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Sample records for inverted repeat motif

  1. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification.

    Directory of Open Access Journals (Sweden)

    Bonita J Brewer

    2015-12-01

    Full Text Available DNA replication errors are a major driver of evolution--from single nucleotide polymorphisms to large-scale copy number variations (CNVs. Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model--Origin-Dependent Inverted-Repeat Amplification (ODIRA-proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error-the ligation of leading and lagging nascent strands to create "closed" forks-can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent--a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins

  2. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification.

    Science.gov (United States)

    Brewer, Bonita J; Payen, Celia; Di Rienzi, Sara C; Higgins, Megan M; Ong, Giang; Dunham, Maitreya J; Raghuraman, M K

    2015-12-01

    DNA replication errors are a major driver of evolution--from single nucleotide polymorphisms to large-scale copy number variations (CNVs). Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model--Origin-Dependent Inverted-Repeat Amplification (ODIRA)-proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error-the ligation of leading and lagging nascent strands to create "closed" forks-can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent--a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins of interstitial

  3. An inverted repeat motif stabilizes binding of E2F and enhances transcription of the dihydrofolate reductase gene

    DEFF Research Database (Denmark)

    Wade, M; Blake, M C; Jambou, R C

    1995-01-01

    consensus E2F site, significantly decrease the binding stability of all of the forms of E2F tested. The rate of association of E2F-1/DP-1 heterodimers with the inverted repeat wild type site was not significantly different from those with the two single site mutated probes. Furthermore, the mutations...

  4. detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

    Science.gov (United States)

    Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

    2014-01-01

    Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.

  5. Fragile DNA Motifs Trigger Mutagenesis at Distant Chromosomal Loci in Saccharomyces cerevisiae

    Science.gov (United States)

    Saini, Natalie; Zhang, Yu; Nishida, Yuri; Sheng, Ziwei; Choudhury, Shilpa; Mieczkowski, Piotr; Lobachev, Kirill S.

    2013-01-01

    DNA sequences capable of adopting non-canonical secondary structures have been associated with gross-chromosomal rearrangements in humans and model organisms. Previously, we have shown that long inverted repeats that form hairpin and cruciform structures and triplex-forming GAA/TTC repeats induce the formation of double-strand breaks which trigger genome instability in yeast. In this study, we demonstrate that breakage at both inverted repeats and GAA/TTC repeats is augmented by defects in DNA replication. Increased fragility is associated with increased mutation levels in the reporter genes located as far as 8 kb from both sides of the repeats. The increase in mutations was dependent on the presence of inverted or GAA/TTC repeats and activity of the translesion polymerase Polζ. Mutagenesis induced by inverted repeats also required Sae2 which opens hairpin-capped breaks and initiates end resection. The amount of breakage at the repeats is an important determinant of mutations as a perfect palindromic sequence with inherently increased fragility was also found to elevate mutation rates even in replication-proficient strains. We hypothesize that the underlying mechanism for mutagenesis induced by fragile motifs involves the formation of long single-stranded regions in the broken chromosome, invasion of the undamaged sister chromatid for repair, and faulty DNA synthesis employing Polζ. These data demonstrate that repeat-mediated breaks pose a dual threat to eukaryotic genome integrity by inducing chromosomal aberrations as well as mutations in flanking genes. PMID:23785298

  6. Inverted repeats in the promoter as an autoregulatory sequence for TcrX in Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Bhattacharya, Monolekha; Das, Amit Kumar

    2011-01-01

    Highlights: ► The regulatory sequences recognized by TcrX have been identified. ► The regulatory region comprises of inverted repeats segregated by 30 bp region. ► The mode of binding of TcrX with regulatory sequence is unique. ► In silico TcrX–DNA docked model binds one of the inverted repeats. ► Both phosphorylated and unphosphorylated TcrX binds regulatory sequence in vitro. -- Abstract: TcrY, a histidine kinase, and TcrX, a response regulator, constitute a two-component system in Mycobacterium tuberculosis. tcrX, which is expressed during iron scarcity, is instrumental in the survival of iron-dependent M. tuberculosis. However, the regulator of tcrX/Y has not been fully characterized. Crosslinking studies of TcrX reveal that it can form oligomers in vitro. Electrophoretic mobility shift assays (EMSAs) show that TcrX recognizes two regions in the promoter that are comprised of inverted repeats separated by ∼30 bp. The dimeric in silico model of TcrX predicts binding to one of these inverted repeat regions. Site-directed mutagenesis and radioactive phosphorylation indicate that D54 of TcrX is phosphorylated by H256 of TcrY. However, phosphorylated and unphosphorylated TcrX bind the regulatory sequence with equal efficiency, which was shown with an EMSA using the D54A TcrX mutant.

  7. Direct and inverted repeats elicit genetic instability by both exploiting and eluding DNA double-strand break repair systems in mycobacteria.

    Directory of Open Access Journals (Sweden)

    Ewelina A Wojcik

    Full Text Available Repetitive DNA sequences with the potential to form alternative DNA conformations, such as slipped structures and cruciforms, can induce genetic instability by promoting replication errors and by serving as a substrate for DNA repair proteins, which may lead to DNA double-strand breaks (DSBs. However, the contribution of each of the DSB repair pathways, homologous recombination (HR, non-homologous end-joining (NHEJ and single-strand annealing (SSA, to this sort of genetic instability is not fully understood. Herein, we assessed the genome-wide distribution of repetitive DNA sequences in the Mycobacterium smegmatis, Mycobacterium tuberculosis and Escherichia coli genomes, and determined the types and frequencies of genetic instability induced by direct and inverted repeats, both in the presence and in the absence of HR, NHEJ, and SSA. All three genomes are strongly enriched in direct repeats and modestly enriched in inverted repeats. When using chromosomally integrated constructs in M. smegmatis, direct repeats induced the perfect deletion of their intervening sequences ~1,000-fold above background. Absence of HR further enhanced these perfect deletions, whereas absence of NHEJ or SSA had no influence, suggesting compromised replication fidelity. In contrast, inverted repeats induced perfect deletions only in the absence of SSA. Both direct and inverted repeats stimulated excision of the constructs from the attB integration sites independently of HR, NHEJ, or SSA. With episomal constructs, direct and inverted repeats triggered DNA instability by activating nucleolytic activity, and absence of the DSB repair pathways (in the order NHEJ>HR>SSA exacerbated this instability. Thus, direct and inverted repeats may elicit genetic instability in mycobacteria by 1 directly interfering with replication fidelity, 2 stimulating the three main DSB repair pathways, and 3 enticing L5 site-specific recombination.

  8. Direct and inverted repeats elicit genetic instability by both exploiting and eluding DNA double-strand break repair systems in mycobacteria.

    Science.gov (United States)

    Wojcik, Ewelina A; Brzostek, Anna; Bacolla, Albino; Mackiewicz, Pawel; Vasquez, Karen M; Korycka-Machala, Malgorzata; Jaworski, Adam; Dziadek, Jaroslaw

    2012-01-01

    Repetitive DNA sequences with the potential to form alternative DNA conformations, such as slipped structures and cruciforms, can induce genetic instability by promoting replication errors and by serving as a substrate for DNA repair proteins, which may lead to DNA double-strand breaks (DSBs). However, the contribution of each of the DSB repair pathways, homologous recombination (HR), non-homologous end-joining (NHEJ) and single-strand annealing (SSA), to this sort of genetic instability is not fully understood. Herein, we assessed the genome-wide distribution of repetitive DNA sequences in the Mycobacterium smegmatis, Mycobacterium tuberculosis and Escherichia coli genomes, and determined the types and frequencies of genetic instability induced by direct and inverted repeats, both in the presence and in the absence of HR, NHEJ, and SSA. All three genomes are strongly enriched in direct repeats and modestly enriched in inverted repeats. When using chromosomally integrated constructs in M. smegmatis, direct repeats induced the perfect deletion of their intervening sequences ~1,000-fold above background. Absence of HR further enhanced these perfect deletions, whereas absence of NHEJ or SSA had no influence, suggesting compromised replication fidelity. In contrast, inverted repeats induced perfect deletions only in the absence of SSA. Both direct and inverted repeats stimulated excision of the constructs from the attB integration sites independently of HR, NHEJ, or SSA. With episomal constructs, direct and inverted repeats triggered DNA instability by activating nucleolytic activity, and absence of the DSB repair pathways (in the order NHEJ>HR>SSA) exacerbated this instability. Thus, direct and inverted repeats may elicit genetic instability in mycobacteria by 1) directly interfering with replication fidelity, 2) stimulating the three main DSB repair pathways, and 3) enticing L5 site-specific recombination.

  9. Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats.

    Science.gov (United States)

    Wang, Jianye; Huang, Yu; Zhou, Mingxu; Zhu, Guoqiang

    2016-09-01

    Genomic information about Muscovy duck parvovirus is still limited. In this study, the genome of the pathogenic MDPV strain YY was sequenced. The full-length genome of YY is 5075 nucleotides (nt) long, 57 nt shorter than that of strain FM. Sequence alignment indicates that the 5' and 3' inverted terminal repeats (ITR) of strain YY contain a 14-nucleotide-pair deletion in the stem of the palindromic hairpin structure in comparison to strain FM and FZ91-30. The deleted region contains one "E-box" site and one repeated motif with the sequence "TTCCGGT" or "ACCGGAA". Phylogenetic trees constructed based the protein coding genes concordantly showed that YY, together with nine other MDPV isolates from various places, clustered in a separate branch, distinct from the branch formed by goose parvovirus (GPV) strains. These results demonstrate that, despite the distinctive deletion, the YY strain still belongs to the classical MDPV group. Moreover, the deletion of ITR may contribute to the genome evolution of MDPV under immunization pressure.

  10. Variable presence of the inverted repeat and plastome stability in Erodium

    OpenAIRE

    Blazier, John C.; Jansen, Robert K.; Mower, Jeffrey P.; Govindu, Madhu; Zhang, Jin; Weng, Mao-Lun; Ruhlman, Tracey A.

    2016-01-01

    Background and Aims Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stabili...

  11. Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion.

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    Ni, ZhouXian; Ye, YouJu; Bai, Tiandao; Xu, Meng; Xu, Li-An

    2017-09-11

    The chloroplast genome (CPG) of Pinus massoniana belonging to the genus Pinus (Pinaceae), which is a primary source of turpentine, was sequenced and analyzed in terms of gene rearrangements, ndh genes loss, and the contraction and expansion of short inverted repeats (IRs). P. massoniana CPG has a typical quadripartite structure that includes large single copy (LSC) (65,563 bp), small single copy (SSC) (53,230 bp) and two IRs (IRa and IRb, 485 bp). The 108 unique genes were identified, including 73 protein-coding genes, 31 tRNAs, and 4 rRNAs. Most of the 81 simple sequence repeats (SSRs) identified in CPG were mononucleotides motifs of A/T types and located in non-coding regions. Comparisons with related species revealed an inversion (21,556 bp) in the LSC region; P. massoniana CPG lacks all 11 intact ndh genes (four ndh genes lost completely; the five remained truncated as pseudogenes; and the other two ndh genes remain as pseudogenes because of short insertions or deletions). A pair of short IRs was found instead of large IRs, and size variations among pine species were observed, which resulted from short insertions or deletions and non-synchronized variations between "IRa" and "IRb". The results of phylogenetic analyses based on whole CPG sequences of 16 conifers indicated that the whole CPG sequences could be used as a powerful tool in phylogenetic analyses.

  12. [Active miniature inverted-repeat transposable elements transposon in plants: a review].

    Science.gov (United States)

    Hu, Bingjie; Zhou, Mingbing

    2018-02-25

    Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

  13. Two new miniature inverted-repeat transposable elements in the genome of the clam Donax trunculus.

    Science.gov (United States)

    Šatović, Eva; Plohl, Miroslav

    2017-10-01

    Repetitive sequences are important components of eukaryotic genomes that drive their evolution. Among them are different types of mobile elements that share the ability to spread throughout the genome and form interspersed repeats. To broaden the generally scarce knowledge on bivalves at the genome level, in the clam Donax trunculus we described two new non-autonomous DNA transposons, miniature inverted-repeat transposable elements (MITEs), named DTC M1 and DTC M2. Like other MITEs, they are characterized by their small size, their A + T richness, and the presence of terminal inverted repeats (TIRs). DTC M1 and DTC M2 are 261 and 286 bp long, respectively, and in addition to TIRs, both of them contain a long imperfect palindrome sequence in their central parts. These elements are present in complete and truncated versions within the genome of the clam D. trunculus. The two new MITEs share only structural similarity, but lack any nucleotide sequence similarity to each other. In a search for related elements in databases, blast search revealed within the Crassostrea gigas genome a larger element sharing sequence similarity only to DTC M1 in its TIR sequences. The lack of sequence similarity with any previously published mobile elements indicates that DTC M1 and DTC M2 elements may be unique to D. trunculus.

  14. A Repeating Sulfated Galactan Motif Resuscitates Dormant Micrococcus luteus Bacteria.

    Science.gov (United States)

    Böttcher, Thomas; Szamosvári, Dávid; Clardy, Jon

    2018-07-01

    Only a small fraction of bacteria can autonomously initiate growth on agar plates. Nongrowing bacteria typically enter a metabolically inactive dormant state and require specific chemical trigger factors or signals to exit this state and to resume growth. Micrococcus luteus has become a model organism for this important yet poorly understood phenomenon. Only a few resuscitation signals have been described to date, and all of them are produced endogenously by bacterial species. We report the discovery of a novel type of resuscitation signal that allows M. luteus to grow on agar but not agarose plates. Fractionation of the agar polysaccharide complex and sulfation of agarose allowed us to identify the signal as highly sulfated saccharides found in agar or carrageenans. Purification of hydrolyzed κ-carrageenan ultimately led to the identification of the signal as a small fragment of a large linear polysaccharide, i.e., an oligosaccharide of five or more sugars with a repeating disaccharide motif containing d-galactose-4-sulfate (G4S) 1,4-linked to 3,6-anhydro-α-d-galactose (DA), G4S-(DA-G4S) n ≥2 IMPORTANCE Most environmental bacteria cannot initiate growth on agar plates, but they can flourish on the same plates once growth is initiated. While there are a number of names for and manifestations of this phenomenon, the underlying cause appears to be the requirement for a molecular signal indicating safe growing conditions. Micrococcus luteus has become a model organism for studying this growth initiation process, often called resuscitation, because of its apparent connection with the persistent or dormant form of Mycobacterium tuberculosis , an important human pathogen. In this report, we identify a highly sulfated saccharide from agar or carrageenans that robustly resuscitates dormant M. luteus on agarose plates. We identified and characterized the signal as a small repeating disaccharide motif. Our results indicate that signals inherent in or absent from the

  15. Armadillo motifs involved in vesicular transport.

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    Harald Striegl

    Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

  16. Topological characteristics of helical repeat proteins

    NARCIS (Netherlands)

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  17. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

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    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  18. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence.

    Directory of Open Access Journals (Sweden)

    Cristina Aguado

    2014-03-01

    Full Text Available In recent years different types of structural variants (SVs have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies.

  19. Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria

    International Nuclear Information System (INIS)

    Zhou Fengfeng; Tran Thao; Xu Ying

    2008-01-01

    Miniature inverted-repeat transposable elements (MITEs) were first identified in plants and exerted extensive proliferations throughout eukaryotic and archaeal genomes. But very few MITEs have been characterized in bacteria. We identified a novel MITE, called Nezha, in cyanobacteria Anabaena variabilis ATCC 29413 and Nostoc sp. PCC 7120. Nezha, like most previously known MITEs in other organisms, is small in size, non-coding, carrying TIR and DR signals, and of potential to form a stable RNA secondary structure, and it tends to insert into A+T-rich regions. Recent transpositions of Nezha were observed in A. variabilis ATCC 29413 and Nostoc sp. PCC 7120, respectively. Nezha might have proliferated recently with aid from the transposase encoded by ISNpu3-like elements. A possible horizontal transfer event of Nezha from cyanobacteria to Polaromonas JS666 is also observed

  20. Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes.

    Science.gov (United States)

    Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

    2017-04-01

    For species with minor inverted repeat (IR) boundary changes in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in the IR than the single copy regions (SC). However, the impact of large-scale IR expansion/contraction on plastid nucleotide substitution rates among closely related species remains unclear. We included plastomes from 22 Pelargonium species, including eight newly sequenced genomes, and used both pairwise and model-based comparisons to investigate the impact of the IR on sequence evolution in plastids. Ten types of plastome organization with different inversions or IR boundary changes were identified in Pelargonium. Inclusion in the IR was not sufficient to explain the variation of nucleotide substitution rates. Instead, the rate heterogeneity in Pelargonium plastomes was a mixture of locus-specific, lineage-specific and IR-dependent effects. Our study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  1. Repeating Spatial-Temporal Motifs of CA3 Activity Dependent on Engineered Inputs from Dentate Gyrus Neurons in Live Hippocampal Networks.

    Science.gov (United States)

    Bhattacharya, Aparajita; Desai, Harsh; DeMarse, Thomas B; Wheeler, Bruce C; Brewer, Gregory J

    2016-01-01

    Anatomical and behavioral studies, and in vivo and slice electrophysiology of the hippocampus suggest specific functions of the dentate gyrus (DG) and the CA3 subregions, but the underlying activity dynamics and repeatability of information processing remains poorly understood. To approach this problem, we engineered separate living networks of the DG and CA3 neurons that develop connections through 51 tunnels for axonal communication. Growing these networks on top of an electrode array enabled us to determine whether the subregion dynamics were separable and repeatable. We found spontaneous development of polarized propagation of 80% of the activity in the native direction from DG to CA3 and different spike and burst dynamics for these subregions. Spatial-temporal differences emerged when the relationships of target CA3 activity were categorized with to the number and timing of inputs from the apposing network. Compared to times of CA3 activity when there was no recorded tunnel input, DG input led to CA3 activity bursts that were 7× more frequent, increased in amplitude and extended in temporal envelope. Logistic regression indicated that a high number of tunnel inputs predict CA3 activity with 90% sensitivity and 70% specificity. Compared to no tunnel input, patterns of >80% tunnel inputs from DG specified different patterns of first-to-fire neurons in the CA3 target well. Clustering dendrograms revealed repeating motifs of three or more patterns at up to 17 sites in CA3 that were importantly associated with specific spatial-temporal patterns of tunnel activity. The number of these motifs recorded in 3 min was significantly higher than shuffled spike activity and not seen above chance in control networks in which CA3 was apposed to CA3 or DG to DG. Together, these results demonstrate spontaneous input-dependent repeatable coding of distributed activity in CA3 networks driven by engineered inputs from DG networks. These functional configurations at measured times

  2. The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.

    Science.gov (United States)

    Zhang, Yanzhen; Ma, Ji; Yang, Bingxian; Li, Ruyi; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Zhang, Lin

    2014-05-01

    Taxus chinensis var. mairei (Taxaceae) is a domestic variety of yew species in local China. This plant is one of the sources for paclitaxel, which is a promising antineoplastic chemotherapy drugs during the last decade. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of T. chinensis var. mairei. The T. chinensis var. mairei cp genome is 129,513 bp in length, with 113 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). Among the 113 single copy genes, 9 are intron-containing. Compared to other land plant cp genomes, the T. chinensis var. mairei cp genome has lost one of the large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperm such as Cycas revoluta and Ginkgo biloba L. Compared to related species, the gene order of T. chinensis var. mairei has a large inversion of ~110kb including 91 genes (from rps18 to accD) with gene contents unarranged. Repeat analysis identified 48 direct and 2 inverted repeats 30 bp long or longer with a sequence identity greater than 90%. Repeated short segments were found in genes rps18, rps19 and clpP. Analysis also revealed 22 simple sequence repeat (SSR) loci and almost all are composed of A or T. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Novel anti-HIV peptides containing multiple copies of artificially designed heptad repeat motifs

    International Nuclear Information System (INIS)

    Shi Weiguo; Qi Zhi; Pan Chungen; Xue Na; Debnath, Asim K.; Qie Jiankun; Jiang Shibo; Liu Keliang

    2008-01-01

    The peptidic anti-HIV drug T20 (Fuzeon) and its analog C34 share a common heptad repeat (HR) sequence, but they have different functional domains, i.e., pocket- and lipid-binding domains (PBD and LBD, respectively). We hypothesize that novel anti-HIV peptides may be designed by using artificial sequences containing multiple copies of HR motifs plus zero, one or two functional domains. Surprisingly, we found that the peptides containing only the non-natural HR sequences could significantly inhibit HIV-1 infection, while addition of PBD and/or LBD to the peptides resulted in significant improvement of anti-HIV-1 activity. These results suggest that these artificial HR sequences, which may serve as structural domains, could be used as templates for the design of novel antiviral peptides against HIV and other viruses with class I fusion proteins

  4. Variable presence of the inverted repeat and plastome stability in Erodium.

    Science.gov (United States)

    Blazier, John C; Jansen, Robert K; Mower, Jeffrey P; Govindu, Madhu; Zhang, Jin; Weng, Mao-Lun; Ruhlman, Tracey A

    2016-06-01

    Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts. © The Author 2016

  5. Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.

    Science.gov (United States)

    Cechová, Jana; Lýsek, Jirí; Bartas, Martin; Brázda, Václav

    2018-04-01

    The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. vaclav@ibp.cz. Supplementary data are available at Bioinformatics online.

  6. Regulation of HFE expression by poly(ADP-ribose) polymerase-1 (PARP1) through an inverted repeat DNA sequence in the distal promoter.

    Science.gov (United States)

    Pelham, Christopher; Jimenez, Tamara; Rodova, Marianna; Rudolph, Angela; Chipps, Elizabeth; Islam, M Rafiq

    2013-12-01

    Hereditary hemochromatosis (HH) is a common autosomal recessive disorder of iron overload among Caucasians of northern European descent. Over 85% of all cases with HH are due to mutations in the hemochromatosis protein (HFE) involved in iron metabolism. Although the importance in iron homeostasis is well recognized, the mechanism of sensing and regulating iron absorption by HFE, especially in the absence of iron response element in its gene, is not fully understood. In this report, we have identified an inverted repeat sequence (ATGGTcttACCTA) within 1700bp (-1675/+35) of the HFE promoter capable to form cruciform structure that binds PARP1 and strongly represses HFE promoter. Knockdown of PARP1 increases HFE mRNA and protein. Similarly, hemin or FeCl3 treatments resulted in increase in HFE expression by reducing nuclear PARP1 pool via its apoptosis induced cleavage, leading to upregulation of the iron regulatory hormone hepcidin mRNA. Thus, PARP1 binding to the inverted repeat sequence on the HFE promoter may serve as a novel iron sensing mechanism as increased iron level can trigger PARP1 cleavage and relief of HFE transcriptional repression. © 2013.

  7. RNA recognition motif (RRM)-containing proteins in Bombyx mori

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...

  8. Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism

    Science.gov (United States)

    Faraldo-Gómez, José D.

    2017-01-01

    The membrane transporter anion exchanger 1 (AE1), or band 3, is a key component in the processes of carbon-dioxide transport in the blood and urinary acidification in the renal collecting duct. In both erythrocytes and the basolateral membrane of the collecting-duct α-intercalated cells, the role of AE1 is to catalyze a one-for-one exchange of chloride for bicarbonate. After decades of biochemical and functional studies, the structure of the transmembrane region of AE1, which catalyzes the anion-exchange reaction, has finally been determined. Each protomer of the AE1 dimer comprises two repeats with inverted transmembrane topologies, but the structures of these repeats differ. This asymmetry causes the putative substrate-binding site to be exposed only to the extracellular space, consistent with the expectation that anion exchange occurs via an alternating-access mechanism. Here, we hypothesize that the unknown, inward-facing conformation results from inversion of this asymmetry, and we propose a model of this state constructed using repeat-swap homology modeling. By comparing this inward-facing model with the outward-facing experimental structure, we predict that the mechanism of AE1 involves an elevator-like motion of the substrate-binding domain relative to the nearly stationary dimerization domain and to the membrane plane. This hypothesis is in qualitative agreement with a wide range of biochemical and functional data, which we review in detail, and suggests new avenues of experimentation. PMID:29167180

  9. Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism.

    Science.gov (United States)

    Ficici, Emel; Faraldo-Gómez, José D; Jennings, Michael L; Forrest, Lucy R

    2017-12-04

    The membrane transporter anion exchanger 1 (AE1), or band 3, is a key component in the processes of carbon-dioxide transport in the blood and urinary acidification in the renal collecting duct. In both erythrocytes and the basolateral membrane of the collecting-duct α-intercalated cells, the role of AE1 is to catalyze a one-for-one exchange of chloride for bicarbonate. After decades of biochemical and functional studies, the structure of the transmembrane region of AE1, which catalyzes the anion-exchange reaction, has finally been determined. Each protomer of the AE1 dimer comprises two repeats with inverted transmembrane topologies, but the structures of these repeats differ. This asymmetry causes the putative substrate-binding site to be exposed only to the extracellular space, consistent with the expectation that anion exchange occurs via an alternating-access mechanism. Here, we hypothesize that the unknown, inward-facing conformation results from inversion of this asymmetry, and we propose a model of this state constructed using repeat-swap homology modeling. By comparing this inward-facing model with the outward-facing experimental structure, we predict that the mechanism of AE1 involves an elevator-like motion of the substrate-binding domain relative to the nearly stationary dimerization domain and to the membrane plane. This hypothesis is in qualitative agreement with a wide range of biochemical and functional data, which we review in detail, and suggests new avenues of experimentation. © 2017 Ficici et al.

  10. Gene Isolation Using Degenerate Primers Targeting Protein Motif: A Laboratory Exercise

    Science.gov (United States)

    Yeo, Brandon Pei Hui; Foong, Lian Chee; Tam, Sheh May; Lee, Vivian; Hwang, Siaw San

    2018-01-01

    Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the…

  11. Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus)

    Science.gov (United States)

    Suntronpong, Aorarat; Thapana, Watcharaporn; Twilprawat, Panupon; Prakhongcheep, Ornjira; Somyong, Suthasinee; Muangmai, Narongrit; Surin Peyachoknagul; Srikulnath, Kornsorn

    2017-01-01

    Abstract Among teleost fishes, Asian swamp eel (Monopterus albus Zuiew, 1793) possesses the lowest chromosome number, 2n = 24. To characterize the chromosome constitution and investigate the genome organization of repetitive sequences in M. albus, karyotyping and chromosome mapping were performed with the 18S – 28S rRNA gene, telomeric repeats, microsatellite repeat motifs, and Rex retroelements. The 18S – 28S rRNA genes were observed to the pericentromeric region of chromosome 4 at the same position with large propidium iodide and C-positive bands, suggesting that the molecular structure of the pericentromeric regions of chromosome 4 has evolved in a concerted manner with amplification of the 18S – 28S rRNA genes. (TTAGGG)n sequences were found at the telomeric ends of all chromosomes. Eight of 19 microsatellite repeat motifs were dispersedly mapped on different chromosomes suggesting the independent amplification of microsatellite repeat motifs in M. albus. Monopterus albus Rex1 (MALRex1) was observed at interstitial sites of all chromosomes and in the pericentromeric regions of most chromosomes whereas MALRex3 was scattered and localized to all chromosomes and MALRex6 to several chromosomes. This suggests that these retroelements were independently amplified or lost in M. albus. Among MALRexs (MALRex1, MALRex3, and MALRex6), MALRex6 showed higher interspecific sequence divergences from other teleost species in comparison. This suggests that the divergence of Rex6 sequences of M. albus might have occurred a relatively long time ago. PMID:29093797

  12. Distinct repeat motifs at the C-terminal region of CagA of Helicobacter pylori strains isolated from diseased patients and asymptomatic individuals in West Bengal, India

    Directory of Open Access Journals (Sweden)

    Chattopadhyay Santanu

    2012-05-01

    Full Text Available Abstract Background Infection with Helicobacter pylori strains that express CagA is associated with gastritis, peptic ulcer disease, and gastric adenocarcinoma. The biological function of CagA depends on tyrosine phosphorylation by a cellular kinase. The phosphate acceptor tyrosine moiety is present within the EPIYA motif at the C-terminal region of the protein. This region is highly polymorphic due to variations in the number of EPIYA motifs and the polymorphism found in spacer regions among EPIYA motifs. The aim of this study was to analyze the polymorphism at the C-terminal end of CagA and to evaluate its association with the clinical status of the host in West Bengal, India. Results Seventy-seven H. pylori strains isolated from patients with various clinical statuses were used to characterize the C-ternimal polymorphic region of CagA. Our analysis showed that there is no correlation between the previously described CagA types and various disease outcomes in Indian context. Further analyses of different CagA structures revealed that the repeat units in the spacer sequences within the EPIYA motifs are actually more discrete than the previously proposed models of CagA variants. Conclusion Our analyses suggest that EPIYA motifs as well as the spacer sequence units are present as distinct insertions and deletions, which possibly have arisen from extensive recombination events. Moreover, we have identified several new CagA types, which could not be typed by the existing systems and therefore, we have proposed a new typing system. We hypothesize that a cagA gene encoding higher number EPIYA motifs may perhaps have arisen from cagA genes that encode lesser EPIYA motifs by acquisition of DNA segments through recombination events.

  13. Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes

    Directory of Open Access Journals (Sweden)

    HUAN GAO

    2009-01-01

    Full Text Available To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia, rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

  14. Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes.

    Science.gov (United States)

    Sabir, Jamal; Schwarz, Erika; Ellison, Nicholas; Zhang, Jin; Baeshen, Nabih A; Mutwakil, Muhammed; Jansen, Robert; Ruhlman, Tracey

    2014-08-01

    Land plant plastid genomes (plastomes) provide a tractable model for evolutionary study in that they are relatively compact and gene dense. Among the groups that display an appropriate level of variation for structural features, the inverted-repeat-lacking clade (IRLC) of papilionoid legumes presents the potential to advance general understanding of the mechanisms of genomic evolution. Here, are presented six complete plastome sequences from economically important species of the IRLC, a lineage previously represented by only five completed plastomes. A number of characters are compared across the IRLC including gene retention and divergence, synteny, repeat structure and functional gene transfer to the nucleus. The loss of clpP intron 2 was identified in one newly sequenced member of IRLC, Glycyrrhiza glabra. Using deeply sequenced nuclear transcriptomes from two species helped clarify the nature of the functional transfer of accD to the nucleus in Trifolium, which likely occurred in the lineage leading to subgenus Trifolium. Legumes are second only to cereal crops in agricultural importance based on area harvested and total production. Genetic improvement via plastid transformation of IRLC crop species is an appealing proposition. Comparative analyses of intergenic spacer regions emphasize the need for complete genome sequences for developing transformation vectors for plastid genetic engineering of legume crops. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  15. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes

    DEFF Research Database (Denmark)

    Peng, Xu; Brügger, Kim; Shen, Biao

    2003-01-01

    terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also...... recognizes both main families of repeat sequences in S. solfataricus. The recombinant protein, expressed in Escherichia coli, showed the same binding properties to the SRSR repeat as the native one. The SSO454 protein exhibits a tripartite internal repeat structure which yields a good sequence match...... with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure...

  16. Spectral Barcoding of Quantum Dots: Deciphering Structural Motifs from the Excitonic Spectra

    International Nuclear Information System (INIS)

    Mlinar, V.; Zunger, A.

    2009-01-01

    Self-assembled semiconductor quantum dots (QDs) show in high-resolution single-dot spectra a multitude of sharp lines, resembling a barcode, due to various neutral and charged exciton complexes. Here we propose the 'spectral barcoding' method that deciphers structural motifs of dots by using such barcode as input to an artificial-intelligence learning system. Thus, we invert the common practice of deducing spectra from structure by deducing structure from spectra. This approach (i) lays the foundation for building a much needed structure-spectra understanding for large nanostructures and (ii) can guide future design of desired optical features of QDs by controlling during growth only those structural motifs that decide given optical features.

  17. Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

    Science.gov (United States)

    Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

    2004-01-05

    The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

  18. Acute proptosis: Unusual initial presentation of sinonasal inverted papilloma

    Institute of Scientific and Technical Information of China (English)

    Norihan Ibrahim; Baharuddin Abdullah; Regunath Kandasamy; Nor Hayati Othman; Mohtar Ibrahim; Adil Hussein

    2017-01-01

    Inverted papilloma is an uncommon histopathological finding of maxillary sinus tumor. We reported here a rare case of inverted papilloma of maxillary sinus presented initially with ipsilateral proptosis. A middle-aged lady with history of having allergic rhinitis presented with progressive left eye proptosis. Assessment revealed presence of orbital mass arising from paranasal sinus, in which the histopathological examination was initially inconclusive, and later it turned up to be inverted papilloma, partly with malignant transformation. High index of suspicion is necessary especially in those patients with recurrent non-specific sinonasal symptoms, which may need repeated biopsy and histopathological examination. Ocular manifestation signifies a more advance disease.

  19. Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

    Science.gov (United States)

    Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

    2015-12-01

    Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

  20. CompariMotif: quick and easy comparisons of sequence motifs.

    Science.gov (United States)

    Edwards, Richard J; Davey, Norman E; Shields, Denis C

    2008-05-15

    CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

  1. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  2. Inverted U-shaped model: How frequent repetition affects perceived risk

    OpenAIRE

    Xi Lu; Xiaofei Xie; Lu Liu

    2015-01-01

    We asked how repeated media reports on technological hazards influence an individual's risk perception. We looked for two contradictory effects, an increasing effect of repetition on perceived risk with the first few repetitions and a decreasing effect with later repetitions, leading to the inverted U-shaped pattern. In an experiment, we demonstrated the inverted U-shaped relationship between the repetition and perceived risk in the context of food risk. The finding broaden...

