can be applied to various storage devices, to various dimensions (i.e, number of cells), and various kind of additional constraints.

Challenge: Code of environmental law; Herausforderung Umweltgesetzbuch

Energy Technology Data Exchange (ETDEWEB)

NONE

2007-07-15

Within the meeting ''Challenge: Code of environmental law'' at 16th February, 2007, in Berlin (Federal Republic of Germany) and organized by the Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (Berlin, Federal Republic of Germany), the following lectures were held: (a) the new code of environmental law as a contribution to more modernness and efficiency in the environmental politics (Sigmar Gabriel); (b) The code of environmental law from the view of the economy (Martin Wansleben); (c) Significance of the code of environmental law from the view of jurisprudence (Michael Kloepfer); (d) Targets, content and utility of the code of environmental law: Summary of the panel discussion (Tanja Goenner, Klaus Mittelbach, Juergen Resch, Hans-Joachim Koch, Alfred Wirtz, Andreas Troge (moderator)); (e) Considerations to the coding of water law in the code of environmental law (Helge Wendenburg); (f) Considerations to the coding of water law: Summary of te discussion; (g) Considerations to the coding of nature conservation law (Jochen Flasbarth); (h) Considerations to the coding of nature conservation law: Summary of the discussion.

The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features

Science.gov (United States)

Tu, Shiqi; Yuan, Guo-Cheng; Shao, Zhen

2017-01-01

Recently, long non-coding RNAs (lncRNAs) have emerged as an important class of molecules involved in many cellular processes. One of their primary functions is to shape epigenetic landscape through interactions with chromatin modifying proteins. However, mechanisms contributing to the specificity of such interactions remain poorly understood. Here we took the human and mouse lncRNAs that were experimentally determined to have physical interactions with Polycomb repressive complex 2 (PRC2), and systematically investigated the sequence features of these lncRNAs by developing a new computational pipeline for sequences composition analysis, in which each sequence is considered as a series of transitions between adjacent nucleotides. Through that, PRC2-binding lncRNAs were found to be associated with a set of distinctive and evolutionarily conserved sequence features, which can be utilized to distinguish them from the others with considerable accuracy. We further identified fragments of PRC2-binding lncRNAs that are enriched with these sequence features, and found they show strong PRC2-binding signals and are more highly conserved across species than the other parts, implying their functional importance.

Field theory of absorbing phase transitions with a non-diffusive conserved field

International Nuclear Information System (INIS)

Pastor-Satorras, R.; Vespignani, A.

2000-04-01

We investigate the critical behavior of a reaction-diffusion system exhibiting a continuous absorbing-state phase transition. The reaction-diffusion system strictly conserves the total density of particles, represented as a non-diffusive conserved field, and allows an infinite number of absorbing configurations. Numerical results show that it belongs to a wide universality class that also includes stochastic sandpile models. We derive microscopically the field theory representing this universality class. (author)

The Non-Coding Regulatory RNA Revolution in Archaea

Directory of Open Access Journals (Sweden)

Diego Rivera Gelsinger

2018-03-01

Full Text Available Small non-coding RNAs (sRNAs are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting, are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3′ untranslated region (UTR, 5′ UTR, CDS-binding. These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting. While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved and how sRNAs integrate with complex regulatory networks.

Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse

Directory of Open Access Journals (Sweden)

Lu Lu

2010-11-01

Full Text Available Abstract Background Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression in mammalian brain is globally regulated or locally regulated in diverse brain structures, and to study the genomic organisation of brain-expressed sex-biased genes, we performed a large scale gene expression analysis of distinct brain regions in adult male and female mice. Results This study revealed spatial specificity in sex-biased transcription in the mouse brain, and identified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampus and 31 in the eye. Genes located on sex chromosomes were consistently over-represented in all brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealed Y-encoded male-biased transcripts and X-encoded female-biased transcripts known to escape X-inactivation. In addition, we identified novel coding and non-coding X-linked genes with female-biased expression in multiple tissues. Interestingly, the chromosomal positions of all of the female-biased non-coding genes are in close proximity to protein-coding genes that escape X-inactivation. This defines X-chromosome domains each of which contains a coding and a non-coding female-biased gene. Lack of repressive chromatin marks in non-coding transcribed loci supports the possibility that they escape X-inactivation. Moreover, RNA-DNA combined FISH experiments confirmed the biallelic expression of one such novel domain. Conclusion This study demonstrated that the amount of genes with sex-biased expression varies between individual brain regions in mouse. The sex-biased genes identified are localized on many chromosomes. At the same time, sexually dimorphic gene expression that is common to several parts of the brain is mostly restricted to the sex chromosomes. Moreover, the study uncovered

Long Non-coding RNAs in Response to Genotoxic Stress

Institute of Scientific and Technical Information of China (English)

Xiaoman Li; Dong Pan; Baoquan Zhao; Burong Hu

2016-01-01

Long non-coding RNAs(lncRNAs) are increasingly involved in diverse biological processes.Upon DNA damage,the DNA damage response(DDR) elicits a complex signaling cascade,which includes the induction of lncRNAs.LncRNA-mediated DDR is involved in non-canonical and canonical manners.DNA-damage induced lncRNAs contribute to the regulation of cell cycle,apoptosis,and DNA repair,thereby playing a key role in maintaining genome stability.This review summarizes the emerging role of lncRNAs in DNA damage and repair.

Development of a 3D non-linear implicit MHD code

International Nuclear Information System (INIS)

Nicolas, T.; Ichiguchi, K.

2016-06-01

This paper details the on-going development of a 3D non-linear implicit MHD code, which aims at making possible large scale simulations of the non-linear phase of the interchange mode. The goal of the paper is to explain the rationale behind the choices made along the development, and the technical difficulties encountered. At the present stage, the development of the code has not been completed yet. Most of the discussion is concerned with the first approach, which utilizes cartesian coordinates in the poloidal plane. This approach shows serious difficulties in writing the preconditioner, closely related to the choice of coordinates. A second approach, based on curvilinear coordinates, also faced significant difficulties, which are detailed. The third and last approach explored involves unstructured tetrahedral grids, and indicates the possibility to solve the problem. The issue to domain meshing is addressed. (author)

TASS/SMR Code Topical Report for SMART Plant, Vol. I: Code Structure, System Models, and Solution Methods

Energy Technology Data Exchange (ETDEWEB)

Chung, Young Jong; Kim, Soo Hyoung; Kim, See Darl (and others)

2008-10-15

The TASS/SMR code has been developed with domestic technologies for the safety analysis of the SMART plant which is an integral type pressurized water reactor. It can be applied to the analysis of design basis accidents including non-LOCA (loss of coolant accident) and LOCA of the SMART plant. The TASS/SMR code can be applied to any plant regardless of the structural characteristics of a reactor since the code solves the same governing equations for both the primary and secondary system. The code has been developed to meet the requirements of the safety analysis code. This report describes the overall structure of the TASS/SMR, input processing, and the processes of a steady state and transient calculations. In addition, basic differential equations, finite difference equations, state relationships, and constitutive models are described in the report. First, the conservation equations, a discretization process for numerical analysis, search method for state relationship are described. Then, a core power model, heat transfer models, physical models for various components, and control and trip models are explained.

Studies on representative disruption scenarios, associated electromagnetic and heat loads and operation window in ITER

International Nuclear Information System (INIS)

Fujieda, Hirobumi; Shimada, Michiya; Kawano, Yasunori; Ohmori, Junji; Neyatani, Yuzuru; Sugihara, Masayoshi; Gribov, Yuri; Ioki, Kimihiro; Khayrutdinov, Rustan; Lukash, Victor

2007-07-01

The impacts of plasma disruptions on ITER have been investigated in detail to confirm the robustness of the design of the machine to the potential consequential loads. The loads include both electromagnetic (EM) and heat loads on the in-vessel components and the vacuum vessel (VV). Several representative disruption scenarios are specified based on newly derived physics guidelines for the shortest current quench time as well as the maximum product of halo current fraction and toroidal peaking factor arising from disruptions in ITER. Disruption simulations with the DINA code and EM load analyses with a 3D finite element method (FEM) code are performed for these scenarios. Some margins are confirmed in the EM load on in-vessel components due to induced eddy and halo currents for these representative scenarios. However, the margins are not very large. The heat load on various parts of the first wall due to the vertical movement and the thermal quench (TQ) is calculated with a 2D heat conduction code based on the database of heat deposition during disruptions and simulation results with the DINA code. It is found that the beryllium (Be) wall will not melt during the vertical movement. Significant melting is anticipated for the upper Be wall and tungsten divertor baffle due to the TQ after the vertical movement. However, its impact could be substantially mitigated by implementing a reliable detection system of the vertical movement and a mitigation system, e.g., massive noble gas injection (MGI). Some melting of the upper Be wall is anticipated at major disruptions (MD). At least several tens of unmitigated disruptions must be considered even if an advanced prediction/mitigation system is implemented. With these unmitigated disruptions, the loss of Be layer is expected to be within approx. = 30-100 μm/event out of 10 mm thick Be first wall. Various post processing programs of the results simulated with the DINA code, which are developed for the design work, are

Building Energy Efficiency in India: Compliance Evaluation of Energy Conservation Building Code

Energy Technology Data Exchange (ETDEWEB)

Yu, Sha; Evans, Meredydd; Delgado, Alison

2014-03-26

India is experiencing unprecedented construction boom. The country doubled its floorspace between 2001 and 2005 and is expected to add 35 billion m2 of new buildings by 2050. Buildings account for 35% of total final energy consumption in India today, and building energy use is growing at 8% annually. Studies have shown that carbon policies will have little effect on reducing building energy demand. Chaturvedi et al. predicted that, if there is no specific sectoral policies to curb building energy use, final energy demand of the Indian building sector will grow over five times by the end of this century, driven by rapid income and population growth. The growing energy demand in buildings is accompanied by a transition from traditional biomass to commercial fuels, particularly an increase in electricity use. This also leads to a rapid increase in carbon emissions and aggravates power shortage in India. Growth in building energy use poses challenges to the Indian government. To curb energy consumption in buildings, the Indian government issued the Energy Conservation Building Code (ECBC) in 2007, which applies to commercial buildings with a connected load of 100 kW or 120kVA. It is predicted that the implementation of ECBC can help save 25-40% of energy, compared to reference buildings without energy-efficiency measures. However, the impact of ECBC depends on the effectiveness of its enforcement and compliance. Currently, the majority of buildings in India are not ECBC-compliant. The United Nations Development Programme projected that code compliance in India would reach 35% by 2015 and 64% by 2017. Whether the projected targets can be achieved depends on how the code enforcement system is designed and implemented. Although the development of ECBC lies in the hands of the national government – the Bureau of Energy Efficiency under the Ministry of Power, the adoption and implementation of ECBC largely relies on state and local governments. Six years after ECBC�

Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions

DEFF Research Database (Denmark)

Lavstsen, Thomas; Salanti, Ali; Jensen, Anja T R

2003-01-01

and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence. METHODS: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains. RESULTS: var genes can be sub...

Baryon- and lepton-number non-conserving processes and intermediate mass scales

International Nuclear Information System (INIS)

Nieves, J.F.

1981-01-01

An analysis of the possible mechanisms to mediate various baryon- and lepton-number non-conserving processes is presented. Processes considered include the Δ(B+L) = 0 proton decay, ΔB = 2 neutron-antineutron oscillations and neutrino Majorana masses. Among our results we find that, in the absence of elementary scalars and exotic fermions, all the renormalizable interactions of vector bosons and ordinary fermions conserve B-L. Therefore, the observation of Δ(B-L) not equal 0 processes would imply the existence of elementary scalars and/or exotic fermions. (orig.)

ncRNA-class Web Tool: Non-coding RNA feature extraction and pre-miRNA classification web tool

KAUST Repository

Kleftogiannis, Dimitrios A.; Theofilatos, Konstantinos A.; Papadimitriou, Stergios; Tsakalidis, Athanasios K.; Likothanassis, Spiridon D.; Mavroudi, Seferina P.

2012-01-01

Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs. © 2012 IFIP International Federation for Information Processing.

Confinement of Reinforced-Concrete Columns with Non-Code Compliant Confining Reinforcement plus Supplemental Pen-Binder

Directory of Open Access Journals (Sweden)

Anang Kristianto

2012-11-01

Full Text Available One of the important requirements for earthquake resistant building related to confinement is the use of seismic hooks in the hoop or confining reinforcement of reinforced-concrete column elements. However, installation of a confining reinforcement with a 135-degree hook is not easy. Therefore, in practice, many construction workers apply a confining reinforcement with a 90-degreehook (non-code compliant. Based on research and records of recent earthquakes in Indonesia, the use of a non-code compliant confining reinforcement for concrete columns produces structures with poor seismic performance. This paper presents a study that introduces an additional element that is expected to improve the effectiveness of concrete columns confined with a non-code compliant confining reinforcement. The additional element, named a pen-binder, is used to keep the non-code compliant confining reinforcement in place. The effectiveness of this element under pure axial concentric loading was investigatedcomprehensively.The specimens tested in this study were 18 concrete columns,with a cross-section of 170 mm x 170 mm and a height of 480 mm. The main test variables were the material type of the pen-binder, the angle of the hook, and the confining reinforcement configuration.The test results indicate that adding pen-binders can effectively improve the strength and ductility of the column specimens confined with a non-code compliant confining reinforcement

TAD disruption as oncogenic driver.

Science.gov (United States)

Valton, Anne-Laure; Dekker, Job

2016-02-01

Topologically Associating Domains (TADs) are conserved during evolution and play roles in guiding and constraining long-range regulation of gene expression. Disruption of TAD boundaries results in aberrant gene expression by exposing genes to inappropriate regulatory elements. Recent studies have shown that TAD disruption is often found in cancer cells and contributes to oncogenesis through two mechanisms. One mechanism locally disrupts domains by deleting or mutating a TAD boundary leading to fusion of the two adjacent TADs. The other mechanism involves genomic rearrangements that break up TADs and creates new ones without directly affecting TAD boundaries. Understanding the mechanisms by which TADs form and control long-range chromatin interactions will therefore not only provide insights into the mechanism of gene regulation in general, but will also reveal how genomic rearrangements and mutations in cancer genomes can lead to misregulation of oncogenes and tumor suppressors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular breeding of the Mureka-non-forming sake koji mold from Aspergillus oryzae by the disruption of the mreA gene.

Science.gov (United States)

Kubodera, Takafumi; Yamashita, Nobuo; Nishimura, Akira

2003-01-01

Mureka-non-forming sake koji molds were constructed from an Aspergillus oryzae industrial strain by the disruption of the mreA gene using a host-vector system with the ptrA gene as a dominant selectable marker. All of the mreA gene disruptants obtained retained the advantages of the host strain in terms of the brewing characteristics, while their isoamyl alcohol oxidase (IAAOD) activities were significantly lower than that of the host strain. Sake brewing was successfully carried out using the koji prepared with the disruptants, followed by storage of the resultant non-pasteurized sake (nama-shu). The isovaleraldehyde (i-Val) concentration in the sake brewed the host strain increased rapidly and reached the threshold values for mureka, 1.8 ppm and 2.6 ppm after storage at 20 degrees C for 42 d and 63 d, respectively, while those of the disruptants were less than 0.5 ppm even after storage at 20 degrees C or 30 degrees C for 63 d. In the sensory evaluation of the sake stored at 20 degrees C or 30 degrees C for 63 d, all members of the panel recognized the strong mureka flavor of the sake brewed with the host strain, while they did not detect this flavor in the sake brewed with the disruptants. Thus, we concluded that the mreA gene disruptants can be used for the production of sake in which mureka is not formed.

Supply disruption cost for power network planning

International Nuclear Information System (INIS)

Kjoelle, G.H.

1992-09-01

A description is given of the method of approach to calculate the total annual socio-economic cost of power supply disruption and non-supplied energy, included the utilities' cost for planning. The total socio-economic supply disruption cost is the sum of the customers' disruption cost and the utilities' cost for failure and disruption. The mean weighted disruption cost for Norway for one hour disruption is NOK 19 per kWh. The customers' annual disruption cost is calculated with basis in the specific disruption cost referred to heavy load (January) and dimensioning maximum loads. The loads are reduced by factors taking into account the time variations of the failure frequency, duration, the loads and the disruption cost. 6 refs

Parity Non-Conservation in Proton-Proton Elastic Scattering

International Nuclear Information System (INIS)

Brown, V.R.; B.F. Gibson; J.A. Carlson; R. Schiavilla

2002-01-01

The parity non-conserving longitudinal asymmetry in proton-proton (pp) elastic scattering is calculated in the lab-energy range 0-350 MeV using contemporary, realistic strong-interaction potentials combined with a weak-interaction potential comprised of rho- and omega-meson exchanges as exemplified by the DDH model. Values for the rho- and omega-meson coupling constants, h rho rho rho and h rho rho omega , are determined from comparison with the measured asymmetries at 13.6 MeV, 45 MeV, and 221 MeV

Long Non-Coding RNAs in Metabolic Organs and Energy Homeostasis

Directory of Open Access Journals (Sweden)

Maude Giroud

2017-11-01

Full Text Available Single cell organisms can surprisingly exceed the number of human protein-coding genes, which are thus not at the origin of the complexity of an organism. In contrast, the relative amount of non-protein-coding sequences increases consistently with organismal complexity. Moreover, the mammalian transcriptome predominantly comprises non-(protein-coding RNAs (ncRNA, of which the long ncRNAs (lncRNAs constitute the most abundant part. lncRNAs are highly species- and tissue-specific with very versatile modes of action in accordance with their binding to a large spectrum of molecules and their diverse localization. lncRNAs are transcriptional regulators adding an additional regulatory layer in biological processes and pathophysiological conditions. Here, we review lncRNAs affecting metabolic organs with a focus on the liver, pancreas, skeletal muscle, cardiac muscle, brain, and adipose organ. In addition, we will discuss the impact of lncRNAs on metabolic diseases such as obesity and diabetes. In contrast to the substantial number of lncRNA loci in the human genome, the functionally characterized lncRNAs are just the tip of the iceberg. So far, our knowledge concerning lncRNAs in energy homeostasis is still in its infancy, meaning that the rest of the iceberg is a treasure chest yet to be discovered.

Coding chaotic billiards: I-Non-Compact billiards on a negative curvature manifold

International Nuclear Information System (INIS)

Giannoni, M.J.; Ullmo, D.

1989-03-01

This paper presents a method for coding billiards. The main device is to use a proper surface of section, the bounce mapping, and foliate the reduced phase space into regions associated with a given code. The alphabet is merely the ensemble of the labels of the sides of the billiard. The procedure is applied here to non-compact polygonal billiard defined on a manifold of constant negative curvature, with all vertices at infinity. A simple grammar rule is necessary and sufficient to insure existence and uniqueness of the coding

Wound Disruption Following Colorectal Operations.

Science.gov (United States)

Moghadamyeghaneh, Zhobin; Hanna, Mark H; Carmichael, Joseph C; Mills, Steven; Pigazzi, Alessio; Nguyen, Ninh T; Stamos, Michael J

2015-12-01

Postoperative wound disruption is associated with high morbidity and mortality. We sought to identify the risk factors and outcomes of wound disruption following colorectal resection. The American College of Surgeons National Surgical Quality Improvement Program (NSQIP) database was used to examine the clinical data of patients who underwent colorectal resection from 2005 to 2013. Multivariate regression analysis was performed to identify risk factors of wound disruption. We sampled a total of 164,297 patients who underwent colorectal resection. Of these, 2073 (1.3 %) had wound disruption. Patients with wound disruption had significantly higher mortality (5.1 vs. 1.9 %, AOR: 1.46, P = 0.01). The highest risk of wound disruption was seen in patients with wound infection (4.8 vs. 0.9 %, AOR: 4.11, P disruption such as chronic steroid use (AOR: 1.71, P disruption compared to open surgery (AOR: 0.61, P disruption occurs in 1.3 % of colorectal resections, and it correlates with mortality of patients. Wound infection is the strongest predictor of wound disruption. Chronic steroid use, obesity, severe COPD, prolonged operation, non-elective admission, and serum albumin level are strongly associated with wound disruption. Utilization of the laparoscopic approach may decrease the risk of wound disruption when possible.

Analysis of recent fuel-disruption experiments

International Nuclear Information System (INIS)

Kramer, J.M.; Kraft, T.E.; DiMelfi, R.J.; Fenske, G.R.; Gruber, E.E.

1982-01-01

Recent USDOE-sponsored DEH, FGR, and TREAT F series fuel-disruption experiments are analyzed with existing analytical models. The experiments are interpreted and the results used to evaluate the models. Calculations are presented using the FRAS3 fission-gas-behavior code and the DiMelfi-Deitrich fuel-response model

Non-coding RNAs and epigenome: de novo DNA methylation, allelic exclusion and X-inactivation

Directory of Open Access Journals (Sweden)

V. A. Halytskiy

2013-12-01

Full Text Available Non-coding RNAs are widespread class of cell RNAs. They participate in many important processes in cells – signaling, posttranscriptional silencing, protein biosynthesis, splicing, maintenance of genome stability, telomere lengthening, X-inactivation. Nevertheless, activity of these RNAs is not restricted to posttranscriptional sphere, but cover also processes that change or maintain the epigenetic information. Non-coding RNAs can directly bind to the DNA targets and cause their repression through recruitment of DNA methyltransferases as well as chromatin modifying enzymes. Such events constitute molecular mechanism of the RNA-dependent DNA methylation. It is possible, that the RNA-DNA interaction is universal mechanism triggering DNA methylation de novo. Allelic exclusion can be also based on described mechanism. This phenomenon takes place, when non-coding RNA, which precursor is transcribed from one allele, triggers DNA methylation in all other alleles present in the cell. Note, that miRNA-mediated transcriptional silencing resembles allelic exclusion, because both miRNA gene and genes, which can be targeted by this miRNA, contain elements with the same sequences. It can be assumed that RNA-dependent DNA methylation and allelic exclusion originated with the purpose of counteracting the activity of mobile genetic elements. Probably, thinning and deregulation of the cellular non-coding RNA pattern allows reactivation of silent mobile genetic elements resulting in genome instability that leads to ageing and carcinogenesis. In the course of X-inactivation, DNA methylation and subsequent hete­rochromatinization of X chromosome can be triggered by direct hybridization of 5′-end of large non-coding RNA Xist with DNA targets in remote regions of the X chromosome.

Mass and energy-capital conservation equations to study the price evolution of non-renewable energy resources

International Nuclear Information System (INIS)

Gori, F.

2006-01-01

Mass conservation equation of non-renewable resources is employed to study the resources remaining in the reservoir according to the extraction policy. The energy conservation equation is transformed into an energy-capital conservation equation. The Hotelling rule is shown to be a special case of the general energy-capital conservation equation when the mass flow rate of extracted resources is equal to unity. Mass and energy-capital conservation equations are then coupled and solved together. It is investigated the price evolution of extracted resources. The conclusion of the Hotelling rule for non-extracted resources, i.e. an exponential increase of the price of non-renewable resources at the rate of current interest, is then generalized. A new parameter, called 'Price Increase Factor', PIF, is introduced as the difference between the current interest rate of capital and the mass flow rate of extraction of non-renewable resources. The price of extracted resources can increase exponentially only if PIF is greater than zero or if the mass flow rate of extraction is lower than the current interest rate of capital. The price is constant if PIF is zero or if the mass flow rate of extraction is equal to the current interest rate. The price is decreasing with time if PIF is smaller than zero or if the mass flow rate of extraction is higher than the current interest rate. (author)

Infinite sets of conservation laws for linear and non-linear field equations

International Nuclear Information System (INIS)

Niederle, J.

1984-01-01

The work was motivated by a desire to understand group theoretically the existence of an infinite set of conservation laws for non-interacting fields and to carry over these conservation laws to the case of interacting fields. The relation between an infinite set of conservation laws of a linear field equation and the enveloping algebra of its space-time symmetry group was established. It is shown that in the case of the Korteweg-de Vries (KdV) equation to each symmetry of the corresponding linear equation delta sub(o)uxxx=u sub() determined by an element of the enveloping algebra of the space translation algebra, there corresponds a symmetry of the full KdV equation

Facial Expression Recognition via Non-Negative Least-Squares Sparse Coding

Directory of Open Access Journals (Sweden)

Ying Chen

2014-05-01

Full Text Available Sparse coding is an active research subject in signal processing, computer vision, and pattern recognition. A novel method of facial expression recognition via non-negative least squares (NNLS sparse coding is presented in this paper. The NNLS sparse coding is used to form a facial expression classifier. To testify the performance of the presented method, local binary patterns (LBP and the raw pixels are extracted for facial feature representation. Facial expression recognition experiments are conducted on the Japanese Female Facial Expression (JAFFE database. Compared with other widely used methods such as linear support vector machines (SVM, sparse representation-based classifier (SRC, nearest subspace classifier (NSC, K-nearest neighbor (KNN and radial basis function neural networks (RBFNN, the experiment results indicate that the presented NNLS method performs better than other used methods on facial expression recognition tasks.

nocoRNAc: Characterization of non-coding RNAs in prokaryotes

Directory of Open Access Journals (Sweden)

Nieselt Kay

2011-01-01

Full Text Available Abstract Background The interest in non-coding RNAs (ncRNAs constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA genes across many species. However, for most organisms the non-coding transcriptome still remains unexplored to a great extent. Various experimental techniques for the identification of ncRNA transcripts are available, but as these methods are costly and time-consuming, there is a need for computational methods that allow the detection of functional RNAs in complete genomes in order to suggest elements for further experiments. Several programs for the genome-wide prediction of functional RNAs have been developed but most of them predict a genomic locus with no indication whether the element is transcribed or not. Results We present NOCORNAc, a program for the genome-wide prediction of ncRNA transcripts in bacteria. NOCORNAc incorporates various procedures for the detection of transcriptional features which are then integrated with functional ncRNA loci to determine the transcript coordinates. We applied RNAz and NOCORNAc to the genome of Streptomyces coelicolor and detected more than 800 putative ncRNA transcripts most of them located antisense to protein-coding regions. Using a custom design microarray we profiled the expression of about 400 of these elements and found more than 300 to be transcribed, 38 of them are predicted novel ncRNA genes in intergenic regions. The expression patterns of many ncRNAs are similarly complex as those of the protein-coding genes, in particular many antisense ncRNAs show a high expression correlation with their protein-coding partner. Conclusions We have developed NOCORNAc, a framework that facilitates the automated characterization of functional ncRNAs. NOCORNAc increases the confidence of predicted ncRNA loci, especially if they contain transcribed ncRNAs. NOCORNAc is not restricted to

Novel naval technologies: Sustaining or disrupting naval doctrine

NARCIS (Netherlands)

te Kulve, Haico; Smit, Willem A.

2010-01-01

The defense sector is generally known to be simultaneously conservative and enthusiastic about novel technologies. Uptake of new technologies by the military may differ depending on the perceived impact of new technologies. Introduction of technological changes can sustain or disrupt doctrine and

Developmental programming of long non-coding RNAs during postnatal liver maturation in mice.

Directory of Open Access Journals (Sweden)

Lai Peng

Full Text Available The liver is a vital organ with critical functions in metabolism, protein synthesis, and immune defense. Most of the liver functions are not mature at birth and many changes happen during postnatal liver development. However, it is unclear what changes occur in liver after birth, at what developmental stages they occur, and how the developmental processes are regulated. Long non-coding RNAs (lncRNAs are involved in organ development and cell differentiation. Here, we analyzed the transcriptome of lncRNAs in mouse liver from perinatal (day -2 to adult (day 60 by RNA-Sequencing, with an attempt to understand the role of lncRNAs in liver maturation. We found around 15,000 genes expressed, including about 2,000 lncRNAs. Most lncRNAs were expressed at a lower level than coding RNAs. Both coding RNAs and lncRNAs displayed three major ontogenic patterns: enriched at neonatal, adolescent, or adult stages. Neighboring coding and non-coding RNAs showed the trend to exhibit highly correlated ontogenic expression patterns. Gene ontology (GO analysis revealed that some lncRNAs enriched at neonatal ages have their neighbor protein coding genes also enriched at neonatal ages and associated with cell proliferation, immune activation related processes, tissue organization pathways, and hematopoiesis; other lncRNAs enriched at adolescent ages have their neighbor protein coding genes associated with different metabolic processes. These data reveal significant functional transition during postnatal liver development and imply the potential importance of lncRNAs in liver maturation.

Non-coding RNA networks in cancer.

Science.gov (United States)

Anastasiadou, Eleni; Jacob, Leni S; Slack, Frank J

2018-01-01

Thousands of unique non-coding RNA (ncRNA) sequences exist within cells. Work from the past decade has altered our perception of ncRNAs from 'junk' transcriptional products to functional regulatory molecules that mediate cellular processes including chromatin remodelling, transcription, post-transcriptional modifications and signal transduction. The networks in which ncRNAs engage can influence numerous molecular targets to drive specific cell biological responses and fates. Consequently, ncRNAs act as key regulators of physiological programmes in developmental and disease contexts. Particularly relevant in cancer, ncRNAs have been identified as oncogenic drivers and tumour suppressors in every major cancer type. Thus, a deeper understanding of the complex networks of interactions that ncRNAs coordinate would provide a unique opportunity to design better therapeutic interventions.

Vocable Code

DEFF Research Database (Denmark)

Soon, Winnie; Cox, Geoff

2018-01-01

a computational and poetic composition for two screens: on one of these, texts and voices are repeated and disrupted by mathematical chaos, together exploring the performativity of code and language; on the other, is a mix of a computer programming syntax and human language. In this sense queer code can...... be understood as both an object and subject of study that intervenes in the world’s ‘becoming' and how material bodies are produced via human and nonhuman practices. Through mixing the natural and computer language, this article presents a script in six parts from a performative lecture for two persons...

Weak asymptotic solution for a non-strictly hyperbolic system of conservation laws-II

Directory of Open Access Journals (Sweden)

Manas Ranjan Sahoo

2016-04-01

Full Text Available In this article we introduce a concept of entropy weak asymptotic solution for a system of conservation laws and construct the same for a prolonged system of conservation laws which is highly non-strictly hyperbolic. This is first done for Riemann type initial data by introducing $\\delta,\\delta',\\delta''$ waves along a discontinuity curve and then for general initial data by piecing together the Riemann solutions.

Development of 3D CFD code based on structured non-orthogonal grids

International Nuclear Information System (INIS)

Vaidya, Abhijeet Mohan; Maheshwari, Naresh Kumar; Rama Rao, A.

2016-01-01

Most of the nuclear industry problems involve complex geometries. Solution of flow and heat transfer over complex geometries is a very important requirement for designing new reactor systems. Hence development of a general purpose three dimensional (3D) CFD code is undertaken. For handling complex shape of computational domain, implementation on structured non-orthogonal coordinates is being done. The code is validated by comparing its results for 3D inclined lid driven cavity at different inclination angles and Reynolds numbers with OpenFOAM results. This paper contains formulation and validation of the new code developed. (author)

Computational Approaches Reveal New Insights into Regulation and Function of Non; coding RNAs and their Targets

KAUST Repository

Alam, Tanvir

2016-01-01

Regulation and function of protein-coding genes are increasingly well-understood, but no comparable evidence exists for non-coding RNA (ncRNA) genes, which appear to be more numerous than protein-coding genes. We developed a novel machine

Energy and angular-momentum non-conservation in four-dimensional gauge theories

International Nuclear Information System (INIS)

Manohar, A.

