Real-time minimal-bit-error probability decoding of convolutional codes

Science.gov (United States)

Lee, L.-N.

1974-01-01

A recursive procedure is derived for decoding of rate R = 1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit, subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e., fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications, such as in the inner coding system for concatenated coding.

Real-time minimal bit error probability decoding of convolutional codes

Science.gov (United States)

Lee, L. N.

1973-01-01

A recursive procedure is derived for decoding of rate R=1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e. fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications such as in the inner coding system for concatenated coding.

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...

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...

Minimal and non-minimal standard models: Universality of radiative corrections

International Nuclear Information System (INIS)

Passarino, G.

1991-01-01

The possibility of describing electroweak processes by means of models with a non-minimal Higgs sector is analyzed. The renormalization procedure which leads to a set of fitting equations for the bare parameters of the lagrangian is first reviewed for the minimal standard model. A solution of the fitting equations is obtained, which correctly includes large higher-order corrections. Predictions for physical observables, notably the W boson mass and the Z O partial widths, are discussed in detail. Finally the extension to non-minimal models is described under the assumption that new physics will appear only inside the vector boson self-energies and the concept of universality of radiative corrections is introduced, showing that to a large extent they are insensitive to the details of the enlarged Higgs sector. Consequences for the bounds on the top quark mass are also discussed. (orig.)

Plateau inflation from random non-minimal coupling

International Nuclear Information System (INIS)

Broy, Benedict J.; Roest, Diederik

2016-06-01

A generic non-minimal coupling can push any higher-order terms of the scalar potential sufficiently far out in field space to yield observationally viable plateau inflation. We provide analytic and numerical evidence that this generically happens for a non-minimal coupling strength ξ of the order N 2 e . In this regime, the non-minimally coupled field is sub-Planckian during inflation and is thus protected from most higher-order terms. For larger values of ξ, the inflationary predictions converge towards the sweet spot of PLANCK. The latter includes ξ≅10 4 obtained from CMB normalization arguments, thus providing a natural explanation for the inflationary observables measured.

Essential idempotents and simplex codes

Directory of Open Access Journals (Sweden)

Gladys Chalom

2017-01-01

Full Text Available We define essential idempotents in group algebras and use them to prove that every mininmal abelian non-cyclic code is a repetition code. Also we use them to prove that every minimal abelian code is equivalent to a minimal cyclic code of the same length. Finally, we show that a binary cyclic code is simplex if and only if is of length of the form $n=2^k-1$ and is generated by an essential idempotent.

Supersymmetric hybrid inflation with non-minimal Kahler potential

International Nuclear Information System (INIS)

Bastero-Gil, M.; King, S.F.; Shafi, Q.

2007-01-01

Minimal supersymmetric hybrid inflation based on a minimal Kahler potential predicts a spectral index n s ∼>0.98. On the other hand, WMAP three year data prefers a central value n s ∼0.95. We propose a class of supersymmetric hybrid inflation models based on the same minimal superpotential but with a non-minimal Kahler potential. Including radiative corrections using the one-loop effective potential, we show that the prediction for the spectral index is sensitive to the small non-minimal corrections, and can lead to a significantly red-tilted spectrum, in agreement with WMAP

Hybrid genetic algorithm for minimizing non productive machining ...

African Journals Online (AJOL)

user

The movement of tool is synchronized with the help of these CNC codes. Total ... Lot of work has been reported for minimizing the productive time by ..... Optimal path for automated drilling operations by a new heuristic approach using particle.

Identification of coding and non-coding mutational hotspots in cancer genomes.

Science.gov (United States)

Piraino, Scott W; Furney, Simon J

2017-01-05

The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

An Implementation of Error Minimization Data Transmission in OFDM using Modified Convolutional Code

Directory of Open Access Journals (Sweden)

Hendy Briantoro

2016-04-01

Full Text Available This paper presents about error minimization in OFDM system. In conventional system, usually using channel coding such as BCH Code or Convolutional Code. But, performance BCH Code or Convolutional Code is not good in implementation of OFDM System. Error bits of OFDM system without channel coding is 5.77%. Then, we used convolutional code with code rate 1/2, it can reduce error bitsonly up to 3.85%. So, we proposed OFDM system with Modified Convolutional Code. In this implementation, we used Software Define Radio (SDR, namely Universal Software Radio Peripheral (USRP NI 2920 as the transmitter and receiver. The result of OFDM system using Modified Convolutional Code with code rate is able recover all character received so can decrease until 0% error bit. Increasing performance of Modified Convolutional Code is about 1 dB in BER of 10-4 from BCH Code and Convolutional Code. So, performance of Modified Convolutional better than BCH Code or Convolutional Code. Keywords: OFDM, BCH Code, Convolutional Code, Modified Convolutional Code, SDR, USRP

Noether symmetry for non-minimally coupled fermion fields

International Nuclear Information System (INIS)

Souza, Rudinei C de; Kremer, Gilberto M

2008-01-01

A cosmological model where a fermion field is non-minimally coupled with the gravitational field is studied. By applying Noether symmetry the possible functions for the potential density of the fermion field and for the coupling are determined. Cosmological solutions are found showing that the non-minimally coupled fermion field behaves as an inflaton describing an inflationary scenario, whereas the minimally coupled fermion field describes a decelerated period, behaving as a standard matter field

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.

On minimizing the maximum broadcast decoding delay for instantly decodable network coding

KAUST Repository

Douik, Ahmed S.; Sorour, Sameh; Alouini, Mohamed-Slim; Ai-Naffouri, Tareq Y.

2014-01-01

In this paper, we consider the problem of minimizing the maximum broadcast decoding delay experienced by all the receivers of generalized instantly decodable network coding (IDNC). Unlike the sum decoding delay, the maximum decoding delay as a

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.

Minimal but non-minimal inflation and electroweak symmetry breaking

Energy Technology Data Exchange (ETDEWEB)

Marzola, Luca [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia); Institute of Physics, University of Tartu,Ravila 14c, 50411 Tartu (Estonia); Racioppi, Antonio [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia)

2016-10-07

We consider the most minimal scale invariant extension of the standard model that allows for successful radiative electroweak symmetry breaking and inflation. The framework involves an extra scalar singlet, that plays the rôle of the inflaton, and is compatibile with current experimental bounds owing to the non-minimal coupling of the latter to gravity. This inflationary scenario predicts a very low tensor-to-scalar ratio r≈10{sup −3}, typical of Higgs-inflation models, but in contrast yields a scalar spectral index n{sub s}≃0.97 which departs from the Starobinsky limit. We briefly discuss the collider phenomenology of the framework.

Supersymmetric Hybrid Inflation with Non-Minimal Kähler potential

CERN Document Server

Bastero-Gil, M; Shafi, Q

2007-01-01

Minimal supersymmetric hybrid inflation based on a minimal Kahler potential predicts a spectral index n_s\\gsim 0.98. On the other hand, WMAP three year data prefers a central value n_s \\approx 0.95. We propose a class of supersymmetric hybrid inflation models based on the same minimal superpotential but with a non-minimal Kahler potential. Including radiative corrections using the one-loop effective potential, we show that the prediction for the spectral index is sensitive to the small non-minimal corrections, and can lead to a significantly red-tilted spectrum, in agreement with WMAP.

KCUT, code to generate minimal cut sets for fault trees

International Nuclear Information System (INIS)

Han, Sang Hoon

2008-01-01

1 - Description of program or function: KCUT is a software to generate minimal cut sets for fault trees. 2 - Methods: Expand a fault tree into cut sets and delete non minimal cut sets. 3 - Restrictions on the complexity of the problem: Size and complexity of the fault tree

Signals of non-minimal Higgs sectors at future colliders

International Nuclear Information System (INIS)

Akeroyd, A.G.

1996-08-01

This thesis concerns study of extended Higgs sectors at future colliders. Such studies are well motivated since enlarged Higgs models are a necessity in many extensions of the Standard Model (SM), although these structures may be considered purely in the context of the SM, to be called the 'non-minimal SM'. The continuous theme of the thesis is the task of distinguishing between the (many) theoretically sound non-minimal Higgs sectors at forthcoming colliders. If a Higgs boson is found it is imperative to know from which model it originates. In particular, the possible differences between the Higgs sectors of the Minimal Supersymmetric Standard Model (MSSM) and the non-minimal SM are highlighted. (author)

The non-minimal heterotic pure spinor string in a curved background

Energy Technology Data Exchange (ETDEWEB)

Chandia, Osvaldo [Facultad de Artes Liberales and Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez,Diagonal Las Torres 2640, Peñalolén, Santiago (Chile)

2014-03-21

We study the non-minimal pure spinor string in a curved background. We find that the minimal BRST invariance implies the existence of a non-trivial stress-energy tensor for the minimal and non-minimal variables in the heterotic curved background. We find constraint equations for the b ghost. We construct the b ghost as a solution of these constraints.

Inflation in non-minimal matter-curvature coupling theories

Energy Technology Data Exchange (ETDEWEB)

Gomes, C.; Bertolami, O. [Departamento de Física e Astronomia and Centro de Física do Porto, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto (Portugal); Rosa, J.G., E-mail: claudio.gomes@fc.up.pt, E-mail: joao.rosa@ua.pt, E-mail: orfeu.bertolami@fc.up.pt [Departamento de Física da Universidade de Aveiro and CIDMA, Campus de Santiago, 3810-183 Aveiro (Portugal)

2017-06-01

We study inflationary scenarios driven by a scalar field in the presence of a non-minimal coupling between matter and curvature. We show that the Friedmann equation can be significantly modified when the energy density during inflation exceeds a critical value determined by the non-minimal coupling, which in turn may considerably modify the spectrum of primordial perturbations and the inflationary dynamics. In particular, we show that these models are characterised by a consistency relation between the tensor-to-scalar ratio and the tensor spectral index that can differ significantly from the predictions of general relativity. We also give examples of observational predictions for some of the most commonly considered potentials and use the results of the Planck collaboration to set limits on the scale of the non-minimal coupling.

An Optical Multicast Routing with Minimal Network Coding Operations in WDM Networks

Directory of Open Access Journals (Sweden)

Huanlin Liu

2014-01-01

Full Text Available Network coding can improve the optical multicast routing performance in terms of network throughput, bandwidth utilization, and traffic load balance. But network coding needs high encoding operations costs in all-optical WDM networks due to shortage of optical RAM. In the paper, the network coding operation is defined to evaluate the number of network coding operation cost in the paper. An optical multicast routing algorithm based on minimal number of network coding operations is proposed to improve the multicast capacity. Two heuristic criteria are designed to establish the multicast routing with low network coding cost and high multicast capacity. One is to select one path from the former K shortest paths with the least probability of dropping the multicast maximal capacity. The other is to select the path with lowest potential coding operations with the highest link shared degree among the multiple wavelength disjoint paths cluster from source to each destination. Comparing with the other multicast routing based on network coding, simulation results show that the proposed multicast routing algorithm can effectively reduce the times of network coding operations, can improve the probability of reaching multicast maximal capacity, and can keep the less multicast routing link cost for optical WDM networks.

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana.

Science.gov (United States)

Hoffmann, Robert D; Palmgren, Michael

2016-06-13

Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown. Here, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3' untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses. Loss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.

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

Strong Sector in non-minimal SUSY model

Directory of Open Access Journals (Sweden)

Costantini Antonio

2016-01-01

Full Text Available We investigate the squark sector of a supersymmetric theory with an extended Higgs sector. We give the mass matrices of stop and sbottom, comparing the Minimal Supersymmetric Standard Model (MSSM case and the non-minimal case. We discuss the impact of the extra superfields on the decay channels of the stop searched at the LHC.

Inflation with non-minimal coupling. Metric vs. Palatini formulations

International Nuclear Information System (INIS)

Bauer, F.; Demir, D.A.; Izmir Institute of Technology

2008-03-01

We analyze non-minimally coupled scalar field theories in metric (second-order) and Palatini (first-order) formalisms in a comparative fashion. After contrasting them in a general setup, we specialize to inflation and find that the two formalisms differ in their predictions for various cosmological parameters. The main reason is that dependencies on the non-minimal coupling parameter are different in the two formalisms. For successful inflation, the Palatini approach prefers a much larger value for the non-minimal coupling parameter than the Metric approach. Unlike the Metric formalism, in Palatini, the inflaton stays well below the Planck scale whereby providing a natural inflationary epoch. (orig.)

Probing the non-minimal Higgs sector at the SSC

International Nuclear Information System (INIS)

Gunion, J.F.; Haber, H.E.; Komamiya, S.; Yamamoto, H.; Barbaro-Galtieri, A.

1987-11-01

Non-minimal Higgs sectors occur in the Standard Model with more than one Higgs doublet, as well as in theories that go beyond the Standard Model. In this report, we discuss how Higgs search strategies must be altered, with respect to the Standard Model approaches, in order to probe the non-minimal Higgs sectors at the SSC

Families of bitangent planes of space curves and minimal non-fibration families

KAUST Repository

Lubbes, Niels

2014-01-01

. Such families are called minimal non-fibration families. Families of bitangent planes of cone curves correspond to minimal non-fibration families. The main motivation of this paper is to classify minimal non-fibration families. We present algorithms which

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.

Quantization of the minimal and non-minimal vector field in curved space

OpenAIRE

Toms, David J.

2015-01-01

The local momentum space method is used to study the quantized massive vector field (the Proca field) with the possible addition of non-minimal terms. Heat kernel coefficients are calculated and used to evaluate the divergent part of the one-loop effective action. It is shown that the naive expression for the effective action that one would write down based on the minimal coupling case needs modification. We adopt a Faddeev-Jackiw method of quantization and consider the case of an ultrastatic...

Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth.

Science.gov (United States)

Du, Wei; Jongbloets, Joeri A; van Boxtel, Coco; Pineda Hernández, Hugo; Lips, David; Oliver, Brett G; Hellingwerf, Klaas J; Branco Dos Santos, Filipe

2018-01-01

Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass. Based on well-established constraint-based analysis techniques such as OptKnock and FVA, we developed an in silico pipeline-FRUITS-that specifically 'Finds Reactions Usable in Tapping Side-products'. It analyses a metabolic network to identify compounds produced in anabolism that are suitable to be coupled to growth by deletion of their re-utilization pathway(s), and computes their respective biomass and product formation rates. When applied to Synechocystis sp. PCC6803, a model cyanobacterium explored for sustainable bioproduction, a total of nine target metabolites were identified. We tested our approach for one of these compounds, acetate, which is used in a wide range of industrial applications. The model-guided engineered strain shows an obligatory coupling between acetate production and photoautotrophic growth as predicted. Furthermore, the stability of acetate productivity in this strain was confirmed by performing prolonged turbidostat cultivations. This work demonstrates a novel approach to stabilize the production of target compounds in cyanobacteria that culminated in the first report of a photoautotrophic growth-coupled cell factory. The method developed is generic and can easily be extended to any other modeled microbial production system.

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...

Particle production after inflation with non-minimal derivative coupling to gravity

International Nuclear Information System (INIS)

Ema, Yohei; Jinno, Ryusuke; Nakayama, Kazunori; Mukaida, Kyohei

2015-01-01

We study cosmological evolution after inflation in models with non-minimal derivative coupling to gravity. The background dynamics is solved and particle production associated with rapidly oscillating Hubble parameter is studied in detail. In addition, production of gravitons through the non-minimal derivative coupling with the inflaton is studied. We also find that the sound speed squared of the scalar perturbation oscillates between positive and negative values when the non-minimal derivative coupling dominates over the minimal kinetic term. This may lead to an instability of this model. We point out that the particle production rates are the same as those in the Einstein gravity with the minimal kinetic term, if we require the sound speed squared is positive definite

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 ...

Content-addressable memory processing: Multilevel coding, logical minimization, and an optical implementation

International Nuclear Information System (INIS)

Mirsalehi, M.M.; Gaylord, T.K.

1986-01-01

This paper describes the effect of coding scheme on the number of reference patterns that need to be stored in a content-addressable memory. It is shown that residue number system in conjunction with multilevel coding and logical minimization significantly reduces the number of reference patterns required for implementation of an operation. The number of reference patterns and the total amount of information that needs to be stored are determined for practical cases of 16-bit and 32-bit fixed-point addition and multiplication. The storage requirements were found to be achievable with the state-of-the-art memory technologies. An optical holographical processor capable of parallel-input/parallel-output operation is described

Classical electromagnetic non-minimal coupling for spin 3/2 fields

International Nuclear Information System (INIS)

Villanueva, V. M.; Obregon, O.; Nieto, J. A.

1996-01-01

We obtain a non-minimal electromagnetic coupling for spin 3/2 particles from linearized N=2 Supergravity. This coupling coincides with the one found by Ferrara et al. by demanding g=2 at the tree level. Linearized Einstein field equations plus interaction terms are obtained by squaring the Rarita-Schwinger with this non-minimal coupling by using generalized Poisson brackets

Non-minimal Higgs inflation and frame dependence in cosmology

International Nuclear Information System (INIS)

Steinwachs, Christian F.; Kamenshchik, Alexander Yu.

2013-01-01

We investigate a very general class of cosmological models with scalar fields non-minimally coupled to gravity. A particular representative in this class is given by the non-minimal Higgs inflation model in which the Standard Model Higgs boson and the inflaton are described by one and the same scalar particle. While the predictions of the non-minimal Higgs inflation scenario come numerically remarkably close to the recently discovered mass of the Higgs boson, there remains a conceptual problem in this model that is associated with the choice of the cosmological frame. While the classical theory is independent of this choice, we find by an explicit calculation that already the first quantum corrections induce a frame dependence. We give a geometrical explanation of this frame dependence by embedding it into a more general field theoretical context. From this analysis, some conceptional points in the long lasting cosmological debate: 'Jordan frame vs. Einstein frame' become more transparent and in principle can be resolved in a natural way.

Effects of thermal fluctuations on non-minimal regular magnetic black hole

International Nuclear Information System (INIS)

Jawad, Abdul; Shahzad, M.U.

2017-01-01

We analyze the effects of thermal fluctuations on a regular black hole (RBH) of the non-minimal Einstein-Yang-Mill theory with gauge field of magnetic Wu-Yang type and a cosmological constant. We consider the logarithmic corrected entropy in order to analyze the thermal fluctuations corresponding to non-minimal RBH thermodynamics. In this scenario, we develop various important thermodynamical quantities, such as entropy, pressure, specific heats, Gibb's free energy and Helmholtz free energy. We investigate the first law of thermodynamics in the presence of logarithmic corrected entropy and non-minimal RBH. We also discuss the stability of this RBH using various frameworks such as the γ factor (the ratio of heat capacities), phase transition, grand canonical ensemble and canonical ensemble. It is observed that the non-minimal RBH becomes globally and locally more stable if we increase the value of the cosmological constant. (orig.)

Effects of thermal fluctuations on non-minimal regular magnetic black hole

Energy Technology Data Exchange (ETDEWEB)

Jawad, Abdul [COMSATS Institute of Information Technology, Department of Mathematics, Lahore (Pakistan); Shahzad, M.U. [COMSATS Institute of Information Technology, Department of Mathematics, Lahore (Pakistan); University of Central Punjab, CAMS, UCP Business School, Lahore (Pakistan)

2017-05-15

We analyze the effects of thermal fluctuations on a regular black hole (RBH) of the non-minimal Einstein-Yang-Mill theory with gauge field of magnetic Wu-Yang type and a cosmological constant. We consider the logarithmic corrected entropy in order to analyze the thermal fluctuations corresponding to non-minimal RBH thermodynamics. In this scenario, we develop various important thermodynamical quantities, such as entropy, pressure, specific heats, Gibb's free energy and Helmholtz free energy. We investigate the first law of thermodynamics in the presence of logarithmic corrected entropy and non-minimal RBH. We also discuss the stability of this RBH using various frameworks such as the γ factor (the ratio of heat capacities), phase transition, grand canonical ensemble and canonical ensemble. It is observed that the non-minimal RBH becomes globally and locally more stable if we increase the value of the cosmological constant. (orig.)

Radio frequency energy for non-invasive and minimally invasive skin tightening.

Science.gov (United States)

Mulholland, R Stephen

2011-07-01

This article reviews the non-invasive and minimally invasive options for skin tightening, focusing on peer-reviewed articles and presentations and those technologies with the most proven or promising RF non-excisional skin-tightening results for excisional surgeons. RF has been the mainstay of non-invasive skin tightening and has emerged as the "cutting edge" technology in the minimally invasive skin-tightening field. Because these RF skin-tightening technologies are capital equipment purchases with a significant cost associated, this article also discusses some business issues and models that have proven to work in the plastic surgeon's office for non-invasive and minimally invasive skin-tightening technologies. Copyright © 2011 Elsevier Inc. All rights reserved.

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.

Constraining non-minimally coupled tachyon fields by the Noether symmetry

International Nuclear Information System (INIS)

De Souza, Rudinei C; Kremer, Gilberto M

2009-01-01

A model for a homogeneous and isotropic Universe whose gravitational sources are a pressureless matter field and a tachyon field non-minimally coupled to the gravitational field is analyzed. The Noether symmetry is used to find expressions for the potential density and for the coupling function, and it is shown that both must be exponential functions of the tachyon field. Two cosmological solutions are investigated: (i) for the early Universe whose only source of gravitational field is a non-minimally coupled tachyon field which behaves as an inflaton and leads to an exponential accelerated expansion and (ii) for the late Universe whose gravitational sources are a pressureless matter field and a non-minimally coupled tachyon field which plays the role of dark energy and is responsible for the decelerated-accelerated transition period.

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.

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...

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...

Non-minimal Higgs inflation and frame dependence in cosmology

Energy Technology Data Exchange (ETDEWEB)

Steinwachs, Christian F. [School of Mathematical Sciences, University of Nottingham University Park, Nottingham, NG7 2RD (United Kingdom); Kamenshchik, Alexander Yu. [Dipartimento di Fisica e Astronomia and INFN, Via Irnerio 46, 40126 Bologna, Italy and L.D. Landau Institute for Theoretical Physics of the Russian Academy of Sciences, Kosygin str. 2, 119334 Moscow (Russian Federation)

2013-02-21

We investigate a very general class of cosmological models with scalar fields non-minimally coupled to gravity. A particular representative in this class is given by the non-minimal Higgs inflation model in which the Standard Model Higgs boson and the inflaton are described by one and the same scalar particle. While the predictions of the non-minimal Higgs inflation scenario come numerically remarkably close to the recently discovered mass of the Higgs boson, there remains a conceptual problem in this model that is associated with the choice of the cosmological frame. While the classical theory is independent of this choice, we find by an explicit calculation that already the first quantum corrections induce a frame dependence. We give a geometrical explanation of this frame dependence by embedding it into a more general field theoretical context. From this analysis, some conceptional points in the long lasting cosmological debate: 'Jordan frame vs. Einstein frame' become more transparent and in principle can be resolved in a natural way.

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...

Non-minimal fields of the pure spinor string in general curved backgrounds

Energy Technology Data Exchange (ETDEWEB)

Chandia, Osvaldo [Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez,Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez,Diagonal Las Torres 2640, Peñalolén, Santiago (Chile); Vallilo, Brenno Carlini [Departamento de Ciencias Físicas, Facultad de Ciencias Exactas, Universidad Andrés Bello,República 220, Santiago (Chile)

2015-02-16

We study the coupling of the non-minimal ghost fields of the pure spinor superstring in general curved backgrounds. The coupling is found solving the consistency relations from the nilpotency of the non-minimal BRST charge.

Axion dark matter and Planck favor non-minimal couplings to gravity

Energy Technology Data Exchange (ETDEWEB)

Folkerts, Sarah, E-mail: sarah.folkerts@lmu.de [Arnold Sommerfeld Center, Ludwig-Maximilians-University, Theresienstr. 37, 80333 München (Germany); Germani, Cristiano, E-mail: cristiano.germani@lmu.de [Arnold Sommerfeld Center, Ludwig-Maximilians-University, Theresienstr. 37, 80333 München (Germany); Redondo, Javier, E-mail: javier.redondo@lmu.de [Arnold Sommerfeld Center, Ludwig-Maximilians-University, Theresienstr. 37, 80333 München (Germany); Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany)

2014-01-20

Constraints on inflationary scenarios and isocurvature perturbations have excluded the simplest and most generic models of dark matter based on QCD axions. Considering non-minimal kinetic couplings of scalar fields to gravity substantially changes this picture. The axion can account for the observed dark matter density avoiding the overproduction of isocurvature fluctuations. Finally, we show that assuming the same non-minimal kinetic coupling to the axion (dark matter) and to the standard model Higgs boson (inflaton) provides a minimal picture of early time cosmology.

Canonical Primal-Dual Method for Solving Non-convex Minimization Problems

OpenAIRE

Wu, Changzhi; Li, Chaojie; Gao, David Yang

2012-01-01

A new primal-dual algorithm is presented for solving a class of non-convex minimization problems. This algorithm is based on canonical duality theory such that the original non-convex minimization problem is first reformulated as a convex-concave saddle point optimization problem, which is then solved by a quadratically perturbed primal-dual method. %It is proved that the popular SDP method is indeed a special case of the canonical duality theory. Numerical examples are illustrated. Comparing...

Cosmological Ohm's law and dynamics of non-minimal electromagnetism

International Nuclear Information System (INIS)

Hollenstein, Lukas; Jain, Rajeev Kumar; Urban, Federico R.

2013-01-01

The origin of large-scale magnetic fields in cosmic structures and the intergalactic medium is still poorly understood. We explore the effects of non-minimal couplings of electromagnetism on the cosmological evolution of currents and magnetic fields. In this context, we revisit the mildly non-linear plasma dynamics around recombination that are known to generate weak magnetic fields. We use the covariant approach to obtain a fully general and non-linear evolution equation for the plasma currents and derive a generalised Ohm law valid on large scales as well as in the presence of non-minimal couplings to cosmological (pseudo-)scalar fields. Due to the sizeable conductivity of the plasma and the stringent observational bounds on such couplings, we conclude that modifications of the standard (adiabatic) evolution of magnetic fields are severely limited in these scenarios. Even at scales well beyond a Mpc, any departure from flux freezing behaviour is inhibited

Minimal length uncertainty and generalized non-commutative geometry

International Nuclear Information System (INIS)

Farmany, A.; Abbasi, S.; Darvishi, M.T.; Khani, F.; Naghipour, A.

2009-01-01

A generalized formulation of non-commutative geometry for the Bargmann-Fock space of quantum field theory is presented. The analysis is related to the symmetry of the simplistic space and a minimal length uncertainty.

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)

A Game Theoretic Approach to Minimize the Completion Time of Network Coded Cooperative Data Exchange

KAUST Repository

Douik, Ahmed S.

2014-05-11

In this paper, we introduce a game theoretic framework for studying the problem of minimizing the completion time of instantly decodable network coding (IDNC) for cooperative data exchange (CDE) in decentralized wireless network. In this configuration, clients cooperate with each other to recover the erased packets without a central controller. Game theory is employed herein as a tool for improving the distributed solution by overcoming the need for a central controller or additional signaling in the system. We model the session by self-interested players in a non-cooperative potential game. The utility function is designed such that increasing individual payoff results in a collective behavior achieving both a desirable system performance in a shared network environment and the Pareto optimal solution. Through extensive simulations, our approach is compared to the best performance that could be found in the conventional point-to-multipoint (PMP) recovery process. Numerical results show that our formulation largely outperforms the conventional PMP scheme in most practical situations and achieves a lower delay.

A Game Theoretic Approach to Minimize the Completion Time of Network Coded Cooperative Data Exchange

KAUST Repository

Douik, Ahmed S.; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim; Sorour, Sameh; Tembine, Hamidou

2014-01-01

In this paper, we introduce a game theoretic framework for studying the problem of minimizing the completion time of instantly decodable network coding (IDNC) for cooperative data exchange (CDE) in decentralized wireless network. In this configuration, clients cooperate with each other to recover the erased packets without a central controller. Game theory is employed herein as a tool for improving the distributed solution by overcoming the need for a central controller or additional signaling in the system. We model the session by self-interested players in a non-cooperative potential game. The utility function is designed such that increasing individual payoff results in a collective behavior achieving both a desirable system performance in a shared network environment and the Pareto optimal solution. Through extensive simulations, our approach is compared to the best performance that could be found in the conventional point-to-multipoint (PMP) recovery process. Numerical results show that our formulation largely outperforms the conventional PMP scheme in most practical situations and achieves a lower delay.

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.

Families of bitangent planes of space curves and minimal non-fibration families

KAUST Repository

Lubbes, Niels

2014-01-01

A cone curve is a reduced sextic space curve which lies on a quadric cone and does not pass through the vertex. We classify families of bitangent planes of cone curves. The methods we apply can be used for any space curve with ADE singularities, though in this paper we concentrate on cone curves. An embedded complex projective surface which is adjoint to a degree one weak Del Pezzo surface contains families of minimal degree rational curves, which cannot be defined by the fibers of a map. Such families are called minimal non-fibration families. Families of bitangent planes of cone curves correspond to minimal non-fibration families. The main motivation of this paper is to classify minimal non-fibration families. We present algorithms which compute all bitangent families of a given cone curve and their geometric genus. We consider cone curves to be equivalent if they have the same singularity configuration. For each equivalence class of cone curves we determine the possible number of bitangent families and the number of rational bitangent families. Finally we compute an example of a minimal non-fibration family on an embedded weak degree one Del Pezzo surface.

Cosmology or Catastrophe? A non-minimally coupled scalar in an inhomogeneous universe

International Nuclear Information System (INIS)

Caputa, Paweł; Haque, Sheikh Shajidul; Olson, Joseph; Underwood, Bret

2013-01-01

A non-minimally coupled scalar field can have, in principle, a negative effective Planck mass squared which depends on the scalar field. Surprisingly, an isotropic and homogeneous cosmological universe with a non-minimally coupled scalar field is perfectly smooth as the rolling scalar field causes the effective Planck mass to change sign and pass through zero. However, we show that any small deviations from homogeneity diverge as the effective Planck mass vanishes, with catastrophic consequences for the cosmology. The physical origin of the divergence is due to the presence of non-zero scalar anisotropic stress from the non-minimally coupled scalar field. Thus, while the homogeneous and isotropic cosmology appears surprisingly sensible when the effective Planck mass vanishes, inhomogeneities tell a different story. (paper)

Annotating non-coding regions of the genome.

Science.gov (United States)

Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B

2010-08-01

Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.

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...

Functional interrogation of non-coding DNA through CRISPR genome editing.

Science.gov (United States)

Canver, Matthew C; Bauer, Daniel E; Orkin, Stuart H

2017-05-15

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Y-formalism and b ghost in the non-minimal pure spinor formalism of superstrings

International Nuclear Information System (INIS)

Oda, Ichiro; Tonin, Mario

2007-01-01

We present the Y-formalism for the non-minimal pure spinor quantization of superstrings. In the framework of this formalism we compute, at the quantum level, the explicit form of the compound operators involved in the construction of the b ghost, their normal-ordering contributions and the relevant relations among them. We use these results to construct the quantum-mechanical b ghost in the non-minimal pure spinor formalism. Moreover we show that this non-minimal b ghost is cohomologically equivalent to the non-covariant b ghost

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...

Phenomenology of anomaly-mediated supersymmetry breaking scenarios with non-minimal flavour violation

Energy Technology Data Exchange (ETDEWEB)

Fuks, Benjamin [Strasbourg Univ. (France). Inst. Pluridisciplinaire Hubert Curien; Herrmann, Bjoern [Savoie Univ., Annecy-le-Vieux (France). LAPTh; Klasen, Michael [Muenster Univ. (Germany). Inst. fuer Theoretische Physik 1

2011-12-15

In minimal anomaly-mediated supersymmetry breaking models, tachyonic sleptons are avoided by introducing a common scalar mass similar to the one introduced in minimal supergravity. This may lead to non-minimal flavour-violating interactions, e.g., in the squark sector. In this paper, we analyze the viable anomaly-mediated supersymmetry breaking parameter space in the light of the latest limits on low-energy observables and LHC searches, complete our analytical calculations of flavour-violating supersymmetric particle production at hadron colliders with those related to gluino production, and study the phenomenological consequences of non-minimal flavour violation in anomaly-mediated supersymmetry breaking scenarios at the LHC. Related cosmological aspects are also briefly discussed.

On minimizing the maximum broadcast decoding delay for instantly decodable network coding

KAUST Repository

Douik, Ahmed S.

2014-09-01

In this paper, we consider the problem of minimizing the maximum broadcast decoding delay experienced by all the receivers of generalized instantly decodable network coding (IDNC). Unlike the sum decoding delay, the maximum decoding delay as a definition of delay for IDNC allows a more equitable distribution of the delays between the different receivers and thus a better Quality of Service (QoS). In order to solve this problem, we first derive the expressions for the probability distributions of maximum decoding delay increments. Given these expressions, we formulate the problem as a maximum weight clique problem in the IDNC graph. Although this problem is known to be NP-hard, we design a greedy algorithm to perform effective packet selection. Through extensive simulations, we compare the sum decoding delay and the max decoding delay experienced when applying the policies to minimize the sum decoding delay and our policy to reduce the max decoding delay. Simulations results show that our policy gives a good agreement among all the delay aspects in all situations and outperforms the sum decoding delay policy to effectively minimize the sum decoding delay when the channel conditions become harsher. They also show that our definition of delay significantly improve the number of served receivers when they are subject to strict delay constraints.

Asymptotically safe non-minimal inflation

Energy Technology Data Exchange (ETDEWEB)

Tronconi, Alessandro, E-mail: Alessandro.Tronconi@bo.infn.it [Dipartimento di Fisica e Astronomia and INFN, Via Irnerio 46,40126 Bologna (Italy)

2017-07-01

We study the constraints imposed by the requirement of Asymptotic Safety on a class of inflationary models with an inflaton field non-minimally coupled to the Ricci scalar. The critical surface in the space of theories is determined by the improved renormalization group flow which takes into account quantum corrections beyond the one loop approximation. The combination of constraints deriving from Planck observations and those from theory puts severe bounds on the values of the parameters of the model and predicts a quite large tensor to scalar ratio. We finally comment on the dependence of the results on the definition of the infrared energy scale which parametrises the running on the critical surface.