  3. A leucine repeat motif in AbiA is required for resistance of Lactococcus lactis to phages representing three species.

    Science.gov (United States)

    Dinsmore, P K; O'Sullivan, D J; Klaenhammer, T R

    1998-05-28

    The abiA gene encodes an abortive bacteriophage infection mechanism that can protect Lactococcus species from infection by a variety of bacteriophages including three unrelated phage species. Five heptad leucine repeats suggestive of a leucine zipper motif were identified between residues 232 and 266 in the predicted amino acid sequence of the AbiA protein. The biological role of residues in the repeats was investigated by incorporating amino acid substitutions via site-directed mutagenesis. Each mutant was tested for phage resistance against three phages, phi 31, sk1, and c2, belonging to species P335, 936, and c2, respectively. The five residues that comprise the heptad repeats were designated L234, L242, A249, L256, and L263. Three single conservative mutations of leucine to valine in positions L235, L242, and L263 and a double mutation of two leucines (L235 and L242) to valines did not affect AbiA activity on any phages tested. Non-conservative single substitutions of charged amino acids for three of the leucines (L235, L242, and L256) virtually eliminated AbiA activity on all phages tested. Substitution of the alanine residue in the third repeat (A249) with a charged residue did not affect AbiA activity. Replacement of L242 with an alanine elimination phage resistance against phi 31, but partial resistance to sk1 and c2 remained. Two single proline substitutions for leucines L242 and L263 virtually eliminated AbiA activity against all phages, indicating that the predicted alpha-helical structure of this region is important. Mutations in an adjacent region of basic amino acids had various effects on phage resistance, suggesting that these basic residues are also important for AbiA activity. This directed mutagenesis analysis of AbiA indicated that the leucine repeat structure is essential for conferring phage resistance against three species of lactococcal bacteriophages.

  4. Analysis of genetic polymorphism of nine short tandem repeat loci in ...

    African Journals Online (AJOL)

    Yomi

    2012-03-15

    Mar 15, 2012 ... Key words: short tandem repeat, repeat motif, genetic polymorphism, Han population, forensic genetics. INTRODUCTION. Short tandem repeat (STR) is widely .... Data analysis. The exact test of Hardy-Weinberg equilibrium was conducted with. Arlequin version 3.5 software (Computational and Molecular.

  5. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Raquel S Linheiro

    Full Text Available Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes.

  6. MotifNet: a web-server for network motif analysis.

    Science.gov (United States)

    Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

    2017-06-15

    Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  7. The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms.

    Science.gov (United States)

    Ma, Ji; Yang, Bingxian; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Wang, Xumin

    2013-10-10

    Mahonia bealei (Berberidaceae) is a frequently-used traditional Chinese medicinal plant with efficient anti-inflammatory ability. This plant is one of the sources of berberine, a new cholesterol-lowering drug with anti-diabetic activity. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of M. bealei. The complete cp genome of M. bealei is 164,792 bp in length, and has a typical structure with large (LSC 73,052 bp) and small (SSC 18,591 bp) single-copy regions separated by a pair of inverted repeats (IRs 36,501 bp) of large size. The Mahonia cp genome contains 111 unique genes and 39 genes are duplicated in the IR regions. The gene order and content of M. bealei are almost unarranged which is consistent with the hypothesis that large IRs stabilize cp genome and reduce gene loss-and-gain probabilities during evolutionary process. A large IR expansion of over 12 kb has occurred in M. bealei, 15 genes (rps19, rpl22, rps3, rpl16, rpl14, rps8, infA, rpl36, rps11, petD, petB, psbH, psbN, psbT and psbB) have expanded to have an additional copy in the IRs. The IR expansion rearrangement occurred via a double-strand DNA break and subsequence repair, which is different from the ordinary gene conversion mechanism. Repeat analysis identified 39 direct/inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Analysis also revealed 75 simple sequence repeat (SSR) loci and almost all are composed of A or T, contributing to a distinct bias in base composition. Comparison of protein-coding sequences with ESTs reveals 9 putative RNA edits and 5 of them resulted in non-synonymous modifications in rpoC1, rps2, rps19 and ycf1. Phylogenetic analysis using maximum parsimony (MP) and maximum likelihood (ML) was performed on a dataset composed of 65 protein-coding genes from 25 taxa, which yields an identical tree topology as previous plastid-based trees, and provides strong support for the sister relationship between Ranunculaceae and Berberidaceae

  8. Characterization of a genome-specific Gypsy-like retrotransposon ...

    Indian Academy of Sciences (India)

    2013-04-12

    Apr 12, 2013 ... E-mail: Guangbing Deng, denggb@cib.ac.cn; ... characterized using FISH image. ... CAAAA (invert) motif is boxed, and the 12-mer direct nucleotide repeats are under- lined. ... The fixed root tips were squashed on microscope.

  9. PMS2 inactivation by a complex rearrangement involving an HERV retroelement and the inverted 100-kb duplicon on 7p22.1.

    Science.gov (United States)

    Vogt, Julia; Wernstedt, Annekatrin; Ripperger, Tim; Pabst, Brigitte; Zschocke, Johannes; Kratz, Christian; Wimmer, Katharina

    2016-11-01

    Biallelic PMS2 mutations are responsible for more than half of all cases of constitutional mismatch repair deficiency (CMMRD), a recessively inherited childhood cancer predisposition syndrome. The mismatch repair gene PMS2 is partly embedded within one copy of an inverted 100-kb low-copy repeat (LCR) on 7p22.1. In an individual with CMMRD syndrome, PMS2 was found to be homozygously inactivated by a complex chromosomal rearrangement, which separates the 5'-part from the 3'-part of the gene. The rearrangement involves sequences of the inverted 100-kb LCR and a human endogenous retrovirus element and may be associated with an inversion that is indistinguishable from the known inversion polymorphism affecting the ~0.7-Mb sequence intervening the LCR. Its formation is best explained by a replication-based mechanism (RBM) such as fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR). This finding supports the hypothesis that the inverted LCR can not only facilitate the formation of the non-allelic homologous recombination-mediated inversion polymorphism but it also promotes the occurrence of more complex rearrangements that can be associated with a large inversion, as well, but are mediated by a RBM. This further suggests that among the inversion polymorphism on 7p22.1, more complex rearrangements might be hidden. Furthermore, as the locus is embedded in a common fragile site (CFS) region, this rearrangement also supports the recently raised hypothesis that CFS sequence motifs may facilitate replication-based rearrangement mechanisms.

  10. A proposed vestigial translation initiation motif in VP1 of hepatitis A virus.

    Science.gov (United States)

    Kang, Jeong-Ah; Funkhouser, Ann W

    2002-07-01

    The internal ribosome entry site (IRES) of picornaviruses has a 3' polypyrimidine tract (PPT) 16-24 bases upstream of an AUG triplet (PPT/AUG motif). This motif is critical in determining the efficiency of cap-independent translation. HAV has a conserved PPT/AUG motif consisting of a nine base sequence (AGGUUUUUC) 23 bases upstream of the preferred AUG start codon. This HAV-specific PPT/AUG motif is repeated and conserved in VP1 of HAV, but not of other picornaviruses. We proposed that the PPT/AUG motif in the open reading frame initiated translation and/or had an impact on the life cycle of the virus. In vitro translation of mutant bicistronic mRNAs and growth in cell culture of mutant viruses provided no evidence that the VP1 PPT/AUG motif had any impact on either translation or growth. HAV differs from other picornaviruses in its inefficient growth in cell culture. Since the HAV-specific PPT/AUG motif is found in only 1 in 300,000 reported viral sequences outside the hepatovirus genus, this motif may be a vestigial translation initiation element and may have played a role in determining the unusual phenotype of HAV.

  11. The leucine-rich repeat structure.

    Science.gov (United States)

    Bella, J; Hindle, K L; McEwan, P A; Lovell, S C

    2008-08-01

    The leucine-rich repeat is a widespread structural motif of 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucines. Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. Thousands of protein sequences containing leucine-rich repeats have been identified by automatic annotation methods. Three-dimensional structures of leucine-rich repeat domains determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. As the essential structural principles become well established, the leucine-rich repeat architecture is emerging as an attractive framework for structural prediction and protein engineering. This review presents an update of the current understanding of leucine-rich repeat structure at the primary, secondary, tertiary and quaternary levels and discusses specific examples from recently determined three-dimensional structures.

  12. BayesMotif: de novo protein sorting motif discovery from impure datasets.

    Science.gov (United States)

    Hu, Jianjun; Zhang, Fan

    2010-01-18

    Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

  13. Exact Tandem Repeats Analyzer (E-TRA): A new program for DNA ...

    Indian Academy of Sciences (India)

    Unknown

    Advanced user defined parameters/options let the researchers use different minimum motif repeats ... E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 ..... repeat rates of T-cells, embryo and testis were higher.

  14. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  15. Identification of multiple binding sites for the THAP domain of the Galileo transposase in the long terminal inverted-repeats.

    Science.gov (United States)

    Marzo, Mar; Liu, Danxu; Ruiz, Alfredo; Chalmers, Ronald

    2013-08-01

    Galileo is a DNA transposon responsible for the generation of several chromosomal inversions in Drosophila. In contrast to other members of the P-element superfamily, it has unusually long terminal inverted-repeats (TIRs) that resemble those of Foldback elements. To investigate the function of the long TIRs we derived consensus and ancestral sequences for the Galileo transposase in three species of Drosophilids. Following gene synthesis, we expressed and purified their constituent THAP domains and tested their binding activity towards the respective Galileo TIRs. DNase I footprinting located the most proximal DNA binding site about 70 bp from the transposon end. Using this sequence we identified further binding sites in the tandem repeats that are found within the long TIRs. This suggests that the synaptic complex between Galileo ends may be a complicated structure containing higher-order multimers of the transposase. We also attempted to reconstitute Galileo transposition in Drosophila embryos but no events were detected. Thus, although the limited numbers of Galileo copies in each genome were sufficient to provide functional consensus sequences for the THAP domains, they do not specify a fully active transposase. Since the THAP recognition sequence is short, and will occur many times in a large genome, it seems likely that the multiple binding sites within the long, internally repetitive, TIRs of Galileo and other Foldback-like elements may provide the transposase with its binding specificity. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  16. Genomic organization and developmental fate of adjacent repeated sequences in a foldback DNA clone of Tetrahymena thermophila

    International Nuclear Information System (INIS)

    Tschunko, A.H.; Loechel, R.H.; McLaren, N.C.; Allen, S.L.

    1987-01-01

    DNA sequence elimination and rearrangement occurs during the development of somatic cell lineages of eukaryotes and was first discovered over a century ago. However, the significance and mechanism of chromatin elimination are not understood. DNA elimination also occurs during the development of the somatic macronucleus from the germinal micronucleus in unicellular ciliated protozoa such as Tetrahymena thermophila. In this study foldback DNA from the micronucleus was used as a probe to isolate ten clones. All of those tested (4/4) contained sequences that were repetitive in the micronucleus and rearranged in the macronucleus. Inverted repeated sequences were present in one clone. This clone, pTtFBl, was subjected to a detailed analysis of its developmental fate. Subregions were subcloned and used as probes against Southern blots of micronuclear and macronuclear DNA. DNA was labeled with [ 33 P]-labeled dATP. The authors found that all subregions defined repeated sequence families in the micronuclear genome. A minimum of four different families was defined, two of which are retained in the macronucleus and two of which are completely eliminated. The inverted repeat family is retained with little rearrangement. Two of the families, defined by subregions that do not contain parts of the inverted repeat are totally eliminated during macronuclear development-and contain open reading frames. The significance of retained inverted repeats to the process of elimination is discussed

  17. MotifMark: Finding regulatory motifs in DNA sequences.

    Science.gov (United States)

    Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

    2017-07-01

    The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

  18. A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation

    Directory of Open Access Journals (Sweden)

    Dong Hai-Tao

    2012-04-01

    Full Text Available Abstract Background Miniature inverted repeat transposable element (MITE is one type of transposable element (TE, which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown. Results We found that the amplicon discrepancy of a gene locus LOC_Os01g0420 in different rice cultivar genomes was resulted from the existence of a member of Gaijin-like MITEs (mGing. This result indicated that mGing transposition was occurred at this gene locus. By using a modified transposon display (TD analysis, the active transpositions of mGing were detected in rice Jiahua No. 1 genome under three conditions: in seedlings germinated from the seeds received a high dose γ-ray irradiation, in plantlets regenerated from anther-derived calli and from scutellum-derived calli, and were confirmed by PCR validation and sequencing. Sequence analysis revealed that single nucleotide polymorphisms (SNPs or short additional DNA sequences at transposition sites post mGing transposition. It suggested that sequence modification was possibly taken place during mGing transposition. Furthermore, cell re-differentiation experiment showed that active transpositions of both mGing and mPing (another well studied MITE were identified only in regenerated plantlets. Conclusions It is for the first time that mGing active transposition was demonstrated under γ-ray irradiation or in cell re-differentiation process in rice. This newly identified active MITE will provide a foundation for further analysis of the roles of MITEs in biological process.

  19. High-Pressure NMR and SAXS Reveals How Capping Modulates Folding Cooperativity of the pp32 Leucine-rich Repeat Protein.

    Science.gov (United States)

    Zhang, Yi; Berghaus, Melanie; Klein, Sean; Jenkins, Kelly; Zhang, Siwen; McCallum, Scott A; Morgan, Joel E; Winter, Roland; Barrick, Doug; Royer, Catherine A

    2018-04-27

    Many repeat proteins contain capping motifs, which serve to shield the hydrophobic core from solvent and maintain structural integrity. While the role of capping motifs in enhancing the stability and structural integrity of repeat proteins is well documented, their contribution to folding cooperativity is not. Here we examined the role of capping motifs in defining the folding cooperativity of the leucine-rich repeat protein, pp32, by monitoring the pressure- and urea-induced unfolding of an N-terminal capping motif (N-cap) deletion mutant, pp32-∆N-cap, and a C-terminal capping motif destabilization mutant pp32-Y131F/D146L, using residue-specific NMR and small-angle X-ray scattering. Destabilization of the C-terminal capping motif resulted in higher cooperativity for the unfolding transition compared to wild-type pp32, as these mutations render the stability of the C-terminus similar to that of the rest of the protein. In contrast, deletion of the N-cap led to strong deviation from two-state unfolding. In both urea- and pressure-induced unfolding, residues in repeats 1-3 of pp32-ΔN-cap lost their native structure first, while the C-terminal half was more stable. The residue-specific free energy changes in all regions of pp32-ΔN-cap were larger in urea compared to high pressure, indicating a less cooperative destabilization by pressure. Moreover, in contrast to complete structural disruption of pp32-ΔN-cap at high urea concentration, its pressure unfolded state remained compact. The contrasting effects of the capping motifs on folding cooperativity arise from the differential local stabilities of pp32, whereas the contrasting effects of pressure and urea on the pp32-ΔN-cap variant arise from their distinct mechanisms of action. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. Inverter for Interchangeable Use as Current Source Inverter and Voltage Source Inverter for Interconnecting to Grid

    Science.gov (United States)

    Teruya, Daisuke; Masukawa, Shigeo; Iida, Shoji

    We propose a novel inverter that can be operated either as a Current Source Inverter (CSI) or as a Voltage Source Inverter (VSI) by changing only the control signals. It is proper to apply it to the interconnecting system with renewal energy, such as photovoltaic cells or wind generation systems, to a grid. This inverter is usually operated as the CSI connected to the grid. Even if the energy source has a lower voltage than the grid, the energy can be supplied to the grid through the proposed inverter. The power factor can be briefly maintained at almost unity. When power supply from the grid is interrupted, the proposed circuit should be operated as the VSI in the stand-alone operation mode. In this way, the circuit can maintain a constant output voltage to the loads. In this paper, the proposed circuit configuration and the control schemes for both the CSI and the VSI are described. Further, the circuit characteristics for both are discussed experimentally.

  1. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    Science.gov (United States)

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  2. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

    Science.gov (United States)

    Tran, Ngoc Tam L; Huang, Chun-Hsi

    2014-02-20

    ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.

  3. Y-source inverter

    DEFF Research Database (Denmark)

    Siwakoti, Yam P.; Town, Graham; Loh, Poh Chiang

    2014-01-01

    This paper introduces a new 3-phase Y-source inverter whose gain is presently not matched by classical impedance-network-based inverters operating at the same duty ratio. The proposed network uses a tightly coupled transformer with three windings. By squeezing the shoot-through range while keeping...... higher boost, the inverter can operate at a higher modulation index, thereby minimizing switching device stress and providing better output power quality. In addition, the inverter has more degrees of freedom for setting the voltage gain and modulation index than other classical impedance-source networks...

  4. Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix

    Science.gov (United States)

    Phan, Anh Tuân; Mergny, Jean-Louis

    2002-01-01

    Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451

  5. Alanine substitutions in the GXXXG motif alter C99 cleavage by γ-secretase but not its dimerization.

    Science.gov (United States)

    Higashide, Hidekazu; Ishihara, Seiko; Nobuhara, Mika; Ihara, Yasuo; Funamoto, Satoru

    2017-03-01

    The amyloid β (Aβ) protein is a major component of senile plaques, one of the neuropathological hallmarks of Alzheimer's disease. Amyloidogenic processing of amyloid precursor protein (APP) by β- and γ-secretases leads to production of Aβ. APP contains tandem triple repeats of the GXXXG motif in its extracellular juxtamembrane and transmembrane regions. It is reported that the GXXXG motif is related to protein-protein interactions, but it remains controversial whether the GXXXG motif in APP is involved in substrate dimerization and whether dimerization affects γ-secretase-dependent cleavage. Therefore, the relationship between the GXXXG motifs, substrate dimerization, and γ-secretase-dependent cleavage sites remains unclear. Here, we applied blue native poly acrylamide gel electrophoresis to examine the effect of alanine substitutions within the GXXXG motifs of APP carboxyl terminal fragment (C99) on its dimerization and Aβ production. Surprisingly, alanine substitutions in the motif failed to alter C99 dimerization in detergent soluble state. Cell-based and solubilized γ-secretase assays demonstrated that increasing alanine substitutions in the motif tended to decrease long Aβ species such as Aβ42 and Aβ43 and to increase in short Aβ species concomitantly. Our data suggest that the GXXXG motif is crucial for Aβ production, but not for C99 dimerization. © 2016 International Society for Neurochemistry.

  6. Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Cristóbal Almendros

    Full Text Available Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR and CRISPR associated (cas genes conform the CRISPR-Cas systems of various bacteria and archaea and produce degradation of invading nucleic acids containing sequences (protospacers that are complementary to repeat intervening spacers. It has been demonstrated that the base sequence identity of a protospacer with the cognate spacer and the presence of a protospacer adjacent motif (PAM influence CRISPR-mediated interference efficiency. By using an original transformation assay with plasmids targeted by a resident spacer here we show that natural CRISPR-mediated immunity against invading DNA occurs in wild type Escherichia coli. Unexpectedly, the strongest activity is observed with protospacer adjoining nucleotides (interference motifs that differ from the PAM both in sequence and location. Hence, our results document for the first time native CRISPR activity in E. coli and demonstrate that positions next to the PAM in invading DNA influence their recognition and degradation by these prokaryotic immune systems.

  7. An unusual internal ribosomal entry site of inverted symmetry directs expression of a potato leafroll polerovirus replication-associated protein

    Science.gov (United States)

    Jaag, Hannah Miriam; Kawchuk, Lawrence; Rohde, Wolfgang; Fischer, Rainer; Emans, Neil; Prüfer, Dirk

    2003-01-01

    Potato leafroll polerovirus (PLRV) genomic RNA acts as a polycistronic mRNA for the production of proteins P0, P1, and P2 translated from the 5′-proximal half of the genome. Within the P1 coding region we identified a 5-kDa replication-associated protein 1 (Rap1) essential for viral multiplication. An internal ribosome entry site (IRES) with unusual structure and location was identified that regulates Rap1 translation. Core structural elements for internal ribosome entry include a conserved AUG codon and a downstream GGAGAGAGAGG motif with inverted symmetry. Reporter gene expression in potato protoplasts confirmed the internal ribosome entry function. Unlike known IRES motifs, the PLRV IRES is located completely within the coding region of Rap1 at the center of the PLRV genome. PMID:12835413

  8. Inverted oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Yuce, C [Physics Department, Anadolu University, Eskisehir (Turkey); Kilic, A [Physics Department, Anadolu University, Eskisehir (Turkey); Coruh, A [Physics Department, Sakarya University, Sakarya (Turkey)

    2006-07-15

    The inverted harmonic oscillator problem is investigated quantum mechanically. The exact wavefunction for the confined inverted oscillator is obtained and it is shown that the associated energy eigenvalues are discrete, and the energy is given as a linear function of the quantum number n.

  9. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

    Science.gov (United States)

    El Kafsi, Hela; Loux, Valentin; Mariadassou, Mahendra; Blin, Camille; Chiapello, Hélène; Abraham, Anne-Laure; Maguin, Emmanuelle; van de Guchte, Maarten

    2017-01-01

    The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp. PMID:28281695

  10. Modular inverter system

    Science.gov (United States)

    Ma, Mingyao; Hu, Haibing; Kutkut, Nasser; Batarseh, Issa; Shen, John; , Bkayrat, Raed

    2017-08-01

    A system connected to an AC power grid having an AC phase signal includes an inverter module including a first inverter coupled to a DC voltage, actuated based on the AC phase signal. The first inverter provides a first voltage signal having predetermined harmonic components. A second inverter includes second switch elements coupled to the DC voltage and actuated by a second set of control signals phase delayed with respect to the first control signals. A transformer module has first and second primary windings coupled to the first and second inverters. The transformer module further includes a secondary winding coupled to first primary winding, the second primary winding, and the AC power grid. The secondary winding is configured to provide a secondary output voltage to the AC power grid by combining the first voltage signal and the second voltage signal such that the predetermined harmonic components are substantially cancelled.

  11. Performance analysis of new type grid-tied inverter-Aalborg Inverter

    DEFF Research Database (Denmark)

    Wu, Weimin; Wang, Zhen; Ji, Junhao

    2014-01-01

    Aalborg Inverter is a grid-tied DC/AC inverter. In order to optimize the design, its power losses are analyzed in detail, combined with a description of the single-phase operating principle and the modulation strategy. A 2 kW / 220 V experimental prototype is constructed to verify the theoretical...... analysis. It is concluded that a minimize inductance in the power loop does help the inverter to achieve the high efficiency with the good dynamic performance....

  12. Revisiting the TALE repeat.

    Science.gov (United States)

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

  13. Functional motifs responsible for human metapneumovirus M2-2-mediated innate immune evasion.

    Science.gov (United States)

    Chen, Yu; Deng, Xiaoling; Deng, Junfang; Zhou, Jiehua; Ren, Yuping; Liu, Shengxuan; Prusak, Deborah J; Wood, Thomas G; Bao, Xiaoyong

    2016-12-01

    Human metapneumovirus (hMPV) is a major cause of lower respiratory infection in young children. Repeated infections occur throughout life, but its immune evasion mechanisms are largely unknown. We recently found that hMPV M2-2 protein elicits immune evasion by targeting mitochondrial antiviral-signaling protein (MAVS), an antiviral signaling molecule. However, the molecular mechanisms underlying such inhibition are not known. Our mutagenesis studies revealed that PDZ-binding motifs, 29-DEMI-32 and 39-KEALSDGI-46, located in an immune inhibitory region of M2-2, are responsible for M2-2-mediated immune evasion. We also found both motifs prevent TRAF5 and TRAF6, the MAVS downstream adaptors, to be recruited to MAVS, while the motif 39-KEALSDGI-46 also blocks TRAF3 migrating to MAVS. In parallel, these TRAFs are important in activating transcription factors NF-kB and/or IRF-3 by hMPV. Our findings collectively demonstrate that M2-2 uses its PDZ motifs to launch the hMPV immune evasion through blocking the interaction of MAVS and its downstream TRAFs. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Quasi-Y-source inverter

    DEFF Research Database (Denmark)

    Siwakoti, Yam Prasad; Blaabjerg, Frede; Loh, Poh Chiang

    2015-01-01

    This paper introduces a new inverter topology called a “quasi-Y-source inverter”. The proposed inverter inherits all the advantages of the original Y-source inverter. In addition, the new topology draws continuous current from the source which is required for many renewable sources. It also has dc......-current-blocking capacitors, which avoids saturation in the transformer core. Simulations and experimental results have proved the validity of the proposed inverter....

  15. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

  16. Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.

    Science.gov (United States)

    Zanuy, David; Gunasekaran, Kannan; Lesk, Arthur M; Nussinov, Ruth

    2006-04-21

    The formation of fibril aggregates by long polyglutamine sequences is assumed to play a major role in neurodegenerative diseases such as Huntington. Here, we model peptides rich in glutamine, through a series of molecular dynamics simulations. Starting from a rigid nanotube-like conformation, we have obtained a new conformational template that shares structural features of a tubular helix and of a beta-helix conformational organization. Our new model can be described as a super-helical arrangement of flat beta-sheet segments linked by planar turns or bends. Interestingly, our comprehensive analysis of the Protein Data Bank reveals that this is a common motif in beta-helices (termed beta-bend), although it has not been identified so far. The motif is based on the alternation of beta-sheet and helical conformation as the protein sequence is followed from the N to the C termini (beta-alpha(R)-beta-polyPro-beta). We further identify this motif in the ssNMR structure of the protofibril of the amyloidogenic peptide Abeta(1-40). The recurrence of the beta-bend suggests a general mode of connecting long parallel beta-sheet segments that would allow the growth of partially ordered fibril structures. The design allows the peptide backbone to change direction with a minimal loss of main chain hydrogen bonds. The identification of a coherent organization beyond that of the beta-sheet segments in different folds rich in parallel beta-sheets suggests a higher degree of ordered structure in protein fibrils, in agreement with their low solubility and dense molecular packing.

  17. Fault-tolerant three-level inverter

    Science.gov (United States)

    Edwards, John; Xu, Longya; Bhargava, Brij B.

    2006-12-05

    A method for driving a neutral point clamped three-level inverter is provided. In one exemplary embodiment, DC current is received at a neutral point-clamped three-level inverter. The inverter has a plurality of nodes including first, second and third output nodes. The inverter also has a plurality of switches. Faults are checked for in the inverter and predetermined switches are automatically activated responsive to a detected fault such that three-phase electrical power is provided at the output nodes.

  18. Analisis Harmonisa Inverter PWM Satu Fasa

    OpenAIRE

    Rejeki Simanjorang

    2008-01-01

    Pada tesis ini dianalisis harmonisa inverter PWM satu fasa. Inverter PWM satu fasa yang akan ditinjau adalah inverter satu fasa jembatan penuh (konvensional) dan inverter komposit. Analisis difokuskan pada penentuan pola penyaklaran yang optimum agar pembangkitan harmonisa dan switching losses inverter rendah. Untuk menentukan pola penyaklaran optimum maka dilakukan analisis yang berbasis pada rangkaian ekivalen harmonisa inverter satu fasa. Dengan menggunakan pola penyaklaran optimum, kedua ...

  19. 2015 Inverter Workshop | Photovoltaic Research | NREL

    Science.gov (United States)

    Inverter Workshop 2015 Inverter Workshop Wednesday, February 25, 2015 Chair: Jack Flicker In about inverters. This workshop represented a follow-on to the inverter workshops that Sandia National conversations between module and inverter experts. Agenda For a detailed schedule of the day's events, access

  20. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

    Directory of Open Access Journals (Sweden)

    Vergnaud Gilles

    2007-05-01

    Full Text Available Abstract Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the

  1. Milliwatt dc/dc Inverter

    Science.gov (United States)

    Mclyman, C. W.

    1983-01-01

    Compact dc/dc inverter uses single integrated-circuit package containing six inverter gates that generate and amplify 100-kHz square-wave switching signal. Square-wave switching inverts 10-volt local power to isolated voltage at another desired level. Relatively high operating frequency reduces size of filter capacitors required, resulting in small package unit.

  2. Overload protection system for power inverter

    Science.gov (United States)

    Nagano, S. (Inventor)

    1977-01-01

    An overload protection system for a power inverter utilized a first circuit for monitoring current to the load from the power inverter to detect an overload and a control circuit to shut off the power inverter, when an overload condition was detected. At the same time, a monitoring current inverter was turned on to deliver current to the load at a very low power level. A second circuit monitored current to the load, from the monitoring current inverter, to hold the power inverter off through the control circuit, until the overload condition was cleared so that the control circuit may be deactivated in order for the power inverter to be restored after the monitoring current inverter is turned off completely.

  3. Three-Phase Cascaded Multilevel Inverter Using Power Cells With Two Inverter Legs in Series

    NARCIS (Netherlands)

    Waltrich, G.; Barbi, I.

    2010-01-01

    In this paper, a modular three-phase multilevel inverter specially suited for electrical drive applications is proposed. Unlike the cascaded H-bridge inverter, this topology is based on power cells connected in cascade using two inverter legs in series. A detailed analysis of the structure and the

  4. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  5. Cloning the human lysozyme cDNA: Inverted Alu repeat in the mRNA and in situ hybridization for macrophages and Paneth cells

    International Nuclear Information System (INIS)

    Chung, L.P.; Keshav, S.; Gordon, S.

    1988-01-01

    Lysozyme is a major secretory product of human and rodent macrophages and a useful marker for myelomonocytic cells. Based on the known human lysozyme amino acid sequence, oligonucleotides were synthesized and used as probes to screen a phorbol 12-myristate 13-acetate-treated U937 cDNA library. A full-length human lysozyme cDNA clone, pHL-2, was obtained and characterized. Sequence analysis shows that human lysozyme, like chicken lysozyme, has in 18-amino-acid-long signal peptide, but unlike the chicken lysozyme cDNA, the human lysozyme cDNA has a >1-kilobase-long 3' nontranslated sequence. Interestingly, within this 3' region, an inverted repeat of the Alu family of repetitive sequences was discovered. In RNA blot analyses, DNA probes prepared from pHL-2 can be used to detect lysozyme mRNA not only from human but also from mouse and rat. Moreover, by in situ hybridization, complementary RNA transcripts have been used as probes to detect lysozyme mRNA in mouse macrophages and Paneth cells. This human lysozyme cDNA clone is therefore likely to be a useful molecular probe for studying macrophage distribution and gene expression

  6. Γ-source Neutral Point Clamped Inverter

    DEFF Research Database (Denmark)

    Mo, Wei; Loh, Poh Chiang; Blaabjerg, Frede

    Transformer based Z-source inverters are recently proposed to achieve promising buck-boost capability. They have improved higher buck-boost capability, smaller size and less components count over Z-source inverters. On the other hand, neutral point clamped inverters have less switching stress...... and better output performance comparing with traditional two-level inverters. Integrating these two types of configurations can help neutral point inverters achieve enhanced votlage buck-boost capability....

  7. SEEPAGE/INVERT INTERACTIONS

    International Nuclear Information System (INIS)

    P.S. Domski

    2000-01-01

    As directed by a written development plan (CRWMS M andO 1999a), a conceptual model for water entering the drift and reacting with the invert materials is to be developed. The purpose of this conceptual model is to assist Performance Assessment Operations (PAO) and its Engineered Barrier Performance Department in modeling the geochemical environment within a repository drift, thus allowing PAO to provide a more detailed and complete in-drift geochemical model abstraction, and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near-Field Environment (NFE), Revision 2 (NRC 1999). This AMR also seeks to: (1) Develop a logical conceptual model for physical/chemical interactions between seepage and the invert materials; (2) screen potential processes and reactions that may occur between seepage and invert to evaluate the potential consequences of the interactions; and (3) outline how seepage/invert processes may be quantified. This document provides the conceptual framework for screening out insignificant processes and for identifying and evaluating those seepage/invert interactions that have the potential to be important to subsequent PAO analyses including the Engineered Barrier System (EBS) physical and chemical model abstraction effort. This model has been developed to serve as a basis for the in-drift geochemical analyses performed by PAO. Additionally, the concepts discussed within this report may also apply to certain near and far-field geochemical processes and may have conceptual application within the unsaturated zone (UZ) and saturated zone (SZ) transport modeling efforts. The seepage/invert interactions will not directly affect any principal factors

  8. Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember

    Directory of Open Access Journals (Sweden)

    Irfa'ina Rohana Salma

    2015-06-01

    Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik  baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi;  (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources

  9. Inverter communications using output signal

    Science.gov (United States)

    Chapman, Patrick L.

    2017-02-07

    Technologies for communicating information from an inverter configured for the conversion of direct current (DC) power generated from an alternative source to alternating current (AC) power are disclosed. The technologies include determining information to be transmitted from the inverter over a power line cable connected to the inverter and controlling the operation of an output converter of the inverter as a function of the information to be transmitted to cause the output converter to generate an output waveform having the information modulated thereon.

  10. Multilevel DC link inverter

    Science.gov (United States)

    Su, Gui-Jia

    2003-06-10

    A multilevel DC link inverter and method for improving torque response and current regulation in permanent magnet motors and switched reluctance motors having a low inductance includes a plurality of voltage controlled cells connected in series for applying a resulting dc voltage comprised of one or more incremental dc voltages. The cells are provided with switches for increasing the resulting applied dc voltage as speed and back EMF increase, while limiting the voltage that is applied to the commutation switches to perform PWM or dc voltage stepping functions, so as to limit current ripple in the stator windings below an acceptable level, typically 5%. Several embodiments are disclosed including inverters using IGBT's, inverters using thyristors. All of the inverters are operable in both motoring and regenerating modes.

  11. CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

    Science.gov (United States)

    Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

    2014-12-01

    Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

  12. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  13. Resonant snubber inverter

    Science.gov (United States)

    Lai, Jih-Sheng; Young, Sr., Robert W.; Chen, Daoshen; Scudiere, Matthew B.; Ott, Jr., George W.; White, Clifford P.; McKeever, John W.

    1997-01-01

    A resonant, snubber-based, soft switching, inverter circuit achieves lossless switching during dc-to-ac power conversion and power conditioning with minimum component count and size. Current is supplied to the resonant snubber branches solely by the main inverter switches. Component count and size are reduced by use of a single semiconductor switch in the resonant snubber branches. Component count is also reduced by maximizing the use of stray capacitances of the main switches as parallel resonant capacitors. Resonance charging and discharging of the parallel capacitances allows lossless, zero voltage switching. In one embodiment, circuit component size and count are minimized while achieving lossless, zero voltage switching within a three-phase inverter.

  14. Next Generation Inverter

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Zilai [General Motors LLC, Detroit, MI (United States); Gough, Charles [General Motors LLC, Detroit, MI (United States)

    2016-04-22

    The goal of this Cooperative Agreement was the development of a Next Generation Inverter for General Motors’ electrified vehicles, including battery electric vehicles, range extended electric vehicles, plug-in hybrid electric vehicles and hybrid electric vehicles. The inverter is a critical electronics component that converts battery power (DC) to and from the electric power for the motor (AC).