1985-01-01

We study energy and angular-momentum non-conservation on four-dimensional chiral gauge theories using Landau levels. These effects are physical manifestations of the usual gauge anomaly, and enable us to understand in a semi-classical approximation why anomaly cancellation is required for a consistent field theory. (orig.)

Development of non-orthogonal and 2-dimensional numerical code TFC2D-BFC for fluid flow

International Nuclear Information System (INIS)

Park, Ju Yeop; In, Wang Kee; Chun, Tae Hyun; Oh, Dong Seok

2000-09-01

The development of algorithm for three dimensional non-orthogonal coordinate system has been made. The algorithm adopts a non-staggered grid system, Cartesian velocity components for independent variables of momentum equations and a SIMPLER algorithm for a pressure correction equation. Except the pressure correction method, the selected grid system and the selected independent variables for momentum equations have been widely used in a commercial code. It is well known that the SIMPLER is superior to the SIMPLE algorithm in the view of convergence rate. Using this algorithm, a two dimensional non-orthogonal numerical code has been completed. The code adopts a structured single square block in a computational domain with a uniform mesh interval. Consequently, any solid body existing in a flow field can be implemented in the numerical code through a blocked-off method which was devised by Patankar

Evaluation of temporary non-code repairs in safety class 3 piping systems

International Nuclear Information System (INIS)

Godha, P.C.; Kupinski, M.; Azevedo, N.F.

1996-01-01

Temporary non-ASME Code repairs in safety class 3 pipe and piping components are permissible during plant operation in accordance with Nuclear Regulatory Commission Generic Letter 90-05. However, regulatory acceptance of such repairs requires the licensee to undertake several timely actions. Consistent with the requirements of GL 90-05, this paper presents an overview of the detailed evaluation and relief request process. The technical criteria encompasses both ductile and brittle piping materials. It also lists appropriate evaluation methods that a utility engineer can select to perform a structural integrity assessment for design basis loading conditions to support the use of temporary non-Code repair for degraded piping components. Most use of temporary non-code repairs at a nuclear generating station is in the service water system which is an essential safety related system providing the ultimate heat sink for various plant systems. Depending on the plant siting, the service water system may use fresh water or salt water as the cooling medium. Various degradation mechanisms including general corrosion, erosion/corrosion, pitting, microbiological corrosion, galvanic corrosion, under-deposit corrosion or a combination thereof continually challenge the pressure boundary structural integrity. A good source for description of corrosion degradation in cooling water systems is provided in a cited reference

SIMMER-II code and its applications

International Nuclear Information System (INIS)

Smith, L.L.

1979-01-01

The significant features of SIMMER-II, a disrupted-core analysis code, are described. The code has the capabalities to begin space-time neutronics calculations from nonstationary reactor states, to track the intermixing of fuel of different enrichments, and to model the complicated heat- and mass-transfer processes that occur in the transition phase. Example calculations are presented for analyses of whole-core accidents and for analyses of experiments supporting the code models

Decoding the non-coding RNAs in Alzheimer's disease.

Science.gov (United States)

Schonrock, Nicole; Götz, Jürgen

2012-11-01

Non-coding RNAs (ncRNAs) are integral components of biological networks with fundamental roles in regulating gene expression. They can integrate sequence information from the DNA code, epigenetic regulation and functions of multimeric protein complexes to potentially determine the epigenetic status and transcriptional network in any given cell. Humans potentially contain more ncRNAs than any other species, especially in the brain, where they may well play a significant role in human development and cognitive ability. This review discusses their emerging role in Alzheimer's disease (AD), a human pathological condition characterized by the progressive impairment of cognitive functions. We discuss the complexity of the ncRNA world and how this is reflected in the regulation of the amyloid precursor protein and Tau, two proteins with central functions in AD. By understanding this intricate regulatory network, there is hope for a better understanding of disease mechanisms and ultimately developing diagnostic and therapeutic tools.

Conservative and non-conservative behaviour of radionuclides in an estuarine environment, with particular respect to the behaviour of plutonium isotopes

International Nuclear Information System (INIS)

Assinder, D.J.; Kelly, M.; Aston, S.R.

1984-01-01

Of the radionuclides entering the Esk Estuary from the Sellafield effluent discharges into the Irish Sea, the behaviour in the dissolved phase of 106 Ru, 134 Cs and 137 Cs is conservative whilst that of 238 Pu and sup(239,240)Pu is non-conservative. The latter leads to the enrichment of Pu in low salinity waters, probably by transfer from the particulate phase. This has repercussions on the distribution of Pu activity in the estuary, and also on the long term fate of sediment stored Pu. (author)

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

KAUST Repository

Alam, Tanvir

2014-10-02

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

Cell disruption for microalgae biorefineries.

Science.gov (United States)

Günerken, E; D'Hondt, E; Eppink, M H M; Garcia-Gonzalez, L; Elst, K; Wijffels, R H

2015-01-01

Microalgae are a potential source for various valuable chemicals for commercial applications ranging from nutraceuticals to fuels. Objective in a biorefinery is to utilize biomass ingredients efficiently similarly to petroleum refineries in which oil is fractionated in fuels and a variety of products with higher value. Downstream processes in microalgae biorefineries consist of different steps whereof cell disruption is the most crucial part. To maintain the functionality of algae biochemicals during cell disruption while obtaining high disruption yields is an important challenge. Despite this need, studies on mild disruption of microalgae cells are limited. This review article focuses on the evaluation of conventional and emerging cell disruption technologies, and a comparison thereof with respect to their potential for the future microalgae biorefineries. The discussed techniques are bead milling, high pressure homogenization, high speed homogenization, ultrasonication, microwave treatment, pulsed electric field treatment, non-mechanical cell disruption and some emerging technologies. Copyright © 2015 Elsevier Inc. All rights reserved.

Development of Non-Conservative Joints in Beam Networks for Vibration Energy Flow Analysis

Directory of Open Access Journals (Sweden)

Jee-Hun Song

2007-01-01

Full Text Available Our work aims to find a general solution for the vibrational energy flow through a plane network of beams on the basis of an energy flow analysis. A joint between two semi-infinite beams are modeled by three sets of springs and dashpots. Thus, the results can incorporate the case of complaint and non-conservative in all the three degrees of freedom. In the cases of finite coupled structures connected at a certain angle, the derived non-conservative joints and developed wave energy equation were applied. The joint properties, the frequency, the coupling angle, and the internal loss factor were changed to evaluate the proposed methods for predicting medium-to-high frequency vibrational energy and intensity distributions.

Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes.

Science.gov (United States)

Peng, Hui; Lan, Chaowang; Liu, Yuansheng; Liu, Tao; Blumenstein, Michael; Li, Jinyan

2017-10-03

Disease-related protein-coding genes have been widely studied, but disease-related non-coding genes remain largely unknown. This work introduces a new vector to represent diseases, and applies the newly vectorized data for a positive-unlabeled learning algorithm to predict and rank disease-related long non-coding RNA (lncRNA) genes. This novel vector representation for diseases consists of two sub-vectors, one is composed of 45 elements, characterizing the information entropies of the disease genes distribution over 45 chromosome substructures. This idea is supported by our observation that some substructures (e.g., the chromosome 6 p-arm) are highly preferred by disease-related protein coding genes, while some (e.g., the 21 p-arm) are not favored at all. The second sub-vector is 30-dimensional, characterizing the distribution of disease gene enriched KEGG pathways in comparison with our manually created pathway groups. The second sub-vector complements with the first one to differentiate between various diseases. Our prediction method outperforms the state-of-the-art methods on benchmark datasets for prioritizing disease related lncRNA genes. The method also works well when only the sequence information of an lncRNA gene is known, or even when a given disease has no currently recognized long non-coding genes.

Disruption-induced poloidal currents in the tokamak wall

International Nuclear Information System (INIS)

Pustovitov, V.D.

2017-01-01

Highlights: • Induction effects during disruptions and rapid transient events in tokamaks. • Plasma-wall electromagnetic interaction. • Flux-conserving evolution of plasma equilibrium. • Poloidal current induced in the vacuum vessel wall in a tokamak. • Complete analytical derivations and estimates. - Abstract: The poloidal current induced in the tokamak wall during fast transient events is analytically evaluated. The analysis is based on the electromagnetic relations coupled with plasma equilibrium equations. The derived formulas describe the consequences of both thermal and current quenches. In the final form, they give explicit dependence of the wall current on the plasma pressure and current. A comparison with numerical results of Villone et al. [F. Villone, G. Ramogida, G. Rubinacci, Fusion Eng. Des. 93, 57 (2015)] for IGNITOR is performed. Our analysis confirms the importance of the effects described there. The estimates show that the disruption-induced poloidal currents in the wall should be necessarily taken into account in the studies of disruptions and disruption mitigation in ITER.

Disruption-induced poloidal currents in the tokamak wall

Energy Technology Data Exchange (ETDEWEB)

Pustovitov, V.D., E-mail: Pustovitov_VD@nrcki.ru [National Research Centre ‘Kurchatov Institute’, Pl. Kurchatova 1, Moscow 123182 (Russian Federation); National Research Nuclear University MEPhI, Kashirskoe sh. 31, Moscow 115409, Russia (Russian Federation)

2017-04-15

Highlights: • Induction effects during disruptions and rapid transient events in tokamaks. • Plasma-wall electromagnetic interaction. • Flux-conserving evolution of plasma equilibrium. • Poloidal current induced in the vacuum vessel wall in a tokamak. • Complete analytical derivations and estimates. - Abstract: The poloidal current induced in the tokamak wall during fast transient events is analytically evaluated. The analysis is based on the electromagnetic relations coupled with plasma equilibrium equations. The derived formulas describe the consequences of both thermal and current quenches. In the final form, they give explicit dependence of the wall current on the plasma pressure and current. A comparison with numerical results of Villone et al. [F. Villone, G. Ramogida, G. Rubinacci, Fusion Eng. Des. 93, 57 (2015)] for IGNITOR is performed. Our analysis confirms the importance of the effects described there. The estimates show that the disruption-induced poloidal currents in the wall should be necessarily taken into account in the studies of disruptions and disruption mitigation in ITER.

An analysis of recent fuel disruption experiments

International Nuclear Information System (INIS)

Kramer, J.M.; Kraft, T.E.; Dimelfi, R.J.; Fenske, G.R.; Gruber, E.E.

1982-01-01

Recent USDOE-Sponsored DEH, FGR, and TREAT F series fuel disruption experiments are analyzed with existing analytical models. The experiments are interpreted and the results used to evaluate the models. Calculations are presented using the FRAS3 fission gas behavior code and the DiMelfi-Deitrich fuel response model

The emerging role of non-coding RNAs in drug addiction

Directory of Open Access Journals (Sweden)

Gregory Charles Sartor

2012-06-01

Full Text Available Prolonged drug use causes long-lasting neuroadaptations in reward-related brain areas that contribute to addiction. Despite significant amount of research dedicated to understanding the underlying mechanisms of addiction, the molecular underpinnings remain unclear. At the same time, much of the pervasive transcription that encompasses the human genome occurs in the nervous system and contributes to its heterogeneity and complexity. Recent evidence suggests that non-coding RNAs (ncRNAs play an important and dynamic role in transcriptional regulation, epigenetic signaling, stress response, and plasticity in the nervous system. Dysregulation of ncRNAs are thought to contribute to many, and perhaps all, neurological disorders, including addiction. Here, we review recent insights in the functional relevance of ncRNAs, including both microRNAs (miRNAs and long non-coding RNAs (lncRNAs, and then illustrate specific examples of ncRNA regulation in the context of drug addiction. We conclude that ncRNAs are importantly involved in the persistent neuroadaptations associated with addiction-related behaviors, and that therapies that target specific ncRNAs may represent new avenues for the treatment of drug addiction.

The roles of non-coding RNAs in cardiac regenerative medicine

Directory of Open Access Journals (Sweden)

Oi Kuan Choong

2017-06-01

Full Text Available The emergence of non-coding RNAs (ncRNAs has challenged the central dogma of molecular biology that dictates that the decryption of genetic information starts from transcription of DNA to RNA, with subsequent translation into a protein. Large numbers of ncRNAs with biological significance have now been identified, suggesting that ncRNAs are important in their own right and their roles extend far beyond what was originally envisaged. ncRNAs do not only regulate gene expression, but are also involved in chromatin architecture and structural conformation. Several studies have pointed out that ncRNAs participate in heart disease; however, the functions of ncRNAs still remain unclear. ncRNAs are involved in cellular fate, differentiation, proliferation and tissue regeneration, hinting at their potential therapeutic applications. Here, we review the current understanding of both the biological functions and molecular mechanisms of ncRNAs in heart disease and describe some of the ncRNAs that have potential heart regeneration effects. Keywords: Non-coding RNAs, Cardiac regeneration, Cardiac fate, Proliferation, Differentiation, Reprograming

Conservation patterns in different functional sequence categoriesof divergent Drosophila species

Energy Technology Data Exchange (ETDEWEB)

Papatsenko, Dmitri; Kislyuk, Andrey; Levine, Michael; Dubchak, Inna

2005-10-01

We have explored the distributions of fully conservedungapped blocks in genome-wide pairwise alignments of recently completedspecies of Drosophila: D.yakuba, D.ananassae, D.pseudoobscura, D.virilisand D.mojavensis. Based on these distributions we have found that nearlyevery functional sequence category possesses its own distinctiveconservation pattern, sometimes independent of the overall sequenceconservation level. In the coding and regulatory regions, the ungappedblocks were longer than in introns, UTRs and non-functional sequences. Atthe same time, the blocks in the coding regions carried 3N+2 signaturecharacteristic to synonymic substitutions in the 3rd codon positions.Larger block sizes in transcription regulatory regions can be explainedby the presence of conserved arrays of binding sites for transcriptionfactors. We also have shown that the longest ungapped blocks, or'ultraconserved' sequences, are associated with specific gene groups,including those encoding ion channels and components of the cytoskeleton.We discussed how restrained conservation patterns may help in mappingfunctional sequence categories and improving genomeannotation.

Prospects for Parity Non-conservation Experiments with Highly Charged Heavy Ions

OpenAIRE

Maul, M.; Schäfer, A.; Greiner, W.; Indelicato, P.

1996-01-01

We discuss the prospects for parity non-conservation experiments with highly charged heavy ions. Energy levels and parity mixing for heavy ions with two to five electrons are calculated. We investigate two-photon-transitions and the possibility to observe interference effects between weak-matrix elements and Stark matrix elements for periodic electric field configurations.

Long Non-Coding RNAs in Cancer and Development: Where Do We Go from Here?

Directory of Open Access Journals (Sweden)

Monika Haemmerle

2015-01-01

Full Text Available Recent genome-wide expression profiling studies have uncovered a huge amount of novel, long non-protein-coding RNA transcripts (lncRNA. In general, these transcripts possess a low, but tissue-specific expression, and their nucleotide sequences are often poorly conserved. However, several studies showed that lncRNAs can have important roles for normal tissue development and regulate cellular pluripotency as well as differentiation. Moreover, lncRNAs are implicated in the control of multiple molecular pathways leading to gene expression changes and thus, ultimately modulate cell proliferation, migration and apoptosis. Consequently, deregulation of lncRNA expression contributes to carcinogenesis and is associated with human diseases, e.g., neurodegenerative disorders like Alzheimer’s Disease. Here, we will focus on some major challenges of lncRNA research, especially loss-of-function studies. We will delineate strategies for lncRNA gene targeting in vivo, and we will briefly discuss important consideration and pitfalls when investigating lncRNA functions in knockout animal models. Finally, we will highlight future opportunities for lncRNAs research by applying the concept of cross-species comparison, which might contribute to novel disease biomarker discovery and might identify lncRNAs as potential therapeutic targets.

Conservation implications of anthropogenic impacts on visual communication and camouflage.

Science.gov (United States)

Delhey, Kaspar; Peters, Anne

2017-02-01

Anthropogenic environmental impacts can disrupt the sensory environment of animals and affect important processes from mate choice to predator avoidance. Currently, these effects are best understood for auditory and chemosensory modalities, and recent reviews highlight their importance for conservation. We examined how anthropogenic changes to the visual environment (ambient light, transmission, and backgrounds) affect visual communication and camouflage and considered the implications of these effects for conservation. Human changes to the visual environment can increase predation risk by affecting camouflage effectiveness, lead to maladaptive patterns of mate choice, and disrupt mutualistic interactions between pollinators and plants. Implications for conservation are particularly evident for disrupted camouflage due to its tight links with survival. The conservation importance of impaired visual communication is less documented. The effects of anthropogenic changes on visual communication and camouflage may be severe when they affect critical processes such as pollination or species recognition. However, when impaired mate choice does not lead to hybridization, the conservation consequences are less clear. We suggest that the demographic effects of human impacts on visual communication and camouflage will be particularly strong when human-induced modifications to the visual environment are evolutionarily novel (i.e., very different from natural variation); affected species and populations have low levels of intraspecific (genotypic and phenotypic) variation and behavioral, sensory, or physiological plasticity; and the processes affected are directly related to survival (camouflage), species recognition, or number of offspring produced, rather than offspring quality or attractiveness. Our findings suggest that anthropogenic effects on the visual environment may be of similar importance relative to conservation as anthropogenic effects on other sensory modalities

SHARP: A Spatially Higher-order, Relativistic Particle-in-cell Code

Energy Technology Data Exchange (ETDEWEB)

Shalaby, Mohamad; Broderick, Avery E. [Department of Physics and Astronomy, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1 (Canada); Chang, Philip [Department of Physics, University of Wisconsin-Milwaukee, 1900 E. Kenwood Boulevard, Milwaukee, WI 53211 (United States); Pfrommer, Christoph [Leibniz-Institut für Astrophysik Potsdam (AIP), An der Sternwarte 16, D-14482 Potsdam (Germany); Lamberts, Astrid [Theoretical Astrophysics, California Institute of Technology, Pasadena, CA 91125 (United States); Puchwein, Ewald, E-mail: mshalaby@live.ca [Institute of Astronomy and Kavli Institute for Cosmology, University of Cambridge, Madingley Road, Cambridge, CB3 0HA (United Kingdom)

2017-05-20

Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially higher-order accurate relativistic PIC algorithm in one spatial dimension, which conserves charge and momentum exactly. We utilize the smoothness implied by the usage of higher-order interpolation functions to achieve a spatially higher-order accurate algorithm (up to the fifth order). We validate our algorithm against several test problems—thermal stability of stationary plasma, stability of linear plasma waves, and two-stream instability in the relativistic and non-relativistic regimes. Comparing our simulations to exact solutions of the dispersion relations, we demonstrate that SHARP can quantitatively reproduce important kinetic features of the linear regime. Our simulations have a superior ability to control energy non-conservation and avoid numerical heating in comparison to common second-order schemes. We provide a natural definition for convergence of a general PIC algorithm: the complement of physical modes captured by the simulation, i.e., those that lie above the Poisson noise, must grow commensurately with the resolution. This implies that it is necessary to simultaneously increase the number of particles per cell and decrease the cell size. We demonstrate that traditional ways for testing for convergence fail, leading to plateauing of the energy error. This new PIC code enables us to faithfully study the long-term evolution of plasma problems that require absolute control of the energy and momentum conservation.

Wind Noise Reduction using Non-negative Sparse Coding

DEFF Research Database (Denmark)

Schmidt, Mikkel N.; Larsen, Jan; Hsiao, Fu-Tien

2007-01-01

We introduce a new speaker independent method for reducing wind noise in single-channel recordings of noisy speech. The method is based on non-negative sparse coding and relies on a wind noise dictionary which is estimated from an isolated noise recording. We estimate the parameters of the model ...... and discuss their sensitivity. We then compare the algorithm with the classical spectral subtraction method and the Qualcomm-ICSI-OGI noise reduction method. We optimize the sound quality in terms of signal-to-noise ratio and provide results on a noisy speech recognition task....

High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs.

Directory of Open Access Journals (Sweden)

Germán Martínez

Full Text Available Micro RNAS (miRNAs are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance. Here we report a combined approach of bioinformatics prediction, high-throughput sequencing data and molecular methods to analyze miRNAs populations in cucumber (Cucumis sativus plants. A set of 19 conserved and 6 known but non-conserved miRNA families were found in our cucumber small RNA dataset. We also identified 7 (3 with their miRNA* strand not previously described miRNAs, candidates to be cucumber-specific. To validate their description these new C. sativus miRNAs were detected by northern blot hybridization. Additionally, potential targets for most conserved and new miRNAs were identified in cucumber genome.In summary, in this study we have identified, by first time, conserved, known non-conserved and new miRNAs arising from an agronomically important species such as C. sativus. The detection of this complex population of regulatory small RNAs suggests that similarly to that observe in other plant species, cucumber miRNAs may possibly play an important role in diverse biological and metabolic processes.

Shock loading of reactor vessel following hypothetical core disruptive accident

International Nuclear Information System (INIS)

Srinivas, G.; Doshi, J.B.

1990-01-01

Hypothetical Core Disruptive Accident (HCDA) has been historically considered as the maximum credible accident in Fast Breeder Reactor systems. Environmental consequences of such an accident depends to a great extent on the ability of the reactor vessel to maintain integrity during the shock loading following an HCDA. In the present paper, a computational model of the reactor core and the surrounding coolant with a free surface is numerical technique. The equations for conservation of mass, momentum and energy along with an equation of state are considered in two dimensional cylindrical geometry. The reactor core at the end of HCDA is taken as a bubble of hot, vaporized fuel at high temperature and pressure, formed at the center of the reactor vessel and expanding against the surrounding liquid sodium coolant. The free surface of sodium at the top of the vessel and the movement of the core bubble-liquid coolant interface are tracked by Marker and Cell (MAC) procedure. The results are obtained for the transient pressure at the vessel wall and also for the loading on the roof plug by the impact of the slug of liquid sodium. The computer code developed is validated against a benchmark experiment chosen to be ISPRA experiment reported in literature. The computer code is next applied to predict the loading on the Indian Prototype Fast Breeder Reactor (PFBR) being developed at Kalpakkam

A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

Science.gov (United States)

Kress, W John; Erickson, David L

2007-06-06

A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

Characterization of non-coding DNA satellites associated with sweepoviruses (genus Begomovirus, Geminiviridae - definition of a distinct class of begomovirus-associated satellites

Directory of Open Access Journals (Sweden)

Gloria eLozano

2016-02-01

Full Text Available Begomoviruses (family Geminiviridae are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas. Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus–satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus, with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem-loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem-loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed.

On conservation of renewable resources with stock-dependent return and non-concave production

International Nuclear Information System (INIS)

Olson, Lars J.; Roy, Santanu

1994-05-01

An analysis is presented of the intertemporal choice foundations underlying the conservation or extinction of renewable resources when the resource production function is non-concave and the immediate return function depends on both current consumption and the size of the resource stock. This case may exhibit nonlinear dynamics and extinction is possible from high stocks even if conservation occurs from lower stocks. The paper focusses on the influence of preferences and the production function on the efficiency of: global conservation, the existence of a safe standard of conservation, or extinction. We show that conservation is efficient under weaker conditions than the 'δ-productivity' requirements derived in models where return function is not stock-dependent. The marginal rate of substitution between investment and the stock plays an important role in addition to the discount factor and the marginal productivity of the resource. Extinction need not be optimal even if the intrinsic growth rate of the resource is less than the external rate of return. Our analysis demonstrates the potential role of taxes, subsidies, demand forces, and harvest costs in determining the efficiency of conservation or extinction. 3 figs., 1 appendix, 24 refs

On conservation of renewable resources with stock-dependent return and non-concave production

Energy Technology Data Exchange (ETDEWEB)

Olson, Lars J. [Department of Agricultural and Resource Economics, University of Maryland, College Park, MD (United States); Roy, Santanu [Econometric Institute, Erasmus University, Rotterdam (Netherlands)

1994-05-01

An analysis is presented of the intertemporal choice foundations underlying the conservation or extinction of renewable resources when the resource production function is non-concave and the immediate return function depends on both current consumption and the size of the resource stock. This case may exhibit nonlinear dynamics and extinction is possible from high stocks even if conservation occurs from lower stocks. The paper focusses on the influence of preferences and the production function on the efficiency of: global conservation, the existence of a safe standard of conservation, or extinction. We show that conservation is efficient under weaker conditions than the `{delta}-productivity` requirements derived in models where return function is not stock-dependent. The marginal rate of substitution between investment and the stock plays an important role in addition to the discount factor and the marginal productivity of the resource. Extinction need not be optimal even if the intrinsic growth rate of the resource is less than the external rate of return. Our analysis demonstrates the potential role of taxes, subsidies, demand forces, and harvest costs in determining the efficiency of conservation or extinction. 3 figs., 1 appendix, 24 refs.

Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response

Directory of Open Access Journals (Sweden)

Benoit T. Roux

2017-08-01

Full Text Available Despite increasing evidence to indicate that long non-coding RNAs (lncRNAs are novel regulators of immunity, there has been no systematic attempt to identify and characterize the lncRNAs whose expression is changed following the induction of the innate immune response. To address this issue, we have employed next-generation sequencing data to determine the changes in the lncRNA profile in four human (monocytes, macrophages, epithelium, and chondrocytes and four mouse cell types (RAW 264.7 macrophages, bone marrow-derived macrophages, peritoneal macrophages, and splenic dendritic cells following exposure to the pro-inflammatory mediators, lipopolysaccharides (LPS, or interleukin-1β. We show differential expression of 204 human and 210 mouse lncRNAs, with positional analysis demonstrating correlation with immune-related genes. These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences, and show poor evolutionary conservation. Comparison within the human and mouse sequences showed less than 1% sequence conservation, although we identified multiple conserved motifs. Of the 204 human lncRNAs, 21 overlapped with syntenic mouse lncRNAs, of which five were differentially expressed in both species. Among these syntenic lncRNA was IL7-AS (antisense, which was induced in multiple cell types and shown to regulate the production of the pro-inflammatory mediator interleukin-6 in both human and mouse cells. In summary, we have identified and characterized those lncRNAs that are differentially expressed following activation of the human and mouse innate immune responses and believe that these catalogs will provide the foundation for the future analysis of the role of lncRNAs in immune and inflammatory responses.

Risk factors for wound disruption following cesarean delivery.

Science.gov (United States)

Subramaniam, Akila; Jauk, Victoria C; Figueroa, Dana; Biggio, Joseph R; Owen, John; Tita, Alan T N

2014-08-01

Risk factors for post-cesarean wound infection, but not disruption, are well-described in the literature. The primary objective of this study was to identify risk factors for non-infectious post-cesarean wound disruption. Secondary analysis was conducted using data from a single-center randomized controlled trial of staple versus suture skin closure in women ≥24 weeks' gestation undergoing cesarean delivery. Wound disruption was defined as subcutaneous skin or fascial dehiscence excluding primary wound infections. Composite wound morbidity (disruption or infection) was examined as a secondary outcome. Patient demographics, medical co-morbidities, and intrapartum characteristics were evaluated as potential risk factors using multivariable logistic regression. Of the 398 randomized patients, 340, including 26 with disruptions (7.6%) met inclusion criteria and were analyzed. After multivariable adjustments, African-American race (aOR 3.9, 95% CI 1.1-13.8) and staple - as opposed to suture - wound closure (aOR 5.4, 95% CI 1.8-16.1) remained significant risk factors for disruption; non-significant increases were observed for body mass index ≥30 (aOR 2.1, 95% CI 0.6-7.5), but not for diabetes mellitus (aOR 0.9, 95% CI 0.3-2.9). RESULTS for composite wound morbidity were similar. Skin closure with staples, African-American race, and considering the relatively small sample size, potentially obesity are associated with increased risk of non-infectious post-cesarean wound disruption.

A method of non-contact reading code based on computer vision

Science.gov (United States)

Zhang, Chunsen; Zong, Xiaoyu; Guo, Bingxuan

2018-03-01

With the purpose of guarantee the computer information exchange security between internal and external network (trusted network and un-trusted network), A non-contact Reading code method based on machine vision has been proposed. Which is different from the existing network physical isolation method. By using the computer monitors, camera and other equipment. Deal with the information which will be on exchanged, Include image coding ,Generate the standard image , Display and get the actual image , Calculate homography matrix, Image distort correction and decoding in calibration, To achieve the computer information security, Non-contact, One-way transmission between the internal and external network , The effectiveness of the proposed method is verified by experiments on real computer text data, The speed of data transfer can be achieved 24kb/s. The experiment shows that this algorithm has the characteristics of high security, fast velocity and less loss of information. Which can meet the daily needs of the confidentiality department to update the data effectively and reliably, Solved the difficulty of computer information exchange between Secret network and non-secret network, With distinctive originality, practicability, and practical research value.

Comprehensive Reconstruction and Visualization of Non-Coding Regulatory Networks in Human

Science.gov (United States)

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape. PMID:25540777

Comprehensive reconstruction and visualization of non-coding regulatory networks in human.

Science.gov (United States)

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.

Non-Coding RNAs in Castration-Resistant Prostate Cancer: Regulation of Androgen Receptor Signaling and Cancer Metabolism.

Science.gov (United States)

Shih, Jing-Wen; Wang, Ling-Yu; Hung, Chiu-Lien; Kung, Hsing-Jien; Hsieh, Chia-Ling

2015-12-04

Hormone-refractory prostate cancer frequently relapses from therapy and inevitably progresses to a bone-metastatic status with no cure. Understanding of the molecular mechanisms conferring resistance to androgen deprivation therapy has the potential to lead to the discovery of novel therapeutic targets for type of prostate cancer with poor prognosis. Progression to castration-resistant prostate cancer (CRPC) is characterized by aberrant androgen receptor (AR) expression and persistent AR signaling activity. Alterations in metabolic activity regulated by oncogenic pathways, such as c-Myc, were found to promote prostate cancer growth during the development of CRPC. Non-coding RNAs represent a diverse family of regulatory transcripts that drive tumorigenesis of prostate cancer and various other cancers by their hyperactivity or diminished function. A number of studies have examined differentially expressed non-coding RNAs in each stage of prostate cancer. Herein, we highlight the emerging impacts of microRNAs and long non-coding RNAs linked to reactivation of the AR signaling axis and reprogramming of the cellular metabolism in prostate cancer. The translational implications of non-coding RNA research for developing new biomarkers and therapeutic strategies for CRPC are also discussed.

Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.

Science.gov (United States)

Gussow, Ayal B; Copeland, Brett R; Dhindsa, Ryan S; Wang, Quanli; Petrovski, Slavé; Majoros, William H; Allen, Andrew S; Goldstein, David B

2017-01-01

There is broad agreement that genetic mutations occurring outside of the protein-coding regions play a key role in human disease. Despite this consensus, we are not yet capable of discerning which portions of non-coding sequence are important in the context of human disease. Here, we present Orion, an approach that detects regions of the non-coding genome that are depleted of variation, suggesting that the regions are intolerant of mutations and subject to purifying selection in the human lineage. We show that Orion is highly correlated with known intolerant regions as well as regions that harbor putatively pathogenic variation. This approach provides a mechanism to identify pathogenic variation in the human non-coding genome and will have immediate utility in the diagnostic interpretation of patient genomes and in large case control studies using whole-genome sequences.