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)

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.

Proton decay in non-minimal SU(5) GUTs

International Nuclear Information System (INIS)

Rudaz, S.

1984-01-01

We first give an overview of the minimal SU(5) GUT, outlining its successes and failures: we argue that in view of the failure of this theory to reproduce correctly light quark and lepton mass ratios, the lack of experimental evidence for the decay mode p → e + π 0 is hardly surprising. We then consider non-minimal extensions of the basic SU(5) model, with or without supersymmetry, which give rise to quite different hierarchies of nucleon decay modes. These considerations serve to emphasize the importance of ''broad band'' searches for proton decay in all possible modes in the next generation of experiments. 31 refs

Heterologous expression of mlrA in a photoautotrophic host - Engineering cyanobacteria to degrade microcystins.

Science.gov (United States)

Dexter, Jason; Dziga, Dariusz; Lv, Jing; Zhu, Junqi; Strzalka, Wojciech; Maksylewicz, Anna; Maroszek, Magdalena; Marek, Sylwia; Fu, Pengcheng

2018-06-01

In this report, we establish proof-of-principle demonstrating for the first time genetic engineering of a photoautotrophic microorganism for bioremediation of naturally occurring cyanotoxins. In model cyanobacterium Synechocystis sp. PCC 6803 we have heterologously expressed Sphingopyxis sp. USTB-05 microcystinase (MlrA) bearing a 23 amino acid N-terminus secretion peptide from native Synechocystis sp. PCC 6803 PilA (sll1694). The resultant whole cell biocatalyst displayed about 3 times higher activity against microcystin-LR compared to a native MlrA host (Sphingomonas sp. ACM 3962), normalized for optical density. In addition, MlrA activity was found to be almost entirely located in the cyanobacterial cytosolic fraction, despite the presence of the secretion tag, with crude cellular extracts showing MlrA activity comparable to extracts from MlrA expressing E. coli. Furthermore, despite approximately 9.4-fold higher initial MlrA activity of a whole cell E. coli biocatalyst, utilization of a photoautotrophic chassis resulted in prolonged stability of MlrA activity when cultured under semi-natural conditions (using lake water), with the heterologous MlrA biocatalytic activity of the E. coli culture disappearing after 4 days, while the cyanobacterial host displayed activity (3% of initial activity) after 9 days. In addition, the cyanobacterial cell density was maintained over the duration of this experiment while the cell density of the E. coli culture rapidly declined. Lastly, failure to establish a stable cyanobacterial isolate expressing native MlrA (without the N-terminus tag) via the strong cpcB560 promoter draws attention to the use of peptide tags to positively modulate expression of potentially toxic proteins. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

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′

Hybrid genetic algorithm for minimizing non productive machining ...

African Journals Online (AJOL)

Minimization of non-productive time of tool during machining for 2.5 D milling significantly reduces the machining cost. The tool gets retracted and repositioned several times in multi pocket jobs during rough machining which consumes 15 to 30% of total machining time depending on the complexity of job. The automatic ...

Dark matter as a Bose-Einstein Condensate: the relativistic non-minimally coupled case

International Nuclear Information System (INIS)

Bettoni, Dario; Colombo, Mattia; Liberati, Stefano

2014-01-01

Bose-Einstein Condensates have been recently proposed as dark matter candidates. In order to characterize the phenomenology associated to such models, we extend previous investigations by studying the general case of a relativistic BEC on a curved background including a non-minimal coupling to curvature. In particular, we discuss the possibility of a two phase cosmological evolution: a cold dark matter-like phase at the large scales/early times and a condensed phase inside dark matter halos. During the first phase dark matter is described by a minimally coupled weakly self-interacting scalar field, while in the second one dark matter condensates and, we shall argue, develops as a consequence the non-minimal coupling. Finally, we discuss how such non-minimal coupling could provide a new mechanism to address cold dark matter paradigm issues at galactic scales

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.

Tc-99m DTPA perfusion scintigraphy and color coded duplex sonography in the evaluation of minimal renal allograft perfusion

International Nuclear Information System (INIS)

Bair, H.J.; Platsch, G.; Wolf, F.; Guenter, E.; Becker, D.; Rupprecht, H.; Neumayer, H.H.

1997-01-01

Aim: The clinical impact of perfusion scintigraphy versus color coded Duplex sonography was evaluated, with respect to their potential in assessing minimal allograft perfusion in vitally threatened kidney transplants, i.e. oligoanuric allografts suspected to have either severe rejection or thrombosis of the renal vein or artery. Methods: From July 1990 to August 1994 the grafts of 15 out of a total of 315 patients were vitally threatened. Technetium-99m DTPA scintigraphy and color coded Duplex sonography were performed in all patients. For scintigraphic evaluation of transplant perfusion analog scans up to 60 min postinjection, and time-activity curves over the first 60 sec after injection of 370-440 MBq Tc-99m diethylenetriaminepentaacetate acid (DTPA) were used and classified by a perfusion score, the time between renal and iliac artery peaks (TDiff) and the washout of the renogram curve. Additionally, evaluation of excretion function and assessment of vascular or urinary leaks were performed. By color coded Duplex sonography the perfusion in all sections of the graft as well as the vascular anastomoses were examined and the maximal blood flow velocity (Vmax) and the resistive index (RI) in the renal artery were determined by means of the pulsed Doppler device. Pathologic-anatomical diagnosis was achieved by either biopsy or post-explant histology in all grafts. Results: Scintigraphy and color coded Duplex sonography could reliably differentiate minimal (8/15) and not perfused (7/15) renal allografts. The results were confirmed either by angiography in digital subtraction technique (DSA) or the clinical follow up. Conclusion: In summary, perfusion scintigraphy and color coded Duplex sonography are comparable modalities to assess kidney graft perfusion. In clinical practice scintigraphy and colorcoded Doppler sonography can replace digital subtraction angiography in the evaluation of minimal allograft perfusion. (orig.) [de

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

On the non-minimal gravitational coupling to matter

International Nuclear Information System (INIS)

Bertolami, O; Paramos, J

2008-01-01

The connection between f(R) theories of gravity and scalar-tensor models with a 'physical' metric coupled to the scalar field is well known. In this work, we pursue the equivalence between a suitable scalar theory and a model that generalizes the f(R) scenario, encompassing both a non-minimal scalar curvature term and a non-minimum coupling of the scalar curvature and matter. This equivalence allows for the calculation of the PPN parameters β and γ and, eventually, a solution to the debate concerning the weak-field limit of f(R) theories

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.

Dryland photoautotrophic soil surface communities endangered by global change

Science.gov (United States)

Rodriguez-Caballero, Emilio; Belnap, Jayne; Büdel, Burkhard; Crutzen, Paul J.; Andreae, Meinrat O.; Pöschl, Ulrich; Weber, Bettina

2018-03-01

Photoautotrophic surface communities forming biological soil crusts (biocrusts) are crucial for soil stability as well as water, nutrient and trace gas cycling at regional and global scales. Quantitative information on their global coverage and the environmental factors driving their distribution patterns, however, are not readily available. We use observations and environmental modelling to estimate the global distribution of biocrusts and their response to global change using future projected scenarios. We find that biocrusts currently covering approximately 12% of Earth's terrestrial surface will decrease by about 25-40% within 65 years due to anthropogenically caused climate change and land-use intensification, responding far more drastically than vascular plants. Our results illustrate that current biocrust occurrence is mainly driven by a combination of precipitation, temperature and land management, and future changes are expected to be affected by land-use and climate change in similar proportion. The predicted loss of biocrusts may substantially reduce the microbial contribution to nitrogen cycling and enhance the emissions of soil dust, which affects the functioning of ecosystems as well as human health and should be considered in the modelling, mitigation and management of global change.

Dryland photoautotrophic soil surface communities endangered by global change

Science.gov (United States)

Rodriguez-Caballero, Emilio; Belnap, Jayne; Büdel, Burkhard; Crutzen, Paul J.; Andreae, Meinrat O.; Pöschl, Ulrich; Weber, Bettina

2018-01-01

Photoautotrophic surface communities forming biological soil crusts (biocrusts) are crucial for soil stability as well as water, nutrient and trace gas cycling at regional and global scales. Quantitative information on their global coverage and the environmental factors driving their distribution patterns, however, are not readily available. We use observations and environmental modelling to estimate the global distribution of biocrusts and their response to global change using future projected scenarios. We find that biocrusts currently covering approximately 12% of Earth’s terrestrial surface will decrease by about 25–40% within 65 years due to anthropogenically caused climate change and land-use intensification, responding far more drastically than vascular plants. Our results illustrate that current biocrust occurrence is mainly driven by a combination of precipitation, temperature and land management, and future changes are expected to be affected by land-use and climate change in similar proportion. The predicted loss of biocrusts may substantially reduce the microbial contribution to nitrogen cycling and enhance the emissions of soil dust, which affects the functioning of ecosystems as well as human health and should be considered in the modelling, mitigation and management of global change.

Precise Higgs mass calculations in (non-)minimal supersymmetry at both high and low scales

Energy Technology Data Exchange (ETDEWEB)

Athron, Peter [Monash Univ., Victoria (Australia). School of Physics and Astronomy; Park, Jae-hyeon [Korea Institute for Advanced Study, Seoul (Korea, Republic of). Quantum Universe Center; Steudtner, Tom; Stoeckinger, Dominik [TU Dresden (Germany). Inst. fuer Kern- und Teilchenphysik; Voigt, Alexander [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2016-09-15

We present FlexibleEFTHiggs, a method for calculating the SM-like Higgs pole mass in SUSY (and even non-SUSY) models, which combines an effective field theory approach with a diagrammatic calculation. It thus achieves an all order resummation of leading logarithms together with the inclusion of all non-logarithmic 1-loop contributions. We implement this method into FlexibleSUSY and study its properties in the MSSM, NMSSM, E{sub 6}SSM and MRSSM. In the MSSM, it correctly interpolates between the known results of effective field theory calculations in the literature for a high SUSY scale and fixed-order calculations in the full theory for a sub-TeV SUSY scale. We compare our MSSM results to those from public codes and identify the origin of the most significant deviations between the DR programs. We then perform a similar comparison in the remaining three non-minimal models. For all four models we estimate the theoretical uncertainty of FlexibleEFTHiggs and the fixed-order DR programs thereby finding that the former becomes more precise than the latter for a SUSY scale above a few TeV. Even for sub-TeV SUSY scales, FlexibleEFTHiggs maintains the uncertainty estimate around 2-3 GeV, remaining a competitive alternative to existing fixed-order computations.

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

On the uniqueness of the non-minimal matter coupling in massive gravity and bigravity

International Nuclear Information System (INIS)

Huang, Qing-Guo; Ribeiro, Raquel H.; Xing, Yu-Hang; Zhang, Ke-Chao; Zhou, Shuang-Yong

2015-01-01

In de Rham–Gabadadze–Tolley (dRGT) massive gravity and bi-gravity, a non-minimal matter coupling involving both metrics generically reintroduces the Boulware–Deser (BD) ghost. A non-minimal matter coupling via a simple, yet specific composite metric has been proposed, which eliminates the BD ghost below the strong coupling scale. Working explicitly in the metric formulation and for arbitrary spacetime dimensions, we show that this composite metric is the unique consistent non-minimal matter coupling below the strong coupling scale, which emerges out of two diagnostics, namely, the absence of Ostrogradski ghosts in the decoupling limit and the absence of the BD ghost from matter quantum loop corrections

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)

On the uniqueness of the non-minimal matter coupling in massive gravity and bigravity

Directory of Open Access Journals (Sweden)

Qing-Guo Huang

2015-09-01

Full Text Available In de Rham–Gabadadze–Tolley (dRGT massive gravity and bi-gravity, a non-minimal matter coupling involving both metrics generically reintroduces the Boulware–Deser (BD ghost. A non-minimal matter coupling via a simple, yet specific composite metric has been proposed, which eliminates the BD ghost below the strong coupling scale. Working explicitly in the metric formulation and for arbitrary spacetime dimensions, we show that this composite metric is the unique consistent non-minimal matter coupling below the strong coupling scale, which emerges out of two diagnostics, namely, the absence of Ostrogradski ghosts in the decoupling limit and the absence of the BD ghost from matter quantum loop corrections.

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

Precise Higgs mass calculations in (non-)minimal supersymmetry at both high and low scales

Energy Technology Data Exchange (ETDEWEB)

Athron, Peter [ARC Centre of Excellence for Particle Physics at the Terascale,School of Physics and Astronomy, Monash University,Melbourne, Victoria 3800 (Australia); Park, Jae-hyeon [Quantum Universe Center, Korea Institute for Advanced Study,85 Hoegiro Dongdaemungu, Seoul 02455 (Korea, Republic of); Steudtner, Tom; Stöckinger, Dominik [Institut für Kern- und Teilchenphysik, TU Dresden,Zellescher Weg 19, 01069 Dresden (Germany); Voigt, Alexander [Deutsches Elektronen-Synchrotron DESY,Notkestraße 85, 22607 Hamburg (Germany)

2017-01-18

We present FlexibleEFTHiggs, a method for calculating the SM-like Higgs pole mass in SUSY (and even non-SUSY) models, which combines an effective field theory approach with a diagrammatic calculation. It thus achieves an all order resummation of leading logarithms together with the inclusion of all non-logarithmic 1-loop contributions. We implement this method into FlexibleSUSY and study its properties in the MSSM, NMSSM, E{sub 6}SSM and MRSSM. In the MSSM, it correctly interpolates between the known results of effective field theory calculations in the literature for a high SUSY scale and fixed-order calculations in the full theory for a sub-TeV SUSY scale. We compare our MSSM results to those from public codes and identify the origin of the most significant deviations between the (DR)-bar programs. We then perform a similar comparison in the remaining three non-minimal models. For all four models we estimate the theoretical uncertainty of FlexibleEFTHiggs and the fixed-order (DR)-bar programs thereby finding that the former becomes more precise than the latter for a SUSY scale above a few TeV. Even for sub-TeV SUSY scales, FlexibleEFTHiggs maintains the uncertainty estimate around 2–3 GeV, remaining a competitive alternative to existing fixed-order computations.

Running non-minimal inflation with stabilized inflaton potential

Energy Technology Data Exchange (ETDEWEB)

Okada, Nobuchika; Raut, Digesh [University of Alabama, Department of Physics and Astronomy, Alabama (United States)

2017-04-15

In the context of the Higgs model involving gauge and Yukawa interactions with the spontaneous gauge symmetry breaking, we consider λφ{sup 4} inflation with non-minimal gravitational coupling, where the Higgs field is identified as the inflaton. Since the inflaton quartic coupling is very small, once quantum corrections through the gauge and Yukawa interactions are taken into account, the inflaton effective potential most likely becomes unstable. In order to avoid this problem, we need to impose stability conditions on the effective inflaton potential, which lead to not only non-trivial relations amongst the particle mass spectrum of the model, but also correlations between the inflationary predictions and the mass spectrum. For concrete discussion, we investigate the minimal B-L extension of the standard model with identification of the B-L Higgs field as the inflaton. The stability conditions for the inflaton effective potential fix the mass ratio amongst the B-L gauge boson, the right-handed neutrinos and the inflaton. This mass ratio also correlates with the inflationary predictions. In other words, if the B-L gauge boson and the right-handed neutrinos are discovered in the future, their observed mass ratio provides constraints on the inflationary predictions. (orig.)

Extended ΛCDM: generalized non-minimal coupling for dark matter fluids

International Nuclear Information System (INIS)

Bettoni, Dario; Liberati, Stefano; Sindoni, Lorenzo

2011-01-01

In this paper we discuss a class of models that address the issue of explaining the gravitational dynamics at the galactic scale starting from a geometric point of view. Instead of claiming the existence of some hidden coupling between dark matter and baryons, or abandoning the existence of dark matter itself, we consider the possibility that dark matter and gravity have some non trivial interaction able to modify the dynamics at astrophysical scales. This interaction is implemented assuming that dark matter gets non-minimally coupled with gravity at suitably small scales and late times. After showing the predictions of the model in the Newtonian limit we also discuss the possible origin of it non-minimal coupling. This investigation seems to suggest that phenomenological mechanisms envisaged for the dark matter dynamics, such as the Bose-Einstein condensation of dark matter halos, could be connected to this class of models

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.

Main photoautotrophic components of biofilms in natural draft cooling towers.

Science.gov (United States)

Hauer, Tomáš; Čapek, Petr; Böhmová, Petra

2016-05-01

While photoautotrophic organisms are an important component of biofilms that live in certain regions of natural draft cooling towers, little is known about these communities. We therefore examined 18 towers at nine sites to identify the general patterns of community assembly in three distinct tower parts, and we examined how community structures differ depending on geography. We also compared the newly acquired data with previously published data. The bottom sections of draft cooling towers are mainly settled by large filamentous algae, primarily Cladophora glomerata. The central portions of towers host a small amount of planktic algae biomass originating in the cooling water. The upper fourths of towers are colonized by biofilms primarily dominated by cyanobacteria, e.g., members of the genera Gloeocapsa and Scytonema. A total of 41 taxa of phototrophic microorganisms were identified. Species composition of the upper fourth of all towers was significantly affected by cardinal position. There was different species composition at positions facing north compared to positions facing south. West- and east-facing positions were transitory and highly similar to each other in terms of species composition. Biofilms contribute to the degradation of paint coatings inside towers.

Cosmological perturbations of non-minimally coupled quintessence in the metric and Palatini formalisms

International Nuclear Information System (INIS)

Fan, Yize; Wu, Puxun; Yu, Hongwei

2015-01-01

Cosmological perturbations of the non-minimally coupled scalar field dark energy in both the metric and Palatini formalisms are studied in this paper. We find that on the large scales with the energy density of dark energy becoming more and more important in the low redshift region, the gravitational potential becomes smaller and smaller, and the effect of non-minimal coupling becomes more and more apparent. In the metric formalism the value of the gravitational potential in the non-minimally coupled case with a positive coupling constant is less than that in the minimally coupled case, while it is larger if the coupling constant is negative. This is different from that in the Palatini formalism where the value of gravitational potential is always smaller. Based upon the quasi-static approximation on the sub-horizon scales, the linear growth of matter is also analyzed. We obtain that the effective Newton's constants in the metric and Palatini formalisms have different forms. A negative coupling constant enhances the gravitational interaction, while a positive one weakens it. Although the metric and Palatini formalisms give different linear growth rates, the difference is very small and the current observation cannot distinguish them effectively

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

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

Non-minimal Maxwell-Chern-Simons theory and the composite Fermion model

International Nuclear Information System (INIS)

Paschoal, Ricardo C.; Helayel Neto, Jose A.

2003-01-01

The magnetic field redefinition in Jain's composite fermion model for the fractional quantum Hall effect is shown to be effective described by a mean-field approximation of a model containing a Maxwell-Chern-Simons gauge field nominally coupled to matter. Also an explicit non-relativistic limit of the non-minimal (2+1) D Dirac's equation is derived. (author)

Highly conserved non-coding sequences are associated with vertebrate development.

Directory of Open Access Journals (Sweden)

Adam Woolfe

2005-01-01

Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

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.

Decoding the usefulness of non-coding RNAs as breast cancer markers.

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Amorim, Maria; Salta, Sofia; Henrique, Rui; Jerónimo, Carmen

2016-09-15

Although important advances in the management of breast cancer (BC) have been recently accomplished, it still constitutes the leading cause of cancer death in women worldwide. BC is a heterogeneous and complex disease, making clinical prediction of outcome a very challenging task. In recent years, gene expression profiling emerged as a tool to assist in clinical decision, enabling the identification of genetic signatures that better predict prognosis and response to therapy. Nevertheless, translation to routine practice has been limited by economical and technical reasons and, thus, novel biomarkers, especially those requiring non-invasive or minimally invasive collection procedures, while retaining high sensitivity and specificity might represent a significant development in this field. An increasing amount of evidence demonstrates that non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are aberrantly expressed in several cancers, including BC. miRNAs are of particular interest as new, easily accessible, cost-effective and non-invasive tools for precise management of BC patients because they circulate in bodily fluids (e.g., serum and plasma) in a very stable manner, enabling BC assessment and monitoring through liquid biopsies. This review focus on how ncRNAs have the potential to answer present clinical needs in the personalized management of patients with BC and comprehensively describes the state of the art on the role of ncRNAs in the diagnosis, prognosis and prediction of response to therapy in BC.

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.

Mimicking dark matter through a non-minimal gravitational coupling with matter

International Nuclear Information System (INIS)

Bertolami, O.; Páramos, J.

2010-01-01

In this study one resorts to the phenomenology of models endowed with a non-minimal coupling between matter and geometry, in order to develop a mechanism through which dynamics similar to that due to the presence of dark matter is generated. As a first attempt, one tries to account for the flattening of the galaxy rotation curves as an effect of the non-(covariant) conservation of the energy-momentum tensor of visible matter. Afterwards, one assumes instead that this non-minimal coupling modifies the scalar curvature in a way that can be interpreted as a dark matter component (albeit with negative pressure). It is concluded that it is possible to mimic known dark matter density profiles through an appropriate power-law coupling f 2 = (R/R 0 ) n , with a negative index n — a fact that reflects the dominance of dark matter at large distances. The properties of the model are extensively discussed, and possible cosmological implications are addressed

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

Cosmological perturbations in theories with non-minimal coupling between curvature and matter

International Nuclear Information System (INIS)

Bertolami, Orfeu; Frazão, Pedro; Páramos, Jorge

2013-01-01

In this work, we examine how the presence of a non-minimal coupling between spacetime curvature and matter affects the evolution of cosmological perturbations on a homogeneous and isotropic Universe, and hence the formation of large-scale structure. This framework places constraints on the terms which arise due to the coupling with matter and, in particular, on the modified growth of matter density perturbations. We derive approximate analytical solutions for the evolution of matter overdensities during the matter dominated era and discuss the compatibility of the obtained results with the hypothesis that the late time acceleration of the Universe is driven by a non-minimal coupling

Light intensity as major factor to maximize biomass and lipid productivity of Ettlia sp. in CO2-controlled photoautotrophic chemostat.

Science.gov (United States)

Seo, Seong-Hyun; Ha, Ji-San; Yoo, Chan; Srivastava, Ankita; Ahn, Chi-Yong; Cho, Dae-Hyun; La, Hyun-Joon; Han, Myung-Soo; Oh, Hee-Mock

2017-11-01

The optimal culture conditions are critical factors for high microalgal biomass and lipid productivity. To optimize the photoautotrophic culture conditions, combination of the pH (regulated by CO 2 supply), dilution rate, and light intensity was systematically investigated for Ettlia sp. YC001 cultivation in a chemostat during 143days. The biomass productivity increased with the increase in dilution rate and light intensity, but decreased with increasing pH. The average lipid content was 19.8% and statistically non-variable among the tested conditions. The highest biomass and lipid productivities were 1.48gL -1 d -1 and 291.4mgL -1 d -1 with a pH of 6.5, dilution rate of 0.78d -1 , and light intensity of 1500μmolphotonsm -2 s -1 . With a sufficient supply of CO 2 and nutrients, the light intensity was the main determinant of the photosynthetic rate. Therefore, the surface-to-volume ratio of a photobioreactor should enable efficient light distribution to enhance microalgal growth. Copyright © 2017 Elsevier Ltd. All rights reserved.

Variation of photoautotrophic fatty acid production from a highly CO2 tolerant alga, Chlorococcum littorale, with inorganic carbon over narrow ranges of pH.

Science.gov (United States)

Ota, Masaki; Takenaka, Motohiro; Sato, Yoshiyuki; Smith, Richard L; Inomata, Hiroshi

2015-01-01

Photoautotrophic fatty acid production of a highly CO2 -tolerant green alga Chlorococcum littorale in the presence of inorganic carbon at 295 K and light intensity of 170 µmol-photon m(-2) s(-1) was investigated. CO2 concentration in the bubbling gas was adjusted by mixing pure gas components of CO2 and N2 to avoid photorespiration and β-oxidation of fatty acids under O2 surrounding conditions. Maximum content of total fatty acid showed pH-dependence after nitrate depletion of the culture media and increased with the corresponding inorganic carbon ratio. Namely, [HCO3 (-) ]/([CO2 ]+n[ CO32-]) ratio in the culture media was found to be a controlling factor for photoautotrophic fatty acid production after the nitrate limitation. At a CO2 concentration of 5% (vol/vol) and a pH of 6.7, the fatty acid content was 47.8 wt % (dry basis) at its maximum that is comparable with land plant seed oils. © 2015 American Institute of Chemical Engineers.

Gauss–Bonnet cosmology with induced gravity and a non-minimally coupled scalar field on the brane

International Nuclear Information System (INIS)

Nozari, Kourosh; Fazlpour, Behnaz

2008-01-01

We construct a cosmological model with a non-minimally coupled scalar field on the brane, where Gauss–Bonnet and induced gravity effects are taken into account. This model has 5D character at both high and low energy limits but reduces to 4D gravity for intermediate scales. While induced gravity is a manifestation of the IR limit of the model, the Gauss–Bonnet term and non-minimal coupling of the scalar field and induced gravity are essentially related to the UV limit of the scenario. We study the cosmological implications of this scenario focusing on the late time behavior of the solutions. In this setup, non-minimal coupling plays the role of an additional fine-tuning parameter that controls the initial density of the predicted finite density big bang. Also, non-minimal coupling has important implications for the bouncing nature of the solutions

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

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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.

Stability of the Minimizers of Least Squares with a Non-Convex Regularization. Part I: Local Behavior

International Nuclear Information System (INIS)

Durand, S.; Nikolova, M.

2006-01-01

Many estimation problems amount to minimizing a piecewise C m objective function, with m ≥ 2, composed of a quadratic data-fidelity term and a general regularization term. It is widely accepted that the minimizers obtained using non-convex and possibly non-smooth regularization terms are frequently good estimates. However, few facts are known on the ways to control properties of these minimizers. This work is dedicated to the stability of the minimizers of such objective functions with respect to variations of the data. It consists of two parts: first we consider all local minimizers, whereas in a second part we derive results on global minimizers. In this part we focus on data points such that every local minimizer is isolated and results from a C m-1 local minimizer function, defined on some neighborhood. We demonstrate that all data points for which this fails form a set whose closure is negligible

Cosmological dynamics with non-minimally coupled scalar field and a constant potential function

International Nuclear Information System (INIS)

Hrycyna, Orest; Szydłowski, Marek

2015-01-01

Dynamical systems methods are used to investigate global behaviour of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We show that the system can be reduced to an autonomous three-dimensional dynamical system and additionally is equipped with an invariant manifold corresponding to an accelerated expansion of the universe. Using this invariant manifold we find an exact solution of the reduced dynamics. We investigate all solutions for all admissible initial conditions using theory of dynamical systems to obtain a classification of all evolutional paths. The right-hand sides of the dynamical system depend crucially on the value of the non-minimal coupling constant therefore we study bifurcation values of this parameter under which the structure of the phase space changes qualitatively. We found a special bifurcation value of the non-minimal coupling constant which is distinguished by dynamics of the model and may suggest some additional symmetry in matter sector of the theory

Cosmological dynamics with non-minimally coupled scalar field and a constant potential function

Energy Technology Data Exchange (ETDEWEB)

Hrycyna, Orest [Theoretical Physics Division, National Centre for Nuclear Research, Hoża 69, 00-681 Warszawa (Poland); Szydłowski, Marek, E-mail: orest.hrycyna@ncbj.gov.pl, E-mail: marek.szydlowski@uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244 Kraków (Poland)

2015-11-01

Dynamical systems methods are used to investigate global behaviour of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We show that the system can be reduced to an autonomous three-dimensional dynamical system and additionally is equipped with an invariant manifold corresponding to an accelerated expansion of the universe. Using this invariant manifold we find an exact solution of the reduced dynamics. We investigate all solutions for all admissible initial conditions using theory of dynamical systems to obtain a classification of all evolutional paths. The right-hand sides of the dynamical system depend crucially on the value of the non-minimal coupling constant therefore we study bifurcation values of this parameter under which the structure of the phase space changes qualitatively. We found a special bifurcation value of the non-minimal coupling constant which is distinguished by dynamics of the model and may suggest some additional symmetry in matter sector of the theory.

Non-minimally coupled tachyon field in teleparallel gravity

Energy Technology Data Exchange (ETDEWEB)

Fazlpour, Behnaz [Department of Physics, Babol Branch, Islamic Azad University, Shariati Street, Babol (Iran, Islamic Republic of); Banijamali, Ali, E-mail: b.fazlpour@umz.ac.ir, E-mail: a.banijamali@nit.ac.ir [Department of Basic Sciences, Babol University of Technology, Shariati Street, Babol (Iran, Islamic Republic of)

2015-04-01

We perform a full investigation on dynamics of a new dark energy model in which the four-derivative of a non-canonical scalar field (tachyon) is non-minimally coupled to the vector torsion. Our analysis is done in the framework of teleparallel equivalent of general relativity which is based on torsion instead of curvature. We show that in our model there exists a late-time scaling attractor (point P{sub 4}), corresponding to an accelerating universe with the property that dark energy and dark matter densities are of the same order. Such a point can help to alleviate the cosmological coincidence problem. Existence of this point is the most significant difference between our model and another model in which a canonical scalar field (quintessence) is used instead of tachyon field.

Non-minimally coupled tachyon field in teleparallel gravity

International Nuclear Information System (INIS)

Fazlpour, Behnaz; Banijamali, Ali

2015-01-01

We perform a full investigation on dynamics of a new dark energy model in which the four-derivative of a non-canonical scalar field (tachyon) is non-minimally coupled to the vector torsion. Our analysis is done in the framework of teleparallel equivalent of general relativity which is based on torsion instead of curvature. We show that in our model there exists a late-time scaling attractor (point P 4 ), corresponding to an accelerating universe with the property that dark energy and dark matter densities are of the same order. Such a point can help to alleviate the cosmological coincidence problem. Existence of this point is the most significant difference between our model and another model in which a canonical scalar field (quintessence) is used instead of tachyon field

Testing non-minimally coupled inflation with CMB data: a Bayesian analysis

International Nuclear Information System (INIS)

Campista, Marcela; Benetti, Micol; Alcaniz, Jailson

2017-01-01

We use the most recent cosmic microwave background (CMB) data to perform a Bayesian statistical analysis and discuss the observational viability of inflationary models with a non-minimal coupling, ξ, between the inflaton field and the Ricci scalar. We particularize our analysis to two examples of small and large field inflationary models, namely, the Coleman-Weinberg and the chaotic quartic potentials. We find that ( i ) the ξ parameter is closely correlated with the primordial amplitude ; ( ii ) although improving the agreement with the CMB data in the r − n s plane, where r is the tensor-to-scalar ratio and n s the primordial spectral index, a non-null coupling is strongly disfavoured with respect to the minimally coupled standard ΛCDM model, since the upper bounds of the Bayes factor (odds) for ξ parameter are greater than 150:1.

Testing non-minimally coupled inflation with CMB data: a Bayesian analysis

Energy Technology Data Exchange (ETDEWEB)

Campista, Marcela; Benetti, Micol; Alcaniz, Jailson, E-mail: campista@on.br, E-mail: micolbenetti@on.br, E-mail: alcaniz@on.br [Observatório Nacional, Rua General José Cristino 77, Rio de Janeiro, RJ, 20921-400 Brazil (Brazil)

2017-09-01

We use the most recent cosmic microwave background (CMB) data to perform a Bayesian statistical analysis and discuss the observational viability of inflationary models with a non-minimal coupling, ξ, between the inflaton field and the Ricci scalar. We particularize our analysis to two examples of small and large field inflationary models, namely, the Coleman-Weinberg and the chaotic quartic potentials. We find that ( i ) the ξ parameter is closely correlated with the primordial amplitude ; ( ii ) although improving the agreement with the CMB data in the r − n {sub s} plane, where r is the tensor-to-scalar ratio and n {sub s} the primordial spectral index, a non-null coupling is strongly disfavoured with respect to the minimally coupled standard ΛCDM model, since the upper bounds of the Bayes factor (odds) for ξ parameter are greater than 150:1.

Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

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Maggi Giorgio P

2008-06-01

Full Text Available Abstract Background The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between conserved coding and non-coding sequences. This discrimination is often based (thus dependent on the availability of annotated proteins. Results In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of conserved sequences and accurate assessment of their coding potential. By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci. Following this analysis we created a collection of human-mouse conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST sequences but not corresponding to as yet annotated genes. Conclusion Here we present a new system which allows comprehensive comparison of genomes to detect conserved coding and non-coding sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.

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

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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.