  15. Inverting the Linear Algebra Classroom

    Science.gov (United States)

    Talbert, Robert

    2014-01-01

    The inverted classroom is a course design model in which students' initial contact with new information takes place outside of class meetings, and students spend class time on high-level sense-making activities. The inverted classroom model is so called because it inverts or "flips" the usual classroom design where typically class…

  16. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop.

    Science.gov (United States)

    Dembska, Anna; Juskowiak, Bernard

    2015-01-01

    In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit). Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Experimental Evaluation of PV Inverter Anti-Islanding with Grid Support Functions in Multi-Inverter Island Scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Hoke, Anderson [National Renewable Energy Lab. (NREL), Golden, CO (United States); Nelson, Austin [National Renewable Energy Lab. (NREL), Golden, CO (United States); Miller, Brian [National Renewable Energy Lab. (NREL), Golden, CO (United States); Chakraborty, Sudipta [National Renewable Energy Lab. (NREL), Golden, CO (United States); Bell, Frances [SolarCity, San Mateo, CA (United States); McCarty, Michael [SolarCity, San Mateo, CA (United States)

    2016-07-01

    As PV and other DER systems are connected to the grid at increased penetration levels, island detection may become more challenging for two reasons: 1.) In islands containing many DERs, active inverter-based anti-islanding methods may have more difficulty detecting islands because each individual inverter's efforts to detect the island may be interfered with by the other inverters in the island. 2.) The increasing numbers of DERs are leading to new requirements that DERs ride through grid disturbances and even actively try to regulate grid voltage and frequency back towards nominal operating conditions. These new grid support requirements may directly or indirectly interfere with anti-islanding controls. This report describes a series of tests designed to examine the impacts of both grid support functions and multi-inverter islands on anti-islanding effectiveness. Crucially, the multi-inverter anti-islanding tests described in this report examine scenarios with multiple inverters connected to multiple different points on the grid. While this so-called 'solar subdivision' scenario has been examined to some extent through simulation, this is the first known work to test it using hardware inverters. This was accomplished through the use of power hardware-in-the-loop (PHIL) simulation, which allows the hardware inverters to be connected to a real-time transient simulation of an electric power system that can be easily reconfigured to test various distribution circuit scenarios. The anti-islanding test design was a modified version of the unintentional islanding test in IEEE Standard 1547.1, which creates a balanced, resonant island with the intent of creating a highly challenging condition for island detection. Three common, commercially available single-phase PV inverters from three different manufacturers were tested. The first part of this work examined each inverter individually using a series of pure hardware resistive-inductive-capacitive (RLC

  18. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  19. Reliable inverter systems

    Science.gov (United States)

    Nagano, S.

    1979-01-01

    Base driver with common-load-current feedback protects paralleled inverter systems from open or short circuits. Circuit eliminates total system oscillation that can occur in conventional inverters because of open circuit in primary transformer winding. Common feedback signal produced by functioning modules forces operating frequency of failed module to coincide with clock drive so module resumes normal operating frequency in spite of open circuit.

  20. Identity and functions of CxxC-derived motifs.

    Science.gov (United States)

    Fomenko, Dmitri E; Gladyshev, Vadim N

    2003-09-30

    Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

  1. Addressable inverter matrix for process and device characterization

    Science.gov (United States)

    Buehler, M. G.; Sayah, H. R.

    1985-01-01

    The addressable inverter matrix consists of 222 inverters each accessible with the aid of a shift register. The structure has proven useful in characterizing the variability of inverter transfer curves and in diagnosing processing faults. For good 3-micron CMOS bulk inverters investigated, the percent standard deviation of the inverter threshold voltage was less than one percent and the inverter gain (the slope of the inverter transfer curve at the inverter threshold vltage) was less than 3 percent. The average noise margin for the inverters was near 2 volts for a power supply voltage of 5 volts. The specific faults studied included undersize pull-down transistor widths and various open contacts in the matrix.

  2. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.

    2008-01-01

    set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...

  3. Deletion of the B-B' and C-C' regions of inverted terminal repeats reduces rAAV productivity but increases transgene expression.

    Science.gov (United States)

    Zhou, Qingzhang; Tian, Wenhong; Liu, Chunguo; Lian, Zhonghui; Dong, Xiaoyan; Wu, Xiaobing

    2017-07-14

    Inverted terminal repeats (ITRs) of the adeno-associated virus (AAV) are essential for rescue, replication, packaging, and integration of the viral genome. While ITR mutations have been identified in previous reports, we designed a new truncated ITR lacking the B-B' and C-C' regions named as ITRΔBC and investigated its effects on viral genome replication, packaging, and expression of recombinant AAV (rAAV). The packaging ability was compared between ITRΔBC rAAV and wild-type (wt) ITR rAAV. Our results showed the productivity of ITRΔBC rAAV was reduced 4-fold, which is consistent with the 8-fold decrease in the replication of viral genomic DNA of ITRΔBC rAAV compared with wt ITR rAAV. Surprisingly, transgene expression was significantly higher for ITRΔBC rAAV. A preliminary exploration of the underlying mechanisms was carried out by inhibiting and degrading the ataxia telangiectasia mutated (ATM) protein and the Mre11 complex (MRN), respectively, since the rAAV expression was inhibited by the ATM and/or MRN through cis interaction or binding with wt ITRs. We demonstrated that the inhibitory effects were weakened on ITRΔBC rAAV expression. This study suggests deletion in ITR can affect the transgene expression of AAV, which provides a new way to improve the AAV expression through ITRs modification.

  4. Inverter design for high frequency power distribution

    Science.gov (United States)

    King, R. J.

    1985-01-01

    A class of simple resonantly commutated inverters are investigated for use in a high power (100 KW - 1000 KW) high frequency (10 KHz - 20 KHz) AC power distribution system. The Mapham inverter is found to provide a unique combination of large thyristor turn-off angle and good utilization factor, much better than an alternate 'current-fed' inverter. The effects of loading the Mapham inverter entirely with rectifier loads are investigated by simulation and with an experimental 3 KW 20 KHz inverter. This inverter is found to be well suited to a power system with heavy rectifier loading.

  5. Transformerless PV inverters. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Borup, U.

    2009-12-15

    Since the start of the project the market for grid connected PV inverters have developed further. When the project started three - phase inverter were only available in high power systems. The technology developed within this project will enable three phase technology also to be implemented in string inverters for system down to 10 kW. We expect this to be very attractive due to the increased demand for symmetrical feed-in to the grid. The project relevance is therefore high and the sector continues to develop very much driven by technology. Especially the inverter technology is getting a lot of focus. The inverter systems are expected to take a much larger role in supporting the electrical grid in the future. The technology platform developed within the project is prepared to be extended with these utility functionalities. The main results of the project were: 1) A new technology concept for transformer-less inverters has been demonstrated with a number of prototypes. 2) Efficiency above 97,7% has been proven. 3) Efficiency and Maximum power point tracking has been optimized to ensure that almost all energy produced of the panels is transferred to the grid. 4) The platform is developed with a very fast control board, which enables extended functionality as demanding grid supporting functions in the future. Details about cost price and details about the control loop implementation is excluded from the report due to the competitive situation for Danfoss Solar Inverters A/S. (LN)

  6. Genome-wide analysis of tandem repeats in plants and green algae

    Science.gov (United States)

    Zhixin Zhao; Cheng Guo; Sreeskandarajan Sutharzan; Pei Li; Craig Echt; Jie Zhang; Chun Liang

    2014-01-01

    Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among...

  7. Multilevel Inverter by Cascading Industrial VSI

    DEFF Research Database (Denmark)

    Teodorescu, Remus; Blaabjerg, Frede; Pedersen, John Kim

    2002-01-01

    In this paper the modularity concept applied to medium-voltage adjustable speed drives is addressed. First, the single-phase cascaded voltage-source inverter that uses series connection of IGBT H-bridge modules with isolated dc-buses is presented. Next, a novel three-phase cascaded voltage......-source inverter that uses three IGBT triphase inverter modules along with an output transformer to obtain a 3 p.u. multilevel output voltage is introduced. The system yields in high-quality multistep voltage with up to 4 levels and low dv/dt, balanced operation of the inverter modules, each supplying a third...... of the motor rated kVA. The concept of using cascaded inverters is further extended to a new modular motor-modular inverter system where the motor winding connections are reconnected into several three-phase groups, either six-lead or 12-lead connection according to the voltage level, each powered...

  8. Gas cooled traction drive inverter

    Science.gov (United States)

    Chinthavali, Madhu Sudhan

    2013-10-08

    The present invention provides a modular circuit card configuration for distributing heat among a plurality of circuit cards. Each circuit card includes a housing adapted to dissipate heat in response to gas flow over the housing. In one aspect, a gas-cooled inverter includes a plurality of inverter circuit cards, and a plurality of circuit card housings, each of which encloses one of the plurality of inverter cards.

  9. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

  10. Embedded EZ-Source Inverters

    DEFF Research Database (Denmark)

    Chiang Loh, Poh; Gao, Feng; Blaabjerg, Frede

    2010-01-01

    overvoltage oscillations to the system. Therefore, Z-source inverters are, in effect, safer and less complex and can be implemented using only passive elements with no additional active semiconductor needed. Believing in the prospects of Z-source inverters, this paper contributes by introducing a new family...

  11. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  12. A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family.

    Science.gov (United States)

    Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L; Salt, Jennifer N; Goring, Daphne R

    2004-01-01

    The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis.

  13. Motif enrichment tool.

    Science.gov (United States)

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. EEVD motif of heat shock cognate protein 70 contributes to bacterial uptake by trophoblast giant cells

    Directory of Open Access Journals (Sweden)

    Kim Suk

    2009-12-01

    Full Text Available Abstract Background The uptake of abortion-inducing pathogens by trophoblast giant (TG cells is a key event in infectious abortion. However, little is known about phagocytic functions of TG cells against the pathogens. Here we show that heat shock cognate protein 70 (Hsc70 contributes to bacterial uptake by TG cells and the EEVD motif of Hsc70 plays an important role in this. Methods Brucella abortus and Listeria monocytogenes were used as the bacterial antigen in this study. Recombinant proteins containing tetratricopeptide repeat (TPR domains were constructed and confirmation of the binding capacity to Hsc70 was assessed by ELISA. The recombinant TPR proteins were used for investigation of the effect of TPR proteins on bacterial uptake by TG cells and on pregnancy in mice. Results The monoclonal antibody that inhibits bacterial uptake by TG cells reacted with the EEVD motif of Hsc70. Bacterial TPR proteins bound to the C-terminal of Hsc70 through its EEVD motif and this binding inhibited bacterial uptake by TG cells. Infectious abortion was also prevented by blocking the EEVD motif of Hsc70. Conclusions Our results demonstrate that surface located Hsc70 on TG cells mediates the uptake of pathogenic bacteria and proteins containing the TPR domain inhibit the function of Hsc70 by binding to its EEVD motif. These molecules may be useful in the development of methods for preventing infectious abortion.

  15. Embedded EZ-Source Inverters

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Loh, Poh Chiang; Gao, F.

    2008-01-01

    -voltage oscillations to the system. Therefore, Z-source inverters are in effect safer and less complex, and can be implemented using only passive elements with no additional active semiconductor needed. Believing in the prospects of Z-source inverters, this paper contributes by introducing a new family of embedded EZ...

  16. Trans-Z-source Neutral Point Clamped inverter

    DEFF Research Database (Denmark)

    Mo, W.; Loh, P. C.; Li, D.

    2012-01-01

    Transformer based Z-source (trans-Z-source) inverters are recently proposed by extending the traditional Z-source inverter with higher buck-boost capability as well as reducing the passive components at the same time. Multi-Level Z-source inverters are single-stage topological solutions used...... for buck-boost energy conversion with all the favourable advantages of multi-level switching retained. This paper presents three-level trans-Z-source Neutral Point Clamped (NPC) inverter topology, which achieves both the advantages of trans-Z-source and three-level NPC inverter configuration. With proper...... modulation scheme, the three-level trans-Z-source inverter can function with minimum of six device commutations per half carrier cycle (same as the traditional buck NPC inverter), while maintaining to produce the designed volt-sec average and inductive voltage boosting at ac output terminals. The designed...

  17. Five-level Z-source diode-clamped inverter

    DEFF Research Database (Denmark)

    Gao, F.; Loh, Poh Chiang; Blaabjerg, Frede

    2010-01-01

    This study proposes a five-level Z-source diode-clamped inverter designed with two intermediate Z-source networks connected between the dc input sources and rear-end inverter circuitry. By partially shorting the Z-source networks, new operating states not previously reported for two-level Z......-source inverter are introduced here for operating the proposed inverter with voltage buck–boost energy conversion ability and five-level phase voltage switching. These characteristic features are in fact always ensured at the inverter terminal output by simply adopting a properly designed carrier modulation...

  18. Component-Minimized Buck-Boost Voltage Source Inverters

    DEFF Research Database (Denmark)

    Gao, F.; Loh, P.C.; Blaabjerg, Frede

    2007-01-01

    This paper presents the design of buck-boost B4 inverters that can be derived from either Ćuk- or SEPIC-derived buck-boost B6 inverters. Unlike traditional inverters, the integration of front-end voltage boost circuitry and inverter circuitry allows it to perform buck-boost voltage inversion...... between capacitors. Modulation wise, the proposed buck-boost B4 inverters can be controlled using a carefully designed carrier-based pulse-width modulation (PWM) scheme that will always ensure balanced threephase outputs as desired, while simultaneously achieving minimal voltage stress across...

  19. Inverted Nipple Correction with Selective Dissection of Lactiferous Ducts Using an Operative Microscope and a Traction Technique.

    Science.gov (United States)

    Sowa, Yoshihiro; Itsukage, Sizu; Morita, Daiki; Numajiri, Toshiaki

    2017-10-01

    An inverted nipple is a common congenital condition in young women that may cause breastfeeding difficulty, psychological distress, repeated inflammation, and loss of sensation. Various surgical techniques have been reported for correction of inverted nipples, and all have advantages and disadvantages. Here, we report a new technique for correction of an inverted nipple using an operative microscope and traction that results in low recurrence and preserves lactation function and sensation. Between January 2010 and January 2013, we treated eight inverted nipples in seven patients with selective lactiferous duct dissection using an operative microscope. An opposite Z-plasty was added at the junction of the nipple and areola. Postoperatively, traction was applied through an apparatus made from a rubber gasket attached to a sterile syringe. Patients were followed up for 15-48 months. Adequate projection was achieved in all patients, and there was no wound dehiscence or complications such as infection. Three patients had successful pregnancies and subsequent breastfeeding that was not adversely affected by the treatment. There was no loss of sensation in any patient during the postoperative period. Our technique for treating an inverted nipple is effective and preserves lactation function and nipple sensation. The method maintains traction for a longer period, which we believe increases the success rate of the surgery for correction of severely inverted nipples. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

  20. On Invertible Sampling and Adaptive Security

    DEFF Research Database (Denmark)

    Ishai, Yuval; Kumarasubramanian, Abishek; Orlandi, Claudio

    2011-01-01

    functionalities was left open. We provide the first convincing evidence that the answer to this question is negative, namely that some (randomized) functionalities cannot be realized with adaptive security. We obtain this result by studying the following related invertible sampling problem: given an efficient...... sampling algorithm A, obtain another sampling algorithm B such that the output of B is computationally indistinguishable from the output of A, but B can be efficiently inverted (even if A cannot). This invertible sampling problem is independently motivated by other cryptographic applications. We show......, under strong but well studied assumptions, that there exist efficient sampling algorithms A for which invertible sampling as above is impossible. At the same time, we show that a general feasibility result for adaptively secure MPC implies that invertible sampling is possible for every A, thereby...

  1. Microbial expression of proteins containing long repetitive Arg-Gly-Asp cell adhesive motifs created by overlap elongation PCR

    International Nuclear Information System (INIS)

    Kurihara, Hiroyuki; Shinkai, Masashige; Nagamune, Teruyuki

    2004-01-01

    We developed a novel method for creating repetitive DNA libraries using overlap elongation PCR, and prepared a DNA library encoding repetitive Arg-Gly-Asp (RGD) cell adhesive motifs. We obtained various length DNAs encoding repetitive RGD from a short monomer DNA (18 bp) after a thermal cyclic reaction without a DNA template for amplification, and isolated DNAs encoding 2, 21, and 43 repeats of the RGD motif. We cloned these DNAs into a protein expression vector and overexpressed them as thioredoxin fusion proteins: RGD2, RGD21, and RGD43, respectively. The solubility of RGD43 in water was low and it formed a fibrous precipitate in water. Scanning electron microscopy revealed that RGD43 formed a branched 3D-network structure in the solid state. To evaluate the function of the cell adhesive motifs in RGD43, mouse fibroblast cells were cultivated on the RGD43 scaffold. The fibroblast cells adhered to the RGD43 scaffold and extended long filopodia

  2. Preparation of inverted medium and processing in the inverted medium

    International Nuclear Information System (INIS)

    Zafarullah, Ijaz; Tian Minghzen; Chang Tiejun; Randall Babbitt, W.

    2007-01-01

    The processing of weak optical signals in spatial-spectral holographic (SSH) materials coherently inverted with optical frequency chirped pulses were investigated. Simulations and experimental studies in Tm 3+ :YAG were conducted to characterize the parameters of the frequency chirped laser pulse used to invert the SSH material in order to obtain high photon echo efficiency for SSH lidar processing. Collinear and angled beam geometries and single shot and accumulated processes were investigated. Echo efficiencies as high as 450% were measured, significantly higher than the typical stimulated photon echo efficiency of 10%

  3. Preparation of inverted medium and processing in the inverted medium

    Energy Technology Data Exchange (ETDEWEB)

    Zafarullah, Ijaz [Department of Physics, Montana State University, Bozeman, MT 59717 (United States)]. E-mail: ijaz@montana.edu; Tian Minghzen [Department of Physics, Montana State University, Bozeman, MT 59717 (United States); Chang Tiejun [The Spectrum Laboratory, Montana State University, Bozeman, MT 59717 (United States); Randall Babbitt, W. [Department of Physics, Montana State University, Bozeman, MT 59717 (United States)

    2007-11-15

    The processing of weak optical signals in spatial-spectral holographic (SSH) materials coherently inverted with optical frequency chirped pulses were investigated. Simulations and experimental studies in Tm{sup 3+}:YAG were conducted to characterize the parameters of the frequency chirped laser pulse used to invert the SSH material in order to obtain high photon echo efficiency for SSH lidar processing. Collinear and angled beam geometries and single shot and accumulated processes were investigated. Echo efficiencies as high as 450% were measured, significantly higher than the typical stimulated photon echo efficiency of 10%.

  4. Solar Charged Stand Alone Inverter

    OpenAIRE

    M.Vasugi; Prof R.Jayaraman

    2014-01-01

    This paper deals with solar powered stand alone inverter which converts the variable dc output of a photovoltaic solar panel into ac that can be fed to loads. Stand alone inverters are used in systems where the inverter get its energy from batteries charged by photo voltaic arrays. A charge controller limits the rate at which electric current is added to or drawn from electric batteries. This charge discharge controller is needed to prevent the battery from being overcharged o...

  5. Nanowire NMOS Logic Inverter Characterization.

    Science.gov (United States)

    Hashim, Yasir

    2016-06-01

    This study is the first to demonstrate characteristics optimization of nanowire N-Channel Metal Oxide Semiconductor (NW-MOS) logic inverter. Noise margins and inflection voltage of transfer characteristics are used as limiting factors in this optimization. A computer-based model used to produce static characteristics of NW-NMOS logic inverter. In this research two circuit configuration of NW-NMOS inverter was studied, in first NW-NMOS circuit, the noise margin for (low input-high output) condition was very low. For second NMOS circuit gives excellent noise margins, and results indicate that optimization depends on applied voltage to the inverter. Increasing gate to source voltage with (2/1) nanowires ratio results better noise margins. Increasing of applied DC load transistor voltage tends to increasing in decreasing noise margins; decreasing this voltage will improve noise margins significantly.

  6. UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO

    Directory of Open Access Journals (Sweden)

    Irfa ina Rohana Salma

    2016-12-01

    Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo

  7. Repeat Sequence Proteins as Matrices for Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Drummy, L.; Koerner, H; Phillips, D; McAuliffe, J; Kumar, M; Farmer, B; Vaia, R; Naik, R

    2009-01-01

    Recombinant protein-inorganic nanocomposites comprised of exfoliated Na+ montmorillonite (MMT) in a recombinant protein matrix based on silk-like and elastin-like amino acid motifs (silk elastin-like protein (SELP)) were formed via a solution blending process. Charged residues along the protein backbone are shown to dominate long-range interactions, whereas the SELP repeat sequence leads to local protein/MMT compatibility. Up to a 50% increase in room temperature modulus and a comparable decrease in high temperature coefficient of thermal expansion occur for cast films containing 2-10 wt.% MMT.

  8. 21 CFR 184.1859 - Invert sugar.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Invert sugar. 184.1859 Section 184.1859 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1859 Invert sugar. (a) Invert sugar (CAS Reg. No. 8013-17-0) is an aqueous...

  9. Simplified High-Power Inverter

    Science.gov (United States)

    Edwards, D. B.; Rippel, W. E.

    1984-01-01

    Solid-state inverter simplified by use of single gate-turnoff device (GTO) to commutate multiple silicon controlled rectifiers (SCR's). By eliminating conventional commutation circuitry, GTO reduces cost, size and weight. GTO commutation applicable to inverters of greater than 1-kilowatt capacity. Applications include emergency power, load leveling, drives for traction and stationary polyphase motors, and photovoltaic-power conditioning.

  10. Aalborg Inverter - A New Type of “Buck in Buck, Boost in Boost” Grid-Tied Inverter

    DEFF Research Database (Denmark)

    Wu, Weimin; Ji, Junhao; Blaabjerg, Frede

    2015-01-01

    This paper presents a new family of high efficiency dc/ac grid-tied inverter with a wide variation of input dc voltage. It is a “boost in boost, buck in buck” inverter, meaning that only one power stage works at high frequency in order to achieve minimum switching loss. The minimum voltage drop...... of the filtering inductor in the power loop is achieved to reduce the conduction power loss in both “boost” and “buck” mode. The principle of operation is demonstrated through the analysis on the equivalent circuits of a “half-bridge” single-phase inverter. The theoretical analysis shows that when input dc voltage...... is larger than the magnitude of the ac voltage, it is a voltage-source inverter, and on the contrary it is current-source inverter in the other mode. A 220 V/50 Hz/ 2000 W prototype has been constructed. Simulations and experiments show that it has a good control and system performance....

  11. A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family1[w

    Science.gov (United States)

    Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L.; Salt, Jennifer N.; Goring, Daphne R.

    2004-01-01

    The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis. PMID:14657406

  12. Online Variable Topology-Type Photovoltaic Grid-Connected Inverter

    DEFF Research Database (Denmark)

    Wu, Fengjiang; Sun, Bo; Duan, Jiandong

    2015-01-01

    In photovoltaic (PV) grid-connected generation system, the key focus is how to expand the generation range of the PV array and enhance the total efficiency of the system. This paper originally derived expressions of the total loss and grid current total harmonics distortions of cascaded inverter...... and H-bridge inverter under the conditions of variable output voltage and power of the PV array. It is proved that, compared with the H-bridge inverter, the operation range of the cascaded inverter is wider, whereas the total loss is larger. Furthermore, a novel online variable topology-type grid......-connected inverter is proposed. A bidirectional power switch is introduced into the conventional cascaded inverter to connect the negative terminals of the PV arrays. When the output voltages of the PV arrays are lower, the proposed inverter works under cascaded inverter mode to obtain wider generation range. When...

  13. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  14. Conserved amino acid motifs from the novel Piv/MooV family of transposases and site-specific recombinases are required for catalysis of DNA inversion by Piv.

    Science.gov (United States)

    Tobiason, D M; Buchner, J M; Thiel, W H; Gernert, K M; Karls, A C

    2001-02-01

    Piv, a site-specific invertase from Moraxella lacunata, exhibits amino acid homology with the transposases of the IS110/IS492 family of insertion elements. The functions of conserved amino acid motifs that define this novel family of both transposases and site-specific recombinases (Piv/MooV family) were examined by mutagenesis of fully conserved amino acids within each motif in Piv. All Piv mutants altered in conserved residues were defective for in vivo inversion of the M. lacunata invertible DNA segment, but competent for in vivo binding to Piv DNA recognition sequences. Although the primary amino acid sequences of the Piv/MooV recombinases do not contain a conserved DDE motif, which defines the retroviral integrase/transposase (IN/Tnps) family, the predicted secondary structural elements of Piv align well with those of the IN/Tnps for which crystal structures have been determined. Molecular modelling of Piv based on these alignments predicts that E59, conserved as either E or D in the Piv/MooV family, forms a catalytic pocket with the conserved D9 and D101 residues. Analysis of Piv E59G confirms a role for E59 in catalysis of inversion. These results suggest that Piv and the related IS110/IS492 transposases mediate DNA recombination by a common mechanism involving a catalytic DED or DDD motif.

  15. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2008-01-01

    . Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...

  16. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    Science.gov (United States)

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

  17. Analysis of alkaptonuria (AKU) mutations and polymorphisms reveals that the CCC sequence motif is a mutational hot spot in the homogentisate 1,2 dioxygenase gene (HGO).

    Science.gov (United States)

    Beltrán-Valero de Bernabé, D; Jimenez, F J; Aquaron, R; Rodríguez de Córdoba, S

    1999-01-01

    We recently showed that alkaptonuria (AKU) is caused by loss-of-function mutations in the homogentisate 1,2 dioxygenase gene (HGO). Herein we describe haplotype and mutational analyses of HGO in seven new AKU pedigrees. These analyses identified two novel single-nucleotide polymorphisms (INV4+31A-->G and INV11+18A-->G) and six novel AKU mutations (INV1-1G-->A, W60G, Y62C, A122D, P230T, and D291E), which further illustrates the remarkable allelic heterogeneity found in AKU. Reexamination of all 29 mutations and polymorphisms thus far described in HGO shows that these nucleotide changes are not randomly distributed; the CCC sequence motif and its inverted complement, GGG, are preferentially mutated. These analyses also demonstrated that the nucleotide substitutions in HGO do not involve CpG dinucleotides, which illustrates important differences between HGO and other genes for the occurrence of mutation at specific short-sequence motifs. Because the CCC sequence motifs comprise a significant proportion (34.5%) of all mutated bases that have been observed in HGO, we conclude that the CCC triplet is a mutational hot spot in HGO. PMID:10205262

  18. Inverted base pavements: construction and performance

    KAUST Repository

    Papadopoulos, Efthymios

    2017-05-11

    Inverted base pavements involve a well-compacted granular aggregate base built between a thin asphalt concrete layer and a cement-treated base. Inverted base pavements can be constructed using conventional equipment and procedures but require proper quality control. This study reviews the extensive South African experience and case histories in the USA. Accumulating evidence suggests that inverted base pavements are a viable alternative and can outperform conventional pavements at a lower cost. Inverted base pavements rely on the complementary interaction between layers. The cement-treated base provides a stiff foundation for efficient compaction and constrains the deformation of the stress-sensitive granular aggregate base. The thin asphalt surface layer deforms as a membrane and develops low tensile stress. Additional large-scale field tests should be conducted to assess the performance of inverted base pavement designs in a wide range of conditions relevant to the USA.

  19. Complete plastid genome sequencing of Trochodendraceae reveals a significant expansion of the inverted repeat and suggests a Paleogene divergence between the two extant species.

    Directory of Open Access Journals (Sweden)

    Yan-xia Sun

    Full Text Available The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots, but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8 that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.

  20. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

  1. Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

    Science.gov (United States)

    Tajaddod, Mansoureh; Tanzer, Andrea; Licht, Konstantin; Wolfinger, Michael T; Badelt, Stefan; Huber, Florian; Pusch, Oliver; Schopoff, Sandy; Janisiw, Michael; Hofacker, Ivo; Jantsch, Michael F

    2016-10-25

    Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels. Here, we undertake a genome-wide analysis of insertion patterns of human Alus within transcribed portions of the genome. Multiple, nearby insertions of SINEs within one transcript are more abundant in tandem orientation than in inverted orientation. Indeed, analysis of transcriptome-wide expression levels of 15 ENCODE cell lines suggests a cis-repressive effect of inverted Alu elements on gene expression. Using reporter assays, we show that the negative effect of inverted SINEs on gene expression is independent of known sensors of double-stranded RNAs. Instead, transcriptional elongation seems impaired, leading to reduced mRNA levels. Our study suggests that there is a bias against multiple SINE insertions that can promote intramolecular base pairing within a transcript. Moreover, at a genome-wide level, mRNAs harboring inverted SINEs are less expressed than mRNAs harboring single or tandemly arranged SINEs. Finally, we demonstrate a novel mechanism by which inverted SINEs can impact on gene expression by interfering with RNA polymerase II.

  2. An Optimal Current Controller Design for a Grid Connected Inverter to Improve Power Quality and Test Commercial PV Inverters.

    Science.gov (United States)

    Algaddafi, Ali; Altuwayjiri, Saud A; Ahmed, Oday A; Daho, Ibrahim

    2017-01-01

    Grid connected inverters play a crucial role in generating energy to be fed to the grid. A filter is commonly used to suppress the switching frequency harmonics produced by the inverter, this being passive, and either an L- or LCL-filter. The latter is smaller in size compared to the L-filter. But choosing the optimal values of the LCL-filter is challenging due to resonance, which can affect stability. This paper presents a simple inverter controller design with an L-filter. The control topology is simple and applied easily using traditional control theory. Fast Fourier Transform analysis is used to compare different grid connected inverter control topologies. The modelled grid connected inverter with the proposed controller complies with the IEEE-1547 standard, and total harmonic distortion of the output current of the modelled inverter has been just 0.25% with an improved output waveform. Experimental work on a commercial PV inverter is then presented, including the effect of strong and weak grid connection. Inverter effects on the resistive load connected at the point of common coupling are presented. Results show that the voltage and current of resistive load, when the grid is interrupted, are increased, which may cause failure or damage for connecting appliances.

  3. Deciphering functional glycosaminoglycan motifs in development.

    Science.gov (United States)

    Townley, Robert A; Bülow, Hannes E

    2018-03-23

    Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Aalborg Inverter - A new type of “Buck in Buck, Boost in Boost” Grid-tied Inverter

    DEFF Research Database (Denmark)

    Wu, Weimin; Blaabjerg, Frede

    2013-01-01

    This paper presents a new family of high efficiency DC/AC grid-tied inverter with a wide variation of input DC voltage. It is a kind of “Boost in Boost, Buck in Buck” inverter, meaning that only one power stage works at the high frequency to achieve the minimum switching loss. Furthermore......, the minimum filtering inductance in the power loop is achieved to reduce the conduction power loss whether in “Boost” or “Buck” mode. In theory, it can achieve higher efficiency than other inverters under the same condition of input DC voltage. The principle of operation is fully illustrated through...... the analysis on the equivalent circuits of a “three-level” single-phase inverter. Simulations show it has good control performance....

  5. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed....

  6. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    Science.gov (United States)

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

  7. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    Directory of Open Access Journals (Sweden)

    Masiswo Masiswo

    2016-04-01

    Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa

  8. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  9. Design and Implementation of nine level multilevel Inverter

    Science.gov (United States)

    Dhineshkumar, K.; Subramani, C.

    2018-04-01

    In this paper the solar based boost converter integrated Nine level multilevel inverter presented. It uses 7 switches to produce nine level output stepped waveform. The aim of the work to produce 9 level wave form using solar and boost converter. The conventional inverter has multiple sources and has 16 switches are required and also more number of voltage sources required. The proposed inverter required single solar panel and reduced number of switches and integrated boost converter which increase the input voltage of the inverter. The proposed inverter simulated and compared with R load using Mat lab and prototype model experimentally verified. The proposed inverter can be used in n number of solar applications.

  10. Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

    Directory of Open Access Journals (Sweden)

    Rudi - Nababan

    2012-04-01

    Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

  11. Efficient/reliable dc-to-dc inverter circuit

    Science.gov (United States)

    Pasciutti, E. R.

    1970-01-01

    Feedback loop, which contains an inductor in series with a saturable reactor, is added to a standard inverter circuit to permit the inverter power transistors to be switched in a controlled and efficient manner. This inverter is applicable where the power source has either high or low impedance properties.

  12. Divergent Synthesis of Chondroitin Sulfate Disaccharides and Identification of Sulfate Motifs that Inhibit Triple Negative Breast Cancer

    Science.gov (United States)

    Wei Poh, Zhong; Heng Gan, Chin; Lee, Eric J.; Guo, Suxian; Yip, George W.; Lam, Yulin

    2015-09-01

    Glycosaminoglycans (GAGs) regulate many important physiological processes. A pertinent issue to address is whether GAGs encode important functional information via introduction of position specific sulfate groups in the GAG structure. However, procurement of pure, homogenous GAG motifs to probe the “sulfation code” is a challenging task due to isolation difficulty and structural complexity. To this end, we devised a versatile synthetic strategy to obtain all the 16 theoretically possible sulfation patterns in the chondroitin sulfate (CS) repeating unit; these include rare but potentially important sulfated motifs which have not been isolated earlier. Biological evaluation indicated that CS sulfation patterns had differing effects for different breast cancer cell types, and the greatest inhibitory effect was observed for the most aggressive, triple negative breast cancer cell line MDA-MB-231.

  13. High voltage series resonant inverter ion engine screen supply. [SCR series resonant inverter for space applications

    Science.gov (United States)

    Biess, J. J.; Inouye, L. Y.; Shank, J. H.

    1974-01-01

    A high-voltage, high-power LC series resonant inverter using SCRs has been developed for an Ion Engine Power Processor. The inverter operates within 200-400Vdc with a maximum output power of 2.5kW. The inverter control logic, the screen supply electrical and mechanical characteristics, the efficiency and losses in power components, regulation on the dual feedback principle, the SCR waveforms and the component weight are analyzed. Efficiency of 90.5% and weight density of 4.1kg/kW are obtained.