Non-coding RNAs and heme oxygenase-1 in vaccinia virus infection

International Nuclear Information System (INIS)

Meseda, Clement A.; Srinivasan, Kumar; Wise, Jasen; Catalano, Jennifer; Yamada, Kenneth M.; Dhawan, Subhash

2014-01-01

Highlights: • Heme oxygenase-1 (HO-1) induction inhibited vaccinia virus infection of macrophages. • Reduced infectivity inversely correlated with increased expression of non-coding RNAs. • The regulation of HO-1 and ncRNAs suggests a novel host defense response against vaccinia virus infection. - Abstract: Small nuclear RNAs (snRNAs) are <200 nucleotide non-coding uridylate-rich RNAs. Although the functions of many snRNAs remain undetermined, a population of snRNAs is produced during the early phase of infection of cells by vaccinia virus. In the present study, we demonstrate a direct correlation between expression of the cytoprotective enzyme heme oxygenase-1 (HO-1), suppression of selective snRNA expression, and inhibition of vaccinia virus infection of macrophages. Hemin induced HO-1 expression, completely reversed virus-induced host snRNA expression, and suppressed vaccinia virus infection. This involvement of specific virus-induced snRNAs and associated gene clusters suggests a novel HO-1-dependent host-defense pathway in poxvirus infection

Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

Energy Technology Data Exchange (ETDEWEB)

Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

2007-02-21

Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

Survey of disruption causes at JET

International Nuclear Information System (INIS)

De Vries, P.C.; Johnson, M.F.; Alper, B.; Hender, T.C.; Riccardo, V.; Buratti, P.; Koslowski, H.R.

2011-01-01

A survey has been carried out into the causes of all 2309 disruptions over the last decade of JET operations. The aim of this survey was to obtain a complete picture of all possible disruption causes, in order to devise better strategies to prevent or mitigate their impact. The analysis allows the effort to avoid or prevent JET disruptions to be more efficient and effective. As expected, a highly complex pattern of chain of events that led to disruptions emerged. It was found that the majority of disruptions had a technical root cause, for example due to control errors, or operator mistakes. These bring a random, non-physics, factor into the occurrence of disruptions and the disruption rate or disruptivity of a scenario may depend more on technical performance than on physics stability issues. The main root cause of JET disruptions was nevertheless due to neo-classical tearing modes that locked, closely followed in second place by disruptions due to human error. The development of more robust operational scenarios has reduced the JET disruption rate over the last decade from about 15% to below 4%. A fraction of all disruptions was caused by very fast, precursorless unpredictable events. The occurrence of these disruptions may set a lower limit of 0.4% to the disruption rate of JET. If one considers on top of that human error and all unforeseen failures of heating or control systems this lower limit may rise to 1.0% or 1.6%, respectively.

Critical review of conservation equations for two-phase flow in the U.S. NRC TRACE code

International Nuclear Information System (INIS)

Wulff, Wolfgang

2011-01-01

Research highlights: → Field equations as implemented in TRACE are incorrect. → Boundary conditions needed for cooling of nuclear fuel elements are wrong. → The two-fluid model in TRACE is not closed. → Three-dimensional flow modeling in TRACE has no basis. - Abstract: The field equations for two-phase flow in the computer code TRAC/RELAP Advanced Computational Engine or TRACE are examined to determine their validity, their capabilities and limitations in resolving nuclear reactor safety issues. TRACE was developed for the NRC to predict thermohydraulic phenomena in nuclear power plants during operational transients and postulated accidents. TRACE is based on the rigorously derived and well-established two-fluid field equations for 1-D and 3-D two-phase flow. It is shown that: (1)The two-fluid field equations for mass conservation as implemented in TRACE are wrong because local mass balances in TRACE are in conflict with mass conservation for the whole reactor system, as shown in Section . (2)Wrong equations of motion are used in TRACE in place of momentum balances, compromising at branch points the prediction of momentum transfer between, and the coupling of, loops in hydraulic networks by impedance (form loss and wall shear) and by inertia and thereby the simulation of reactor component interactions. (3)Most seriously, TRACE calculation of heat transfer from fuel elements is incorrect for single and two-phase flows, because Eq. of the TRACE Manual is wrong (see Section ). (4)Boundary conditions for momentum and energy balances in TRACE are restricted to flow regimes with single-phase wall contact because TRACE lacks constitutive relations for solid-fluid exchange of momentum and heat in prevailing flow regimes. Without a quantified assessment of consequences from (3) to (4), predictions of phasic fluid velocities, fuel temperatures and important safety parameters, e.g., peak clad temperature, are questionable. Moreover, TRACE cannot predict 3-D single- or

Majorana fermion codes

International Nuclear Information System (INIS)

Bravyi, Sergey; Terhal, Barbara M; Leemhuis, Bernhard

2010-01-01

We initiate the study of Majorana fermion codes (MFCs). These codes can be viewed as extensions of Kitaev's one-dimensional (1D) model of unpaired Majorana fermions in quantum wires to higher spatial dimensions and interacting fermions. The purpose of MFCs is to protect quantum information against low-weight fermionic errors, that is, operators acting on sufficiently small subsets of fermionic modes. We examine to what extent MFCs can surpass qubit stabilizer codes in terms of their stability properties. A general construction of 2D MFCs is proposed that combines topological protection based on a macroscopic code distance with protection based on fermionic parity conservation. Finally, we use MFCs to show how to transform any qubit stabilizer code to a weakly self-dual CSS code.

Biocomputational prediction of small non-coding RNAs in Streptomyces

Czech Academy of Sciences Publication Activity Database

Pánek, Josef; Bobek, Jan; Mikulík, Karel; Basler, Marek; Vohradský, Jiří

2008-01-01

Roč. 9, č. 217 (2008), s. 1-14 ISSN 1471-2164 R&D Projects: GA ČR GP204/07/P361; GA ČR GA203/05/0106; GA ČR GA310/07/1009 Grant - others:XE(XE) EC Integrated Project ActinoGEN, LSHM-CT-2004-005224. Institutional research plan: CEZ:AV0Z50200510 Keywords : non-coding RNA * streptomyces * biocomputational prediction Subject RIV: IN - Informatics, Computer Science Impact factor: 3.926, year: 2008

One-dimensional thermohydraulic code THESEUS and its application to chilldown process simulation in two-phase hydrogen flows

Science.gov (United States)

Papadimitriou, P.; Skorek, T.

THESUS is a thermohydraulic code for the calculation of steady state and transient processes of two-phase cryogenic flows. The physical model is based on four conservation equations with separate liquid and gas phase mass conservation equations. The thermohydraulic non-equilibrium is calculated by means of evaporation and condensation models. The mechanical non-equilibrium is modeled by a full-range drift-flux model. Also heat conduction in solid structures and heat exchange for the full spectrum of heat transfer regimes can be simulated. Test analyses of two-channel chilldown experiments and comparisons with the measured data have been performed.

Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury.

Science.gov (United States)

Arthur-Farraj, Peter J; Morgan, Claire C; Adamowicz, Martyna; Gomez-Sanchez, Jose A; Fazal, Shaline V; Beucher, Anthony; Razzaghi, Bonnie; Mirsky, Rhona; Jessen, Kristjan R; Aitman, Timothy J

2017-09-12

Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Effect of music on mealtime disruptions.

Science.gov (United States)

Hooper, Jeff; Carson, Derek; Lindsay, Bill

People with learning disabilities can disrupt mealtimes with non-cooperative, aggressive and self-injurious behaviours that challenge other people to tolerate and manage them. These behaviours appear to arise because the proximity of other people, and the heightened activity and noise of a dining room, causes anxiety and agitation. To examine how delivering calming background music via headphones affected anxiety-driven behaviours that disrupted mealtimes. A sample of 30 adults with mild, moderate or severe learning disabilities were videotaped during mealtimes on two consecutive days. On the first day, half the group ate without any calming music while the other half sat opposite them wearing earphones and listening to calming music. On the second day, the non-music and music groups swapped around. Of the participants who tolerated the earphones, only three showed disruptive behaviour; all three had been sitting at the table waiting for their food. With so few examples, meaningful inferential analysis was not possible. However, there were signs that calming music had a positive effect on disruptive mealtime behaviours. It eliminated physical harm, complaining and verbal repetition in one person, and stopped another from shouting/swearing. It also reduced the incidence of shouting/swearing, restlessness and vocalising. Calming music and reduced waiting at tables for food may reduce disruptive behaviours.

Determination of non-market values to inform conservation strategies for the threatened Alistana-Sanabresa cattle breed.

Science.gov (United States)

Martin-Collado, D; Diaz, C; Drucker, A G; Carabaño, M J; Zander, K K

2014-08-01

Livestock breed-related public good functions are often used to justify support for endangered breed conservation despite the fact that little is known about such non-market values. We show how stated preference techniques can be used to assess the non-market values that people place on livestock breeds. Through the application of a case study choice experiment survey in Zamora province, Spain, the total economic value (TEV) of the threatened Alistana-Sanabresa (AS) cattle breed was investigated. An analysis of the relative importance of the non-market components of its TEV and an assessment of the socio-economic variables that influence people's valuation of such components is used to inform conservation strategy design. Overall, the findings reveal that the AS breed had significant non-market values associated with it and that the value that respondents placed on each specific public good function also varied significantly. Functions related with indirect use cultural and existence values were much more highly valued than landscape maintenance values. These high cultural and existence values (totalling over 80% of TEV) suggest that an AS in situ conservation strategy will be required to secure such values. As part of such a strategy, incentive mechanisms will be needed to permit farmers to capture some of these public good values and thus be able to afford to maintain breed population numbers at socially desirable levels. One such mechanism could be related to the development of breed-related agritourism initiatives, with a view to enhancing private good values and providing an important addition to continued direct support. Where linked with cultural dimensions, niche product market development, including through improving AS breed-related product quality and brand recognition may also have a role to play as part of such an overall conservation and use strategy. We conclude that livestock breed conservation strategies with the highest potential to maximise

Extension of CE/SE method to non-equilibrium dissociating flows

KAUST Repository

Wen, C.Y.

2017-12-08

In this study, the hypersonic non-equilibrium flows over rounded nose geometries are numerically investigated by a robust conservation element and solution element (CE/SE) code, which is based on hybrid meshes consisting of triangular and quadrilateral elements. The dissociating and recombination chemical reactions as well as the vibrational energy relaxation are taken into account. The stiff source terms are solved by an implicit trapezoidal method of integration. Comparison with laboratory and numerical cases are provided to demonstrate the accuracy and reliability of the present CE/SE code in simulating hypersonic non-equilibrium flows.

p53-dependent non-coding RNA networks in chronic lymphocytic leukemia

NARCIS (Netherlands)

Blume, C. J.; Hotz-Wagenblatt, A.; Hüllein, J.; Sellner, L.; Jethwa, A.; Stolz, T.; Slabicki, M.; Lee, K.; Sharathchandra, A.; Benner, A.; Dietrich, S.; Oakes, C. C.; Dreger, P.; te Raa, D.; Kater, A. P.; Jauch, A.; Merkel, O.; Oren, M.; Hielscher, T.; Zenz, T.

2015-01-01

Mutations of the tumor suppressor p53 lead to chemotherapy resistance and a dismal prognosis in chronic lymphocytic leukemia (CLL). Whereas p53 targets are used to identify patient subgroups with impaired p53 function, a comprehensive assessment of non-coding RNA targets of p53 in CLL is missing. We

Modeling of thermal effects on TIBER II [Tokamak Ignition/Burn Experimental Reactor] divertor during plasma disruption

International Nuclear Information System (INIS)

Bruhn, M.L.; Perkins, L.J.

1987-01-01

Mapping the disruption power flow from the mid-plane of the TIBER Engineering Test Reactor to its divertor and calculating the resulting thermal effects are accomplished through the modification and coupling of three presently existing computer codes. The resulting computer code TADDPAK (Thermal Analysis Divertor during Disruption PAcKage) provides three-dimensional graphic presentations of time and positional dependent thermal effects on a poloidal cross section of the double-null-divertor configured reactor. These thermal effects include incident heat flux, surface temperature, vaporization rate, total vaporization, and melting depth. The dependence of these thermal effects on material choice, disruption pulse shape, and the characteristic thickness of the plasma scrape-off layer is determined through parametric analysis with TADDPAK. This computer code is designed to be a convenient, rapid, and user-friendly modeling tool which can be easily adapted to most tokamak double-null-divertor reactor designs. 14 refs

DNA watermarks in non-coding regulatory sequences

Directory of Open Access Journals (Sweden)

Pyka Martin

2009-07-01

Full Text Available Abstract Background DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli. Findings The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity. Conclusion Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

Non-conserved magnetization operator and 'fire-and-ice' ground states in the Ising-Heisenberg diamond chain

Science.gov (United States)

Torrico, Jordana; Ohanyan, Vadim; Rojas, Onofre

2018-05-01

We consider the diamond chain with S = 1/2 XYZ vertical dimers which interact with the intermediate sites via the interaction of the Ising type. We also suppose all four spins form the diamond-shaped plaquette to have different g-factors. The non-uniform g-factors within the quantum spin dimer as well as the XY-anisotropy of the exchange interaction lead to the non-conserving magnetization for the chain. We analyze the effects of non-conserving magnetization as well as the effects of the appearance of negative g-factors among the spins from the unit cell. A number of unusual frustrated states for ferromagnetic couplings and g-factors with non-uniform signs are found out. These frustrated states generalize the "half-fire-half-ice" state introduced in reference Yin et al. (2015). The corresponding zero-temperature ground state phase diagrams are presented.

Novel classes of non-coding RNAs and cancer

Directory of Open Access Journals (Sweden)

Sana Jiri

2012-05-01

Full Text Available Abstract For the many years, the central dogma of molecular biology has been that RNA functions mainly as an informational intermediate between a DNA sequence and its encoded protein. But one of the great surprises of modern biology was the discovery that protein-coding genes represent less than 2% of the total genome sequence, and subsequently the fact that at least 90% of the human genome is actively transcribed. Thus, the human transcriptome was found to be more complex than a collection of protein-coding genes and their splice variants. Although initially argued to be spurious transcriptional noise or accumulated evolutionary debris arising from the early assembly of genes and/or the insertion of mobile genetic elements, recent evidence suggests that the non-coding RNAs (ncRNAs may play major biological roles in cellular development, physiology and pathologies. NcRNAs could be grouped into two major classes based on the transcript size; small ncRNAs and long ncRNAs. Each of these classes can be further divided, whereas novel subclasses are still being discovered and characterized. Although, in the last years, small ncRNAs called microRNAs were studied most frequently with more than ten thousand hits at PubMed database, recently, evidence has begun to accumulate describing the molecular mechanisms by which a wide range of novel RNA species function, providing insight into their functional roles in cellular biology and in human disease. In this review, we summarize newly discovered classes of ncRNAs, and highlight their functioning in cancer biology and potential usage as biomarkers or therapeutic targets.

The role of the uncertainty in code development

Energy Technology Data Exchange (ETDEWEB)

Barre, F. [CEA-Grenoble (France)

1997-07-01

From a general point of view, all the results of a calculation should be given with their uncertainty. It is of most importance in nuclear safety where sizing of the safety systems, therefore protection of the population and the environment essentially depends on the calculation results. Until these last years, the safety analysis was performed with conservative tools. Two types of critics can be made. Firstly, conservative margins can be too large and it may be possible to reduce the cost of the plant or its operation with a best estimate approach. Secondly, some of the conservative hypotheses may not really conservative in the full range of physical events which can occur during an accident. Simpson gives an interesting example: in some cases, the majoration of the residual power during a small break LOCA can lead to an overprediction of the swell level and thus of an overprediction of the core cooling, which is opposite to a conservative prediction. A last question is: does the accumulation of conservative hypotheses for a problem always give a conservative result? The two phase flow physics, mainly dealing with situation of mechanical and thermal non-equilibrium, is too much complicated to answer these questions with a simple engineer judgement. The objective of this paper is to make a review of the quantification of the uncertainties which can be made during code development and validation.

The role of the uncertainty in code development

International Nuclear Information System (INIS)

Barre, F.

1997-01-01

From a general point of view, all the results of a calculation should be given with their uncertainty. It is of most importance in nuclear safety where sizing of the safety systems, therefore protection of the population and the environment essentially depends on the calculation results. Until these last years, the safety analysis was performed with conservative tools. Two types of critics can be made. Firstly, conservative margins can be too large and it may be possible to reduce the cost of the plant or its operation with a best estimate approach. Secondly, some of the conservative hypotheses may not really conservative in the full range of physical events which can occur during an accident. Simpson gives an interesting example: in some cases, the majoration of the residual power during a small break LOCA can lead to an overprediction of the swell level and thus of an overprediction of the core cooling, which is opposite to a conservative prediction. A last question is: does the accumulation of conservative hypotheses for a problem always give a conservative result? The two phase flow physics, mainly dealing with situation of mechanical and thermal non-equilibrium, is too much complicated to answer these questions with a simple engineer judgement. The objective of this paper is to make a review of the quantification of the uncertainties which can be made during code development and validation

Understanding Epistatic Interactions between Genes Targeted by Non-coding Regulatory Elements in Complex Diseases

Directory of Open Access Journals (Sweden)

Min Kyung Sung

2014-12-01

Full Text Available Genome-wide association studies have proven the highly polygenic architecture of complex diseases or traits; therefore, single-locus-based methods are usually unable to detect all involved loci, especially when individual loci exert small effects. Moreover, the majority of associated single-nucleotide polymorphisms resides in non-coding regions, making it difficult to understand their phenotypic contribution. In this work, we studied epistatic interactions associated with three common diseases using Korea Association Resource (KARE data: type 2 diabetes mellitus (DM, hypertension (HT, and coronary artery disease (CAD. We showed that epistatic single-nucleotide polymorphisms (SNPs were enriched in enhancers, as well as in DNase I footprints (the Encyclopedia of DNA Elements [ENCODE] Project Consortium 2012, which suggested that the disruption of the regulatory regions where transcription factors bind may be involved in the disease mechanism. Accordingly, to identify the genes affected by the SNPs, we employed whole-genome multiple-cell-type enhancer data which discovered using DNase I profiles and Cap Analysis Gene Expression (CAGE. Assigned genes were significantly enriched in known disease associated gene sets, which were explored based on the literature, suggesting that this approach is useful for detecting relevant affected genes. In our knowledge-based epistatic network, the three diseases share many associated genes and are also closely related with each other through many epistatic interactions. These findings elucidate the genetic basis of the close relationship between DM, HT, and CAD.

Disruption of mouse Cenpj, a regulator of centriole biogenesis, phenocopies Seckel syndrome

OpenAIRE

McIntyre, Rebecca E; Lakshminarasimhan Chavali, Pavithra; Ismail, Ozama; Carragher, Damian M; Sanchez-Andrade, Gabriela; Forment, Josep V; Fu, Beiyuan; Del Castillo Velasco-Herrera, Martin; Edwards, Andrew; van der Weyden, Louise; Yang, Fengtang; Ramirez-Solis, Ramiro; Estabel, Jeanne; Gallagher, Ferdia A; Logan, Darren W

2012-01-01

Disruption of the centromere protein J gene, CENPJ (CPAP, MCPH6, SCKL4), which is a highly conserved and ubiquitiously expressed centrosomal protein, has been associated with primary microcephaly and the microcephalic primordial dwarfism disorder Seckel syndrome. The mechanism by which disruption of CENPJ causes the proportionate, primordial growth failure that is characteristic of Seckel syndrome is unknown. By generating a hypomorphic allele of Cenpj, we have developed a mouse (Cenpj(tm/tm)...

Surface heat loads during major disruptions in INTOR

International Nuclear Information System (INIS)

Mioduszewski, P.

1981-01-01

The thermal energy contained in the INTOR plasma is assumed to be about 200 MJ. In a major plasma disruption this energy is dumped into parts of the first wall in a time short compared to the energy confinement time. To estimate the surface heat load due to this energy dump, two major parameters are not sufficiently well known at present: the disruption time and the affected first wall surface area. To get a certain idea of the heat loads to be expected, we have employed the model of conserved flux tubes which are successively scraped-off at the first wall. The results reveal that even for a homogeneous deposition in the toroidal direction the heat load is too high for some parts of the first wall. Since, however, the presumptions are very uncertain to date, experiments will have to be set up to study the energy deposition during disruptions. (author)

Improvements in disruption prediction at ASDEX Upgrade

Energy Technology Data Exchange (ETDEWEB)

Aledda, R., E-mail: raffaele.aledda@diee.unica.it; Cannas, B., E-mail: cannas@diee.unica.it; Fanni, A., E-mail: fanni@diee.unica.it; Pau, A., E-mail: alessandro.pau@diee.unica.it; Sias, G., E-mail: giuliana.sias@diee.unica.it

2015-10-15

Highlights: • A disruption prediction system for AUG, based on a logistic model, is designed. • The length of the disruptive phase is set for each disruption in the training set. • The model is tested on dataset different from that used during the training phase. • The generalization capability and the aging of the model have been tested. • The predictor performance is compared with the locked mode detector. - Abstract: In large-scale tokamaks disruptions have the potential to create serious damage to the facility. Hence disruptions must be avoided, but, when a disruption is unavoidable, minimizing its severity is mandatory. A reliable detection of a disruptive event is required to trigger proper mitigation actions. To this purpose machine learning methods have been widely studied to design disruption prediction systems at ASDEX Upgrade. The training phase of the proposed approaches is based on the availability of disrupted and non-disrupted discharges. In literature disruptive configurations were assumed appearing into the last 45 ms of each disruption. Even if the achieved results in terms of correct predictions were good, it has to be highlighted that the choice of such a fixed temporal window might have limited the prediction performance. In fact, it generates confusing information in cases of disruptions with disruptive phase different from 45 ms. The assessment of a specific disruptive phase for each disruptive discharge represents a relevant issue in understanding the disruptive events. In this paper, the Mahalanobis distance is applied to define a specific disruptive phase for each disruption, and a logistic regressor has been trained as disruption predictor. The results show that enhancements on the achieved performance on disruption prediction are possible by defining a specific disruptive phase for each disruption.

Improvements in disruption prediction at ASDEX Upgrade

International Nuclear Information System (INIS)

Aledda, R.; Cannas, B.; Fanni, A.; Pau, A.; Sias, G.

2015-01-01

Highlights: • A disruption prediction system for AUG, based on a logistic model, is designed. • The length of the disruptive phase is set for each disruption in the training set. • The model is tested on dataset different from that used during the training phase. • The generalization capability and the aging of the model have been tested. • The predictor performance is compared with the locked mode detector. - Abstract: In large-scale tokamaks disruptions have the potential to create serious damage to the facility. Hence disruptions must be avoided, but, when a disruption is unavoidable, minimizing its severity is mandatory. A reliable detection of a disruptive event is required to trigger proper mitigation actions. To this purpose machine learning methods have been widely studied to design disruption prediction systems at ASDEX Upgrade. The training phase of the proposed approaches is based on the availability of disrupted and non-disrupted discharges. In literature disruptive configurations were assumed appearing into the last 45 ms of each disruption. Even if the achieved results in terms of correct predictions were good, it has to be highlighted that the choice of such a fixed temporal window might have limited the prediction performance. In fact, it generates confusing information in cases of disruptions with disruptive phase different from 45 ms. The assessment of a specific disruptive phase for each disruptive discharge represents a relevant issue in understanding the disruptive events. In this paper, the Mahalanobis distance is applied to define a specific disruptive phase for each disruption, and a logistic regressor has been trained as disruption predictor. The results show that enhancements on the achieved performance on disruption prediction are possible by defining a specific disruptive phase for each disruption.

TASS code topical report. V.1 TASS code technical manual

International Nuclear Information System (INIS)

Sim, Suk K.; Chang, W. P.; Kim, K. D.; Kim, H. C.; Yoon, H. Y.

1997-02-01

TASS 1.0 code has been developed at KAERI for the initial and reload non-LOCA safety analysis for the operating PWRs as well as the PWRs under construction in Korea. TASS code will replace various vendor's non-LOCA safety analysis codes currently used for the Westinghouse and ABB-CE type PWRs in Korea. This can be achieved through TASS code input modifications specific to each reactor type. The TASS code can be run interactively through the keyboard operation. A simimodular configuration used in developing the TASS code enables the user easily implement new models. TASS code has been programmed using FORTRAN77 which makes it easy to install and port for different computer environments. The TASS code can be utilized for the steady state simulation as well as the non-LOCA transient simulations such as power excursions, reactor coolant pump trips, load rejections, loss of feedwater, steam line breaks, steam generator tube ruptures, rod withdrawal and drop, and anticipated transients without scram (ATWS). The malfunctions of the control systems, components, operator actions and the transients caused by the malfunctions can be easily simulated using the TASS code. This technical report describes the TASS 1.0 code models including reactor thermal hydraulic, reactor core and control models. This TASS code models including reactor thermal hydraulic, reactor core and control models. This TASS code technical manual has been prepared as a part of the TASS code manual which includes TASS code user's manual and TASS code validation report, and will be submitted to the regulatory body as a TASS code topical report for a licensing non-LOCA safety analysis for the Westinghouse and ABB-CE type PWRs operating and under construction in Korea. (author). 42 refs., 29 tabs., 32 figs

Family number non-conservation induced by the super-symmetric mixing of scalar leptons

International Nuclear Information System (INIS)

Levine, M.J.S.

1987-01-01

We examine a model of supersymmetry with soft breaking terms in the electroweak sector. Explicit mixing among the scalar leptons results in a number of effects, principally non-conservation of lepton family number. Comparison with experiment permits us to place constraints upon the model

Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells

Directory of Open Access Journals (Sweden)

Sarah Inwood

2018-01-01

Full Text Available The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK, while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.

Training program for energy conservation in new-building construction. Volume II. Energy conservation technology: for the building inspector

Energy Technology Data Exchange (ETDEWEB)

None

1977-12-01

A Model Code for Energy Conservation in New Building Construction has been developed by those national organizations primarily concerned with the development and promulgation of model codes. The technical provisions are based on ASHRAE Standard 90-75 and are intended for use by state and local officials. This training manual contains the basic information necessary to acquaint the field building inspector with the concepts of energy conservation in buildings and instructs him in the basic techniques of field inspection of energy compliance.

Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs.

LENUS (Irish Health Repository)

Weissenmayer, Barbara A

2011-01-01

Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes of several bacterial and archaeal species. One of the central findings has been the identification of complex networks of small non-coding RNAs that play central roles in transcriptional regulation in all growth conditions and for the pathogen\\'s interaction with and survival within host cells. Legionella pneumophila is a gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila during exponential and post-exponential broth growth and during the replicative and transmissive phase of infection inside A. castellanii. We extend previous microarray based studies as well as uncovering evidence of a complex regulatory architecture underpinned by numerous non-coding RNAs. Over seventy new non-coding RNAs could be identified; many of them appear to be strain specific and in configurations not previously reported. We discover a family of non-coding RNAs preferentially expressed during infection conditions and identify a second copy of 6S RNA in L. pneumophila. We show that the newly discovered putative 6S RNA as well as a number of other non-coding RNAs show evidence for antisense transcription. The nature and extent of the non-coding RNAs and their expression patterns suggests that these may well play central roles in the regulation of Legionella spp. specific traits and offer clues as to how L. pneumophila adapts to its intracellular niche. The expression profiles outlined in the study have been deposited into Genbank\\'s Gene Expression Omnibus (GEO) database under the series accession GSE27232.

Enforcing dust mass conservation in 3D simulations of tightly coupled grains with the PHANTOM SPH code

Science.gov (United States)

Ballabio, G.; Dipierro, G.; Veronesi, B.; Lodato, G.; Hutchison, M.; Laibe, G.; Price, D. J.

2018-06-01

We describe a new implementation of the one-fluid method in the SPH code PHANTOM to simulate the dynamics of dust grains in gas protoplanetary discs. We revise and extend previously developed algorithms by computing the evolution of a new fluid quantity that produces a more accurate and numerically controlled evolution of the dust dynamics. Moreover, by limiting the stopping time of uncoupled grains that violate the assumptions of the terminal velocity approximation, we avoid fatal numerical errors in mass conservation. We test and validate our new algorithm by running 3D SPH simulations of a large range of disc models with tightly and marginally coupled grains.

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.

Joint beam design and user selection over non-binary coded MIMO interference channel

Science.gov (United States)

Li, Haitao; Yuan, Haiying

2013-03-01

In this paper, we discuss the problem of sum rate improvement for coded MIMO interference system, and propose joint beam design and user selection over interference channel. Firstly, we have formulated non-binary LDPC coded MIMO interference networks model. Then, the least square beam design for MIMO interference system is derived, and the low complexity user selection is presented. Simulation results confirm that the sum rate can be improved by the joint user selection and beam design comparing with single interference aligning beamformer.

Long non-coding RNA expression profiles in hereditary haemorrhagic telangiectasia

DEFF Research Database (Denmark)

Tørring, Pernille M; Larsen, Martin Jakob; Kjeldsen, Anette D

2014-01-01

transcriptome, we wanted to assess whether lncRNAs play a role in the molecular pathogenesis of HHT manifestations. By microarray technology, we profiled lncRNA transcripts from HHT nasal telangiectasial and non-telangiectasial tissue using a paired design. The microarray probes were annotated using the GENCODE...... v.16 dataset, identifying 4,810 probes mapping to 2,811 lncRNAs. Comparing HHT telangiectasial tissue with HHT non-telangiectasial tissue, we identified 42 lncRNAs that are differentially expressed (qUsing GREAT, a tool that assumes cis-regulation, we showed that differently expressed lncRNAs...... to the TGF-β signalling pathway. The exact mechanism of how haploinsufficiency of ENG and ACVRL1 leads to HHT manifestations remains to be identified. As long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression and constitute a sizable fraction of the human...

miR126-5p down-regulation facilitates axon degeneration and NMJ disruption via a non-cell-autonomous mechanism in ALS.

Science.gov (United States)

Maimon, Roy; Ionescu, Ariel; Bonnie, Avichai; Sweetat, Sahar; Wald-Altman, Shane; Inbar, Shani; Gradus, Tal; Trotti, Davide; Weil, Miguel; Behar, Oded; Perlson, Eran

2018-05-17

Axon degeneration and disruption of neuromuscular junctions (NMJs) are key events in Amyotrophic Lateral Sclerosis (ALS) pathology. Although the disease's etiology is not fully understood, it is thought to involve a non-cell-autonomous mechanism and alterations in RNA metabolism. Here, we identified reduced levels of miR-126-5p in pre-symptomatic ALS male mice models, and an increase in its targets: axon destabilizing type-3 Semaphorins and their co-receptor Neuropilins. Utilizing compartmentalized in vitro co-cultures, we demonstrated that myocytes expressing diverse ALS-causing mutations promote axon degeneration and NMJ dysfunction, which were inhibited by applying Neuropilin1 (NRP1) blocking antibody. Finally, overexpressing miR126-5p is sufficient to transiently rescue axon degeneration and NMJ disruption both in vitro and in vivo Thus, we demonstrate a novel mechanism underlying ALS pathology, in which alterations in miR126-5p facilitate a non-cell-autonomous mechanism of motor neuron degeneration in ALS. SIGNIFICANCE STATEMENT In spite of some progress, currently no effective treatment is available for ALS. We suggest a novel regulatory role for miR126-5p in ALS and demonstrate for the first time a mechanism by which alterations in miR126-5p contribute to axon degeneration and NMJ disruption observed in ALS. We show that miR126-5p is altered in ALS models and that it can modulate Sema3 and NRP protein expression. Furthermore, NRP1 elevations in motor neurons and muscle secretion of Sema3A contribute to axon degeneration and NMJ disruption in ALS. Finally, overexpressing miR126-5p is sufficient to transiently rescue NMJ disruption and axon degeneration both in vitro and in vivo. Copyright © 2018 Maimon et al.