Tc-99m DTPA perfusion scintigraphy and color coded duplex sonography in the evaluation of minimal renal allograft perfusion

Energy Technology Data Exchange (ETDEWEB)

Bair, H.J.; Platsch, G.; Wolf, F. [Erlangen-Nuernberg Univ., Erlangen (Germany). Dept. of Nuclear Medicine; Guenter, E.; Becker, D. [Erlangen-Nuernberg Univ., Erlangen (Germany). Dept. of Internal Medicine 1; Rupprecht, H.; Neumayer, H.H. [Erlangen-Nuernberg Univ., Erlangen (Germany). Dept. of Internal Medicine 4

1997-08-01

Aim: The clinical impact of perfusion scintigraphy versus color coded Duplex sonography was evaluated, with respect to their potential in assessing minimal allograft perfusion in vitally threatened kidney transplants, i.e. oligoanuric allografts suspected to have either severe rejection or thrombosis of the renal vein or artery. Methods: From July 1990 to August 1994 the grafts of 15 out of a total of 315 patients were vitally threatened. Technetium-99m DTPA scintigraphy and color coded Duplex sonography were performed in all patients. For scintigraphic evaluation of transplant perfusion analog scans up to 60 min postinjection, and time-activity curves over the first 60 sec after injection of 370-440 MBq Tc-99m diethylenetriaminepentaacetate acid (DTPA) were used and classified by a perfusion score, the time between renal and iliac artery peaks (TDiff) and the washout of the renogram curve. Additionally, evaluation of excretion function and assessment of vascular or urinary leaks were performed. By color coded Duplex sonography the perfusion in all sections of the graft as well as the vascular anastomoses were examined and the maximal blood flow velocity (Vmax) and the resistive index (RI) in the renal artery were determined by means of the pulsed Doppler device. Pathologic-anatomical diagnosis was achieved by either biopsy or post-explant histology in all grafts. Results: Scintigraphy and color coded Duplex sonography could reliably differentiate minimal (8/15) and not perfused (7/15) renal allografts. The results were confirmed either by angiography in digital subtraction technique (DSA) or the clinical follow up. Conclusion: In summary, perfusion scintigraphy and color coded Duplex sonography are comparable modalities to assess kidney graft perfusion. In clinical practice scintigraphy and colorcoded Doppler sonography can replace digital subtraction angiography in the evaluation of minimal allograft perfusion. (orig.) [Deutsch] Ziel der Studie war es, das

Long Non-Coding RNA in Cancer

Directory of Open Access Journals (Sweden)

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.

Late-time acceleration and phantom divide line crossing with non-minimal coupling and Lorentz-invariance violation

International Nuclear Information System (INIS)

Nozari, Kourosh; Sadatian, S.D.

2008-01-01

We consider two alternative dark-energy models: a Lorentz-invariance preserving model with a non-minimally coupled scalar field and a Lorentz-invariance violating model with a minimally coupled scalar field. We study accelerated expansion and the dynamics of the equation of state parameter in these scenarios. While a minimally coupled scalar field does not have the capability to be a successful dark-energy candidate with line crossing of the cosmological constant, a non-minimally coupled scalar field in the presence of Lorentz invariance or a minimally coupled scalar field with Lorentz-invariance violation have this capability. In the latter case, accelerated expansion and phantom divide line crossing are the results of the interactive nature of this Lorentz-violating scenario. (orig.)

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.

Uptake of /sup 86/Rb/sup +/ into photoautotrophic mesophyll cells of Papaver somniferum

Energy Technology Data Exchange (ETDEWEB)

Kaiser, W.M.; Jeschke, W.D.; Hartung, W.

1982-06-01

Uptake of /sup 86/Rb/sup +/, used as a tracer for potassium, into isolated photoautotrophic mesophyll cells of Papaver somniferum was weakly but consistently stimulated in the light. It showed mono-phasic saturation kinetics with a pH optimum of 7.0, a Vsub(max) of 6.7 ..mu..mol mg/sup -1/ Chl x h/sup -1/ and a Ksub(m) of 2.7 mmol l/sup -1/. Different anions as Cl/sup -/, NO/sub 3//sup -/ and PO/sub 4//sup 3 -/ had no effects on /sup 86/Rb/sup +/ uptake. Sodium ions influenced Rb/sup +/-uptake very weakly, indicating a high K/sup +/ -specificity of the mesophyll cell plasmalemma. Fusicoccin stimulated /sup 86/Rb/sup +/ -uptake strongly whereas abscisic acid inhibited uptake only following preincubation for two hours. Nitrite, CCCP and Dio-9 inhibited /sup 86/Rb/sup +/-uptake which gives evidence that this process is dependent on intact pH-gradients within the cells and on ATP-formation.

Non - minimal interaction of gravity with other physical fields: an overview

International Nuclear Information System (INIS)

Novello, M.; Oliveira, L.A.R. de.

1986-01-01

A review on some modern developments concerning the interaction of gravity with other physical fields. It is argued that a suitable context for an account of their dynamical interplay is that of the non-minimal (e.g., conformal) coupling of these fields to gravity. Some interesting features of non-minimal coupling, such as the connection with Weyl-integrable spacetime (WIST) structure, the generation of eternal Universes, the appearance of a cosmological constant and the possible induction of repulsive gravity via spontaneous symmetry breaking (SSB) mechanisms, are discussed. In particular, examines a simple case of strong interacting scalar particles (such as the well-Known elastic reaction ΠK → ΠK), in a curved background, thereby obtaining the curious result that the actual, observed value of the strong coupling constant and the minimum value allowable, in order to preclude antigravity, are related by Eddington's number 10 39 . (Author) [pt

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.

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.

Denjoy minimal sets and Birkhoff periodic orbits for non-exact monotone twist maps

Science.gov (United States)

Qin, Wen-Xin; Wang, Ya-Nan

2018-06-01

A non-exact monotone twist map φbarF is a composition of an exact monotone twist map φ bar with a generating function H and a vertical translation VF with VF ((x , y)) = (x , y - F). We show in this paper that for each ω ∈ R, there exists a critical value Fd (ω) ≥ 0 depending on H and ω such that for 0 ≤ F ≤Fd (ω), the non-exact twist map φbarF has an invariant Denjoy minimal set with irrational rotation number ω lying on a Lipschitz graph, or Birkhoff (p , q)-periodic orbits for rational ω = p / q. Like the Aubry-Mather theory, we also construct heteroclinic orbits connecting Birkhoff periodic orbits, and show that quasi-periodic orbits in these Denjoy minimal sets can be approximated by periodic orbits. In particular, we demonstrate that at the critical value F =Fd (ω), the Denjoy minimal set is not uniformly hyperbolic and can be approximated by smooth curves.

Recent results on a non-minimal coupling between curvature and matter

International Nuclear Information System (INIS)

Páramos, Jorge

2013-01-01

This work presents a review of recent findings from the consideration of a non-minimal coupling between matter and geometry, namely the possibility of mimicking dark matter in clusters and the description of gravitational collapse — thus adding to the wide range of phenomena already covered by the theory.

Phenomenology of non-minimal supersymmetric models at linear colliders

International Nuclear Information System (INIS)

Porto, Stefano

2015-06-01

The focus of this thesis is on the phenomenology of several non-minimal supersymmetric models in the context of future linear colliders (LCs). Extensions of the minimal supersymmetric Standard Model (MSSM) may accommodate the observed Higgs boson mass at about 125 GeV in a more natural way than the MSSM, with a richer phenomenology. We consider both F-term extensions of the MSSM, as for instance the non-minimal supersymmetric Standard Model (NMSSM), as well as D-terms extensions arising at low energies from gauge extended supersymmetric models. The NMSSM offers a solution to the μ-problem with an additional gauge singlet supermultiplet. The enlarged neutralino sector of the NMSSM can be accurately studied at a LC and used to distinguish the model from the MSSM. We show that exploiting the power of the polarised beams of a LC can be used to reconstruct the neutralino and chargino sector and eventually distinguish the NMSSM even considering challenging scenarios that resemble the MSSM. Non-decoupling D-terms extensions of the MSSM can raise the tree-level Higgs mass with respect to the MSSM. This is done through additional contributions to the Higgs quartic potential, effectively generated by an extended gauge group. We study how this can happen and we show how these additional non-decoupling D-terms affect the SM-like Higgs boson couplings to fermions and gauge bosons. We estimate how the deviations from the SM couplings can be spotted at the Large Hadron Collider (LHC) and at the International Linear Collider (ILC), showing how the ILC would be suitable for the model identication. Since our results prove that a linear collider is a fundamental machine for studying supersymmetry phenomenology at a high level of precision, we argue that also a thorough comprehension of the physics at the interaction point (IP) of a LC is needed. Therefore, we finally consider the possibility of observing intense electromagnetic field effects and nonlinear quantum electrodynamics

Experimental validation of the DPM Monte Carlo code using minimally scattered electron beams in heterogeneous media

International Nuclear Information System (INIS)

Chetty, Indrin J.; Moran, Jean M.; Nurushev, Teamor S.; McShan, Daniel L.; Fraass, Benedick A.; Wilderman, Scott J.; Bielajew, Alex F.

2002-01-01

A comprehensive set of measurements and calculations has been conducted to investigate the accuracy of the Dose Planning Method (DPM) Monte Carlo code for electron beam dose calculations in heterogeneous media. Measurements were made using 10 MeV and 50 MeV minimally scattered, uncollimated electron beams from a racetrack microtron. Source distributions for the Monte Carlo calculations were reconstructed from in-air ion chamber scans and then benchmarked against measurements in a homogeneous water phantom. The in-air spatial distributions were found to have FWHM of 4.7 cm and 1.3 cm, at 100 cm from the source, for the 10 MeV and 50 MeV beams respectively. Energy spectra for the electron beams were determined by simulating the components of the microtron treatment head using the code MCNP4B. Profile measurements were made using an ion chamber in a water phantom with slabs of lung or bone-equivalent materials submerged at various depths. DPM calculations are, on average, within 2% agreement with measurement for all geometries except for the 50 MeV incident on a 6 cm lung-equivalent slab. Measurements using approximately monoenergetic, 50 MeV, 'pencil-beam'-type electrons in heterogeneous media provide conditions for maximum electronic disequilibrium and hence present a stringent test of the code's electron transport physics; the agreement noted between calculation and measurement illustrates that the DPM code is capable of accurate dose calculation even under such conditions. (author)

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.

The self-force on a non-minimally coupled static scalar charge outside a Schwarzschild black hole

International Nuclear Information System (INIS)

Cho, Demian H J; Tsokaros, Antonios A; Wiseman, Alan G

2007-01-01

The finite part of the self-force on a static, non-minimally coupled scalar test charge outside a Schwarzschild black hole is zero. This result is determined from the work required to slowly raise or lower the charge through an infinitesimal distance. Unlike similar force calculations for minimally-coupled scalar charges or electric charges, we find that we must account for a flux of field energy that passes through the horizon and changes the mass and area of the black hole when the charge is displaced. This occurs even for an arbitrarily slow displacement of the non-minimally coupled scalar charge. For a positive coupling constant, the area of the hole increases when the charge is lowered and decreases when the charge is raised. The fact that the self-force vanishes for a static, non-minimally coupled scalar charge in Schwarzschild spacetime agrees with a simple prediction of the Quinn-Wald axioms. However, Zel'nikov and Frolov computed a non-vanishing self-force for a non-minimally coupled charge. Our method of calculation closely parallels the derivation of Zel'nikov and Frolov, and we show that their omission of this unusual flux is responsible for their (incorrect) result. When the flux is accounted for, the self-force vanishes. This correction eliminates a potential counter example to the Quinn-Wald axioms. The fact that the area of the black hole changes when the charge is displaced brings up two interesting questions that did not arise in similar calculations for static electric charges and minimally coupled scalar charges. (1) How can we reconcile a decrease in the area of the black hole horizon with the area theorem which concludes that δArea horizon ≥ 0? The key hypothesis of the area theorem is that the stress-energy tensor must satisfy a null-energy condition T αβ l α l β ≥ 0 for any null vector l α . We explicitly show that the stress-energy associated with a non-minimally coupled field does not satisfy this condition, and this violation of

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

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.

A Matrix Splitting Method for Composite Function Minimization

KAUST Repository

Yuan, Ganzhao

2016-12-07

Composite function minimization captures a wide spectrum of applications in both computer vision and machine learning. It includes bound constrained optimization and cardinality regularized optimization as special cases. This paper proposes and analyzes a new Matrix Splitting Method (MSM) for minimizing composite functions. It can be viewed as a generalization of the classical Gauss-Seidel method and the Successive Over-Relaxation method for solving linear systems in the literature. Incorporating a new Gaussian elimination procedure, the matrix splitting method achieves state-of-the-art performance. For convex problems, we establish the global convergence, convergence rate, and iteration complexity of MSM, while for non-convex problems, we prove its global convergence. Finally, we validate the performance of our matrix splitting method on two particular applications: nonnegative matrix factorization and cardinality regularized sparse coding. Extensive experiments show that our method outperforms existing composite function minimization techniques in term of both efficiency and efficacy.

A Matrix Splitting Method for Composite Function Minimization

KAUST Repository

Yuan, Ganzhao; Zheng, Wei-Shi; Ghanem, Bernard

2016-01-01

Composite function minimization captures a wide spectrum of applications in both computer vision and machine learning. It includes bound constrained optimization and cardinality regularized optimization as special cases. This paper proposes and analyzes a new Matrix Splitting Method (MSM) for minimizing composite functions. It can be viewed as a generalization of the classical Gauss-Seidel method and the Successive Over-Relaxation method for solving linear systems in the literature. Incorporating a new Gaussian elimination procedure, the matrix splitting method achieves state-of-the-art performance. For convex problems, we establish the global convergence, convergence rate, and iteration complexity of MSM, while for non-convex problems, we prove its global convergence. Finally, we validate the performance of our matrix splitting method on two particular applications: nonnegative matrix factorization and cardinality regularized sparse coding. Extensive experiments show that our method outperforms existing composite function minimization techniques in term of both efficiency and efficacy.

Non-minimally coupled varying constants quantum cosmologies

International Nuclear Information System (INIS)

Balcerzak, Adam

2015-01-01

We consider gravity theory with varying speed of light and varying gravitational constant. Both constants are represented by non-minimally coupled scalar fields. We examine the cosmological evolution in the near curvature singularity regime. We find that at the curvature singularity the speed of light goes to infinity while the gravitational constant vanishes. This corresponds to the Newton's Mechanics limit represented by one of the vertex of the Bronshtein-Zelmanov-Okun cube [1,2]. The cosmological evolution includes both the pre-big-bang and post-big-bang phases separated by the curvature singularity. We also investigate the quantum counterpart of the considered theory and find the probability of transition of the universe from the collapsing pre-big-bang phase to the expanding post-big-bang phase

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.

Description of the TREBIL, CRESSEX and STREUSL computer programs, that belongs to RALLY computer code pack for the analysis of reliability systems

International Nuclear Information System (INIS)

Fernandes Filho, T.L.

1982-11-01

The RALLY computer code pack (RALLY pack) is a set of computer codes destinate to the reliability of complex systems, aiming to a risk analysis. Three of the six codes, are commented, presenting their purpose, input description, calculation methods and results obtained with each one of those computer codes. The computer codes are: TREBIL, to obtain the fault tree logical equivalent; CRESSEX, to obtain the minimal cut and the punctual values of the non-reliability and non-availability of the system; and STREUSL, for the dispersion calculation of those values around the media. In spite of the CRESSEX, in its version available at CNEN, uses a little long method to obtain the minimal cut in an HB-CNEN system, the three computer programs show good results, mainly the STREUSL, which permits the simulation of various components. (E.G.) [pt

Self-duality in Maxwell-Chern-Simons theories with non minimal coupling with matter field

CERN Document Server

Chandelier, F; Masson, T; Wallet, J C

2000-01-01

We consider a general class of non-local MCS models whose usual minimal coupling to a conserved current is supplemented with a (non-minimal) magnetic Pauli-type coupling. We find that the considered models exhibit a self-duality whenever the magnetic coupling constant reaches a special value: the partition function is invariant under a set of transformations among the parameter space (the duality transformations) while the original action and its dual counterpart have the same form. The duality transformations have a structure similar to the one underlying self-duality of the (2+1)-dimensional Z sub n - Abelian Higgs model with Chern-Simons and bare mass term.

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)

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...

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.

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.

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

Stability of Einstein static universe in gravity theory with a non-minimal derivative coupling

Energy Technology Data Exchange (ETDEWEB)

Huang, Qihong [Hunan Normal University, Department of Physics and Synergetic Innovation Center for Quantum Effects and Applications, Changsha, Hunan (China); Zunyi Normal College, School of Physics and Electronic Science, Zunyi (China); Wu, Puxun [Hunan Normal University, Department of Physics and Synergetic Innovation Center for Quantum Effects and Applications, Changsha, Hunan (China); Peking University, Center for High Energy Physics, Beijing (China); Yu, Hongwei [Hunan Normal University, Department of Physics and Synergetic Innovation Center for Quantum Effects and Applications, Changsha, Hunan (China)

2018-01-15

The emergent mechanism provides a possible way to resolve the big-bang singularity problem by assuming that our universe originates from the Einstein static (ES) state. Thus, the existence of a stable ES solution becomes a very crucial prerequisite for the emergent scenario. In this paper, we study the stability of an ES universe in gravity theory with a non-minimal coupling between the kinetic term of a scalar field and the Einstein tensor. We find that the ES solution is stable under both scalar and tensor perturbations when the model parameters satisfy certain conditions, which indicates that the big-bang singularity can be avoided successfully by the emergent mechanism in the non-minimally kinetic coupled gravity. (orig.)

Stability of Einstein static universe in gravity theory with a non-minimal derivative coupling

Science.gov (United States)

Huang, Qihong; Wu, Puxun; Yu, Hongwei

2018-01-01

The emergent mechanism provides a possible way to resolve the big-bang singularity problem by assuming that our universe originates from the Einstein static (ES) state. Thus, the existence of a stable ES solution becomes a very crucial prerequisite for the emergent scenario. In this paper, we study the stability of an ES universe in gravity theory with a non-minimal coupling between the kinetic term of a scalar field and the Einstein tensor. We find that the ES solution is stable under both scalar and tensor perturbations when the model parameters satisfy certain conditions, which indicates that the big-bang singularity can be avoided successfully by the emergent mechanism in the non-minimally kinetic coupled gravity.

Modified cyanobacteria

Science.gov (United States)

Vermaas, Willem F J.

2014-06-17

Disclosed is a modified photoautotrophic bacterium comprising genes of interest that are modified in terms of their expression and/or coding region sequence, wherein modification of the genes of interest increases production of a desired product in the bacterium relative to the amount of the desired product production in a photoautotrophic bacterium that is not modified with respect to the genes of interest.

Job shop scheduling model for non-identic machine with fixed delivery time to minimize tardiness

Science.gov (United States)

Kusuma, K. K.; Maruf, A.

2016-02-01

Scheduling non-identic machines problem with low utilization characteristic and fixed delivery time are frequent in manufacture industry. This paper propose a mathematical model to minimize total tardiness for non-identic machines in job shop environment. This model will be categorized as an integer linier programming model and using branch and bound algorithm as the solver method. We will use fixed delivery time as main constraint and different processing time to process a job. The result of this proposed model shows that the utilization of production machines can be increase with minimal tardiness using fixed delivery time as constraint.

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

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

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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.

An Error-Entropy Minimization Algorithm for Tracking Control of Nonlinear Stochastic Systems with Non-Gaussian Variables

Energy Technology Data Exchange (ETDEWEB)

Liu, Yunlong; Wang, Aiping; Guo, Lei; Wang, Hong

2017-07-09

This paper presents an error-entropy minimization tracking control algorithm for a class of dynamic stochastic system. The system is represented by a set of time-varying discrete nonlinear equations with non-Gaussian stochastic input, where the statistical properties of stochastic input are unknown. By using Parzen windowing with Gaussian kernel to estimate the probability densities of errors, recursive algorithms are then proposed to design the controller such that the tracking error can be minimized. The performance of the error-entropy minimization criterion is compared with the mean-square-error minimization in the simulation results.

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

LENUS (Irish Health Repository)

Ivanov, Ivaylo P

2011-05-01

In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5\\' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5\\' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.

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.

Codes on the Klein quartic, ideals, and decoding

DEFF Research Database (Denmark)

Hansen, Johan P.

1987-01-01

descriptions as left ideals in the group-algebra GF(2^{3})[G]. This description allows for easy decoding. For instance, in the case of the single error correcting code of length21and dimension16with minimal distance3. decoding is obtained by multiplication with an idempotent in the group algebra.......A sequence of codes with particular symmetries and with large rates compared to their minimal distances is constructed over the field GF(2^{3}). In the sequence there is, for instance, a code of length 21 and dimension10with minimal distance9, and a code of length21and dimension16with minimal...... distance3. The codes are constructed from algebraic geometry using the dictionary between coding theory and algebraic curves over finite fields established by Goppa. The curve used in the present work is the Klein quartic. This curve has the maximal number of rational points over GF(2^{3})allowed by Serre...

nocoRNAc: Characterization of non-coding RNAs in prokaryotes

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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

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.

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)

Reconstruction of the biogeochemistry and ecology of photoautotrophs based on the nitrogen and carbon isotopic compositions of vanadyl porphyrins from Miocene siliceous sediments

Directory of Open Access Journals (Sweden)

Y. Kashiyama

2008-05-01

Full Text Available We determined both the nitrogen and carbon isotopic compositions of various vanadyl alkylporphyrins isolated from siliceous marine sediments of the Onnagawa Formation (middle Miocene, northeastern Japan to investigate the biogeochemistry and ecology of photoautotrophs living in the paleo-ocean. The distinctive isotopic signals support the interpretations of previous works that the origin of 17-nor-deoxophylloerythroetioporphyrin (DPEP is chlorophylls-c_1-3, whereas 8-nor-DPEP may have originated from chlorophylls-a₂ or b₂ or bacteriochlorophyll-a. Although DPEP and cycloheptanoDPEP are presumably derived from common precursory pigments, their isotopic compositions differed in the present study, suggesting that the latter represents a specific population within the photoautotrophic community. The average δ¹⁵N value for the entire photoautotrophic community is estimated to be –2 to +1‰ from the δ¹⁵N values of DPEP (–6.9 to –3.6‰; n=7, considering that the empirical isotopic relationships that the tetrapyrrole nuclei of chloropigments are depleted in ¹⁵N by ~4.8‰ and enriched in ¹³C by ~1.8‰ relative to the whole cells. This finding suggests that nitrogen utilized in the primary production was supplied mainly through N₂-fixation by diazotrophic cyanobacteria. Based on the δ¹³C values of DPEP (–17.9 to –15.6‰; n=7, we estimated isotopic fractionation associated with photosynthetic carbon fixation to be 8–14‰. This range suggests the importance of β-carboxylation and/or active transport of the carbon substrate, indicating in turn the substantial contribution of diazotrophic cyanobacteria to primary production. Based on the δ¹⁵N values of 17-nor-DPEP (–7.4 to –2.4‰ n=7, the δ¹⁵N range of chlorophylls-c-producing algae was estimated to be –3

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

QCD-resummation and non-minimal flavour-violation for supersymmetric particle production at hadron colliders

International Nuclear Information System (INIS)

Fuks, B.

2007-06-01

Cross sections for supersymmetric particles production at hadron colliders have been extensively studied in the past at leading order and also at next-to-leading order of perturbative QCD. The radiative corrections include large logarithms which have to be re-summed to all orders in the strong coupling constant in order to get reliable perturbative results. In this work, we perform a first and extensive study of the resummation effects for supersymmetric particle pair production at hadron colliders. We focus on Drell-Yan like slepton-pair and slepton-sneutrino associated production in minimal supergravity and gauge-mediated supersymmetry-breaking scenarios, and present accurate transverse-momentum and invariant-mass distributions, as well as total cross sections. In non-minimal supersymmetric models, novel effects of flavour violation may occur. In this case, the flavour structure in the squark sector cannot be directly deduced from the trilinear Yukawa couplings of the fermion and Higgs supermultiplets. We perform a precise numerical analysis of the experimentally allowed parameter space in the case of minimal supergravity scenarios with non-minimal flavour violation, looking for regions allowed by low-energy, electroweak precision, and cosmological data. Leading order cross sections for the production of squarks and gauginos at hadron colliders are implemented in a flexible computer program, allowing us to study in detail the dependence of these cross sections on flavour violation. (author)

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

Solar system tests for realistic f(T) models with non-minimal torsion-matter coupling

Energy Technology Data Exchange (ETDEWEB)

Lin, Rui-Hui; Zhai, Xiang-Hua; Li, Xin-Zhou [Shanghai Normal University, Shanghai United Center for Astrophysics (SUCA), Shanghai (China)

2017-08-15

In the previous paper, we have constructed two f(T) models with non-minimal torsion-matter coupling extension, which are successful in describing the evolution history of the Universe including the radiation-dominated era, the matter-dominated era, and the present accelerating expansion. Meantime, the significant advantage of these models is that they could avoid the cosmological constant problem of ΛCDM. However, the non-minimal coupling between matter and torsion will affect the tests of the Solar system. In this paper, we study the effects of the Solar system in these models, including the gravitation redshift, geodetic effect and perihelion precession. We find that Model I can pass all three of the Solar system tests. For Model II, the parameter is constrained by the uncertainties of the planets' estimated perihelion precessions. (orig.)

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.

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.

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.

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

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.

Stars of bosons with non-minimal energy-momentum tensor

International Nuclear Information System (INIS)

van der Bij, J.J.; Gleiser, M.

1987-02-01

We obtain spherically symmetric solutions for scalar fields with a non-minimal coupling ξ absolute value of phi 2 R to gravity. We find, for fields of mass m, maximum masses and number of particles of order M/sub max/ ∼ 0.73ξ/sup 1/2/ M/sub Planck/ 2 /m, and N/sub max/ ∼ 0.88ξ/sup 1/2/ M/sub Planck/ 2 /m 2 respectively, for large positive ξ. For large negative ξ we find, M/sub max/ ∼ 0.66 absolute value of ξ/sup 1/2/ M/sub Planck/ 2 /m, and N/sub max/ ∼ 0.72 absolute value of ξ/sup 1/2/ M/sub Planck/ 2 /m 2

Non-technical skills in minimally invasive surgery teams

DEFF Research Database (Denmark)

Gjeraa, Kirsten; Spanager, Lene; Konge, Lars

2016-01-01

BACKGROUND: Root cause analyses show that up to 70 % of adverse events are caused by human error. Strong non-technical skills (NTS) can prevent or reduce these errors, considerable numbers of which occur in the operating theatre. Minimally invasive surgery (MIS) requires manipulation of more...... complex equipment than open procedures, likely requiring a different set of NTS for each kind of team. The aims of this study were to identify the MIS teams' key NTS and investigate the effect of training and assessment of NTS on MIS teams. METHODS: The databases of PubMed, Cochrane Library, Embase, Psyc...... were included. All were observational studies without blinding, and they differed in aims, types of evaluation, and outcomes. Only two studies evaluated patient outcomes other than operative time, and overall, the studies' quality of evidence was low. Different communication types were encountered...

Brassinosteriod Insensitive 2 (BIN2) acts as a downstream effector of the Target of Rapamycin (TOR) signaling pathway to regulate photoautotrophic growth in Arabidopsis.

Science.gov (United States)

Xiong, Fangjie; Zhang, Rui; Meng, Zhigang; Deng, Kexuan; Que, Yumei; Zhuo, Fengping; Feng, Li; Guo, Sundui; Datla, Raju; Ren, Maozhi

2017-01-01

The components of the target of rapamycin (TOR) signaling pathway have been well characterized in heterotrophic organisms from yeast to humans. However, because of rapamycin insensitivity, embryonic lethality in tor null mutants and a lack of reliable ways of detecting TOR protein kinase in higher plants, the key players upstream and downstream of TOR remain largely unknown in plants. Using engineered rapamycin-sensitive Binding Protein 12-2 (BP12-2) plants, the present study showed that combined treatment with rapamycin and active-site TOR inhibitors (asTORis) results in synergistic inhibition of TOR activity and plant growth in Arabidopsis. Based on this system, we revealed that TOR signaling plays a crucial role in modulating the transition from heterotrophic to photoautotrophic growth in Arabidopsis. Ribosomal protein S6 kinase 2 (S6K2) was identified as a direct downstream target of TOR, and the growth of TOR-suppressed plants could be rescued by up-regulating S6K2. Systems, genetic, and biochemical analyses revealed that Brassinosteriod Insensitive 2 (BIN2) acts as a novel downstream effector of S6K2, and the phosphorylation of BIN2 depends on TOR-S6K2 signaling in Arabidopsis. By combining pharmacological with genetic and biochemical approaches, we determined that the TOR-S6K2-BIN2 signaling pathway plays important roles in regulating the photoautotrophic growth of Arabidopsis. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

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....

Kinetically modified non-minimal inflation with exponential frame function

Energy Technology Data Exchange (ETDEWEB)

Pallis, C. [University of Cyprus, Department of Physics, Nicosia (Cyprus)

2017-09-15

We consider supersymmetric (SUSY) and non-SUSY models of chaotic inflation based on the φ{sup n} potential with n = 2 or 4. We show that the coexistence of an exponential non-minimal coupling to gravity f{sub R} = e{sup c{sub R}φ{sup p}} with a kinetic mixing of the form f{sub K} = c{sub K}f{sub R}{sup m} can accommodate inflationary observables favored by the Planck and Bicep2/Keck Array results for p = 1 and 2, 1 ≤ m ≤ 15 and 2.6 x 10{sup -3} ≤ r{sub RK} = c{sub R}/c{sub K}{sup p/2} ≤ 1, where the upper limit is not imposed for p = 1. Inflation is of hilltop type and it can be attained for subplanckian inflaton values with the corresponding effective theories retaining the perturbative unitarity up to the Planck scale. The supergravity embedding of these models is achieved employing two chiral gauge singlet supefields, a monomial superpotential and several (semi)logarithmic or semi-polynomial Kaehler potentials. (orig.)

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.

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

Minimizing human error in radiopharmaceutical preparation and administration via a bar code-enhanced nuclear pharmacy management system.

Science.gov (United States)

Hakala, John L; Hung, Joseph C; Mosman, Elton A

2012-09-01

The objective of this project was to ensure correct radiopharmaceutical administration through the use of a bar code system that links patient and drug profiles with on-site information management systems. This new combined system would minimize the amount of manual human manipulation, which has proven to be a primary source of error. The most common reason for dosing errors is improper patient identification when a dose is obtained from the nuclear pharmacy or when a dose is administered. A standardized electronic transfer of information from radiopharmaceutical preparation to injection will further reduce the risk of misadministration. Value stream maps showing the flow of the patient dose information, as well as potential points of human error, were developed. Next, a future-state map was created that included proposed corrections for the most common critical sites of error. Transitioning the current process to the future state will require solutions that address these sites. To optimize the future-state process, a bar code system that links the on-site radiology management system with the nuclear pharmacy management system was proposed. A bar-coded wristband connects the patient directly to the electronic information systems. The bar code-enhanced process linking the patient dose with the electronic information reduces the number of crucial points for human error and provides a framework to ensure that the prepared dose reaches the correct patient. Although the proposed flowchart is designed for a site with an in-house central nuclear pharmacy, much of the framework could be applied by nuclear medicine facilities using unit doses. An electronic connection between information management systems to allow the tracking of a radiopharmaceutical from preparation to administration can be a useful tool in preventing the mistakes that are an unfortunate reality for any facility.

Non-minimally coupled tachyonic inflation in warped string background

International Nuclear Information System (INIS)

Chingangbam, Pravabati; Panda, Sudhakar; Deshamukhya, Atri

2005-01-01

We show that the non-minimal coupling of tachyon field to the scalar curvature, as proposed by Piao et al, with the chosen coupling parameter does not produce the effective potential where the tachyon field can roll down from T=0 to large T along the slope of the potential. We find a correct choice of the parameters which ensures this requirement and support slow-roll inflation. However, we find that the cosmological parameter found from the analysis of the theory are not in the range obtained from observations. We then invoke warped compactification and varying dilaton field over the compact manifold, as proposed by Raeymaekers, to show that in such a setup the observed parameter space can be ensured. (author)

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

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.

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

Quick response codes in Orthodontics

Directory of Open Access Journals (Sweden)

Moidin Shakil

2015-01-01

Full Text Available Quick response (QR code codes are two-dimensional barcodes, which encodes for a large amount of information. QR codes in Orthodontics are an innovative approach in which patient details, radiographic interpretation, and treatment plan can be encoded. Implementing QR code in Orthodontics will save time, reduces paperwork, and minimizes manual efforts in storage and retrieval of patient information during subsequent stages of treatment.

Scanning Electron Microscope Calibration Using a Multi-Image Non-Linear Minimization Process

Science.gov (United States)

Cui, Le; Marchand, Éric

2015-04-01

A scanning electron microscope (SEM) calibrating approach based on non-linear minimization procedure is presented in this article. A part of this article has been published in IEEE International Conference on Robotics and Automation (ICRA), 2014. . Both the intrinsic parameters and the extrinsic parameters estimations are achieved simultaneously by minimizing the registration error. The proposed approach considers multi-images of a multi-scale calibration pattern view from different positions and orientations. Since the projection geometry of the scanning electron microscope is different from that of a classical optical sensor, the perspective projection model and the parallel projection model are considered and compared with distortion models. Experiments are realized by varying the position and the orientation of a multi-scale chessboard calibration pattern from 300× to 10,000×. The experimental results show the efficiency and the accuracy of this approach.

Surface acoustic wave coding for orthogonal frequency coded devices

Science.gov (United States)

Malocha, Donald (Inventor); Kozlovski, Nikolai (Inventor)

2011-01-01

Methods and systems for coding SAW OFC devices to mitigate code collisions in a wireless multi-tag system. Each device producing plural stepped frequencies as an OFC signal with a chip offset delay to increase code diversity. A method for assigning a different OCF to each device includes using a matrix based on the number of OFCs needed and the number chips per code, populating each matrix cell with OFC chip, and assigning the codes from the matrix to the devices. The asynchronous passive multi-tag system includes plural surface acoustic wave devices each producing a different OFC signal having the same number of chips and including a chip offset time delay, an algorithm for assigning OFCs to each device, and a transceiver to transmit an interrogation signal and receive OFC signals in response with minimal code collisions during transmission.