  14. Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis.

    Science.gov (United States)

    Zheng, Jin-Shuang; Sun, Cheng-Zhen; Zhang, Shu-Ning; Hou, Xi-Lin; Bonnema, Guusje

    2016-01-01

    A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis.

  15. Motif statistics and spike correlations in neuronal networks

    International Nuclear Information System (INIS)

    Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir

    2013-01-01

    Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)

  16. Modulation of Current Source Inverter

    Directory of Open Access Journals (Sweden)

    Golam Reza Arab Markadeh

    2011-04-01

    Full Text Available Direct torque control with Current Source Inverter (CSI instead of voltage source inverter is so appropriate because of determining the torque of induction motor with machine current and air gap flux. In addition, Space-Vector Modulation (SVM is a more proper method for CSI because of low order harmonics reduction, lower switching frequency and easier implementation. This paper introduces the SVM method for CSI and uses the proposed inverter for vector control of an induction motor. The simulation results illustrate fast dynamic response and desirable torque and speed output. Fast and accurate response to changes of speed and load torque reference completely proves the prominence of this method.

  17. Detecting and mitigating inverter aging

    International Nuclear Information System (INIS)

    Gunther, W.E.; Taylor, J.H.; Aggarwal, S.K.

    1988-01-01

    Nuclear power plants use inverters to supply power to safety-related equipment, instrumentation, and controls. They convert direct current (dc) to alternating current (ac) power, thereby making low voltage ac power available even under a station blackout condition. As part of the U.S. NRC's nuclear plant aging research (NPAR) program, the operating experience of this equipment has been analyzed to determine the dominant failure modes and causes. This paper summarizes that data, and then describes methods which can be employed to detect inverter degradation prior to failure, as well as methods to minimize the failure effects. In both cases, the mitigation of inverter aging is emphasized

  18. Diode-Assisted Buck-Boost Current Source Inverters

    DEFF Research Database (Denmark)

    Gao, F.; Cai, Liang; Loh, P.C.

    2007-01-01

    This paper presents a couple of novel current source inverters (CSIs) with the enhanced current buckboost capability. With the unique diode-inductor network added between current source inverter circuitry and current boost elements, the proposed buck-boost current source inverters demonstrate...... uninfluenced. Lastly, all theoretical findings were verified experimentally using constructed laboratory prototypes....

  19. Bayesian centroid estimation for motif discovery.

    Science.gov (United States)

    Carvalho, Luis

    2013-01-01

    Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  20. Bayesian centroid estimation for motif discovery.

    Directory of Open Access Journals (Sweden)

    Luis Carvalho

    Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  1. Repeat-containing protein effectors of plant-associated organisms

    Directory of Open Access Journals (Sweden)

    Carl H. Mesarich

    2015-10-01

    Full Text Available Many plant-associated organisms, including microbes, nematodes, and insects, deliver effector proteins into the apoplast, vascular tissue, or cell cytoplasm of their prospective hosts. These effectors function to promote colonization, typically by altering host physiology or by modulating host immune responses. The same effectors however, can also trigger host immunity in the presence of cognate host immune receptor proteins, and thus prevent colonization. To circumvent effector-triggered immunity, or to further enhance host colonization, plant-associated organisms often rely on adaptive effector evolution. In recent years, it has become increasingly apparent that several effectors of plant-associated organisms are repeat-containing proteins (RCPs that carry tandem or non-tandem arrays of an amino acid sequence or structural motif. In this review, we highlight the diverse roles that these repeat domains play in RCP effector function. We also draw attention to the potential role of these repeat domains in adaptive evolution with regards to RCP effector function and the evasion of effector-triggered immunity. The aim of this review is to increase the profile of RCP effectors from plant-associated organisms.

  2. The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

    Directory of Open Access Journals (Sweden)

    Turmel Monique

    2007-07-01

    Full Text Available Abstract Background In the Chlorophyta – the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae – the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs deviate considerably from the ancestral pattern described for the prasinophyte Nephroselmis olivacea, the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs. Chlorella vulgaris (Chlorellales is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga Leptosira terrestris (Ctenocladales. Results The 195,081-bp Leptosira chloroplast genome resembles the 150,613-bp Chlorella genome in lacking a large inverted repeat (IR but differs greatly in gene order. Six of the conserved genes present in Chlorella cpDNA are missing from the Leptosira gene repertoire. The 106 conserved genes, four introns and 11 free standing open reading frames (ORFs account for 48.3% of the genome sequence. This is the lowest gene density yet observed among chlorophyte cpDNAs. Contrary to the situation in Chlorella but similar to that in the chlorophycean Scenedesmus obliquus, the gene distribution is highly biased over the two DNA strands in Leptosira. Nine genes, compared to only three in Chlorella, have significantly expanded coding regions relative to their homologues in ancestral-type green algal cpDNAs. As observed in chlorophycean genomes, the rpoB gene is fragmented into two ORFs. Short repeats account for 5.1% of the Leptosira genome sequence and are present mainly in intergenic regions. Conclusion Our results highlight the great plasticity of the chloroplast genome in the Trebouxiophyceae and indicate

  3. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms.

    Science.gov (United States)

    Vergara-Jaque, Ariela; Fenollar-Ferrer, Cristina; Kaufmann, Desirée; Forrest, Lucy R

    2015-01-01

    Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called "repeat-swap modeling" to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also

  4. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms

    Directory of Open Access Journals (Sweden)

    Cristina eFenollar Ferrer

    2015-09-01

    Full Text Available Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to either the outside or inside of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (asymmetry of these systems has been successfully used as a bioinformatic tool, called repeat-swap modeling to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that

  5. Live Imaging of Shoot Meristems on an Inverted Confocal Microscope Using an Objective Lens Inverter Attachment

    Science.gov (United States)

    Nimchuk, Zachary L.; Perdue, Tony D.

    2017-01-01

    Live imaging of above ground meristems can lead to new insights in plant development not possible from static imaging of fixed tissue. The use of an upright confocal microscope offers several technical and biological advantages for live imaging floral or shoot meristems. However, many departments and core facilities possess only inverted confocal microscopes and lack the funding for an additional upright confocal microscope. Here we show that imaging of living apical meristems can be performed on existing inverted confocal microscopes with the use of an affordable and detachable InverterScope accessory. PMID:28579995

  6. Live Imaging of Shoot Meristems on an Inverted Confocal Microscope Using an Objective Lens Inverter Attachment.

    Science.gov (United States)

    Nimchuk, Zachary L; Perdue, Tony D

    2017-01-01

    Live imaging of above ground meristems can lead to new insights in plant development not possible from static imaging of fixed tissue. The use of an upright confocal microscope offers several technical and biological advantages for live imaging floral or shoot meristems. However, many departments and core facilities possess only inverted confocal microscopes and lack the funding for an additional upright confocal microscope. Here we show that imaging of living apical meristems can be performed on existing inverted confocal microscopes with the use of an affordable and detachable InverterScope accessory.

  7. DC-to-AC inverter ratio failure detector

    Science.gov (United States)

    Ebersole, T. J.; Andrews, R. E.

    1975-01-01

    Failure detection technique is based upon input-output ratios, which is independent of inverter loading. Since inverter has fixed relationship between V-in/V-out and I-in/I-out, failure detection criteria are based on this ratio, which is simply inverter transformer turns ratio, K, equal to primary turns divided by secondary turns.

  8. NREL Evaluates Advanced Solar Inverter Performance for Hawaiian Electric

    Science.gov (United States)

    Companies | Energy Systems Integration Facility | NREL NREL Evaluates Advanced Solar Inverter Performance for Hawaiian Electric Companies NREL Evaluates Advanced Solar Inverter Performance for Hawaiian performance and impacts of today's advanced solar inverters, as well as proprietary feedback to the inverter

  9. Pulsewidth-modulated 2-source neutral-point-clamped inverter

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Loh, Poh Chang; Gao, Feng

    2007-01-01

    This paper presents the careful integration of a newly proposed Z-source topological concept to the basic neutral-point-clamped (NPC) inverter topology for designing a three-level inverter with both voltage-buck and voltage-boost capabilities. The designed Z-source NPC inverter uses two unique X......-shaped inductance-capacitance (LC) impedance networks that are connected between two isolated dc input power sources and its inverter circuitry for boosting its AC output voltage. Through the design of an appropriate pulsewidth-modulation (PWM) algorithm, the two impedance networks can be short......-circuited sequentially (without shooting through the inverter full DC link) for implementing the ldquonearest-three-vectorrdquo modulation principle with minimized harmonic distortion and device commutations per half carrier cycle while performing voltage boosting. With only a slight modification to the inverter PWM...

  10. Flanking Variation Influences Rates of Stutter in Simple Repeats

    Directory of Open Access Journals (Sweden)

    August E. Woerner

    2017-11-01

    Full Text Available It has been posited that the longest uninterrupted stretch (LUS of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL. While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the PAL, examples to the contrary are apparent in commonly assayed forensic markers. Further, flanking variation that is 7 bp from the repeat region can impact rates of stutter. These findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers.

  11. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

    Directory of Open Access Journals (Sweden)

    Perumal Sampath

    Full Text Available Miniature inverted-repeat transposable elements (MITEs are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5 were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1 were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.

  12. Status and Needs of Power Electronics for Photovoltaic Inverters

    Science.gov (United States)

    Qin, Y. C.; Mohan, N.; West, R.; Bonn, R.

    2002-06-01

    Photovoltaics is the utility connected distributed energy resource (DER) that is in widespread use today. It has one element, the inverter, which is common with all DER sources except rotating generators. The inverter is required to transfer dc energy to ac energy. With all the DER technologies, (solar, wind, fuel cells, and microturbines) the inverter is still an immature product that will result in reliability problems in fielded systems. Today, the PV inverter is a costly and complex component of PV systems that produce ac power. Inverter MTFF (mean time to first failure) is currently unacceptable. Low inverter reliability contributes to unreliable fielded systems and a loss of confidence in renewable technology. The low volume of PV inverters produced restricts the manufacturing to small suppliers without sophisticated research and reliability programs or manufacturing methods. Thus, the present approach to PV inverter supply has low probability of meeting DOE reliability goals.

  13. Inverters for photovoltaics: quality assurance

    International Nuclear Information System (INIS)

    Graf, J.D.; Haeberlin, H.

    2000-01-01

    This project-overview published by the University of Applied Science in Burgdorf, Switzerland, looks back at the history of the university's testing laboratory for inverters for use in photovoltaic installations and discusses the work done there. After its move from Oberburg to Burgdorf in the early nineties, the laboratory was equipped to provide testing facilities for inverters up to 60 kW. Additions have been made to the infrastructure since then to facilitate the testing of various types of inverter produced in Switzerland and other countries. The measurements that can be carried out, including DC-AC conversion efficiency, harmonics, RF interference, islanding, sensitivity to tele-control signals, turn-on power and operating voltage range are described. The improvement in the quality of the inverters tested is discussed and the importance of continued testing as new manufacturers come onto the market is emphasised. The installation of further testing equipment, such as a 25 kW solar generator simulator and apparatus for the testing of maximum-power-tracking efficiency is discussed

  14. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  15. RNA motif search with data-driven element ordering.

    Science.gov (United States)

    Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

    2016-05-18

    In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

  16. On Stability of Voltage Source Inverters in Weak Grids

    DEFF Research Database (Denmark)

    Adib, Aswad; Mirafza, Behrooz; Wang, Xiongfei

    2018-01-01

    As the number of inverters increases in the power grid, the stability of grid-tied inverters becomes an important concern for the power industry. In particular, a weak grid can lead to voltage fluctuations at the inverter terminals and consequently cause inverter instability. In this paper, impac...

  17. Hardness of deriving invertible sequences from finite state machines

    DEFF Research Database (Denmark)

    Hierons, Robert M.; Mousavi, Mohammad Reza; Thomsen, Michael Kirkedal

    2017-01-01

    invertible sequences; these allow one to construct additional UIOs once a UIO has been found. We consider three optimisation problems associated with invertible sequences: deciding whether there is a (proper) invertible sequence of length at least K; deciding whether there is a set of invertible sequences...

  18. Design of a Bioactive Small Molecule that Targets the Myotonic Dystrophy Type 1 RNA Via an RNA Motif-Ligand Database & Chemical Similarity Searching

    Science.gov (United States)

    Parkesh, Raman; Childs-Disney, Jessica L.; Nakamori, Masayuki; Kumar, Amit; Wang, Eric; Wang, Thomas; Hoskins, Jason; Tran, Tuan; Housman, David; Thornton, Charles A.; Disney, Matthew D.

    2012-01-01

    Myotonic dystrophy type 1 (DM1) is a triplet repeating disorder caused by expanded CTG repeats in the 3′ untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. The transcribed repeats fold into an RNA hairpin with multiple copies of a 5′CUG/3′GUC motif that binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Sequestration of MBNL1 by expanded r(CUG) repeats causes splicing defects in a subset of pre-mRNAs including the insulin receptor, the muscle-specific chloride ion channel, Sarco(endo)plasmic reticulum Ca2+ ATPase 1 (Serca1/Atp2a1), and cardiac troponin T (cTNT). Based on these observations, the development of small molecule ligands that target specifically expanded DM1 repeats could serve as therapeutics. In the present study, computational screening was employed to improve the efficacy of pentamidine and Hoechst 33258 ligands that have been shown previously to target the DM1 triplet repeat. A series of inhibitors of the RNA-protein complex with low micromolar IC50’s, which are >20-fold more potent than the query compounds, were identified. Importantly, a bis-benzimidazole identified from the Hoechst query improves DM1-associated pre-mRNA splicing defects in cell and mouse models of DM1 (when dosed with 1 mM and 100 mg/kg, respectively). Since Hoechst 33258 was identified as a DM1 binder through analysis of an RNA motif-ligand database, these studies suggest that lead ligands targeting RNA with improved biological activity can be identified by using a synergistic approach that combines analysis of known RNA-ligand interactions with virtual screening. PMID:22300544

  19. Identification of sequence motifs significantly associated with antisense activity

    Directory of Open Access Journals (Sweden)

    Peek Andrew S

    2007-06-01

    Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

  20. Towards Efficient Positional Inverted Index †

    Directory of Open Access Journals (Sweden)

    Petr Procházka

    2017-02-01

    Full Text Available We address the problem of positional indexing in the natural language domain. The positional inverted index contains the information of the word positions. Thus, it is able to recover the original text file, which implies that it is not necessary to store the original file. Our Positional Inverted Self-Index (PISI stores the word position gaps encoded by variable byte code. Inverted lists of single terms are combined into one inverted list that represents the backbone of the text file since it stores the sequence of the indexed words of the original file. The inverted list is synchronized with a presentation layer that stores separators, stop words, as well as variants of the indexed words. The Huffman coding is used to encode the presentation layer. The space complexity of the PISI inverted list is O ( ( N − n ⌈ log 2 b N ⌉ + ( ⌊ N − n α ⌋ + n × ( ⌈ log 2 b n ⌉ + 1 where N is a number of stems, n is a number of unique stems, α is a step/period of the back pointers in the inverted list and b is the size of the word of computer memory given in bits. The space complexity of the presentation layer is O ( − ∑ i = 1 N ⌈ log 2 p i n ( i ⌉ − ∑ j = 1 N ′ ⌈ log 2 p j ′ ⌉ + N with respect to p i n ( i as a probability of a stem variant at position i, p j ′ as the probability of separator or stop word at position j and N ′ as the number of separators and stop words.

  1. A Hybrid, Current-Source/Voltage-Source Power Inverter Circuit

    DEFF Research Database (Denmark)

    Trzynadlowski, Andrzej M.; Patriciu, Niculina; Blaabjerg, Frede

    2001-01-01

    A combination of a large current-source inverter and a small voltage-source inverter circuits is analyzed. The resultant hybrid inverter inherits certain operating advantages from both the constituent converters. In comparison with the popular voltage-source inverter, these advantages include...... reduced switching losses, improved quality of output current waveforms, and faster dynamic response to current control commands. Description of operating principles and characteristics of the hybrid inverter is illustrated with results of experimental investigation of a laboratory model....

  2. Switching Characteristics of Ferroelectric Transistor Inverters

    Science.gov (United States)

    Laws, Crystal; Mitchell, Coey; MacLeod, Todd C.; Ho, Fat D.

    2010-01-01

    This paper presents the switching characteristics of an inverter circuit using a ferroelectric field effect transistor, FeFET. The propagation delay time characteristics, phl and plh are presented along with the output voltage rise and fall times, rise and fall. The propagation delay is the time-delay between the V50% transitions of the input and output voltages. The rise and fall times are the times required for the output voltages to transition between the voltage levels V10% and V90%. Comparisons are made between the MOSFET inverter and the ferroelectric transistor inverter.

  3. Novel, Four-Switch, Z-Source Three-Phase Inverter

    DEFF Research Database (Denmark)

    Antal, Robert; Muntean, Nicolae; Boldea, Ion

    2010-01-01

    This paper presents a new z-source three phase inverter topology. The proposed topology combines the advantages of a traditional four-switch three-phase inverter with the advantages of the z impedance network (one front-end diode, two inductors and two X connected capacitors). This new topology......, besides the self-boost property, has low switch count and it can operate as a buck-boost inverter. In contrast to standard four-switch three-phase inverter which operates at half dc input voltage the proposed four-switch z-source inverter, by self boosting, brings the output voltage at same (or higher......) value as in six switch standard three-phase inverter. The article presents the derivation of the equations describing the operation of the converter based on space vector analysis, validation through digital simulations in PSIM and preliminary experimental results on a laboratory setup with a dsPIC30F...

  4. The proliferation marker pKi-67 becomes masked to MIB-1 staining after expression of its tandem repeats.

    Science.gov (United States)

    Schmidt, Mirko H H; Broll, Rainer; Bruch, Hans-Peter; Duchrow, Michael

    2002-11-01

    The Ki-67 antigen, pKi-67, is one of the most commonly used markers of proliferating cells. The protein can only be detected in dividing cells (G(1)-, S-, G(2)-, and M-phase) but not in quiescent cells (G(0)). The standard antibody to detect pKi-67 is MIB-1, which detects the so-called 'Ki-67 motif' FKELF in 9 of the protein's 16 tandem repeats. To investigate the function of these repeats we expressed three of them in an inducible gene expression system in HeLa cells. Surprisingly, addition of a nuclear localization sequence led to a complete absence of signal in the nuclei of MIB-1-stained cells. At the same time antibodies directed against different epitopes of pKi-67 did not fail to detect the protein. We conclude that the overexpression of the 'Ki-67 motif', which is present in the repeats, can lead to inability of MIB-1 to detect its antigen as demonstrated in adenocarcinoma tissue samples. Thereafter, in order to prevent the underestimation of Ki-67 proliferation indices in MIB-1-labeled preparations, additional antibodies (for example, MIB-21) should be used. Additionally, we could show in a mammalian two-hybrid assay that recombinant pKi-67 repeats are capable of self-associating with endogenous pKi-67. Speculating that the tandem repeats are intimately involved in its protein-protein interactions, this offers new insights in how access to these repeats is regulated by pKi-67 itself.

  5. Analisis Unsur Matematika pada Motif Sulam Usus

    Directory of Open Access Journals (Sweden)

    Fredi Ganda Putra

    2017-12-01

    Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the

  6. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  7. Transistorized PWM inverter-induction motor drive system

    Science.gov (United States)

    Peak, S. C.; Plunkett, A. B.

    1982-01-01

    This paper describes the development of a transistorized PWM inverter-induction motor traction drive system. A vehicle performance analysis was performed to establish the vehicle tractive effort-speed requirements. These requirements were then converted into a set of inverter and motor specifications. The inverter was a transistorized three-phase bridge using General Electric power Darlington transistors. The description of the design and development of this inverter is the principal object of this paper. The high-speed induction motor is a design which is optimized for use with an inverter power source. The primary feedback control is a torque angle control with voltage and torque outer loop controls. A current-controlled PWM technique is used to control the motor voltage. The drive has a constant torque output with PWM operation to base motor speed and a constant horsepower output with square wave operation to maximum speed. The drive system was dynamometer tested and the results are presented.

  8. Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Shuyan; Sun, Cancan; Tan, Kemin; Ye, Sheng; Zhang, Rongguang

    2017-09-01

    Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

  9. Integral inverter/battery charger for use in electric vehicles

    Science.gov (United States)

    Thimmesch, D.

    1983-01-01

    The design and test results of a thyristor based inverter/charger are discussed. A battery charger is included integral to the inverter by using a subset of the inverter power circuit components. The resulting charger provides electrical isolation between the vehicle propulsion battery and ac line and is capable of charging a 25 kWh propulsion battery in 8 hours from a 220 volt ac line. The integral charger employs the inverter commutation components at a resonant ac/dc isolated converter rated at 3.6 kW. Charger efficiency and power factor at an output power of 3.6 kW are 86% and 95% respectively. The inverter, when operated with a matching polyphase ac induction motor and nominal 132 volt propulsion battery, can provide a peak shaft power of 34 kW (45 ph) during motoring operation and 45 kW (60 hp) during regeneration. Thyristors are employed for the inverter power switching devices and are arranged in an input-commutated topology. This configuration requires only two thyristors to commutate the six main inverter thyristors. Inverter efficiency during motoring operation at motor shaft speeds above 450 rad/sec (4300 rpm) is 92-94% for output power levels above 11 KW (15 hp). The combined ac inverter/charger package weighs 47 kg (103 lbs).

  10. Design optimization of grid-connected PV inverters

    DEFF Research Database (Denmark)

    Koutroulis, Eftichios; Blaabjerg, Frede

    2011-01-01

    The DC/AC inverters are the key elements in grid-connected PV energy production systems. In this paper, new design optimization techniques focused on transformerless (very high efficiency) PV inverters are proposed. They have been developed based on an analysis of the deficiencies of the current......, state-of-the-art PV inverters design technology, which limits the amount of PV energy supplied into the electric grid. The influences of the electric grid regulations and standards and the PV array operational characteristics on the design of grid-connected PV inverters have also been considered....... The simulation results verify that the proposed optimization techniques enable the maximization of the PV energy injected into the electric grid by the optimized PV installation....

  11. Advanced DC/AC inverters applications in renewable energy

    CERN Document Server

    Luo, Fang Lin

    2013-01-01

    DC/AC inversion technology is of vital importance for industrial applications, including electrical vehicles and renewable energy systems, which require a large number of inverters. In recent years, inversion technology has developed rapidly, with new topologies improving the power factor and increasing power efficiency. Proposing many novel approaches, Advanced DC/AC Inverters: Applications in Renewable Energy describes advanced DC/AC inverters that can be used for renewable energy systems. The book introduces more than 100 topologies of advanced inverters originally developed by the authors,

  12. Five-Level Z-Source Neutral Point-Clamped Inverter

    DEFF Research Database (Denmark)

    Gao, F.; Loh, P.C.; Blaabjerg, Frede

    2007-01-01

    This paper proposes a five-level Z-source neutralpoint- clamped (NPC) inverter with two Z-source networks functioning as intermediate energy storages coupled between dc sources and NPC inverter circuitry. Analyzing the operational principles of Z-source network with partial dclink shoot......-through scheme reveals the hidden theories in the five-level Z-source NPC inverter unlike the operational principle appeared in the general two-level Z-source inverter, so that the five-level Z-source NPC inverter can be designed with the modulation of carrier-based phase disposition (PD) or alternative phase...

  13. Large-Signal Lyapunov-Based Stability Analysis of DC/AC Inverters and Inverter-Based Microgrids

    Science.gov (United States)

    Kabalan, Mahmoud

    Microgrid stability studies have been largely based on small-signal linearization techniques. However, the validity and magnitude of the linearization domain is limited to small perturbations. Thus, there is a need to examine microgrids with large-signal nonlinear techniques to fully understand and examine their stability. Large-signal stability analysis can be accomplished by Lyapunov-based mathematical methods. These Lyapunov methods estimate the domain of asymptotic stability of the studied system. A survey of Lyapunov-based large-signal stability studies showed that few large-signal studies have been completed on either individual systems (dc/ac inverters, dc/dc rectifiers, etc.) or microgrids. The research presented in this thesis addresses the large-signal stability of droop-controlled dc/ac inverters and inverter-based microgrids. Dc/ac power electronic inverters allow microgrids to be technically feasible. Thus, as a prelude to examining the stability of microgrids, the research presented in Chapter 3 analyzes the stability of inverters. First, the 13 th order large-signal nonlinear model of a droop-controlled dc/ac inverter connected to an infinite bus is presented. The singular perturbation method is used to decompose the nonlinear model into 11th, 9th, 7th, 5th, 3rd and 1st order models. Each model ignores certain control or structural components of the full order model. The aim of the study is to understand the accuracy and validity of the reduced order models in replicating the performance of the full order nonlinear model. The performance of each model is studied in three different areas: time domain simulations, Lyapunov's indirect method and domain of attraction estimation. The work aims to present the best model to use in each of the three domains of study. Results show that certain reduced order models are capable of accurately reproducing the performance of the full order model while others can be used to gain insights into those three areas of

  14. Analysis of Magnetically-Coupled Impedance Source Three-Phase Four-Switch Inverters

    DEFF Research Database (Denmark)

    Li, Kerui; Abdelhakim, Ahmed; Yang, Yongheng

    2017-01-01

    In this paper, magnetically-coupled impedance source (MCIS) three-phase four-switch inverters are introduced for renewable energy applications. This inverter utilizes two single-phase MCIS inverters to obtain a three-phase output, where less component-count is achieved in order to reduce the inve......In this paper, magnetically-coupled impedance source (MCIS) three-phase four-switch inverters are introduced for renewable energy applications. This inverter utilizes two single-phase MCIS inverters to obtain a three-phase output, where less component-count is achieved in order to reduce...... the inverter volume. On the other hand, as a result of the reduced number of switches, the proposed inverter suffers from higher voltage stresses. The MCIS inverters are first reviewed. Then, the modulation and operation principle of the MCIS three-phase inverter topology are introduced before sizing...

  15. Comparative study of SiC- and Si-based photovoltaic inverters

    Science.gov (United States)

    Ando, Yuji; Oku, Takeo; Yasuda, Masashi; Shirahata, Yasuhiro; Ushijima, Kazufumi; Murozono, Mikio

    2017-01-01

    This article reports comparative study of 150-300 W class photovoltaic inverters (Si inverter, SiC inverter 1, and SiC inverter 2). In these sub-kW class inverters, the ON-resistance was considered to have little influence on the efficiency. The developed SiC inverters, however, have exhibited an approximately 3% higher direct current (DC)-alternating current (AC) conversion efficiency as compared to the Si inverter. Power loss analysis indicated a reduction in the switching and reverse recovery losses of SiC metal-oxide-semiconductor field-effect transistors used for the DC-AC converter is responsible for this improvement. In the SiC inverter 2, an increase of the switching frequency up to 100 kHz achieved a state-of-the-art combination of the weight (1.25 kg) and the volume (1260 cm3) as a 150-250 W class inverter. Even though the increased switching frequency should cause the increase of the switching losses, the SiC inverter 2 exhibited an efficiency comparable to the SiC inverter 1 with a switching frequency of 20 kHz. The power loss analysis also indicated a decreased loss of the DC-DC converter built with SiC Schottky barrier diodes led to the high efficiency for its increased switching frequency. These results clearly indicated feasibility of SiC devices even for sub-kW photovoltaic inverters, which will be available for the applications where compactness and efficiency are of tremendous importance.

  16. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  17. Triadic motifs in the dependence networks of virtual societies.

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-10

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  18. Direct AUC optimization of regulatory motifs.

    Science.gov (United States)

    Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

    2017-07-15

    The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  19. A single-phase embedded Z-source DC-AC inverter.

    Science.gov (United States)

    Kim, Se-Jin; Lim, Young-Cheol

    2014-01-01

    In the conventional DC-AC inverter consisting of two DC-DC converters with unipolar output capacitors, the output capacitor voltages of the DC-DC converters must be higher than the DC input voltage. To overcome this weakness, this paper proposes a single-phase DC-AC inverter consisting of two embedded Z-source converters with bipolar output capacitors. The proposed inverter is composed of two embedded Z-source converters with a common DC source and output AC load. Though the output capacitor voltages of the converters are relatively low compared to those of a conventional inverter, an equivalent level of AC output voltages can be obtained. Moreover, by controlling the output capacitor voltages asymmetrically, the AC output voltage of the proposed inverter can be higher than the DC input voltage. To verify the validity of the proposed inverter, experiments were performed with a DC source voltage of 38 V. By controlling the output capacitor voltages of the converters symmetrically or asymmetrically, the proposed inverter can produce sinusoidal AC output voltages. The experiments show that efficiencies of up to 95% and 97% can be achieved with the proposed inverter using symmetric and asymmetric control, respectively.

  20. Evidence that human papillomavirus causes inverted papilloma is sparse.

    Science.gov (United States)

    Justice, Jeb M; Davis, Kern M; Saenz, Daniel A; Lanza, Donald C

    2014-12-01

    Controversy exists regarding the pathogenesis of inverted papilloma as it relates to the involvement of human papillomavirus (HPV). The purpose of this report is to describe the prevalence of HPV in nondysplastic, "early inverted papilloma" and to summarize HPV detection rates in the general population and in other HPV related neoplasia. This case series report characterizes consecutive inverted papilloma patients from January 2005 to August 2012 with regard to smoking history, dysplasia, and HPV detection rates. Presence or absence of low/high risk HPV was determined by standardized in situ hybridization DNA probes. Medline literature review was performed to determine the prevalence of HPV in inverted papilloma without moderate or severe dysplasia. Thirty-six consecutive patients were identified with an average age of 63.6 (range, 40-84) years; gender: 23 men, 13 women. More than half (55%) were active or former smokers (14% active and 41% former). High/low risk HPV was present in 1 in 36 (2.7%) patients and 1 in 36 (2.7%) had mild dysplasia. In the literature review: (1) HPV was detected in 16.4% of inverted papilloma without dysplasia; (2) oral cavity HPV detection was 4.2% to 11.4% in the normal population; and (3) HPV was normally detected in 85% to 95% of HPV-related neoplasia. Given histological features of inverted papilloma and comparatively low detection rates of HPV in inverted papilloma without dysplasia (2.7%), as well as the summary of the world literature, HPV is not related to the initial pathogenesis of inverted papilloma or inverted papilloma's tendency to persist or recur. It is postulated that since inverted papilloma is more an inflammatory polyp, it is susceptible to secondary HPV infection because of its metaplasia. Tobacco and other causes of respiratory epithelium remodeling are more plausible explanations for the initial tissue transformation to inverted papilloma. © 2014 ARS-AAOA, LLC.

  1. DMINDA: an integrated web server for DNA motif identification and analyses.

    Science.gov (United States)

    Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

    2014-07-01

    DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeats.

    Science.gov (United States)

    Casas-Vila, Núria; Scheibe, Marion; Freiwald, Anja; Kappei, Dennis; Butter, Falk

    2015-11-17

    To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical TTAGGG motif found in vertebrates and also several other fungi. Using label-free quantitative proteomics, we here investigate the telosome of Neurospora crassa, a fungus with canonical telomeric repeats. We show that at least six of the candidates detected in our screen are direct TTAGGG-repeat binding proteins. While three of the direct interactors (NCU03416 [ncTbf1], NCU01991 [ncTbf2] and NCU02182 [ncTay1]) feature the known myb/homeobox DNA interaction domain also found in the vertebrate telomeric factors, we additionally show that a zinc-finger protein (NCU07846) and two proteins without any annotated DNA-binding domain (NCU02644 and NCU05718) are also direct double-strand TTAGGG binders. We further find two single-strand binders (NCU02404 [ncGbp2] and NCU07735 [ncTcg1]). By quantitative label-free interactomics we identify TTAGGG-binding proteins in Neurospora crassa, suggesting candidates for telomeric factors that are supported by phylogenomic comparison with yeast species. Intriguingly, homologs in yeast species with degenerated telomeric repeats are also TTAGGG-binding proteins, e.g. in S. cerevisiae Tbf1 recognizes the TTAGGG motif found in its subtelomeres. However, there is also a subset of proteins that is not conserved. While a rudimentary core TTAGGG-recognition machinery may be conserved across yeast species, our data suggests Neurospora as an emerging model organism with unique features.

  3. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  4. Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats

    DEFF Research Database (Denmark)

    Dagil, Robert; O'Shea, Charlotte; Nykjær, Anders

    2013-01-01

    megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described...... to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists....

  5. Membrane fusion and inverted phases

    International Nuclear Information System (INIS)

    Ellens, H.; Siegel, D.P.; Alford, D.; Yeagle, P.L.; Boni, L.; Lis, L.J.; Quinn, P.J.; Bentz, J.

    1989-01-01

    We have found a correlation between liposome fusion kinetics and lipid phase behavior for several inverted phase forming lipids. N-Methylated dioleoylphosphatidylethanolamine (DOPE-Me), or mixtures of dioleoylphosphatidylethanolamine (DOPE) and dioleoylphosphatidylcholine (DOPC), will form an inverted hexagonal phase (HII) at high temperatures (above TH), a lamellar phase (L alpha) at low temperatures, and an isotropic/inverted cubic phase at intermediate temperatures, which is defined by the appearance of narrow isotropic 31 P NMR resonances. The phase behavior has been verified by using high-sensitivity DSC, 31 P NMR, freeze-fracture electron microscopy, and X-ray diffraction. The temperature range over which the narrow isotropic resonances occur is defined as delta TI, and the range ends at TH. Extruded liposomes (approximately 0.2 microns in diameter) composed of these lipids show fusion and leakage kinetics which are strongly correlated with the temperatures of these phase transitions. At temperatures below delta TI, where the lipid phase is L alpha, there is little or no fusion, i.e., mixing of aqueous contents, or leakage. However, as the temperature reaches delta TI, there is a rapid increase in both fusion and leakage rates. At temperatures above TH, the liposomes show aggregation-dependent lysis, as the rapid formation of HII phase precursors disrupts the membranes. We show that the correspondence between the fusion and leakage kinetics and the observed phase behavior is easily rationalized in terms of a recent kinetic theory of L alpha/inverted phase transitions. In particular, it is likely that membrane fusion and the L alpha/inverted cubic phase transition proceed via a common set of intermembrane intermediates

  6. Asymmetrical and symmetrical embedded Z-source inverters

    DEFF Research Database (Denmark)

    Gao, F.; Loh, P.C.; Li, D.