Modeling SOL evolution during disruptions

International Nuclear Information System (INIS)

Rognlien, T.D.; Cohen, R.H.; Crotinger, J.A.

1996-01-01

We present the status of our models and transport simulations of the 2-D evolution of the scrape-off layer (SOL) during tokamak disruptions. This evolution is important for several reasons: It determines how the power from the core plasma is distributed on material surfaces, how impurities from those surfaces or from gas injection migrate back to the core region, and what are the properties of the SOL for carrying halo currents. We simulate this plasma in a time-dependent fashion using the SOL transport code UEDGE. This code models the SOL plasma using fluid equations of plasma density, parallel momentum (along the magnetic field), electron energy, ion energy, and neutral gas density. A multispecies model is used to follow the density of different charge-states of impurities. The parallel transport is classical but with kinetic modifications; these are presently treated by flux limits, but we have initiated more sophisticated models giving the correct long-mean-free path limit. The cross-field transport is anomalous, and one of the results of this work is to determine reasonable values to characterize disruptions. Our primary focus is on the initial thermal quench phase when most of the core energy is lost, but the total current is maintained. The impact of edge currents on the MHD equilibrium will be discussed

Code Cactus; Code Cactus

Energy Technology Data Exchange (ETDEWEB)

Fajeau, M; Nguyen, L T; Saunier, J [Commissariat a l' Energie Atomique, Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)

1966-09-01

This code handles the following problems: -1) Analysis of thermal experiments on a water loop at high or low pressure; steady state or transient behavior; -2) Analysis of thermal and hydrodynamic behavior of water-cooled and moderated reactors, at either high or low pressure, with boiling permitted; fuel elements are assumed to be flat plates: - Flowrate in parallel channels coupled or not by conduction across plates, with conditions of pressure drops or flowrate, variable or not with respect to time is given; the power can be coupled to reactor kinetics calculation or supplied by the code user. The code, containing a schematic representation of safety rod behavior, is a one dimensional, multi-channel code, and has as its complement (FLID), a one-channel, two-dimensional code. (authors) [French] Ce code permet de traiter les problemes ci-dessous: 1. Depouillement d'essais thermiques sur boucle a eau, haute ou basse pression, en regime permanent ou transitoire; 2. Etudes thermiques et hydrauliques de reacteurs a eau, a plaques, a haute ou basse pression, ebullition permise: - repartition entre canaux paralleles, couples on non par conduction a travers plaques, pour des conditions de debit ou de pertes de charge imposees, variables ou non dans le temps; - la puissance peut etre couplee a la neutronique et une representation schematique des actions de securite est prevue. Ce code (Cactus) a une dimension d'espace et plusieurs canaux, a pour complement Flid qui traite l'etude d'un seul canal a deux dimensions. (auteurs)

Post-disruptive plasma loss in the Princeton Beta Experiment (PBX)

International Nuclear Information System (INIS)

Jardin, S.C.; DeLucia, J.; Okabayashi, M.; Pomphrey, N.; Reusch, M.; Kaye, S.; Takahashi, H.

1986-07-01

The free-boundary, axisymmetric tokamak simulation code TSC is used to model the transport time scale evolution and positional stability of PBX. A disruptive thermal quench will cause the plasma column to move inward in major radius. It is shown that the plasma can then lose axisymmetric stability, causing it to displace exponentially off the midplane, terminating the discharge. We verify the accuracy of the code by modeling several controlled experiments shots in PBX

The Aster code; Code Aster

Energy Technology Data Exchange (ETDEWEB)

Delbecq, J.M

1999-07-01

The Aster code is a 2D or 3D finite-element calculation code for structures developed by the R and D direction of Electricite de France (EdF). This dossier presents a complete overview of the characteristics and uses of the Aster code: introduction of version 4; the context of Aster (organisation of the code development, versions, systems and interfaces, development tools, quality assurance, independent validation); static mechanics (linear thermo-elasticity, Euler buckling, cables, Zarka-Casier method); non-linear mechanics (materials behaviour, big deformations, specific loads, unloading and loss of load proportionality indicators, global algorithm, contact and friction); rupture mechanics (G energy restitution level, restitution level in thermo-elasto-plasticity, 3D local energy restitution level, KI and KII stress intensity factors, calculation of limit loads for structures), specific treatments (fatigue, rupture, wear, error estimation); meshes and models (mesh generation, modeling, loads and boundary conditions, links between different modeling processes, resolution of linear systems, display of results etc..); vibration mechanics (modal and harmonic analysis, dynamics with shocks, direct transient dynamics, seismic analysis and aleatory dynamics, non-linear dynamics, dynamical sub-structuring); fluid-structure interactions (internal acoustics, mass, rigidity and damping); linear and non-linear thermal analysis; steels and metal industry (structure transformations); coupled problems (internal chaining, internal thermo-hydro-mechanical coupling, chaining with other codes); products and services. (J.S.)

ChIP-seq Identification of Weakly Conserved Heart Enhancers

Energy Technology Data Exchange (ETDEWEB)

Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.

2010-07-01

Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type.

The interplay of long non-coding RNAs and MYC in cancer

Directory of Open Access Journals (Sweden)

Michael J. Hamilton

2015-12-01

Full Text Available Long non-coding RNAs (lncRNAs are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Investigations exploring the dynamic interactions between lncRNAs and MYC, referred to as the lncRNA-MYC network, have proven to be especially complex. Genome-wide studies have shown that MYC transcriptionally regulates many lncRNA genes. Conversely, recent reports identified lncRNAs that regulate MYC expression both at the transcriptional and post-transcriptional levels. These findings are of particular interest because they suggest roles of lncRNAs as regulators of MYC oncogenic functions and the possibility that targeting lncRNAs could represent a novel avenue to cancer treatment. Here, we briefly review the current understanding of how lncRNAs regulate chromatin structure and gene transcription, and then focus on the new developments in the emerging field exploring the lncRNA-MYC network in cancer.

The AutoProof Verifier: Usability by Non-Experts and on Standard Code

Directory of Open Access Journals (Sweden)

Carlo A. Furia

2015-08-01

Full Text Available Formal verification tools are often developed by experts for experts; as a result, their usability by programmers with little formal methods experience may be severely limited. In this paper, we discuss this general phenomenon with reference to AutoProof: a tool that can verify the full functional correctness of object-oriented software. In particular, we present our experiences of using AutoProof in two contrasting contexts representative of non-expert usage. First, we discuss its usability by students in a graduate course on software verification, who were tasked with verifying implementations of various sorting algorithms. Second, we evaluate its usability in verifying code developed for programming assignments of an undergraduate course. The first scenario represents usability by serious non-experts; the second represents usability on "standard code", developed without full functional verification in mind. We report our experiences and lessons learnt, from which we derive some general suggestions for furthering the development of verification tools with respect to improving their usability.

Geothermal energy of Slovakia - CO2 emissions reduction contribution potential (background study for conservative and non-conservative approach

Directory of Open Access Journals (Sweden)

Branislav Fričovský

2012-12-01

Full Text Available Total geothermal energy potential is estimated for 209 714 TJ per year or 6 650 MWth. Natural conditions define a use of thermalwaters for heat generation only. Accepting proportion of real achievable output of geothermal projects in the non-conservative scenarioat a rate of 1 861 MWth or 13 440 TJ per year, yearly carbon dioxide savings are up to reach 0,357 MtCO2.yr-1 or 12,5 of cumulativeMtCO2 in 35 years. By a contrast, introduction of conservative approach points to increase in a geothermal heat production from 145 to243 TJ per period or 6 944 TJ of cumulative 35 years production, with a real outcome of 0,45 MtCO2 cumulative carbon dioxidesavings, corresponding to yearly real savings from 9,4 .10-3 to 15,8 .10-3 MtCO2.

MHD stability analyses of a tokamak plasma by time-dependent codes

International Nuclear Information System (INIS)

Kurita, Gen-ichi

1982-07-01

The MHD properties of a tokamak plasma are investigated by using time evolutional codes. As for the ideal MHD modes we have analyzed the external modes including the positional instability. Linear and nonlinear ideal MHD codes have been developed. Effects of the toroidicity and conducting shell on the external kink mode are studied minutely by the linear code. A new rezoning algorithm is devised and it is successfully applied to express numerically the axisymmetric plasma perturbation in a cylindrical geometry. As for the resistive MHD modes we have developed nonlinear codes on the basis of the reduced set of the resistive MHD equations. By using the codes we have studied the major disruption processes and properties of the low n resistive modes. We have found that the effects of toroidicity and finite poloidal beta are very important. Considering the above conclusion we propose a new scenario of the initiation of the major disruption. (author)

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.

Science.gov (United States)

Ferlaino, Michael; Rogers, Mark F; Shihab, Hashem A; Mort, Matthew; Cooper, David N; Gaunt, Tom R; Campbell, Colin

2017-10-06

Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome.

Quantification of non-coding RNA target localization diversity and its application in cancers.

Science.gov (United States)

Cheng, Lixin; Leung, Kwong-Sak

2018-04-01

Subcellular localization is pivotal for RNAs and proteins to implement biological functions. The localization diversity of protein interactions has been studied as a crucial feature of proteins, considering that the protein-protein interactions take place in various subcellular locations. Nevertheless, the localization diversity of non-coding RNA (ncRNA) target proteins has not been systematically studied, especially its characteristics in cancers. In this study, we provide a new algorithm, non-coding RNA target localization coefficient (ncTALENT), to quantify the target localization diversity of ncRNAs based on the ncRNA-protein interaction and protein subcellular localization data. ncTALENT can be used to calculate the target localization coefficient of ncRNAs and measure how diversely their targets are distributed among the subcellular locations in various scenarios. We focus our study on long non-coding RNAs (lncRNAs), and our observations reveal that the target localization diversity is a primary characteristic of lncRNAs in different biotypes. Moreover, we found that lncRNAs in multiple cancers, differentially expressed cancer lncRNAs, and lncRNAs with multiple cancer target proteins are prone to have high target localization diversity. Furthermore, the analysis of gastric cancer helps us to obtain a better understanding that the target localization diversity of lncRNAs is an important feature closely related to clinical prognosis. Overall, we systematically studied the target localization diversity of the lncRNAs and uncovered its association with cancer.

Non-coding RNAs: New therapeutic targets and opportunities for hepatocellular carcinoma

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Yu Cuiyun

2016-02-01

Full Text Available Non-coding RNAs (ncRNA are RNA molecules without protein coding functions owing to the lack of an open reading frame (ORF. Based on the length, ncRNAs can be divided into long and short ncRNAs; short ncRNAs include miRNAs and piRNAs. Hepatocellular carcinoma (HCC is among the most frequent forms of cancer worldwide and its incidence is increasing rapidly. Studies have found that ncRNAs are likely to play a crucial role in a variety of biological processes including the pathogenesis and progression of HCC. In this review, we summarized the regulation mechanism and biological functions of ncRNAs in HCC with respect to its application in HCC diagnosis, therapy and prognosis.

New Clox Systems for rapid and efficient gene disruption in Candida albicans.

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Shahida Shahana

Full Text Available Precise genome modification is essential for the molecular dissection of Candida albicans, and is yielding invaluable information about the roles of specific gene functions in this major fungal pathogen of humans. C. albicans is naturally diploid, unable to undergo meiosis, and utilizes a non-canonical genetic code. Hence, specialized tools have had to be developed for gene disruption in C. albicans that permit the deletion of both target alleles, and in some cases, the recycling of the Candida-specific selectable markers. Previously, we developed a tool based on the Cre recombinase, which recycles markers in C. albicans with 90-100% efficiency via site-specific recombination between loxP sites. Ironically, the utility of this system was hampered by the extreme efficiency of Cre, which prevented the construction in Escherichia coli of stable disruption cassettes carrying a methionine-regulatable CaMET3p-cre gene flanked by loxP sites. Therefore, we have significantly enhanced this system by engineering new Clox cassettes that carry a synthetic, intron-containing cre gene. The Clox kit facilitates efficient transformation and marker recycling, thereby simplifying and accelerating the process of gene disruption in C. albicans. Indeed, homozygous mutants can be generated and their markers resolved within two weeks. The Clox kit facilitates strategies involving single marker recycling or multi-marker gene disruption. Furthermore, it includes the dominant NAT1 marker, as well as URA3, HIS1 and ARG4 cassettes, thereby permitting the manipulation of clinical isolates as well as genetically marked strains of C. albicans. The accelerated gene disruption strategies afforded by this new Clox system are likely to have a profound impact on the speed with which C. albicans pathobiology can be dissected.

Territorialisation, Conservation, and Neoliberalism in the Tehuacán-Cuicatlán Biosphere Reserve, Mexico

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Alison Elizabeth Lee

2014-01-01

Full Text Available The territorialisation of a botanical garden and the Tehuacán-Cuicatlán Biosphere Reserve (TCBR in southern Mexico is examined from the perspective of local residents of one rural town and the biologists whose professional careers involved extensive research in the region. While there were brief periods of conflict between residents and outsiders over the use of local lands for conservation, the cumulative effects demonstrate a general acceptance of the conservation paradigm. Local residents re-appropriated an older discourse linking their land rights to indigenous ancestors in order to mobilise collective support to ensure local control of the botanical garden. The discourse was subsequently incorporated into a local ecotourism project providing cultural substance complementary to the biological and visual aspects of the landscape. Contradictions between conservation and livelihoods were minimal due to neoliberal policies that encouraged migration to the United States of America and wage work in regional maquiladoras. Consequently, the territorialisation of conservation spaces was not disruptive to the increasingly proletarianised, non-agricultural livelihoods of local residents.

Prevention of the current-quench phase of a major disruption in a tokamak reactor

International Nuclear Information System (INIS)

Miller, J.B.

1987-01-01

The 2-D Tokamak Simulation Code written by the Princeton Plasma Physics Laboratory was joined to a 3-D eddy-current code, which models periodic torus sectors. The combined system was found to be an efficient and accurate method for modeling the plasma/eddy current interaction during a major disruption. For modeling large highly compartmentalized structures, artificially increasing the self-inductance and limiting the mutual inductance of current elements were necessary to enhance numerical stability. Even with these modifications, a slowly growing instability made the results unreliable after 58 ms. This model was used to demonstrate prevention of the current quench phase of a major disruption in INTOR. The average plasma temperature was reduced to 150 eV over 3 ms. The (outboard) breeding blanket structure was constructed of CuBeNi and was electrically connected between torus sectors. Disruption recovery coils were provided inboard of the inboard shield (linking the toroidal field coils). It was necessary to supply to these coils a total of 500 MW for 0.6 s and to reheat the plasma to full beta in 6 s. The calculation shows a method of recovery from the most severe disruption probable. Determining the severity of the disruption from which recovery would be cost effective is beyond the scope of this study

Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups

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Singh Nagendra

2009-03-01

Full Text Available Abstract Background Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS markers for the rice (Oryza sativa L. genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences. Results We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS. Primers were designed for 17,966 (92% GNMS repeats, including 4,288 (94% hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3% followed by markers in the promoter region (53.3% and least in the CDS (26.6%. The robust polymerase chain reaction (PCR amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya compared to short

Beamforming-Based Physical Layer Network Coding for Non-Regenerative Multi-Way Relaying

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Klein Anja

2010-01-01

Full Text Available We propose non-regenerative multi-way relaying where a half-duplex multi-antenna relay station (RS assists multiple single-antenna nodes to communicate with each other. The required number of communication phases is equal to the number of the nodes, N. There are only one multiple-access phase, where the nodes transmit simultaneously to the RS, and broadcast (BC phases. Two transmission methods for the BC phases are proposed, namely, multiplexing transmission and analog network coded transmission. The latter is a cooperation method between the RS and the nodes to manage the interference in the network. Assuming that perfect channel state information is available, the RS performs transceive beamforming to the received signals and transmits simultaneously to all nodes in each BC phase. We address the optimum transceive beamforming maximising the sum rate of non-regenerative multi-way relaying. Due to the nonconvexity of the optimization problem, we propose suboptimum but practical signal processing schemes. For multiplexing transmission, we propose suboptimum schemes based on zero forcing, minimising the mean square error, and maximising the signal to noise ratio. For analog network coded transmission, we propose suboptimum schemes based on matched filtering and semidefinite relaxation of maximising the minimum signal to noise ratio. It is shown that analog network coded transmission outperforms multiplexing transmission.

FEAST: a two-dimensional non-linear finite element code for calculating stresses

International Nuclear Information System (INIS)

Tayal, M.

1986-06-01

The computer code FEAST calculates stresses, strains, and displacements. The code is two-dimensional. That is, either plane or axisymmetric calculations can be done. The code models elastic, plastic, creep, and thermal strains and stresses. Cracking can also be simulated. The finite element method is used to solve equations describing the following fundamental laws of mechanics: equilibrium; compatibility; constitutive relations; yield criterion; and flow rule. FEAST combines several unique features that permit large time-steps in even severely non-linear situations. The features include a special formulation for permitting many finite elements to simultaneously cross the boundary from elastic to plastic behaviour; accomodation of large drops in yield-strength due to changes in local temperature and a three-step predictor-corrector method for plastic analyses. These features reduce computing costs. Comparisons against twenty analytical solutions and against experimental measurements show that predictions of FEAST are generally accurate to ± 5%

Mutualism Disruption Threatens Global Plant Biodiversity: A Systematic Review.

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Clare E Aslan

Full Text Available As global environmental change accelerates, biodiversity losses can disrupt interspecific interactions. Extinctions of mutualist partners can create "widow" species, which may face reduced ecological fitness. Hypothetically, such mutualism disruptions could have cascading effects on biodiversity by causing additional species coextinctions. However, the scope of this problem - the magnitude of biodiversity that may lose mutualist partners and the consequences of these losses - remains unknown.We conducted a systematic review and synthesis of data from a broad range of sources to estimate the threat posed by vertebrate extinctions to the global biodiversity of vertebrate-dispersed and -pollinated plants. Though enormous research gaps persist, our analysis identified Africa, Asia, the Caribbean, and global oceanic islands as geographic regions at particular risk of disruption of these mutualisms; within these regions, percentages of plant species likely affected range from 2.1-4.5%. Widowed plants are likely to experience reproductive declines of 40-58%, potentially threatening their persistence in the context of other global change stresses.Our systematic approach demonstrates that thousands of species may be impacted by disruption in one class of mutualisms, but extinctions will likely disrupt other mutualisms, as well. Although uncertainty is high, there is evidence that mutualism disruption directly threatens significant biodiversity in some geographic regions. Conservation measures with explicit focus on mutualistic functions could be necessary to bolster populations of widowed species and maintain ecosystem functions.

Mutating the Conserved Q-loop Glutamine 1291 Selectively Disrupts Adenylate Kinase-dependent Channel Gating of the ATP-binding Cassette (ABC) Adenylate Kinase Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and Reduces Channel Function in Primary Human Airway Epithelia.

Science.gov (United States)

Dong, Qian; Ernst, Sarah E; Ostedgaard, Lynda S; Shah, Viral S; Ver Heul, Amanda R; Welsh, Michael J; Randak, Christoph O

2015-05-29

The ATP-binding cassette (ABC) transporter cystic fibrosis transmembrane conductance regulator (CFTR) and two other non-membrane-bound ABC proteins, Rad50 and a structural maintenance of chromosome (SMC) protein, exhibit adenylate kinase activity in the presence of physiologic concentrations of ATP and AMP or ADP (ATP + AMP ⇆ 2 ADP). The crystal structure of the nucleotide-binding domain of an SMC protein in complex with the adenylate kinase bisubstrate inhibitor P(1),P(5)-di(adenosine-5') pentaphosphate (Ap5A) suggests that AMP binds to the conserved Q-loop glutamine during the adenylate kinase reaction. Therefore, we hypothesized that mutating the corresponding residue in CFTR, Gln-1291, selectively disrupts adenylate kinase-dependent channel gating at physiologic nucleotide concentrations. We found that substituting Gln-1291 with bulky side-chain amino acids abolished the effects of Ap5A, AMP, and adenosine 5'-monophosphoramidate on CFTR channel function. 8-Azidoadenosine 5'-monophosphate photolabeling of the AMP-binding site and adenylate kinase activity were disrupted in Q1291F CFTR. The Gln-1291 mutations did not alter the potency of ATP at stimulating current or ATP-dependent gating when ATP was the only nucleotide present. However, when physiologic concentrations of ADP and AMP were added, adenylate kinase-deficient Q1291F channels opened significantly less than wild type. Consistent with this result, we found that Q1291F CFTR displayed significantly reduced Cl(-) channel function in well differentiated primary human airway epithelia. These results indicate that a highly conserved residue of an ABC transporter plays an important role in adenylate kinase-dependent CFTR gating. Furthermore, the results suggest that adenylate kinase activity is important for normal CFTR channel function in airway epithelia. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

3-D rod ejection analysis using a conservative methodology

Energy Technology Data Exchange (ETDEWEB)

Park, Min Ho; Park, Jin Woo; Park, Guen Tae; Um, Kil Sup; Ryu, Seok Hee; Lee, Jae Il; Choi, Tong Soo [KEPCO, Daejeon (Korea, Republic of)

2016-05-15

The point kinetics model which simplifies the core phenomena and physical specifications is used for the conventional rod ejection accident analysis. The point kinetics model is convenient to assume conservative core parameters but this simplification loses large amount of safety margin. The CHASER system couples the three-dimensional core neutron kinetics code ASTRA, the sub-channel analysis code THALES and the fuel performance analysis code FROST. The validation study for the CHASER system is addressed using the NEACRP three-dimensional PWR core transient benchmark problem. A series of conservative rod ejection analyses for the APR1400 type plant is performed for both hot full power (HFP) and hot zero power (HZP) conditions to determine the most limiting cases. The conservative rod ejection analysis methodology is designed to properly consider important phenomena and physical parameters.

Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend

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McCallion Andrew S

2009-01-01

Full Text Available Abstract Background Transcriptional regulatory elements are central to development and interspecific phenotypic variation. Current regulatory element prediction tools rely heavily upon conservation for prediction of putative elements. Recent in vitro observations from the ENCODE project combined with in vivo analyses at the zebrafish phox2b locus suggests that a significant fraction of regulatory elements may fall below commonly applied metrics of conservation. We propose to explore these observations in vivo at the human PHOX2B locus, and also evaluate the potential evidence for genome-wide applicability of these observations through a novel analysis of extant data. Results Transposon-based transgenic analysis utilizing a tiling path proximal to human PHOX2B in zebrafish recapitulates the observations at the zebrafish phox2b locus of both conserved and non-conserved regulatory elements. Analysis of human sequences conserved with previously identified zebrafish phox2b regulatory elements demonstrates that the orthologous sequences exhibit overlapping regulatory control. Additionally, analysis of non-conserved sequences scattered over 135 kb 5' to PHOX2B, provides evidence of non-conserved regulatory elements positively biased with close proximity to the gene. Furthermore, we provide a novel analysis of data from the ENCODE project, finding a non-uniform distribution of regulatory elements consistent with our in vivo observations at PHOX2B. These observations remain largely unchanged when one accounts for the sequence repeat content of the assayed intervals, when the intervals are sub-classified by biological role (developmental versus non-developmental, or by gene density (gene desert versus non-gene desert. Conclusion While regulatory elements frequently display evidence of evolutionary conservation, a fraction appears to be undetected by current metrics of conservation. In vivo observations at the PHOX2B locus, supported by our analyses of in

List Decoding of Matrix-Product Codes from nested codes: an application to Quasi-Cyclic codes

DEFF Research Database (Denmark)

Hernando, Fernando; Høholdt, Tom; Ruano, Diego

2012-01-01

A list decoding algorithm for matrix-product codes is provided when $C_1,..., C_s$ are nested linear codes and $A$ is a non-singular by columns matrix. We estimate the probability of getting more than one codeword as output when the constituent codes are Reed-Solomon codes. We extend this list...... decoding algorithm for matrix-product codes with polynomial units, which are quasi-cyclic codes. Furthermore, it allows us to consider unique decoding for matrix-product codes with polynomial units....

Disruption of a -35kb enhancer impairs CTCF binding and MLH1 expression in colorectal cells.

Science.gov (United States)

Liu, Qing; Thoms, Julie A; Nunez, Andrea C; Huang, Yizhou; Knezevic, Kathy; Packham, Deborah; Poulos, Rebecca C; Williams, Rachel; Beck, Dominik; Hawkins, Nicholas J; Ward, Robyn L; Wong, Jason W H; Hesson, Luke B; Sloane, Mathew A; Pimanda, John

2018-06-13

MLH1 is a major tumour suppressor gene involved in the pathogenesis of Lynch syndrome and various sporadic cancers. Despite their potential pathogenic importance, genomic regions capable of regulating MLH1 expression over long distances have yet to be identified. Here we use chromosome conformation capture (3C) to screen a 650-kb region flanking the MLH1 locus to identify interactions between the MLH1 promoter and distal regions in MLH1 expressing and non-expressing cells. Putative enhancers were functionally validated using luciferase reporter assays, chromatin immunoprecipitation and CRISPR-Cas9 mediated deletion of endogenous regions. To evaluate whether germline variants in the enhancer might contribute to impaired MLH1 expression in patients with suspected Lynch syndrome, we also screened germline DNA from a cohort of 74 patients with no known coding mutations or epimutations at the MLH1 promoter. A 1.8kb DNA fragment, 35kb upstream of the MLH1 transcription start site enhances MLH1 gene expression in colorectal cells. The enhancer was bound by CTCF and CRISPR-Cas9 mediated deletion of a core binding region impairs endogenous MLH1 expression. 5.4% of suspected Lynch syndrome patients have a rare single nucleotide variant (G>A; rs143969848; 2.5% in gnomAD European, non-Finnish) within a highly conserved CTCF binding motif, which disrupts enhancer activity in SW620 colorectal carcinoma cells. A CTCF bound region within the MLH1 -35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. Copyright ©2018, American Association for Cancer Research.

Functional Analysis of an ATP-Binding Cassette Transporter Gene in Botrytis cinerea by Gene Disruption

OpenAIRE

Masami, NAKAJIMA; Junko, SUZUKI; Takehiko, HOSAKA; Tadaaki, HIBI; Katsumi, AKUTSU; School of Agriculture, Ibaraki University; School of Agriculture, Ibaraki University; School of Agriculture, Ibaraki University; Department of Agriculture and Environmental Biology, The University of Tokyo; School of Agriculture, Ibaraki University

2001-01-01

The BMR1 gene encoding an ABC transporter was cloned from Botrytis cinerea. To examine the function of BMR1 in B.cinerea, we isolated BMR1-deficient mutants after gene disruption. Disruption vector pBcDF4 was constructed by replacing the BMR1-coding region with a hygromycin B phosphotransferase gene(hph)cassette. The BMR1 disruptants had an increased sensitivity to polyoxin and iprobenfos. Polyoxin and iprobenfos, structurally unrelated compounds, may therefore be substrates of BMR1.

LEVERAGING RURAL LIVELIHOODS WITH FOREST CONSERVATION IN NIGERIA: THE ROLE OF NON-TIMBER FOREST PRODUCTS

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Egbe BASSEY ETOWA

2015-03-01

Full Text Available In recent times some economists view Non-Timber Forest Products (NTFPs extraction and marketing as a better alternative to timber exploitation as a rural livelihood strategy. Harvesting and sale of NTFPs have the potential for accomplishing the dual goals of natural forest conservation and income generation for the rural inhabitants. Meanwhile, realization of these dual goals in Nigeria, require an understanding of how NTFPs functions in the face of marketing, ecological, geographic and institutional constraints. Following a conceptualization of NTFPs, this paper provides a vivid overview of the simultaneous roles of NTFPs in rural livelihood enhancement and forest conservation in Nigeria. It highlights governmental initiatives with respect to conservation, the challenges and prospects of NTFPs as a conservation strategy. Conclusively, the paper suggests that appropriate NTFPs development policies are required to simultaneously address forest depletion and poverty in rural areas of Nigeria.

Overexpression of long non-coding RNAs following exposure to xenobiotics in the aquatic midge Chironomus riparius

International Nuclear Information System (INIS)

Martínez-Guitarte, José-Luis; Planelló, Rosario; Morcillo, Gloria

2012-01-01

Non-coding RNAs (ncRNAs) represent an important transcriptional output of eukaryotic genomes. In addition to their functional relevance as housekeeping and regulatory elements, recent studies have suggested their involvement in rather unexpected cellular functions. The aim of this work was to analyse the transcriptional behaviour of non-coding RNAs in the toxic response to pollutants in Chironomus riparius, a reference organism in aquatic toxicology. Three well-characterized long non-coding sequences were studied: telomeric repeats, Cla repetitive elements and the SINE CTRT1. Transcription levels were evaluated by RT-PCR after 24-h exposures to three current aquatic contaminants: bisphenol A (BPA), benzyl butyl phthalate (BBP) and the heavy metal cadmium (Cd). Upregulation of telomeric transcripts was found after BPA treatments. Moreover, BPA significantly activated Cla transcription, which also appeared to be increased by cadmium, whereas BBP did not affect the transcription levels of these sequences. Transcription of SINE CTRT1 was not altered by any of the chemicals tested. These data are discussed in the light of previous studies that have shown a response by long ncRNAS (lncRNAs) to cellular stressors, indicating a relationship with environmental stimuli. Our results demonstrated for the first time the ability of bisphenol A to activate non-coding sequences mainly located at telomeres and centromeres. Overall, this study provides evidence that xenobiotics can induce specific responses in ncRNAs derived from repetitive sequences that could be relevant in the toxic response, and also suggests that ncRNAs could represent a novel class of potential biomarkers in toxicological assessment.