Scheduling Non-Preemptible Jobs to Minimize Peak Demand

Directory of Open Access Journals (Sweden)

Sean Yaw

2017-10-01

Full Text Available This paper examines an important problem in smart grid energy scheduling; peaks in power demand are proportionally more expensive to generate and provision for. The issue is exacerbated in local microgrids that do not benefit from the aggregate smoothing experienced by large grids. Demand-side scheduling can reduce these peaks by taking advantage of the fact that there is often flexibility in job start times. We focus attention on the case where the jobs are non-preemptible, meaning once started, they run to completion. The associated optimization problem is called the peak demand minimization problem, and has been previously shown to be NP-hard. Our results include an optimal fixed-parameter tractable algorithm, a polynomial-time approximation algorithm, as well as an effective heuristic that can also be used in an online setting of the problem. Simulation results show that these methods can reduce peak demand by up to 50% versus on-demand scheduling for household power jobs.

Development of the DTNTES code

International Nuclear Information System (INIS)

Ortega Prieto, P.; Morales Dorado, M.D.; Alonso Santos, A.

1987-01-01

The DTNTES code has been developed in the Department of Nuclear Technology of the Polytechnical University in Madrid as a part of the Research Program on Quantitative Risk Analysis. DTNTES code calculates several time-dependent probabilistic characteristics of basic events, minimal cut sets and the top event of a fault tree. The code assumes that basic events are statistically independent, and they have failure and repair distributions. It computes the minimal cut upper bound approach for the top event unavailability, and the time-dependent unreliability of the top event by means of different methods, selected by the user. These methods are: expected number of system failures, failure rate, Barlow-Proschan bound, steady-state upper bound, and T* method. (author)

Toxicity of the fluoroquinolone antibiotics enrofloxacin and ciprofloxacin to photoautotrophic aquatic organisms.

Science.gov (United States)

Ebert, Ina; Bachmann, Jean; Kühnen, Ute; Küster, Anette; Kussatz, Carola; Maletzki, Dirk; Schlüter, Christoph

2011-12-01

The present study investigated the growth inhibition effect of the fluoroquinolone antibiotics enrofloxacin and ciprofloxacin on four photoautotrophic aquatic species: the freshwater microalga Desmodesmus subspicatus, the cyanobacterium Anabaena flos-aquae, the monocotyledonous macrophyte Lemna minor, and the dicotyledonous macrophyte Myriophyllum spicatum. Both antibiotics, which act by inhibiting the bacterial DNA gyrase, demonstrated high toxicity to A. flos-aquae and L. minor and moderate to slight toxicity to D. subspicatus and M. spicatum. The cyanobacterium was the most sensitive species with median effective concentration (EC50) values of 173 and 10.2 µg/L for enrofloxacin and ciprofloxacin, respectively. Lemna minor proved to be similarly sensitive, with EC50 values of 107 and 62.5 µg/L for enrofloxacin and ciprofloxacin, respectively. While enrofloxacin was more toxic to green algae, ciprofloxacin was more toxic to cyanobacteria. Calculated EC50s for D. subspicatus were 5,568 µg/L and >8,042 µg/L for enrofloxacin and ciprofloxacin, respectively. These data, as well as effect data from the literature, were compared with predicted and reported environmental concentrations. For two of the four species, a risk was identified at ciprofloxacin concentrations found in surface waters, sewage treatment plant influents and effluents, as well as in hospital effluents. For ciprofloxacin the results of the present study indicate a risk even at the predicted environmental concentration. In contrast, for enrofloxacin no risk was identified at predicted and measured concentrations. Copyright © 2011 SETAC.

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.

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.

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.

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

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.

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.

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.

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.

A non-minimally coupled quintom dark energy model on the warped DGP brane

International Nuclear Information System (INIS)

Nozari, K; Azizi, T; Setare, M R; Behrouz, N

2009-01-01

We construct a quintom dark energy model with two non-minimally coupled scalar fields, one quintessence and the other phantom field, confined to the warped Dvali-Gabadadze-Porrati (DGP) brane. We show that this model accounts for crossing of the phantom divide line in appropriate subspaces of the model parameter space. This crossing occurs for both normal and self-accelerating branches of this DGP-inspired setup.

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...

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)

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.)

Stars of bosons with non-minimal energy-momentum tensor

International Nuclear Information System (INIS)

Van der Bij, J.J.; Gleiser, M.

1987-01-01

We obtain spherically symmetric solutions for scalar fields with a non-minimal coupling ξvertical strokeφvertical stroke 2 R to gravity. We find, for zeronode fields of mass m, maximum masses and number of particles of order M max ≅ 0.73ξ 1/2 M Planck 2 /m, and N max ≅ 0.88ξ 1/2 x M Planck 2 /m 2 respectively, for large positive ξ. For large negative ξ we find M max ≅ 0.66vertical strokeξvertical stroke 1/2 M Planck 2 /m, and N max ≅ 0.72vertical strokeξvertical stroke 1/2 x M Planck 2 /m 2 . We also calculate the critical mass and particle number for higher radial nodes of the scalar field and find that both quantities grow approximately linearly for large node number n. (orig.)

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.

Non-minimal CW inflation, electroweak symmetry breaking and the 750 GeV anomaly

Energy Technology Data Exchange (ETDEWEB)

Marzola, L. [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia); Laboratory of Theoretical Physics, Institute of Physics, University of Tartu,Ravila 14c, 50411 Tartu (Estonia); Racioppi, A. [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia); Raidal, M. [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia); Laboratory of Theoretical Physics, Institute of Physics, University of Tartu,Ravila 14c, 50411 Tartu (Estonia); Urban, F.R.; Veermäe, H. [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia)

2016-03-29

We study whether the hinted 750 GeV resonance at the LHC can be a Coleman-Weinberg inflaton which is non-minimally coupled to gravity. Since the inflaton must couple to new charged and coloured states to reproduce the LHC diphoton signature, the same interaction can generate its effective potential and trigger the electroweak symmetry breaking via the portal coupling to the Higgs boson. This inflationary scenario predicts a lower bound on the tensor-to-scalar ratio of r≳0.006, where the minimal value corresponds to the measured spectral index n{sub s}≃0.97. However, we find that the compatibility with the LHC diphoton signal requires exotic new physics at energy scales accessible at the LHC. We study and quantify the properties of the predicted exotic particles.

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.

Early Universe Higgs dynamics in the presence of the Higgs-inflaton and non-minimal Higgs-gravity couplings

Energy Technology Data Exchange (ETDEWEB)

Ema, Yohei [Department of Physics, Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 (Japan); Karčiauskas, Mindaugas [University of Jyväskylä, Department of Physics, P.O. Box 35 (YFL), FI-40014, Jyväskylä (Finland); Lebedev, Oleg; Zatta, Marco, E-mail: ema@hep-th.phys.s.u-tokyo.ac.jp, E-mail: mindaugas.m.karciauskas@jyu.fi, E-mail: oleg.lebedev@helsinki.fi, E-mail: marco.zatta@helsinki.fi [University of Helsinki and Helsinki Institute of Physics, P.O. Box 64, FI-00014, Helsinki (Finland)

2017-06-01

Apparent metastability of the electroweak vacuum poses a number of cosmological questions. These concern evolution of the Higgs field to the current vacuum, and its stability during and after inflation. Higgs-inflaton and non-minimal Higgs-gravity interactions can make a crucial impact on these considerations potentially solving the problems. In this work, we allow for these couplings to be present simultaneously and study their interplay. We find that different combinations of the Higgs-inflaton and non-minimal Higgs-gravity couplings induce effective Higgs mass during and after inflation. This crucially affects the Higgs stability considerations during preheating. In particular, a wide range of the couplings leading to stable solutions becomes allowed.

Concatenated coding systems employing a unit-memory convolutional code and a byte-oriented decoding algorithm

Science.gov (United States)

Lee, L.-N.

1977-01-01

Concatenated coding systems utilizing a convolutional code as the inner code and a Reed-Solomon code as the outer code are considered. In order to obtain very reliable communications over a very noisy channel with relatively modest coding complexity, it is proposed to concatenate a byte-oriented unit-memory convolutional code with an RS outer code whose symbol size is one byte. It is further proposed to utilize a real-time minimal-byte-error probability decoding algorithm, together with feedback from the outer decoder, in the decoder for the inner convolutional code. The performance of the proposed concatenated coding system is studied, and the improvement over conventional concatenated systems due to each additional feature is isolated.

Constraining N=1 supergravity inflation with non-minimal Kähler operators using δN formalism

International Nuclear Information System (INIS)

Choudhury, Sayantan

2014-01-01

In this paper I provide a general framework based on δN formalism to study the features of unavoidable higher dimensional non-renormalizable Kähler operators for N=1 supergravity (SUGRA) during primordial inflation from the combined constraint on non-Gaussianity, sound speed and CMB dipolar asymmetry as obtained from the recent Planck data. In particular I study the nonlinear evolution of cosmological perturbations on large scales which enables us to compute the curvature perturbation, ζ, without solving the exact perturbed field equations. Further I compute the non-Gaussian parameters f NL , τ NL and g NL for local type of non-Gaussianities and CMB dipolar asymmetry parameter, A CMB , using the δN formalism for a generic class of sub-Planckian models induced by the Hubble-induced corrections for a minimal supersymmetric D-flat direction where inflation occurs at the point of inflection within the visible sector. Hence by using multi parameter scan I constrain the non-minimal couplings appearing in non-renormalizable Kähler operators within, O(1), for the speed of sound, 0.02≤c s ≤1, and tensor to scalar, 10 −22 ≤r ⋆ ≤0.12. Finally applying all of these constraints I will fix the lower as well as the upper bound of the non-Gaussian parameters within, O(1−5)≤f NL ≤8.5, O(75−150)≤τ NL ≤2800 and O(17.4−34.7)≤g NL ≤648.2, and CMB dipolar asymmetry parameter within the range, 0.05≤A CMB ≤0.09

Constraining N=1 supergravity inflation with non-minimal Kähler operators using δN formalism

Energy Technology Data Exchange (ETDEWEB)

Choudhury, Sayantan [Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700 108 (India)

2014-04-15

In this paper I provide a general framework based on δN formalism to study the features of unavoidable higher dimensional non-renormalizable Kähler operators for N=1 supergravity (SUGRA) during primordial inflation from the combined constraint on non-Gaussianity, sound speed and CMB dipolar asymmetry as obtained from the recent Planck data. In particular I study the nonlinear evolution of cosmological perturbations on large scales which enables us to compute the curvature perturbation, ζ, without solving the exact perturbed field equations. Further I compute the non-Gaussian parameters f{sub NL} , τ{sub NL} and g{sub NL} for local type of non-Gaussianities and CMB dipolar asymmetry parameter, A{sub CMB}, using the δN formalism for a generic class of sub-Planckian models induced by the Hubble-induced corrections for a minimal supersymmetric D-flat direction where inflation occurs at the point of inflection within the visible sector. Hence by using multi parameter scan I constrain the non-minimal couplings appearing in non-renormalizable Kähler operators within, O(1), for the speed of sound, 0.02≤c{sub s}≤1, and tensor to scalar, 10{sup −22}≤r{sub ⋆}≤0.12. Finally applying all of these constraints I will fix the lower as well as the upper bound of the non-Gaussian parameters within, O(1−5)≤f{sub NL}≤8.5, O(75−150)≤τ{sub NL}≤2800 and O(17.4−34.7)≤g{sub NL}≤648.2, and CMB dipolar asymmetry parameter within the range, 0.05≤A{sub CMB}≤0.09.

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

Directory of Open Access Journals (Sweden)

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.

Quasi-cyclic unit memory convolutional codes

DEFF Research Database (Denmark)

Justesen, Jørn; Paaske, Erik; Ballan, Mark

1990-01-01

Unit memory convolutional codes with generator matrices, which are composed of circulant submatrices, are introduced. This structure facilitates the analysis of efficient search for good codes. Equivalences among such codes and some of the basic structural properties are discussed. In particular......, catastrophic encoders and minimal encoders are characterized and dual codes treated. Further, various distance measures are discussed, and a number of good codes, some of which result from efficient computer search and some of which result from known block codes, are presented...

TMRBAR power balance code for tandem mirror reactors

International Nuclear Information System (INIS)

Blackkfield, D.T.; Campbell, R.; Fenstermacher, M.; Bulmer, R.; Perkins, L.; Peng, Y.K.M.; Reid, R.L.; Wu, K.F.

1984-01-01

A revised version of the tandem mirror multi-point code TMRBAR developed at LLNL has been used to examine various reactor designs using MARS-like ''c'' coils. We solve 14 to 16 non-linear equations to obtain the densities, temperatures, plasma potential and magnetic field on axis at the cardinal points. Since ICRH, ECRH, and neutral beams may be used to stabilize the central cell, various combinations of rf and neutral beam powers may satisfy the physics. To select a desired set of physics parameters, we use nonlinear optimization techniques. Whit these routines, we minimize or maximize a physics variable subject to the physics constraints being satisfied. For example, for a given fusion power we may find the minimum length needed to have an ignited central cell or the maximum fusion Q. Finally, we have coupled this physics model to the LLNL magnetics-MHD code. This code runs the EFFI magnetic field generator and uses TEBASCO to calculate 1-D MHD equilibria and stability

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

Directory of Open Access Journals (Sweden)

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.

The in-core fuel management code system for VVER reactors

International Nuclear Information System (INIS)

Cada, R.; Krysl, V.; Mikolas, P.; Sustek, J.; Svarny, J.

2004-01-01

The structure and methodology of a fuel management system for NPP VVER 1000 (NPP Temelin) and VVER 440 (NPP Dukovany) is described. It is under development in SKODA JS a.s. and is followed by practical applications. The general objectives of the system are maximization of end of cycle reactivity, the minimization of fresh fuel inventory for the minimization of fed enrichment and minimization of burnable poisons (BPs) inventory. They are also safety related constraints in witch minimization of power peaking plays a dominant role. General structure of the system consists in preparation of input data for macrocode calculation, algorithms (codes) for optimization of fuel loading, calculation of fuel enrichment and BPs assignment. At present core loading can be calculated (optimized) by Tabu search algorithm (code ATHENA), genetic algorithm (code Gen1) and hybrid algorithm - simplex procedure with application of Tabu search algorithm on binary shuffling (code OPAL B ). Enrichment search is realized by the application of simplex algorithm (OPAL B code) and BPs assignment by module BPASS and simplex algorithm in OPAL B code. Calculations of the real core loadings are presented and a comparison of different optimization methods is provided. (author)

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%

Minimal Composite Inflation

DEFF Research Database (Denmark)

Channuie, Phongpichit; Jark Joergensen, Jakob; Sannino, Francesco

2011-01-01

We investigate models in which the inflaton emerges as a composite field of a four dimensional, strongly interacting and nonsupersymmetric gauge theory featuring purely fermionic matter. We show that it is possible to obtain successful inflation via non-minimal coupling to gravity, and that the u......We investigate models in which the inflaton emerges as a composite field of a four dimensional, strongly interacting and nonsupersymmetric gauge theory featuring purely fermionic matter. We show that it is possible to obtain successful inflation via non-minimal coupling to gravity...

Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

Science.gov (United States)

Santos, José; Monteagudo, Ángel

2017-03-27

The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.

Gingival recession in smokers and non-smokers with minimal periodontal disease.

Science.gov (United States)

Müller, Hans-Peter; Stadermann, Sabine; Heinecke, Achim

2002-02-01

Smoking is a major risk factor for destructive periodontal disease. There is limited information with regard to effects of smoking in subjects with minimal periodontal destruction. The aim of the present investigation was to assess the development of gingival recession in young adult smokers and non-smokers. 61 systemically healthy young adults, 19 to 30 years of age completed the final examination. 30 volunteers smoked at least 20 cigarettes per day, whereas 31 subjects were non-smokers. Clinical periodontal conditions were assessed 4x within a time period of 6 months. Site-specific analyses considering the correlated structure of data were performed. At the outset, 50% of subjects presented with gingival recession at 1 or more sites. There was no significant difference in the prevalence of gingival recession between non-smokers and smokers. Severe recession in excess of 2 mm affected about 23% non-smokers but only 7% smokers. Some further gingival recession developed during the 6-month observation period. In a multivariate logistic regression analysis, the risk for recession development appeared not to be influenced by smoking status after adjusting for periodontal probing depth, recession at baseline, tooth brushing frequency, gender, jaw, tooth type and site. Present data did not support the hypothesis that smokers are at an increased risk for the development of gingival recession.

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....

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...

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.

Effect of non-local equilibrium on minimal thermal resistance porous layered systems

International Nuclear Information System (INIS)

Leblond, Genevieve; Gosselin, Louis

2008-01-01

In this paper, the cooling of a heat-generating surface by a stacking of porous media (e.g., metallic foam) through which fluid flows parallel to the surface is considered. A two-temperature model is proposed to account for non-local thermal equilibrium (non-LTE). A scale analysis is performed to determine temperatures profiles in the boundary layer regime. The hot spot temperature is minimized with respect to the three design variables of each layer: porosity, pore diameter, and material. Global cost and mass are constrained. The optimization is performed with a hybrid genetic algorithm (GA) including local search to enhance convergence and repeatability. Results demonstrate that the optimized stacks do not operate in LTE. Therefore, we show that assuming LTE might result in underestimation of the hot spot temperature, and into different final designs as well

Minimal string theories and integrable hierarchies

Science.gov (United States)

Iyer, Ramakrishnan

Well-defined, non-perturbative formulations of the physics of string theories in specific minimal or superminimal model backgrounds can be obtained by solving matrix models in the double scaling limit. They provide us with the first examples of completely solvable string theories. Despite being relatively simple compared to higher dimensional critical string theories, they furnish non-perturbative descriptions of interesting physical phenomena such as geometrical transitions between D-branes and fluxes, tachyon condensation and holography. The physics of these theories in the minimal model backgrounds is succinctly encoded in a non-linear differential equation known as the string equation, along with an associated hierarchy of integrable partial differential equations (PDEs). The bosonic string in (2,2m-1) conformal minimal model backgrounds and the type 0A string in (2,4 m) superconformal minimal model backgrounds have the Korteweg-de Vries system, while type 0B in (2,4m) backgrounds has the Zakharov-Shabat system. The integrable PDE hierarchy governs flows between backgrounds with different m. In this thesis, we explore this interesting connection between minimal string theories and integrable hierarchies further. We uncover the remarkable role that an infinite hierarchy of non-linear differential equations plays in organizing and connecting certain minimal string theories non-perturbatively. We are able to embed the type 0A and 0B (A,A) minimal string theories into this single framework. The string theories arise as special limits of a rich system of equations underpinned by an integrable system known as the dispersive water wave hierarchy. We find that there are several other string-like limits of the system, and conjecture that some of them are type IIA and IIB (A,D) minimal string backgrounds. We explain how these and several other string-like special points arise and are connected. In some cases, the framework endows the theories with a non

Users' manual for fault tree analysis code: CUT-TD

International Nuclear Information System (INIS)

Watanabe, Norio; Kiyota, Mikio.

1992-06-01

The CUT-TD code has been developed to find minimal cut sets for a given fault tree and to calculate the occurrence probability of its top event. This code uses an improved top-down algorithm which can enhance the efficiency in deriving minimal cut sets. The features in processing techniques incorporated into CUT-TD are as follows: (1) Consecutive OR gates or consecutive AND gates can be coalesced into a single gate. As a result, this processing directly produces cut sets for the redefined single gate with each gate not being developed. (2) The independent subtrees are automatically identified and their respective cut sets are separately found to enhance the efficiency in processing. (3) The minimal cut sets can be obtained for the top event of a fault tree by combining their respective minimal cut sets for several gates of the fault tree. (4) The user can reduce the computing time for finding minimal cut sets and control the size and significance of cut sets by inputting a minimum probability cut off and/or a maximum order cut off. (5) The user can select events that need not to be further developed in the process of obtaining minimal cut sets. This option can reduce the number of minimal cut sets, save the computing time and assists the user in reviewing the result. (6) Computing time is monitored by the CUT-TD code so that it can prevent the running job from abnormally ending due to excessive CPU time and produce an intermediate result. The CUT-TD code has the ability to restart the calculation with use of the intermediate result. This report provides a users' manual for the CUT-TD code. (author)

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.

Code Calibration as a Decision Problem

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard; Kroon, I. B.; Faber, Michael Havbro

1993-01-01

Calibration of partial coefficients for a class of structures where no code exists is considered. The partial coefficients are determined such that the difference between the reliability for the different structures in the class considered and a target reliability level is minimized. Code...... calibration on a decision theoretical basis is discussed. Results from code calibration for rubble mound breakwater designs are shown....

Erosion corrosion in power plant piping systems - Calculation code for predicting wall thinning

International Nuclear Information System (INIS)

Kastner, W.; Erve, M.; Henzel, N.; Stellwag, B.

1990-01-01

Extensive experimental and theoretical investigations have been performed to develop a calculation code for wall thinning due to erosion corrosion in power plant piping systems. The so-called WATHEC code can be applied to single-phase water flow as well as to two-phase water/steam flow. Only input data which are available to the operator of the plant are taken into consideration. Together with a continuously updated erosion corrosion data base the calculation code forms one element of a weak point analysis for power plant piping systems which can be applied to minimize material loss due to erosion corrosion, reduce non-destructive testing and curtail monitoring programs for piping systems, recommend life-extending measures. (author). 12 refs, 17 figs

Anisotropic inflation with a non-minimally coupled electromagnetic field to gravity

Science.gov (United States)

Adak, Muzaffer; Akarsu, Özgür; Dereli, Tekin; Sert, Özcan

2017-11-01

We consider the non-minimal model of gravity in Y(R) F2-form. We investigate a particular case of the model, for which the higher order derivatives are eliminated but the scalar curvature R is kept to be dynamical via the constraint YRFmnFmn =-2/κ2. The effective fluid obtained can be represented by interacting electromagnetic field and vacuum depending on Y(R), namely, the energy density of the vacuum tracks R while energy density of the conventional electromagnetic field is dynamically scaled with the factor Y(R)/2. We give exact solutions for anisotropic inflation by assuming the volume scale factor of the Universe exhibits a power-law expansion. The directional scale factors do not necessarily exhibit power-law expansion, which would give rise to a constant expansion anisotropy, but expand non-trivially and give rise to a non-monotonically evolving expansion anisotropy that eventually converges to a non-zero constant. Relying on this fact, we discuss the anisotropic e-fold during the inflation by considering observed scale invariance in CMB and demanding the Universe to undergo the same amount of e-folds in all directions. We calculate the residual expansion anisotropy at the end of inflation, though as a result of non-monotonic behaviour of expansion anisotropy all the axes of the Universe undergo the same of amount of e-folds by the end of inflation. We also discuss the generation of the modified electromagnetic field during the first few e-folds of the inflation and its persistence against to the vacuum till end of inflation.

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.

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.

Inverse modelling and pulsating torque minimization of salient pole non-sinusoidal synchronous machines

Energy Technology Data Exchange (ETDEWEB)

Ait-gougam, Y.; Ibtiouen, R.; Touhami, O. [Laboratoire de Recherche en Electrotechnique, Ecole Nationale Polytechnique, BP 182, El-Harrach 16200 (Algeria); Louis, J.-P.; Gabsi, M. [Systemes et Applications des Technologies de l' Information et de l' Energie (SATIE), CNRS UMR 8029, Ecole Normale Superieure de Cachan, 61 Avenue du President Wilson, 94235 Cachan Cedex (France)

2008-01-15

Sinusoidal motor's mathematical models are usually obtained using classical d-q transformation in the case of salient pole synchronous motors having sinusoidal field distribution. In this paper, a new inverse modelling for synchronous motors is presented. This modelling is derived from the properties of constant torque curves in the Concordia's reference frame. It takes into account the non-sinusoidal field distribution; EMF, self and mutual inductances having non-sinusoidal variations with respect to the angular rotor position. Both copper losses and torque ripples are minimized by adapted currents waveforms calculated from this model. Experimental evaluation was carried out on a DSP-controlled PMSM drive platform. Test results obtained demonstrate the effectiveness of the proposed method in reducing torque ripple. (author)

Non-unitary neutrino mixing and CP violation in the minimal inverse seesaw model

International Nuclear Information System (INIS)

Malinsky, Michal; Ohlsson, Tommy; Xing, Zhi-zhong; Zhang He

2009-01-01

We propose a simplified version of the inverse seesaw model, in which only two pairs of the gauge-singlet neutrinos are introduced, to interpret the observed neutrino mass hierarchy and lepton flavor mixing at or below the TeV scale. This 'minimal' inverse seesaw scenario (MISS) is technically natural and experimentally testable. In particular, we show that the effective parameters describing the non-unitary neutrino mixing matrix are strongly correlated in the MISS, and thus, their upper bounds can be constrained by current experimental data in a more restrictive way. The Jarlskog invariants of non-unitary CP violation are calculated, and the discovery potential of such new CP-violating effects in the near detector of a neutrino factory is discussed.

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.

The simplest non-minimal matter-geometry coupling in the f(R, T) cosmology

Energy Technology Data Exchange (ETDEWEB)

Moraes, P.H.R.S. [ITA - Instituto Tecnologico de Aeronautica, Departamento de Fisica, Sao Paulo (Brazil); Sahoo, P.K. [Birla Institute of Technology and Science-Pilani, Department of Mathematics, Hyderabad (India)

2017-07-15

f(R, T) gravity is an extended theory of gravity in which the gravitational action contains general terms of both the Ricci scalar R and the trace of the energy-momentum tensor T. In this way, f(R, T) models are capable of describing a non-minimal coupling between geometry (through terms in R) and matter (through terms in T). In this article we construct a cosmological model from the simplest non-minimal matter-geometry coupling within the f(R, T) gravity formalism, by means of an effective energy-momentum tensor, given by the sum of the usual matter energy-momentum tensor with a dark energy contribution, with the latter coming from the matter-geometry coupling terms. We apply the energy conditions to our solutions in order to obtain a range of values for the free parameters of the model which yield a healthy and well-behaved scenario. For some values of the free parameters which are submissive to the energy conditions application, it is possible to predict a transition from a decelerated period of the expansion of the universe to a period of acceleration (dark energy era). We also propose further applications of this particular case of the f(R, T) formalism in order to check its reliability in other fields, rather than cosmology. (orig.)

The simplest non-minimal matter-geometry coupling in the f(R, T) cosmology

International Nuclear Information System (INIS)

Moraes, P.H.R.S.; Sahoo, P.K.

2017-01-01

f(R, T) gravity is an extended theory of gravity in which the gravitational action contains general terms of both the Ricci scalar R and the trace of the energy-momentum tensor T. In this way, f(R, T) models are capable of describing a non-minimal coupling between geometry (through terms in R) and matter (through terms in T). In this article we construct a cosmological model from the simplest non-minimal matter-geometry coupling within the f(R, T) gravity formalism, by means of an effective energy-momentum tensor, given by the sum of the usual matter energy-momentum tensor with a dark energy contribution, with the latter coming from the matter-geometry coupling terms. We apply the energy conditions to our solutions in order to obtain a range of values for the free parameters of the model which yield a healthy and well-behaved scenario. For some values of the free parameters which are submissive to the energy conditions application, it is possible to predict a transition from a decelerated period of the expansion of the universe to a period of acceleration (dark energy era). We also propose further applications of this particular case of the f(R, T) formalism in order to check its reliability in other fields, rather than cosmology. (orig.)

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.)

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)

Minimally Adhesive, Advanced Non-toxic Coatings of Dendrimeric Catalysts in Sol-Gel Matrices

Science.gov (United States)

2015-10-19

Catalysts in Sol -Gel Matrices 5a. CONTRACT NUMBER 5b. GRANT NUMBER N00014-09-1-0217 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Detty, Michael R. 5d...Technical Report for ONR N00014-09-1-0217 Minimally Adhesive, Advanced Non-toxic Coatings of Dendrimeric Catalysts in Sol -Gel Matrices Michael R. Detty, PI...Environmentally benign sol -gel antifouling and foul-releasing coatings. Ace. Chem. Res. 2014, 47, 678-687. 11) Alberto, E. E.; Müller, L. M

Non-minimally coupled quintessence dark energy model with a cubic galileon term: a dynamical system analysis

Science.gov (United States)

Bhattacharya, Somnath; Mukherjee, Pradip; Roy, Amit Singha; Saha, Anirban

2018-03-01

We consider a scalar field which is generally non-minimally coupled to gravity and has a characteristic cubic Galilean-like term and a generic self-interaction, as a candidate of a Dark Energy model. The system is dynamically analyzed and novel fixed points with perturbative stability are demonstrated. Evolution of the system is numerically studied near a novel fixed point which owes its existence to the Galileon character of the model. It turns out that demanding the stability of this novel fixed point puts a strong restriction on the allowed non-minimal coupling and the choice of the self-interaction. The evolution of the equation of state parameter is studied, which shows that our model predicts an accelerated universe throughout and the phantom limit is only approached closely but never crossed. Our result thus extends the findings of Coley, Dynamical systems and cosmology. Kluwer Academic Publishers, Boston (2013) for more general NMC than linear and quadratic couplings.

Hexavalent Chromium Minimization Strategy

Science.gov (United States)

2011-05-01

Logistics 4 Initiative - DoD Hexavalent Chromium Minimization Non- Chrome Primer IIEXAVAJ ENT CHRO:M I~UMI CHROMIUM (VII Oil CrfVli.J CANCEfl HAnRD CD...Management Office of the Secretary of Defense Hexavalent Chromium Minimization Strategy Report Documentation Page Form ApprovedOMB No. 0704-0188...00-2011 4. TITLE AND SUBTITLE Hexavalent Chromium Minimization Strategy 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6

Optimal Reliability-Based Code Calibration

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard; Kroon, I. B.; Faber, Michael Havbro

1994-01-01

Calibration of partial safety factors is considered in general, including classes of structures where no code exists beforehand. The partial safety factors are determined such that the difference between the reliability for the different structures in the class considered and a target reliability...... level is minimized. Code calibration on a decision theoretical basis is also considered and it is shown how target reliability indices can be calibrated. Results from code calibration for rubble mound breakwater designs are shown....

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.

The Art of Readable Code

CERN Document Server

Boswell, Dustin

2011-01-01

As programmers, we've all seen source code that's so ugly and buggy it makes our brain ache. Over the past five years, authors Dustin Boswell and Trevor Foucher have analyzed hundreds of examples of "bad code" (much of it their own) to determine why they're bad and how they could be improved. Their conclusion? You need to write code that minimizes the time it would take someone else to understand it-even if that someone else is you. This book focuses on basic principles and practical techniques you can apply every time you write code. Using easy-to-digest code examples from different languag

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.

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...

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

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

Waste minimization assessment procedure

International Nuclear Information System (INIS)

Kellythorne, L.L.

1993-01-01

Perry Nuclear Power Plant began developing a waste minimization plan early in 1991. In March of 1991 the plan was documented following a similar format to that described in the EPA Waste Minimization Opportunity Assessment Manual. Initial implementation involved obtaining management's commitment to support a waste minimization effort. The primary assessment goal was to identify all hazardous waste streams and to evaluate those streams for minimization opportunities. As implementation of the plan proceeded, non-hazardous waste streams routinely generated in large volumes were also evaluated for minimization opportunities. The next step included collection of process and facility data which would be useful in helping the facility accomplish its assessment goals. This paper describes the resources that were used and which were most valuable in identifying both the hazardous and non-hazardous waste streams that existed on site. For each material identified as a waste stream, additional information regarding the materials use, manufacturer, EPA hazardous waste number and DOT hazard class was also gathered. Once waste streams were evaluated for potential source reduction, recycling, re-use, re-sale, or burning for heat recovery, with disposal as the last viable alternative

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.

Probing gravitational non-minimal coupling with dark energy surveys

Energy Technology Data Exchange (ETDEWEB)

Geng, Chao-Qiang [Chongqing University of Posts and Telecommunications, Chongqing (China); National Tsing Hua University, Department of Physics, Hsinchu (China); National Center for Theoretical Sciences, Hsinchu (China); Lee, Chung-Chi [National Center for Theoretical Sciences, Hsinchu (China); Wu, Yi-Peng [Academia Sinica, Institute of Physics, Taipei (China)

2017-03-15

We investigate observational constraints on a specific one-parameter extension to the minimal quintessence model, where the quintessence field acquires a quadratic coupling to the scalar curvature through a coupling constant ξ. The value of ξ is highly suppressed in typical tracker models if the late-time cosmic acceleration is driven at some field values near the Planck scale. We test ξ in a second class of models in which the field value today becomes a free model parameter. We use the combined data from type-Ia supernovae, cosmic microwave background, baryon acoustic oscillations and matter power spectrum, to weak lensing measurements and find a best-fit value ξ > 0.289 where ξ = 0 is excluded outside the 95% confidence region. The effective gravitational constant G{sub eff} subject to the hint of a non-zero ξ is constrained to -0.003 < 1 - G{sub eff}/G < 0.033 at the same confidence level on cosmological scales, and it can be narrowed down to 1 - G{sub eff}/G < 2.2 x 10{sup -5} when combining with Solar System tests. (orig.)

CONDOR: a database resource of developmentally associated conserved non-coding elements

Directory of Open Access Journals (Sweden)

Smith Sarah

2007-08-01

Full Text Available Abstract Background Comparative genomics is currently one of the most popular approaches to study the regulatory architecture of vertebrate genomes. Fish-mammal genomic comparisons have proved powerful in identifying conserved non-coding elements likely to be distal cis-regulatory modules such as enhancers, silencers or insulators that control the expression of genes involved in the regulation of early development. The scientific community is showing increasing interest in characterizing the function, evolution and language of these sequences. Despite this, there remains little in the way of user-friendly access to a large dataset of such elements in conjunction with the analysis and the visualization tools needed to study them. Description Here we present CONDOR (COnserved Non-coDing Orthologous Regions available at: http://condor.fugu.biology.qmul.ac.uk. In an interactive and intuitive way the website displays data on > 6800 non-coding elements associated with over 120 early developmental genes and conserved across vertebrates. The database regularly incorporates results of ongoing in vivo zebrafish enhancer assays of the CNEs carried out in-house, which currently number ~100. Included and highlighted within this set are elements derived from duplication events both at the origin of vertebrates and more recently in the teleost lineage, thus providing valuable data for studying the divergence of regulatory roles between paralogs. CONDOR therefore provides a number of tools and facilities to allow scientists to progress in their own studies on the function and evolution of developmental cis-regulation. Conclusion By providing access to data with an approachable graphics interface, the CONDOR database presents a rich resource for further studies into the regulation and evolution of genes involved in early development.