    2011-01-01

    ends, which indirectly translates to a lowering of overall system cost. These noted advantages are indeed appropriate for applications like photovoltaic and fuel cell energy harnessing, and have already been confirmed in simulation and experimentally using a laboratory-implemented inverter prototype.......This study presents two types of embedded Z-source inverters with each type further divided into asymmetrical and symmetrical realisations. Being different from their traditional counterparts, the presented inverters have their dc sources inserted within their X-shaped impedance networks so...

  7. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

    Science.gov (United States)

    Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

    2008-02-15

    KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

  8. Optimal Design of Modern Transformerless PV Inverter Topologies

    DEFF Research Database (Denmark)

    Saridakis, Stefanos; Koutroulis, Eftichios; Blaabjerg, Frede

    2013-01-01

    the operational lifetime period of the PV installation, is also considered in the optimization process. According to the results of the proposed design method, different optimal values of the PV inverter design variables are derived for each PV inverter topology and installation site. The H5, H6, neutral point...... clamped, active-neutral point clamped and conergy-NPC PV inverters designed using the proposed optimization process feature lower levelized cost of generated electricity and lifetime cost, longer mean time between failures and inject more PV-generated energy into the electric grid than their nonoptimized......The design optimization of H5, H6, neutral point clamped, active-neutral point clamped, and conergy-NPC transformerless photovoltaic (PV) inverters is presented in this paper. The components reliability in terms of the corresponding malfunctions, affecting the PV inverter maintenance cost during...

  9. Diode-Assisted Buck-Boost Voltage-Source Inverters

    DEFF Research Database (Denmark)

    Gao, Feng; Loh, Poh Chiang; Teodorescu, Remus

    2009-01-01

    , a number of diode-assisted inverter variants can be designed with each having its own operational principle and voltage gain expression. For controlling them, a generic modulation scheme that can be used for controlling all diode-assisted variants with minimized harmonic distortion and component stress......This paper proposes a number of diode-assisted buck-boost voltage-source inverters with a unique X-shaped diode-capacitor network inserted between the inverter circuitry and dc source for producing a voltage gain that is comparatively higher than those of other buck-boost conversion techniques....... Using the diode-assisted network, the proposed inverters can naturally configure themselves to perform capacitive charging in parallel and discharging in series to give a higher voltage multiplication factor without compromising waveform quality. In addition, by adopting different front-end circuitries...

  10. Development of inverter for elevator door control

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J.K.; Choi, U.D.; Jung, M.K.; Choi, S.K. [HHI R and D Center (Korea, Republic of); Yun, J.H.; Han, S.B. [HELCO R and D Center (Korea, Republic of)

    1995-07-01

    Most of the elevator door controllers have been controlled by DC Motors as an actuator. Recently, The control system using AC induction motor and general purpose inverter has been applied to control of elevator door. But there are some difficulties in making use of this system, such as adjustment of door speed pattern, door open-close time, and security of passenger safety. In order to solve these problems, a special inverter has been developed with an encoder feedback. From the result of field-test, we proved that a special inverter with encoder feedback device has come to considerable effect. Until now about 1,200 sets of these inverters are operated in Korea and about 100 sets are operated in South-east Asia. (author). 3 refs., 10 figs., 3 tabs.

  11. Operational analysis and comparative evaluation of embedded Z-Source inverters

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Gao, F.; Loh, P.C.

    2008-01-01

    ) circuitry connected instead of the generic voltage source inverter (VSI) circuitry. Further proceeding on to the topological variation, parallel embedded Z-source inverters are presented with the detailed analysis of topological configuration and operational principles showing that they are the superior......This paper presents various embedded Z-source (EZ-source) inverters broadly classified as shunt or parallel embedded Z-source inverter. Being different from the traditional Z-source inverter, EZ-source inverters are constructed by inserting dc sources into the X-shaped impedance network so...... that the dc input current flows smoothly during the whole switching period unlike the traditional Z-source inverter. This feature is interesting when PV panels or fuel cells are assumed to power load since the continuous input current flow reduces control complexity of dc source and system design burden...

  12. Advanced Power Electronics and Smart Inverters | Grid Modernization | NREL

    Science.gov (United States)

    Advanced Power Electronics and Smart Inverters Advanced Power Electronics and Smart Inverters , into the electric distribution system requires advanced power electronics, or smart inverters, that . Contact Sudipta Chakraborty Power Electronics Team Lead sudipta.chakraborty@nrel.gov | 303-384-7093

  13. Thin type inverter for machine-room-less elevator; Machine roomless elevator yo usugata inverter

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-01-10

    In the elevator industry, a machine-room-less elevator, which does not necessitate a machine room usually installed on the roof, has come into the spotlight in the domain of low and intermediate speed elevators. The lack of a machine room, however, will necessarily limit the space for the installation of the traction motor and control panel. Fuji Electric Co., Ltd., in order to properly cope with the situation, has developed in cooperation with Fujitec Co., Ltd., a very thin type inverter installable on an elevator hall floor. The inverter, based on Fuji Electric's high-performance vector control inverter FRENIC5000VG5, is as thin as 100mm, and is available in three series up to 11kW. For the embodiment of such a thin structure, a cooling structure of Fuji Electric's own is employed, and prudence is exercised as required at many locations so that maintainability will not be impaired throughout the very thin control panel design. (translated by NEDO)

  14. DNA motif alignment by evolving a population of Markov chains.

    Science.gov (United States)

    Bi, Chengpeng

    2009-01-30

    Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

  15. LCCT-derived three-level three-phase inverters

    DEFF Research Database (Denmark)

    Shults, Tatiana; Husev, Oleksandr; Blaabjerg, Frede

    2017-01-01

    Solutions for a family of the novel three-level neutral-point-clamped (NPC) inductor-capacitor-capacitor-transformer (LCCT)-derived three-phase inverters are described and compared. Component design guidelines and steady state analysis, current and voltage waveforms are given. The authors......' simulation results confirm the theoretical predictions. It was found that an asymmetrical three-level NPC LCCT-derived inverter with a single diode in the impedance source network is the most promising solution. Experimental results for an asymmetrical three-level NPC LCCT-derived inverter with a single...

  16. Advanced Energy Validated Photovoltaic Inverter Technology at NREL | Energy

    Science.gov (United States)

    Inverter Technology at NREL Advanced Energy Industries-NREL's first partner at the Energy Systems Integration Facility (ESIF)-validated its advanced photovoltaic (PV) inverter technology using the ESIF's computer screen in a laboratory, with power inverter hardware in the background Photo by Dennis Schroeder

  17. Photovoltaic power generating system; Sanso zetsuengata taiyoko inverter

    Energy Technology Data Exchange (ETDEWEB)

    Nojima, T; Nakashima, T; Muta, Y; Takase, K; Hirayama, K [Nishimu Electronics Industries Co. Ltd., Saga (Japan)

    1996-10-27

    Nishimu Electronics Industries Co., Ltd. has developed a new series of inverters of three phase photovoltaic power generating system with the output ranging from 10 kVA to 50 kVA. For these inverters, the inverter and the system interconnection protector were integrated to make them smaller, lighter and cheaper. Stand-alone operation function was also added. The DC input voltage ranges were between 240 and 400 V for the crystalline solar cell, and between 170 and 400 V for the amorphous one. From the viewpoint of control of inverters, the inverters are generally controlled by the voltage-type current control method during the interconnection operation, while they must be controlled by the voltage-type voltage control method during the stand-alone operation which is the same as the UPS usually operated alone. For the present inverters, two control circuits for the interconnection operation and for the stand-alone operation were prepared. The control circuits for interconnection and stand-alone operations were switched using a cam-operation switch for change-over of operation. The results of the system interconnection verification tests satisfied the criteria of Japan`s Electronic Products Test Center. 3 refs., 4 figs., 2 tabs.

  18. Accelerating development of advanced inverters :

    Energy Technology Data Exchange (ETDEWEB)

    Neely, Jason C.; Gonzalez, Sigifredo; Ropp, Michael; Schutz, Dustin

    2013-11-01

    The high penetration of utility interconnected photovoltaic (PV) systems is causing heightened concern over the effect that variable renewable generation will have on the electrical power system (EPS). These concerns have initiated the need to amend the utility interconnection standard to allow advanced inverter control functionalities that provide: (1) reactive power control for voltage support, (2) real power control for frequency support and (3) better tolerance of grid disturbances. These capabilities are aimed at minimizing the negative impact distributed PV systems may have on EPS voltage and frequency. Unfortunately, these advanced control functions may interfere with island detection schemes, and further development of advanced inverter functions requires a study of the effect of advanced functions on the efficacy of antiislanding schemes employed in industry. This report summarizes the analytical, simulation and experimental work to study interactions between advanced inverter functions and anti-islanding schemes being employed in distributed PV systems.

  19. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  20. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  1. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  2. The identification of functional motifs in temporal gene expression analysis

    Directory of Open Access Journals (Sweden)

    Michael G. Surette

    2005-01-01

    Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

  3. Leakage current measurement in transformerless PV inverters

    DEFF Research Database (Denmark)

    Kerekes, Tamas; Sera, Dezso; Mathe, Laszlo

    2012-01-01

    Photovoltaic (PV) installations have seen a huge increase during the last couple of years. Transformerless PV inverters are gaining more share of the total inverter market, due to their high conversion efficiency, small weight and size. Nevertheless safety should have an important role in case...... of these tranformerless systems, due to the missing galvanic isolation. Leakage and fault current measurement is a key issue for these inverter topologies to be able to comply with the required safety standards. This article presents the test results of two different current measurement sensors that were suggested...

  4. Static Characteristics of the Ferroelectric Transistor Inverter

    Science.gov (United States)

    Mitchell, Cody; Laws, crystal; MacLeond, Todd C.; Ho, Fat D.

    2010-01-01

    The inverter is one of the most fundamental building blocks of digital logic, and it can be used as the foundation for understanding more complex logic gates and circuits. This paper presents the characteristics of an inverter circuit using a ferroelectric field-effect transistor. The voltage transfer characteristics are analyzed with respect to varying parameters such as supply voltage, input voltage, and load resistance. The effects of the ferroelectric layer between the gate and semiconductor are examined, and comparisons are made between the inverters using ferroelectric transistors and those using traditional MOSFETs.

  5. Electrical power inverter having a phase modulated, twin-inverter, high frequency link and an energy storage module

    Science.gov (United States)

    Pitel, I.J.

    1987-02-03

    The present invention provides an electrical power inverter method and apparatus, which includes a high frequency link, for converting DC power into AC power. Generally stated, the apparatus includes a first high frequency module which produces an AC voltage at a first output frequency, and a second high frequency inverter module which produces an AC voltage at a second output frequency that is substantially the same as the first output frequency. The second AC voltage is out of phase with the first AC voltage by a selected angular phase displacement. A mixer mixes the first and second output voltages to produce a high frequency carrier which has a selected base frequency impressed on the sidebands thereof. A rectifier rectifies the carrier, and a filter filters the rectified carrier. An output inverter inverts the filtered carrier to produce an AC line voltage at the selected base frequency. A phase modulator adjusts the relative angular phase displacement between the outputs of the first and second high frequency modules to control the base frequency and magnitude of the AC line voltage. 19 figs.

  6. Electrical power inverter having a phase modulated, twin-inverter, high frequency link and an energy storage module

    Science.gov (United States)

    Pitel, Ira J.

    1987-02-03

    The present invention provides an electrical power inverter method and apparatus, which includes a high frequency link, for converting DC power into AC power. Generally stated, the apparatus includes a first high frequency module which produces an AC voltage at a first output frequency, and a second high frequency inverter module which produces an AC voltage at a second output frequency that is substantially the same as the first output frequency. The second AC voltage is out of phase with the first AC voltage by a selected angular phase displacement. A mixer mixes the first and second output voltages to produce a high frequency carrier which has a selected base frequency impressed on the sidebands thereof. A rectifier rectifies the carrier, and a filter filters the rectified carrier. An output inverter inverts the filtered carrier to produce an AC line voltage at the selected base frequency. A phase modulator adjusts the relative angular phase displacement between the outputs of the first and second high frequency modules to control the base frequency and magnitude of the AC line voltage.

  7. Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

    Science.gov (United States)

    Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

    2016-05-23

    Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

  8. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

  9. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

    Science.gov (United States)

    2012-01-01

    Background Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation. Conclusions This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding

  10. Epitopes of MUC1 Tandem Repeats in Cancer as Revealed by Antibody Crystallography: Toward Glycopeptide Signature-Guided Therapy

    Directory of Open Access Journals (Sweden)

    Dapeng Zhou

    2018-05-01

    Full Text Available Abnormally O-glycosylated MUC1 tandem repeat glycopeptide epitopes expressed by multiple types of cancer have long been attractive targets for therapy in the race against genetic mutations of tumor cells. Glycopeptide signature-guided therapy might be a more promising avenue than mutation signature-guided therapy. Three O-glycosylated peptide motifs, PDTR, GSTA, and GVTS, exist in a tandem repeat HGVTSAPDTRPAPGSTAPPA, containing five O-glycosylation sites. The exact peptide and sugar residues involved in antibody binding are poorly defined. Co-crystal structures of glycopeptides and respective monoclonal antibodies are very few. Here we review 3 groups of monoclonal antibodies: antibodies which only bind to peptide portion, antibodies which only bind to sugar portion, and antibodies which bind to both peptide and sugar portions. The antigenicity of peptide and sugar portions of glyco-MUC1 tandem repeat were analyzed according to available biochemical and structural data, especially the GSTA and GVTS motifs independent from the most studied PDTR. Tn is focused as a peptide-modifying residue in vaccine design, to induce glycopeptide-binding antibodies with cross reactivity to Tn-related tumor glycans, but not glycans of healthy cells. The unique requirement for the designs of antibody in antibody-drug conjugate, bi-specific antibodies, and chimeric antigen receptors are also discussed.

  11. A set of tetra-nucleotide core motif SSR markers for efficient identification of potato (Solanum tuberosum) cultivars.

    Science.gov (United States)

    Kishine, Masahiro; Tsutsumi, Katsuji; Kitta, Kazumi

    2017-12-01

    Simple sequence repeat (SSR) is a popular tool for individual fingerprinting. The long-core motif (e.g. tetra-, penta-, and hexa-nucleotide) simple sequence repeats (SSRs) are preferred because they make it easier to separate and distinguish neighbor alleles. In the present study, a new set of 8 tetra-nucleotide SSRs in potato ( Solanum tuberosum ) is reported. By using these 8 markers, 72 out of 76 cultivars obtained from Japan and the United States were clearly discriminated, while two pairs, both of which arose from natural variation, showed identical profiles. The combined probability of identity between two random cultivars for the set of 8 SSR markers was estimated to be 1.10 × 10 -8 , confirming the usefulness of the proposed SSR markers for fingerprinting analyses of potato.

  12. [Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].

    Science.gov (United States)

    Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin

    2015-04-01

    This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

  13. Myotonin protein-kinase [AGC]n trinucleotide repeat in seven nonhuman primates

    Energy Technology Data Exchange (ETDEWEB)

    Novelli, G.; Sineo, L.; Pontieri, E. [Catholic Univ. of Rome (Italy)]|[Univ. of Milan (Italy)]|[Univ. Florence (Italy)] [and others

    1994-09-01

    Myotonic dystrophy (DM) is due to a genomic instability of a trinucleotide [AGC]n motif, located at the 3{prime} UTR region of a protein-kinase gene (myotonin protein kinase, MT-PK). The [AGC] repeat is meiotically and mitotically unstable, and it is directly related to the manifestations of the disorder. Although a gene dosage effect of the MT-PK has been demonstrated n DM muscle, the mechanism(s) by which the intragenic repeat expansion leads to disease is largely unknown. This non-standard mutational event could reflect an evolutionary mechanism widespread among animal genomes. We have isolated and sequenced the complete 3{prime}UTR region of the MT-PK gene in seven primates (macaque, orangutan, gorilla, chimpanzee, gibbon, owl monkey, saimiri), and examined by comparative sequence nucleotide analysis the [AGC]n intragenic repeat and the surrounding nucleotides. The genomic organization, including the [AGC]n repeat structure, was conserved in all examined species, excluding the gibbon (Hylobates agilis), in which the [AGC]n upstream sequence (GGAA) is replaced by a GA dinucleotide. The number of [AGC]n in the examined species ranged between 7 (gorilla) and 13 repeats (owl monkeys), with a polymorphism informative content (PIC) similar to that observed in humans. These results indicate that the 3{prime}UTR [AGC] repeat within the MT-PK gene is evolutionarily conserved, supporting that this region has important regulatory functions.

  14. Distributed Storage Inverter and Legacy Generator Integration Plus Renewables Solution for Microgrids

    Science.gov (United States)

    2015-07-01

    inverter (advantage of short term storage) and enables microgrid upgrade of legacy generator assets (integration of inverter and generator controllers ...today. The storage inverter controls and hardware are also leveraged to provide an islanding inverter ( microgrid compatibility) for renewable...transiently rated inverters, integration with legacy generator controls , and microgrid compatible inverters for PV. Key system design drivers are lowering

  15. Low voltage ride-through of single-phase transformerless photovoltaic inverters

    DEFF Research Database (Denmark)

    Yang, Yongheng; Blaabjerg, Frede; Wang, Huai

    2013-01-01

    Transformerless photovoltaic (PV) inverters are going to be more widely adopted in order to achieve high efficiency, as the penetration level of PV systems is continuously booming. However, problems may arise in highly PV-integrated distribution systems. For example, a sudden stoppage of all PV...... discussed. The selected inverters are the full-bridge inverter with bipolar modulation, full-bridge inverter with DC bypass and the Highly Efficient and Reliable Inverter Concept (HERIC). A 1 kW single-phase grid-connected PV system is analyzed to verify the discussions. The tests confirmed that, although...

  16. Low Voltage Ride-Through of Single-Phase Transformerless Photovoltaic Inverters

    DEFF Research Database (Denmark)

    Yang, Yongheng; Blaabjerg, Frede; Wang, Huai

    2014-01-01

    Transformerless photovoltaic (PV) inverters are going to be more widely adopted in order to achieve high efficiency, as the penetration level of PV systems is continuously booming. However, problems may arise in highly PV-integrated distribution systems. For example, a sudden stoppage of all PV...... are also discussed. The selected inverters are the full-bridge inverter with bipolar modulation, full-bridge inverter with DC bypass and the Highly Efficient and Reliable Inverter Concept (HERIC). A 1 kW singlephase grid-connected PV system is analyzed to verify the discussions. The tests confirmed that...

  17. Hawaiian Electric Advanced Inverter Test Plan - Result Summary

    Energy Technology Data Exchange (ETDEWEB)

    Hoke, Anderson; Nelson, Austin; Prabakar, Kumaraguru; Nagarajan, Adarsh

    2016-10-14

    This presentation is intended to share the results of lab testing of five PV inverters with the Hawaiian Electric Companies and other stakeholders and interested parties. The tests included baseline testing of advanced inverter grid support functions, as well as distribution circuit-level tests to examine the impact of the PV inverters on simulated distribution feeders using power hardware-in-the-loop (PHIL) techniques. hardware-in-the-loop (PHIL) techniques.

  18. Design optimization of transformerless grid-connected PV inverters including reliability

    DEFF Research Database (Denmark)

    Koutroulis, Eftichios; Blaabjerg, Frede

    2012-01-01

    Of the Electricity (LCOE) generated during the PV system lifetime period is minimized. The LCOE is calculated also considering the failure rates of the components, which affect the reliability performance and lifetime maintenance cost of the PV inverter. A design example is presented, demonstrating that compared...... to the non-optimized PV inverter structures, the PV inverters designed using the proposed optimization methodology exhibit lower total manufacturing and lifetime maintenance cost and inject more energy into the electric-grid and by that minimizing LCOE.......This paper presents a new methodology for optimal design of transformerless Photovoltaic (PV) inverters targeting a cost-effective deployment of grid-connected PV systems. The optimal values and types of the PV inverter components are calculated such that the PV inverter Levelized Cost...

  19. Design Optimization of Transformerless Grid-Connected PV Inverters Including Reliability

    DEFF Research Database (Denmark)

    Koutroulis, Eftichios; Blaabjerg, Frede

    2013-01-01

    such that the PV inverter LCOE generated during the PV system lifetime period is minimized. The LCOE is also calculated considering the failure rates of the components, which affect the reliability performance and lifetime maintenance cost of the PV inverter. A design example is presented, demonstrating...... that compared to the nonoptimized PV inverter structures, the PV inverters designed using the proposed optimization methodology exhibit lower total manufacturing and lifetime maintenance cost and inject more energy into the electric-grid and by that minimizing LCOE.......This paper presents a new methodology for optimal design of transformerless photovoltaic (PV) inverters targeting a cost-effective deployment of grid-connected PV systems. The optimal switching frequency as well as the optimal values and types of the PV inverter components is calculated...

  20. Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia.

    Science.gov (United States)

    Meyer, C; Pouteau, S; Rouzé, P; Caboche, M

    1994-01-01

    By Northern blot analysis of nitrate reductase-deficient mutants of Nicotiana plumbaginifolia, we identified a mutant (mutant D65), obtained after gamma-ray irradiation of protoplasts, which contained an insertion sequence in the nitrate reductase (NR) mRNA. This insertion sequence was localized by polymerase chain reaction (PCR) in the first exon of NR and was also shown to be present in the NR gene. The mutant gene contained a 565 bp insertion sequence that exhibits the sequence characteristics of a transposable element, which was thus named dTnp1. The dTnp1 element has 14 bp terminal inverted repeats and is flanked by an 8-bp target site duplication generated upon transposition. These inverted repeats have significant sequence homology with those of other transposable elements. Judging by its size and the absence of a long open reading frame, dTnp1 appears to represent a defective, although mobile, transposable element. The octamer motif TTTAGGCC was found several times in direct orientation near the 5' and 3' ends of dTnp1 together with a perfect palindrome located after the 5' inverted repeat. Southern blot analysis using an internal probe of dTnp1 suggested that this element occurs as a single copy in the genome of N. plumbaginifolia. It is also present in N. tabacum, but absent in tomato or petunia. The dTnp1 element is therefore of potential use for gene tagging in Nicotiana species.

  1. Closed-loop waveform control of boost inverter

    DEFF Research Database (Denmark)

    Zhu, Guo Rong; Xiao, Cheng Yuan; Wang, Haoran

    2016-01-01

    The input current of single-phase inverter typically has an AC ripple component at twice the output frequency, which causes a reduction in both the operating lifetime of its DC source and the efficiency of the system. In this paper, the closed-loop performance of a proposed waveform control method...... to eliminate such a ripple current in boost inverter is investigated. The small-signal stability and the dynamic characteristic of the inverter system for input voltage or wide range load variations under the closed-loop waveform control method are studied. It is validated that with the closedloop waveform...... control, not only was stability achieved, the reference voltage of the boost inverter capacitors can be instantaneously adjusted to match the new load, thereby achieving improved ripple mitigation for a wide load range. Furthermore, with the control and feedback mechanism, there is minimal level of ripple...

  2. Alanine repeats influence protein localization in splicing speckles and paraspeckles.

    Science.gov (United States)

    Chang, Shuo-Hsiu; Chang, Wei-Lun; Lu, Chia-Chen; Tarn, Woan-Yuh

    2014-12-16

    Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated-fully or partially-from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

    Science.gov (United States)

    Gade, Chandrasekhar Reddy; Sharma, Nagendra K

    2017-12-15

    This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  5. Distortion and regulation characterization of a Mapham inverter

    Science.gov (United States)

    Sundberg, Richard C.; Brush, Andrew S.; Button, Robert M.; Patterson, Alexander G.

    1989-01-01

    Output voltage Total Harmonic Distortion (THD) of a 20kHz, 6kVA Mapham resonant inverter is characterized as a function of its switching-to-resonant frequency ratio, f sub s/f sub r, using the EASY5 engineering analysis system. EASY5 circuit simulation results are compared with hardware test results to verify the accuracy of the simulations. The effects of load on the THD versus f sub s/f sub r ratio is investigated for resistive, leading, and lagging power factor load impedances. The effect of the series output capacitor on the Mapham inverter output voltage distortion and inherent load regulation is characterized under loads of various power factors and magnitudes. An optimum series capacitor value which improves the inherent load regulation to better than 3 percent is identified. The optimum series capacitor value is different than the value predicted from a modeled frequency domain analysis. An explanation is proposed which takes into account the conduction overlap in the inductor pairs during steady-state inverter operation, which decreases the effective inductance of a Mapham inverter. A fault protection and current limit method is discussed which allows the Mapham inverter to operate into a short circuit, even when the inverter resonant circuit becomes overdamped.

  6. Verification of the MOTIF code version 3.0

    International Nuclear Information System (INIS)

    Chan, T.; Guvanasen, V.; Nakka, B.W.; Reid, J.A.K.; Scheier, N.W.; Stanchell, F.W.

    1996-12-01

    As part of the Canadian Nuclear Fuel Waste Management Program (CNFWMP), AECL has developed a three-dimensional finite-element code, MOTIF (Model Of Transport In Fractured/ porous media), for detailed modelling of groundwater flow, heat transport and solute transport in a fractured rock mass. The code solves the transient and steady-state equations of groundwater flow, solute (including one-species radionuclide) transport, and heat transport in variably saturated fractured/porous media. The initial development was completed in 1985 (Guvanasen 1985) and version 3.0 was completed in 1986. This version is documented in detail in Guvanasen and Chan (in preparation). This report describes a series of fourteen verification cases which has been used to test the numerical solution techniques and coding of MOTIF, as well as demonstrate some of the MOTIF analysis capabilities. For each case the MOTIF solution has been compared with a corresponding analytical or independently developed alternate numerical solution. Several of the verification cases were included in Level 1 of the International Hydrologic Code Intercomparison Project (HYDROCOIN). The MOTIF results for these cases were also described in the HYDROCOIN Secretariat's compilation and comparison of results submitted by the various project teams (Swedish Nuclear Power Inspectorate 1988). It is evident from the graphical comparisons presented that the MOTIF solutions for the fourteen verification cases are generally in excellent agreement with known analytical or numerical solutions obtained from independent sources. This series of verification studies has established the ability of the MOTIF finite-element code to accurately model the groundwater flow and solute and heat transport phenomena for which it is intended. (author). 20 refs., 14 tabs., 32 figs

  7. A new Zero Voltage Switching three-level NPC inverter

    DEFF Research Database (Denmark)

    He, Ning; Chen, Yenan; Xu, Dehong

    2015-01-01

    A novel Zero Voltage Switching (ZVS) three-level NPC inverter topology using a new ZVS Space Vector Modulation (SVM) scheme is proposed. A detailed operation analysis of ZVS three-level NPC inverter is given. The ZVS condition of the proposed ZVS inverter is derived and it can be achieved of all...

  8. PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae.

    Science.gov (United States)

    Zucchini, Laure; Mercy, Chryslène; Garcia, Pierre Simon; Cluzel, Caroline; Gueguen-Chaignon, Virginie; Galisson, Frédéric; Freton, Céline; Guiral, Sébastien; Brochier-Armanet, Céline; Gouet, Patrice; Grangeasse, Christophe

    2018-02-01

    Eukaryotic-like serine/threonine kinases (eSTKs) with extracellular PASTA repeats are key membrane regulators of bacterial cell division. How PASTA repeats govern eSTK activation and function remains elusive. Using evolution- and structural-guided approaches combined with cell imaging, we disentangle the role of each PASTA repeat of the eSTK StkP from Streptococcus pneumoniae. While the three membrane-proximal PASTA repeats behave as interchangeable modules required for the activation of StkP independently of cell wall binding, they also control the septal cell wall thickness. In contrast, the fourth and membrane-distal PASTA repeat directs StkP localization at the division septum and encompasses a specific motif that is critical for final cell separation through interaction with the cell wall hydrolase LytB. We propose a model in which the extracellular four-PASTA domain of StkP plays a dual function in interconnecting the phosphorylation of StkP endogenous targets along with septal cell wall remodelling to allow cell division of the pneumococcus.

  9. Purification and functional motifs of the recombinant ATPase of orf virus.

    Science.gov (United States)

    Lin, Fong-Yuan; Chan, Kun-Wei; Wang, Chi-Young; Wong, Min-Liang; Hsu, Wei-Li

    2011-10-01

    Our previous study showed that the recombinant ATPase encoded by the A32L gene of orf virus displayed ATP hydrolysis activity as predicted from its amino acids sequence. This viral ATPase contains four known functional motifs (motifs I-IV) and a novel AYDG motif; they are essential for ATP hydrolysis reaction by binding ATP and magnesium ions. The motifs I and II correspond with the Walker A and B motifs of the typical ATPase, respectively. To examine the biochemical roles of these five conserved motifs, recombinant ATPases of five deletion mutants derived from the Taiping strain were expressed and purified. Their ATPase functions were assayed and compared with those of two wild type strains, Taiping and Nantou isolated in Taiwan. Our results showed that deletions at motifs I-III or IV exhibited lower activity than that of the wild type. Interestingly, deletion of AYDG motif decreased the ATPase activity more significantly than those of motifs I-IV deletions. Divalent ions such as magnesium and calcium were essential for ATPase activity. Moreover, our recombinant proteins of orf virus also demonstrated GTPase activity, though weaker than the original ATPase activity. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Voltage Balancing Control of Diode-Clamped Multilevel Inverter

    Directory of Open Access Journals (Sweden)

    ŞCHIOP Adrian

    2013-10-01

    Full Text Available In this paper is developed a control scheme for mono-phase diode clamped inverter to achieve balancing voltages on inverter capacitors. First, it develops a control scheme without taking into account the need to balance voltage on two capacitors. It examines the effects on the output voltage inverter, and then it realizes two control schemes that will balance the voltages. The simulations of control schemes were performed in OrCAD Pspice.

  11. Combining flagelliform and dragline spider silk motifs to produce tunable synthetic biopolymer fibers.

    Science.gov (United States)

    Teulé, Florence; Addison, Bennett; Cooper, Alyssa R; Ayon, Joel; Henning, Robert W; Benmore, Chris J; Holland, Gregory P; Yarger, Jeffery L; Lewis, Randolph V

    2012-06-01

    The two Flag/MaSp 2 silk proteins produced recombinantly were based on the basic consensus repeat of the dragline silk spidroin 2 protein (MaSp 2) from the Nephila clavipes orb weaving spider. However, the proline-containing pentapeptides juxtaposed to the polyalanine segments resembled those found in the flagelliform silk protein (Flag) composing the web spiral: (GPGGX(1) GPGGX(2))(2) with X(1) /X(2) = A/A or Y/S. Fibers were formed from protein films in aqueous solutions or extruded from resolubilized protein dopes in organic conditions when the Flag motif was (GPGGX(1) GPGGX(2))(2) with X(1) /X(2) = Y/S or A/A, respectively. Post-fiber processing involved similar drawing ratios (2-2.5×) before or after water-treatment. Structural (ssNMR and XRD) and morphological (SEM) changes in the fibers were compared to the mechanical properties of the fibers at each step. Nuclear magnetic resonance indicated that the fraction of β-sheet nanocrystals in the polyalanine regions formed upon extrusion, increased during stretching, and was maximized after water-treatment. X-ray diffraction showed that nanocrystallite orientation parallel to the fiber axis increased the ultimate strength and initial stiffness of the fibers. Water furthered nanocrystal orientation and three-dimensional growth while plasticizing the amorphous regions, thus producing tougher fibers due to increased extensibility. These fibers were highly hygroscopic and had similar internal network organization, thus similar range of mechanical properties that depended on their diameters. The overall structure of the consensus repeat of the silk-like protein dictated the mechanical properties of the fibers while protein molecular weight limited these same properties. Subtle structural motif re-design impacted protein self-assembly mechanisms and requirements for fiber formation. Copyright © 2011 Wiley Periodicals, Inc.

  12. Simulation of Fuzzy Adaptive PI Controlled Grid Interactive Inverter

    Directory of Open Access Journals (Sweden)

    Necmi ALTIN

    2009-03-01

    Full Text Available In this study, a voltage source grid interactive inverter is modeled and simulated in MATLAB/Simulink. Inverter is designed as current controlled and a fuzzy-PI current controller used for the generation of switching pattern to shape the inverter output current. The grid interactive inverter consists of a line frequency transformer and a LC type filter. Galvanic isolation between the grid and renewable energy source is obtained by the line frequency transformer and LC filter is employed to filter the high frequency harmonic components in current waveform due to PWM switching and to reduce the output current THD. Results of the MATLAB/Simulink simulation show that inverter output current is in sinusoidal waveform and in phase with line voltage, and current harmonics are in the limits of international standards (

  13. Triple inverter pierce oscillator circuit suitable for CMOS

    Science.gov (United States)

    Wessendorf,; Kurt, O [Albuquerque, NM

    2007-02-27

    An oscillator circuit is disclosed which can be formed using discrete field-effect transistors (FETs), or as a complementary metal-oxide-semiconductor (CMOS) integrated circuit. The oscillator circuit utilizes a Pierce oscillator design with three inverter stages connected in series. A feedback resistor provided in a feedback loop about a second inverter stage provides an almost ideal inverting transconductance thereby allowing high-Q operation at the resonator-controlled frequency while suppressing a parasitic oscillation frequency that is inherent in a Pierce configuration using a "standard" triple inverter for the sustaining amplifier. The oscillator circuit, which operates in a range of 10 50 MHz, has applications for use as a clock in a microprocessor and can also be used for sensor applications.

  14. Integrated Inverter For Driving Multiple Electric Machines

    Science.gov (United States)

    Su, Gui-Jia [Knoxville, TN; Hsu, John S [Oak Ridge, TN

    2006-04-04

    An electric machine drive (50) has a plurality of inverters (50a, 50b) for controlling respective electric machines (57, 62), which may include a three-phase main traction machine (57) and two-phase accessory machines (62) in a hybrid or electric vehicle. The drive (50) has a common control section (53, 54) for controlling the plurality of inverters (50a, 50b) with only one microelectronic processor (54) for controlling the plurality of inverters (50a, 50b), only one gate driver circuit (53) for controlling conduction of semiconductor switches (S1-S10) in the plurality of inverters (50a, 50b), and also includes a common dc bus (70), a common dc bus filtering capacitor (C1) and a common dc bus voltage sensor (67). The electric machines (57, 62) may be synchronous machines, induction machines, or PM machines and may be operated in a motoring mode or a generating mode.