Overexpression of long non-coding RNAs following exposure to xenobiotics in the aquatic midge Chironomus riparius

Energy Technology Data Exchange (ETDEWEB)

Martinez-Guitarte, Jose-Luis, E-mail: jlmartinez@ccia.uned.es [Grupo de Biologia y Toxicologia Ambiental, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia, UNED, Senda del Rey 9, 28040 Madrid (Spain); Planello, Rosario; Morcillo, Gloria [Grupo de Biologia y Toxicologia Ambiental, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia, UNED, Senda del Rey 9, 28040 Madrid (Spain)

2012-04-15

Non-coding RNAs (ncRNAs) represent an important transcriptional output of eukaryotic genomes. In addition to their functional relevance as housekeeping and regulatory elements, recent studies have suggested their involvement in rather unexpected cellular functions. The aim of this work was to analyse the transcriptional behaviour of non-coding RNAs in the toxic response to pollutants in Chironomus riparius, a reference organism in aquatic toxicology. Three well-characterized long non-coding sequences were studied: telomeric repeats, Cla repetitive elements and the SINE CTRT1. Transcription levels were evaluated by RT-PCR after 24-h exposures to three current aquatic contaminants: bisphenol A (BPA), benzyl butyl phthalate (BBP) and the heavy metal cadmium (Cd). Upregulation of telomeric transcripts was found after BPA treatments. Moreover, BPA significantly activated Cla transcription, which also appeared to be increased by cadmium, whereas BBP did not affect the transcription levels of these sequences. Transcription of SINE CTRT1 was not altered by any of the chemicals tested. These data are discussed in the light of previous studies that have shown a response by long ncRNAS (lncRNAs) to cellular stressors, indicating a relationship with environmental stimuli. Our results demonstrated for the first time the ability of bisphenol A to activate non-coding sequences mainly located at telomeres and centromeres. Overall, this study provides evidence that xenobiotics can induce specific responses in ncRNAs derived from repetitive sequences that could be relevant in the toxic response, and also suggests that ncRNAs could represent a novel class of potential biomarkers in toxicological assessment.

Disruption simulation experiment using high-frequency rastering electron beam as the heat source

International Nuclear Information System (INIS)

Yamazaki, S.; Seki, M.

1987-01-01

The disruption is a serious event which possibly reduces the lifetime of plasm interactive components, so the effects of the resulting high heat flux on the wall materials must be clearly identified. The authors performed disruption simulation experiments to investigate melting, evaporation, and crack initiation behaviors using an electron beam facility as the heat source. The facility was improved with a high-frequency beam rastering system which provided spatially and temporally uniform heat flux on wider test surfaces. Along with the experiments, thermal and mechanical analyses were also performed. A two-dimensional disruption thermal analysis code (DREAM) was developed for the analyses

Costal cartilage fractures and disruptions in a rugby football player.

Science.gov (United States)

Lopez, Victor; Ma, Richard; Li, Xinning; Steele, John; Allen, Answorth A

2013-05-01

Costal cartilage fracture of the rib cage, or costochondral, is a rare sporting injury. For contact athletes, the instability of the rib cage may lead to potential serious complications, similar to rib fractures or thorax disruption. Most authors recommend initial conservative treatment with surgery reserved for only recalcitrant cases. We report a case of an amateur American male rugby football player who sustained a costal cartilage fracture and disruption involving the anterior left fifth and sixth rib costal cartilages. The case highlights the difficulty in establishing the diagnosis based on clinical examination and standard radiographs alone. Computed tomography was used to assist in diagnosing this destabilizing injury to the rib cage. Costal cartilage fractures and disruptions in athletes are rarely reported in the literature and can have serious implications for the athlete's ability to return to play if the rib cage is destabilized.

Disruptive Innovation in Numerical Hydrodynamics

Energy Technology Data Exchange (ETDEWEB)

Waltz, Jacob I. [Los Alamos National Laboratory

2012-09-06

We propose the research and development of a high-fidelity hydrodynamic algorithm for tetrahedral meshes that will lead to a disruptive innovation in the numerical modeling of Laboratory problems. Our proposed innovation has the potential to reduce turnaround time by orders of magnitude relative to Advanced Simulation and Computing (ASC) codes; reduce simulation setup costs by millions of dollars per year; and effectively leverage Graphics Processing Unit (GPU) and future Exascale computing hardware. If successful, this work will lead to a dramatic leap forward in the Laboratory's quest for a predictive simulation capability.

Non-Coding RNAs are Differentially Expressed by Nocardia brasiliensis in Vitro and in Experimental Actinomycetoma.

Science.gov (United States)

Cruz-Rabadán, Josué S; Miranda-Ríos, Juan; Espín-Ocampo, Guadalupe; Méndez-Tovar, Luis J; Maya-Pineda, Héctor Rubén; Hernández-Hernández, Francisca

2017-01-01

Nocardia spp. are common soil-inhabiting bacteria that frequently infect humans through traumatic injuries or inhalation routes and cause infections, such as actinomycetoma and nocardiosis, respectively. Nocardia brasiliensis is the main aetiological agent of actinomycetoma in various countries. Many bacterial non-coding RNAs are regulators of genes associated with virulence factors. The aim of this work was to identify non-coding RNAs (ncRNAs) expressed during infection conditions and in free-living form ( in vitro ) in Nocardia brasiliensis . The N. brasiliensis transcriptome (predominately brasiliensis infection compared with the in vitro conditions. The results of this work suggest a possible role for these transcripts in the regulation of virulence genes in actinomycetoma pathogenesis.

Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy

Science.gov (United States)

Miller-Delaney, Suzanne F.C.; Bryan, Kenneth; Das, Sudipto; McKiernan, Ross C.; Bray, Isabella M.; Reynolds, James P.; Gwinn, Ryder; Stallings, Raymond L.

2015-01-01

Temporal lobe epilepsy is associated with large-scale, wide-ranging changes in gene expression in the hippocampus. Epigenetic changes to DNA are attractive mechanisms to explain the sustained hyperexcitability of chronic epilepsy. Here, through methylation analysis of all annotated C-phosphate-G islands and promoter regions in the human genome, we report a pilot study of the methylation profiles of temporal lobe epilepsy with or without hippocampal sclerosis. Furthermore, by comparative analysis of expression and promoter methylation, we identify methylation sensitive non-coding RNA in human temporal lobe epilepsy. A total of 146 protein-coding genes exhibited altered DNA methylation in temporal lobe epilepsy hippocampus (n = 9) when compared to control (n = 5), with 81.5% of the promoters of these genes displaying hypermethylation. Unique methylation profiles were evident in temporal lobe epilepsy with or without hippocampal sclerosis, in addition to a common methylation profile regardless of pathology grade. Gene ontology terms associated with development, neuron remodelling and neuron maturation were over-represented in the methylation profile of Watson Grade 1 samples (mild hippocampal sclerosis). In addition to genes associated with neuronal, neurotransmitter/synaptic transmission and cell death functions, differential hypermethylation of genes associated with transcriptional regulation was evident in temporal lobe epilepsy, but overall few genes previously associated with epilepsy were among the differentially methylated. Finally, a panel of 13, methylation-sensitive microRNA were identified in temporal lobe epilepsy including MIR27A, miR-193a-5p (MIR193A) and miR-876-3p (MIR876), and the differential methylation of long non-coding RNA documented for the first time. The present study therefore reports select, genome-wide DNA methylation changes in human temporal lobe epilepsy that may contribute to the molecular architecture of the epileptic brain. PMID

Non-binary unitary error bases and quantum codes

Energy Technology Data Exchange (ETDEWEB)

Knill, E.

1996-06-01

Error operator bases for systems of any dimension are defined and natural generalizations of the bit-flip/ sign-change error basis for qubits are given. These bases allow generalizing the construction of quantum codes based on eigenspaces of Abelian groups. As a consequence, quantum codes can be constructed form linear codes over {ital Z}{sub {ital n}} for any {ital n}. The generalization of the punctured code construction leads to many codes which permit transversal (i.e. fault tolerant) implementations of certain operations compatible with the error basis.

Polarization-multiplexed rate-adaptive non-binary-quasi-cyclic-LDPC-coded multilevel modulation with coherent detection for optical transport networks.

Science.gov (United States)

Arabaci, Murat; Djordjevic, Ivan B; Saunders, Ross; Marcoccia, Roberto M

2010-02-01

In order to achieve high-speed transmission over optical transport networks (OTNs) and maximize its throughput, we propose using a rate-adaptive polarization-multiplexed coded multilevel modulation with coherent detection based on component non-binary quasi-cyclic (QC) LDPC codes. Compared to prior-art bit-interleaved LDPC-coded modulation (BI-LDPC-CM) scheme, the proposed non-binary LDPC-coded modulation (NB-LDPC-CM) scheme not only reduces latency due to symbol- instead of bit-level processing but also provides either impressive reduction in computational complexity or striking improvements in coding gain depending on the constellation size. As the paper presents, compared to its prior-art binary counterpart, the proposed NB-LDPC-CM scheme addresses the needs of future OTNs, which are achieving the target BER performance and providing maximum possible throughput both over the entire lifetime of the OTN, better.

NPTFit: A Code Package for Non-Poissonian Template Fitting

International Nuclear Information System (INIS)

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R.

2017-01-01

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

NPTFit: A Code Package for Non-Poissonian Template Fitting

Energy Technology Data Exchange (ETDEWEB)

Mishra-Sharma, Siddharth [Department of Physics, Princeton University, Princeton, NJ 08544 (United States); Rodd, Nicholas L.; Safdi, Benjamin R., E-mail: smsharma@princeton.edu, E-mail: nrodd@mit.edu, E-mail: bsafdi@mit.edu [Center for Theoretical Physics, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

2017-06-01

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing.

Science.gov (United States)

Zhang, Rui; Deng, Patricia; Jacobson, Dionna; Li, Jin Billy

2017-02-01

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3'UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3'UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions.

Processivity and Subcellular Localization of Glycogen Synthase Depend on a Non-catalytic High Affinity Glycogen-binding Site*

OpenAIRE

Díaz, Adelaida; Martínez-Pons, Carlos; Fita, Ignacio; Ferrer, Juan C.; Guinovart, Joan J.

2011-01-01

Glycogen synthase, a central enzyme in glucose metabolism, catalyzes the successive addition of α-1,4-linked glucose residues to the non-reducing end of a growing glycogen molecule. A non-catalytic glycogen-binding site, identified by x-ray crystallography on the surface of the glycogen synthase from the archaeon Pyrococcus abyssi, has been found to be functionally conserved in the eukaryotic enzymes. The disruption of this binding site in both the archaeal and the human muscle glycogen synth...

Sequence-based heuristics for faster annotation of non-coding RNA families.

Science.gov (United States)

Weinberg, Zasha; Ruzzo, Walter L

2006-01-01

Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. The source code is available under GNU Public License at the supplementary web site.

Fragile X mental retardation protein participates in non-coding RNA pathways.

Science.gov (United States)

Li, En-Hui; Zhao, Xin; Zhang, Ce; Liu, Wei

2018-02-20

Fragile X syndrome is one of the most common forms of inherited intellectual disability. It is caused by mutations of the Fragile X mental retardation 1(FMR1) gene, resulting in either the loss or abnormal expression of the Fragile X mental retardation protein (FMRP). Recent research showed that FMRP participates in non-coding RNA pathways and plays various important roles in physiology, thereby extending our knowledge of the pathogenesis of the Fragile X syndrome. Initial studies showed that the Drosophila FMRP participates in siRNA and miRNA pathways by interacting with Dicer, Ago1 and Ago2, involved in neural activity and the fate determination of the germline stem cells. Subsequent studies showed that the Drosophila FMRP participates in piRNA pathway by interacting with Aub, Ago1 and Piwi in the maintenance of normal chromatin structures and genomic stability. More recent studies showed that FMRP is associated with lncRNA pathway, suggesting a potential role for the involvement in the clinical manifestations. In this review, we summarize the novel findings and explore the relationship between FMRP and non-coding RNA pathways, particularly the piRNA pathway, thereby providing critical insights on the molecular pathogenesis of Fragile X syndrome, and potential translational applications in clinical management of the disease.

CRNDE: a long non-coding RNA involved in CanceR, Neurobiology and DEvelopment

Directory of Open Access Journals (Sweden)

Blake C. Ellis

2012-11-01

Full Text Available CRNDE is the gene symbol for Colorectal Neoplasia Differentially Expressed (non protein-coding, a long non-coding RNA (lncRNA gene that expresses multiple splice variants and displays a very tissue-specific pattern of expression. CRNDE was initially identified as a lncRNA whose expression is highly elevated in colorectal cancer, but it is also upregulated in many other solid tumors and in leukemias. Indeed, CRNDE is the most upregulated lncRNA in gliomas and here, as in other cancers, it is associated with a stemness signature. CRNDE is expressed in specific regions within the human and mouse brain; the mouse ortholog is high in induced pluripotent stem cells and increases further during neuronal differentiation. We suggest that CRNDE is a multifunctional lncRNA whose different splice forms provide specific functional scaffolds for regulatory complexes, such as the polycomb repressive complex 2 (PRC2 and CoREST chromatin-modifying complexes, which CRNDE helps pilot to target genes.

Experimental benchmark of non-local-thermodynamic-equilibrium plasma atomic physics codes

International Nuclear Information System (INIS)

Nagels-Silvert, V.

2004-09-01

The main purpose of this thesis is to get experimental data for the testing and validation of atomic physics codes dealing with non-local-thermodynamical-equilibrium plasmas. The first part is dedicated to the spectroscopic study of xenon and krypton plasmas that have been produced by a nanosecond laser pulse interacting with a gas jet. A Thomson scattering diagnostic has allowed us to measure independently plasma parameters such as electron temperature, electron density and the average ionisation state. We have obtained time integrated spectra in the range between 5 and 10 angstroms. We have identified about one hundred xenon rays between 8.6 and 9.6 angstroms via the use of the Relac code. We have discovered unknown rays for the krypton between 5.2 and 7.5 angstroms. In a second experiment we have extended the wavelength range to the X UV domain. The Averroes/Transpec code has been tested in the ranges from 9 to 15 angstroms and from 10 to 130 angstroms, the first range has been well reproduced while the second range requires a more complex data analysis. The second part is dedicated to the spectroscopic study of aluminium, selenium and samarium plasmas in femtosecond operating rate. We have designed an interferometry diagnostic in the frequency domain that has allowed us to measure the expanding speed of the target's backside. Via the use of an adequate isothermal model this parameter has led us to know the plasma electron temperature. Spectra and emission times of various rays from the aluminium and selenium plasmas have been computed satisfactorily with the Averroes/Transpec code coupled with Film and Multif hydrodynamical codes. (A.C.)

Improvements on non-equilibrium and transport Green function techniques: The next-generation TRANSIESTA

OpenAIRE

Papior, Nick Rübner; Lorente, Nicolás; Frederiksen, Thomas; García, Alberto; Brandbyge, Mads

2017-01-01

We present novel methods implemented within the non-equilibrium Green function code (NEGF) TRANSIESTA based on density functional theory (DFT). Our flexible, next-generation DFT–NEGF code handles devices with one or multiple electrodes (Ne≥1) with individual chemical potentials and electronic temperatures. We describe its novel methods for electrostatic gating, contour optimizations, and assertion of charge conservation, as well as the newly implemented algorithms for optimized and scalable m...

Disruptive Effects of Colorful versus Non-Colorful Play Area on Structured Play – a Pilot Study with Preschoolers

Directory of Open Access Journals (Sweden)

Keren Stern-Ellran

2016-10-01

Full Text Available To contribute to young children's development, sensory enrichment is often provided via colorful play areas. However, little is known about the effects of colorful environments on children while they engage in age-appropriate tasks and games. Studies in adults suggest that aspects of color can distract attention and impair performance, and children are known to have less developed attentional and executive abilities than adults. Preliminary studies conducted in children aged 5-8 suggest that the colorfulness of both distal (e.g., wall decorations and proximal (e.g., the surface of the desktop environments can have a disruptive effect on children's performance. The present research seeks to extend the previous studies to an even younger age group and focus on proximal colorfulness. With a sample of 15 pre-schoolers (3-4 years old we examined whether a colorful play surface compared to a non-colorful (white play surface would affect engagement in developmentally appropriate structured play. Our pilot findings suggest that a colorful play surface interfered with preschoolers' structured play, inducing more behaviors indicating disruption in task execution compared with a non-colorful play surface. The implications of the current study for practice and further research are discussed.

Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

Science.gov (United States)

Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

2013-09-01

Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

Non-coding RNAs in endometriosis: a narrative review.

Science.gov (United States)

Panir, Kavita; Schjenken, John E; Robertson, Sarah A; Hull, M Louise

2018-04-25

Endometriosis is a benign gynaecological disorder, which affects 10% of reproductive-aged women and is characterized by endometrial cells from the lining of the uterus being found outside the uterine cavity. However, the pathophysiological mechanisms causing the development of this heterogeneous disease remain enigmatic, and a lack of effective biomarkers necessitates surgical intervention for diagnosis. There is international recognition that accurate non-invasive diagnostic tests and more effective therapies are urgently needed. Non-coding RNA (ncRNA) molecules, which are important regulators of cellular function, have been implicated in many chronic conditions. In endometriosis, transcriptome profiling of tissue samples and functional in vivo and in vitro studies demonstrate that ncRNAs are key contributors to the disease process. In this review, we outline the biogenesis of various ncRNAs relevant to endometriosis and then summarize the evidence indicating their roles in regulatory pathways that govern disease establishment and progression. Articles from 2000 to 2016 were selected for relevance, validity and quality, from results obtained in PubMed, MEDLINE and Google Scholar using the following search terms: ncRNA and reproduction; ncRNA and endometriosis; miRNA and endometriosis; lncRNA and endometriosis; siRNA and endometriosis; endometriosis; endometrial; cervical; ovary; uterus; reproductive tract. All articles were independently screened for eligibility by the authors. This review integrates extensive information from all relevant published studies focusing on microRNAs, long ncRNAs and short inhibitory RNAs in endometriosis. We outline the biological function and synthesis of microRNAs, long ncRNAs and short inhibitory RNAs and provide detailed findings from human research as well as functional studies carried out both in vitro and in vivo, including animal models. Although variability in findings between individual studies exists, collectively, the

Non-standard model for electron heat transport for multidimensional hydrodynamic codes

Energy Technology Data Exchange (ETDEWEB)

Nicolai, Ph.; Busquet, M.; Schurtz, G. [CEA/DAM-Ile de France, 91 - Bruyeres Le Chatel (France)

2000-07-01

In simulations of laser-produced plasma, modeling of heat transport requires an artificial limitation of standard Spitzer-Haerm fluxes. To improve heat conduction processing, we have developed a multidimensional model which accounts for non-local features of heat transport and effects of self-generated magnetic fields. This consistent treatment of both mechanisms has been implemented in a two-dimensional radiation-hydrodynamic code. First results indicate good agreements between simulations and experimental data. (authors)

Non-standard model for electron heat transport for multidimensional hydrodynamic codes

International Nuclear Information System (INIS)

Nicolai, Ph.; Busquet, M.; Schurtz, G.

2000-01-01

In simulations of laser-produced plasma, modeling of heat transport requires an artificial limitation of standard Spitzer-Haerm fluxes. To improve heat conduction processing, we have developed a multidimensional model which accounts for non-local features of heat transport and effects of self-generated magnetic fields. This consistent treatment of both mechanisms has been implemented in a two-dimensional radiation-hydrodynamic code. First results indicate good agreements between simulations and experimental data. (authors)

Trans-acting GC-rich non-coding RNA at var expression site modulates gene counting in malaria parasite.

Science.gov (United States)

Guizetti, Julien; Barcons-Simon, Anna; Scherf, Artur

2016-11-16

Monoallelic expression of the var multigene family enables immune evasion of the malaria parasite Plasmodium falciparum in its human host. At a given time only a single member of the 60-member var gene family is expressed at a discrete perinuclear region called the 'var expression site'. However, the mechanism of var gene counting remains ill-defined. We hypothesize that activation factors associating specifically with the expression site play a key role in this process. Here, we investigate the role of a GC-rich non-coding RNA (ncRNA) gene family composed of 15 highly homologous members. GC-rich genes are positioned adjacent to var genes in chromosome-central gene clusters but are absent near subtelomeric var genes. Fluorescence in situ hybridization demonstrates that GC-rich ncRNA localizes to the perinuclear expression site of central and subtelomeric var genes in trans. Importantly, overexpression of distinct GC-rich ncRNA members disrupts the gene counting process at the single cell level and results in activation of a specific subset of var genes in distinct clones. We identify the first trans-acting factor targeted to the elusive perinuclear var expression site and open up new avenues to investigate ncRNA function in antigenic variation of malaria and other protozoan pathogens. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sideways wall force produced during tokamak disruptions

Science.gov (United States)

Strauss, H.; Paccagnella, R.; Breslau, J.; Sugiyama, L.; Jardin, S.

2013-07-01

A critical issue for ITER is to evaluate the forces produced on the surrounding conducting structures during plasma disruptions. We calculate the non-axisymmetric ‘sideways’ wall force Fx, produced in disruptions. Simulations were carried out of disruptions produced by destabilization of n = 1 modes by a vertical displacement event (VDE). The force depends strongly on γτwall, where γ is the mode growth rate and τwall is the wall penetration time, and is largest for γτwall = constant, which depends on initial conditions. Simulations of disruptions caused by a model of massive gas injection were also performed. It was found that the wall force increases approximately offset linearly with the displacement from the magnetic axis produced by a VDE. These results are also obtained with an analytical model. Disruptions are accompanied by toroidal variation of the plasma current Iφ. This is caused by toroidal variation of the halo current, as verified computationally and analytically.

Neural-net predictor for beta limit disruptions in JT-60U

International Nuclear Information System (INIS)

Yoshino, R.

2005-01-01

Prediction of major disruptions occurring at the β -limit for tokamak plasmas with a normal magnetic shear in JT-60U was conducted using neural networks. Since no clear precursors are generally observed a few tens of milliseconds before the β -limit disruption, a sub-neural network is trained to output the value of the β N limit every 2 ms. The target β N limit is artificially set by the operator in the first step to train a network with non-disruptive shots as well as disruptive shots, and then in the second step the target limit is modified using the β N limit output from the trained network. The adjusted target greatly improves the consistency between the input data and the output. This training, the 'self-teaching method', has greatly reduced the false alarm rate triggered for non-disruptive shots. To improve the prediction performance further, the difference between the output β N limit and the measured β N , and 11 parameters, are inputted to the main neural network to calculate the 'stability level'. The occurrence of a major disruption is predicted when the stability level decreases to the 'alarm level'. Major disruptions at the β -limit have been predicted by the main network with a prediction success rate of 80% at 10 ms prior to the disruption while the false alarm rate is lower than 4% for non-disruptive shots. This 80% value is much higher than that obtained for a network trained with a fixed target β N limit set to be the maximum β N observed at the start of a major disruption, lower than 10%. A prediction success rate of 90% with a false alarm rate of 12% at 10 ms prior to the disruption has also been obtained. This 12% value is about half of that obtained for a network trained with a fixed target β N limit

DSTAR: A comprehensive tokamak resistive disruption model for vacuum vessel components

International Nuclear Information System (INIS)

Merrill, B.J.; Jardin, S.C.

1987-01-01

A computer code, DSTAR, has recently been developed to quantify the surface erosion and induced forces than can occur during major tokamak plasma disruptions. A disruption analysis has been performed for the TFCX fusion device. The limiters and inboard first wall were assumed to be clad with beryllium. Disruption simulations were performed with and without these structures present, to determine their electromagnetic influence. The results with structure show that the ablated wall material is transported poloidally, as well as radially, in the plasma causing the outermost regions of the plasma to cool. The plasma moves downward and deforms while maintaining contact with the lower limiter. This motion maintains the peak impurity radiant source directly above the exposed surface. For the disruption simulation without the vacuum vessel included, the plasma moves radially along the lower limiter until it contacts the inboard wall, causing ablation of this surface as well. The conclusion is drawn that disruption simulations that do not include both the thermal and electromagnetic response of the vaccum vessel will not result in an accurate prediction. (orig.)

Long non-coding RNAs and mRNAs profiling during spleen development in pig.

Science.gov (United States)

Che, Tiandong; Li, Diyan; Jin, Long; Fu, Yuhua; Liu, Yingkai; Liu, Pengliang; Wang, Yixin; Tang, Qianzi; Ma, Jideng; Wang, Xun; Jiang, Anan; Li, Xuewei; Li, Mingzhou

2018-01-01

Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar. A total of 15,040 lncRNA transcripts were identified among these samples. We found that the temporal expression pattern of lncRNAs was more restricted than observed for protein-coding genes. Time-series analysis showed two large modules for protein-coding genes and lncRNAs. The up-regulated module was enriched for genes related to immune and inflammatory function, while the down-regulated module was enriched for cell proliferation processes such as cell division and DNA replication. Co-expression networks indicated the functional relatedness between protein-coding genes and lncRNAs, which were enriched for similar functions over the series of time points examined. We identified numerous differentially expressed protein-coding genes and lncRNAs in all five developmental stages. Notably, ceruloplasmin precursor (CP), a protein-coding gene participating in antioxidant and iron transport processes, was differentially expressed in all stages. This study provides the first catalog of the developing pig spleen, and contributes to a fuller understanding of the molecular mechanisms underpinning mammalian spleen development.

NONCODE v2.0: decoding the non-coding.

Science.gov (United States)

He, Shunmin; Liu, Changning; Skogerbø, Geir; Zhao, Haitao; Wang, Jie; Liu, Tao; Bai, Baoyan; Zhao, Yi; Chen, Runsheng

2008-01-01

The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs. The improvements brought to the database include not only new and updated ncRNA data sets, but also an incorporation of BLAST alignment search service and access through our custom UCSC Genome Browser. NONCODE can be found under http://www.noncode.org or http://noncode.bioinfo.org.cn.

LETTER TO THE EDITOR: Bicomplexes and conservation laws in non-Abelian Toda models

Science.gov (United States)

Gueuvoghlanian, E. P.

2001-08-01

A bicomplex structure is associated with the Leznov-Saveliev equation of integrable models. The linear problem associated with the zero-curvature condition is derived in terms of the bicomplex linear equation. The explicit example of a non-Abelian conformal affine Toda model is discussed in detail and its conservation laws are derived from the zero-curvature representation of its equation of motion.

Multidisciplinary approach to non-surgical management of inguinal disruption in a professional hockey player treated with platelet-rich plasma, manual therapy and exercise: a case report.

Science.gov (United States)

St-Onge, Eric; MacIntyre, Ian G; Galea, Anthony M

2015-12-01

To present the clinical management of inguinal disruption in a professional hockey player and highlight the importance of a multidisciplinary approach to diagnosis and management. A professional hockey player with recurrent groin pain presented to the clinic after an acute exacerbation of pain while playing hockey. The patient received a clinical diagnosis of inguinal disruption. Imaging revealed a tear in the rectus abdominis. Management included two platelet-rich plasma (PRP) injections to the injured tissue, and subsequent manual therapy and exercise. The patient returned to his prior level of performance in 3.5 weeks. This case demonstrated the importance of a multidisciplinary team and the need for advanced imaging in athletes with groin pain. Research quality concerning the non-surgical management of inguinal disruption remains low. This case adds evidence that PRP, with the addition of manual therapy and exercise may serve as a relatively quick and effective non-surgical management strategy.

Basic Pilot Code Development for Two-Fluid, Three-Field Model

International Nuclear Information System (INIS)

Jeong, Jae Jun; Bae, S. W.; Lee, Y. J.; Chung, B. D.; Hwang, M.; Ha, K. S.; Kang, D. H.

2006-03-01

A basic pilot code for one-dimensional, transient, two-fluid, three-field model has been developed. Using 9 conceptual problems, the basic pilot code has been verified. The results of the verification are summarized below: - It was confirmed that the basic pilot code can simulate various flow conditions (such as single-phase liquid flow, bubbly flow, slug/churn turbulent flow, annular-mist flow, and single-phase vapor flow) and transitions of the flow conditions. A mist flow was not simulated, but it seems that the basic pilot code can simulate mist flow conditions. - The pilot code was programmed so that the source terms of the governing equations and numerical solution schemes can be easily tested. - The mass and energy conservation was confirmed for single-phase liquid and single-phase vapor flows. - It was confirmed that the inlet pressure and velocity boundary conditions work properly. - It was confirmed that, for single- and two-phase flows, the velocity and temperature of non-existing phase are calculated as intended. - During the simulation of a two-phase flow, the calculation reaches a quasisteady state with small-amplitude oscillations. The oscillations seem to be induced by some numerical causes. The research items for the improvement of the basic pilot code are listed in the last section of this report

Basic Pilot Code Development for Two-Fluid, Three-Field Model

Energy Technology Data Exchange (ETDEWEB)

Jeong, Jae Jun; Bae, S. W.; Lee, Y. J.; Chung, B. D.; Hwang, M.; Ha, K. S.; Kang, D. H

2006-03-15

A basic pilot code for one-dimensional, transient, two-fluid, three-field model has been developed. Using 9 conceptual problems, the basic pilot code has been verified. The results of the verification are summarized below: - It was confirmed that the basic pilot code can simulate various flow conditions (such as single-phase liquid flow, bubbly flow, slug/churn turbulent flow, annular-mist flow, and single-phase vapor flow) and transitions of the flow conditions. A mist flow was not simulated, but it seems that the basic pilot code can simulate mist flow conditions. - The pilot code was programmed so that the source terms of the governing equations and numerical solution schemes can be easily tested. - The mass and energy conservation was confirmed for single-phase liquid and single-phase vapor flows. - It was confirmed that the inlet pressure and velocity boundary conditions work properly. - It was confirmed that, for single- and two-phase flows, the velocity and temperature of non-existing phase are calculated as intended. - During the simulation of a two-phase flow, the calculation reaches a quasisteady state with small-amplitude oscillations. The oscillations seem to be induced by some numerical causes. The research items for the improvement of the basic pilot code are listed in the last section of this report.

Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification.

Science.gov (United States)

Zhang, Jingpu; Zhang, Zuping; Wang, Zixiang; Liu, Yuting; Deng, Lei

2018-05-15

Long non-coding RNAs (lncRNAs) are an enormous collection of functional non-coding RNAs. Over the past decades, a large number of novel lncRNA genes have been identified. However, most of the lncRNAs remain function uncharacterized at present. Computational approaches provide a new insight to understand the potential functional implications of lncRNAs. Considering that each lncRNA may have multiple functions and a function may be further specialized into sub-functions, here we describe NeuraNetL2GO, a computational ontological function prediction approach for lncRNAs using hierarchical multi-label classification strategy based on multiple neural networks. The neural networks are incrementally trained level by level, each performing the prediction of gene ontology (GO) terms belonging to a given level. In NeuraNetL2GO, we use topological features of the lncRNA similarity network as the input of the neural networks and employ the output results to annotate the lncRNAs. We show that NeuraNetL2GO achieves the best performance and the overall advantage in maximum F-measure and coverage on the manually annotated lncRNA2GO-55 dataset compared to other state-of-the-art methods. The source code and data are available at http://denglab.org/NeuraNetL2GO/. leideng@csu.edu.cn. Supplementary data are available at Bioinformatics online.

Taking the conservation biology perspective to secondary school classrooms.

Science.gov (United States)

Wyner, Yael; Desalle, Rob

2010-06-01

The influence of conservation biology can be enhanced greatly if it reaches beyond undergraduate biology to students at the middle and high school levels. If a conservation perspective were taught in secondary schools, students who are not interested in biology could be influenced to pursue careers or live lifestyles that would reduce the negative impact of humans on the world. We use what we call the ecology-disrupted approach to transform the topics of conservation biology research into environmental-issue and ecology topics, the major themes of secondary school courses in environmental science. In this model, students learn about the importance and complexity of normal ecological processes by studying what goes wrong when people disrupt them (environmental issues). Many studies published in Conservation Biology are related in some way to the ecological principles being taught in secondary schools. Describing research in conservation biology in the language of ecology curricula in secondary schools can help bring these science stories to the classroom and give them a context in which they can be understood by students. Without this context in the curriculum, a science story can devolve into just another environmental issue that has no immediate effect on the daily lives of students. Nevertheless, if the research is placed in the context of larger ecological processes that are being taught, students can gain a better understanding of ecology and a better understanding of their effect on the world.