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

Collaborative multi-layer network coding for cellular cognitive radio networks

KAUST Repository

Sorour, Sameh

2013-06-01

In this paper, we propose a prioritized multi-layer network coding scheme for collaborative packet recovery in underlay cellular cognitive radio networks. This scheme allows the collocated primary and cognitive radio base-stations to collaborate with each other, in order to minimize their own and each other\\'s packet recovery overheads, and thus improve their throughput, without any coordination between them. This non-coordinated collaboration is done using a novel multi-layer instantly decodable network coding scheme, which guarantees that each network\\'s help to the other network does not result in any degradation in its own performance. It also does not cause any violation to the primary networks interference thresholds in the same and adjacent cells. Yet, our proposed scheme both guarantees the reduction of the recovery overhead in collocated primary and cognitive radio networks, and allows early recovery of their packets compared to non-collaborative schemes. Simulation results show that a recovery overhead reduction of 15% and 40% can be achieved by our proposed scheme in the primary and cognitive radio networks, respectively, compared to the corresponding non-collaborative scheme. © 2013 IEEE.

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

Who's keeping the code? Compliance with the international code for the marketing of breast-milk substitutes in Greater Glasgow.

Science.gov (United States)

McInnes, Rhona J; Wright, Charlotte; Haq, Shogufta; McGranachan, Margaret

2007-07-01

To evaluate compliance with the World Health Organization's International Code of Marketing of Breast-milk Substitutes in primary care, after the introduction of strict local infant feeding guidelines. An audit form was sent to all community-based health professionals with an infant feeding remit. Walking tours were conducted in a random sample of community care facilities. Greater Glasgow Primary Care Division. (1) Primary-care staff with an infant feeding remit; (2) community health-care facilities. Contact with manufacturers of breast-milk substitutes (BMS) and BMS company personnel, free samples or incentives, and advertising of BMS. Contact with company personnel was minimal, usually unsolicited and was mainly to provide product information. Free samples of BMS or feeding equipment were rare but childcare or parenting literature was more prevalent. Staff voiced concerns about the lack of relevant information for bottle-feeding mothers and the need to support the mother's feeding choice. One-third of facilities were still displaying materials non-compliant with the Code, with the most common materials being weight conversion charts and posters. Contact between personnel from primary care and BMS companies was minimal and generally unsolicited. The presence of materials from BMS companies in health-care premises was more common. Due to the high level of bottle-feeding in Glasgow, primary-care staff stated a need for information about BMS.

Perceptual coding of stereo endoscopy video for minimally invasive surgery

Science.gov (United States)

Bartoli, Guido; Menegaz, Gloria; Yang, Guang Zhong

2007-03-01

In this paper, we propose a compression scheme that is tailored for stereo-laparoscope sequences. The inter-frame correlation is modeled by the deformation field obtained by elastic registration between two subsequent frames and exploited for prediction of the left sequence. The right sequence is lossy encoded by prediction from the corresponding left images. Wavelet-based coding is applied to both the deformation vector fields and residual images. The resulting system supports spatio temporal scalability, while providing lossless performance. The implementation of the wavelet transform by integer lifting ensures a low computational complexity, thus reducing the required run-time memory allocation and on line implementation. Extensive psychovisual tests were performed for system validation and characterization with respect to the MPEG4 standard for video coding. Results are very encouraging: the PSVC system features the functionalities making it suitable for PACS while providing a good trade-off between usability and performance in lossy mode.

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.

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

Minimal important difference in field walking tests in non-cystic fibrosis bronchiectasis following exercise training.

Science.gov (United States)

Lee, A L; Hill, C J; Cecins, N; Jenkins, S; McDonald, C F; Burge, A T; Rautela, L; Stirling, R G; Thompson, P J; Holland, A E

2014-09-01

The 6-min walk distance (6MWD) and incremental shuttle walk distance (ISWD) are clinically meaningful measures of exercise capacity in people with non-cystic fibrosis (CF) bronchiectasis, but the change in walking distance which constitutes clinical benefit is undefined. This study aimed to determine the minimal important difference for the 6MWD and ISWD in non-CF bronchiectasis. Thirty-seven participants with mean FEV1 70% predicted completed both field walking tests before and after an 8-week exercise program. The minimal important difference was calculated using a distribution-based and anchor-based method, with the global rating of change scale used. The mean change in 6MWD in participants who reported themselves to be unchanged was 10 m, compared to 36 m (small change) and 45 m (substantial change) (p = 0.01). For the ISWD, the mean change in participants who reported themselves to be unchanged was 33 m, compared to 54 m (small change) and 73 m (substantial change) (p = 0.04). The anchor-based method defined the minimal important difference for 6MWD as 24.5 m (AUC 0.76, 95% CI 0.61-0.91) and for ISWD as 35 m (AUC 0.88, 95% CI 0.73-0.99), based on participant's global rating of change. The distribution-based method indicated a value of 22.3 m for the 6MWD and 37 m for the ISWD. There was excellent agreement between the two methods for the 6MWD (kappa = 0.91) and the ISWD (kappa = 0.92). Small changes in 6MWD and ISWD may represent clinically important benefits in people with non-CF bronchiectasis. These data are likely to assist in the interpretation of change in exercise capacity following intervention. Copyright © 2014 Elsevier Ltd. All rights reserved.

Algorithm for finding minimal cut sets in a fault tree

International Nuclear Information System (INIS)

Rosenberg, Ladislav

1996-01-01

This paper presents several algorithms that have been used in a computer code for fault-tree analysing by the minimal cut sets method. The main algorithm is the more efficient version of the new CARA algorithm, which finds minimal cut sets with an auxiliary dynamical structure. The presented algorithm for finding the minimal cut sets enables one to do so by defined requirements - according to the order of minimal cut sets, or to the number of minimal cut sets, or both. This algorithm is from three to six times faster when compared with the primary version of the CARA algorithm

ComboCoding: Combined intra-/inter-flow network coding for TCP over disruptive MANETs

Directory of Open Access Journals (Sweden)

Chien-Chia Chen

2011-07-01

Full Text Available TCP over wireless networks is challenging due to random losses and ACK interference. Although network coding schemes have been proposed to improve TCP robustness against extreme random losses, a critical problem still remains of DATA–ACK interference. To address this issue, we use inter-flow coding between DATA and ACK to reduce the number of transmissions among nodes. In addition, we also utilize a “pipeline” random linear coding scheme with adaptive redundancy to overcome high packet loss over unreliable links. The resulting coding scheme, ComboCoding, combines intra-flow and inter-flow coding to provide robust TCP transmission in disruptive wireless networks. The main contributions of our scheme are twofold; the efficient combination of random linear coding and XOR coding on bi-directional streams (DATA and ACK, and the novel redundancy control scheme that adapts to time-varying and space-varying link loss. The adaptive ComboCoding was tested on a variable hop string topology with unstable links and on a multipath MANET with dynamic topology. Simulation results show that TCP with ComboCoding delivers higher throughput than with other coding options in high loss and mobile scenarios, while introducing minimal overhead in normal operation.

Parallelization methods study of thermal-hydraulics codes

International Nuclear Information System (INIS)

Gaudart, Catherine

2000-01-01

The variety of parallelization methods and machines leads to a wide selection for programmers. In this study we suggest, in an industrial context, some solutions from the experience acquired through different parallelization methods. The study is about several scientific codes which simulate a large variety of thermal-hydraulics phenomena. A bibliography on parallelization methods and a first analysis of the codes showed the difficulty of our process on the whole applications to study. Therefore, it would be necessary to identify and extract a representative part of these applications and parallelization methods. The linear solver part of the codes forced itself. On this particular part several parallelization methods had been used. From these developments one could estimate the necessary work for a non initiate programmer to parallelize his application, and the impact of the development constraints. The different methods of parallelization tested are the numerical library PETSc, the parallelizer PAF, the language HPF, the formalism PEI and the communications library MPI and PYM. In order to test several methods on different applications and to follow the constraint of minimization of the modifications in codes, a tool called SPS (Server of Parallel Solvers) had be developed. We propose to describe the different constraints about the optimization of codes in an industrial context, to present the solutions given by the tool SPS, to show the development of the linear solver part with the tested parallelization methods and lastly to compare the results against the imposed criteria. (author) [fr

Asymptotic safety of higher derivative quantum gravity non-minimally coupled with a matter system

Science.gov (United States)

Hamada, Yuta; Yamada, Masatoshi

2017-08-01

We study asymptotic safety of models of the higher derivative quantum gravity with and without matter. The beta functions are derived by utilizing the functional renormalization group, and non-trivial fixed points are found. It turns out that all couplings in gravity sector, namely the cosmological constant, the Newton constant, and the R 2 and R μν 2 coupling constants, are relevant in case of higher derivative pure gravity. For the Higgs-Yukawa model non-minimal coupled with higher derivative gravity, we find a stable fixed point at which the scalar-quartic and the Yukawa coupling constants become relevant. The relevant Yukawa coupling is crucial to realize the finite value of the Yukawa coupling constants in the standard model.

Radiation fluid stars in the non-minimally coupled Y(R)F{sup 2} gravity

Energy Technology Data Exchange (ETDEWEB)

Sert, Oezcan [Pamukkale University, Department of Mathematics, Faculty of Arts and Sciences, Denizli (Turkey)

2017-02-15

We propose a non-minimally coupled gravity model in Y(R)F{sup 2} form to describe the radiation fluid stars which have the radiative equation of state between the energy density ρ and the pressure p given by ρ = 3p. Here F{sup 2} is the Maxwell invariant and Y(R) is a function of the Ricci scalar R. We give the gravitational and electromagnetic field equations in differential form notation taking the infinitesimal variations of the model. We look for electrically charged star solutions to the field equations under the constraint eliminating complexity of the higher order terms in the field equations. We determine the non-minimally coupled function Y(R) and the corresponding model which admits new exact solutions in the interior of the star and the Reissner-Nordstrom solution at the exterior region. Using the vanishing pressure condition at the boundary together with the continuity conditions of the metric functions and the electric charge, we find the mass-radius ratio, charge-radius ratio, and the gravitational surface redshift depending on the parameter of the model for the radiation fluid star. We derive general restrictions for the ratios and redshift of the charged compact stars. We obtain a slightly smaller upper mass-radius ratio limit than the Buchdahl bound 4/9 and a smaller upper redshift limit than the bound of the standard general relativistic stars. (orig.)

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...

Aeroelastic code development activities in the United States

Energy Technology Data Exchange (ETDEWEB)

Wright, A.D. [National Renewable Energy Lab., Golden, Colorado (United States)

1996-09-01

Designing wind turbines to be fatigue resistant and to have long lifetimes at minimal cost is a major goal of the federal wind program and the wind industry in the United States. To achieve this goal, we must be able to predict critical loads for a wide variety of different wind turbines operating under extreme conditions. The codes used for wind turbine dynamic analysis must be able to analyze a wide range of different wind turbine configurations as well as rapidly predict the loads due to turbulent wind inflow with a minimal set of degrees of freedom. Code development activities in the US have taken a two-pronged approach in order to satisfy both of these criteria: (1) development of a multi-purpose code which can be used to analyze a wide variety of wind turbine configurations without having to develop new equations of motion with each configuration change, and (2) development of specialized codes with minimal sets of specific degrees of freedom for analysis of two- and three-bladed horizontal axis wind turbines and calculation of machine loads due to turbulent inflow. In the first method we have adapted a commercial multi-body dynamics simulation package for wind turbine analysis. In the second approach we are developing specialized codes with limited degrees of freedom, usually specified in the modal domain. This paper will summarize progress to date in the development, validation, and application of these codes. (au) 13 refs.

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

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...

Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes

Science.gov (United States)

Lin, Shu

1998-01-01

A code trellis is a graphical representation of a code, block or convolutional, in which every path represents a codeword (or a code sequence for a convolutional code). This representation makes it possible to implement Maximum Likelihood Decoding (MLD) of a code with reduced decoding complexity. The most well known trellis-based MLD algorithm is the Viterbi algorithm. The trellis representation was first introduced and used for convolutional codes [23]. This representation, together with the Viterbi decoding algorithm, has resulted in a wide range of applications of convolutional codes for error control in digital communications over the last two decades. There are two major reasons for this inactive period of research in this area. First, most coding theorists at that time believed that block codes did not have simple trellis structure like convolutional codes and maximum likelihood decoding of linear block codes using the Viterbi algorithm was practically impossible, except for very short block codes. Second, since almost all of the linear block codes are constructed algebraically or based on finite geometries, it was the belief of many coding theorists that algebraic decoding was the only way to decode these codes. These two reasons seriously hindered the development of efficient soft-decision decoding methods for linear block codes and their applications to error control in digital communications. This led to a general belief that block codes are inferior to convolutional codes and hence, that they were not useful. Chapter 2 gives a brief review of linear block codes. The goal is to provide the essential background material for the development of trellis structure and trellis-based decoding algorithms for linear block codes in the later chapters. Chapters 3 through 6 present the fundamental concepts, finite-state machine model, state space formulation, basic structural properties, state labeling, construction procedures, complexity, minimality, and

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.

Under-coding of secondary conditions in coded hospital health data: Impact of co-existing conditions, death status and number of codes in a record.

Science.gov (United States)

Peng, Mingkai; Southern, Danielle A; Williamson, Tyler; Quan, Hude

2017-12-01

This study examined the coding validity of hypertension, diabetes, obesity and depression related to the presence of their co-existing conditions, death status and the number of diagnosis codes in hospital discharge abstract database. We randomly selected 4007 discharge abstract database records from four teaching hospitals in Alberta, Canada and reviewed their charts to extract 31 conditions listed in Charlson and Elixhauser comorbidity indices. Conditions associated with the four study conditions were identified through multivariable logistic regression. Coding validity (i.e. sensitivity, positive predictive value) of the four conditions was related to the presence of their associated conditions. Sensitivity increased with increasing number of diagnosis code. Impact of death on coding validity is minimal. Coding validity of conditions is closely related to its clinical importance and complexity of patients' case mix. We recommend mandatory coding of certain secondary diagnosis to meet the need of health research based on administrative health data.

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.

Minimally invasive non-surgical lung volume reduction

International Nuclear Information System (INIS)

Shen Liming; Zhou Dayong; Shen Junkang

2006-01-01

Minimally invasive treatment with lung volume reduction is the promising future for severe pulmonary emphysema patients. With emerging and improving of new techniques and instruments, it would become an important choice for managing severe emphysema. A comprehensive review is here documented through the correlative techniques, instruments, new achievements and latest research work. (authors)

Gravity localization in non-minimally coupled scalar thick braneworlds with a Gauss-Bonnet term

International Nuclear Information System (INIS)

Malagon-Morejon, D; Quiros, I; Herrera-Aguilar, A

2011-01-01

We consider a warped five-dimensional thick braneworld with a four-dimensional Poincare invariant space-time in the framework of scalar matter non-minimally coupled to gravity plus a Gauss-Bonnet term in the bulk. Scalar field and higher curvature corrections to the background equations as well as the perturbed equations are shown. A relationship between 4-dimensional and 5-dimensional Planck masses is studied in general terms. By imposing finiteness of the 4-dimensional Planck mass and regularity of the geometry, the localization properties of the tensor modes of the first order perturbed geometry are analized for an important class of solutions motivated by models with scalar fields which are minimally coupled to gravity. In order to study the gravity localization properties for this model, the normalizability condition for the lowest level of the tensor fluctuations is analized. We see that for the class of solutions examined, gravity in 4 dimensions is recovered if the curvature invariants are regular and Planck masses are finite.

Network Coding Protocols for Data Gathering Applications

DEFF Research Database (Denmark)

Nistor, Maricica; Roetter, Daniel Enrique Lucani; Barros, João

2015-01-01

Tunable sparse network coding (TSNC) with various sparsity levels of the coded packets and different feedback mechanisms is analysed in the context of data gathering applications in multi-hop networks. The goal is to minimize the completion time, i.e., the total time required to collect all data ...

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.

Non-invasive or minimally invasive autopsy compared to conventional autopsy of suspected natural deaths in adults: a systematic review.

Science.gov (United States)

Blokker, Britt M; Wagensveld, Ivo M; Weustink, Annick C; Oosterhuis, J Wolter; Hunink, M G Myriam

2016-04-01

Autopsies are used for healthcare quality control and improving medical knowledge. Because autopsy rates are declining worldwide, various non-invasive or minimally invasive autopsy methods are now being developed. To investigate whether these might replace the invasive autopsies conventionally performed in naturally deceased adults, we systematically reviewed original prospective validation studies. We searched six databases. Two reviewers independently selected articles and extracted data. Methods and patient groups were too heterogeneous for meaningful meta-analysis of outcomes. Sixteen of 1538 articles met our inclusion criteria. Eight studies used a blinded comparison; ten included less than 30 appropriate cases. Thirteen studies used radiological imaging (seven dealt solely with non-invasive procedures), two thoracoscopy and laparoscopy, and one sampling without imaging. Combining CT and MR was the best non-invasive method (agreement for cause of death: 70 %, 95%CI: 62.6; 76.4), but minimally invasive methods surpassed non-invasive methods. The highest sensitivity for cause of death (90.9 %, 95%CI: 74.5; 97.6, suspected duplicates excluded) was achieved in recent studies combining CT, CT-angiography and biopsies. Minimally invasive autopsies including biopsies performed best. To establish a feasible alternative to conventional autopsy and to increase consent to post-mortem investigations, further research in larger study groups is needed. • Health care quality control benefits from clinical feedback provided by (alternative) autopsies. • So far, sixteen studies investigated alternative autopsy methods for naturally deceased adults. • Thirteen studies used radiological imaging modalities, eight tissue biopsies, and three CT-angiography. • Combined CT, CT-angiography and biopsies were most sensitive diagnosing cause of death.

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...

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)

Probing gravitational non-minimal coupling with dark energy surveys

International Nuclear Information System (INIS)

Geng, Chao-Qiang; Lee, Chung-Chi; Wu, Yi-Peng

2017-01-01

We investigate observational constraints on a specific one-parameter extension to the minimal quintessence model, where the quintessence field acquires a quadratic coupling to the scalar curvature through a coupling constant ξ. The value of ξ is highly suppressed in typical tracker models if the late-time cosmic acceleration is driven at some field values near the Planck scale. We test ξ in a second class of models in which the field value today becomes a free model parameter. We use the combined data from type-Ia supernovae, cosmic microwave background, baryon acoustic oscillations and matter power spectrum, to weak lensing measurements and find a best-fit value ξ > 0.289 where ξ = 0 is excluded outside the 95% confidence region. The effective gravitational constant G_e_f_f subject to the hint of a non-zero ξ is constrained to -0.003 < 1 - G_e_f_f/G < 0.033 at the same confidence level on cosmological scales, and it can be narrowed down to 1 - G_e_f_f/G < 2.2 x 10"-"5 when combining with Solar System tests. (orig.)

Trellises for stabilizer codes: Definition and uses

International Nuclear Information System (INIS)

Ollivier, Harold; Tillich, Jean-Pierre

2006-01-01

Trellises play an important theoretical and practical role for classical codes. Their main utility is to devise complexity-efficient error estimation algorithms. Here, we describe trellis representations for quantum stabilizer codes. We show that they share the same properties as their classical analogs. In particular, for any stabilizer code it is possible to find a minimal trellis representation. Our construction is illustrated by two fundamental error estimation algorithms

Phenomenological optical potentials and optical model computer codes

International Nuclear Information System (INIS)

Prince, A.

1980-01-01

An introduction to the Optical Model is presented. Starting with the purpose and nature of the physical problems to be analyzed, a general formulation and the various phenomenological methods of solution are discussed. This includes the calculation of observables based on assumed potentials such as local and non-local and their forms, e.g. Woods-Saxon, folded model etc. Also discussed are the various calculational methods and model codes employed to describe nuclear reactions in the spherical and deformed regions (e.g. coupled-channel analysis). An examination of the numerical solutions and minimization techniques associated with the various codes, is briefly touched upon. Several computer programs are described for carrying out the calculations. The preparation of input, (formats and options), determination of model parameters and analysis of output are described. The class is given a series of problems to carry out using the available computer. Interpretation and evaluation of the samples includes the effect of varying parameters, and comparison of calculations with the experimental data. Also included is an intercomparison of the results from the various model codes, along with their advantages and limitations. (author)

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

Quasinormal modes of the BTZ black hole under scalar perturbations with a non-minimal coupling: exact spectrum

Science.gov (United States)

Panotopoulos, Grigoris

2018-06-01

We perturb the non-rotating BTZ black hole with a non-minimally coupled massless scalar field, and we compute the quasinormal spectrum exactly. We solve the radial equation in terms of hypergeometric functions, and we obtain an analytical expression for the quasinormal frequencies. In addition, we compare our analytical results with the 6th order semi-analytical WKB method, and we find an excellent agreement. The impact of the nonminimal coupling as well as of the cosmological constant on the quasinormal spectrum is briefly discussed.

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

New Technique for Improving Performance of LDPC Codes in the Presence of Trapping Sets

Directory of Open Access Journals (Sweden)

Mohamed Adnan Landolsi

2008-06-01

Full Text Available Trapping sets are considered the primary factor for degrading the performance of low-density parity-check (LDPC codes in the error-floor region. The effect of trapping sets on the performance of an LDPC code becomes worse as the code size decreases. One approach to tackle this problem is to minimize trapping sets during LDPC code design. However, while trapping sets can be reduced, their complete elimination is infeasible due to the presence of cycles in the underlying LDPC code bipartite graph. In this work, we introduce a new technique based on trapping sets neutralization to minimize the negative effect of trapping sets under belief propagation (BP decoding. Simulation results for random, progressive edge growth (PEG and MacKay LDPC codes demonstrate the effectiveness of the proposed technique. The hardware cost of the proposed technique is also shown to be minimal.

A unified form of exact-MSR codes via product-matrix frameworks

KAUST Repository

Lin, Sian Jheng

2015-02-01

Regenerating codes represent a class of block codes applicable for distributed storage systems. The [n, k, d] regenerating code has data recovery capability while possessing arbitrary k out of n code fragments, and supports the capability for code fragment regeneration through the use of other arbitrary d fragments, for k ≤ d ≤ n - 1. Minimum storage regenerating (MSR) codes are a subset of regenerating codes containing the minimal size of each code fragment. The first explicit construction of MSR codes that can perform exact regeneration (named exact-MSR codes) for d ≥ 2k - 2 has been presented via a product-matrix framework. This paper addresses some of the practical issues on the construction of exact-MSR codes. The major contributions of this paper include as follows. A new product-matrix framework is proposed to directly include all feasible exact-MSR codes for d ≥ 2k - 2. The mechanism for a systematic version of exact-MSR code is proposed to minimize the computational complexities for the process of message-symbol remapping. Two practical forms of encoding matrices are presented to reduce the size of the finite field.

A unified form of exact-MSR codes via product-matrix frameworks

KAUST Repository

Lin, Sian Jheng; Chung, Weiho; Han, Yunghsiangsam; Al-Naffouri, Tareq Y.

2015-01-01

Regenerating codes represent a class of block codes applicable for distributed storage systems. The [n, k, d] regenerating code has data recovery capability while possessing arbitrary k out of n code fragments, and supports the capability for code fragment regeneration through the use of other arbitrary d fragments, for k ≤ d ≤ n - 1. Minimum storage regenerating (MSR) codes are a subset of regenerating codes containing the minimal size of each code fragment. The first explicit construction of MSR codes that can perform exact regeneration (named exact-MSR codes) for d ≥ 2k - 2 has been presented via a product-matrix framework. This paper addresses some of the practical issues on the construction of exact-MSR codes. The major contributions of this paper include as follows. A new product-matrix framework is proposed to directly include all feasible exact-MSR codes for d ≥ 2k - 2. The mechanism for a systematic version of exact-MSR code is proposed to minimize the computational complexities for the process of message-symbol remapping. Two practical forms of encoding matrices are presented to reduce the size of the finite field.

Characterization of photoautotrophic picoplankton assemblages in turbid, alkaline lakes of the Carpathian Basin (Central Europe

Directory of Open Access Journals (Sweden)

Lajos VÖRÖS

2009-08-01

Full Text Available The photoautotrophic picoplankton (PPP of ten shallow, hyposaline soda lakes located in three different geographical regions in the Carpathian Basin (Central Europe was characterized. These lakes, which frequently dry out completely, are extremely rich in PPP. Epifluorescence microscopy was applied to determine picocyanobacterial and picoeukaryotic cell abundance and PCR-based molecular techniques (denaturing gradient gel electrophoresis and cloning with phylospecies delineation to identify the members of PPP. Most of these lakes were eu- and hypertrophic with varying contribution of picocyanobacteria to the total PPP cell number. We found an unusually high PPP abundance with peaks of 8.16 × 106 cells mL-1 for picoeukaryotes and 1.78 × 107 cells mL-1 for picocyanobacteria. The majority of the retrieved PPP sequences belonged to picocyanobacteria (nonmarine Synechococcus/ Cyanobium, while others showed similarity to eukaryotic algal plastids (close to Trebouxiophycean isolates. Molecular analysis revealed significant genetic diversity in the PPP fraction of these lakes and showed that the closest relatives of our picocyanobacterial clones were recovered from different habitats, indicating seemingly no correlation between the 'saline' ecotypes and their phylogenetic position. Our results also confirmed that PPP might exploit different aquatic ecosystems and be successful even in the case of abrupt changes of environmental parameters (in our case, salinity. According to our knowledge, this is the first survey focusing on the identification of the PPP community members in turbid and alkaline lakes with extraordinarily high picoplankton productivity.

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.

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.

Assessment of variable fluorescence fluorometry as an approach for rapidly detecting living photoautotrophs in ballast water

Science.gov (United States)

First, Matthew R.; Robbins-Wamsley, Stephanie H.; Riley, Scott C.; Drake, Lisa A.

2018-03-01

Variable fluorescence fluorometry, an analytical approach that estimates the fluorescence yield of chlorophyll a (F0, a proximal measure of algal concentration) and photochemical yield (FV/FM, an indicator of the physiological status of algae) was evaluated as a means to rapidly assess photoautotrophs. Specifically, it was used to gauge the efficacy of ballast water treatment designed to reduce the transport and delivery of potentially invasive organisms. A phytoflagellate, Tetraselmis spp. (10-12 μm) and mixed communities of ambient protists were examined in both laboratory experiments and large-scale field trials simulating 5-d hold times in mock ballast tanks. In laboratory incubations, ambient organisms held in the dark exhibited declining F0 and FV/FM measurements relative to organisms held under lighted conditions. In field experiments, increases and decreases in F0 and FV/FM over the tank hold time corresponded to those of microscope counts of organisms in two of three trials. In the third trial, concentrations of organisms ≥ 10 and protists) increased while F0 and FV/FM decreased. Rapid and sensitive, variable fluorescence fluorometry is appropriate for detecting changes in organism concentrations and physiological status in samples dominated by microalgae. Changes in the heterotrophic community, which may become more prevalent in light-limited ballast tanks, would not be detected via variable fluorescence fluorometry, however.

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...

Qualitative analysis of cosmological models in Brans-Dicke theory, solutions from non-minimal coupling and viscous universe

International Nuclear Information System (INIS)

Romero Filho, C.A.

1988-01-01

Using dynamical system theory we investigate homogeneous and isotropic models in Brans-Dicke theory for perfect fluids with general equation of state and arbitrary ω. Phase diagrams are drawn on the Poincare sphere which permits a qualitative analysis of the models. Based on this analysis we construct a method for generating classes of solutions in Brans-Dicke theory. The same technique is used for studying models arising from non-minimal coupling of electromagnetism with gravity. In addition, viscous fluids are considered and non-singular solutions with bulk viscosity are found. (author)

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.

Gravitino problem in minimal supergravity inflation

Energy Technology Data Exchange (ETDEWEB)

Hasegawa, Fuminori [Institute for Cosmic Ray Research, The University of Tokyo, Kashiwa, Chiba 277-8582 (Japan); Mukaida, Kyohei [Kavli IPMU (WPI), UTIAS, The University of Tokyo, Kashiwa, Chiba 277-8583 (Japan); Nakayama, Kazunori [Department of Physics, Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo 133-0033 (Japan); Terada, Takahiro, E-mail: terada@kias.re.kr [School of Physics, Korea Institute for Advanced Study (KIAS), Seoul 02455 (Korea, Republic of); Yamada, Yusuke [Stanford Institute for Theoretical Physics and Department of Physics, Stanford University, Stanford, CA 94305 (United States)

2017-04-10

We study non-thermal gravitino production in the minimal supergravity inflation. In this minimal model utilizing orthogonal nilpotent superfields, the particle spectrum includes only graviton, gravitino, inflaton, and goldstino. We find that a substantial fraction of the cosmic energy density can be transferred to the longitudinal gravitino due to non-trivial change of its sound speed. This implies either a breakdown of the effective theory after inflation or a serious gravitino problem.

Gravitino problem in minimal supergravity inflation

Directory of Open Access Journals (Sweden)

Fuminori Hasegawa

2017-04-01

Full Text Available We study non-thermal gravitino production in the minimal supergravity inflation. In this minimal model utilizing orthogonal nilpotent superfields, the particle spectrum includes only graviton, gravitino, inflaton, and goldstino. We find that a substantial fraction of the cosmic energy density can be transferred to the longitudinal gravitino due to non-trivial change of its sound speed. This implies either a breakdown of the effective theory after inflation or a serious gravitino problem.

Origin of intense magnetic fields near black holes due to non-minimal gravitational-electromagnetic coupling

International Nuclear Information System (INIS)

Souza, Rafael S. de; Opher, Reuven

2011-01-01

The origin of magnetic fields in astrophysical objects is a challenging problem in astrophysics. Throughout the years, many scientists have suggested that non-minimal gravitational-electromagnetic coupling (NMGEC) could be the origin of the ubiquitous astrophysical magnetic fields. We investigate the possible origin of intense magnetic fields by NMGEC near rotating black holes, connected with quasars and gamma-ray bursts. Whereas these intense magnetic fields are difficult to explain astrophysically, we find that they are easily explained by NMGEC.

The new CMSS code for interactions with companies managing relationships to minimize conflicts.

Science.gov (United States)

Kahn, Norman B; Lichter, Allen S

2011-09-01

Conflicts of interest in medicine have received significant attention in recent years, through the public and professional media, federal and state governments, and through a 2009 report of the Institute of Medicine on Conflict of Interest in Medical Research, Education and Practice. The Council of Medical Specialty Societies (CMSS) Code for Interactions with Companies was adopted by the CMSS in April 2010. The Code guides specialty societies in the profession of medicine in ethical relationships between societies and the pharmaceutical and medical device industries. The Code serves to protect and promote the independence of specialty societies and their leaders in corporate sponsorships, licensing, advertising, society meetings, exhibits, educational programs, journals, clinical practice guidelines, and research. Copyright © 2011 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

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

Inflationary predictions of double-well, Coleman-Weinberg, and hilltop potentials with non-minimal coupling

Science.gov (United States)

Bostan, Nilay; Güleryüz, Ömer; Nefer Şenoğuz, Vedat

2018-05-01

We discuss how the non-minimal coupling ξphi2R between the inflaton and the Ricci scalar affects the predictions of single field inflation models where the inflaton has a non-zero vacuum expectation value (VEV) v after inflation. We show that, for inflaton values both above the VEV and below the VEV during inflation, under certain conditions the inflationary predictions become approximately the same as the predictions of the Starobinsky model. We then analyze inflation with double-well and Coleman-Weinberg potentials in detail, displaying the regions in the v-ξ plane for which the spectral index ns and the tensor-to-scalar ratio r values are compatible with the current observations. r is always larger than 0.002 in these regions. Finally, we consider the effect of ξ on small field inflation (hilltop) potentials.

Thermodynamics of Horndeski black holes with non-minimal derivative coupling

Energy Technology Data Exchange (ETDEWEB)

Miao, Yan-Gang [Nankai University, School of Physics, Tianjin (China); Max-Planck-Institut fuer Gravitationsphysik (Albert-Einstein-Institut), Potsdam (Germany); Xu, Zhen-Ming [Nankai University, School of Physics, Tianjin (China)

2016-11-15

We explore thermodynamic properties of a new class of Horndeski black holes whose action contains a non-minimal kinetic coupling of a massless real scalar and the Einstein tensor. Our treatment is based on the well-accepted consideration, where the cosmological constant is dealt with as thermodynamic pressure and the mass of black holes as thermodynamic enthalpy. We resort to a newly introduced intensive thermodynamic variable, i.e., the coupling strength of the scalar and tensor whose dimension is length square, and thus yield both the generalized first law of thermodynamics and the generalized Smarr relation. Our result indicates that this class of Horndeski black holes presents rich thermodynamic behaviors and critical phenomena. Especially in the case of the presence of an electric field, these black holes undergo two phase transitions. Once the charge parameter exceeds its critical value, or the cosmological parameter does not exceed its critical value, no phase transitions happen and the black holes are stable. As a by-product, we point out, the coupling strength acts as the thermodynamic pressure in thermodynamics. (orig.)