  15. An experimental test of a fundamental food web motif.

    Science.gov (United States)

    Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

    2010-06-07

    Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

  16. An SCR inverter for electric vehicles

    Science.gov (United States)

    Latos, T.; Bosack, D.; Ehrlich, R.; Jahns, T.; Mezera, J.; Thimmesch, D.

    1980-01-01

    An inverter for an electric vehicle propulsion application has been designed and constructed to excite a polyphase induction motor from a fixed propulsion battery source. The inverter, rated at 35kW peak power, is fully regenerative and permits vehicle operation in both the forward and reverse directions. Thyristors are employed as the power switching devices arranged in a dc bus commutated topology. This paper describes the major role the controller plays in generating the motor excitation voltage and frequency to deliver performance similar to dc systems. Motoring efficiency test data for the controller are presented. It is concluded that an SCR inverter in conjunction with an ac induction motor is a viable alternative to present dc vehicle propulsion systems on the basis of performance and size criteria.

  17. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  18. Mechanisms of zero-lag synchronization in cortical motifs.

    Directory of Open Access Journals (Sweden)

    Leonardo L Gollo

    2014-04-01

    Full Text Available Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying"--a mechanism that relies on a specific network motif--has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair--a "resonance pair"--plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying from those that do not (such as the common driving triad. Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain.

  19. Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup Repeat Specificity

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Möller, Ingvar Rúnar; Kristensen, Ole

    2013-01-01

    Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat...... peptide. Despite high structural similarity, the FxFG binding site is located between two alpha helices in the G3BP1 NTF2-like domain and not at the dimer interface as observed for nuclear transport factor 2. ITC studies showed specificity towards the FxFG motif but not FG and GLFG motifs. The unliganded...

  20. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  1. Transduction motif analysis of gastric cancer based on a human signaling network

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

    2014-04-04

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  2. CT and MR findings of the inverted papilloma

    International Nuclear Information System (INIS)

    Lim, Seong Youb; Kim, Hak Jin; Lee, Jun Woo; Park, Jae Yeong; Lee, Sung Gap; Kim, Byung Soo; Roh, Hwan Jung; Baik, Seung Kook

    1997-01-01

    The purpose of this study is to describe the CT and MR findings of inverted papilloma and to determine the specific differential finding between inverted papilloma with and without coexisting malignancy. Twenty-two histopathologically proven inverted papillomas were included in this study ; in six patients there was coexisting malignancy. Twenty-two CT images and eight MR images were retrospectively reviewed. On CT images, the inverted papillomas were seen as unilateral sinonasal masses with bone remodeling (n=15) rather than bone destruction (n=1) and showed iso- or slightly high attenuation. Three of the six malignant cases showed aggressive bone destruction and widespread extension into the orbit, intracranial and buccal spaces, and pterygopalatine fossa. On MR images, the inverted papillomas (n=3) were iso- (n=2) or slightly high (n=1) in signal intensity in relation to muscle on T1-weighted images, and high (n=3) on T2-weighted images. Gadolinium enhanced images showed heterogenous moderate enhancement. In the cases of coexisting malignancy (n=5), the masses were iso- (n=5) on T1-weighted images, high (n=5) on T2-weighted images and also showed heterogenous moderate enhancement. Inverted papilloma should be considered in the differential diagnosis of a bulky unilateral nasal mass extending into the adjacent paranasal sinuses, especially in an elderly patient with chronic nasal obstruction. Although there were no specific differential findings in signal intensity and enhancement pattern on CT and MR images between benign and malignant inverted papilloma, aggressive bone destruction and widespread extension beyond the sinonasal cavity are findings which are highly suggestive of coexisting malignancy

  3. Automatic load sharing in inverter modules

    Science.gov (United States)

    Nagano, S.

    1979-01-01

    Active feedback loads transistor equally with little power loss. Circuit is suitable for balancing modular inverters in spacecraft, computer power supplies, solar-electric power generators, and electric vehicles. Current-balancing circuit senses differences between collector current for power transistor and average value of load currents for all power transistors. Principle is effective not only in fixed duty-cycle inverters but also in converters operating at variable duty cycles.

  4. Base drive for paralleled inverter systems

    Science.gov (United States)

    Nagano, S. (Inventor)

    1980-01-01

    In a paralleled inverter system, a positive feedback current derived from the total current from all of the modules of the inverter system is applied to the base drive of each of the power transistors of all modules, thereby to provide all modules protection against open or short circuit faults occurring in any of the modules, and force equal current sharing among the modules during turn on of the power transistors.

  5. Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2014-10-01

    Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

  6. Discriminative motif discovery via simulated evolution and random under-sampling.

    Directory of Open Access Journals (Sweden)

    Tao Song

    Full Text Available Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  7. Discriminative motif discovery via simulated evolution and random under-sampling.

    Science.gov (United States)

    Song, Tao; Gu, Hong

    2014-01-01

    Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  8. Improved i-motif thermal stability by insertion of anthraquinone monomers

    DEFF Research Database (Denmark)

    Gouda, Alaa S; Amine, Mahasen S.; Pedersen, Erik Bjerregaard

    2017-01-01

    In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA...... loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends...... unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified...

  9. A New N-Level Inverter Based on Z-NPC

    Directory of Open Access Journals (Sweden)

    E. Babaei

    2017-12-01

    Full Text Available First of all, in this paper, the topology and operation of the three-phase three-level Z-source inverter based on neutral-point-clamped (Z-NPC are studied. Moreover, different combinations of permissible switching states and control signals are explained for this inverter. In this paper, the topology of the three-phase three-level Z-NPC inverter is extended for an n-level state. Also, a combination of allowed switching states with relevant mathematical equations is presented for the proposed n-level Z-NPC inverter. In comparison with multilevel voltage-source inverters (only voltage-boost capability, the proposed multilevel Z-NPC inverter is a single-stage converter and it has a buck-boost capability of voltage. On the other hand, the control of two-stage converters compared to single-stage converters can be more difficult because of existing more active and passive components. In this paper, two new PWM control methods are also proposed for various multilevel Z-NPC inverters. One advantage of the proposed PWM control methods in comparison with conventional PWM control methods is maintaining the charge balance of the dc-link capacitors in neutral point. The correct performance of the proposed multilevel Z-NPC topology and PWM control methods are verified by the obtained results of analysis and simulations performed in the PSCAD software.

  10. Six transformer based asymmetrical embedded Z-source inverters

    DEFF Research Database (Denmark)

    Wei, Mo; Poh Chiang, Loh; Chi, Jin

    2013-01-01

    Embedded/Asymmetrical embedded Z-source inverters were proposed to maintain smooth input current/voltage across the dc source and within the impedance network, remain the shoot-through feature used to boost up the dc-link voltage without adding bulky filter at input side. This paper introduces a ...... a class of transformer based asymmetrical embedded Z-source inverters which keep the smooth input current and voltage while achieving enhanced voltage boost capability. The presented inverters are verified by laboratory prototypes experimentally....

  11. Designing a Smaller Power Inverter: the Google Littlebox Challenge - Text

    Science.gov (United States)

    Version | Energy Systems Integration Facility | NREL Designing a Smaller Power Inverter: the Google Littlebox Challenge - Text Version er Power Inverter: the Google Littlebox Challenge - Text Version Below is the text version for the Designing a Smaller Power Inverter: the Google Littlebox

  12. Solution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin

    International Nuclear Information System (INIS)

    Wolf, Christian A.; Dancea, Felician; Shi Meichen; Bade-Noskova, Veronika; Rueterjans, Heinz; Kerjaschki, Dontscho; Luecke, Christian

    2007-01-01

    Megalin, an approx. 600 kDa transmembrane glycoprotein that acts as multi-ligand transporter, is a member of the low density lipoprotein receptor gene family. Several cysteine-rich repeats, each consisting of about 40 residues, are responsible for the multispecific binding of ligands. The solution structure of the twelfth cysteine-rich ligand-binding repeat with class A motif found in megalin features two short β-strands and two helical turns, yielding the typical fold with a I-III, II-V and IV-VI disulfide bridge connectivity pattern and a calcium coordination site at the C-terminal end. The resulting differences in electrostatic surface potential compared to other ligand-binding modules of this gene family, however, may be responsible for the functional divergence

  13. An inverter/controller subsystem optimized for photovoltaic applications

    Science.gov (United States)

    Pickrell, R. L.; Merrill, W. C.; Osullivan, G.

    1978-01-01

    Conversion of solar array dc power to ac power stimulated the specification, design, and simulation testing of an inverter/controller subsystem tailored to the photovoltaic power source characteristics. This paper discusses the optimization of the inverter/controller design as part of an overall Photovoltaic Power System (PPS) designed for maximum energy extraction from the solar array. The special design requirements for the inverter/controller include: (1) a power system controller (PSC) to control continuously the solar array operating point at the maximum power level based on variable solar insolation and cell temperatures; and (2) an inverter designed for high efficiency at rated load and low losses at light loadings to conserve energy. It must be capable of operating connected to the utility line at a level set by an external controller (PSC).

  14. An SCR inverter with an integral battery charger for electric vehicles

    Science.gov (United States)

    Thimmeach, D.

    1983-01-01

    The feasibility of incorporating an onboard battery charger into the inverter previously developed under a NASA contract is successfully demonstrated. The rated output power of the resulting isolated battery charger is 3.6 kW at 220 Vac with an 86 percent efficiency and a 95 percent power factor. Also achieved are improved inverter efficiency (from 90 to 93 percent at 15 kW motor shaft power), inverter peak power capability (from 26 to 34 kW), and reduced weight and volume of the combined inverter/charger package (47 kg, 49 x 44 x 24 cm). Some major conclusions are that using the inverter commutation circuitry to perform the battery charging function is advantageous, and that the input-commutated thyristor inverter has the potential to be an excellent inverter and battery charger for use in electric vehicle applications.

  15. Inverter-based successive approximation capacitance-to-digital converter

    KAUST Repository

    Omran, Hesham; Alhoshany, Abdulaziz; Salama, Khaled N.

    2017-01-01

    offset voltage will result in signal-dependent and parasitic-dependent conversion errors, which necessitates an op-amp-based implementation. The inverter-based SAR CDC contemplated herein provides robust, energy-efficient, and fast operation. The inverter

  16. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

    Science.gov (United States)

    de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

    2015-11-16

    Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Efficiency analysis on a two-level three-phase quasi-soft-switching inverter

    DEFF Research Database (Denmark)

    Geng, Pan; Wu, Weimin; Huang, Min

    2013-01-01

    When designing an inverter, an engineer often needs to select and predict the efficiency beforehand. For the standard inverters, plenty of researches are analyzing the power losses and also many software tools are being used for efficiency calculation. In this paper, the efficiency calculation...... for non-conventional inverters with special shoot-through state is introduced and illustrated through the analysis on a special two-level three-phase quasi-soft-switching inverter. Efficiency comparison between the classical two-stage two-level three-phase inverter and the two-level three-phase quasi......-soft-switching inverter is carried out. A 10 kW/380 V prototype is constructed to verify the analysis. The experimental results show that the efficiency of the new inverter is higher than that of the traditional two-stage two- level three-phase inverter....

  18. MSDB: A Comprehensive Database of Simple Sequence Repeats.

    Science.gov (United States)

    Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh Kumar

    2017-06-01

    Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Modeling Single-Phase PV HB-ZVR Inverter Connected to Grid

    DEFF Research Database (Denmark)

    Guo, Yougui; Zeng, Ping; Zhu, Jieqiong

    2011-01-01

    PLECS is used to model the PV H-bridge zero voltage rectifier (HB-ZVR) inverter connected to grid and good results are obtained. First, several common topologies of PV inverters are introduced. Then the unipolar PWM control strategy is described for PV HB-ZVR inverter. Third, PLECS is briefly...... introduced. Fourth, the modeling of PV HB-ZVR inverter is presented with PLECS. Finally, a series of simulations are carried out. The simulation results tell us PLECS is very powerful tool to real power circuits and it is very easy to simulate LCL filter. They have also verified that the unipolar PWM control...... strategy is feasible to control the PV HB-ZVR inverter....

  20. 27-Level DC–AC inverter with single energy source

    International Nuclear Information System (INIS)

    Tsang, K.M.; Chan, W.L.

    2012-01-01

    Highlights: ► This paper reports a novel 27-level DC–AC inverter using only single renewable energy source. ► The efficiency of the inverter is very high. The output waveform is almost sinusoidal. ► The cost is low as the number of power switches required is only 12. - Abstract: A novel design of multilevel DC–AC inverter using only single renewable energy source is presented in this paper. The proposed approach enables multilevel output to be realised by a few cascaded H-bridges and a single energy source. As an illustration, a 27-level inverter has been implemented based on three cascaded H-bridges with a single energy source and two capacitors. Using the proposed novel switching strategy, 27 levels can be realized and the two virtual energy sources can be well regulated. Experimental results are included to demonstrate the effectiveness of the proposed inverter.

  1. Compensation techniques for non-linearities in H-bridge inverters

    Directory of Open Access Journals (Sweden)

    Daniel Zammit

    2016-12-01

    Full Text Available This paper presents compensation techniques for component non-linearities in H-bridge inverters as those used in grid-connected photovoltaic (PV inverters. Novel compensation techniques depending on the switching device current were formulated to compensate for the non-linearities in inverter circuits caused by the voltage drops on the switching devices. Both simulation and experimental results will be presented. Testing was carried out on a PV inverter which was designed and constructed for this research. Very satisfactory results were obtained from all the compensation techniques presented, however the exact compensation method was the most effective, providing the highest reduction in harmonics.

  2. LLCL-Filter Based Single-Phase Grid-Tied Aalborg Inverter

    DEFF Research Database (Denmark)

    Wu, Weimin; Feng, Shuangshuang; Ji, Junhao

    2014-01-01

    The Aalborg Inverter is a new type of high efficient DC/AC grid-tied inverter, where the input DC voltage can vary in a wide range. Compared with the LCL-filter, the LLCL-filter can save the total inductance for the conventional voltage source inverter. In this paper, an LLCL-filter based Aalborg...... Inverter is proposed and its character is illustrated through the small signal analysis in both “Buck” and “Buck-Boost” mode. From the modeling, it can be seen that the resonant inductor in the capacitor loop has not brought extra control difficulties, whereas more inductance in the power loop can be saved...

  3. Energy-Saving Inverter

    Science.gov (United States)

    Rippel, W. E.; Edwards, D. B.

    1984-01-01

    Commutation by field-effect transistor allows more efficient operation. High voltage field-effect transistor (FET) controls silicon controlled rectifiers (SCR's). Circuit requires only one capacitor and one inductor in commutation circuit: simpler, more efficient, and more economical than conventional inverters. Adaptable to dc-to-dc converters.

  4. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  5. Finishing report for the 'SolcelleInverter' project

    Energy Technology Data Exchange (ETDEWEB)

    Boekhoej Kjaer, S.

    2005-03-01

    The main objective for this research project was to develop an inverter for the AC module, where one PV module is equipped with its own dedicated inverter, and connected to the grid. A topology, among many different candidates, has been selected, based on analysis's. The inverter has been optimized in respect to cost, reliability, and efficiency, and a prototype has been build. (au)

  6. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  7. Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

    Directory of Open Access Journals (Sweden)

    O. V. Galzitskaya

    2015-01-01

    Full Text Available How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern and third (the two amino acids occur randomly groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62 is higher than between fungi and plants (0.54. Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

  8. THE DETERMINATION OF DIFFUSION COEFFICIENT OF INVERT MATERIALS

    International Nuclear Information System (INIS)

    P. Heller and J. Wright

    2000-01-01

    The Engineered Barrier System (EBS) Testing Department is performing tests in the Department of Energy's Atlas Facility to evaluate the performance of various means for increasing the time for breakthrough of radionuclides from the waste package to the base of the invert. This includes testing various barriers in the invert as a means of increasing breakthrough time through the process of diffusion. A diffusion barrier may serve as an invert material for the emplacement drifts. The invert material may consist of crushed tuff from the repository excavation at Yucca Mountain or silica sand. The objective of this report is to determine the diffusion coefficient of the crushed tuff and silica sand invert materials specified by the EBS Testing Department. The laboratory derived information from the testing was used in the Nernst-Einstein equation (Jurinak et al. 1987, p. 626) to determine the diffusion coefficient of the invert material. This report transmits the results and describes the methodology and interpretation. The scope of this report is to determine the diffusion coefficients of the invert materials mentioned above using the centrifuge at UFA Ventures. Standard laboratory procedures, described in Section 2 of this report, were used. The diffusion coefficients are to be determined over a range of moisture contents. The report contains the diffusion coefficients calculated by the Nernst-Einstein equation (Jurinak et al. 1987, p. 626) that become a part of the Technical Database. Raw data is also included in the report, however this data does not become part of the Technical Database as per Section 3.23 of AP-SIII.3Q ''Submittal and Incorporation of Data to the Technical Data Management System''. A sieve analysis of the samples was not conducted as part of this report, but sieve analysis may be accomplished as part of other reports. Two samples of crushed tuff and two samples of silica sand were tested

  9. Comparison of three-phase three-level voltage source inverter with intermediate dc–dc boost converter and quasi-Z-source inverter

    DEFF Research Database (Denmark)

    Panfilov, Dmitry; Husev, Oleksandr; Blaabjerg, Frede

    2016-01-01

    This study compares a three-phase three-level voltage source inverter with an intermediate dc-dc boost converter and a quasi-Z-source inverter in terms of passive elements values and dimensions, semiconductor stresses, and overall efficiency. A comparative analysis was conducted with relative...

  10. Current Harmonics from Single-Phase Grid-Connected Inverters

    DEFF Research Database (Denmark)

    Yang, Yongheng; Zhou, Keliang; Blaabjerg, Frede

    2016-01-01

    Environmental conditions and operational modes may significantly impact the distortion level of the injected current from single-phase grid-connected inverter systems, such as photovoltaic (PV) inverters, which may operate in cloudy days with a maximum power point tracking, in a non-unity power...... factor, or in the low voltage ride through mode with reactive current injection. In this paper, the mechanism of the harmonic current injection from grid-connected single-phase inverter systems is thus explored, and the analysis is conducted on single-phase PV systems. In particular, the analysis...... is focused on the impacts of the power factor and the feed-in grid current level on the quality of the feed-in grid current from single-phase inverters. As a consequence, an internal model principle based high performance current control solution is tailor-made and developed for single-phase grid-connected...

  11. Homogeneous Crystallization of Micro-DispensedTIPS-Pentacene Using a Two-Solvent System toEnable Printed Inverters on Foil Substrates

    Directory of Open Access Journals (Sweden)

    Indranil Bose

    2015-08-01

    Full Text Available We report on a micro-dispensing system for 6,13-Bis(triisopropylsilylethynylpentacene (TIPS-pentacene to enable homogenous crystallization and uniform filmmorphology of the dispensed droplets using a two-solvent mixture along with the use of aninsulating binder. This solution composition results in a controlled evaporation of the dropletin ambient air such that the Marangoni flow counteracts the outward convective flow toenable uniform radial crystal growth from the edge towards the center of the drops.The consequence of this process is the high degree of uniformity in the crystallization of thedrops, which results in a reduction in the performance spread of the organic field effecttransistors (OFET created using this process. The addition of the insulating binder furtherimproves the reduction in the spread of the results as a trade-off to the reduction in mobilityof the transistors. The transfer curves of the OFETs show a tight grouping due to thecontrolled self-alignment of the TIPS-pentacene crystals; this repeatability was furtherhighlighted by fabricating p-type inverters with driver to load ratios of 8:1, wherein theoutput inverter curves were also grouped tightly while exhibiting a gain of greater than 4 inthe switching region. Therefore, the reliability and repeatability of this process justifies itsuse to enable large area solution-processed printed circuits at the cost of reduced mobility.

  12. An iterative method to invert the LTSn matrix

    Energy Technology Data Exchange (ETDEWEB)

    Cardona, A.V.; Vilhena, M.T. de [UFRGS, Porto Alegre (Brazil)

    1996-12-31

    Recently Vilhena and Barichello proposed the LTSn method to solve, analytically, the Discrete Ordinates Problem (Sn problem) in transport theory. The main feature of this method consist in the application of the Laplace transform to the set of Sn equations and solve the resulting algebraic system for the transport flux. Barichello solve the linear system containing the parameter s applying the definition of matrix invertion exploiting the structure of the LTSn matrix. In this work, it is proposed a new scheme to invert the LTSn matrix, decomposing it in blocks and recursively inverting this blocks.

  13. Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

    Science.gov (United States)

    Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

    2015-06-01

    Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Methods and statistics for combining motif match scores.

    Science.gov (United States)

    Bailey, T L; Gribskov, M

    1998-01-01

    Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

  15. Work Station For Inverting Solar Cells

    Science.gov (United States)

    Feder, H.; Frasch, W.

    1982-01-01

    Final work station along walking-beam conveyor of solar-array assembly line turns each pretabbed solar cell over, depositing it back-side-up onto landing pad, which centers cell without engaging collector surface. Solar cell arrives at inverting work station collector-side-up with two interconnect tabs attached to collector side. Cells are inverted so that second soldering operation takes place in plain view of operator. Inversion protects collector from damage when handled at later stages of assembly.

  16. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

    Science.gov (United States)

    Ozaki, Haruka; Iwasaki, Wataru

    2016-08-01

    As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. NRC Information No. 87-24: Operational experience involving losses of electrical inverters

    International Nuclear Information System (INIS)

    Rossi, C.E.

    1992-01-01

    The NRC case study report identified three potential failure mechanisms for inverters. One of these involves relatively high ambient temperature and/or humidity within inverter enclosures. This condition appears to result in accelerated aging of components that form a part of the inverter circuitry causing a significant reduction in component life expectancy and inverter loss. Another mechanism for inverter failure involves the electrical interconnecting and physical arrangements for the inverter circuitry components. In some installations, these arrangements are such that when certain components fail, other components also may fail or degrade. The third failure mechanism involves voltage spikes and perturbations. Many of the electrical loads in a plant have inductive characteristics. During plant operations that involve energizing and deenergizing these loads, voltage spikes and perturbations are generated. The solid-state devices in the inverter circuitry are sensitive to these voltage spikes, and this has resulted in component failure, blown fuses, and inverter losses. Additionally, secondary voltage perturbations caused by lighting strikes or switching surges can have an adverse effect on inverter operation

  18. Power inverter implementing phase skipping control

    Science.gov (United States)

    Somani, Utsav; Amirahmadi, Ahmadreza; Jourdan, Charles; Batarseh, Issa

    2016-10-18

    A power inverter includes a DC/AC inverter having first, second and third phase circuitry coupled to receive power from a power source. A controller is coupled to a driver for each of the first, second and third phase circuitry (control input drivers). The controller includes an associated memory storing a phase skipping control algorithm, wherein the controller is coupled to receive updating information including a power level generated by the power source. The drivers are coupled to control inputs of the first, second and third phase circuitry, where the drivers are configured for receiving phase skipping control signals from the controller and outputting mode selection signals configured to dynamically select an operating mode for the DC/AC inverter from a Normal Control operation and a Phase Skipping Control operation which have different power injection patterns through the first, second and third phase circuitry depending upon the power level.

  19. Design consideration of resonance inverters with electro-technological application

    Science.gov (United States)

    Hinov, Nikolay

    2017-12-01

    This study presents design consideration of resonance inverters with electro-technological application. The presented methodology was achieved as a result of investigations and analyses of different types and working regimes of resonance inverters, made by the author. Are considered schemes of resonant inverters without inverse diodes. The first harmonic method is used in the analysis and design. This method for the case of inverters with electro-technological application gives very good accuracy. This does not require the use of a complex and heavy mathematical apparatus. The proposed methodology is easy to use and is suitable for use in training students in power electronics. Authenticity of achieved results is confirmed by simulating and physical prototypes research work.

  20. Active Damping Techniques for LCL-Filtered Inverters-Based Microgrids

    DEFF Research Database (Denmark)

    Lorzadeh, Iman; Firoozabadi, Mehdi Savaghebi; Askarian Abyaneh, Hossein

    2015-01-01

    LCL-type filters are widely used in gridconnected voltage source inverters, since it provides switching ripples reduction with lower cost and weight than the L-type counterpart. However, the inclusion of LCL-filters in voltage source inverters complicates the current control design regarding system...... the different active damping approaches for grid-connected inverters with LCL filters, which are based on high-order filters and additional feedbacks methods. These techniques are analyzed and discussed in detail....... stability issues; because an inherent resonance peak appears due to zero impedance at that resonance frequency. Moreover, in grid-interactive low-voltage microgrids, the interactions among the LCL-filtered-based parallel inverters may result in a more complex multiresonance issue which may compromise...

  1. Impacts of PV Array Sizing on PV Inverter Lifetime and Reliability

    DEFF Research Database (Denmark)

    Sangwongwanich, Ariya; Yang, Yongheng; Sera, Dezso

    2017-01-01

    . However, oversizing the PV array will increase the loading of PV inverters, which may have undesired influence on the PV inverter lifetime and reliability. In that case, it may result in a negative impact on the overall PV energy cost, due to the increased maintenance for the PV inverters. This paper...... evaluates the lifetime of PV inverters considering the PV array sizing and installation sites, e.g., Denmark and Arizona. The results reveal that the PV array sizing has a considerable impact on the PV inverter lifetime and reliability, especially in Denmark, where the average solar irradiance level...

  2. Model Predictive Control of Z-source Neutral Point Clamped Inverter

    DEFF Research Database (Denmark)

    Mo, Wei; Loh, Poh Chiang; Blaabjerg, Frede

    2011-01-01

    This paper presents Model Predictive Control (MPC) of Z-source Neutral Point Clamped (NPC) inverter. For illustration, current control of Z-source NPC grid-connected inverter is analyzed and simulated. With MPC’s advantage of easily including system constraints, load current, impedance network...... response are obtained at the same time with a formulated Z-source NPC inverter network model. Operation steady state and transient state simulation results of MPC are going to be presented, which shows good reference tracking ability of this method. It provides new control method for Z-source NPC inverter...

  3. Thermal hydraulic design of a hydride-fueled inverted PWR core

    International Nuclear Information System (INIS)

    Malen, J.A.; Todreas, N.E.; Hejzlar, P.; Ferroni, P.; Bergles, A.

    2009-01-01

    An inverted PWR core design utilizing U(45%, w/o)ZrH 1.6 fuel (here referred to as U-ZrH 1.6 ) is proposed and its thermal hydraulic performance is compared to that of a standard rod bundle core design also fueled with U-ZrH 1.6 . The inverted design features circular cooling channels surrounded by prisms of fuel. Hence the relative position of coolant and fuel is inverted with respect to the standard rod bundle design. Inverted core designs with and without twisted tape inserts, used to enhance critical heat flux, were analyzed. It was found that higher power and longer cycle length can be concurrently achieved by the inverted core with twisted tape relative to the optimal standard core, provided that higher core pressure drop can be accommodated. The optimal power of the inverted design with twisted tape is 6869 MW t , which is 135% of the optimally powered standard design (5080 MW t -determined herein). Uncertainties in this design regarding fuel and clad dimensions needed to accommodate mechanical loads and fuel swelling are presented. If mechanical and neutronic feasibility of these designs can be confirmed, these thermal assessments imply significant economic advantages for inverted core designs.

  4. Mobile Inverted Constructivism: Education of Interaction Technology in Social Media

    Science.gov (United States)

    Chai, Jia-Xiang; Fan, Kuo-Kuang

    2016-01-01

    The combination of social media and invert teaching is a new path to inverting interation technology education and reconstructing the curriculum of context. In this paper, based on the theory of constructivism learning, a model named Mobile Inverted Constructivism (MIC) is provided. Moreover, in view of the functional quality of social media in…

  5. Tensor product of left n-invertible operators

    Czech Academy of Sciences Publication Activity Database

    Duggal, B.P.; Müller, Vladimír

    2013-01-01

    Roč. 215, č. 2 (2013), s. 113-125 ISSN 0039-3223 R&D Projects: GA ČR GA201/09/0473 Institutional support: RVO:67985840 Keywords : Banach space * essentially left n- invertible operator * left n-invertible operator Subject RIV: BA - General Mathematics Impact factor: 0.630, year: 2013 http://journals.impan.pl/cgi-bin/doi?sm215-2-2

  6. Single phase inverter for a three phase power generation and distribution system

    Science.gov (United States)

    Lindena, S. J.

    1976-01-01

    A breadboard design of a single-phase inverter with sinusoidal output voltage for a three-phase power generation and distribution system was developed. The three-phase system consists of three single-phase inverters, whose output voltages are connected in a delta configuration. Upon failure of one inverter the two remaining inverters will continue to deliver three-phase power. Parallel redundancy as offered by two three-phase inverters is substituted by one three-phase inverter assembly with high savings in volume, weight, components count and complexity, and a considerable increase in reliability. The following requirements must be met: (1) Each single-phase, current-fed inverter must be capable of being synchronized to a three-phase reference system such that its output voltage remains phaselocked to its respective reference voltage. (2) Each single-phase, current-fed inverter must be capable of accepting leading and lagging power factors over a range from -0.7 through 1 to +0.7.

  7. Breaking Barriers to Low-Cost Modular Inverter Production & Use

    Energy Technology Data Exchange (ETDEWEB)

    Bogdan Borowy; Leo Casey; Jerry Foshage; Steve Nichols; Jim Perkinson

    2005-05-31

    The goal of this cost share contract is to advance key technologies to reduce size, weight and cost while enhancing performance and reliability of Modular Inverter Product for Distributed Energy Resources (DER). Efforts address technology development to meet technical needs of DER market protection, isolation, reliability, and quality. Program activities build on SatCon Technology Corporation inverter experience (e.g., AIPM, Starsine, PowerGate) for Photovoltaic, Fuel Cell, Energy Storage applications. Efforts focused four technical areas, Capacitors, Cooling, Voltage Sensing and Control of Parallel Inverters. Capacitor efforts developed a hybrid capacitor approach for conditioning SatCon's AIPM unit supply voltages by incorporating several types and sizes to store energy and filter at high, medium and low frequencies while minimizing parasitics (ESR and ESL). Cooling efforts converted the liquid cooled AIPM module to an air-cooled unit using augmented fin, impingement flow cooling. Voltage sensing efforts successfully modified the existing AIPM sensor board to allow several, application dependent configurations and enabling voltage sensor galvanic isolation. Parallel inverter control efforts realized a reliable technique to control individual inverters, connected in a parallel configuration, without a communication link. Individual inverter currents, AC and DC, were balanced in the paralleled modules by introducing a delay to the individual PWM gate pulses. The load current sharing is robust and independent of load types (i.e., linear and nonlinear, resistive and/or inductive). It is a simple yet powerful method for paralleling both individual devices dramatically improves reliability and fault tolerance of parallel inverter power systems. A patent application has been made based on this control technology.

  8. Single stage buck-boost DC-AC neutral point clamped inverter

    DEFF Research Database (Denmark)

    Mo, Wei; Loh, Poh Chiang; Andrew, A.

    2012-01-01

    This paper proposes a new single stage buck-boost DC-AC neutral point clamped inverter topology which integrates the cascaded configurations of recently introduced inductor-capacitor-capacitor-transformer impedance source network (by Adamowicz) and classic NPC configuration. As a consequence......, it has enhanced buck-boost functionality and low output voltage distortions compared to the traditional Z-source inverter; it has continuous input current which reduces the source stress and inverter noise; it also contains two built-in capacitors which can block the DC current in the transformer...... windings thus preventing the core from saturation; lowers the voltage stresses and power losses of inverter switches and reduces the sizes of filtering devices and as well as obtains better output performance compared to the original two-level Z-source inverters. A phase disposition pulse width modulation...

  9. Low-dimensional morphospace of topological motifs in human fMRI brain networks

    Directory of Open Access Journals (Sweden)

    Sarah E. Morgan

    2018-06-01

    Full Text Available We present a low-dimensional morphospace of fMRI brain networks, where axes are defined in a data-driven manner based on the network motifs. The morphospace allows us to identify the key variations in healthy fMRI networks in terms of their underlying motifs, and we observe that two principal components (PCs can account for 97% of the motif variability. The first PC of the motif distribution is correlated with efficiency and inversely correlated with transitivity. Hence this axis approximately conforms to the well-known economical small-world trade-off between integration and segregation in brain networks. Finally, we show that the economical clustering generative model proposed by Vértes et al. (2012 can approximately reproduce the motif morphospace of the real fMRI brain networks, in contrast to other generative models. Overall, the motif morphospace provides a powerful way to visualize the relationships between network properties and to investigate generative or constraining factors in the formation of complex human brain functional networks. Motifs have been described as the building blocks of complex networks. Meanwhile, a morphospace allows networks to be placed in a common space and can reveal the relationships between different network properties and elucidate the driving forces behind network topology. We combine the concepts of motifs and morphospaces to create the first motif morphospace of fMRI brain networks. Crucially, the morphospace axes are defined by the motifs, in a data-driven manner. We observe strong correlations between the networks’ positions in morphospace and their global topological properties, suggesting that motif morphospaces are a powerful way to capture the topology of networks in a low-dimensional space and to compare generative models of brain networks. Motif morphospaces could also be used to study other complex networks’ topologies.

  10. Mitigation of Grid Current Distortion for LCL-Filtered Voltage Source Inverter with Inverter Current Feedback Control

    DEFF Research Database (Denmark)

    Xin, Zhen; Mattavelli, Paolo; Yao, WenLi

    2018-01-01

    LCL filters feature low inductance; thus, the injected grid current from an LCL-filtered Voltage Source Inverter (VSI) can be easily distorted by grid voltage harmonics. This problem is especially tough for the control system with Inverter-side Current Feedback (ICF), since the grid current...... harmonics can freely flow into the filter capacitor. In this case, because of the loss of harmonic information, traditional harmonic controllers fail to mitigate the grid current distortion. Although this problem may be avoided using the grid voltage feedforward scheme, the required differentiators may...