Endotherapy is effective for pancreatic ductal disruption: A dual center experience.

Science.gov (United States)

Das, Rohit; Papachristou, Georgios I; Slivka, Adam; Easler, Jeffrey J; Chennat, Jennifer; Malin, Jessica; Herman, Justin B; Laique, Sobia N; Hayat, Umar; Ooi, Yinn Shaung; Rabinovitz, Mordechai; Yadav, Dhiraj; Siddiqui, Ali A

2016-01-01

Pancreatic duct (PD) disruptions occur as a result of different etiologies and can be managed medically, endoscopically, or surgically. The aim of this study was to provide an evaluation on the efficacy of endotherapy for treatment of PD disruption in a large cohort of patients and identify factors that predict successful treatment outcome. We retrospectively evaluated consecutive patients who underwent endoscopic retrograde pancreatography (ERP) for transpapillary pancreatic stent placement for PD disruption from 2008 to 2013 at two tertiary referral institutions. PD disruption was defined as extravasation of contrast from the pancreatic duct as seen on ERP. Therapeutic success was defined by resolution of PD leak on ERP, clinical, and/or imaging evaluation. We evaluated 107 patients (58% male, mean age 53 years) with PD disruption. Etiologies of PD disruption were acute pancreatitis (36%), post-operative (31%), chronic pancreatitis (29%), and trauma (4%). PD disruption was successfully bridged by a stent in 45 (44%) patients. Two patients developed post-sphincterotomy bleeding, two had stent migration, and two patients died as a result of post-ERP related complications. Placement of a PD stent was successful in 103/107 (96%) patients. Therapeutic success was achieved in 80/107 (75%) patients. Non-acute pancreatitis etiologies and absence of complete duct disruption were independent predictors of therapeutic success. Endoscopic therapy using a transpapillary stent for PD disruption is safe and effective. Absence of complete duct disruption and non-AP etiologies determine a favorable endoscopic outcome. Published by Elsevier India Pvt Ltd.

3D code for simulations of fluid flows

International Nuclear Information System (INIS)

Skandera, D.

2004-01-01

In this paper, a present status in the development of the new numerical code is reported. The code is considered for simulations of fluid flows. The finite volume approach is adopted for solving standard fluid equations. They are treated in a conservative form to ensure a correct conservation of fluid quantities. Thus, a nonlinear hyperbolic system of conservation laws is numerically solved. The code uses the Eulerian description of the fluid and is designed as a high order central numerical scheme. The central approach employs no (approximate) Riemann solver and is less computational expensive. The high order WENO strategy is adopted in the reconstruction step to achieve results comparable with more accurate Riemann solvers. A combination of the central approach with an iterative solving of a local Riemann problem is tested and behaviour of such numerical flux is reported. An extension to three dimensions is implemented using a dimension by dimension approach, hence, no complicated dimensional splitting need to be introduced. The code is fully parallelized with the MPI library. Several standard hydrodynamic tests in one, two and three dimensions were performed and their results are presented. (author)

On the Comparative Performance Analysis of Turbo-Coded Non-Ideal Sigle-Carrier and Multi-Carrier Waveforms over Wideband Vogler-Hoffmeyer HF Channels

Directory of Open Access Journals (Sweden)

F. Genc

2014-09-01

Full Text Available The purpose of this paper is to compare the turbo-coded Orthogonal Frequency Division Multiplexing (OFDM and turbo-coded Single Carrier Frequency Domain Equalization (SC-FDE systems under the effects of Carrier Frequency Offset (CFO, Symbol Timing Offset (STO and phase noise in wide-band Vogler-Hoffmeyer HF channel model. In mobile communication systems multi-path propagation occurs. Therefore channel estimation and equalization is additionally necessary. Furthermore a non-ideal local oscillator generally is misaligned with the operating frequency at the receiver. This causes carrier frequency offset. Hence in coded SC-FDE and coded OFDM systems; a very efficient, low complex frequency domain channel estimation and equalization is implemented in this paper. Also Cyclic Prefix (CP based synchronization synchronizes the clock and carrier frequency offset.The simulations show that non-ideal turbo-coded OFDM has better performance with greater diversity than non-ideal turbo-coded SC-FDE system in HF channel.

Integration and visualization of non-coding RNA and protein interaction networks

OpenAIRE

Junge, Alexander; Refsgaard, Jan Christian; Garde, Christian; Pan, Xiaoyong; Santos Delgado, Alberto; Anthon, Christian; Alkan, Ferhat; von Mering, Christian; Workman, Christopher; Jensen, Lars Juhl; Gorodkin, Jan

2015-01-01

Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Association and Interaction Networks) - a database that combines ncRNA-ncRNA, ncRNA-mRNA and ncRNA-protein interactions with large-scale protein association networks available in the STRING database. By int...

The Redox Code.

Science.gov (United States)

Jones, Dean P; Sies, Helmut

2015-09-20

The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O₂ and H₂O₂ contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine.

Long Non-Coding RNAs: The Key Players in Glioma Pathogenesis

Energy Technology Data Exchange (ETDEWEB)

Kiang, Karrie Mei-Yee; Zhang, Xiao-Qin; Leung, Gilberto Ka-Kit, E-mail: gilberto@hku.hk [Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong (China)

2015-07-29

Long non-coding RNAs (LncRNAs) represent a novel class of RNAs with no functional protein-coding ability, yet it has become increasingly clear that interactions between lncRNAs with other molecules are responsible for important gene regulatory functions in various contexts. Given their relatively high expressions in the brain, lncRNAs are now thought to play important roles in normal brain development as well as diverse disease processes including gliomagenesis. Intriguingly, certain lncRNAs are closely associated with the initiation, differentiation, progression, recurrence and stem-like characteristics in glioma, and may therefore be exploited for the purposes of sub-classification, diagnosis and prognosis. LncRNAs may also serve as potential therapeutic targets as well as a novel biomarkers in the treatment of glioma. In this article, the functional aspects of lncRNAs, particularly within the central nervous system (CNS), will be briefly discussed, followed by highlights of the important roles of lncRNAs in mediating critical steps during glioma development. In addition, the key lncRNA players and their possible mechanistic pathways associated with gliomagenesis will be addressed.

Long Non-Coding RNAs: The Key Players in Glioma Pathogenesis

International Nuclear Information System (INIS)

Kiang, Karrie Mei-Yee; Zhang, Xiao-Qin; Leung, Gilberto Ka-Kit

2015-01-01

Long non-coding RNAs (LncRNAs) represent a novel class of RNAs with no functional protein-coding ability, yet it has become increasingly clear that interactions between lncRNAs with other molecules are responsible for important gene regulatory functions in various contexts. Given their relatively high expressions in the brain, lncRNAs are now thought to play important roles in normal brain development as well as diverse disease processes including gliomagenesis. Intriguingly, certain lncRNAs are closely associated with the initiation, differentiation, progression, recurrence and stem-like characteristics in glioma, and may therefore be exploited for the purposes of sub-classification, diagnosis and prognosis. LncRNAs may also serve as potential therapeutic targets as well as a novel biomarkers in the treatment of glioma. In this article, the functional aspects of lncRNAs, particularly within the central nervous system (CNS), will be briefly discussed, followed by highlights of the important roles of lncRNAs in mediating critical steps during glioma development. In addition, the key lncRNA players and their possible mechanistic pathways associated with gliomagenesis will be addressed

Training program for energy conservation in new-building construction. Volume IV. Energy conservation technology: advanced course for plan examiners

Energy Technology Data Exchange (ETDEWEB)

None

1977-12-01

A Model Code for Energy Conservation in New Building Construction has been developed by those national organizations primarily concerned with the development and promulgation of model codes. The technical provisions are based on ASHRAE Standard 90-75 and are intended for use by state and local officials. This manual contains a more in-depth training in the review techniques and concepts required by the plan examiners and code officials in administering the code for conventional (buildings of 3 stories or less) construction.

The θ-γ neural code.

Science.gov (United States)

Lisman, John E; Jensen, Ole

2013-03-20

Theta and gamma frequency oscillations occur in the same brain regions and interact with each other, a process called cross-frequency coupling. Here, we review evidence for the following hypothesis: that the dual oscillations form a code for representing multiple items in an ordered way. This form of coding has been most clearly demonstrated in the hippocampus, where different spatial information is represented in different gamma subcycles of a theta cycle. Other experiments have tested the functional importance of oscillations and their coupling. These involve correlation of oscillatory properties with memory states, correlation with memory performance, and effects of disrupting oscillations on memory. Recent work suggests that this coding scheme coordinates communication between brain regions and is involved in sensory as well as memory processes. Copyright © 2013 Elsevier Inc. All rights reserved.

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

KAUST Repository

Ma, L.; Li, A.; Zou, D.; Xu, X.; Xia, L.; Yu, J.; Bajic, Vladimir B.; Zhang, Z.

2014-01-01

Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open

Evaluation of Agency Non-Code Layered Pressure Vessels (LPVs)

Science.gov (United States)

Prosser, William H.

2014-01-01

In coordination with the Office of Safety and Mission Assurance and the respective Center Pressure System Managers (PSMs), the NASA Engineering and Safety Center (NESC) was requested to formulate a consensus draft proposal for the development of additional testing and analysis methods to establish the technical validity, and any limitation thereof, for the continued safe operation of facility non-code layered pressure vessels. The PSMs from each NASA Center were asked to participate as part of the assessment team by providing, collecting, and reviewing data regarding current operations of these vessels. This report contains the outcome of the assessment and the findings, observations, and NESC recommendations to the Agency and individual NASA Centers.

Upregulation of Haploinsufficient Gene Expression in the Brain by Targeting a Long Non-coding RNA Improves Seizure Phenotype in a Model of Dravet Syndrome.

Science.gov (United States)

Hsiao, J; Yuan, T Y; Tsai, M S; Lu, C Y; Lin, Y C; Lee, M L; Lin, S W; Chang, F C; Liu Pimentel, H; Olive, C; Coito, C; Shen, G; Young, M; Thorne, T; Lawrence, M; Magistri, M; Faghihi, M A; Khorkova, O; Wahlestedt, C

2016-07-01

Dravet syndrome is a devastating genetic brain disorder caused by heterozygous loss-of-function mutation in the voltage-gated sodium channel gene SCN1A. There are currently no treatments, but the upregulation of SCN1A healthy allele represents an appealing therapeutic strategy. In this study we identified a novel, evolutionary conserved mechanism controlling the expression of SCN1A that is mediated by an antisense non-coding RNA (SCN1ANAT). Using oligonucleotide-based compounds (AntagoNATs) targeting SCN1ANAT we were able to induce specific upregulation of SCN1A both in vitro and in vivo, in the brain of Dravet knock-in mouse model and a non-human primate. AntagoNAT-mediated upregulation of Scn1a in postnatal Dravet mice led to significant improvements in seizure phenotype and excitability of hippocampal interneurons. These results further elucidate the pathophysiology of Dravet syndrome and outline a possible new approach for the treatment of this and other genetic disorders with similar etiology. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Upregulation of Haploinsufficient Gene Expression in the Brain by Targeting a Long Non-coding RNA Improves Seizure Phenotype in a Model of Dravet Syndrome

Directory of Open Access Journals (Sweden)

J. Hsiao

2016-07-01

Full Text Available Dravet syndrome is a devastating genetic brain disorder caused by heterozygous loss-of-function mutation in the voltage-gated sodium channel gene SCN1A. There are currently no treatments, but the upregulation of SCN1A healthy allele represents an appealing therapeutic strategy. In this study we identified a novel, evolutionary conserved mechanism controlling the expression of SCN1A that is mediated by an antisense non-coding RNA (SCN1ANAT. Using oligonucleotide-based compounds (AntagoNATs targeting SCN1ANAT we were able to induce specific upregulation of SCN1A both in vitro and in vivo, in the brain of Dravet knock-in mouse model and a non-human primate. AntagoNAT-mediated upregulation of Scn1a in postnatal Dravet mice led to significant improvements in seizure phenotype and excitability of hippocampal interneurons. These results further elucidate the pathophysiology of Dravet syndrome and outline a possible new approach for the treatment of this and other genetic disorders with similar etiology.

Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris

Czech Academy of Sciences Publication Activity Database

Stone, James D.; Koloušková, Pavla; Sloan, D.B.; Štorchová, Helena

2017-01-01

Roč. 68, č. 7 (2017), s. 1599-1612 ISSN 0022-0957 R&D Projects: GA ČR(CZ) GA16-09220S Institutional support: RVO:61389030 Keywords : Cytoplasmic male sterility * Editing * Mitochondrion * Non-coding RNA * Silene vulgaris * Splicing * Transcriptome Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 5.830, year: 2016

Do the weak neutral currents cause parity non-conserving eN and μN forces

International Nuclear Information System (INIS)

Henley, E.M.

1977-01-01

It is stated that although the evidence for weak neutral currents is now well established its effects have been observed primarily in reactions initiated by muon neutrinos in which the neutrino is also present in the final state. There is, as yet, no comparable evidence for a weak force due to neutral currents, mediated by an uncharged boson, between charged leptons (electrons, muons) and nucleons. Theory predicts such a force, but its detection requires it to be parity non-conserving, since any weak parity conserving force is masked by the much larger electromagnetic interaction between the charged lepton and proton. Although high energy neutrino experiments favor a parity non-conserving interaction, the evidence is not overwhelming, and pure vector current theories cannot be ruled out. The electromagnetic current which is related directly to the weak force in modern gauge theories, behaves, as a pure vector under rotations and reflections, but the charged weak currents, responsible for ordinary β decays, are known to be of a mixed vector-axial vector nature. It is therefore of great interest to learn the spatial characteristics of the neutral weak currents. The search for parity non-conserving (PNC) effects in electron-nucleon scattering, in muonic atoms and in normal electronic atoms, has received much attention, but the experiments require very high precision and great care and ingenuity. The variety of ways for searching for PNC effects are discussed, together with the basic framework for most PNC theories, restricted to vector and axial-vector currents. One method to learn about the e-N weak force is to scatter longitudinally polarized electrons from protons, and the advantages of this are discussed - such tests are being undertaken. Experiments with muonic and normal electronic atoms are referred to, and their advantages and disadvantages are discussed. It is pointed out that a pleasant feature of the weak interaction is that perturbation theory can be used

Manufacturing doubt about endocrine disrupter science

DEFF Research Database (Denmark)

Bergman, Åke; Becher, Georg; Blumberg, Bruce

2015-01-01

We present a detailed response to the critique of "State of the Science of Endocrine Disrupting Chemicals 2012" (UNEP/WHO, 2013) by financial stakeholders, authored by Lamb et al. (2014). Lamb et al.'s claim that UNEP/WHO (2013) does not provide a balanced perspective on endocrine disruption......) report is not particularly erudite and that their critique is not intended to be convincing to the scientific community, but to confuse the scientific data. Consequently, it promotes misinterpretation of the UNEP/WHO (2013) report by non-specialists, bureaucrats, politicians and other decision makers...

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

Science.gov (United States)

Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

2012-08-01

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue

Directory of Open Access Journals (Sweden)

Hui Gao

2018-04-01

Full Text Available Long non-coding RNAs (lncRNAs belong to a recently discovered class of molecules proposed to regulate various cellular processes. Here, we systematically analyzed their expression in human subcutaneous white adipose tissue (WAT and found that a limited set was differentially expressed in obesity and/or the insulin resistant state. Two lncRNAs herein termed adipocyte-specific metabolic related lncRNAs, ASMER-1 and ASMER-2 were enriched in adipocytes and regulated by both obesity and insulin resistance. Knockdown of either ASMER-1 or ASMER-2 by antisense oligonucleotides in in vitro differentiated human adipocytes revealed that both genes regulated adipogenesis, lipid mobilization and adiponectin secretion. The observed effects could be attributed to crosstalk between ASMERs and genes within the master regulatory pathways for adipocyte function including PPARG and INSR. Altogether, our data demonstrate that lncRNAs are modulators of the metabolic and secretory functions in human fat cells and provide an emerging link between WAT and common metabolic conditions. Keywords: White adipose tissue, Adipocytes, Long non-coding RNAs, Metabolic traits, Lipolysis, Adiponectin

Iterative demodulation and decoding of coded non-square QAM

Science.gov (United States)

Li, L.; Divsalar, D.; Dolinar, S.

2003-01-01

Simulation results show that, with iterative demodulation and decoding, coded NS-8QAM performs 0.5 dB better than standard 8QAM and 0.7 dB better than 8PSK at BER= 10(sup -5), when the FEC code is the (15, 11) Hamming code concatenated with a rate-1 accumulator code, while coded NS-32QAM performs 0.25 dB better than standard 32QAM.

Newly-Developed 3D GRMHD Code and its Application to Jet Formation

Science.gov (United States)

Mizuno, Y.; Nishikawa, K.-I.; Koide, S.; Hardee, P.; Fishman, G. J.

2006-01-01

We have developed a new three-dimensional general relativistic magnetohydrodynamic code by using a conservative, high-resolution shock-capturing scheme. The numerical fluxes are calculated using the HLL approximate Riemann solver scheme. The flux-interpolated constrained transport scheme is used to maintain a divergence-free magnetic field. We have performed various 1-dimensional test problems in both special and general relativity by using several reconstruction methods and found that the new 3D GRMHD code shows substantial improvements over our previous model. The . preliminary results show the jet formations from a geometrically thin accretion disk near a non-rotating and a rotating black hole. We will discuss the jet properties depended on the rotation of a black hole and the magnetic field strength.

The role of non-coding RNAs in cytoplasmic male sterility in flowering plants

Czech Academy of Sciences Publication Activity Database

Štorchová, Helena

2017-01-01

Roč. 18, č. 11 (2017), č. článku 2429. E-ISSN 1422-0067 R&D Projects: GA ČR GA16-09220S Institutional support: RVO:61389030 Keywords : Cytoplasmic male sterility * Gene expression * Global transcriptome * Non-coding RNA * Pollen development Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 3.226, year: 2016

Non-pharmacological strategies for blood conservation in cardiac surgery.

Science.gov (United States)

Ruel, M A; Rubens, F D

2001-04-01

Of all surgical specialties, cardiac operations are most often associated with coagulopathy, blood loss, and the need for transfusions. This not only represents a major burden on blood procurement and banking organizations at all levels, but also constitutes a risk for each patient receiving allogeneic blood products. This paper reviews current non-pharmacological strategies aimed at decreasing blood use in patients undergoing cardiac surgery. The literature pertaining to each blood conservation strategy was searched, reviewed, and appraised. Meta- analyses were also consulted and their results complemented with subsequent reports when available. Preoperative autologous donation programs are effective in decreasing allogeneic transfusions, but are costly and applicable to elective patients only. Off-pump revascularization strategies also appear to decrease transfusion requirements in suitable patients. The effectiveness of acute normovolemic hemodilution, retrograde autologous priming, small volume cardiopulmonary bypass circuits, platelet-rich plasmapheresis, alternative heparin strategies, and postoperative cell salvage are more difficult to appraise as a high proportion of available studies suffer from lack of transfusion guidelines or the absence of blinding. Biological glues, surgical adhesives, and postoperative increases in positive end-expiratory pressure (PEEP) have no demonstrated efficacy. The applicability or effectiveness of many of these modalities remains controversial and more studies are needed before they may be employed routinely in cardiac surgical patients. The judicious use of rational transfusion guidelines may still be the simplest and most cost-effective means of blood conservation today.

Electromagnetic loads and structural response of the CIT [Compact Ignition Tokamak] vacuum vessel to plasma disruptions

International Nuclear Information System (INIS)

Salem, S.L.; Listvinsky, G.; Lee, M.Y.; Bailey, C.

1987-01-01

Studies of the electromagnetic loads produced by a variety of plasma disruptions, and the resulting structural effects on the compact Ignition Tokamak (CIT) vacuum vessel (VV), have been performed to help optimize the VV design. A series of stationary and moving plasmas, with disruption rates from 0.7--10.0 MA/ms, have been analyzed using the EMPRES code to compute eddy currents and electromagnetic pressures, and the NASTRAN code to evaluate the structural response of the vacuum vessel. Key factors contributing to the magnitude of EM forces and resulting stresses on the vessel have been found to include disruption rate, and direction and synchronization of plasma motion with the onset of plasma current decay. As a result of these analyses, a number of design changes have been made, and design margins for the present 1.75 meter design have been improved over the original CIT configuration. 1 ref., 10 figs., 4 tabs

The ALI-ARMS Code for Modeling Atmospheric non-LTE Molecular Band Emissions: Current Status and Applications

Science.gov (United States)

Kutepov, A. A.; Feofilov, A. G.; Manuilova, R. O.; Yankovsky, V. A.; Rezac, L.; Pesnell, W. D.; Goldberg, R. A.

2008-01-01

The Accelerated Lambda Iteration (ALI) technique was developed in stellar astrophysics at the beginning of 1990s for solving the non-LTE radiative transfer problem in atomic lines and multiplets in stellar atmospheres. It was later successfully applied to modeling the non-LTE emissions and radiative cooling/heating in the vibrational-rotational bands of molecules in planetary atmospheres. Similar to the standard lambda iterations ALI operates with the matrices of minimal dimension. However, it provides higher convergence rate and stability due to removing from the iterating process the photons trapped in the optically thick line cores. In the current ALI-ARMS (ALI for Atmospheric Radiation and Molecular Spectra) code version additional acceleration of calculations is provided by utilizing the opacity distribution function (ODF) approach and "decoupling". The former allows replacing the band branches by single lines of special shape, whereas the latter treats non-linearity caused by strong near-resonant vibration-vibrational level coupling without additional linearizing the statistical equilibrium equations. Latest code application for the non-LTE diagnostics of the molecular band emissions of Earth's and Martian atmospheres as well as for the non-LTE IR cooling/heating calculations are discussed.

An evolutionary conserved region (ECR in the human dopamine receptor D4 gene supports reporter gene expression in primary cultures derived from the rat cortex

Directory of Open Access Journals (Sweden)

Haddley Kate

2011-05-01

Full Text Available Abstract Background Detecting functional variants contributing to diversity of behaviour is crucial for dissecting genetics of complex behaviours. At a molecular level, characterisation of variation in exons has been studied as they are easily identified in the current genome annotation although the functional consequences are less well understood; however, it has been difficult to prioritise regions of non-coding DNA in which genetic variation could also have significant functional consequences. Comparison of multiple vertebrate genomes has allowed the identification of non-coding evolutionary conserved regions (ECRs, in which the degree of conservation can be comparable with exonic regions suggesting functional significance. Results We identified ECRs at the dopamine receptor D4 gene locus, an important gene for human behaviours. The most conserved non-coding ECR (D4ECR1 supported high reporter gene expression in primary cultures derived from neonate rat frontal cortex. Computer aided analysis of the sequence of the D4ECR1 indicated the potential transcription factors that could modulate its function. D4ECR1 contained multiple consensus sequences for binding the transcription factor Sp1, a factor previously implicated in DRD4 expression. Co-transfection experiments demonstrated that overexpression of Sp1 significantly decreased the activity of the D4ECR1 in vitro. Conclusion Bioinformatic analysis complemented by functional analysis of the DRD4 gene locus has identified a a strong enhancer that functions in neurons and b a transcription factor that may modulate the function of that enhancer.

Comparison of Crack Growth Test Results at Elevated Temperature and Design Code Material Properties for Grade 91 Steel

Energy Technology Data Exchange (ETDEWEB)

Lee, Hyeong-Yeon; Kim, Woo-Gon; Kim, Nak-Hyun [Korea Atomic Energy Reserach Institute, Daejeon (Korea, Republic of)

2015-01-15

The material properties of crack growth models at an elevated temperature were derived from the results of numerous crack growth tests for Mod.9Cr-1Mo (ASME Grade 91) steel specimens under fatigue loading and creep loading at an elevated temperature. These crack growth models were needed for defect assessment under creep-fatigue loading. The mathematical crack growth rate models for fatigue crack growth (FCG) and creep crack growth (CCG) were determined based on the test results, and the models were compared with those of the French design code RCCMRx to investigate the conservatism of the code. The French design code RCC-MRx provides an FCG model and a CCG model for Grade 91 steel in Section III Tome 6. It was shown that the FCG model of RCC-MRx is conservative, while the CCG model is non-conservative compared with the present test data. Thus, it was shown that further validation of the property was required. Mechanical strength tests and creep tests were also conducted, and the test results were compared with those of RCC-MRx.

Prediction of density limit disruptions on the J-TEXT tokamak

International Nuclear Information System (INIS)

Wang, S Y; Chen, Z Y; Huang, D W; Tong, R H; Yan, W; Wei, Y N; Ma, T K; Zhang, M; Zhuang, G

2016-01-01

Disruption mitigation is essential for the next generation of tokamaks. The prediction of plasma disruption is the key to disruption mitigation. A neural network combining eight input signals has been developed to predict the density limit disruptions on the J-TEXT tokamak. An optimized training method has been proposed which has improved the prediction performance. The network obtained has been tested on 64 disruption shots and 205 non-disruption shots. A successful alarm rate of 82.8% with a false alarm rate of 12.3% can be achieved at 4.8 ms prior to the current spike of the disruption. It indicates that more physical parameters than the current physical scaling should be considered for predicting the density limit. It was also found that the critical density for disruption can be predicted several tens of milliseconds in advance in most cases. Furthermore, if the network is used for real-time density feedback control, more than 95% of the density limit disruptions can be avoided by setting a proper threshold. (paper)

Quasi-integrable non-linear Schrödinger models, infinite towers of exactly conserved charges and bright solitons

Science.gov (United States)

Blas, H.; do Bonfim, A. C. R.; Vilela, A. M.

2017-05-01

Deformations of the focusing non-linear Schrödinger model (NLS) are considered in the context of the quasi-integrability concept. We strengthen the results of JHEP 09 (2012) 103 10.1007/JHEP06(2015)177" TargetType="URL"/> for bright soliton collisions. We addressed the focusing NLS as a complement to the one in JHEP 03 (2016) 005 10.1007/JHEP06(2015)177" TargetType="URL"/> , in which the modified defocusing NLS models with dark solitons were shown to exhibit an infinite tower of exactly conserved charges. We show, by means of analytical and numerical methods, that for certain two-bright-soliton solutions, in which the modulus and phase of the complex modified NLS field exhibit even parities under a space-reflection symmetry, the first four and the sequence of even order charges are exactly conserved during the scattering process of the solitons. We perform extensive numerical simulations and consider the bright solitons with deformed potential V=2η /2+\\upepsilon{({|ψ |}^2)}^{2+\\upepsilon},\\upepsilon \\in \\mathbb{R},η <0 . However, for two-soliton field components without definite parity we also show numerically the vanishing of the first non-trivial anomaly and the exact conservation of the relevant charge. So, the parity symmetry seems to be a sufficient but not a necessary condition for the existence of the infinite tower of conserved charges. The model supports elastic scattering of solitons for a wide range of values of the amplitudes and velocities and the set { η, ɛ}. Since the NLS equation is ubiquitous, our results may find potential applications in several areas of non-linear science.

Scaling Non-Regular Shared-Memory Codes by Reusing Custom Loop Schedules

Directory of Open Access Journals (Sweden)

Dimitrios S. Nikolopoulos

2003-01-01

Full Text Available In this paper we explore the idea of customizing and reusing loop schedules to improve the scalability of non-regular numerical codes in shared-memory architectures with non-uniform memory access latency. The main objective is to implicitly setup affinity links between threads and data, by devising loop schedules that achieve balanced work distribution within irregular data spaces and reusing them as much as possible along the execution of the program for better memory access locality. This transformation provides a great deal of flexibility in optimizing locality, without compromising the simplicity of the shared-memory programming paradigm. In particular, the programmer does not need to explicitly distribute data between processors. The paper presents practical examples from real applications and experiments showing the efficiency of the approach.

Integration and visualization of non-coding RNA and protein interaction networks

DEFF Research Database (Denmark)

Junge, Alexander; Refsgaard, Jan Christian; Garde, Christian

Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Associ......) co-occurrences found by text mining Medline abstracts. Each resource was assigned a reliability score by assessing its agreement with a gold standard set of microRNA-target interactions. RAIN is available at: http://rth.dk/resources/rain...

NOAA Weather Radio - EAS Event Codes

Science.gov (United States)

Non-Zero All Hazards Logo Emergency Alert Description Event Codes Fact Sheet FAQ Organization Search Coding Using SAME SAME Non-Zero Codes DOCUMENTS NWR Poster NWR Brochure NWR Brochure Printing Notes

Analysis of energy released from core disruptive accident of sodium cooled fast reactor using CDA-ER and VENUS-II codes

Energy Technology Data Exchange (ETDEWEB)

Kang, S. H.; Ha, K. S. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2013-05-15

feedback (Doppler and displacement) VENUS-II has the following assumptions. The reactor materials behave like a homogeneous mixture with the property of an isotropic and nonviscous fluid. The reactivity change caused by a material displacement can be calculated with first-order perturbation theory. Further, the reactivity worth of spatial gradients remain constant and distort with the grid. The heat transfer from the fuel can be ignored. Although several heat transfer mechanisms can become significant, one of the greatest potential influence would appear to be a rapid molten-fuel-coolant interaction (MFCI). The non fuel core constituents are considered to be compressible, but inert, materials. The fuel vapor pressure and compression of the reactor materials are the only sources of internal pressure. Thus, such potential pressure sources such as fission gas and sodium vapor pressure are ignored. The time history of the power level can be described using point kinetics, and the spatial power-density distribution remains constant. In this work, the energy released from core disruptive accident (CDA) of sodium cooled fast reactor was investigated using CDA-ER and VENUS-II code for various reactivity insertion rates up to 100$/s, and their results were compared. The calculation results of two codes showed similar trends of energy, power and pressure from CDA. But most results of VENUS-II were found to be larger than those of CDA-ER. The released energy results calculated from VENUS-II were about 2 ∼ 3 times higher than those from CDA-ER.

Analysis of energy released from core disruptive accident of sodium cooled fast reactor using CDA-ER and VENUS-II codes

International Nuclear Information System (INIS)

Kang, S. H.; Ha, K. S.

2013-01-01

displacement) VENUS-II has the following assumptions. The reactor materials behave like a homogeneous mixture with the property of an isotropic and nonviscous fluid. The reactivity change caused by a material displacement can be calculated with first-order perturbation theory. Further, the reactivity worth of spatial gradients remain constant and distort with the grid. The heat transfer from the fuel can be ignored. Although several heat transfer mechanisms can become significant, one of the greatest potential influence would appear to be a rapid molten-fuel-coolant interaction (MFCI). The non fuel core constituents are considered to be compressible, but inert, materials. The fuel vapor pressure and compression of the reactor materials are the only sources of internal pressure. Thus, such potential pressure sources such as fission gas and sodium vapor pressure are ignored. The time history of the power level can be described using point kinetics, and the spatial power-density distribution remains constant. In this work, the energy released from core disruptive accident (CDA) of sodium cooled fast reactor was investigated using CDA-ER and VENUS-II code for various reactivity insertion rates up to 100$/s, and their results were compared. The calculation results of two codes showed similar trends of energy, power and pressure from CDA. But most results of VENUS-II were found to be larger than those of CDA-ER. The released energy results calculated from VENUS-II were about 2 ∼ 3 times higher than those from CDA-ER

Fuel retention and recovery in natural and MGI disruptions on KSTAR

International Nuclear Information System (INIS)

Yu, Y.W.; Hong, S.H.; Yoon, S.W.; Kim, K.P.; Kim, W.C.; Seo, D.C.