Thermodynamics of Horndeski black holes with non-minimal derivative coupling

International Nuclear Information System (INIS)

Miao, Yan-Gang; Xu, Zhen-Ming

2016-01-01

We explore thermodynamic properties of a new class of Horndeski black holes whose action contains a non-minimal kinetic coupling of a massless real scalar and the Einstein tensor. Our treatment is based on the well-accepted consideration, where the cosmological constant is dealt with as thermodynamic pressure and the mass of black holes as thermodynamic enthalpy. We resort to a newly introduced intensive thermodynamic variable, i.e., the coupling strength of the scalar and tensor whose dimension is length square, and thus yield both the generalized first law of thermodynamics and the generalized Smarr relation. Our result indicates that this class of Horndeski black holes presents rich thermodynamic behaviors and critical phenomena. Especially in the case of the presence of an electric field, these black holes undergo two phase transitions. Once the charge parameter exceeds its critical value, or the cosmological parameter does not exceed its critical value, no phase transitions happen and the black holes are stable. As a by-product, we point out, the coupling strength acts as the thermodynamic pressure in thermodynamics. (orig.)

Non-minimal supersymmetric models. LHC phenomenolgy and model discrimination

Energy Technology Data Exchange (ETDEWEB)

Krauss, Manuel Ernst

2015-12-18

It is generally agreed upon the fact that the Standard Model of particle physics can only be viewed as an effective theory that needs to be extended as it leaves some essential questions unanswered. The exact realization of the necessary extension is subject to discussion. Supersymmetry is among the most promising approaches to physics beyond the Standard Model as it can simultaneously solve the hierarchy problem and provide an explanation for the dark matter abundance in the universe. Despite further virtues like gauge coupling unification and radiative electroweak symmetry breaking, minimal supersymmetric models cannot be the ultimate answer to the open questions of the Standard Model as they still do not incorporate neutrino masses and are besides heavily constrained by LHC data. This does, however, not derogate the beauty of the concept of supersymmetry. It is therefore time to explore non-minimal supersymmetric models which are able to close these gaps, review their consistency, test them against experimental data and provide prospects for future experiments. The goal of this thesis is to contribute to this process by exploring an extraordinarily well motivated class of models which bases upon a left-right symmetric gauge group. While relaxing the tension with LHC data, those models automatically include the ingredients for neutrino masses. We start with a left-right supersymmetric model at the TeV scale in which scalar SU(2){sub R} triplets are responsible for the breaking of left-right symmetry as well as for the generation of neutrino masses. Although a tachyonic doubly-charged scalar is present at tree-level in this kind of models, we show by performing the first complete one-loop evaluation that it gains a real mass at the loop level. The constraints on the predicted additional charged gauge bosons are then evaluated using LHC data, and we find that we can explain small excesses in the data of which the current LHC run will reveal if they are actual new

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

The maximum number of minimal codewords in an [n, k]-code

DEFF Research Database (Denmark)

Alahmadi, A.; Aldred, R. E. L.; de la Cruz, R.

2013-01-01

We survey some upper and lower bounds on the function in the title, and make them explicit for n≤15 and 1≤k≤15. Exact values are given for cycle codes of graphs for 3≤n≤15 and 1≤k≤13....

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)

Panda code

International Nuclear Information System (INIS)

Altomare, S.; Minton, G.

1975-02-01

PANDA is a new two-group one-dimensional (slab/cylinder) neutron diffusion code designed to replace and extend the FAB series. PANDA allows for the nonlinear effects of xenon, enthalpy and Doppler. Fuel depletion is allowed. PANDA has a completely general search facility which will seek criticality, maximize reactivity, or minimize peaking. Any single parameter may be varied in a search. PANDA is written in FORTRAN IV, and as such is nearly machine independent. However, PANDA has been written with the present limitations of the Westinghouse CDC-6600 system in mind. Most computation loops are very short, and the code is less than half the useful 6600 memory size so that two jobs can reside in the core at once. (auth)

Non-thermal production of minimal dark matter via right-handed neutrino decay

International Nuclear Information System (INIS)

Aoki, Mayumi; Toma, Takashi; Vicente, Avelino

2015-01-01

Minimal Dark Matter (MDM) stands as one of the simplest dark matter scenarios. In MDM models, annihilation and co-annihilation processes among the members of the MDM multiplet are usually very efficient, pushing the dark matter mass above O(10) TeV in order to reproduce the observed dark matter relic density. Motivated by this little drawback, in this paper we consider an extension of the MDM scenario by three right-handed neutrinos. Two specific choices for the MDM multiplet are studied: a fermionic SU(2) L quintuplet and a scalar SU(2) L septuplet. The lightest right-handed neutrino, with tiny Yukawa couplings, never reaches thermal equilibrium in the early universe and is produced by freeze-in. This creates a link between dark matter and neutrino physics: dark matter can be non-thermally produced by the decay of the lightest right-handed neutrino after freeze-out, allowing to lower significantly the dark matter mass. We discuss the phenomenology of the non-thermally produced MDM and, taking into account significant Sommerfeld corrections, we find that the dark matter mass must have some specific values in order not to be in conflict with the current bounds from gamma-ray observations

Stable 1-Norm Error Minimization Based Linear Predictors for Speech Modeling

DEFF Research Database (Denmark)

Giacobello, Daniele; Christensen, Mads Græsbøll; Jensen, Tobias Lindstrøm

2014-01-01

In linear prediction of speech, the 1-norm error minimization criterion has been shown to provide a valid alternative to the 2-norm minimization criterion. However, unlike 2-norm minimization, 1-norm minimization does not guarantee the stability of the corresponding all-pole filter and can generate...... saturations when this is used to synthesize speech. In this paper, we introduce two new methods to obtain intrinsically stable predictors with the 1-norm minimization. The first method is based on constraining the roots of the predictor to lie within the unit circle by reducing the numerical range...... based linear prediction for modeling and coding of speech....

Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

Directory of Open Access Journals (Sweden)

Michael John Milligan

2016-03-01

Full Text Available Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72; Retroposed Pseudogenes V5 (processed only and Yale Pseudo60 (processed and unprocessed, Ensembl 60; two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation.

Non-coding RNAs and plant male sterility: current knowledge and future prospects.

Science.gov (United States)

Mishra, Ankita; Bohra, Abhishek

2018-02-01

Latest outcomes assign functional role to non-coding (nc) RNA molecules in regulatory networks that confer male sterility to plants. Male sterility in plants offers great opportunity for improving crop performance through application of hybrid technology. In this respect, cytoplasmic male sterility (CMS) and sterility induced by photoperiod (PGMS)/temperature (TGMS) have greatly facilitated development of high-yielding hybrids in crops. Participation of non-coding (nc) RNA molecules in plant reproductive development is increasingly becoming evident. Recent breakthroughs in rice definitively associate ncRNAs with PGMS and TGMS. In case of CMS, the exact mechanism through which the mitochondrial ORFs exert influence on the development of male gametophyte remains obscure in several crops. High-throughput sequencing has enabled genome-wide discovery and validation of these regulatory molecules and their target genes, describing their potential roles performed in relation to CMS. Discovery of ncRNA localized in plant mtDNA with its possible implication in CMS induction is intriguing in this respect. Still, conclusive evidences linking ncRNA with CMS phenotypes are currently unavailable, demanding complementing genetic approaches like transgenics to substantiate the preliminary findings. Here, we review the recent literature on the contribution of ncRNAs in conferring male sterility to plants, with an emphasis on microRNAs. Also, we present a perspective on improved understanding about ncRNA-mediated regulatory pathways that control male sterility in plants. A refined understanding of plant male sterility would strengthen crop hybrid industry to deliver hybrids with improved performance.

Minimal constrained supergravity

Energy Technology Data Exchange (ETDEWEB)

Cribiori, N. [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Dall' Agata, G., E-mail: dallagat@pd.infn.it [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Farakos, F. [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Porrati, M. [Center for Cosmology and Particle Physics, Department of Physics, New York University, 4 Washington Place, New York, NY 10003 (United States)

2017-01-10

We describe minimal supergravity models where supersymmetry is non-linearly realized via constrained superfields. We show that the resulting actions differ from the so called “de Sitter” supergravities because we consider constraints eliminating directly the auxiliary fields of the gravity multiplet.

Minimal constrained supergravity

International Nuclear Information System (INIS)

Cribiori, N.; Dall'Agata, G.; Farakos, F.; Porrati, M.

2017-01-01

We describe minimal supergravity models where supersymmetry is non-linearly realized via constrained superfields. We show that the resulting actions differ from the so called “de Sitter” supergravities because we consider constraints eliminating directly the auxiliary fields of the gravity multiplet.

On the classification of long non-coding RNAs

KAUST Repository

Ma, Lina

2013-06-01

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, it is convenient to classify lncRNAs into different groups. Here, we summarize classification methods of lncRNAs according to their four major features, namely, genomic location and context, effect exerted on DNA sequences, mechanism of functioning and their targeting mechanism. In combination with the presently available function annotations, we explore potential relationships between different classification categories, and generalize and compare biological features of different lncRNAs within each category. Finally, we present our view on potential further studies. We believe that the classifications of lncRNAs as indicated above are of fundamental importance for lncRNA studies, helpful for further investigation of specific lncRNAs, for formulation of new hypothesis based on different features of lncRNA and for exploration of the underlying lncRNA functional mechanisms. © 2013 Landes Bioscience.

Non-compliance with the International Code of Marketing of Breast Milk Substitutes is not confined to the infant formula industry.

Science.gov (United States)

Forsyth, Stewart

2013-06-01

Infant feeding policy and practice continues to be a contentious area of global health care. The infant formula industry is widely considered to be the bête noire with frequent claims that they adopt marketing and sales practices that are not compliant with the WHO Code. However, failure to resolve these issues over three decades suggests that there may be wider systemic failings. Review of published papers, commentaries and reports relating to the implementation and governance of the WHO Code with specific reference to issues of non-compliance. The analysis set out in this paper indicates that there are systemic failings at all levels of the implementation and monitoring process including the failure of WHO to successfully 'urge' governments to implement the Code in its entirety; a lack of political will by Member States to implement and monitor the Code and a lack of formal and transparent governance structures. Non-compliance with the WHO Code is not confined to the infant formula industry and several actions are identified, including the need to address issues of partnership working and the establishment of governance systems that are robust, independent and transparent.

Kinetic models of gene expression including non-coding RNAs

Energy Technology Data Exchange (ETDEWEB)

Zhdanov, Vladimir P., E-mail: zhdanov@catalysis.r

2011-03-15

In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

Neutralino Dark Matter in non-universal and non-minimal SUSY

International Nuclear Information System (INIS)

King, S.F.

2010-01-01

We discuss neutralino dark matter in non-universal SUSY including the NUHM, SU(5) with non-universal gauginos. In the MSSM we argue from naturalness that non-universal soft mass parameters are preferred, with non-universal gaugino masses enabling supernatural dark matter beyond the MSSM, we also discuss neutralino dark matter in the U SSM and E 6 SSM. In the E 6 SSM a light neutralino LSP coming from the inert Higgsino and singlino sector is unavoidable and makes an attractive dark matter candidate.

Minimal constrained supergravity

Directory of Open Access Journals (Sweden)

N. Cribiori

2017-01-01

Full Text Available We describe minimal supergravity models where supersymmetry is non-linearly realized via constrained superfields. We show that the resulting actions differ from the so called “de Sitter” supergravities because we consider constraints eliminating directly the auxiliary fields of the gravity multiplet.

The Aster code

International Nuclear Information System (INIS)

Delbecq, J.M.

1999-01-01

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.)

Non-Coding RNAs in Saliva: Emerging Biomarkers for Molecular Diagnostics

Directory of Open Access Journals (Sweden)

Blanca Majem

2015-04-01

Full Text Available Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have reported that saliva body fluid can be useful for discriminating several oral diseases, but also systemic diseases including cancer. Most of these studies revealed messenger RNA (mRNA and proteomic biomarker signatures rather than specific non-coding RNA (ncRNA profiles. NcRNAs are emerging as new regulators of diverse biological functions, playing an important role in oncogenesis and tumor progression. Indeed, the small size of these molecules makes them very stable in different body fluids and not as susceptible as mRNAs to degradation by ribonucleases (RNases. Therefore, the development of a non-invasive salivary test, based on ncRNAs profiles, could have a significant applicability to clinical practice, not only by reducing the cost of the health system, but also by benefitting the patient. Here, we summarize the current status and clinical implications of the ncRNAs present in human saliva as a source of biological information.

On the non-minimal character of the SMEFT

DEFF Research Database (Denmark)

Jiang, Yun; Trott, Michael Robert

2017-01-01

When integrating out unknown new physics sectors, what is the minimal character of the Standard Model Effective Field Theory (SMEFT) that can result? In this paper we focus on a particular aspect of this question: “How can one obtain only one dimension six operator in the SMEFT from a consistent...

Specificity Protein (Sp) Transcription Factors and Metformin Regulate Expression of the Long Non-coding RNA HULC

Science.gov (United States)

There is evidence that specificity protein 1 (Sp1) transcription factor (TF) regulates expression of long non-coding RNAs (lncRNAs) in hepatocellular carcinoma (HCC) cells. RNA interference (RNAi) studies showed that among several lncRNAs expressed in HepG2, SNU-449 and SK-Hep-1...

Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection

Science.gov (United States)

It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs ...

O2-GIDNC: Beyond instantly decodable network coding

KAUST Repository

Aboutorab, Neda

2013-06-01

In this paper, we are concerned with extending the graph representation of generalized instantly decodable network coding (GIDNC) to a more general opportunistic network coding (ONC) scenario, referred to as order-2 GIDNC (O2-GIDNC). In the O2-GIDNC scheme, receivers can store non-instantly decodable packets (NIDPs) comprising two of their missing packets, and use them in a systematic way for later decodings. Once this graph representation is found, it can be used to extend the GIDNC graph-based analyses to the proposed O2-GIDNC scheme with a limited increase in complexity. In the proposed O2-GIDNC scheme, the information of the stored NIDPs at the receivers and the decoding opportunities they create can be exploited to improve the broadcast completion time and decoding delay compared to traditional GIDNC scheme. The completion time and decoding delay minimizing algorithms that can operate on the new O2-GIDNC graph are further described. The simulation results show that our proposed O2-GIDNC improves the completion time and decoding delay performance of the traditional GIDNC. © 2013 IEEE.

LeARN: a platform for detecting, clustering and annotating non-coding RNAs

Directory of Open Access Journals (Sweden)

Schiex Thomas

2008-01-01

Full Text Available Abstract Background In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules. Results LeARN is a flexible software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation. Conclusion This software provides the infrastructure to deal properly with ncRNAs in the framework of any annotation project. It fills the gap between existing prediction software, that detect independent ncRNA occurrences, and public ncRNA repositories, that do not offer the flexibility and interactivity required for annotation projects. The software is freely available from the download section of the website http://bioinfo.genopole-toulouse.prd.fr/LeARN

Codeword Structure Analysis for LDPC Convolutional Codes

Directory of Open Access Journals (Sweden)

Hua Zhou

2015-12-01

Full Text Available The codewords of a low-density parity-check (LDPC convolutional code (LDPC-CC are characterised into structured and non-structured. The number of the structured codewords is dominated by the size of the polynomial syndrome former matrix H T ( D , while the number of the non-structured ones depends on the particular monomials or polynomials in H T ( D . By evaluating the relationship of the codewords between the mother code and its super codes, the low weight non-structured codewords in the super codes can be eliminated by appropriately choosing the monomials or polynomials in H T ( D , resulting in improved distance spectrum of the mother code.

Non-binary decomposition trees - a method of reliability computation for systems with known minimal paths/cuts

International Nuclear Information System (INIS)

Malinowski, Jacek

2004-01-01

A coherent system with independent components and known minimal paths (cuts) is considered. In order to compute its reliability, a tree structure T is constructed whose nodes contain the modified minimal paths (cuts) and numerical values. The value of a non-leaf node is a function of its child nodes' values. The values of leaf nodes are calculated from a simple formula. The value of the root node is the system's failure probability (reliability). Subsequently, an algorithm computing the system's failure probability (reliability) is constructed. The algorithm scans all nodes of T using a stack structure for this purpose. The nodes of T are alternately put on and removed from the stack, their data being modified in the process. Once the algorithm has terminated, the stack contains only the final modification of the root node of T, and its value is equal to the system's failure probability (reliability)

SPORTS - a simple non-linear thermalhydraulic stability code

International Nuclear Information System (INIS)

Chatoorgoon, V.

1986-01-01

A simple code, called SPORTS, has been developed for two-phase stability studies. A novel method of solution of the finite difference equations was deviced and incorporated, and many of the approximations that are common in other stability codes are avoided. SPORTS is believed to be accurate and efficient, as small and large time-steps are permitted, and hence suitable for micro-computers. (orig.)

Non-thermal production of minimal dark matter via right-handed neutrino decay

Energy Technology Data Exchange (ETDEWEB)

Aoki, Mayumi [Institute for Theoretical Physics, Kanazawa University,Kanazawa 920-1192 (Japan); Toma, Takashi [Laboratoire de Physique Théorique, CNRS - UMR 8627, Université de Paris-Sud 11,F-91405 Orsay Cedex (France); Vicente, Avelino [IFPA, Dep. AGO, Université de Liège,Bat B5, Sart-Tilman B-4000 Liège 1 (Belgium); Instituto de Física Corpuscular, CSIC-Universitat de València,Apdo. 22085, E-46071 Valencia (Spain)

2015-09-29

Minimal Dark Matter (MDM) stands as one of the simplest dark matter scenarios. In MDM models, annihilation and co-annihilation processes among the members of the MDM multiplet are usually very efficient, pushing the dark matter mass above O(10) TeV in order to reproduce the observed dark matter relic density. Motivated by this little drawback, in this paper we consider an extension of the MDM scenario by three right-handed neutrinos. Two specific choices for the MDM multiplet are studied: a fermionic SU(2){sub L} quintuplet and a scalar SU(2){sub L} septuplet. The lightest right-handed neutrino, with tiny Yukawa couplings, never reaches thermal equilibrium in the early universe and is produced by freeze-in. This creates a link between dark matter and neutrino physics: dark matter can be non-thermally produced by the decay of the lightest right-handed neutrino after freeze-out, allowing to lower significantly the dark matter mass. We discuss the phenomenology of the non-thermally produced MDM and, taking into account significant Sommerfeld corrections, we find that the dark matter mass must have some specific values in order not to be in conflict with the current bounds from gamma-ray observations.

Non-thermal production of minimal dark matter via right-handed neutrino decay

Energy Technology Data Exchange (ETDEWEB)

Aoki, Mayumi [Institute for Theoretical Physics, Kanazawa University, Kanazawa 920-1192 (Japan); Toma, Takashi [Laboratoire de Physique Théorique, CNRS - UMR 8627, Université de Paris-Sud 11, F-91405 Orsay Cedex (France); Vicente, Avelino, E-mail: mayumi@hep.s.kanazawa-u.ac.jp, E-mail: takashi.toma@th.u-psud.fr, E-mail: Avelino.Vicente@ulg.ac.be [IFPA, Dep. AGO, Université de Liège, Bat B5, Sart-Tilman B-4000 Liège 1 (Belgium)

2015-09-01

Minimal Dark Matter (MDM) stands as one of the simplest dark matter scenarios. In MDM models, annihilation and co-annihilation processes among the members of the MDM multiplet are usually very efficient, pushing the dark matter mass above O(10) TeV in order to reproduce the observed dark matter relic density. Motivated by this little drawback, in this paper we consider an extension of the MDM scenario by three right-handed neutrinos. Two specific choices for the MDM multiplet are studied: a fermionic SU(2){sub L} quintuplet and a scalar SU(2){sub L} septuplet. The lightest right-handed neutrino, with tiny Yukawa couplings, never reaches thermal equilibrium in the early universe and is produced by freeze-in. This creates a link between dark matter and neutrino physics: dark matter can be non-thermally produced by the decay of the lightest right-handed neutrino after freeze-out, allowing to lower significantly the dark matter mass. We discuss the phenomenology of the non-thermally produced MDM and, taking into account significant Sommerfeld corrections, we find that the dark matter mass must have some specific values in order not to be in conflict with the current bounds from gamma-ray observations.

Small non coding RNAs in adipocyte biology and obesity.

Science.gov (United States)

Amri, Ez-Zoubir; Scheideler, Marcel

2017-11-15

Obesity has reached epidemic proportions world-wide and constitutes a substantial risk factor for hypertension, type 2 diabetes, cardiovascular diseases and certain cancers. So far, regulation of energy intake by dietary and pharmacological treatments has met limited success. The main interest of current research is focused on understanding the role of different pathways involved in adipose tissue function and modulation of its mass. Whole-genome sequencing studies revealed that the majority of the human genome is transcribed, with thousands of non-protein-coding RNAs (ncRNA), which comprise small and long ncRNAs. ncRNAs regulate gene expression at the transcriptional and post-transcriptional level. Numerous studies described the involvement of ncRNAs in the pathogenesis of many diseases including obesity and associated metabolic disorders. ncRNAs represent potential diagnostic biomarkers and promising therapeutic targets. In this review, we focused on small ncRNAs involved in the formation and function of adipocytes and obesity. Copyright © 2017 Elsevier B.V. All rights reserved.

Dynamical analysis for a scalar-tensor model with Gauss-Bonnet and non-minimal couplings

Energy Technology Data Exchange (ETDEWEB)

Granda, L.N.; Jimenez, D.F. [Universidad del Valle, Departamento de Fisica, Cali (Colombia)

2017-10-15

We study the autonomous system for a scalar-tensor model of dark energy with Gauss-Bonnet and non-minimal couplings. The critical points describe important stable asymptotic scenarios including quintessence, phantom and de Sitter attractor solutions. Two functional forms for the coupling functions and the scalar potential are considered: power-law and exponential functions of the scalar field. For the exponential functions the existence of stable quintessence, phantom or de Sitter solutions, allows for an asymptotic behavior where the effective Newtonian coupling becomes constant. The phantom solutions could be realized without appealing to ghost degrees of freedom. Transient inflationary and radiation-dominated phases can also be described. (orig.)

Screening and Identification of putative long non coding RNAs from transcriptome data of a high yielding blackgram (Vigna mungo, Cv. T9

Directory of Open Access Journals (Sweden)

Pankaj Kumar Singh

2018-04-01

Full Text Available Blackgram (Vigna mungo is one of primary legumes cultivated throughout India, Cv.T9 being one of its common high yielding cultivar. This article reports RNA sequencing data and a pipeline for prediction of novel long non-coding RNAs from the sequenced data. The raw data generated during sequencing are available at Sequence Read Archive (SRA of NCBI with accession number- SRX1558530 Keywords: Blackgram, Long non-coding RNA, Legumes, RNA sequencing data

Recent advances in extracellular vesicles enriched with non-coding RNAs related to cancers

Directory of Open Access Journals (Sweden)

Song Yang

2018-03-01

Full Text Available As membrane-bound structures that could be shedded by a parental cell, and fuse with others after shedding, and then release its contents, extracellular vesicles (EVs are considered as an indispensable part of intercellular communication system. The EV contents might be all kinds of bioactive molecules including non-coding RNAs (ncRNAs, a large and complex group of RNAs with various subtypes that function to regulate biological events but classically do not code for proteins. In this review we covered the recently published works that validated the underlying molecular mechanisms regulating EV-associated ncRNAs' biogenesis, signaling, and particularly the systemic bio-effects related mostly to any stage of cancer progression, and the clinical potential of ncRNA-carrying EVs as diagnostic biomarkers and drug-delivery system that is being engineered for better loading and targeting capacity. Our views on the future direction of basic research and applications of EVs containing ncRNAs have also been shared.

De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

Directory of Open Access Journals (Sweden)

Josephine A Reinhardt

Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

Evaluation of Agency Non-Code Layered Pressure Vessels (LPVs) . Volume 2; Appendices

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 document contains the appendices to the main report.

High-throughput bioscreening system utilizing high-performance affinity magnetic carriers exhibiting minimal non-specific protein binding

International Nuclear Information System (INIS)

Hanyu, Naohiro; Nishio, Kosuke; Hatakeyama, Mamoru; Yasuno, Hiroshi; Tanaka, Toshiyuki; Tada, Masaru; Nakagawa, Takashi; Sandhu, Adarsh; Abe, Masanori; Handa, Hiroshi

2009-01-01

For affinity purification of drug target protein we have developed magnetic carriers, narrow in size distribution (184±9 nm), which exhibit minimal non-specific binding of unwanted proteins. The carriers were highly dispersed in aqueous solutions and highly resistant to organic solvents, which enabled immobilization of various hydrophobic chemicals as probes on the carrier surfaces. Utilizing the carriers we have automated the process of separation and purification of the target proteins that had been done by manual operation previously.

Minimal DBM Substraction

DEFF Research Database (Denmark)

David, Alexandre; Håkansson, John; G. Larsen, Kim

In this paper we present an algorithm to compute DBM substractions with a guaranteed minimal number of splits and disjoint DBMs to avoid any redundance. The substraction is one of the few operations that result in a non-convex zone, and thus, requires splitting. It is of prime importance to reduce...

User's guide for SLWDN9, a code for calculating flux-surfaced-averaging of alpha densities, currents, and heating in non-circular tokamaks

International Nuclear Information System (INIS)

Hively, L.M.; Miley, G.M.

1980-03-01

The code calculates flux-surfaced-averaged values of alpha density, current, and electron/ion heating profiles in realistic, non-circular tokamak plasmas. The code is written in FORTRAN and execute on the CRAY-1 machine at the Magnetic Fusion Energy Computer Center

New quantum codes derived from a family of antiprimitive BCH codes

Science.gov (United States)

Liu, Yang; Li, Ruihu; Lü, Liangdong; Guo, Luobin

The Bose-Chaudhuri-Hocquenghem (BCH) codes have been studied for more than 57 years and have found wide application in classical communication system and quantum information theory. In this paper, we study the construction of quantum codes from a family of q2-ary BCH codes with length n=q2m+1 (also called antiprimitive BCH codes in the literature), where q≥4 is a power of 2 and m≥2. By a detailed analysis of some useful properties about q2-ary cyclotomic cosets modulo n, Hermitian dual-containing conditions for a family of non-narrow-sense antiprimitive BCH codes are presented, which are similar to those of q2-ary primitive BCH codes. Consequently, via Hermitian Construction, a family of new quantum codes can be derived from these dual-containing BCH codes. Some of these new antiprimitive quantum BCH codes are comparable with those derived from primitive BCH codes.

Feedback in LT codes for prioritized and non-prioritized data

DEFF Research Database (Denmark)

Sørensen, Jesper Hemming; Popovski, Petar; Østergaard, Jan

2012-01-01

In this paper feedback in LT codes is investigated. The considered type of feedback is acknowledgments, where information on which symbols have been decoded is given to the transmitter. Our analysis reveals that acknowledgments has a very low potential in LT codes with standard degree distributions....... Motivated by this, we analyze the impact of acknowledgments on multi-layer LT codes. In this case, feedback proves advantageous. By using only a single feedback message, it is possible to achieve a significant performance improvement compared to traditional LT codes....

Overview of long non-coding RNA and mRNA expression in response to methamphetamine treatment in vitro

NARCIS (Netherlands)

Xiong, Kun; Long, Lingling; Zhang, Xudong; Qu, Hongke; Deng, Haixiao; Ding, Yanjun; Cai, Jifeng; Wang, Shuchao; Wang, Mi; Liao, Lvshuang; Huang, Jufang; Yi, Chun-Xia; Yan, Jie

2017-01-01

Long non-coding RNAs (IncRNAs) display multiple functions including regulation of neuronal injury. However, their impact in methamphetamine (METH)-induced neurotoxicity has rarely been reported. Here, using microarray analysis, we investigated the expression profiling of lncRNAs and mRNAs in primary

Minimal cut-set methodology for artificial intelligence applications

International Nuclear Information System (INIS)

Weisbin, C.R.; de Saussure, G.; Barhen, J.; Oblow, E.M.; White, J.C.

1984-01-01

This paper reviews minimal cut-set theory and illustrates its application with an example. The minimal cut-set approach uses disjunctive normal form in Boolean algebra and various Boolean operators to simplify very complicated tree structures composed of AND/OR gates. The simplification process is automated and performed off-line using existing computer codes to implement the Boolean reduction on the finite, but large tree structure. With this approach, on-line expert diagnostic systems whose response time is critical, could determine directly whether a goal is achievable by comparing the actual system state to a concisely stored set of preprocessed critical state elements

Construction and decoding of matrix-product codes from nested codes

DEFF Research Database (Denmark)

Hernando, Fernando; Lally, Kristine; Ruano, Diego

2009-01-01

We consider matrix-product codes [C1 ... Cs] · A, where C1, ..., Cs  are nested linear codes and matrix A has full rank. We compute their minimum distance and provide a decoding algorithm when A is a non-singular by columns matrix. The decoding algorithm decodes up to half of the minimum distance....

Minimally inconsistent reasoning in Semantic Web.

Science.gov (United States)

Zhang, Xiaowang

2017-01-01

Reasoning with inconsistencies is an important issue for Semantic Web as imperfect information is unavoidable in real applications. For this, different paraconsistent approaches, due to their capacity to draw as nontrivial conclusions by tolerating inconsistencies, have been proposed to reason with inconsistent description logic knowledge bases. However, existing paraconsistent approaches are often criticized for being too skeptical. To this end, this paper presents a non-monotonic paraconsistent version of description logic reasoning, called minimally inconsistent reasoning, where inconsistencies tolerated in the reasoning are minimized so that more reasonable conclusions can be inferred. Some desirable properties are studied, which shows that the new semantics inherits advantages of both non-monotonic reasoning and paraconsistent reasoning. A complete and sound tableau-based algorithm, called multi-valued tableaux, is developed to capture the minimally inconsistent reasoning. In fact, the tableaux algorithm is designed, as a framework for multi-valued DL, to allow for different underlying paraconsistent semantics, with the mere difference in the clash conditions. Finally, the complexity of minimally inconsistent description logic reasoning is shown on the same level as the (classical) description logic reasoning.

Non-binary decomposition trees - a method of reliability computation for systems with known minimal paths/cuts

Energy Technology Data Exchange (ETDEWEB)

Malinowski, Jacek

2004-05-01

A coherent system with independent components and known minimal paths (cuts) is considered. In order to compute its reliability, a tree structure T is constructed whose nodes contain the modified minimal paths (cuts) and numerical values. The value of a non-leaf node is a function of its child nodes' values. The values of leaf nodes are calculated from a simple formula. The value of the root node is the system's failure probability (reliability). Subsequently, an algorithm computing the system's failure probability (reliability) is constructed. The algorithm scans all nodes of T using a stack structure for this purpose. The nodes of T are alternately put on and removed from the stack, their data being modified in the process. Once the algorithm has terminated, the stack contains only the final modification of the root node of T, and its value is equal to the system's failure probability (reliability)

Optical coding theory with Prime

CERN Document Server

Kwong, Wing C

2013-01-01

Although several books cover the coding theory of wireless communications and the hardware technologies and coding techniques of optical CDMA, no book has been specifically dedicated to optical coding theory-until now. Written by renowned authorities in the field, Optical Coding Theory with Prime gathers together in one volume the fundamentals and developments of optical coding theory, with a focus on families of prime codes, supplemented with several families of non-prime codes. The book also explores potential applications to coding-based optical systems and networks. Learn How to Construct

The long non-coding RNA TUG1 indicates a poor prognosis for colorectal cancer and promotes metastasis by affecting epithelial-mesenchymal transition

OpenAIRE

Sun, Junfeng; Ding, Chaohui; Yang, Zhen; Liu, Tao; Zhang, Xiefu; Zhao, Chunlin; Wang, Jiaxiang

2016-01-01

Background Long intergenic non-coding RNAs (lncRNAs) are a class of non-coding RNAs that are involved in gene expression regulation. Taurine up-regulated gene 1 (TUG1) is a cancer progression related lncRNA in some tumor oncogenesis; however, its role in colorectal cancer (CRC) remains unclear. In this study, we determined the expression patterns of TUG1 in CRC patients and explored its effect on CRC cell metastasis using cultured representative CRC cell lines. Methods The expression levels o...

A Looking-Glass of Non-Coding RNAs in Oral Cancer

Science.gov (United States)

Irimie, Alexandra Iulia; Braicu, Cornelia; Sonea, Laura; Zimta, Alina Andreea; Diudea, Diana; Buduru, Smaranda; Berindan-Neagoe, Ioana

2017-01-01

Oral cancer is a multifactorial pathology and is characterized by the lack of efficient treatment and accurate diagnostic tools. This is mainly due the late diagnosis; therefore, reliable biomarkers for the timely detection of the disease and patient stratification are required. Non-coding RNAs (ncRNAs) are key elements in the physiological and pathological processes of various cancers, which is also reflected in oral cancer development and progression. A better understanding of their role could give a more thorough perspective on the future treatment options for this cancer type. This review offers a glimpse into the ncRNA involvement in oral cancer, which can help the medical community tap into the world of ncRNAs and lay the ground for more powerful diagnostic, prognostic and treatment tools for oral cancer that will ultimately help build a brighter future for these patients. PMID:29206174

An information theoretic approach to use high-fidelity codes to calibrate low-fidelity codes

Energy Technology Data Exchange (ETDEWEB)

Lewis, Allison, E-mail: lewis.allison10@gmail.com [Department of Mathematics, North Carolina State University, Raleigh, NC 27695 (United States); Smith, Ralph [Department of Mathematics, North Carolina State University, Raleigh, NC 27695 (United States); Williams, Brian [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Figueroa, Victor [Sandia National Laboratories, Albuquerque, NM 87185 (United States)

2016-11-01

For many simulation models, it can be prohibitively expensive or physically infeasible to obtain a complete set of experimental data to calibrate model parameters. In such cases, one can alternatively employ validated higher-fidelity codes to generate simulated data, which can be used to calibrate the lower-fidelity code. In this paper, we employ an information-theoretic framework to determine the reduction in parameter uncertainty that is obtained by evaluating the high-fidelity code at a specific set of design conditions. These conditions are chosen sequentially, based on the amount of information that they contribute to the low-fidelity model parameters. The goal is to employ Bayesian experimental design techniques to minimize the number of high-fidelity code evaluations required to accurately calibrate the low-fidelity model. We illustrate the performance of this framework using heat and diffusion examples, a 1-D kinetic neutron diffusion equation, and a particle transport model, and include initial results from the integration of the high-fidelity thermal-hydraulics code Hydra-TH with a low-fidelity exponential model for the friction correlation factor.