  11. FET commutated current-FED inverter

    Science.gov (United States)

    Rippel, Wally E. (Inventor); Edwards, Dean B. (Inventor)

    1983-01-01

    A shunt switch comprised of a field-effect transistor (Q.sub.1) is employed to commutate a current-fed inverter (10) using thyristors (SCR1, SCR2) or bijunction transistors (Q.sub.2, Q.sub.3) in a full bridge (1, 2, 3, 4) or half bridge (5, 6) and transformer (T.sub.1) configuration. In the case of thyristors, a tapped inverter (12) is employed to couple the inverter to a dc source to back bias the thyristors during commutation. Alternatively, a commutation power supply (20) may be employed for that purpse. Diodes (D.sub.1, D.sub.2) in series with some voltage dropping element (resistor R.sub.12 or resistors R.sub.1, R.sub.2 or Zener diodes D.sub.4, D.sub.5) are connected in parallel with the thyristors in the half bridge and transformer configuration to assure sharing the back bias voltage. A clamp circuit comprised of a winding (18) negatively coupled to the inductor and a diode (D.sub.3) return stored energy from the inductor to the power supply for efficient operation with buck or boost mode.

  12. Inverted annular flow experimental study

    International Nuclear Information System (INIS)

    De Jarlais, G.; Ishii, M.

    1985-04-01

    Steady-state inverted annular flow of Freon 113 in up flow was established in a transparent test section. Using a special inlet configuration consisting of long aspect-ratio liquid nozzles coaxially centered within a heated quartz tube, idealized inverted annular flow initial geometry (cylindrical liquid core surrounded by coaxial annulus of gas) could be established. Inlet liquid and gas flowrates, liquid subcooling, and gas density (using various gas species) were measured and varied systematically. The hydrodynamic behavior of the liquid core, and the subsequent downstream break-up of this core into slugs, ligaments and/or droplets of various sizes, was observed. In general, for low inlet liquid velocities it was observed that after the initial formation of roll waves on the liquid core surface, an agitated region of high surface area, with attendant high momentum and energy transfers, occurs. This agitated region appears to propagate downsteam in a quasi-periodic pattern. Increased inlet liquid flow rates, and high gas annulus flow rates tend to diminish the significance of this agitated region. Observed inverted annular flow (and subsequent downstream flow pattern) hydrodynamic behavior is reported, and comparisons are drawn to data generated by previous experimenters studying post-CHF flow

  13. Power Inverter Topologies for Photovoltaic Modules - A Review

    DEFF Research Database (Denmark)

    Kjær, Søren Bækhøj; Pedersen, John Kim; Blaabjerg, Frede

    2002-01-01

    This review-paper focuses on the latest development of inverters for photovoltaic AC-Modules. The power range for these inverters is usually within 90 Watt to 500 Watt, which covers the most commercial photovoltaic-modules. Self-commutated inverters have replaced the grid-commutated ones. The same...... is true for the bulky low-frequency transformers versus the high-frequency transformers, which are used to adapt the voltage level. The AC-Module provides a modular design and a flexible behaviour in various grid conditions. It hereby opens the market for photovoltaic-power for everyone at a low cost due...

  14. Robustness analysis of the efficiency in PV inverters

    DEFF Research Database (Denmark)

    Pigazo, Alberto; Liserre, Marco; Blaabjerg, Frede

    2013-01-01

    topology and control strategy but also on the characteristics of the employed components. The aim of this paper is evaluate the effect of physical variations associated to the main components on the overall efficiency of PV inverters. It is concluded that a statistical evaluation of the power converter......During last years an increasing attention has been paid to the efficiency of grid-connected PV inverters. They are manufactured from a number of discrete components and by using a certain topology and control strategy. Hence, the performance of a certain PV inverter not only depends on the selected...

  15. PLTS Transformerless Tegangan 20 kV menggunakan Cascaded H-Bridge Multilevel Inverter

    Directory of Open Access Journals (Sweden)

    ANGGARA BRAJAMUSTHI

    2018-03-01

    Full Text Available ABSTRAK Aplikasi dari inverter multilevel pada sistem Pusat Listrik Tenaga Surya (PLTS dapat menghilangkan kebutuhan terhadap transformator, sehingga dapat mengurangi biaya investasi, mengurangi kompleksitas instalasi dan menghilangkan rugi-rugi daya transformator. Pada penelitian ini, sebuah inverter dengan topologi Cascaded H-Bridge Multilevel Inverter dirancang agar mampu mengubah tegangan rendah DC dari beberapa Photovoltaic (PV array menjadi tegangan fasa-fasa 20 kV AC. Perancangan menghasilkan sebuah inverter 3 fasa 27-level dimana setiap level masing-masing memiliki PV array, DC-DC boost converter, H-bridge inverter, dan keluaran 3 fasa terhubung dengan filter LCL. Setiap komponen dari inverter dan sistem tersebut kemudian dimodelkan pada MATLAB Simulink untuk mensimulasikan kinerja dari setiap komponen dan sistem pada Standard Test Condition (STC dari modul PV. Pada keadaan STC, daya 3 fasa maksimum yang dapat dihasilkan adalah 1,716 MW atau 68,54% dari daya DC maksimum sebesar 2,5 MWp. Sistem dapat menghasilkan tegangan fasa-fasa keluaran sebesar 20 kV dengan Total Harmonic Distortion (THD di bawah 5%. Kata kunci: Pusat Listrik Tenaga Surya (PLTS, photovoltaic, Cascaded H-Bridge Multilevel Inverter ABSTRACT The application of Multilevel Inverter in a Photovoltaic Solar Power Plant system could eliminate the needs of step-up transformer, which will reduce the system investment cost, simplify the system installation and also eliminate power losses of the transformer. In this paper, an inverter design was proposed with Cascaded H-Bridge Multilevel Inverter topology that is capable of converting low voltage DC power from several PV arrays into 20 kV AC power. The design resulted a 3 phase 27-level inverter where each level in the inverter has its own photovoltaic array, DC-DC boost converter, H-bridge inverter, and the 3 phase output is connected to LCL filter. Each component of the Inverter and the system were then modelled in MATLAB

  16. Development and Evaluation of a 2KVA Inverter

    Directory of Open Access Journals (Sweden)

    Ajayi Adedayo

    2013-09-01

    Full Text Available A 2KV inverter was designed, developed and tested for household applications. It consists of a heavy duty (24 V, 80 AH, oscillator unit, PWM (Pulse-width modulation controller unit, driver unit, amplifier unit, center-tap step up transformer and battery charger unit. The battery powered the circuitry and the oscillator section generates the drive signal that is amplified and set up the transformer to produce 240 V supply at the secondary winding connected to the output socket of inverter. The feedback control circuit uses discrete components such as: full wave rectifier, pulse width modulator (IC, diodes and other components to sense the output voltage (or load current. When the feedback senses that the load on the inverter output has increased, the inverter control circuitry acts by increasing the width of the switching pulse in the oscillator section which turn on the MOSFETS. MOSFETS turns on for longer time each cycle, automatically correcting the R.M.S value of the output to compensate for any drop in peak-peak output voltage as well as continuous charging of battery, consequently, maintaining a steady output voltage level in inverter irrespective of the load characteristics. The outputs of the tests carried on the unit shows that that instrument performs satisfactory well.

  17. Memetic algorithms for de novo motif-finding in biomedical sequences.

    Science.gov (United States)

    Bi, Chengpeng

    2012-09-01

    The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro

  18. Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

    Science.gov (United States)

    Roy, Indranil; Aluru, Srinivas

    2016-01-01

    Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

  19. PISMA: A Visual Representation of Motif Distribution in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Rogelio Alcántara-Silva

    2017-03-01

    Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

  20. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

    Directory of Open Access Journals (Sweden)

    Barabási Albert-László

    2004-01-01

    Full Text Available Abstract Background Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs. However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.

  1. dSPACE based adaptive neuro-fuzzy controller of grid interactive inverter

    International Nuclear Information System (INIS)

    Altin, Necmi; Sefa, İbrahim

    2012-01-01

    Highlights: ► We propose a dSPACE based neuro-fuzzy controlled grid interactive inverter. ► The membership functions and rule base of fuzzy logic controller by using ANFIS. ► A LCL output filter is designed. ► A high performance controller is designed. - Abstract: In this study, design, simulation and implementation of a dSPACE based grid interactive voltage source inverter are proposed. This inverter has adaptive neuro-fuzzy controller and capable of importing electrical energy, generated from renewable energy sources such as the wind, the solar and the fuel cells to the grid. A line frequency transformer and a LCL filter are used at the output of the grid interactive inverter which is designed as current controlled to decrease the susceptibility to phase errors. Membership functions and rule base of the fuzzy logic controller, which control the inverter output current, are determined by using artificial neural networks. Both simulation and experimental results show that, the grid interactive inverter operates synchronously with the grid. The inverter output current which is imported to the grid is in sinusoidal waveform and the harmonic level of it meets the international standards (4.3 < 5.0%). In addition, simulation and experimental results of the neuro-fuzzy and the PI controlled inverter are given together and compared in detail. Simulation and experimental results show that the proposed inverter has faster response to the reference variations and lower steady state error than PI controller.

  2. Three-level grid-connected photovoltaic inverter with maximum power point tracking

    International Nuclear Information System (INIS)

    Tsang, K.M.; Chan, W.L.

    2013-01-01

    Highlight: ► This paper reports a novel 3-level grid connected photovoltaic inverter. ► The inverter features maximum power point tracking and grid current shaping. ► The inverter can be acted as an active filter and a renewable power source. - Abstract: This paper presents a systematic way of designing control scheme for a grid-connected photovoltaic (PV) inverter featuring maximum power point tracking (MPPT) and grid current shaping. Unlike conventional design, only four power switches are required to achieve three output levels and it is not necessary to use any phase-locked-loop circuitry. For the proposed scheme, a simple integral controller has been designed for the tracking of the maximum power point of a PV array based on an improved extremum seeking control method. For the grid-connected inverter, a current loop controller and a voltage loop controller have been designed. The current loop controller is designed to shape the inverter output current while the voltage loop controller can maintain the capacitor voltage at a certain level and provide a reference inverter output current for the PV inverter without affecting the maximum power point of the PV array. Experimental results are included to demonstrate the effectiveness of the tracking and control scheme.

  3. Simulation and Study of Multilevel Inverter System Fed By Photovoltaic Source

    Directory of Open Access Journals (Sweden)

    Ali Abdulrazzak Jasim

    2018-01-01

    Full Text Available This paper proposes a simulation of Photovoltaic energy used to supply an induction motor with acomparison of two types of inverters.In general, the greater number of motorswhich"are used incommercial and industrial applicationsare"induction motors. To use PV source to run the induction motor, an interface circuits are used which are a dc-dc"converter and an inverter, the PV cell has nonlinear behavior,"adc-dc converter is used along with Maximum Power Point Tracker controllerto improve theefficiency by boosting the output voltage of the PV module and to match the load demand."The dc output voltage of PV modulethen"converted to AC, two types of inverter are presented, A conventional Voltage Source Inverter system and multilevel inverter system which employselective harmonic eliminationmethod fed three phase induction motor, these two types of inverters are simulated using Matlab/Simulink and their results are presented. The FFT spectrum is presented of the output currents to analyze the harmonics reduction, which shows that the"multilevel inverter is better than VSI system"according to harmonics reduction and increment in output voltage and power.

  4. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  5. Dual Z-Source Inverter With Three-Level Reduced Common-Mode Switching

    DEFF Research Database (Denmark)

    Gao, Feng; Loh, Poh Chiang; Blaabjerg, Frede

    2007-01-01

    This paper presents the design of a dual Z-source inverter that can be used with either a single dc source or two isolated dc sources. Unlike traditional inverters, the integration of a properly designed Z-source network and semiconductor switches to the proposed dual inverter allows buck......-boost power conversion to be performed over a wide modulation range, with three-level output waveforms generated. The connection of an additional transformer to the inverter ac output also allows all generic wye-or delta-connected loads with three-wire or four-wire configuration to be supplied by the inverter....... Modulationwise, the dual inverter can be controlled using a carefully designed carrier-based pulsewidth-modulation (PWM) scheme that will always ensure balanced voltage boosting of the Z-source network while simultaneously achieving reduced common-mode switching. Because of the omission of dead-time delays...

  6. MODA: an efficient algorithm for network motif discovery in biological networks.

    Science.gov (United States)

    Omidi, Saeed; Schreiber, Falk; Masoudi-Nejad, Ali

    2009-10-01

    In recent years, interest has been growing in the study of complex networks. Since Erdös and Rényi (1960) proposed their random graph model about 50 years ago, many researchers have investigated and shaped this field. Many indicators have been proposed to assess the global features of networks. Recently, an active research area has developed in studying local features named motifs as the building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding rather large motifs (larger than 8 nodes) by means of current algorithms is impractical as it demands too much computational effort. In this paper, we present a new algorithm (MODA) that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. We have tested our algorithm and found it able to identify larger motifs with more than 8 nodes more efficiently than most of the current state-of-the-art motif discovery algorithms. While most of the algorithms rely on induced subgraphs as motifs of the networks, MODA is able to extract both induced and non-induced subgraphs simultaneously. The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/

  7. Smart Inverter Control and Operation for Distributed Energy Resources

    Science.gov (United States)

    Tazay, Ahmad F.

    The motivation of this research is to carry out the control and operation of smart inverters and voltage source converters (VSC) for distributed energy resources (DERs) such as photovoltaic (PV), battery, and plug-in hybrid electric vehicles (PHEV). The main contribution of the research includes solving a couple of issues for smart grids by controlling and implementing multifunctions of VSC and smart inverter as well as improving the operational scheme of the microgrid. The work is mainly focused on controlling and operating of smart inverter since it promises a new technology for the future microgrid. Two major applications of the smart inverter will be investigated in this work based on the connection modes: microgrid at grid-tied mode and autonomous mode. In grid-tied connection, the smart inverter and VSC are used to integrate DER such as Photovoltaic (PV) and battery to provide suitable power to the system by controlling the supplied real and reactive power. The role of a smart inverter at autonomous mode includes supplying a sufficient voltage and frequency, mitigate abnormal condition of the load as well as equally sharing the total load's power. However, the operational control of the microgrid still has a major issue on the operation of the microgrid. The dissertation is divided into two main sections which are: 1. Low-level control of a single smart Inverter. 2. High-level control of the microgrid. The first part investigates a comprehensive research for a smart inverter and VSC technology at the two major connections of the microgrid. This involves controlling and modeling single smart inverter and VSC to solve specific issues of microgrid as well as improve the operation of the system. The research provides developed features for smart inverter comparing with a conventional voltage sourced converter (VSC). The two main connections for a microgrid have been deeply investigated to analyze a better way to develop and improve the operational procedure of

  8. MODELLING AND SIMULATION OF HIGH FREQUENCY INVERTER FOR INDUCTION HEATING APPLICATION

    OpenAIRE

    SACHIN S. BANKAR; Dr. PRASAD M. JOSHI

    2016-01-01

    This paper presents modelling and simulation of high frequency inverter for induction heating applications. Induction heating has advantages like higher efficiency, controlled heating, safety and pollution free therefore this technology is used in industrial, domestic and medical applications. The high frequency full bridge inverter is used for induction heating, also MOSFET is used as a switching device for inverter and the control strategy used for inverter is Bipolar PWM control. The size ...

  9. Reduced-Order Structure-Preserving Model for Parallel-Connected Three-Phase Grid-Tied Inverters

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Brian B [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Purba, Victor [University of Minnesota; Jafarpour, Saber [University of California Santa-Barbara; Bullo, Francesco [University of California Santa-Barbara; Dhople, Sairaj V. [University of Minnesota

    2017-08-21

    Next-generation power networks will contain large numbers of grid-connected inverters satisfying a significant fraction of system load. Since each inverter model has a relatively large number of dynamic states, it is impractical to analyze complex system models where the full dynamics of each inverter are retained. To address this challenge, we derive a reduced-order structure-preserving model for parallel-connected grid-tied three-phase inverters. Here, each inverter in the system is assumed to have a full-bridge topology, LCL filter at the point of common coupling, and the control architecture for each inverter includes a current controller, a power controller, and a phase-locked loop for grid synchronization. We outline a structure-preserving reduced-order inverter model with lumped parameters for the setting where the parallel inverters are each designed such that the filter components and controller gains scale linearly with the power rating. By structure preserving, we mean that the reduced-order three-phase inverter model is also composed of an LCL filter, a power controller, current controller, and PLL. We show that the system of parallel inverters can be modeled exactly as one aggregated inverter unit and this equivalent model has the same number of dynamical states as any individual inverter in the system. Numerical simulations validate the reduced-order model.

  10. Frequency patterns of T-cell exposed motifs in immunoglobulin heavy chain peptides presented by MHCs

    Directory of Open Access Journals (Sweden)

    Robert D. Bremel

    2014-10-01

    Full Text Available Immunoglobulins are highly diverse protein sequences that are processed and presented to T-cells by B-cells and other antigen presenting cells. We examined a large dataset of immunoglobulin heavy chain variable regions (IGHV to assess the diversity of T-cell exposed motifs (TCEM. TCEM comprise those amino acids in a MHC-bound peptide which face outwards, surrounded by the MHC histotope, and which engage the T-cell receptor. Within IGHV there is a distinct pattern of predicted MHC class II binding and a very high frequency of re-use of the TCEMs. The re-use frequency indicates that only a limited number of different cognate T-cells are required to engage many different clonal B-cells. The amino acids in each outward-facing TCEM are intercalated with the amino acids of inward-facing MHC groove-exposed motifs (GEM. Different GEM may have differing, allele-specific, MHC binding affinities. The intercalation of TCEM and GEM in a peptide allows for a vast combinatorial repertoire of epitopes, each eliciting a different response. Outcome of T-cell receptor binding is determined by overall signal strength, which is a function of the number of responding T-cells and the duration of engagement. Hence, the frequency of T-cell exposed motif re-use appears to be an important determinant of whether a T-cell response is stimulatory or suppressive. The frequency distribution of TCEMs implies that somatic hypermutation is followed by clonal expansion that develop along repeated pathways. The observations of TCEM and GEM derived from immunoglobulins suggest a relatively simple, yet powerful, mechanism to correlate T-cell polyspecificity, through re-use of TCEMs, with a very high degree of specificity achieved by combination with a diversity of GEMs. The frequency profile of TCEMs also points to an economical mechanism for maintaining T-cell memory, recall, and self-discrimination based on an endogenously generated profile of motifs.

  11. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  12. A New Green Power Inverter for Fuel Cells

    DEFF Research Database (Denmark)

    Andersen, Gert Karmisholt; Klumpner, Christian; Kjær, Søren Bækhøj

    2002-01-01

    This paper presents a new grid connected inverter for fuel cells. It consists of a two stage power conversion topology. Since the fuel cell operates with a low voltage in a wide voltage range (25 V-45 V) this volt- age must be transformed to around 350-400 V in order to invert this dc power into ac...... power to the grid. The proposed converter consists of an isolated dc-dc converter cascaded with a single phase H-bridge inverter. The dc-dc converter is a current-fed push-pull converter. A new dedicated voltage mode startup procedure has been developed in order to limit the inrush current during...... startup. The inverter is controlled as a power factor controller with resistor emulation.Experimental results of converter efficiency, grid performance and fuel cell response are shown for a 1 kW prototype. The proposed converter exhibits a high efficiency in a wide power range (higher than 92...

  13. Control Aspects of a LCL Grid-Connected Green Power Inverter

    DEFF Research Database (Denmark)

    Kjær, Søren Bækhøj; Andersen, Gert Karmisholt; Klumpner, Christian

    2002-01-01

    A full-bridge inverter for interfacing the utility grid is developed for using in a Green Power Inverter application. The inverter is feed from an arbitrary green power source (fuel cell, photovoltaic, small wind turbine etc.) through a rectifier into the dc-link. In order to maintain a sinusoidal...... grid current with low harmonic distortion and a high power factor, the inverter is controlled to emulate a negative resistance towards the grid. The size of the emulated resistor is determined by the dc-link voltage controller, which tries to maintain a constant dc-link voltage. This is however...

  14. Distributed Storage Inverter and Legacy Generator Integration Plus Renewable Solution for Microgrids

    Science.gov (United States)

    2015-07-01

    Observation ................. 5 2.1.5 PV Inverter with Microgrid Controls .......................................................... 5 2.2 TECHNOLOGY... CONTROL OF PV POWER RAMP RATE FOR GENERATOR STABILITY ..................... 27 6.11 DEMONSTRATION 11: MICROGRID VOLTAGE SUPPORT FROM PV INVERTER...power delivery optimized storage, transiently rated inverters, integration with legacy generator controls , and microgrid compatible inverters for PV

  15. Optimal design of NPC and Active-NPC transformerless PV inverters

    DEFF Research Database (Denmark)

    Saridakis, Stefanos; Koutroulis, Eftichios; Blaabjerg, Frede

    2012-01-01

    Targeting at a cost-effective deployment of grid-connected PhotoVoltaic (PV) systems, this paper presents a new methodology for the optimal design of transformerless PV inverters, which are based on the Neutral Point Clamped (NPC) and the Active-Neutral Point Clamped (ANPC) topologies. The design...... optimization results demonstrate that a different set of optimal values of the PV inverter switching frequency and output filter components are derived for the NPC and ANPC topologies, respectively, as well as for each of the PV inverter installation sites under study. The NPC and ANPC PV inverter structures......, which are derived using the proposed design optimization methodology exhibit lower Levelized Cost Of generated Electricity (LCOE) and manufacturing cost and they are simultaneously capable to inject more energy into the electric grid than the corresponding non-optimized PV inverters. Thus, the proposed...

  16. Coupled-Inductor-Based Aalborg Inverter With Input DC Energy Regulation

    DEFF Research Database (Denmark)

    Wang, Houqing; Wu, Weimin; Chung, Henry Shu-hung

    2018-01-01

    Due to the global environmental issues and energy crisis, the injection of renewable energy sources (RESs) into the power system is continuously increasing. As the interface between RESs and power grid, grid-tied inverters using MOSFET switches, without traditional line frequency transformers, show...... some potential advantages, in terms of low cost, high efficiency, and lightweight and small size. Among several proposed configurations, the Aalborg inverter was proposed as a new family of high efficiency MOSFET-switch-based hybrid source inverters. For a conventional “half bridge” type Aalborg...... inverter, due to the imbalance of two independent dc sources, the input dc energies may not be fully utilized, which may reduce the efficiency of whole system. In order to extract the maximum energy from two independent dc sources, a coupled-inductor-based “half bridge” type Aalborg inverter is proposed...

  17. Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

    Science.gov (United States)

    Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

    2017-11-01

    Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  18. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

    Science.gov (United States)

    Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

    2011-01-01

    PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

  19. Fully patterned and low temperature transparent ZnO-based inverters

    Energy Technology Data Exchange (ETDEWEB)

    Gutierrez-Heredia, G. [Centro de Investigación en Materiales Avanzados, Unidad Monterrey, México (Mexico); Department of Materials Science and Engineering, University of Texas at Dallas (United States); Mejia, I.; Rivas-Aguilar, M.E.; Hernandez-Como, N. [Department of Materials Science and Engineering, University of Texas at Dallas (United States); Martinez-Landeros, V.H. [Centro de Investigación en Materiales Avanzados, Unidad Monterrey, México (Mexico); Department of Materials Science and Engineering, University of Texas at Dallas (United States); Aguirre-Tostado, F.S. [Centro de Investigación en Materiales Avanzados, Unidad Monterrey, México (Mexico); Quevedo-Lopez, M.A., E-mail: mquevedo@utdallas.edu [Department of Materials Science and Engineering, University of Texas at Dallas (United States)

    2013-10-31

    The fabrication and characterization of transparent logic inverters based on zinc oxide (ZnO) thin film transistors (TFTs) is reported. The inverters are fabricated using standard photolithographic techniques on glass substrates, and the entire fabrication process temperature is maintained < 100 °C, which render the devices suitable for flexible and transparent electronics applications. Pulsed laser deposition is used to deposit aluminum-doped zinc oxide and ZnO as electrode and active semiconductor materials, respectively. Electrical characterization for individual TFTs demonstrate mobilities of ∼ 10 cm{sup 2}/V-s, threshold voltages of 6 V, sub-threshold slopes of 630 mV/decade and I{sub ON}/I{sub OFF} ratios of 5 × 10{sup 6}. Films characterized by UV-Vis showed optical transmission > 80% in the visible spectrum. The inverters are analyzed with AC input signals at frequencies of 100 and 500 Hz. The AC response shows an average rise and fall time transitions of 0.65 and 0.44 ms, respectively. Measured inverters delay is in the order of 0.21 ms. - Highlights: • Logic inverters based on zinc oxide thin film transistors. • Inverters fabricated using temperatures below 100 °C and standard photolithography. • Transparent aluminum-doped zinc oxide as gate, drain and source electrodes. • Devices with total transmittance in the visible range above 80%. • AC inverter response up to 500 Hz.

  20. Fully patterned and low temperature transparent ZnO-based inverters

    International Nuclear Information System (INIS)

    Gutierrez-Heredia, G.; Mejia, I.; Rivas-Aguilar, M.E.; Hernandez-Como, N.; Martinez-Landeros, V.H.; Aguirre-Tostado, F.S.; Quevedo-Lopez, M.A.

    2013-01-01

    The fabrication and characterization of transparent logic inverters based on zinc oxide (ZnO) thin film transistors (TFTs) is reported. The inverters are fabricated using standard photolithographic techniques on glass substrates, and the entire fabrication process temperature is maintained < 100 °C, which render the devices suitable for flexible and transparent electronics applications. Pulsed laser deposition is used to deposit aluminum-doped zinc oxide and ZnO as electrode and active semiconductor materials, respectively. Electrical characterization for individual TFTs demonstrate mobilities of ∼ 10 cm 2 /V-s, threshold voltages of 6 V, sub-threshold slopes of 630 mV/decade and I ON /I OFF ratios of 5 × 10 6 . Films characterized by UV-Vis showed optical transmission > 80% in the visible spectrum. The inverters are analyzed with AC input signals at frequencies of 100 and 500 Hz. The AC response shows an average rise and fall time transitions of 0.65 and 0.44 ms, respectively. Measured inverters delay is in the order of 0.21 ms. - Highlights: • Logic inverters based on zinc oxide thin film transistors. • Inverters fabricated using temperatures below 100 °C and standard photolithography. • Transparent aluminum-doped zinc oxide as gate, drain and source electrodes. • Devices with total transmittance in the visible range above 80%. • AC inverter response up to 500 Hz

  1. Potentials and limitations of histone repeat sequences for phylogenetic reconstruction of Sophophora.

    Science.gov (United States)

    Baldo, A M; Les, D H; Strausbaugh, L D

    1999-11-01

    Simplified DNA sequence acquisition has provided many new data sets that are useful for phylogenetic reconstruction, including single- and multiple-copy nuclear and organellar genes. Although transcribed regions receive much attention, nontranscribed regions have recently been added to the repertoire of sequences suitable for phylogenetic studies, especially for closely related taxa. We evaluated the efficacy of a small portion of the histone repeat for phylogenetic reconstruction among Drosophila species. Histone repeats in invertebrates offer distinct advantages similar to those of widely used ribosomal repeats. First, the units are tandemly repeated and undergo concerted evolution. Second, histone repeats include both highly conserved coding and variable intergenic regions. This composition facilitates application of "universal" primers spanning potentially informative sites. We examined a small region of the histone repeat, including the intergenic spacer segments of coding regions from the divergently transcribed H2A and H2B histone genes. The spacer (about 230 bp) exists as a mosaic with highly conserved functional motifs interspersed with rapidly diverging regions; the former aid in alignment of the spacer. There are no ambiguities in alignment of coding regions. Coding and noncoding regions were analyzed together and separately for phylogenetic information. Parsimony, distance, and maximum-likelihood methods successfully retrieve the corroborated phylogeny for the taxa examined. This study demonstrates the resolving power of a small histone region which may now be added to the growing collection of phylogenetically useful DNA sequences.

  2. Novel T-Z source inverter with high voltage gain and reduced transformer turn ratio

    DEFF Research Database (Denmark)

    Mostaan, Ali; Sharifi Malfejani, Saeed; Soltani, Mohsen

    2015-01-01

    Novel voltage source inverter based on the Z source inverter structure is introduced in this paper. In this new inverter, two inductors of the impedance network in conventional Z source inverter are replaced with two transformers or coupled inductors, but unlike the T-Z source inverter that it......'s voltage gain is raised with increasing the transformers turn ratio, the voltage gain in the proposed inverter is raised with lowering the transformer turn ratio. Therefore, transformers with lower turn ratio are required in the proposed inverter in compare with T- Z source inverter that can lead to lower...

  3. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

    Directory of Open Access Journals (Sweden)

    Natalie L. Dillon

    2014-01-01

    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  4. Inverter ratio failure detector

    Science.gov (United States)

    Wagner, A. P.; Ebersole, T. J.; Andrews, R. E. (Inventor)

    1974-01-01

    A failure detector which detects the failure of a dc to ac inverter is disclosed. The inverter under failureless conditions is characterized by a known linear relationship of its input and output voltages and by a known linear relationship of its input and output currents. The detector includes circuitry which is responsive to the detector's input and output voltages and which provides a failure-indicating signal only when the monitored output voltage is less by a selected factor, than the expected output voltage for the monitored input voltage, based on the known voltages' relationship. Similarly, the detector includes circuitry which is responsive to the input and output currents and provides a failure-indicating signal only when the input current exceeds by a selected factor the expected input current for the monitored output current based on the known currents' relationship.

  5. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  6. Stochastic p -Bits for Invertible Logic

    Science.gov (United States)

    Camsari, Kerem Yunus; Faria, Rafatul; Sutton, Brian M.; Datta, Supriyo

    2017-07-01

    Conventional semiconductor-based logic and nanomagnet-based memory devices are built out of stable, deterministic units such as standard metal-oxide semiconductor transistors, or nanomagnets with energy barriers in excess of ≈40 - 60 kT . In this paper, we show that unstable, stochastic units, which we call "p -bits," can be interconnected to create robust correlations that implement precise Boolean functions with impressive accuracy, comparable to standard digital circuits. At the same time, they are invertible, a unique property that is absent in standard digital circuits. When operated in the direct mode, the input is clamped, and the network provides the correct output. In the inverted mode, the output is clamped, and the network fluctuates among all possible inputs that are consistent with that output. First, we present a detailed implementation of an invertible gate to bring out the key role of a single three-terminal transistorlike building block to enable the construction of correlated p -bit networks. The results for this specific, CMOS-assisted nanomagnet-based hardware implementation agree well with those from a universal model for p -bits, showing that p -bits need not be magnet based: any three-terminal tunable random bit generator should be suitable. We present a general algorithm for designing a Boltzmann machine (BM) with a symmetric connection matrix [J ] (Ji j=Jj i) that implements a given truth table with p -bits. The [J ] matrices are relatively sparse with a few unique weights for convenient hardware implementation. We then show how BM full adders can be interconnected in a partially directed manner (Ji j≠Jj i) to implement large logic operations such as 32-bit binary addition. Hundreds of stochastic p -bits get precisely correlated such that the correct answer out of 233 (≈8 ×1 09) possibilities can be extracted by looking at the statistical mode or majority vote of a number of time samples. With perfect directivity (Jj i=0 ) a small

  7. Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

    Science.gov (United States)

    Spielmann, A; Stutz, E

    1983-10-25

    The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2.

  8. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  9. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2010-09-01

    Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

  10. Integration of Xantrex HY-100 Hybrid Inverter with an AC Induction Wind Turbine

    Energy Technology Data Exchange (ETDEWEB)

    Corbus, D.; Newcomb, C.; Friedly, S.

    2003-05-01

    Several issues must be addressed before solid-state inverters can be used in wind-diesel systems with larger wind turbines. This project addresses those issues by using a commercial hybrid inverter designed for PV-diesel systems and modifying the inverter for use with an AC induction wind turbine. Another approach would have entailed building an inverter specifically for use with an AC induction wind turbine, but that was beyond the scope of this project. The inverter chosen for this project was a Xantrex HY-100, an inverter designed for PV systems. The unit consists of an inverter/rectifier bridge, a generator interface contactor, a battery charge controller, a hybrid controller, and the associated control electronics. Details of the inverter may be found in Appendix A. A twofold approach was taken to integrating the existing inverter for use with an AC induction wind turbine: 1) development of a detailed model to model both steady-state and transient behavior of the system, and 2) modification and testing of the inverter with an induction wind turbine based on the modeling results. This report describes these two tasks.

  11. Several tetratricopeptide repeat (TPR) motifs of FANCG are required for assembly of the BRCA2/D1-D2-G-X3 complex, FANCD2 monoubiquitylation and phleomycin resistance

    International Nuclear Information System (INIS)

    Wilson, James B.; Blom, Eric; Cunningham, Ryan; Xiao, Yuxuan; Kupfer, Gary M.; Jones, Nigel J.