2013-01-01

Fuel retention and recovery are studied during natural and Massive Gas Injection (MGI) induced disruptions in KSTAR with full graphite wall. The amount of released particles in natural disruptions in 15 s after the discharge is ∼5–10 times higher than that of non-disruption shots, but the difference is only ∼ 2 MGI induced disruptions depends on magnetic field (B t ) and MGI amount. The MGI disruption under a low B t and a medium MGI amount shows shorter thermal quench (TQ) and current quench (CQ), thereby higher fuel recovery. High B t plasma requires higher MGI amount for both disruption mitigation and fuel recovery. A high recovery of 4.2 × 10 22 D (∼0.78 monolayers) is obtained by MGI disruption in KSTAR 2011

The Impact of Transformational Leadership, Experiential Learning, and Reflective Journaling on the Conservation Ethic of Tertiary-Level Non-Science Majors

Science.gov (United States)

Reynolds, Bradley Robert

2013-01-01

The impact of transformational leadership, experiential learning, and reflective journaling on the conservation ethic of non-science majors in a general education survey course was investigated. The main research questions were: (1) Is the Conservation of Biodiversity professor a transformational leader? (2) Is there a difference in the…

Do Farmers Using Conventional and Non-Conventional Systems of Agriculture Have Different Perceptions of the Diversity of Wild Birds? Implications for Conservation

Science.gov (United States)

de Andrade, Luciano Pires; Muniz, Lauana Souza; Telino-Júnior, Wallace Rodrigues; Albuquerque, Ulysses Paulino; Lyra-Neves, Rachel Maria

2016-01-01

Farmers’ perceptions of birds’ interactions with agricultural production systems are fundamental to species conservation efforts. In the present study, we evaluated the perceptions of birds held by farmers who engage in conventional and non-conventional agricultural production processes and the implications of potential differences in these perceptions on species conservation. To accomplish this, data were collected using questionnaires, semi-structured interviews, and other complementary sources of information gathered from 191 farmers in northeastern Brazil. Although some similarities were identified among the farmers in their perceptions and local ecological knowledge (LEK) of birds, differences existed between the conventional and non-conventional farmers in their attitudes toward, conflicts with, and usage of bird species. Compared to the conventional farmers, the non-conventional farmers could identify more bird species, possessed more favorable attitudes toward birds, and engaged in practices more beneficial to the conservation of avifauna. The perceptions that were identified were related to the type of agriculture practiced, and such perceptions may affect the conservation of bird species. Therefore, the adoption of certain agricultural practices has important implications for conservation. Our results indicate the need for investment in public policies, programs and actions that account for farmers’ knowledge and perceptions. Such investments will contribute to the development and adoption of practices supporting wild bird conservation in agricultural areas. PMID:27243222

Do Farmers Using Conventional and Non-Conventional Systems of Agriculture Have Different Perceptions of the Diversity of Wild Birds? Implications for Conservation.

Science.gov (United States)

Silva-Andrade, Horasa Lima; de Andrade, Luciano Pires; Muniz, Lauana Souza; Telino-Júnior, Wallace Rodrigues; Albuquerque, Ulysses Paulino; Lyra-Neves, Rachel Maria

2016-01-01

Farmers' perceptions of birds' interactions with agricultural production systems are fundamental to species conservation efforts. In the present study, we evaluated the perceptions of birds held by farmers who engage in conventional and non-conventional agricultural production processes and the implications of potential differences in these perceptions on species conservation. To accomplish this, data were collected using questionnaires, semi-structured interviews, and other complementary sources of information gathered from 191 farmers in northeastern Brazil. Although some similarities were identified among the farmers in their perceptions and local ecological knowledge (LEK) of birds, differences existed between the conventional and non-conventional farmers in their attitudes toward, conflicts with, and usage of bird species. Compared to the conventional farmers, the non-conventional farmers could identify more bird species, possessed more favorable attitudes toward birds, and engaged in practices more beneficial to the conservation of avifauna. The perceptions that were identified were related to the type of agriculture practiced, and such perceptions may affect the conservation of bird species. Therefore, the adoption of certain agricultural practices has important implications for conservation. Our results indicate the need for investment in public policies, programs and actions that account for farmers' knowledge and perceptions. Such investments will contribute to the development and adoption of practices supporting wild bird conservation in agricultural areas.

Do Farmers Using Conventional and Non-Conventional Systems of Agriculture Have Different Perceptions of the Diversity of Wild Birds? Implications for Conservation.

Directory of Open Access Journals (Sweden)

Horasa Lima Silva-Andrade

Full Text Available Farmers' perceptions of birds' interactions with agricultural production systems are fundamental to species conservation efforts. In the present study, we evaluated the perceptions of birds held by farmers who engage in conventional and non-conventional agricultural production processes and the implications of potential differences in these perceptions on species conservation. To accomplish this, data were collected using questionnaires, semi-structured interviews, and other complementary sources of information gathered from 191 farmers in northeastern Brazil. Although some similarities were identified among the farmers in their perceptions and local ecological knowledge (LEK of birds, differences existed between the conventional and non-conventional farmers in their attitudes toward, conflicts with, and usage of bird species. Compared to the conventional farmers, the non-conventional farmers could identify more bird species, possessed more favorable attitudes toward birds, and engaged in practices more beneficial to the conservation of avifauna. The perceptions that were identified were related to the type of agriculture practiced, and such perceptions may affect the conservation of bird species. Therefore, the adoption of certain agricultural practices has important implications for conservation. Our results indicate the need for investment in public policies, programs and actions that account for farmers' knowledge and perceptions. Such investments will contribute to the development and adoption of practices supporting wild bird conservation in agricultural areas.

Development of a computer program to support an efficient non-regression test of a thermal-hydraulic system code

Energy Technology Data Exchange (ETDEWEB)

Lee, Jun Yeob; Jeong, Jae Jun [School of Mechanical Engineering, Pusan National University, Busan (Korea, Republic of); Suh, Jae Seung [System Engineering and Technology Co., Daejeon (Korea, Republic of); Kim, Kyung Doo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2014-10-15

During the development process of a thermal-hydraulic system code, a non-regression test (NRT) must be performed repeatedly in order to prevent software regression. The NRT process, however, is time-consuming and labor-intensive. Thus, automation of this process is an ideal solution. In this study, we have developed a program to support an efficient NRT for the SPACE code and demonstrated its usability. This results in a high degree of efficiency for code development. The program was developed using the Visual Basic for Applications and designed so that it can be easily customized for the NRT of other computer codes.

The Long Non-coding RNA HOTTIP Enhances Pancreatic Cancer Cell Proliferation, Survival and Migration

Science.gov (United States)

ABSTRACTHOTTIP is a long non-coding RNA (lncRNA) transcribed from the 5' tip of the HOXA locus and is associated with the polycomb repressor complex 2 (PRC2) and WD repeat containing protein 5 (WDR5)/mixed lineage leukemia 1 (MLL1) chromatin modifying complexes. HOTTIP is expres...

Coded excitation for infrared non-destructive testing of carbon fiber reinforced plastics.

Science.gov (United States)

Mulaveesala, Ravibabu; Venkata Ghali, Subbarao

2011-05-01

This paper proposes a Barker coded excitation for defect detection using infrared non-destructive testing. Capability of the proposed excitation scheme is highlighted with recently introduced correlation based post processing approach and compared with the existing phase based analysis by taking the signal to noise ratio into consideration. Applicability of the proposed scheme has been experimentally validated on a carbon fiber reinforced plastic specimen containing flat bottom holes located at different depths.

Regulatory interventions necessitated by non-conservative operator decisions

International Nuclear Information System (INIS)

Ojha, D.; Chande, S.K.; Sharma, S.K.

2005-01-01

Presently, India has 15 nuclear power units in operation and 8 units under construction. Though the safety performance of the Nuclear Power Plants (NPPs) in India has been excellent, a few recent events indicate that conservative decision making process can possibly get affected by perceived production goals. In one of the events, a need for some maintenance work arose while reactor start-up was in progress. After it was realized that the maintenance would require considerable time, the proper course of action would have been to shutdown the reactor and add neutron poison to moderator to ensure sufficient sub criticality. This was not done, as it would have delayed the start up of the reactor on completion of maintenance. In another incident, an unintended slow increase in reactor power occurred due to the adjuster rods becoming inoperable on account of blowing-off of fuses in their power supply. Under this condition, the reactor should have been tripped which was not done. Further, the automatic addition of boron poison to the reactor was inhibited. Regulatory review showed that both the incidents were indicative of degradation in safety culture and reflected operator's overriding concern for keeping the units in operation. Appropriate corrective actions were taken to prevent recurrence of such events in the respective units as also in all other operating units of similar type. In the wake of improved production performance operators may develop a tendency to create new operational records and compete with other units. This aspect points out to a need for careful study of events to check the presence of any element of non-conservative decision-making and to identify leading indicators of degradation in safety performance. (author)

An improved weighted essentially non-oscillatory scheme for hyperbolic conservation laws

Science.gov (United States)

Borges, Rafael; Carmona, Monique; Costa, Bruno; Don, Wai Sun

2008-03-01

In this article we develop an improved version of the classical fifth-order weighted essentially non-oscillatory finite difference scheme of [G.S. Jiang, C.W. Shu, Efficient implementation of weighted ENO schemes, J. Comput. Phys. 126 (1996) 202-228] (WENO-JS) for hyperbolic conservation laws. Through the novel use of a linear combination of the low order smoothness indicators already present in the framework of WENO-JS, a new smoothness indicator of higher order is devised and new non-oscillatory weights are built, providing a new WENO scheme (WENO-Z) with less dissipation and higher resolution than the classical WENO. This new scheme generates solutions that are sharp as the ones of the mapped WENO scheme (WENO-M) of Henrick et al. [A.K. Henrick, T.D. Aslam, J.M. Powers, Mapped weighted essentially non-oscillatory schemes: achieving optimal order near critical points, J. Comput. Phys. 207 (2005) 542-567], however with a 25% reduction in CPU costs, since no mapping is necessary. We also provide a detailed analysis of the convergence of the WENO-Z scheme at critical points of smooth solutions and show that the solution enhancements of WENO-Z and WENO-M at problems with shocks comes from their ability to assign substantially larger weights to discontinuous stencils than the WENO-JS scheme, not from their superior order of convergence at critical points. Numerical solutions of the linear advection of discontinuous functions and nonlinear hyperbolic conservation laws as the one dimensional Euler equations with Riemann initial value problems, the Mach 3 shock-density wave interaction and the blastwave problems are compared with the ones generated by the WENO-JS and WENO-M schemes. The good performance of the WENO-Z scheme is also demonstrated in the simulation of two dimensional problems as the shock-vortex interaction and a Mach 4.46 Richtmyer-Meshkov Instability (RMI) modeled via the two dimensional Euler equations.

Comparison between conservative perturbation and sampling based methods for propagation of Non-Neutronic uncertainties

International Nuclear Information System (INIS)

Campolina, Daniel de A.M.; Pereira, Claubia; Veloso, Maria Auxiliadora F.

2013-01-01

For all the physical components that comprise a nuclear system there is an uncertainty. Assessing the impact of uncertainties in the simulation of fissionable material systems is essential for a best estimate calculation that has been replacing the conservative model calculations as the computational power increases. The propagation of uncertainty in a simulation using sampling based method is recent because of the huge computational effort required. In this work a sample space of MCNP calculations were used as a black box model to propagate the uncertainty of system parameters. The efficiency of the method was compared to a conservative method. Uncertainties in input parameters of the reactor considered non-neutronic uncertainties, including geometry dimensions and density. The effect of the uncertainties on the effective multiplication factor of the system was analyzed respect to the possibility of using many uncertainties in the same input. If the case includes more than 46 parameters with uncertainty in the same input, the sampling based method is proved to be more efficient than the conservative method. (author)

Decoding the Emerging Patterns Exhibited in Non-coding RNAs Characteristic of Lung Cancer with Regard to their Clinical Significance.

Science.gov (United States)

Sonea, Laura; Buse, Mihail; Gulei, Diana; Onaciu, Anca; Simon, Ioan; Braicu, Cornelia; Berindan-Neagoe, Ioana

2018-05-01

Lung cancer continues to be the leading topic concerning global mortality rate caused by can-cer; it needs to be further investigated to reduce these dramatic unfavorable statistic data. Non-coding RNAs (ncRNAs) have been shown to be important cellular regulatory factors and the alteration of their expression levels has become correlated to extensive number of pathologies. Specifically, their expres-sion profiles are correlated with development and progression of lung cancer, generating great interest for further investigation. This review focuses on the complex role of non-coding RNAs, namely miR-NAs, piwi-interacting RNAs, small nucleolar RNAs, long non-coding RNAs and circular RNAs in the process of developing novel biomarkers for diagnostic and prognostic factors that can then be utilized for personalized therapies toward this devastating disease. To support the concept of personalized medi-cine, we will focus on the roles of miRNAs in lung cancer tumorigenesis, their use as diagnostic and prognostic biomarkers and their application for patient therapy.

Coherent Synchrotron Radiation A Simulation Code Based on the Non-Linear Extension of the Operator Splitting Method

CERN Document Server

Dattoli, Giuseppe

2005-01-01

The coherent synchrotron radiation (CSR) is one of the main problems limiting the performance of high intensity electron accelerators. A code devoted to the analysis of this type of problems should be fast and reliable: conditions that are usually hardly achieved at the same time. In the past, codes based on Lie algebraic techniques have been very efficient to treat transport problem in accelerators. The extension of these method to the non-linear case is ideally suited to treat CSR instability problems. We report on the development of a numerical code, based on the solution of the Vlasov equation, with the inclusion of non-linear contribution due to wake field effects. The proposed solution method exploits an algebraic technique, using exponential operators implemented numerically in C++. We show that the integration procedure is capable of reproducing the onset of an instability and effects associated with bunching mechanisms leading to the growth of the instability itself. In addition, parametric studies a...

Parametric analysis of the thermal effects on the divertor in tokamaks during plasma disruptions

International Nuclear Information System (INIS)

Bruhn, M.L.

1988-04-01

Plasma disruptions are an ever present danger to the plasma-facing components in today's tokamak fusion reactors. This threat results from our lack of understanding and limited ability to control this complex phenomenon. In particular, severe energy deposition occurs on the divertor component of the double-null configured tokamak reactor during such disruptions. A hybrid computational model developed to estimate and graphically illustrate global thermal effects of disruptions on the divertor plates is described in detail. The quasi-two-dimensional computer code, TADDPAK (Thermal Analysis Divertor during Disruptions PAcKage), is used to conduct parametric analysis for the TIBER II Tokamak Engineering Test Reactor Design. The dependence of these thermal effects on divertor material choice, disruption pulse length, disruption pulse shape, and the characteristic thickness of the plasma scrape-off layer is investigated for this reactor design. Results and conclusions from this analysis are presented. Improvements to this model and issues that require further investigation are discussed. Cursory analysis for ITER (International Thermonuclear Experimental Reactor) is also presented in the appendix. 75 refs., 49 figs., 10 tabs

Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer

Directory of Open Access Journals (Sweden)

Yiwen Fang

2016-02-01

Full Text Available Long non-coding RNAs (lncRNAs play important roles in cancer. They are involved in chromatin remodeling, as well as transcriptional and post-transcriptional regulation, through a variety of chromatin-based mechanisms and via cross-talk with other RNA species. lncRNAs can function as decoys, scaffolds, and enhancer RNAs. This review summarizes the characteristics of lncRNAs, including their roles, functions, and working mechanisms, describes methods for identifying and annotating lncRNAs, and discusses future opportunities for lncRNA-based therapies using antisense oligonucleotides.

Computer codes for three dimensional mass transport with non-linear sorption

International Nuclear Information System (INIS)

Noy, D.J.

1985-03-01

The report describes the mathematical background and data input to finite element programs for three dimensional mass transport in a porous medium. The transport equations are developed and sorption processes are included in a general way so that non-linear equilibrium relations can be introduced. The programs are described and a guide given to the construction of the required input data sets. Concluding remarks indicate that the calculations require substantial computer resources and suggest that comprehensive preliminary analysis with lower dimensional codes would be important in the assessment of field data. (author)

The PSML format and library for norm-conserving pseudopotential data curation and interoperability

Science.gov (United States)

García, Alberto; Verstraete, Matthieu J.; Pouillon, Yann; Junquera, Javier

2018-06-01

Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability.

Mechanisms of disruptions caused by noble gas injection into tokamak plasmas

International Nuclear Information System (INIS)

Morozov, D.Kh.; Yurchenko, E.I.; Lukash, V.E.; Baronova, E.O.; Pozdnyakov, Yu.I.; Rozhansky, V.A.; Senichenkov, I.Yu.; Veselova, I.Yu.; Schneider, R.

2005-01-01

Noble gas injection for disruption mitigation in DIII-D is simulated. The simulation of the first two stages of the disruption is performed: the first one is the neutral gas jet penetration through the background plasmas, and the second one is the instability growth. In order to simulate the first stage, the MHD pellet code LLP with improved radiation model for noble gas is used. Plasma cooling at this stage is provided by the energy exchange with the jet. The opacity effects in radiation losses are found to be important in the energy balance calculations. The magnetic surfaces in contact with the jet are cooled significantly; however, the temperature as well as the electric conductivity, remains high. The cooling front propagates towards the plasma centre. It has been shown that the cooling front is accompanied by strongly localized 'shark fin-like' perturbation in toroidal current density profile. The simplified cylindrical model shows that the cooling front is able to produce the internal kink-like mode with growth rate significantly higher than the tearing mode. The unstable kink perturbation obtained is non-resonant for any magnetic surface, both inside the plasma column, and in the vacuum space outside the separatrix. The mode disturbs mainly the core region. The growth time of the 'shark fin-like' mode is higher than the Alfven time by a factor of 10-100 for DIII-D parameters

Conservation of σ28-Dependent Non-Coding RNA Paralogs and Predicted σ54-Dependent Targets in Thermophilic Campylobacter Species.

Directory of Open Access Journals (Sweden)

My Thanh Le

Full Text Available Assembly of flagella requires strict hierarchical and temporal control via flagellar sigma and anti-sigma factors, regulatory proteins and the assembly complex itself, but to date non-coding RNAs (ncRNAs have not been described to regulate genes directly involved in flagellar assembly. In this study we have investigated the possible role of two ncRNA paralogs (CjNC1, CjNC4 in flagellar assembly and gene regulation of the diarrhoeal pathogen Campylobacter jejuni. CjNC1 and CjNC4 are 37/44 nt identical and predicted to target the 5' untranslated region (5' UTR of genes transcribed from the flagellar sigma factor σ54. Orthologs of the σ54-dependent 5' UTRs and ncRNAs are present in the genomes of other thermophilic Campylobacter species, and transcription of CjNC1 and CNC4 is dependent on the flagellar sigma factor σ28. Surprisingly, inactivation and overexpression of CjNC1 and CjNC4 did not affect growth, motility or flagella-associated phenotypes such as autoagglutination. However, CjNC1 and CjNC4 were able to mediate sequence-dependent, but Hfq-independent, partial repression of fluorescence of predicted target 5' UTRs in an Escherichia coli-based GFP reporter gene system. This hints towards a subtle role for the CjNC1 and CjNC4 ncRNAs in post-transcriptional gene regulation in thermophilic Campylobacter species, and suggests that the currently used phenotypic methodologies are insufficiently sensitive to detect such subtle phenotypes. The lack of a role of Hfq in the E. coli GFP-based system indicates that the CjNC1 and CjNC4 ncRNAs may mediate post-transcriptional gene regulation in ways that do not conform to the paradigms obtained from the Enterobacteriaceae.

Conservation of σ28-Dependent Non-Coding RNA Paralogs and Predicted σ54-Dependent Targets in Thermophilic Campylobacter Species

Science.gov (United States)

Le, My Thanh; van Veldhuizen, Mart; Porcelli, Ida; Bongaerts, Roy J.; Gaskin, Duncan J. H.; Pearson, Bruce M.; van Vliet, Arnoud H. M.

2015-01-01

Assembly of flagella requires strict hierarchical and temporal control via flagellar sigma and anti-sigma factors, regulatory proteins and the assembly complex itself, but to date non-coding RNAs (ncRNAs) have not been described to regulate genes directly involved in flagellar assembly. In this study we have investigated the possible role of two ncRNA paralogs (CjNC1, CjNC4) in flagellar assembly and gene regulation of the diarrhoeal pathogen Campylobacter jejuni. CjNC1 and CjNC4 are 37/44 nt identical and predicted to target the 5' untranslated region (5' UTR) of genes transcribed from the flagellar sigma factor σ54. Orthologs of the σ54-dependent 5' UTRs and ncRNAs are present in the genomes of other thermophilic Campylobacter species, and transcription of CjNC1 and CNC4 is dependent on the flagellar sigma factor σ28. Surprisingly, inactivation and overexpression of CjNC1 and CjNC4 did not affect growth, motility or flagella-associated phenotypes such as autoagglutination. However, CjNC1 and CjNC4 were able to mediate sequence-dependent, but Hfq-independent, partial repression of fluorescence of predicted target 5' UTRs in an Escherichia coli-based GFP reporter gene system. This hints towards a subtle role for the CjNC1 and CjNC4 ncRNAs in post-transcriptional gene regulation in thermophilic Campylobacter species, and suggests that the currently used phenotypic methodologies are insufficiently sensitive to detect such subtle phenotypes. The lack of a role of Hfq in the E. coli GFP-based system indicates that the CjNC1 and CjNC4 ncRNAs may mediate post-transcriptional gene regulation in ways that do not conform to the paradigms obtained from the Enterobacteriaceae. PMID:26512728

Patterns of evolutionary conservation of essential genes correlate with their compensability.

Directory of Open Access Journals (Sweden)

Tobias Bergmiller

2012-06-01

Full Text Available Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.

The Role of Non-­Coding RNA in Plant Stress

KAUST Repository

MacPherson, Cameron R.

2012-12-01

Post-transcriptional gene silencing (PTGS) is a powerful mechanism that can be adapted to genetically modify crop plants. PTGS operates in many plant signaling pathways including those mediating stress responses. Given the small number of miRNAs known, research on the characterization of stress-related micro-RNA (miRNA) and their targets could provide the basis for engineering stress tolerant traits in crops. Indeed, several examples of miRNA mediated crop tolerance have been reported. In the research presented here, we aimed to analyze the role of small non-coding RNA (smRNA) pathways involved in plant stress. In particular, we focused on miRNA-mediated PTGS in phosphate (Pi) starvation. The analysis was split into two research projects. First, to identify potential miRNA targets we began by analyzing the response and recovery of coding and long non-coding RNAs (lncRNA) to Pi starvation in shoot and root. The results obtained were the first genome-wide description of the root’s Pi starvation response and recovery. We found that the root\\'s response involved a widely different set of genes than that of the shoot. In the second research project, the results of the first project were correlated with the responses of miRNA and trans-acting small-interfering RNA (tasiRNA) during Pi starvation. Many miRNA circuits have been predicted before, however, tasiRNA circuits are not as well defined. Therefore, we made use of the double-stranded RNA-binding protein 4 (DRB4) smRNA libraries to enhance our prediction of tasiRNAs. Altogether, we provided evidence to support the following miRNA-mRNA pairs that may function in Pi starvation: IPS1:miR399:PHO2; miR399:RS4; miR399:NF-YA10; miR398:CSD1/2; miR2111:TPS11; miR164:NAC6; miR157:TMO7; miR157:PSB28; RPS2:miR169:IPS2; miR397:LAC2; TAS4:PAP1; NR1:PAP1; and Chr3_1967672:TMO7. In general, we found that non-miR399 related circuits were active only during the root’s recovery from Pi starvation. The functional roles of the genes

Non-disruptive regime changes-The case of competing energy efficient lighting trajectories

DEFF Research Database (Denmark)

Franceschini, Simone; Alkemade, Floortje

2016-01-01

Technologies within the same industry are expected to follow similar patterns of innovation, and when the dominant patterns change, this is often expected to have disruptive effects on the industry. However, the three most recent lighting technologies (fluorescent, compact fluorescent, and LED......) show different patterns of innovative activities despite similarities in the determinants of innovation; and we observed multiple technological regimes within the lighting industry. Furthermore, we observed changes in these innovative patterns without widespread disruptive effects. While FL and LED...... for policymakers in stimulating new technologies in industries with undesirable Mark II pattern through the influence of all the dimensions of the technological regimes....

Effects of recent modeling developments in prompt burst hypothetical core disruptive accident calculations

International Nuclear Information System (INIS)

Sienicki, J.J.; Abramson, P.B.

1978-01-01

The main objective of the development of multifield, multicomponent thermohydrodynamic computer codes is the detailed study of hypothetical core disruptive accidents (HCDAs) in liquid-metal fast breeder reactors. The main contributions such codes are expected to make are the inclusion of detailed modeling of the relative motion of liquid and vapor (slip), the inclusion of modeling of nonequilibrium/nonsaturation thermodynamics, and the use of more detailed neutronics methods. Scoping studies of the importance of including these phenomena performed with the parametric two-field, two-component coupled neutronic/thermodynamic/hydrodynamic code FX2-TWOPOOL indicate for the prompt burst portion of an HCDA that: (1) Vapor-liquid slip plays a relatively insignificant role in establishing energetics, implying that analyses that do not model vapor-liquid slip may be adequate. Furthermore, if conditions of saturation are assumed to be maintained, calculations that do not permit vapor-liquid slip appear to be conservative. (2) The modeling of conduction-limited fuel vaporization and condensation causes the energetics to be highly sensitive to variations in the droplet size (i.e., in the parametric values) for the sizes of interest in HCDA analysis. Care must therefore be exercised in the inclusion of this phenomenon in energetics calculations. (3) Insignificant differences are observed between the use of space-time kinetics (quasi-static diffusion theory) and point kinetics, indicating again that point kinetics is normally adequate for analysis of the prompt burst portion of an HCDA. (4) No significant differences were found to result from assuming that delayed neutron precursors remain stationary where they are created rather than assuming that they move together with fuel. (5) There is no need for implicit coupling between the neutronics and the hydrodynamics/thermodynamics routines, even outside the prompt burst portion

First disruption studies and simulations in view of the development of the DEMO Physics Basis

Energy Technology Data Exchange (ETDEWEB)

Ramogida, G., E-mail: giuseppe.ramogida@enea.it [ENEA for EUROfusion, via E. Fermi 45, 00044 Frascati, Roma (Italy); Maddaluno, G. [ENEA for EUROfusion, via E. Fermi 45, 00044 Frascati, Roma (Italy); Villone, F. [University of Cassino Consorzio CREATE, Cassino (Italy); Albanese, R. [University Federico II Consorzio CREATE, Naples (Italy); Barbato, L. [University of Cassino Consorzio CREATE, Cassino (Italy); Crisanti, F. [ENEA for EUROfusion, via E. Fermi 45, 00044 Frascati, Roma (Italy); Mastrostefano, S. [University of Cassino Consorzio CREATE, Cassino (Italy); Mazzuca, R. [ENEA for EUROfusion, via E. Fermi 45, 00044 Frascati, Roma (Italy); Palmaccio, R. [University of Cassino Consorzio CREATE, Cassino (Italy); Rubinacci, G.; Ventre, S. [University Federico II Consorzio CREATE, Naples (Italy); Wenninger, R. [IPP, Garching (Germany); EFDA, Garching (Germany)

2015-10-15

Highlights: • The prediction of disruption features and loads is essential in the design of DEMO. • Different disruptions need to be simulated to evaluate the EM and thermal loads. • Extrapolation of the thermal quench duration to DEMO gives values from 0.8 to 1.1 ms. • Extrapolation of the current quench duration to DEMO gives values from 47 to 107 ms. • First CarMa0NL simulations points out the effect of large 3D conductive structures. - Abstract: In the development of the DEMO Physics Basis an important role is played by the prediction of the plasma disruption features and by the evaluation of the electro-magnetic (EM) and thermal loads associated with these events. Indeed, the kind and number of foreseen plasma disruptions drive the development of the DEMO operation scenarios and the design of vessel and in-vessel components. To characterize a plausible macroscopic plasma dynamics during these events, we will carry out an extrapolation from present-day machines of the main parameters characterizing the disruptions: thermal and current quench time, evolution of plasma current, β and l{sub i}, safety factor limits, halo current fraction and width, radiated heat fraction. In particular, we will focus on extrapolations for the thermal and current quench characteristic times, due to their importance for the subsequent simulations aimed at the evaluation of the EM and thermal loads. The different options for DEMO design will be taken into account and the possible range of variation of the parameters will be estimated. The 2D axysimmetric MAXFEA and the 3D CarMa0NL codes will be used to evaluate the effects of the induced currents and the EM loads during a disruptive event and to analyze the various design options obtained by the PROCESS code. The results of these simulations, modeled as worst expected events, will be used as input for the system level analysis and design of the vessel and relevant in-vessel components. First simulations with CarMa0NL code

The Effectiveness of Cultural Property and Conservation Learning in Elementary Education and Evaluation of the Contribution of Non-Governmental Organizations

Directory of Open Access Journals (Sweden)

Meltem UÇAR

2014-05-01

Full Text Available A definition of cultural heritage, with its tangible and intangible meanings, encompasses places that are a part of daily life, and brings them into the realm of conservation efforts. In this context, conservation becomes a concern of daily life and means that users of these places must shoulder more responsibility for them. With this in mind, people need to be aware of the values and importance of cultural heritage and their individual role in its conservation. To develop public awareness of conservation of cultural heritage, awareness studies need to begin in childhood education, and in recognition of this, cultural heritage concepts have been included in Turkish primary school education programs. Additionally, a number of awareness studies have been carried out by non-governmental organizations to date. This paper aims to evaluate the concept of cultural heritage in social science programs in elementary education, and discuss the potential contributions to the education system of awareness studies carried out by non-governmental organizations. The first part of the paper deals with the place of the individual in conservation studies, and is followed by cultural heritage learning areas in social science programs in elementary education. The third section examines the results of a survey held to evaluate students’ degrees of learning. The fourth part evaluates some awareness-raising studies carried out by national and international non-governmental organizations. The final part proposes a number of criteria to be considered when attempting to raise cultural heritage education among children.

Calculation of fluid-structure interaction for reactor safety with the Cassiopee code

International Nuclear Information System (INIS)

Graveleau, J.L.; Louvet, P.D.