Up-regulation of Long Non-coding RNA TUG1 in Hibernating Thirteen-lined Ground Squirrels

Directory of Open Access Journals (Sweden)

Jacques J. Frigault

2016-04-01

Full Text Available Mammalian hibernation is associated with multiple physiological, biochemical, and molecular changes that allow animals to endure colder temperatures. We hypothesize that long non-coding RNAs (lncRNAs, a group of non-coding transcripts with diverse functions, are differentially expressed during hibernation. In this study, expression levels of lncRNAs H19 and TUG1 were assessed via qRT-PCR in liver, heart, and skeletal muscle tissues of the hibernating thirteen-lined ground squirrels (Ictidomys tridecemlineatus. TUG1 transcript levels were significantly elevated 1.94-fold in skeletal muscle of hibernating animals when compared with euthermic animals. Furthermore, transcript levels of HSF2 also increased 2.44-fold in the skeletal muscle in hibernating animals. HSF2 encodes a transcription factor that can be negatively regulated by TUG1 levels and that influences heat shock protein expression. Thus, these observations support the differential expression of the TUG1–HSF2 axis during hibernation. To our knowledge, this study provides the first evidence for differential expression of lncRNAs in torpid ground squirrels, adding lncRNAs as another group of transcripts modulated in this mammalian species during hibernation.

ETFOD: a point model physics code with arbitrary input

International Nuclear Information System (INIS)

Rothe, K.E.; Attenberger, S.E.

1980-06-01

ETFOD is a zero-dimensional code which solves a set of physics equations by minimization. The technique used is different than normally used, in that the input is arbitrary. The user is supplied with a set of variables from which he specifies which variables are input (unchanging). The remaining variables become the output. Presently the code is being used for ETF reactor design studies. The code was written in a manner to allow easy modificaton of equations, variables, and physics calculations. The solution technique is presented along with hints for using the code

Codon size reduction as the origin of the triplet genetic code.

Directory of Open Access Journals (Sweden)

Pavel V Baranov

Full Text Available The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon

First step of the project for implementation of two non-symmetric cooling loops modeled by the ALMOD3 code

International Nuclear Information System (INIS)

Dominguez, L.; Camargo, C.T.M.

1984-09-01

The first step of the project for implementation of two non-symmetric cooling loops modeled by the ALMOD3 computer code is presented. This step consists of the introduction of a simplified model for simulating the steam generator. This model is the GEVAP computer code, integrant part of LOOP code, which simulates the primary coolant circuit of PWR nuclear power plants during transients. The ALMOD3 computer code has a model for the steam generator, called UTSG, which is very detailed. This model has spatial dependence, correlations for 2-phase flow, distinguished correlations for different heat transfer process. The GEVAP model has thermal equilibrium between phases (gaseous and liquid homogeneous mixture), no spatial dependence and uses only one generalized correlation to treat several heat transfer processes. (Author) [pt

Stability of braneworlds with non-minimally coupled multi-scalar fields

Energy Technology Data Exchange (ETDEWEB)

Chen, Feng-Wei; Gu, Bao-Min [Lanzhou University, Institute of Theoretical Physics, Lanzhou (China); Lanzhou University, Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Lanzhou (China); Liu, Yu-Xiao [Lanzhou University, Research Center of Gravitation, Lanzhou (China)

2018-02-15

Linear stability of braneworld models constructed with multi-scalar fields is very different from that of single-scalar field models. It is well known that both the tensor and the scalar perturbations of the latter are stable at linear level. However, in general there is no effective method to deal with the stability problem of the scalar perturbations for braneworld models constructed with non-minimally coupled multi-scalar fields. In this work we present a systematic covariant approach to deal with the scalar perturbations. By introducing the orthonormal bases in field space and making the Kaluza-Klein decomposition, we get a set of coupled Schroedinger-like equations of the scalar perturbation modes. Using the nodal theorem, we show that the result is model-dependent. For superpotential derived brane models, the scalar perturbations are stable, but there exist normalizable scalar zero modes, which will result in unacceptable fifth force on the brane. We also use this method to analyze the f(R) braneworld model with an explicit solution and find that the scalar perturbations are stable and the scalar zero modes cannot be localized on the brane, which ensures that there is no extra long-range force and the Newtonian potential on the brane can be recovered. (orig.)

Effects on vegetable seeds due to non ionizing radiation

Energy Technology Data Exchange (ETDEWEB)

Acri, G.; Oliva, A.; Falcone, G. [Universita della Calabria, Dipt. di Fisica, Cosenza (Italy); Acri, G.; Testagrossa, B.; Vermiglio, G.; Tripepi, M.G. [Universita della Calabria, Dipt. di Ecologia, Cosenza (Italy); Bitonti, M.B.; Chiappetta, A. [Universita di Messina, Dipt. di Protezionistica Ambientale, Sanitaria, Sociale ed Industriale, Messina (Italy)

2006-07-01

Based on the tightly relationship between light and plants growth and development, the present work aims to obtain some further insight into the effects of non ionizing radiation the photo-autotrophic organisms, due to the relevant implications for both scientific knowledge and economical and social effects. In this context, a set of experiments was conducted to investigate the influence of a long-lasting exposition to both RF at 1850 MHz and polarized light source on roots elongation of corn kernels. The radical apparatus was chosen as a sensible parameter and the elongation of the roots was monitored as a function of time. Mitotic index and length of meta-xylem cells were estimated in root apex as an index of cell proliferation and cell expansion activity, respectively. (N.C.)

Effects on vegetable seeds due to non ionizing radiation

International Nuclear Information System (INIS)

Acri, G.; Oliva, A.; Falcone, G.; Acri, G.; Testagrossa, B.; Vermiglio, G.; Tripepi, M.G.; Bitonti, M.B.; Chiappetta, A.

2006-01-01

Based on the tightly relationship between light and plants growth and development, the present work aims to obtain some further insight into the effects of non ionizing radiation the photo-autotrophic organisms, due to the relevant implications for both scientific knowledge and economical and social effects. In this context, a set of experiments was conducted to investigate the influence of a long-lasting exposition to both RF at 1850 MHz and polarized light source on roots elongation of corn kernels. The radical apparatus was chosen as a sensible parameter and the elongation of the roots was monitored as a function of time. Mitotic index and length of meta-xylem cells were estimated in root apex as an index of cell proliferation and cell expansion activity, respectively. (N.C.)

A complete classification of minimal non-PS-groups

Indian Academy of Sciences (India)

Abstract. Let G be a finite group. A subgroup H of G is called s-permutable in G if it permutes with every Sylow subgroup of G, and G is called a PS-group if all minimal subgroups and cyclic subgroups with order 4 of G are s-permutable in G. In this paper, we give a complete classification of finite groups which are not ...

Bursts generate a non-reducible spike-pattern code

Directory of Open Access Journals (Sweden)

Hugo G Eyherabide

2009-05-01

Full Text Available On the single-neuron level, precisely timed spikes can either constitute firing-rate codes or spike-pattern codes that utilize the relative timing between consecutive spikes. There has been little experimental support for the hypothesis that such temporal patterns contribute substantially to information transmission. Using grasshopper auditory receptors as a model system, we show that correlations between spikes can be used to represent behaviorally relevant stimuli. The correlations reflect the inner structure of the spike train: a succession of burst-like patterns. We demonstrate that bursts with different spike counts encode different stimulus features, such that about 20% of the transmitted information corresponds to discriminating between different features, and the remaining 80% is used to allocate these features in time. In this spike-pattern code, the "what" and the "when" of the stimuli are encoded in the duration of each burst and the time of burst onset, respectively. Given the ubiquity of burst firing, we expect similar findings also for other neural systems.

Network-Coded Content Delivery in Femtocaching-Assisted Cellular Networks

KAUST Repository

Shnaiwer, Yousef N.; Sorour, Sameh; Aboutorab, Neda; Sadeghi, Parastoo; Al-Naffouri, Tareq Y.

2015-01-01

Next-generation cellular networks are expected to be assisted by femtocaches (FCs), which collectively store the most popular files for the clients. Given any arbitrary non-fragmented placement of such files, a strict no-latency constraint, and clients' prior knowledge, new file download requests could be efficiently handled by both the FCs and the macrocell base station (MBS) using opportunistic network coding (ONC). In this paper, we aim to find the best allocation of coded file downloads to the FCs so as to minimize the MBS involvement in this download process. We first formulate this optimization problem over an ONC graph, and show that it is NP-hard. We then propose a greedy approach that maximizes the number of files downloaded by the FCs, with the goal to reduce the download share of the MBS. This allocation is performed using a dual conflict ONC graph to avoid conflicts among the FC downloads. Simulations show that our proposed scheme almost achieves the optimal performance and significantly saves on the MBS bandwidth.

Network-Coded Content Delivery in Femtocaching-Assisted Cellular Networks

KAUST Repository

Shnaiwer, Yousef N.

2015-12-06

Next-generation cellular networks are expected to be assisted by femtocaches (FCs), which collectively store the most popular files for the clients. Given any arbitrary non-fragmented placement of such files, a strict no-latency constraint, and clients\\' prior knowledge, new file download requests could be efficiently handled by both the FCs and the macrocell base station (MBS) using opportunistic network coding (ONC). In this paper, we aim to find the best allocation of coded file downloads to the FCs so as to minimize the MBS involvement in this download process. We first formulate this optimization problem over an ONC graph, and show that it is NP-hard. We then propose a greedy approach that maximizes the number of files downloaded by the FCs, with the goal to reduce the download share of the MBS. This allocation is performed using a dual conflict ONC graph to avoid conflicts among the FC downloads. Simulations show that our proposed scheme almost achieves the optimal performance and significantly saves on the MBS bandwidth.

Long Non-Coding RNAs: A Novel Paradigm for Toxicology.

Science.gov (United States)

Dempsey, Joseph L; Cui, Julia Yue

2017-01-01

Long non-coding RNAs (lncRNAs) are over 200 nucleotides in length and are transcribed from the mammalian genome in a tissue-specific and developmentally regulated pattern. There is growing recognition that lncRNAs are novel biomarkers and/or key regulators of toxicological responses in humans and animal models. Lacking protein-coding capacity, the numerous types of lncRNAs possess a myriad of transcriptional regulatory functions that include cis and trans gene expression, transcription factor activity, chromatin remodeling, imprinting, and enhancer up-regulation. LncRNAs also influence mRNA processing, post-transcriptional regulation, and protein trafficking. Dysregulation of lncRNAs has been implicated in various human health outcomes such as various cancers, Alzheimer's disease, cardiovascular disease, autoimmune diseases, as well as intermediary metabolism such as glucose, lipid, and bile acid homeostasis. Interestingly, emerging evidence in the literature over the past five years has shown that lncRNA regulation is impacted by exposures to various chemicals such as polycyclic aromatic hydrocarbons, benzene, cadmium, chlorpyrifos-methyl, bisphenol A, phthalates, phenols, and bile acids. Recent technological advancements, including next-generation sequencing technologies and novel computational algorithms, have enabled the profiling and functional characterizations of lncRNAs on a genomic scale. In this review, we summarize the biogenesis and general biological functions of lncRNAs, highlight the important roles of lncRNAs in human diseases and especially during the toxicological responses to various xenobiotics, evaluate current methods for identifying aberrant lncRNA expression and molecular target interactions, and discuss the potential to implement these tools to address fundamental questions in toxicology. © The Author 2016. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e

Dark matter as a dynamic effect due to a non-minimal gravitational coupling with matter (II): Numerical results

International Nuclear Information System (INIS)

Paramos, J; Bertolami, O

2010-01-01

Following the previous contribution discussing the rich phenomenology of models possessing a non-minimal coupling between matter and geometry, with emphasis on its characteristics and analytical results, the obtained 'dark matter' mimicking mechanism is numerically studied. This allows for ascertaining the order of magnitude of the relevant parameters, leading to a validation of the analytical results and the discussion of possible cosmological implications and deviation from universality.

A non-linear, finite element, heat conduction code to calculate temperatures in solids of arbitrary geometry

International Nuclear Information System (INIS)

Tayal, M.

1987-01-01

Structures often operate at elevated temperatures. Temperature calculations are needed so that the design can accommodate thermally induced stresses and material changes. A finite element computer called FEAT has been developed to calculate temperatures in solids of arbitrary shapes. FEAT solves the classical equation for steady state conduction of heat. The solution is obtained for two-dimensional (plane or axisymmetric) or for three-dimensional problems. Gap elements are use to simulate interfaces between neighbouring surfaces. The code can model: conduction; internal generation of heat; prescribed convection to a heat sink; prescribed temperatures at boundaries; prescribed heat fluxes on some surfaces; and temperature-dependence of material properties like thermal conductivity. The user has a option of specifying the detailed variation of thermal conductivity with temperature. For convenience to the nuclear fuel industry, the user can also opt for pre-coded values of thermal conductivity, which are obtained from the MATPRO data base (sponsored by the U.S. Nuclear Regulatory Commission). The finite element method makes FEAT versatile, and enables it to accurately accommodate complex geometries. The optional link to MATPRO makes it convenient for the nuclear fuel industry to use FEAT, without loss of generality. Special numerical techniques make the code inexpensive to run, for the type of material non-linearities often encounter in the analysis of nuclear fuel. The code, however, is general, and can be used for other components of the reactor, or even for non-nuclear systems. The predictions of FEAT have been compared against several analytical solutions. The agreement is usually better than 5%. Thermocouple measurements show that the FEAT predictions are consistent with measured changes in temperatures in simulated pressure tubes. FEAT was also found to predict well, the axial variations in temperatures in the end-pellets(UO 2 ) of two fuel elements irradiated

Photoautotrophic Polyhydroxybutyrate Granule Formation Is Regulated by Cyanobacterial Phasin PhaP in Synechocystis sp. Strain PCC 6803

Science.gov (United States)

Hauf, Waldemar; Watzer, Björn; Roos, Nora; Klotz, Alexander

2015-01-01

Cyanobacteria are photoautotrophic microorganisms which fix atmospheric carbon dioxide via the Calvin-Benson cycle to produce carbon backbones for primary metabolism. Fixed carbon can also be stored as intracellular glycogen, and in some cyanobacterial species like Synechocystis sp. strain PCC 6803, polyhydroxybutyrate (PHB) accumulates when major nutrients like phosphorus or nitrogen are absent. So far only three enzymes which participate in PHB metabolism have been identified in this organism, namely, PhaA, PhaB, and the heterodimeric PHB synthase PhaEC. In this work, we describe the cyanobacterial PHA surface-coating protein (phasin), which we term PhaP, encoded by ssl2501. Translational fusion of Ssl2501 with enhanced green fluorescent protein (eGFP) showed a clear colocalization to PHB granules. A deletion of ssl2501 reduced the number of PHB granules per cell, whereas the mean PHB granule size increased as expected for a typical phasin. Although deletion of ssl2501 had almost no effect on the amount of PHB, the biosynthetic activity of PHB synthase was negatively affected. Secondary-structure prediction and circular dichroism (CD) spectroscopy of PhaP revealed that the protein consists of two α-helices, both of them associating with PHB granules. Purified PhaP forms oligomeric structures in solution, and both α-helices of PhaP contribute to oligomerization. Together, these results support the idea that Ssl2501 encodes a cyanobacterial phasin, PhaP, which regulates the surface-to-volume ratio of PHB granules. PMID:25911471

Application of golay complementary coded excitation schemes for non-destructive testing of sandwich structures

Science.gov (United States)

Arora, Vanita; Mulaveesala, Ravibabu

2017-06-01

In recent years, InfraRed Thermography (IRT) has become a widely accepted non-destructive testing technique to evaluate the structural integrity of composite sandwich structures due to its full-field, remote, fast and in-service inspection capabilities. This paper presents a novel infrared thermographic approach named as Golay complementary coded thermal wave imaging is presented to detect disbonds in a sandwich structure having face sheets from Glass/Carbon Fibre Reinforced (GFR/CFR) laminates and core of the wooden block.

Grassmannian frames with applications to coding and communication

OpenAIRE

Strohmer, Thomas; Heath Jr., Robert W

2003-01-01

For a given class ${\\cal F}$ of uniform frames of fixed redundancy we define a Grassmannian frame as one that minimizes the maximal correlation $||$ among all frames $\\{f_k\\}_{k \\in {\\cal I}} \\in {\\cal F}$. We first analyze finite-dimensional Grassmannian frames. Using links to packings in Grassmannian spaces and antipodal spherical codes we derive bounds on the minimal achievable correlation for Grassmannian frames. These...

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.

Experimental benchmark of non-local-thermodynamic-equilibrium plasma atomic physics codes; Validation experimentale des codes de physique atomique des plasmas hors equilibre thermodynamique local

Energy Technology Data Exchange (ETDEWEB)

Nagels-Silvert, V

2004-09-15

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.)

Experimental benchmark of non-local-thermodynamic-equilibrium plasma atomic physics codes; Validation experimentale des codes de physique atomique des plasmas hors equilibre thermodynamique local

Energy Technology Data Exchange (ETDEWEB)

Nagels-Silvert, V

2004-09-15

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.)

Synthesizing Modular Invariants for Synchronous Code

Directory of Open Access Journals (Sweden)

Pierre-Loic Garoche

2014-12-01

Full Text Available In this paper, we explore different techniques to synthesize modular invariants for synchronous code encoded as Horn clauses. Modular invariants are a set of formulas that characterizes the validity of predicates. They are very useful for different aspects of analysis, synthesis, testing and program transformation. We describe two techniques to generate modular invariants for code written in the synchronous dataflow language Lustre. The first technique directly encodes the synchronous code in a modular fashion. While in the second technique, we synthesize modular invariants starting from a monolithic invariant. Both techniques, take advantage of analysis techniques based on property-directed reachability. We also describe a technique to minimize the synthesized invariants.

Relay-assisted Network Coding Multicast in the Presence of Neighbours

DEFF Research Database (Denmark)

Khamfroush, Hana; Roetter, Daniel Enrique Lucani; Pahlevani, Peyman

2015-01-01

We study the problem of minimizing the cost of packet transmission from a source to two receivers with the help of a relay and using network coding in wireless mesh networks consisting of many active neighbours sharing the same channel. The cost minimization problem is modeled as a Markov Decisio...

A Looking-Glass of Non-Coding RNAs in Oral Cancer

Directory of Open Access Journals (Sweden)

Alexandra Iulia Irimie

2017-12-01

Full Text Available Oral cancer is a multifactorial pathology and is characterized by the lack of efficient treatment and accurate diagnostic tools. This is mainly due the late diagnosis; therefore, reliable biomarkers for the timely detection of the disease and patient stratification are required. Non-coding RNAs (ncRNAs are key elements in the physiological and pathological processes of various cancers, which is also reflected in oral cancer development and progression. A better understanding of their role could give a more thorough perspective on the future treatment options for this cancer type. This review offers a glimpse into the ncRNA involvement in oral cancer, which can help the medical community tap into the world of ncRNAs and lay the ground for more powerful diagnostic, prognostic and treatment tools for oral cancer that will ultimately help build a brighter future for these patients.

Minimizing The Completion Time Of A Wireless Cooperative Network Using Network Coding

DEFF Research Database (Denmark)

Roetter, Daniel Enrique Lucani; Khamfroush, Hana; Barros, João

2013-01-01

We consider the performance of network coding for a wireless cooperative network in which a source wants to transmit M data packets to two receivers. We assume that receivers can share their received packets with each other or simply wait to receive the packets from the source. The problem of fin...

Minimally conscious state or cortically mediated state?

Science.gov (United States)

Naccache, Lionel

2018-04-01

Durable impairments of consciousness are currently classified in three main neurological categories: comatose state, vegetative state (also recently coined unresponsive wakefulness syndrome) and minimally conscious state. While the introduction of minimally conscious state, in 2002, was a major progress to help clinicians recognize complex non-reflexive behaviours in the absence of functional communication, it raises several problems. The most important issue related to minimally conscious state lies in its criteria: while behavioural definition of minimally conscious state lacks any direct evidence of patient's conscious content or conscious state, it includes the adjective 'conscious'. I discuss this major problem in this review and propose a novel interpretation of minimally conscious state: its criteria do not inform us about the potential residual consciousness of patients, but they do inform us with certainty about the presence of a cortically mediated state. Based on this constructive criticism review, I suggest three proposals aiming at improving the way we describe the subjective and cognitive state of non-communicating patients. In particular, I present a tentative new classification of impairments of consciousness that combines behavioural evidence with functional brain imaging data, in order to probe directly and univocally residual conscious processes.

INTRANS. A computer code for the non-linear structural response analysis of reactor internals under transient loads

International Nuclear Information System (INIS)

Ramani, D.T.

1977-01-01

The 'INTRANS' system is a general purpose computer code, designed to perform linear and non-linear structural stress and deflection analysis of impacting or non-impacting nuclear reactor internals components coupled with reactor vessel, shield building and external as well as internal gapped spring support system. This paper describes in general a unique computational procedure for evaluating the dynamic response of reactor internals, descretised as beam and lumped mass structural system and subjected to external transient loads such as seismic and LOCA time-history forces. The computational procedure is outlined in the INTRANS code, which computes component flexibilities of a discrete lumped mass planar model of reactor internals by idealising an assemblage of finite elements consisting of linear elastic beams with bending, torsional and shear stiffnesses interacted with external or internal linear as well as non-linear multi-gapped spring support system. The method of analysis is based on the displacement method and the code uses the fourth-order Runge-Kutta numerical integration technique as a basis for solution of dynamic equilibrium equations of motion for the system. During the computing process, the dynamic response of each lumped mass is calculated at specific instant of time using well-known step-by-step procedure. At any instant of time then, the transient dynamic motions of the system are held stationary and based on the predicted motions and internal forces of the previous instant. From which complete response at any time-step of interest may then be computed. Using this iterative process, the relationship between motions and internal forces is satisfied step by step throughout the time interval

Non invasive blood flow measurement in cerebellum detects minimal hepatic encephalopathy earlier than psychometric tests.

Science.gov (United States)

Felipo, Vicente; Urios, Amparo; Giménez-Garzó, Carla; Cauli, Omar; Andrés-Costa, Maria-Jesús; González, Olga; Serra, Miguel A; Sánchez-González, Javier; Aliaga, Roberto; Giner-Durán, Remedios; Belloch, Vicente; Montoliu, Carmina

2014-09-07

To assess whether non invasive blood flow measurement by arterial spin labeling in several brain regions detects minimal hepatic encephalopathy. Blood flow (BF) was analyzed by arterial spin labeling (ASL) in different brain areas of 14 controls, 24 cirrhotic patients without and 16 cirrhotic patients with minimal hepatic encephalopathy (MHE). Images were collected using a 3 Tesla MR scanner (Achieva 3T-TX, Philips, Netherlands). Pulsed ASL was performed. Patients showing MHE were detected using the battery Psychometric Hepatic Encephalopathy Score (PHES) consisting of five tests. Different cognitive and motor functions were also assessed: alterations in selective attention were evaluated using the Stroop test. Patients and controls also performed visuo-motor and bimanual coordination tests. Several biochemical parameters were measured: serum pro-inflammatory interleukins (IL-6 and IL-18), 3-nitrotyrosine, cGMP and nitrates+nitrites in plasma, and blood ammonia. Bivariate correlations were evaluated. In patients with MHE, BF was increased in cerebellar hemisphere (P = 0.03) and vermis (P = 0.012) and reduced in occipital lobe (P = 0.017). BF in cerebellar hemisphere was also increased in patients without MHE (P = 0.02). Bimanual coordination was impaired in patients without MHE (P = 0.05) and much more in patients with MHE (P battery and with CFF. BF in cerebellar hemisphere correlates with plasma cGMP and nitric oxide (NO) metabolites. BF in vermis cerebellar also correlates with NO metabolites and with 3-nitrotyrosine. IL-18 in plasma correlates with BF in thalamus and occipital lobe. Non invasive BF determination in cerebellum using ASL may detect MHE earlier than the PHES. Altered NO-cGMP pathway seems to be associated to altered BF in cerebellum.

Minimally inconsistent reasoning in Semantic Web.

Directory of Open Access Journals (Sweden)

Xiaowang Zhang

Full Text Available Reasoning with inconsistencies is an important issue for Semantic Web as imperfect information is unavoidable in real applications. For this, different paraconsistent approaches, due to their capacity to draw as nontrivial conclusions by tolerating inconsistencies, have been proposed to reason with inconsistent description logic knowledge bases. However, existing paraconsistent approaches are often criticized for being too skeptical. To this end, this paper presents a non-monotonic paraconsistent version of description logic reasoning, called minimally inconsistent reasoning, where inconsistencies tolerated in the reasoning are minimized so that more reasonable conclusions can be inferred. Some desirable properties are studied, which shows that the new semantics inherits advantages of both non-monotonic reasoning and paraconsistent reasoning. A complete and sound tableau-based algorithm, called multi-valued tableaux, is developed to capture the minimally inconsistent reasoning. In fact, the tableaux algorithm is designed, as a framework for multi-valued DL, to allow for different underlying paraconsistent semantics, with the mere difference in the clash conditions. Finally, the complexity of minimally inconsistent description logic reasoning is shown on the same level as the (classical description logic reasoning.

Emerging putative associations between non-coding RNAs and protein-coding genes in Neuropathic Pain. Added value from re-using microarray data.

Directory of Open Access Journals (Sweden)

Enrico Capobianco

2016-10-01

Full Text Available Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs. This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve injury, and studied in a rat model, using two neuronal tissues, namely dorsal root ganglion (DRG and sciatic nerve (SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes, and re-purposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parent genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to neuropathic pain. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN, and 8 in DRG, antisense RNA (31 asRNA in SN, and 12 in DRG and pseudogenes (456 in SN, 56 in DRG. In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly

Warm inflation with an oscillatory inflaton in the non-minimal kinetic coupling model

Energy Technology Data Exchange (ETDEWEB)

Goodarzi, Parviz [University of Ayatollah Ozma Borujerdi, Department of Science, Boroujerd (Iran, Islamic Republic of); Sadjadi, H.M. [University of Tehran, Department of Physics, Tehran (Iran, Islamic Republic of)

2017-07-15

In the cold inflation scenario, the slow roll inflation and reheating via coherent rapid oscillation, are usually considered as two distinct eras. When the slow roll ends, a rapid oscillation phase begins and the inflaton decays to relativistic particles reheating the Universe. In another model dubbed warm inflation, the rapid oscillation phase is suppressed, and we are left with only a slow roll period during which the reheating occurs. Instead, in this paper, we propose a new picture for inflation in which the slow roll era is suppressed and only the rapid oscillation phase exists. Radiation generation during this era is taken into account, so we have warm inflation with an oscillatory inflaton. To provide enough e-folds, we employ the non-minimal derivative coupling model. We study the cosmological perturbations and compute the temperature at the end of warm oscillatory inflation. (orig.)

Warm inflation with an oscillatory inflaton in the non-minimal kinetic coupling model

International Nuclear Information System (INIS)

Goodarzi, Parviz; Sadjadi, H.M.

2017-01-01

In the cold inflation scenario, the slow roll inflation and reheating via coherent rapid oscillation, are usually considered as two distinct eras. When the slow roll ends, a rapid oscillation phase begins and the inflaton decays to relativistic particles reheating the Universe. In another model dubbed warm inflation, the rapid oscillation phase is suppressed, and we are left with only a slow roll period during which the reheating occurs. Instead, in this paper, we propose a new picture for inflation in which the slow roll era is suppressed and only the rapid oscillation phase exists. Radiation generation during this era is taken into account, so we have warm inflation with an oscillatory inflaton. To provide enough e-folds, we employ the non-minimal derivative coupling model. We study the cosmological perturbations and compute the temperature at the end of warm oscillatory inflation. (orig.)

Coding chaotic billiards. Pt. 3

International Nuclear Information System (INIS)

Ullmo, D.; Giannoni, M.J.

1993-01-01

Non-tiling compact billiard defined on the pseudosphere is studied 'a la Morse coding'. As for most bounded systems, the coding is non exact. However, two sets of approximate grammar rules can be obtained, one specifying forbidden codes, and the other allowed ones. In-between some sequences remain in the 'unknown' zone, but their relative amount can be reduced to zero if one lets the length of the approximate grammar rules goes to infinity. The relationship between these approximate grammar rules and the 'pruning front' introduced by Cvitanovic et al. is discussed. (authors). 13 refs., 10 figs., 1 tab

Radio frequency channel coding made easy

CERN Document Server

Faruque, Saleh

2016-01-01

This book introduces Radio Frequency Channel Coding to a broad audience. The author blends theory and practice to bring readers up-to-date in key concepts, underlying principles and practical applications of wireless communications. The presentation is designed to be easily accessible, minimizing mathematics and maximizing visuals.

New applications of Equinox code for real-time plasma equilibrium and profile reconstruction for tokamaks

International Nuclear Information System (INIS)

Bosak, K.; Blum, J.; Joffrin, E.

2004-01-01

Recent development of real-time equilibrium code Equinox using a fixed-point algorithm allow major plasma magnetic parameters to be identified in real-time, using rigorous analytical method. The code relies on the boundary flux code providing magnetic flux values on the first wall of vacuum vessel. By means of least-square minimization of differences between magnetic field obtained from previous solution and the next measurements the code identifies the source term of the non-linear Grad-Shafranov equation. The strict use of analytical equations together with a flexible algorithm offers an opportunity to include new measurements into stable magnetic equilibrium code and compare the results directly between several tokamaks while maintaining the same physical model (i.e. no iron model is necessary inside the equilibrium code). The successful implementation of this equilibrium code for JET and Tore Supra has already been published. In this paper, we show the preliminary results of predictive runs of the Equinox code using the ITER geometry. Because the real-time control experiments of plasma profile at JET using the code has been shown unstable when using magnetic and polarimetric measurements (that could be indirectly translated into accuracy vs robustness tradeoff), we plan an outline of the algorithm that will allow us to further constrain the plasma current profile using the central value of pressure of the plasma in real-time in order to better define the poloidal beta (this constraint is not necessary with purely magnetic equilibrium). (authors)

New applications of Equinox code for real-time plasma equilibrium and profile reconstruction for tokamaks

Energy Technology Data Exchange (ETDEWEB)

Bosak, K.; Blum, J. [Universite de Nice-Sophia-Antipolis, Lab. J. A. Dieudonne, 06 - Nice (France); Joffrin, E. [Association Euratom-CEA Cadarache, 13 - Saint-Paul-lez-Durance (France). Dept. de Recherches sur la Fusion Controlee

2004-07-01

Recent development of real-time equilibrium code Equinox using a fixed-point algorithm allow major plasma magnetic parameters to be identified in real-time, using rigorous analytical method. The code relies on the boundary flux code providing magnetic flux values on the first wall of vacuum vessel. By means of least-square minimization of differences between magnetic field obtained from previous solution and the next measurements the code identifies the source term of the non-linear Grad-Shafranov equation. The strict use of analytical equations together with a flexible algorithm offers an opportunity to include new measurements into stable magnetic equilibrium code and compare the results directly between several tokamaks while maintaining the same physical model (i.e. no iron model is necessary inside the equilibrium code). The successful implementation of this equilibrium code for JET and Tore Supra has already been published. In this paper, we show the preliminary results of predictive runs of the Equinox code using the ITER geometry. Because the real-time control experiments of plasma profile at JET using the code has been shown unstable when using magnetic and polarimetric measurements (that could be indirectly translated into accuracy vs robustness tradeoff), we plan an outline of the algorithm that will allow us to further constrain the plasma current profile using the central value of pressure of the plasma in real-time in order to better define the poloidal beta (this constraint is not necessary with purely magnetic equilibrium). (authors)

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer.

Science.gov (United States)

Wojcik, Sylwia E; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z; Rai, Kanti R; Kipps, Thomas J; Keating, Michael J; Croce, Carlo M; Calin, George A

2010-02-01

Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas.

Balanced and sparse Tamo-Barg codes

KAUST Repository

Halbawi, Wael; Duursma, Iwan; Dau, Hoang; Hassibi, Babak

2017-01-01

We construct balanced and sparse generator matrices for Tamo and Barg's Locally Recoverable Codes (LRCs). More specifically, for a cyclic Tamo-Barg code of length n, dimension k and locality r, we show how to deterministically construct a generator matrix where the number of nonzeros in any two columns differs by at most one, and where the weight of every row is d + r - 1, where d is the minimum distance of the code. Since LRCs are designed mainly for distributed storage systems, the results presented in this work provide a computationally balanced and efficient encoding scheme for these codes. The balanced property ensures that the computational effort exerted by any storage node is essentially the same, whilst the sparse property ensures that this effort is minimal. The work presented in this paper extends a similar result previously established for Reed-Solomon (RS) codes, where it is now known that any cyclic RS code possesses a generator matrix that is balanced as described, but is sparsest, meaning that each row has d nonzeros.

Balanced and sparse Tamo-Barg codes

KAUST Repository

Halbawi, Wael

2017-08-29

We construct balanced and sparse generator matrices for Tamo and Barg\\'s Locally Recoverable Codes (LRCs). More specifically, for a cyclic Tamo-Barg code of length n, dimension k and locality r, we show how to deterministically construct a generator matrix where the number of nonzeros in any two columns differs by at most one, and where the weight of every row is d + r - 1, where d is the minimum distance of the code. Since LRCs are designed mainly for distributed storage systems, the results presented in this work provide a computationally balanced and efficient encoding scheme for these codes. The balanced property ensures that the computational effort exerted by any storage node is essentially the same, whilst the sparse property ensures that this effort is minimal. The work presented in this paper extends a similar result previously established for Reed-Solomon (RS) codes, where it is now known that any cyclic RS code possesses a generator matrix that is balanced as described, but is sparsest, meaning that each row has d nonzeros.