1979-01-01

The cassiopee code is an eulerian-lagrangian coupled code for computations where the hydrodynamic is coupled with structural domains. It is completely explicit. The fluid zones may be computed either in lagrangian or in eulerian coordinates; thin shells can be computed wih their flexural behaviour; elastic plastic zones must be calculated in a lagrangian way. This code is under development in Cadarache. Its purpose is to compute the hypothetical core disruptive accident of a LMFBR when lagrangian codes are not sufficient. This paper contains a description of the code and two examples of computations, one of which has been compared with experimental results

Neutronic analysis of LMFBRs during severe core disruptive accidents

International Nuclear Information System (INIS)

Tomlinson, E.T.

1979-01-01

A number of numerical experiments were performed to assess the validity of diffusion theory and various perturbation methods for calculating the reactivity state of a severely disrupted liquid metal cooled fast breeder reactor (LMFBR). The disrupted configurations correspond, in general, to phases through which an LMFBR core could pass during a core disruptive accident (CDA). Two-reactor models were chosen for this study, the two zone, homogeneous Clinch River Breeder Reactor and the Large Heterogeneous Reactor Design Study Core. The various phases were chosen to approximate the CDA results predicted by the safety analysis code SAS3D. The calculational methods investigated in this study include the eigenvalue difference technique based on both discrete ordinate transport theory and diffusion theory, first-order perturbation theory, exact perturbation theory, and a new hybrid perturbation theory. Selected cases were analyzed using Monte Carlo methods. It was found that in all cases, diffusion theory and perturbation theory yielded results for the change in reactivity that significantly disagreed with both the discrete ordinate and Monte Carlo results. These differences were, in most cases, in a nonconservative direction

Constraints of a Parity-Conserving Interaction

Science.gov (United States)

van Oers, Willem T. H.

2002-09-01

Time-Reversal-Invariance non-conservation has for the first time been unequivocally demonstrated in a direct measurement at CPLEAR. One then can ask the question: What about tests of time-reversal-invariance in systems other than the kaon system? Tests of time-reversal-invariance can be distinguished as belonging to two classes: the first one deals with time-reversal-invariance-non-conserving (T-odd)/parity violating (P-odd) interactions, while the second one deals with T-odd/P-even interactions (assuming CPT conservation this implies C-conjugation non-conservation). Limits on a T-odd/P-odd interaction follow from measurements of the electric dipole moment of the neutron (room for further experimentation?

Application of HTSC coils for mitigation of VDE during a major disruption

International Nuclear Information System (INIS)

Yamada, T.; Uchimoto, T.; Miya, K.; Nakamura, Y.

1998-01-01

The authors proposed the new method to control plasma position passively with use of high Tc superconducting coils (HTSCs). HTSCs are robust against the thermal disturbance, so that they can be installed in the vicinity of plasmas. In this study, we examine that the VDEs during disruptions can be mitigated or not by using HTSC coils as a stabilizer. Shape and profile of plasmas will change considerably during a disruption, so that the linearized model cannot be applied to this problem. Tokamak Simulation Code (TSC) is employed to evaluate the stabilizing effect of HTSC during a major disruption. The configuration of International Thermonuclear Experimental Reactor (ITER) is taken as an example for numerical analyses. The result of simulations using linear model agreed with that of TSC computation. The results of the simulation show that VDEs during disruptions are mitigated due to the stabilizing effect of HTSC. The vertical instability growth rate is improved if HTSC coils are installed on the backplate. The electromagnetic forces on HTSCs during a disruption were also estimated. A design to accommodate these forces is possible without any difficulty. (author)

Assessment of 12 CHF prediction methods, for an axially non-uniform heat flux distribution, with the RELAP5 computer code

Energy Technology Data Exchange (ETDEWEB)

Ferrouk, M. [Laboratoire du Genie Physique des Hydrocarbures, University of Boumerdes, Boumerdes 35000 (Algeria)], E-mail: m_ferrouk@yahoo.fr; Aissani, S. [Laboratoire du Genie Physique des Hydrocarbures, University of Boumerdes, Boumerdes 35000 (Algeria); D' Auria, F.; DelNevo, A.; Salah, A. Bousbia [Dipartimento di Ingegneria Meccanica, Nucleare e della Produzione, Universita di Pisa (Italy)

2008-10-15

The present article covers the evaluation of the performance of twelve critical heat flux methods/correlations published in the open literature. The study concerns the simulation of an axially non-uniform heat flux distribution with the RELAP5 computer code in a single boiling water reactor channel benchmark problem. The nodalization scheme employed for the considered particular geometry, as modelled in RELAP5 code, is described. For this purpose a review of critical heat flux models/correlations applicable to non-uniform axial heat profile is provided. Simulation results using the RELAP5 code and those obtained from our computer program, based on three type predictions methods such as local conditions, F-factor and boiling length average approaches were compared.

77 FR 74456 - Notice of Proposed Changes to the National Handbook of Conservation Practices for the Natural...

Science.gov (United States)

2012-12-14

..., National Agricultural Engineer, Conservation Engineering Division, Department of Agriculture, Natural... may be directed to Wayne Bogovich, National Agricultural Engineer, Conservation Engineering Division...: Amendments for the Treatment of Agricultural Waste (Code 591), Building Envelope Improvement (Code 672...

Self-organized criticality occurs in non-conservative neuronal networks during `up' states

Science.gov (United States)

Millman, Daniel; Mihalas, Stefan; Kirkwood, Alfredo; Niebur, Ernst

2010-10-01

During sleep, under anaesthesia and in vitro, cortical neurons in sensory, motor, association and executive areas fluctuate between so-called up and down states, which are characterized by distinct membrane potentials and spike rates. Another phenomenon observed in preparations similar to those that exhibit up and down states-such as anaesthetized rats, brain slices and cultures devoid of sensory input, as well as awake monkey cortex-is self-organized criticality (SOC). SOC is characterized by activity `avalanches' with a branching parameter near unity and size distribution that obeys a power law with a critical exponent of about -3/2. Recent work has demonstrated SOC in conservative neuronal network models, but critical behaviour breaks down when biologically realistic `leaky' neurons are introduced. Here, we report robust SOC behaviour in networks of non-conservative leaky integrate-and-fire neurons with short-term synaptic depression. We show analytically and numerically that these networks typically have two stable activity levels, corresponding to up and down states, that the networks switch spontaneously between these states and that up states are critical and down states are subcritical.

Long Non-Coding RNAs: Emerging and Versatile Regulators in Host–Virus Interactions

Directory of Open Access Journals (Sweden)

Xing-Yu Meng

2017-11-01

Full Text Available Long non-coding RNAs (lncRNAs are a class of non-protein-coding RNA molecules, which are involved in various biological processes, including chromatin modification, cell differentiation, pre-mRNA transcription and splicing, protein translation, etc. During the last decade, increasing evidence has suggested the involvement of lncRNAs in both immune and antiviral responses as positive or negative regulators. The immunity-associated lncRNAs modulate diverse and multilayered immune checkpoints, including activation or repression of innate immune signaling components, such as interleukin (IL-8, IL-10, retinoic acid inducible gene I, toll-like receptors 1, 3, and 8, and interferon (IFN regulatory factor 7, transcriptional regulation of various IFN-stimulated genes, and initiation of the cell apoptosis pathways. Additionally, some virus-encoded lncRNAs facilitate viral replication through individually or synergistically inhibiting the host antiviral responses or regulating multiple steps of the virus life cycle. Moreover, some viruses are reported to hijack host-encoded lncRNAs to establish persistent infections. Based on these amazing discoveries, lncRNAs are an emerging hotspot in host–virus interactions. In this review, we summarized the current findings of the host- or virus-encoded lncRNAs and the underlying mechanisms, discussed their impacts on immune responses and viral replication, and highlighted their critical roles in host–virus interactions.

Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum.

Directory of Open Access Journals (Sweden)

Jianqin Li

Full Text Available Ganoderma lucidum is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in G. lucidum genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA in G. lucidum systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from G. lucidum samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3' RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8 and 5 are negatively correlated (r<-0.8. The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in G. lucidum.

Investigating Disruption

DEFF Research Database (Denmark)

Lundgaard, Stine Schmieg; Rosenstand, Claus Andreas Foss

This book shares knowledge collected from 2015 and onward within the Consortium for Digital Disruption anchored at Aalborg University (www.dd.aau.dk). Evidenced by this publication, the field of disruptive innovation research has gone through several stages of operationalizing the theory. In recent...... years, researchers are increasingly looking back towards the origins of the theory in attempts to cure it from its most obvious flaws. This is especially true for the use of the theory in making predictions about future disruptions. In order to continue to develop a valuable theory of disruption, we...... find it useful to first review what the theory of disruptive innovation initially was, how it has developed, and where we are now. A cross section of disruptive innovation literature has been reviewed in order to form a general foundation from which we might better understand the changing world...

photon-plasma: A modern high-order particle-in-cell code

International Nuclear Information System (INIS)

Haugbølle, Troels; Frederiksen, Jacob Trier; Nordlund, Åke

2013-01-01

We present the photon-plasma code, a modern high order charge conserving particle-in-cell code for simulating relativistic plasmas. The code is using a high order implicit field solver and a novel high order charge conserving interpolation scheme for particle-to-cell interpolation and charge deposition. It includes powerful diagnostics tools with on-the-fly particle tracking, synthetic spectra integration, 2D volume slicing, and a new method to correctly account for radiative cooling in the simulations. A robust technique for imposing (time-dependent) particle and field fluxes on the boundaries is also presented. Using a hybrid OpenMP and MPI approach, the code scales efficiently from 8 to more than 250.000 cores with almost linear weak scaling on a range of architectures. The code is tested with the classical benchmarks particle heating, cold beam instability, and two-stream instability. We also present particle-in-cell simulations of the Kelvin-Helmholtz instability, and new results on radiative collisionless shocks

Speeding up Monte Carlo molecular simulation by a non-conservative early rejection scheme

KAUST Repository

Kadoura, Ahmad Salim

2015-04-23

Monte Carlo (MC) molecular simulation describes fluid systems with rich information, and it is capable of predicting many fluid properties of engineering interest. In general, it is more accurate and representative than equations of state. On the other hand, it requires much more computational effort and simulation time. For that purpose, several techniques have been developed in order to speed up MC molecular simulations while preserving their precision. In particular, early rejection schemes are capable of reducing computational cost by reaching the rejection decision for the undesired MC trials at an earlier stage in comparison to the conventional scheme. In a recent work, we have introduced a ‘conservative’ early rejection scheme as a method to accelerate MC simulations while producing exactly the same results as the conventional algorithm. In this paper, we introduce a ‘non-conservative’ early rejection scheme, which is much faster than the conservative scheme, yet it preserves the precision of the method. The proposed scheme is tested for systems of structureless Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. Numerical experiments were conducted at several thermodynamic conditions for different number of particles. Results show that at certain thermodynamic conditions, the non-conservative method is capable of doubling the speed of the MC molecular simulations in both canonical and NVT-Gibbs ensembles. © 2015 Taylor & Francis

Local non-Calderbank-Shor-Steane quantum error-correcting code on a three-dimensional lattice

International Nuclear Information System (INIS)

Kim, Isaac H.

2011-01-01

We present a family of non-Calderbank-Shor-Steane quantum error-correcting code consisting of geometrically local stabilizer generators on a 3D lattice. We study the Hamiltonian constructed from ferromagnetic interaction of overcomplete set of local stabilizer generators. The degenerate ground state of the system is characterized by a quantum error-correcting code whose number of encoded qubits are equal to the second Betti number of the manifold. These models (i) have solely local interactions; (ii) admit a strong-weak duality relation with an Ising model on a dual lattice; (iii) have topological order in the ground state, some of which survive at finite temperature; and (iv) behave as classical memory at finite temperature.

Local non-Calderbank-Shor-Steane quantum error-correcting code on a three-dimensional lattice

Science.gov (United States)

Kim, Isaac H.

2011-05-01

We present a family of non-Calderbank-Shor-Steane quantum error-correcting code consisting of geometrically local stabilizer generators on a 3D lattice. We study the Hamiltonian constructed from ferromagnetic interaction of overcomplete set of local stabilizer generators. The degenerate ground state of the system is characterized by a quantum error-correcting code whose number of encoded qubits are equal to the second Betti number of the manifold. These models (i) have solely local interactions; (ii) admit a strong-weak duality relation with an Ising model on a dual lattice; (iii) have topological order in the ground state, some of which survive at finite temperature; and (iv) behave as classical memory at finite temperature.

Fuel penetration of intersubassembly gaps in LMFBRs: a calculational method with the SIMMER-II code

International Nuclear Information System (INIS)

DeVault, G.P.

1983-01-01

Early fuel removal from the active core of a liquid-metal-cooled fast breeder reactor (LMFBR) undergoing a core-disruptive accident may reduce the potential for large energetics resulting from recriticalities. A possible avenue for early fuel removal in heterogeneous core LMFBRs is the failure of duct walls in disrupted driver subassemblies followed by fuel penetration into the gaps between blanket subassemblies. The SIMMER-II code was modified to simulate flow between subassembly gaps. Calculations with the modified SIMMER-II code indicate the capabilities of the method and the potential for fuel mass reduction in the active core

Conservative constraints on early cosmology with MONTE PYTHON

International Nuclear Information System (INIS)

Audren, Benjamin; Lesgourgues, Julien; Benabed, Karim; Prunet, Simon

2013-01-01

Models for the latest stages of the cosmological evolution rely on a less solid theoretical and observational ground than the description of earlier stages like BBN and recombination. As suggested in a previous work by Vonlanthen et al., it is possible to tweak the analysis of CMB data in such way to avoid making assumptions on the late evolution, and obtain robust constraints on ''early cosmology parameters''. We extend this method in order to marginalise the results over CMB lensing contamination, and present updated results based on recent CMB data. Our constraints on the minimal early cosmology model are weaker than in a standard ΛCDM analysis, but do not conflict with this model. Besides, we obtain conservative bounds on the effective neutrino number and neutrino mass, showing no hints for extra relativistic degrees of freedom, and proving in a robust way that neutrinos experienced their non-relativistic transition after the time of photon decoupling. This analysis is also an occasion to describe the main features of the new parameter inference code MONTE PYTHON, that we release together with this paper. MONTE PYTHON is a user-friendly alternative to other public codes like COSMOMC, interfaced with the Boltzmann code CLASS

TASS/SMR Code Topical Report for SMART Plant, Vol II: User's Guide and Input Requirement

International Nuclear Information System (INIS)

Kim, See Darl; Kim, Soo Hyoung; Kim, Hyung Rae

2008-10-01

The TASS/SMR code has been developed with domestic technologies for the safety analysis of the SMART plant which is an integral type pressurized water reactor. It can be applied to the analysis of design basis accidents including non-LOCA (loss of coolant accident) and LOCA of the SMART plant. The TASS/SMR code can be applied to any plant regardless of the structural characteristics of a reactor since the code solves the same governing equations for both the primary and secondary system. The code has been developed to meet the requirements of the safety analysis code. This report describes the overall structure of the TASS/SMR, input processing, and the processes of a steady state and transient calculations. In addition, basic differential equations, finite difference equations, state relationships, and constitutive models are described in the report. First, the conservation equations, a discretization process for numerical analysis, search method for state relationship are described. Then, a core power model, heat transfer models, physical models for various components, and control and trip models are explained

Insights into inner ear-specific gene regulation: epigenetics and non-coding RNAs in inner ear development and regeneration

Science.gov (United States)

Avraham, Karen B.

2016-01-01

The vertebrate inner ear houses highly specialized sensory organs, tuned to detect and encode sound, head motion and gravity. Gene expression programs under the control of transcription factors orchestrate the formation and specialization of the non-sensory inner ear labyrinth and its sensory constituents. More recently, epigenetic factors and non-coding RNAs emerged as an additional layer of gene regulation, both in inner ear development and disease. In this review, we provide an overview on how epigenetic modifications and non-coding RNAs, in particular microRNAs (miRNAs), influence gene expression and summarize recent discoveries that highlight their critical role in the proper formation of the inner ear labyrinth and its sensory organs. In contrast to non-mammalian vertebrates, adult mammals lack the ability to regenerate inner ear mechano-sensory hair cells. Finally, we discuss recent insights into how epigenetic factors and miRNAs may facilitate, or in the case of mammals, restrict sensory hair cell regeneration. PMID:27836639

Designing reliable supply chain network with disruption risk

Directory of Open Access Journals (Sweden)

Ali Bozorgi Amiri

2013-01-01

Full Text Available Although supply chains disruptions rarely occur, their negative effects are prolonged and severe. In this paper, we propose a reliable capacitated supply chain network design (RSCND model by considering random disruptions in both distribution centers and suppliers. The proposed model determines the optimal location of distribution centers (DC with the highest reliability, the best plan to assign customers to opened DCs and assigns opened DCs to suitable suppliers with lowest transportation cost. In this study, random disruption occurs at the location, capacity of the distribution centers (DCs and suppliers. It is assumed that a disrupted DC and a disrupted supplier may lose a portion of their capacities, and the rest of the disrupted DC's demand can be supplied by other DCs. In addition, we consider shortage in DCs, which can occur in either normal or disruption conditions and DCs, can support each other in such circumstances. Unlike other studies in the extent of literature, we use new approach to model the reliability of DCs; we consider a range of reliability instead of using binary variables. In order to solve the proposed model for real-world instances, a Non-dominated Sorting Genetic Algorithm-II (NSGA-II is applied. Preliminary results of testing the proposed model of this paper on several problems with different sizes provide seem to be promising.

Simulations of ITER disruption and VDE scenarios with TSC and comparison with DINA results

International Nuclear Information System (INIS)

Bandyopadhyay, I.

2008-01-01

Vertical Displacement Events (VDEs) and plasma current disruptions pose one of the major concerns for the lifetime of in-vessel components in ITER, as well as for machine robustness, as large electromagnetic and thermal loads will induced at such events. Hence, accurate modelling of such events is crucial for estimating disruption induced forces. In the past, ITER disruption modelling has been carried out for ITER using the DINA code. However, since predictive simulations of such events depend on a large number of model assumptions, there exists chances of large error bars on the model predictions. As such it is imperative to validate the code results with other models. Towards this objective, we have carried out the VDE and Disruption simulations using the TSC code and the results are compared with the earlier DINA predictions. A detailed electromagnetic model of the ITER vessel, blankets and the first wall components has been created in TSC. In both VDE and disruption cases, the initial plasma is taken as ITER reference scenario 2 end of burn (EOB) specifications with I p = 15 MA, B t = 5 .3 T, e > 8.8 keV, e > = 1.1 x 10 20 m -3 . The plasma current disruption is initiated by dropping the plasma β in 1 msec, so that after the β crash e > = 6 eV, following which the plasma position control is switched off, resulting in a plasma current quench in about 65 msec. On the other hand, in the VDE case, the plasma control is switched off which results in either upward or downward VDE depending on the initial position of the plasma current centroid. In this case the plasma current remains close to 15 MA for a much longer time, about 700 msec in the simulations till the edge safety factor (q) becomes less than 1.5, following which the β is crashed resulting in plasma current quench. Significant differences exist in the DINA and TSC models, for example, even though the plasma current quench rate predicted by the models matches well in till the halo currents start flowing

Conservation laws with non-convex flux and applications to two-phase flow in porous media

Energy Technology Data Exchange (ETDEWEB)

Tegnander, Cathrine

1998-12-31

This thesis deals with conservation laws, which form a family of partial differential equations (PDEs) describing conservation of mass, momentum and energy. The first part studies some theoretical aspects of conservation laws: (1) Scalar hyperbolic conservation laws with a non-convex flux function, where time dependent decay estimates are mainly obtained by a front tracking technique, (2) Convergence of solutions for a finite difference scheme given by a class of one dimensional parabolic systems. The second part of the thesis applies the theory to multiphase flow in porous media. A number of mathematical models for multiphase flow in groundwater are studied. Techniques to improve the study of simulations of oil, gas and water phases in reservoirs such as in the North Sea are discussed. Upscaling of a refinement of the permeability field is evaluated using a flow simulation. This is done by a study of the preserving of the rank of a number of realizations with respect to the cumulative production parameter. Finally, the importance of selection of numerical methods in the simulations are exemplified by considering various splitting techniques. The numerical methods of front tracking and finite difference schemes and finite element methods are used. 98 refs., 24 figs., 18 tabs.

Comparison of Management Styles in Organic and Conventional Farming with Respect to Disruptive External Influences. The Case of Organic Dairy Farming and Conventional Horticulture in the Netherlands

NARCIS (Netherlands)

Blom, M.; Gremmen, H.G.J.

2012-01-01

Conventional Dutch farming systems are constantly improving their technology to withstand disruptive external influences, while organic farming tends to focus on methods that stress conservation of natural and nonrenewable resources. We hypothesize that management styles to withstand disruptive

J simplified assessment for cracked pipes and elbows in the RSE-M code

International Nuclear Information System (INIS)

Delliou, P.L.; Sermage, J.-P.; Gilles, P.; Marie, S.; Kayser, Y.; Barthelet, B.

2005-01-01

RSE-M Code provides rules and requirements for in-service inspection of French Pressurized Water Reactor power plant components. Non mandatory guidance is given in the Code for defect assessment in a wide range of configurations: surface cracked pipes and elbows under pressure, moment and thermal loading. The Code provides influence coefficients to calculate stress intensity factors in pipes and elbows containing semi-elliptical surface defects (circumferential or longitudinal). The J assessment method is based on the reference stress concept with two options for reference loads evaluation: 'CEP elastic plastic stress' and 'CLC modified limit load'. This paper presents an overview of all the formulations and namely the case of pipe-to elbow junctions. The paper provides also a description of the very large data base of 2D and 3D J elastic-plastic finite element calculations performed to establish and validate the formulations. Finally an applicability domain of the methods is given ensuring a conservative prediction of J. (authors)

Code of practice for the design and safe operation of non-medical irradiation facilities (1988)

International Nuclear Information System (INIS)

1988-01-01

This Code establishes requirements for the design and operation of irradiation facilities which use X-rays, electrons or gamma radiation for non-medical purposes such as the sterilisation of therapeutic goods. These requirements aim to ensure that exposure of workers and members of the public to ionizing and non-ionizing radiation as well as to noxious gases and radioactive contamination of the environment and facilities are controlled through the design of engineering safety features, approved administrative controls and appropriate radiation monitoring [fr

Tetrahedral gray code for visualization of genome information.

Directory of Open Access Journals (Sweden)

Natsuhiro Ichinose

Full Text Available We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each [Formula: see text]-mer in the genomic sequence is represented by a color of the corresponding cell of a triangular lattice. For biological significance, the code is designed such that the [Formula: see text]-mers corresponding to any adjacent pair of cells differ from each other by only one nucleotide. We present a simple procedure to draw such a pattern on the development surfaces of a tetrahedron. The thus constructed tetrahedral Gray code can demonstrate evolutionary conservation and variation of the genome information of many organisms at a glance. We also apply the tetrahedral Gray code to the honey bee (Apis mellifera genome to analyze its methylation structure. The results indicate that the honey bee genome exhibits CpG overrepresentation in spite of its methylation ability and that two conserved motifs, CTCGAG and CGCGCG, in the unmethylated regions are responsible for the overrepresentation of CpG.

Regulation of G-protein coupled receptor traffic by an evolutionary conserved hydrophobic signal.

Science.gov (United States)

Angelotti, Tim; Daunt, David; Shcherbakova, Olga G; Kobilka, Brian; Hurt, Carl M

2010-04-01

Plasma membrane (PM) expression of G-protein coupled receptors (GPCRs) is required for activation by extracellular ligands; however, mechanisms that regulate PM expression of GPCRs are poorly understood. For some GPCRs, such as alpha2c-adrenergic receptors (alpha(2c)-ARs), heterologous expression in non-native cells results in limited PM expression and extensive endoplasmic reticulum (ER) retention. Recently, ER export/retentions signals have been proposed to regulate cellular trafficking of several GPCRs. By utilizing a chimeric alpha(2a)/alpha(2c)-AR strategy, we identified an evolutionary conserved hydrophobic sequence (ALAAALAAAAA) in the extracellular amino terminal region that is responsible in part for alpha(2c)-AR subtype-specific trafficking. To our knowledge, this is the first luminal ER retention signal reported for a GPCR. Removal or disruption of the ER retention signal dramatically increased PM expression and decreased ER retention. Conversely, transplantation of this hydrophobic sequence into alpha(2a)-ARs reduced their PM expression and increased ER retention. This evolutionary conserved hydrophobic trafficking signal within alpha(2c)-ARs serves as a regulator of GPCR trafficking.

A direct Arbitrary-Lagrangian-Eulerian ADER-WENO finite volume scheme on unstructured tetrahedral meshes for conservative and non-conservative hyperbolic systems in 3D

Science.gov (United States)

Boscheri, Walter; Dumbser, Michael

2014-10-01

In this paper we present a new family of high order accurate Arbitrary-Lagrangian-Eulerian (ALE) one-step ADER-WENO finite volume schemes for the solution of nonlinear systems of conservative and non-conservative hyperbolic partial differential equations with stiff source terms on moving tetrahedral meshes in three space dimensions. A WENO reconstruction technique is used to achieve high order of accuracy in space, while an element-local space-time Discontinuous Galerkin finite element predictor on moving curved meshes is used to obtain a high order accurate one-step time discretization. Within the space-time predictor the physical element is mapped onto a reference element using a high order isoparametric approach, where the space-time basis and test functions are given by the Lagrange interpolation polynomials passing through a predefined set of space-time nodes. Since our algorithm is cell-centered, the final mesh motion is computed by using a suitable node solver algorithm. A rezoning step as well as a flattener strategy are used in some of the test problems to avoid mesh tangling or excessive element deformations that may occur when the computation involves strong shocks or shear waves. The ALE algorithm presented in this article belongs to the so-called direct ALE methods because the final Lagrangian finite volume scheme is based directly on a space-time conservation formulation of the governing PDE system, with the rezoned geometry taken already into account during the computation of the fluxes. We apply our new high order unstructured ALE schemes to the 3D Euler equations of compressible gas dynamics, for which a set of classical numerical test problems has been solved and for which convergence rates up to sixth order of accuracy in space and time have been obtained. We furthermore consider the equations of classical ideal magnetohydrodynamics (MHD) as well as the non-conservative seven-equation Baer-Nunziato model of compressible multi-phase flows with

Digital Disruption

DEFF Research Database (Denmark)

Rosenstand, Claus Andreas Foss

det digitale domæne ud over det niveau, der kendetegner den nuværende debat, så præsenteres der ny viden om digital disruption. Som noget nyt udlægges Clayton Christens teori om disruptiv innovation med et særligt fokus på små organisationers mulighed for eksponentiel vækst. Specielt udfoldes...... forholdet mellem disruption og den stadig accelererende digitale udvikling i konturerne til ny teoridannelse om digital disruption. Bogens undertitel ”faretruende og fascinerende forandringer” peger på, at der er behov for en nuanceret debat om digital disruption i modsætning til den tone, der er slået an i...... videre kalder et ”disruption-råd”. Faktisk er rådet skrevet ind i 2016 regeringsgrundlaget for VLK-regeringen. Disruption af organisationer er ikke et nyt fænomen; men hastigheden, hvormed det sker, er stadig accelererende. Årsagen er den globale mega-trend: Digitalisering. Og derfor er specielt digital...

Numerical simulations for ITER divertor armour erosion and SOL contamination due to disruptions and ELMs

International Nuclear Information System (INIS)

Landman, I.S.; Pestchanyi, S.E.; Bazylev, B.N.

2005-01-01

The divertor armour materials for ITER are going to be tungsten (as brushe or plates) and CFC. Disruptive loads with the heat deposition Q up to 30 MJ/m 2 on the time scale τ of 3 ms or operation with ELMs at repetitive loads of Q ∼ 3 MJ/m 2 and τ ∼ 0.3 ms cause enhanced armour erosion and produce contamination of SOL. Recent numerical investigations of erosion mechanisms with the anisotropic thermomechanics code PEGASUS-3D and the surface melt motion code MEMOS-1.5D as well as hot hydrogen plasma dynamics, heat loads at the armour surface and backward propagation of material plasma in SOL with the radiation-magnetohydrodynamics code FOREV-2D are survived. For CFC targets, the local overheating model is explained and numerically demonstrated. For the tungsten targets the numerical analysis of melt motion erosion of W-brushe and bulk tungsten targets on the base of MEMOS-1.5D calculations is developed and accompanied by numerical results. For validation of the codes at the regimes relevant to ITER disruptions and ELMs, the simulation results are compared with available experiments carried out at plasma guns, electron beam test facilities and the tokamak JET. (author)

Implementation of non-condensable gases condensation suppression model into the WCOBRA/TRAC-TF2 LOCA safety evaluation code

Energy Technology Data Exchange (ETDEWEB)

Liao, J.; Cao, L.; Ohkawa, K.; Frepoli, C. [LOCA Integrated Services I, Westinghouse Electric Company, 1000 Westinghouse Drive, Cranberry Township, PA 16066 (United States)

2012-07-01

The non-condensable gases condensation suppression model is important for a realistic LOCA safety analysis code. A condensation suppression model for direct contact condensation was previously developed by Westinghouse using first principles. The model is believed to be an accurate description of the direct contact condensation process in the presence of non-condensable gases. The Westinghouse condensation suppression model is further revised by applying a more physical model. The revised condensation suppression model is thus implemented into the WCOBRA/TRAC-TF2 LOCA safety evaluation code for both 3-D module (COBRA-TF) and 1-D module (TRAC-PF1). Parametric study using the revised Westinghouse condensation suppression model is conducted. Additionally, the performance of non-condensable gases condensation suppression model is examined in the ACHILLES (ISP-25) separate effects test and LOFT L2-5 (ISP-13) integral effects test. (authors)

Atomic parity non-conservation: the francium anapole project of the FrPNC collaboration at TRIUMF

Energy Technology Data Exchange (ETDEWEB)

Aubin, S. [College of William and Mary, Dept. Physics (United States); Behr, J. A. [TRIUMF (Canada); Collister, R. [University of Manitoba, Dept. of Physics and Astronomy (Canada); Flambaum, V. V. [University of New South Wales, School of Physics (Australia); Gomez, E. [Universidad Autonoma de San Luis Potosi, Instituto de Fisica (Mexico); Gwinner, G. [University of Manitoba, Dept. of Physics and Astronomy (Canada); Jackson, K. P. [TRIUMF (Canada); Melconian, D. [Texas A and M University, Cyclotron Institute (United States); Orozco, L. A., E-mail: lorozco@umd.edu [University of Maryland, JQI, Dept. of Physics, and NIST (United States); Pearson, M. R. [TRIUMF (Canada); Sheng, D. [Princeton University (United States); Sprouse, G. D. [Stony Brook University, Dept. of Physics and Astronomy (United States); Tandecki, M. [TRIUMF (Canada); Zhang, J. [University of Maryland, JQI, Dept. of Physics, and NIST (United States); Zhao, Y. [Shanxi University, State Key Laboratory of Quantum Optics and Quantum Optics Devices (China)

2013-03-15

We present a method for measuring the nuclear anapole in a string of francium isotopes. The anapole is a parity non-conserving electromagnetic moment that enables parity-forbidden transitions between ground state hyperfine levels of an atom. The experiment is run by the FrPNC collaboration and relies on a beam of artificially-produced francium from the ISAC facility at TRIUMF.

Axisymmetric MHD simulation of ITB crash and following disruption dynamics of Tokamak plasmas with high bootstrap current