An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

DEFF Research Database (Denmark)

Frøkjær-Jensen, Christian; Jain, Nimit; Hansen, Loren

2016-01-01

/or structure. Here, we demonstrate that a pervasive non-coding DNA feature in Caenorhabditis elegans, characterized by 10-base pair periodic An/Tn-clusters (PATCs), can license transgenes for germline expression within repressive chromatin domains. Transgenes containing natural or synthetic PATCs are resistant...

CVD-associated non-coding RNA, ANRIL, modulates expression of atherogenic pathways in VSMC

International Nuclear Information System (INIS)

Congrains, Ada; Kamide, Kei; Katsuya, Tomohiro; Yasuda, Osamu; Oguro, Ryousuke; Yamamoto, Koichi; Ohishi, Mitsuru; Rakugi, Hiromi

2012-01-01

Highlights: ► ANRIL maps in the strongest susceptibility locus for cardiovascular disease. ► Silencing of ANRIL leads to altered expression of tissue remodeling-related genes. ► The effects of ANRIL on gene expression are splicing variant specific. ► ANRIL affects progression of cardiovascular disease by regulating proliferation and apoptosis pathways. -- Abstract: ANRIL is a newly discovered non-coding RNA lying on the strongest genetic susceptibility locus for cardiovascular disease (CVD) in the chromosome 9p21 region. Genome-wide association studies have been linking polymorphisms in this locus with CVD and several other major diseases such as diabetes and cancer. The role of this non-coding RNA in atherosclerosis progression is still poorly understood. In this study, we investigated the implication of ANRIL in the modulation of gene sets directly involved in atherosclerosis. We designed and tested siRNA sequences to selectively target two exons (exon 1 and exon 19) of the transcript and successfully knocked down expression of ANRIL in human aortic vascular smooth muscle cells (HuAoVSMC). We used a pathway-focused RT-PCR array to profile gene expression changes caused by ANRIL knock down. Notably, the genes affected by each of the siRNAs were different, suggesting that different splicing variants of ANRIL might have distinct roles in cell physiology. Our results suggest that ANRIL splicing variants play a role in coordinating tissue remodeling, by modulating the expression of genes involved in cell proliferation, apoptosis, extra-cellular matrix remodeling and inflammatory response to finally impact in the risk of cardiovascular disease and other pathologies.

Crosstalk between long non-coding RNAs and Wnt/β-catenin signalling in cancer.

Science.gov (United States)

Yang, Gang; Shen, Tianyi; Yi, Xiaoming; Zhang, Zhengyu; Tang, Chaopeng; Wang, Longxin; Zhou, Yulin; Zhou, Wenquan

2018-04-01

Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the human genome which perform crucial functions in diverse biological processes. The abnormal expression of some lncRNAs has been found in tumorigenesis, development and therapy resistance of cancers. They may act as oncogenes or tumour suppressors and can be used as diagnostic or prognostic markers, prompting their therapeutic potentials in cancer treatments. Studies have indicated that many lncRNAs are involved in the regulation of several signal pathways, including Wnt/β-catenin signalling pathway, which has been reported to play a significant role in regulating embryogenesis, cell proliferation and controlling tumour biology. Emerging evidences have suggested that lncRNAs can interact with several components of the Wnt/β-catenin signalling pathway to regulate the expression of Wnt target genes in cancer. Moreover, the expression of lncRNAs can also be influenced by the pathway. Nevertheless, Wnt/β-catenin signalling pathway-related lncRNAs and their interactions in cancer are not systematically analysed before. Considering these, this review emphasized the associations between lncRNAs and Wnt/β-catenin signalling pathway in cancer initiation, progression and their therapeutic influence. We also provided an overview on characteristics of lncRNAs and Wnt/β-catenin signalling pathway and discussed their functions in tumour biology. Finally, targeting lncRNAs or/and molecules associated with the Wnt/β-catenin signalling pathway may be a feasible therapeutic method in the future. © 2018 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Circular codes revisited: a statistical approach.

Science.gov (United States)

Gonzalez, D L; Giannerini, S; Rosa, R

2011-04-21

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

A perturbation technique for shield weight minimization

International Nuclear Information System (INIS)

Watkins, E.F.; Greenspan, E.

1993-01-01

The radiation shield optimization code SWAN (Ref. 1) was originally developed for minimizing the thickness of a shield that will meet a given dose (or another) constraint or for extremizing a performance parameter of interest (e.g., maximizing energy multiplication or minimizing dose) while maintaining the shield volume constraint. The SWAN optimization process proved to be highly effective (e.g., see Refs. 2, 3, and 4). The purpose of this work is to investigate the applicability of the SWAN methodology to problems in which the weight rather than the volume is the relevant shield characteristic. Such problems are encountered in shield design for space nuclear power systems. The investigation is carried out using SWAN with the coupled neutron-photon cross-section library FLUNG (Ref. 5)

Up-regulation of Long Non-coding RNA TUG1 in Hibernating Thirteen-lined Ground Squirrels.

Science.gov (United States)

Frigault, Jacques J; Lang-Ouellette, Daneck; Morin, Pier

2016-04-01

Mammalian hibernation is associated with multiple physiological, biochemical, and molecular changes that allow animals to endure colder temperatures. We hypothesize that long non-coding RNAs (lncRNAs), a group of non-coding transcripts with diverse functions, are differentially expressed during hibernation. In this study, expression levels of lncRNAsH19 and TUG1 were assessed via qRT-PCR in liver, heart, and skeletal muscle tissues of the hibernating thirteen-lined ground squirrels (Ictidomys tridecemlineatus). TUG1 transcript levels were significantly elevated 1.94-fold in skeletal muscle of hibernating animals when compared with euthermic animals. Furthermore, transcript levels of HSF2 also increased 2.44-fold in the skeletal muscle in hibernating animals. HSF2 encodes a transcription factor that can be negatively regulated by TUG1 levels and that influences heat shock protein expression. Thus, these observations support the differential expression of the TUG1-HSF2 axis during hibernation. To our knowledge, this study provides the first evidence for differential expression of lncRNAs in torpid ground squirrels, adding lncRNAs as another group of transcripts modulated in this mammalian species during hibernation. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Parallelization of Subchannel Analysis Code MATRA

International Nuclear Information System (INIS)

Kim, Seongjin; Hwang, Daehyun; Kwon, Hyouk

2014-01-01

A stand-alone calculation of MATRA code used up pertinent computing time for the thermal margin calculations while a relatively considerable time is needed to solve the whole core pin-by-pin problems. In addition, it is strongly required to improve the computation speed of the MATRA code to satisfy the overall performance of the multi-physics coupling calculations. Therefore, a parallel approach to improve and optimize the computability of the MATRA code is proposed and verified in this study. The parallel algorithm is embodied in the MATRA code using the MPI communication method and the modification of the previous code structure was minimized. An improvement is confirmed by comparing the results between the single and multiple processor algorithms. The speedup and efficiency are also evaluated when increasing the number of processors. The parallel algorithm was implemented to the subchannel code MATRA using the MPI. The performance of the parallel algorithm was verified by comparing the results with those from the MATRA with the single processor. It is also noticed that the performance of the MATRA code was greatly improved by implementing the parallel algorithm for the 1/8 core and whole core problems

Application of Inverse Gamma Transport to Material Thickness Identification with SGRD Code

Directory of Open Access Journals (Sweden)

Humbert Philippe

2017-01-01

Full Text Available SGRD (Spectroscopy, Gamma rays, Rapid, Deterministic code is used to infer the dimensions of a one dimensional model of a shielded gamma ray source. The method is based on the simulation of the uncollided leakage current of discrete gamma lines that are produced by nuclear decay. Experimentally, the unscattered gamma lines leakage current is obtained by processing high precision gamma spectroscopy measurements. The material thicknesses are computed with SGRD using a fast ray-tracing algorithm embedded in a non-linear multidimensional iterative optimization procedure that minimizes the error metric between calculated and measured signatures. For verification, numerical results on a test problem are presented.

Search for a non-minimal Higgs boson produced in the reaction e+e- → hZ∗

Science.gov (United States)

Buskulic, D.; de Bonis, I.; Decamp, D.; Ghez, P.; Goy, C.; Lees, J.-P.; Minard, M.-N.; Pietrzyk, B.; Ariztizabal, F.; Comas, P.; Crespo, J. M.; Delfino, M.; Efthymiopoulos, I.; Fernandez, E.; Fernandez-Bosman, M.; Gaitan, V.; Garrido, Ll.; Mattison, T.; Pacheco, A.; Padilla, C.; Pascual, A.; Creanza, D.; de Palma, M.; Farilla, A.; Iaselli, G.; Maggi, G.; Natali, S.; Nuzzo, S.; Quattromini, M.; Ranieri, A.; Raso, G.; Romano, F.; Ruggieri, F.; Selvaggi, G.; Silvestris, L.; Tempesta, P.; Zito, G.; Chai, Y.; Hu, H.; Huang, D.; Huang, X.; Lin, J.; Wang, T.; Xie, Y.; Xu, D.; Xu, R.; Zhang, J.; Zhang, L.; Zhao, W.; Blucher, E.; Bonvicini, G.; Boudreau, J.; Casper, D.; Drevermann, H.; Forty, R. W.; Ganis, G.; Gay, C.; Hagelberg, R.; Harvey, J.; Hilgart, J.; Jacobsen, R.; Jost, B.; Knobloch, J.; Lehraus, I.; Lohse, T.; Maggi, M.; Markou, C.; Martinez, M.; Mato, P.; Meinhard, H.; Minten, A.; Miotto, A.; Miquel, R.; Moser, H.-G.; Palazzi, P.; Pater, J. R.; Perlas, J. A.; Pusztaszeri, J.-F.; Ranjard, F.; Redlinger, G.; Rolandi, L.; Rothberg, J.; Ruan, T.; Saich, M.; Schlatter, D.; Schmelling, M.; Sefkow, F.; Tejessy, W.; Tomalin, I. R.; Veenhof, R.; Wachsmuth, H.; Wasserbaech, S.; Wiedenmann, W.; Wildish, T.; Witzeling, W.; Wotschack, J.; Ajaltouni, Z.; Badaud, F.; Bardadin-Otwinowska, M.; El Fellous, R.; Falvard, A.; Gay, P.; Guicheney, C.; Henrard, P.; Jousset, J.; Michel, B.; Montret, J.-C.; Pallin, D.; Perret, P.; Podlyski, F.; Proriol, J.; Prulhière, F.; Saadi, F.; Fearnley, T.; Hansen, J. B.; Hansen, J. D.; Hansen, J. R.; Hansen, P. H.; Møllerud, R.; Nilsson, B. S.; Kyriakis, A.; Simopoulo, E.; Siotis, I.; Vayaki, A.; Zachariadou, K.; Badier, J.; Blondel, A.; Bonneaud, G.; Brient, J. C.; Fouque, G.; Orteu, S.; Rougé, A.; Rumpf, M.; Tanaka, R.; Verderi, M.; Videau, H.; Candlin, D. J.; Parsons, M. I.; Veitch, E.; Focardi, E.; Moneta, L.; Parrini, G.; Corden, M.; Georgiopoulos, C.; Ikeda, M.; Levinthal, D.; Antonelli, A.; Baldini, R.; Bencivenni, G.; Bologna, G.; Bossi, F.; Campana, P.; Capon, G.; Cerutti, F.; Chiarella, V.; D'Ettorre-Piazzoli, B.; Felici, G.; Laurelli, P.; Mannocchi, G.; Murtas, F.; Murtas, G. P.; Passalacqua, L.; Pepe-Altarelli, M.; Picchi, P.; Colrain, P.; Ten Have, I.; Lynch, J. G.; Maitland, W.; Morton, W. T.; Raine, C.; Reeves, P.; Scarr, J. M.; Smith, K.; Smith, M. G.; Thompson, A. S.; Turnbull, R. M.; Brandl, B.; Braun, O.; Geweniger, C.; Hanke, P.; Hepp, V.; Kluge, E. E.; Maumary, Y.; Putzer, A.; Rensch, B.; Stahl, A.; Tittel, K.; Wunsch, M.; Beuselinck, R.; Binnie, D. M.; Cameron, W.; Cattaneo, M.; Colling, D. J.; Dornan, P. J.; Greene, A. M.; Hassard, J. F.; Lieske, N. M.; Moutoussi, A.; Nash, J.; Patton, S.; Payne, D. G.; Phillips, M. J.; San Martin, G.; Sedgbeer, J. K.; Wright, A. G.; Girtler, P.; Kuhn, D.; Rudolph, G.; Vogl, R.; Bowdery, C. K.; Brodbeck, T. J.; Finch, A. J.; Foster, F.; Hughes, G.; Jackson, D.; Keemer, N. R.; Nuttall, M.; Patel, A.; Sloan, T.; Snow, S. W.; Whelan, E. P.; Kleinknecht, K.; Raab, J.; Renk, B.; Sander, H.-G.; Schmidt, H.; Steeg, F.; Walther, S. M.; Wanke, R.; Wolf, B.; Bencheikh, A. M.; Benchouk, C.; Bonissent, A.; Carr, J.; Coyle, P.; Drinkard, J.; Etienne, F.; Nicod, D.; Papalexiou, S.; Payre, P.; Roos, L.; Rousseau, D.; Schwemling, P.; Talby, M.; Adlung, S.; Assmann, R.; Bauer, C.; Blum, W.; Brown, D.; Cattaneo, P.; Dehning, B.; Dietl, H.; Dydak, F.; Frank, M.; Halley, A. W.; Jakobs, K.; Lauber, J.; Lütjens, G.; Lutz, G.; Männer, W.; Richter, R.; Schröder, J.; Schwarz, A. S.; Settles, R.; Seywerd, H.; Stierlin, U.; Stiegler, U.; Denis, R. St.; Wolf, G.; Alemany, R.; Boucrot, J.; Callot, O.; Cordier, A.; Davier, M.; Duflot, L.; Grivaz, J.-F.; Heusse, Ph.; Jaffe, D. E.; Janot, P.; Kim, D. W.; Le Diberder, F.; Lefrançois, J.; Lutz, A.-M.; Schune, M.-H.; Veillet, J.-J.; Videau, I.; Zhang, Z.; Abbaneo, D.; Bagliesi, G.; Batignani, G.; Bottigli, U.; Bozzi, C.; Calderini, G.; Carpinelli, M.; Ciocci, M. A.; Dell'Orso, R.; Ferrante, I.; Fidecaro, F.; Foà, L.; Forti, F.; Giassi, A.; Giorgi, M. A.; Gregorio, A.; Ligabue, F.; Lusiani, A.; Mannelli, E. B.; Marrocchesi, P. S.; Messineo, A.; Palla, F.; Rizzo, G.; Sanguinetti, G.; Spagnolo, P.; Steinberger, J.; Tenchini, R.; Tonelli, G.; Triggiani, G.; Vannini, C.; Venturi, A.; Verdini, P. G.; Walsh, J.; Betteridge, A. P.; Gao, Y.; Green, M. G.; March, P. V.; Mir, Ll. M.; Medcalf, T.; Quazi, I. S.; Strong, J. A.; West, L. R.; Botterill, D. R.; Clifft, R. W.; Edgecock, T. R.; Haywood, S.; Norton, P. R.; Thompson, J. C.; Bloch-Devaux, B.; Colas, P.; Duarte, H.; Emery, S.; Kozanecki, W.; Lançon, E.; Lemaire, M. C.; Locci, E.; Marx, B.; Perez, P.; Rander, J.; Renardy, J.-F.; Rosowsky, A.; Roussarie, A.; Schuller, J.-P.; Schwindling, J.; Si Mohand, D.; Vallage, B.; Johnson, R. P.; Litke, A. M.; Taylor, G.; Wear, J.; Ashman, J. G.; Babbage, W.; Booth, C. N.; Buttar, C.; Cartwright, S.; Combley, F.; Dawson, I.; Thompson, L. F.; Barberio, E.; Böhrer, A.; Brandt, S.; Cowan, G.; Grupen, C.; Lutters, G.; Rivera, F.; Schäfer, U.; Smolik, L.; Bosisio, L.; Della Marina, R.; Giannini, G.; Gobbo, B.; Ragusa, F.; Bellantoni, L.; Chen, W.; Conway, J. S.; Feng, Z.; Ferguson, D. P. S.; Gao, Y. S.; Grahl, J.; Harton, J. L.; Hayes, O. J.; Nachtman, J. M.; Pan, Y. B.; Saadi, Y.; Schmitt, M.; Scott, I.; Sharma, V.; Shi, Z. H.; Turk, J. D.; Walsh, A. M.; Weber, F. V.; Sau Lan Wu; Wu, X.; Zheng, M.; Zobernig, G.; Aleph Collaboration

1993-08-01

A data sample corresponding to 1.23 million hadronic Z decays collected by the ALEPH detector at LEP has been searched for signals of the production of a non-minimal CP-even Higgs boson h in the reaction e+e- → hZ∗. The h decay modes considered were: those of the minimal standard model Higgs boson, with modified branching ratios; decays into a pair of CP-odd Higgs bosons A; and decays into invisible final states. Only one event was found, a very acoplanar e +e - pair which could originate from the standard model background process e+e- → e+e-v v¯. Upper limits for the cross-section of the reaction e+e- → hZ∗ have been derived as a function of mh, the mass of the Higgs boson h. In the case of invisible decays, the 95% CL lower limit on mh is 65 GeV/ c2 for a production cross-section equal to that of a minimal standard model Higgs boson. When combined with previous ALEPH results on the reaction e +e - → hA, these cross-section upper limits exclude a domain in the ( mhmA) plane of the MSSM such that if invisible h and A decays can be neglected, 95% CL lower limits of 44 and 21 GeV/ c2 result for mh and mA, respectively, independent of the other parameters of the model.

Super-linear Precision in Simple Neural Population Codes

Science.gov (United States)

Schwab, David; Fiete, Ila

2015-03-01

A widely used tool for quantifying the precision with which a population of noisy sensory neurons encodes the value of an external stimulus is the Fisher Information (FI). Maximizing the FI is also a commonly used objective for constructing optimal neural codes. The primary utility and importance of the FI arises because it gives, through the Cramer-Rao bound, the smallest mean-squared error achievable by any unbiased stimulus estimator. However, it is well-known that when neural firing is sparse, optimizing the FI can result in codes that perform very poorly when considering the resulting mean-squared error, a measure with direct biological relevance. Here we construct optimal population codes by minimizing mean-squared error directly and study the scaling properties of the resulting network, focusing on the optimal tuning curve width. We then extend our results to continuous attractor networks that maintain short-term memory of external stimuli in their dynamics. Here we find similar scaling properties in the structure of the interactions that minimize diffusive information loss.

Long non-coding RNAs as regulators of the endocrine system.

Science.gov (United States)

Knoll, Marko; Lodish, Harvey F; Sun, Lei

2015-03-01

Long non-coding RNAs (lncRNAs) are a large and diverse group of RNAs that are often lineage-specific and that regulate multiple biological functions. Many are nuclear and are essential parts of ribonucleoprotein complexes that modify chromatin segments and establish active or repressive chromatin states; others are cytosolic and regulate the stability of mRNA or act as microRNA sponges. This Review summarizes the current knowledge of lncRNAs as regulators of the endocrine system, with a focus on the identification and mode of action of several endocrine-important lncRNAs. We highlight lncRNAs that have a role in the development and function of pancreatic β cells, white and brown adipose tissue, and other endocrine organs, and discuss the involvement of these molecules in endocrine dysfunction (for example, diabetes mellitus). We also address the associations of lncRNAs with nuclear receptors involved in major hormonal signalling pathways, such as estrogen and androgen receptors, and the relevance of these associations in certain endocrine cancers.

Improved Iterative Hard- and Soft-Reliability Based Majority-Logic Decoding Algorithms for Non-Binary Low-Density Parity-Check Codes

Science.gov (United States)

Xiong, Chenrong; Yan, Zhiyuan

2014-10-01

Non-binary low-density parity-check (LDPC) codes have some advantages over their binary counterparts, but unfortunately their decoding complexity is a significant challenge. The iterative hard- and soft-reliability based majority-logic decoding algorithms are attractive for non-binary LDPC codes, since they involve only finite field additions and multiplications as well as integer operations and hence have significantly lower complexity than other algorithms. In this paper, we propose two improvements to the majority-logic decoding algorithms. Instead of the accumulation of reliability information in the existing majority-logic decoding algorithms, our first improvement is a new reliability information update. The new update not only results in better error performance and fewer iterations on average, but also further reduces computational complexity. Since existing majority-logic decoding algorithms tend to have a high error floor for codes whose parity check matrices have low column weights, our second improvement is a re-selection scheme, which leads to much lower error floors, at the expense of more finite field operations and integer operations, by identifying periodic points, re-selecting intermediate hard decisions, and changing reliability information.

Scaling Optimization of the SIESTA MHD Code

Science.gov (United States)

Seal, Sudip; Hirshman, Steven; Perumalla, Kalyan

2013-10-01

SIESTA is a parallel three-dimensional plasma equilibrium code capable of resolving magnetic islands at high spatial resolutions for toroidal plasmas. Originally designed to exploit small-scale parallelism, SIESTA has now been scaled to execute efficiently over several thousands of processors P. This scaling improvement was accomplished with minimal intrusion to the execution flow of the original version. First, the efficiency of the iterative solutions was improved by integrating the parallel tridiagonal block solver code BCYCLIC. Krylov-space generation in GMRES was then accelerated using a customized parallel matrix-vector multiplication algorithm. Novel parallel Hessian generation algorithms were integrated and memory access latencies were dramatically reduced through loop nest optimizations and data layout rearrangement. These optimizations sped up equilibria calculations by factors of 30-50. It is possible to compute solutions with granularity N/P near unity on extremely fine radial meshes (N > 1024 points). Grid separation in SIESTA, which manifests itself primarily in the resonant components of the pressure far from rational surfaces, is strongly suppressed by finer meshes. Large problem sizes of up to 300 K simultaneous non-linear coupled equations have been solved on the NERSC supercomputers. Work supported by U.S. DOE under Contract DE-AC05-00OR22725 with UT-Battelle, LLC.

TUG1: a pivotal oncogenic long non-coding RNA of human cancers.

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Li, Zheng; Shen, Jianxiong; Chan, Matthew T V; Wu, William Ka Kei

2016-08-01

Long non-coding RNAs (lncRNAs) are a group greater than 200 nucleotides in length. An increasing number of studies has shown that lncRNAs play important roles in diverse cellular processes, including proliferation, differentiation, apoptosis, invasion and chromatin remodelling. In this regard, deregulation of lncRNAs has been documented in human cancers. TUG1 is a recently identified oncogenic lncRNA whose aberrant upregulation has been detected in different types of cancer, including B-cell malignancies, oesophageal squamous cell carcinoma, bladder cancer, hepatocellular carcinoma and osteosarcoma. In these malignancies, knock-down of TUG1 has been shown to suppress cell proliferation, invasion and/or colony formation. Interestingly, TUG1 has been found to be downregulated in non-small cell lung carcinoma, indicative of its tissue-specific function in tumourigenesis. Pertinent to clinical practice, TUG1 may act as a prognostic biomarker for tumours. In this review, we summarize current knowledge concerning the role of TUG1 in tumour progression and discuss mechanisms associated with it. © 2016 John Wiley & Sons Ltd.

Evaluation of Long Stress-Induced Non-coding Transcripts 5 Polymorphism in Iranian Patients with Bladder Cancer

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Mahla Nazari

2016-07-01

Full Text Available Background: Bladder cancer (BC is the most commonly diagnosed genitourinary cancer in Iran, presented in both men and women. BC is a multifactorial trait resulting from the complex interaction between several genes and environmental factors. Long stress-induced non-coding transcript 5 (LSINCT5, a member of the long non-coding RNAs, is abundantly expressed in high proliferative cells, as well as the cells vulnerable to cellular stress in response to chemical carcinogens. This case-control study aimed to determine any association between LSINCT5 rs2962586 polymorphism and bladder cancer. Materials and Methods: A group of 150 patients with BC were compared with 143 subjects as a control group. Genotyping of the rs2962586 polymorphism was done using tetra- primer amplification refractory mutation system-polymerase chain reaction (T-ARMS PCR method. Results: Genotype and allele distribution were not significantly different between the case and control groups. Smoking was found to be the confounding risk factor for bladder cancer. Conclusion: Considering the result of our analyses, it seems that LSINCT5 could not affect individual susceptibility to BC among Iranian patients, however, it can be considered as a disease predictor among smokers.

Resistor-logic demultiplexers for nanoelectronics based on constant-weight codes.

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Kuekes, Philip J; Robinett, Warren; Roth, Ron M; Seroussi, Gadiel; Snider, Gregory S; Stanley Williams, R

2006-02-28

The voltage margin of a resistor-logic demultiplexer can be improved significantly by basing its connection pattern on a constant-weight code. Each distinct code determines a unique demultiplexer, and therefore a large family of circuits is defined. We consider using these demultiplexers for building nanoscale crossbar memories, and determine the voltage margin of the memory system based on a particular code. We determine a purely code-theoretic criterion for selecting codes that will yield memories with large voltage margins, which is to minimize the ratio of the maximum to the minimum Hamming distance between distinct codewords. For the specific example of a 64 × 64 crossbar, we discuss what codes provide optimal performance for a memory.

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

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Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

2016-06-15

Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available

Decoding the non-coding genome: elucidating genetic risk outside the coding genome.

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Barr, C L; Misener, V L

2016-01-01

Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Theory of epigenetic coding.

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Elder, D

1984-06-07

The logic of genetic control of development may be based on a binary epigenetic code. This paper revises the author's previous scheme dealing with the numerology of annelid metamerism in these terms. Certain features of the code had been deduced to be combinatorial, others not. This paradoxical contrast is resolved here by the interpretation that these features relate to different operations of the code; the combinatiorial to coding identity of units, the non-combinatorial to coding production of units. Consideration of a second paradox in the theory of epigenetic coding leads to a new solution which further provides a basis for epimorphic regeneration, and may in particular throw light on the "regeneration-duplication" phenomenon. A possible test of the model is also put forward.

Joint design of QC-LDPC codes for coded cooperation system with joint iterative decoding

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Zhang, Shunwai; Yang, Fengfan; Tang, Lei; Ejaz, Saqib; Luo, Lin; Maharaj, B. T.

2016-03-01

In this paper, we investigate joint design of quasi-cyclic low-density-parity-check (QC-LDPC) codes for coded cooperation system with joint iterative decoding in the destination. First, QC-LDPC codes based on the base matrix and exponent matrix are introduced, and then we describe two types of girth-4 cycles in QC-LDPC codes employed by the source and relay. In the equivalent parity-check matrix corresponding to the jointly designed QC-LDPC codes employed by the source and relay, all girth-4 cycles including both type I and type II are cancelled. Theoretical analysis and numerical simulations show that the jointly designed QC-LDPC coded cooperation well combines cooperation gain and channel coding gain, and outperforms the coded non-cooperation under the same conditions. Furthermore, the bit error rate performance of the coded cooperation employing jointly designed QC-LDPC codes is better than those of random LDPC codes and separately designed QC-LDPC codes over AWGN channels.

The NIMROD Code

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Schnack, D. D.; Glasser, A. H.

1996-11-01

NIMROD is a new code system that is being developed for the analysis of modern fusion experiments. It is being designed from the beginning to make the maximum use of massively parallel computer architectures and computer graphics. The NIMROD physics kernel solves the three-dimensional, time-dependent two-fluid equations with neo-classical effects in toroidal geometry of arbitrary poloidal cross section. The NIMROD system also includes a pre-processor, a grid generator, and a post processor. User interaction with NIMROD is facilitated by a modern graphical user interface (GUI). The NIMROD project is using Quality Function Deployment (QFD) team management techniques to minimize re-engineering and reduce code development time. This paper gives an overview of the NIMROD project. Operation of the GUI is demonstrated, and the first results from the physics kernel are given.

A Fast Optimization Method for General Binary Code Learning.

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Shen, Fumin; Zhou, Xiang; Yang, Yang; Song, Jingkuan; Shen, Heng; Tao, Dacheng

2016-09-22

Hashing or binary code learning has been recognized to accomplish efficient near neighbor search, and has thus attracted broad interests in recent retrieval, vision and learning studies. One main challenge of learning to hash arises from the involvement of discrete variables in binary code optimization. While the widely-used continuous relaxation may achieve high learning efficiency, the pursued codes are typically less effective due to accumulated quantization error. In this work, we propose a novel binary code optimization method, dubbed Discrete Proximal Linearized Minimization (DPLM), which directly handles the discrete constraints during the learning process. Specifically, the discrete (thus nonsmooth nonconvex) problem is reformulated as minimizing the sum of a smooth loss term with a nonsmooth indicator function. The obtained problem is then efficiently solved by an iterative procedure with each iteration admitting an analytical discrete solution, which is thus shown to converge very fast. In addition, the proposed method supports a large family of empirical loss functions, which is particularly instantiated in this work by both a supervised and an unsupervised hashing losses, together with the bits uncorrelation and balance constraints. In particular, the proposed DPLM with a supervised `2 loss encodes the whole NUS-WIDE database into 64-bit binary codes within 10 seconds on a standard desktop computer. The proposed approach is extensively evaluated on several large-scale datasets and the generated binary codes are shown to achieve very promising results on both retrieval and classification tasks.

Optimal super dense coding over memory channels

OpenAIRE

Shadman, Zahra; Kampermann, Hermann; Macchiavello, Chiara; Bruß, Dagmar

2011-01-01

We study the super dense coding capacity in the presence of quantum channels with correlated noise. We investigate both the cases of unitary and non-unitary encoding. Pauli channels for arbitrary dimensions are treated explicitly. The super dense coding capacity for some special channels and resource states is derived for unitary encoding. We also provide an example of a memory channel where non-unitary encoding leads to an improvement in the super dense coding capacity.

Cost-benefit of minimally invasive staging of non-small cell lung cancer: a decision tree sensitivity analysis.

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Steinfort, Daniel P; Liew, Danny; Conron, Matthew; Hutchinson, Anastasia F; Irving, Louis B

2010-10-01

Accurate staging of non-small cell lung cancer (NSCLC) is critical for optimal management. Minimally invasive pathologic assessment of mediastinal lymphadenopathy is increasingly being performed. The cost-benefit (minimization of health care costs) of such approaches, in comparison with traditional surgical methods, is yet to be established. Decision-tree analysis was applied to compare downstream costs of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA), conventional TBNA, and surgical mediastinoscopy. Calculations were based on real costs derived from actual patient data at a major teaching hospital in Melbourne, Australia. One- and two-way sensitivity analyses were undertaken to account for potential variation in input parameter values. For the base-case analysis, initial evaluation with EBUS-TBNA (with negative results being surgically confirmed) was the most cost-beneficial approach (AU$2961) in comparison with EBUS-TBNA (negative results not surgically confirmed) ($3344), conventional TBNA ($3754), and mediastinoscopy ($8859). The sensitivity of EBUS-TBNA for detecting disease had the largest impact on cost, whereas the prevalence of mediastinal lymph node metastases determined whether surgical confirmation of negative EBUS-TBNA results remained cost-beneficial. Our study confirms that minimally invasive staging of NSCLC is cost-beneficial in comparison with traditional surgical techniques. EBUS-TBNA was the most cost-beneficial approach for mediastinal staging of patients with NSCLC across all studied parameters.

Combinatorial Control of mRNA Fates by RNA-Binding Proteins and Non-Coding RNAs

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Valentina Iadevaia

2015-09-01

Full Text Available Post-transcriptional control of gene expression is mediated by RNA-binding proteins (RBPs and small non-coding RNAs (e.g., microRNAs that bind to distinct elements in their mRNA targets. Here, we review recent examples describing the synergistic and/or antagonistic effects mediated by RBPs and miRNAs to determine the localisation, stability and translation of mRNAs in mammalian cells. From these studies, it is becoming increasingly apparent that dynamic rearrangements of RNA-protein complexes could have profound implications in human cancer, in synaptic plasticity, and in cellular differentiation.

Regulatory Non-Coding RNAs in Pluripotent Stem Cells

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Alessandro Rosa

2013-07-01

Full Text Available The most part of our genome encodes for RNA transcripts are never translated into proteins. These include families of RNA molecules with a regulatory function, which can be arbitrarily subdivided in short (less than 200 nucleotides and long non-coding RNAs (ncRNAs. MicroRNAs, which act post-transcriptionally to repress the function of target mRNAs, belong to the first group. Included in the second group are multi-exonic and polyadenylated long ncRNAs (lncRNAs, localized either in the nucleus, where they can associate with chromatin remodeling complexes to regulate transcription, or in the cytoplasm, acting as post-transcriptional regulators. Pluripotent stem cells, such as embryonic stem cells (ESCs or induced pluripotent stem cells (iPSCs, represent useful systems for modeling normal development and human diseases, as well as promising tools for regenerative medicine. To fully explore their potential, however, a deep understanding of the molecular basis of stemness is crucial. In recent years, increasing evidence of the importance of regulation by ncRNAs in pluripotent cells is accumulating. In this review, we will discuss recent findings pointing to multiple roles played by regulatory ncRNAs in ESC and iPSCs, where they act in concert with signaling pathways, transcriptional regulatory circuitries and epigenetic factors to modulate the balance between pluripotency and differentiation.

CVD-associated non-coding RNA, ANRIL, modulates expression of atherogenic pathways in VSMC