    2010-01-01

    The Fanconi anaemia (FA) FANCG protein is an integral component of the FA nuclear core complex that is required for monoubiquitylation of FANCD2. FANCG is also part of another protein complex termed D1-D2-G-X3 that contains FANCD2 and the homologous recombination repair proteins BRCA2 (FANCD1) and XRCC3. Formation of the D1-D2-G-X3 complex is mediated by serine-7 phosphorylation of FANCG and occurs independently of the FA core complex and FANCD2 monoubiquitylation. FANCG contains seven tetratricopeptide repeat (TPR) motifs that mediate protein-protein interactions and here we show that mutation of several of the TPR motifs at a conserved consensus residue ablates the in vivo binding activity of FANCG. Expression of mutated TPR1, TPR2, TPR5 and TPR6 in Chinese hamster fancg mutant NM3 fails to functionally complement its hypersensitivities to mitomycin C (MMC) and phleomycin and fails to restore FANCD2 monoubiquitylation. Using co-immunoprecipitation analysis, we demonstrate that these TPR-mutated FANCG proteins fail to interact with BRCA2, XRCC3, FANCA or FANCF. The interactions of other proteins in the D1-D2-G-X3 complex are also absent, including the interaction of BRCA2 with both the monoubiquitylated (FANCD2-L) and non-ubiquitylated (FANCD2-S) isoforms of FANCD2. Interestingly, a mutation of TPR7 (R563E), that complements the MMC and phleomycin hypersensitivity of human FA-G EUFA316 cells, fails to complement NM3, despite the mutated FANCG protein co-precipitating with FANCA, BRCA2 and XRCC3. Whilst interaction of TPR7-mutated FANCG with FANCF does appear to be reduced in NM3, FANCD2 is monoubiquitylated suggesting that sub-optimal interactions of FANCG in the core complex and the D1-D2-G-X3 complex are responsible for the observed MMC- and phleomycin-hypersensitivity, rather than a defect in FANCD2 monoubiquitylation. Our data demonstrate that FANCG functions as a mediator of protein-protein interactions and is vital for the assembly of multi-protein complexes

  12. Several tetratricopeptide repeat (TPR) motifs of FANCG are required for assembly of the BRCA2/D1-D2-G-X3 complex, FANCD2 monoubiquitylation and phleomycin resistance

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, James B. [Molecular Oncology and Stem Cell Research Group, School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB (United Kingdom); Blom, Eric [Department of Clinical Genetics and Human Genetics, VU University Medical Center, Van der Boechorststraat 7, NL-1081 BT Amsterdam (Netherlands); Cunningham, Ryan; Xiao, Yuxuan [Molecular Oncology and Stem Cell Research Group, School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB (United Kingdom); Kupfer, Gary M. [Departments of Pediatrics and Pathology, Yale University School of Medicine, Section of Hematology/Oncology, 333 Cedar Street, New Haven, CT 0652 (United States); Jones, Nigel J., E-mail: njjones@liv.ac.uk [Molecular Oncology and Stem Cell Research Group, School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB (United Kingdom)

    2010-07-07

    The Fanconi anaemia (FA) FANCG protein is an integral component of the FA nuclear core complex that is required for monoubiquitylation of FANCD2. FANCG is also part of another protein complex termed D1-D2-G-X3 that contains FANCD2 and the homologous recombination repair proteins BRCA2 (FANCD1) and XRCC3. Formation of the D1-D2-G-X3 complex is mediated by serine-7 phosphorylation of FANCG and occurs independently of the FA core complex and FANCD2 monoubiquitylation. FANCG contains seven tetratricopeptide repeat (TPR) motifs that mediate protein-protein interactions and here we show that mutation of several of the TPR motifs at a conserved consensus residue ablates the in vivo binding activity of FANCG. Expression of mutated TPR1, TPR2, TPR5 and TPR6 in Chinese hamster fancg mutant NM3 fails to functionally complement its hypersensitivities to mitomycin C (MMC) and phleomycin and fails to restore FANCD2 monoubiquitylation. Using co-immunoprecipitation analysis, we demonstrate that these TPR-mutated FANCG proteins fail to interact with BRCA2, XRCC3, FANCA or FANCF. The interactions of other proteins in the D1-D2-G-X3 complex are also absent, including the interaction of BRCA2 with both the monoubiquitylated (FANCD2-L) and non-ubiquitylated (FANCD2-S) isoforms of FANCD2. Interestingly, a mutation of TPR7 (R563E), that complements the MMC and phleomycin hypersensitivity of human FA-G EUFA316 cells, fails to complement NM3, despite the mutated FANCG protein co-precipitating with FANCA, BRCA2 and XRCC3. Whilst interaction of TPR7-mutated FANCG with FANCF does appear to be reduced in NM3, FANCD2 is monoubiquitylated suggesting that sub-optimal interactions of FANCG in the core complex and the D1-D2-G-X3 complex are responsible for the observed MMC- and phleomycin-hypersensitivity, rather than a defect in FANCD2 monoubiquitylation. Our data demonstrate that FANCG functions as a mediator of protein-protein interactions and is vital for the assembly of multi-protein complexes

  13. Microcontroller Based SPWM Single-Phase Inverter For Wind Power Application

    Directory of Open Access Journals (Sweden)

    Khin Ohmar Lin

    2017-04-01

    Full Text Available In this paper microcontroller based sinusoidal pulse width modulation SPWM single-phase inverter is emphasized to constant frequency conversion scheme for wind power application. The wind-power generator output voltage and frequency are fluctuated due to the variation of wind velocity. Therefore the AC output voltage of wind-generator is converted into DC voltage by using rectifier circuit and this DC voltage is converted back to AC voltage by using inverter circuit. SPWM technique is used in inverter to get nearly sine wave and reduce harmonic content. The rating of inverter is 500W single-phase 220V 50 Hz. The required SPWM timing pulses for the inverter are generated from the PIC16F877A microcontroller. Circuit simulation was done by using Proteus 7 Professional and MATLABR 2008 software. The software for microcontroller is implemented by using MPASM assembler.

  14. Proposed Novel Multiphase-Multilevel Inverter Configuration for Open-End Winding Loads

    DEFF Research Database (Denmark)

    Padamanaban, Sanjeevi Kumar; Wheeler, Patrick; Blaabjerg, Frede

    2016-01-01

    This paper presents a new multiphase-multilevel inverter configuration for open-winding loads and suitable for medium power (low-voltage/high-current) applications such as `More Electric Aircraft'. Modular structure comprised of standard dual three-phase voltage source inverter (VSI) along with one...... is developed in this work and overcomes the complexity of standard space vector modulations, easy for real implementation purposes in digital processors. Proposed six-phase multilevel inverter configuration generates multilevel outputs with benefit in comprises with standard multilevel inverter topologies...

  15. Remote Control of an Inverted Pendulum System for Intelligent Control Education

    Directory of Open Access Journals (Sweden)

    Seul Jung

    2011-08-01

    Full Text Available This paper presents a remote control task of an inverted pendulum system for intelligent control education. The inverted pendulum moving on the guided rail is required to maintain balancing while it follows the desired trajectory commanded remotely by a joystick operated by a user. Position commands for the inverted pendulum system are given by a joystick through the network. The inverted pendulum system is controlled by a neural network control method. The corresponding control results are confirmed through experimental studies.

  16. Resonance Interaction of Multi-Parallel Grid-Connected Inverters with LCL Filter

    DEFF Research Database (Denmark)

    Lu, Minghui; Wang, Xiongfei; Loh, Poh Chiang

    2017-01-01

    This letter investigates the resonance characteristics and stability problem caused by the interactions of multiparallel LCL-filtered inverters. Compared to single grid-connected inverter, the multiinverter system presents a more challenging resonance issue, where the inverter interactions may...... excite multiple resonances at various frequencies. This letter proposes a modeling and analysis method based on the current separation scheme. It reveals that an interactive resonant current that circulates between the paralleled three-phase inverters may arise, depending on the current distribution...

  17. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

    Science.gov (United States)

    Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

    2017-04-01

    There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

  18. [Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

    Science.gov (United States)

    Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

    2009-11-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

  19. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

    2013-01-01

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...

  20. Vacuum arc switched inverter tests at 2.5 MVA

    International Nuclear Information System (INIS)

    Miller, R.N.; Gilmour, A.S. Jr.

    1979-01-01

    A mathematical analysis of the unloaded vacuum arc switch (VAS) inverter is undertaken; a key element in this analysis is the assumption of a constant voltage drop of 50 volts across each VAS while it is conducting. From this analysis a constant VAS-voltage model is developed to explain the VAS inverter operation. A comparison of data obtained from laboratory tests of the inverter is made with data obtained from this model, and agreement is found to be within 10% for up to 15 alternations

  1. Buck-Boost Current-Source Inverters With Diode-Inductor Network

    DEFF Research Database (Denmark)

    Gao, Feng; Liang, Chao; Loh, Poh Chiang

    2009-01-01

    This paper presents a number of novel currentsource inverters (CSIs) with enhanced current buck-boost capability. By adding a unique diode-inductor network between the inverter circuitry and current-boost elements, the proposed buck-boost CSIs demonstrate a doubling of current-boost capability......, as compared with other recently reported buck-boost CSIs. For controlling the proposed CSIs, two modulation schemes are designed for achieving either optimized harmonic performance or minimized commutation count without influencing the inverter current buck-boost gain. These theoretical findings were...

  2. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    Ahmad A. Malik

    2017-05-01

    Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

  3. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  4. Solar Power Station Output Inverter Control Design

    Directory of Open Access Journals (Sweden)

    J. Bauer

    2011-04-01

    Full Text Available The photovoltaic applications spreads in these days fast, therefore they also undergo great development. Because the amount of the energy obtained from the panel depends on the surrounding conditions, as intensity of the sun exposure or the temperature of the solar array, the converter must be connected to the panel output. The Solar system equipped with inverter can supply small loads like notebooks, mobile chargers etc. in the places where the supplying network is not present. Or the system can be used as a generator and it shall deliver energy to the supply network. Each type of the application has different requirements on the converter and its control algorithm. But for all of them the one thing is common – the maximal efficiency. The paper focuses on design and simulation of the low power inverter that acts as output part of the whole converter. In the paper the design of the control algorithm of the inverter for both types of inverter application – for islanding mode and for operation on the supply grid – is discussed. Attention is also paid to the design of the output filter that should reduce negative side effects of the converter on the supply network.

  5. Pulse width modulation inverter with battery charger

    Science.gov (United States)

    Slicker, James M.

    1985-01-01

    An inverter is connected between a source of DC power and a three-phase AC induction motor, and a microprocessor-based circuit controls the inverter using pulse width modulation techniques. In the disclosed method of pulse width modulation, both edges of each pulse of a carrier pulse train are equally modulated by a time proportional to sin .theta., where .theta. is the angular displacement of the pulse center at the motor stator frequency from a fixed reference point on the carrier waveform. The carrier waveform frequency is a multiple of the motor stator frequency. The modulated pulse train is then applied to each of the motor phase inputs with respective phase shifts of 120.degree. at the stator frequency. Switching control commands for electronic switches in the inverter are stored in a random access memory (RAM) and the locations of the RAM are successively read out in a cyclic manner, each bit of a given RAM location controlling a respective phase input of the motor. The DC power source preferably comprises rechargeable batteries and all but one of the electronic switches in the inverter can be disabled, the remaining electronic switch being part of a "flyback" DC-DC converter circuit for recharging the battery.

  6. Crystal structure of the G3BP2 NTF2-like domain in complex with a canonical FGDF motif peptide.

    Science.gov (United States)

    Kristensen, Ole

    2015-11-06

    The crystal structure of the NTF2-like domain of the human Ras GTPase SH3 Binding Protein (G3BP), isoform 2, was determined at a resolution of 2.75 Å in complex with a peptide containing a FGDF sequence motif. The overall structure of the protein is highly similar to the homodimeric N-terminal domains of the G3BP1 and Rasputin proteins. Recently, a subset of G3BP interacting proteins was recognized to share a common sequence motif, FGDF. The most studied binding partners, USP10 and viral nsP3, interfere with essential G3BP functions related to assembly of cellular stress granules. Reported molecular modeling suggested that FGDF-motif containing peptides bind in an extended conformation into a hydrophobic groove on the surface of the G3BP NTF2-like domain in a manner similar to the known binding of FxFG nucleoporin repeats. The results in this paper provide evidence for a different binding mode. The FGDF peptide binds and changes conformation of the protruding N-terminal residues by providing hydrophobic interactions to a symmetry related molecule that facilitated crystallization of the G3BP2 isoform. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Christian J. Michel

    2017-12-01

    Full Text Available A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C 3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X , using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X , in the complete genome of the yeast Saccharomyces cerevisiae. Several properties of X motifs are identified by basic statistics (at the frequency level, and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R . We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae. We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae, but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions. This property is true for all cardinalities of X motifs (from 4 to 20 and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non- X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together

  8. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

    2017-12-03

    A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

  9. Three-phase multilevel inverter configuration for open-winding high power application

    DEFF Research Database (Denmark)

    Sanjeevikumar, Padmanaban; Blaabjerg, Frede; Wheeler, Patrick William

    2015-01-01

    This paper work exploits a new dual open-winding three-phase multilevel inverter configuration suitable for high power medium-voltage applications. Modular structure comprised of standard three-phase voltage source inverter (VSI) along with one additional bi-directional semiconductor device (MOSFET...... for implementation purpose. Proposed dual-inverter configuration generates multilevel outputs with benefit includes reduced THD and dv/dt in comparison to other dual-inverter topologies. Complete model of the multilevel ac drive is developed with simple MSCFM modulation in Matlab/PLECs numerical software...

  10. Design and Implementation of 13 Levels Multilevel Inverter for Photovoltaic System

    Science.gov (United States)

    Subramani, C.; Dhineshkumar, K.; Palanivel, P.

    2018-04-01

    This paper approaches the appearing and modernization of S-Type PV based 13- level multilevel inverter with less quantity of switch. The current S-Type Multi level inverter contains more number of switches and voltage sources. Multilevel level inverter is a be understandable among the most gainful power converters for high power application and present day applications with reduced switches. The fundamental good arrangement of the 13-level multilevel inverter is to get ventured voltage from a couple of levels of DC voltages.. The controller gives actual way day and age to switches through driver circuit using PWM methodology. The execution assessment of proposed multilevel inverter is checked using MATLAB/Simulink. This is the outstanding among other techniquem appeared differently in relation to all other existing system

  11. Module Embedded Micro-inverter Smart Grid Ready Residential Solar Electric System

    Energy Technology Data Exchange (ETDEWEB)

    Agamy, Mohammed [GE Global Research Center, Niskayuna, NY (United States)

    2015-10-27

    The “Module Embedded Micro-inverter Smart Grid Ready Residential Solar Electric System” program is focused on developing innovative concepts for residential photovoltaic (PV) systems with the following objectives: to create an Innovative micro-inverter topology that reduces the cost from the best in class micro-inverter and provides high efficiency (>96% CEC - California Energy Commission), and 25+ year warranty, as well as reactive power support; integrate micro-inverter and PV module to reduce system price by at least $0.25/W through a) accentuating dual use of the module metal frame as a large area heat spreader reducing operating temperature, and b) eliminating redundant wiring and connectors; and create micro-inverter controller handles smart grid and safety functions to simplify implementation and reduce cost.

  12. Solar-Based Boost Differential Single Phase Inverter | Eya | Nigerian ...

    African Journals Online (AJOL)

    Solar-Based Boost Differential Single Phase Inverter. ... Solar-based boost differential inverter is reduced down to 22.37% in closed loop system with the aid of Proportional –integral-Differential (PID) ... The dc power source is photovoltaic cell.

  13. Simulation of push-pull inverter using wide bandgap devices

    Science.gov (United States)

    Al-badri, Mustafa; Matin, Mohammed A.

    2016-09-01

    This paper discusses the use of wide bandgap devices (SiC-MOSFET) in the design of a push-pull inverter which provides inexpensive low power dc-ac inverters. The parameters used were 1200V SiC MOSFET(C2M0040120D) made by power company ROHM. This modeling was created using parameters that were provided from a device datasheet. The spice model is provided by this company to study the effect of adding this component on push-pull inverter ordinary circuit and compared results between SiC MOSFET and silicon MOSFET (IRFP260M). The results focused on Vout and Vmos stability as well as on output power and MOSFET power loss because it is a very crucial aspect on DC-AC inverter design. These results are done using the National Instrument simulation program (Multisim 14). It was found that power loss is better in the 12 and 15 vdc inverter. The Vout in the SIC MOSFET circuit shows more stability in the high current low resistance load in comparison to the Silicon MOSFET circuit and this will improve the overall performance of the circuit.

  14. Tri-State Current Source Inverter With Improved Dynamic Performance

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Loh, Poh Chiang; Wong, Chow Pang

    2008-01-01

    Traditional dc-ac current source inverter (CSI) has a right-half-plane (RHP) zero in its control-to-output transfer function. This RHP zero causes the inverter output to fall before rising when a step increase in command reference is required (commonly known as non-minimum-phase effect). To achieve...... a better dynamic response, this paper proposes the design of a tri-state CSI using only an additional semiconductor switch for introducing unique freewheeling states to the traditional six active and three null states of a CSI. With the freewheeling states inserted appropriately within the inverter state...... sequence, the inductive boosting and discharging intervals can be decoupled, allowing the RHP zero to be eliminated with only minor circuit modifications (high level control schemes like predictive and multiloop voltage/current control remain unchanged). The designed inverter can be controlled using...

  15. Performance analysis of samarium cobalt P.M. synchronous motor fed from PWM inverters

    International Nuclear Information System (INIS)

    Rahman, M.A.; Choudhury, M.A.

    1985-01-01

    This paper presents an analysis and performance of samarium cobalt permanent magnet (P.M.) synchronous motors fed from two types of voltage source pulse width modulated (PWM) inverters. The analysis and test results on the steady state performance of a P.M. motor fed from PWM inverters are presented. PWM inverters are used in variable voltage variable frequency applications to avoid a double conversion process of ordinary inverters. In drives, they are used for voltage and speed regulation of motors. Use of modulation technique in inverters also allow to eliminate or minimize selected harmonics from the inverter output voltage

  16. Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

    Directory of Open Access Journals (Sweden)

    Nils E. R. Zimmermann

    2017-11-01

    Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  17. Etiological role of human papillomavirus infection for inverted papilloma of the bladder.

    Science.gov (United States)

    Shigehara, Kazuyoshi; Sasagawa, Toshiyuki; Doorbar, John; Kawaguchi, Shohei; Kobori, Yoshitomo; Nakashima, Takao; Shimamura, Masayoshi; Maeda, Yuji; Miyagi, Tohru; Kitagawa, Yasuhide; Kadono, Yoshifumi; Konaka, Hiroyuki; Mizokami, Atsushi; Koh, Eitetsu; Namiki, Mikio

    2011-02-01

    The status of human papillomavirus (HPV) infection in urothelial inverted papilloma was examined in the present study. Formalin-fixed and paraffin-embedded tissues from eight cases of inverted papilloma of the bladder were studied. The presence of HPV-DNA was examined by modified GP5/6+PCR using archival tissue sections by microdissection. HPV genotype was determined with a Hybri-Max HPV genotyping kit. Immunohistochemical analysis for p16-INK4a, mcm7, HPV-E4, and L1, and in situ hybridization for the HPV genome were performed. HPV was detected in seven of eight cases (87.5%) of inverted papilloma. Three cases were diagnosed as inverted papilloma with atypia, while the remaining five were typical cases. HPV-18 was detected in two cases, including one inverted papilloma with atypia, and HPV-16 was detected in four cases, including one inverted papilloma with atypia. Multiple HPV type infection was detected in one typical case and one atypical case. High-risk HPV was present in all HPV-positive cases. Cellular proteins, p16-INK4a and mcm7, which are surrogate markers for HPV-E7 expression, were detected in all HPV-positive cases, and their levels were higher in inverted papilloma with atypia than in typical cases. In contrast, HPV-E4 and L1, which are markers for HPV propagation, were observed in some parts of the typical inverted papilloma tissue. High-risk HPV infection may be one of the causes of urothelial inverted papilloma, and inverted papilloma with atypia may have malignant potential. 2010 Wiley-Liss, Inc.

  18. High-speed elevators controlled by inverters

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, Yoshio; Takahashi, Hideaki; Nakamura, Kiyoshi; Kinoshita, Hiroshi

    1988-10-25

    The super-high-speed elevator with superiority to 300m/min of speed, requires both the large capacity power and wide range speed controls. Therefore, in order to materialize the smooth and quiet operation characteristics, by applying the inverter control, the low torque ripple control in the low frequency range and high frequency large capacity inverting for lowering the motor in noise are necessary with their being assured of reliability. To satisfy the above necessary items, together with the development of a sine wave pulse width and frequency modulation (PWM/PFM) control system, to more precisely enable the sine wave electric current control, and 3kHz switching power converter, using a 800A power transistor module, a supervoltage control circuit under the extraordinary condition was designed. As a result of commercializing a 360m/min super-high speed inverter elevator, the power source unit, due to the effect of high power factor, could be reduced by 30% in capacity and also the higher harmonic wave including ratio could be considerably lowered to the inferiority to 5%. 2 references, 7 figures, 1 table.

  19. Inverter drive of the motor for pellet chain and rotary shaft

    Energy Technology Data Exchange (ETDEWEB)

    Horie, Katsuzo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Kobayashi, Chiaki

    1996-12-01

    On renewal of driving control board for main body system of tandem accelerator of JAERI (Japan Atomic Energy Research Institute), drive of pellet chain and rotary shaft (for electric power supply to high voltage terminal and others) was changed to inverter driving. It is main aim of this change to prevent from mechanical impact at driving. Here is described on some problems seemed to form on change to inverter driving and some attentions on future adaptation of inverter to accelerator system after simply considering execution of improvement of main body driving system. As a result, the following items were found: (1) To need to confirm a character of possibility to adapt the inverter driving due to many case of accelerators fabricated with imported motor. (2) To preferably adapt motor with forced insulation or exclusive motor for the inverter, especially on case of 400 V class, to prevent insulation deterioration formed at motor terminal of serge voltage caused by circuit constant. (3) To install serge voltage control filter at secondary side of the inverter in the case of 400 V class motor, which is expected to protect the inverter from mixing of the serge accompanying with discharge of the accelerator. (4) To make the wire length of the motor from the inverter as short as possible, if possible within 30 m. And, (5) to install the converter at control panel at place easy to exchange its cooling fan and electrolytic condenser. (G.K.)

  20. Electric machine and current source inverter drive system

    Science.gov (United States)

    Hsu, John S

    2014-06-24

    A drive system includes an electric machine and a current source inverter (CSI). This integration of an electric machine and an inverter uses the machine's field excitation coil for not only flux generation in the machine but also for the CSI inductor. This integration of the two technologies, namely the U machine motor and the CSI, opens a new chapter for the component function integration instead of the traditional integration by simply placing separate machine and inverter components in the same housing. Elimination of the CSI inductor adds to the CSI volumetric reduction of the capacitors and the elimination of PMs for the motor further improve the drive system cost, weight, and volume.

  1. Stability of Brillouin flow in planar, conventional, and inverted magnetrons

    International Nuclear Information System (INIS)

    Simon, D. H.; Lau, Y. Y.; Greening, G.; Wong, P.; Gilgenbach, R. M.; Hoff, B. W.

    2015-01-01

    The Brillouin flow is the prevalent flow in crossed-field devices. We systematically study its stability in the conventional, planar, and inverted magnetron geometry. To investigate the intrinsic negative mass effect in Brillouin flow, we consider electrostatic modes in a nonrelativistic, smooth bore magnetron. We found that the Brillouin flow in the inverted magnetron is more unstable than that in a planar magnetron, which in turn is more unstable than that in the conventional magnetron. Thus, oscillations in the inverted magnetron may startup faster than the conventional magnetron. This result is consistent with simulations, and with the negative mass property in the inverted magnetron configuration. Inclusion of relativistic effects and electromagnetic effects does not qualitatively change these conclusions

  2. Understanding and managing the effects of battery charger and inverter aging

    International Nuclear Information System (INIS)

    Gunther, W.; Aggarwal, S.

    1992-01-01

    An aging assessment of battery chargers and inverters was conducted under the auspices of the NRC's Nuclear Plant Aging Research (NPAR) Program. The intentions of this program are to resolve issues related to the aging and service wear of equipment and systems at operating reactor facilities and to assess their impact on safety. Inverters and battery chargers are used in nuclear power plants to perform significant functions related to plant safety and availability. The specific impact of a battery charger or inverter failure varies with plant configuration. Operating experience data have demonstrated that reactor trips, safety injection system actuations, and inoperable emergency core cooling systems have resulted from inverter failures; and dc bus degradation leading to diesel generator inoperability or loss of control room annunication and indication have resulted from battery and battery charger failures. For the battery charger and inverter, the aging and service wear of subcomponents have contributed significantly to equipment failures. This paper summarizes the data and then describes methods that can be used to detect battery charger and inverter degradation prior to failure, as well as methods to minimize the failure effects. In both cases, the managing of battery charger and inverter aging is emphasized. 5 refs

  3. Challenging Ubiquitous Inverted Files

    NARCIS (Netherlands)

    de Vries, A.P.

    2000-01-01

    Stand-alone ranking systems based on highly optimized inverted file structures are generally considered ‘the’ solution for building search engines. Observing various developments in software and hardware, we argue however that IR research faces a complex engineering problem in the quest for more

  4. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

  5. Modeling of SVM Diode Clamping Three-Level Inverter Connected to Grid

    DEFF Research Database (Denmark)

    Guo, Yougui; Zeng, Ping; Zhu, Jieqiong

    2011-01-01

    PLECS is used to model the diode clamping three-level inverter connected to grid and good results are obtained. First the output voltage SVM is described for diode clamping three-level inverter with loads connected to Y. Then the output voltage SVM of diode clamping three-level inverter is simply...... analyzed with loads connected to △. But it will be further researched in the future. Third, PLECS is briefly introduced. Fourth, the modeling of diode clamping three-level inverter is briefly presented with PLECS. Finally, a series of simulations are carried out. The simulation results tell us PLECS...... is very powerful tool to real power circuits and it is very easy to simulate them. They have also verified that SVM control strategy is feasible to control the diode clamping three-level inverter....

  6. State-space-based harmonic stability analysis for paralleled grid-connected inverters

    DEFF Research Database (Denmark)

    Wang, Yanbo; Wang, Xiongfei; Chen, Zhe

    2016-01-01

    This paper addresses a state-space-based harmonic stability analysis of paralleled grid-connected inverters system. A small signal model of individual inverter is developed, where LCL filter, the equivalent delay of control system, and current controller are modeled. Then, the overall small signal...... model of paralleled grid-connected inverters is built. Finally, the state space-based stability analysis approach is developed to explain the harmonic resonance phenomenon. The eigenvalue traces associated with time delay and coupled grid impedance are obtained, which accounts for how the unstable...... inverter produces the harmonic resonance and leads to the instability of whole paralleled system. The proposed approach reveals the contributions of the grid impedance as well as the coupled effect on other grid-connected inverters under different grid conditions. Simulation and experimental results...

  7. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

    Directory of Open Access Journals (Sweden)

    Launey Thomas

    2011-06-01

    Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  8. Magnetically coupled impedance-source inverters

    DEFF Research Database (Denmark)

    Loh, Poh Chiang; Blaabjerg, Frede

    2012-01-01

    input-to-output gain, and the presence of an impedance network. The former means a high dc-link voltage, which can stress the semiconductor switches unnecessarily. The latter leads to increases in cost and size, which similarly are undesirable. To lessen these concerns, an interesting approach is to use...... magnetically coupled transformers or inductors to raise the gain and modulation ratio simultaneously, while reducing the number of passive components needed. A study of the approach is now presented to show how various existing magnetically coupled inverters can be derived by applying a generic methodology....... The same methodology is then applied to develop more magnetically coupled Z-source inverters with advantages that have not been identified in the literature. These findings have already been proven in experiments....

  9. Fingerprint motifs of phytases | Fan | African Journal of Biotechnology

    African Journals Online (AJOL)

    Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.

  10. Disturbance estimator based predictive current control of grid-connected inverters

    OpenAIRE

    Al-Khafaji, Ahmed Samawi Ghthwan

    2013-01-01

    ABSTRACT: The work presented in my thesis considers one of the modern discrete-time control approaches based on digital signal processing methods, that have been developed to improve the performance control of grid-connected three-phase inverters. Disturbance estimator based predictive current control of grid-connected inverters is proposed. For inverter modeling with respect to the design of current controllers, we choose the d-q synchronous reference frame to make it easier to understand an...

  11. Design Optimization of Transformerless Grid-Connected PV Inverters Including Reliability

    OpenAIRE

    Koutroulis, Eftichios; Blaabjerg, Frede

    2013-01-01

    This paper presents a new methodology for optimal design of transformerless photovoltaic (PV) inverters targeting a cost-effective deployment of grid-connected PV systems. The optimal switching frequency as well as the optimal values and types of the PV inverter components is calculated such that the PV inverter LCOE generated during the PV system lifetime period is minimized. The LCOE is also calculated considering the failure rates of the components, which affect the reliability performance...

  12. Optimized Pulse Width Modulation for transformerless active-NPC inverters

    DEFF Research Database (Denmark)

    Achilladelis, Nikolaos; Koutroulis, Eftichios; Blaabjerg, Frede

    2014-01-01

    The transformerless DC/AC inverter topologies are employed in Photovoltaic systems in order to improve the power conversion efficiency, power density and cost. The Active-Neutral Point Clamped (Active-NPC) transformerless inverters have the advantage of achieving better thermal balance among thei...

  13. Multiple degree of freedom inverted pendulum dynamics: Modeling, computation, and experimentation

    Science.gov (United States)

    Chen, Cheng-Yuan Jerry

    A pendulum is statically unstable in its upright inverted state due to the Earth's gravitational attraction which points downward. However, with proper forcing, the pendulum can be stabilized in its upright inverted state. Special interest is on periodic vertical forcing applied to the pendulum's base to stabilize it around the upright inverted equilibrium. Many researchers have studied how to stabilize the system by varying various parameters, in particular its amplitude and frequency. Most have focused on the single degree of freedom inverted pendulum case, which with linear assumption can be described via Mathieu's equation. The system stability can then be characterized by Floquet theory. Our focus is on searching for the periodic solutions inside the linearly stable region of the pendulum's inverted state when the pendulum is under proper periodic forcing. Our research shows that under appropriate excitation by controlling the forcing amplitude and frequency, the pendulum can maintain certain periodic orbits around its inverted state which we characterize in a systematic way. In this thesis, we applied four different kinds of geometric realizations of the system response: system time traces, system phase portraits, three dimensional views of the system phase portrait as a function of input forcing, and the system's power spectral density diagram. By analyzing these four diagrams simultaneously, we characterize different kinds of multi-frequency periodic behavior around the pendulum's inverted state. To further discuss the effect of the nonlinearity, we applied perturbation techniques using the normalized forcing amplitude as a perturbation parameter to carry out the approximate periodic solutions on a single degree of freedom inverted pendulum nonlinear model. We also discuss the multiple degree of freedom inverted pendulum system. Both numerical simulation and experiments were performed and detailed comparisons are discussed. Our numerical simulations show

  14. Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia

    Directory of Open Access Journals (Sweden)

    Junjie Cui

    2017-06-01

    Full Text Available Bitter gourd (Momordica charantia is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus, watermelon (Citrullus lanatus, and melon (Cucumis melo genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.

  15. Alternative Conformations of the Tau Repeat Domain in Complex with an Engineered Binding Protein*

    Science.gov (United States)

    Grüning, Clara S. R.; Mirecka, Ewa A.; Klein, Antonia N.; Mandelkow, Eckhard; Willbold, Dieter; Marino, Stephen F.; Stoldt, Matthias; Hoyer, Wolfgang

    2014-01-01

    The aggregation of Tau into paired helical filaments is involved in the pathogenesis of several neurodegenerative diseases, including Alzheimer disease. The aggregation reaction is characterized by conformational conversion of the repeat domain, which partially adopts a cross-β-structure in the resulting amyloid-like fibrils. Here, we report the selection and characterization of an engineered binding protein, β-wrapin TP4, targeting the Tau repeat domain. TP4 was obtained by phage display using the four-repeat Tau construct K18ΔK280 as a target. TP4 binds K18ΔK280 as well as the longest isoform of human Tau, hTau40, with nanomolar affinity. NMR spectroscopy identified two alternative TP4-binding sites in the four-repeat domain, with each including two hexapeptide motifs with high β-sheet propensity. Both binding sites contain the aggregation-determining PHF6 hexapeptide within repeat 3. In addition, one binding site includes the PHF6* hexapeptide within repeat 2, whereas the other includes the corresponding hexapeptide Tau(337–342) within repeat 4, denoted PHF6**. Comparison of TP4-binding with Tau aggregation reveals that the same regions of Tau are involved in both processes. TP4 inhibits Tau aggregation at substoichiometric concentration, demonstrating that it interferes with aggregation nucleation. This study provides residue-level insight into the interaction of Tau with an aggregation inhibitor and highlights the structural flexibility of Tau. PMID:24966331

  16. A Comparison between Buck-Boost Inverter with and without Buffer Inductor

    Directory of Open Access Journals (Sweden)

    Purwadi Agus Darwito

    2012-05-01

    Full Text Available The electric vehicle inverter requires an induction motor drive with a high output of voltage and current to reduce the number of batteries used and in turn reduce the vehicle’s weight. In this paper compared two single Phase BuckBoost Inverter (SPBBI, that is between the SPBBI conventional topology with SPBBI new topology uses a buffer inductor. The results of comparison are expected that the new inverter topology can strengthen the voltage greater than the conventional inverter topology. The inverter’s components of capacitor and inductor were reconfigured. The circuit was simulated for various carrier and signal frequencies with various load. The simulation results of the proposed topology compared with the simulation results of conventional topologies commonly used in a variety of frequency and load values. It is shown that the output voltage and current can be strengthened significantly, with a value of more than five times of the output voltage compared to the conventional inverter. The new inverter topology is useful to be implemented for the electric vehicle.

  17. The CMOS Integration of a Power Inverter

    OpenAIRE

    Mannarino, Eric Francis

    2016-01-01

    Due to their falling costs, the use of renewable energy systems is expanding around the world. These systems require the conversion of DC power into grid-synchronous AC power. Currently, the inverters that carry out this task are built using discrete transistors. TowerJazz Semiconductor Corp. has created a commercial CMOS process that allows for blocking voltages of up to 700 V, effectively removing the barrier to integrating power inverters onto a single chip. This thesis explores this proce...

  18. Z-Source Inverter Based Power Quality Compensator with Enhanced Ride-Through Capability

    DEFF Research Database (Denmark)

    Gajanayake, C.J.; Vilathgamuwa, D.M.; Loh, P.C.

    2007-01-01

    Distributed generation has been gaining acceptance over the years and it has the potential to provide reliable power to sensitive loads. However, distributed networks are prone to unbalanced faults conditions. This makes single inverter DG systems unsuitable as UPS systems. This paper proposes...... a Zsource inverter based power quality compensator and a control structure that supplies high quality voltage to the connected sensitive load in the presence of other non linear loads. The proposed topology consists of combination of shunt and series inverters connected to a common Z-source impedance...... network. The shunt inverter is controlled to maintain a quality voltage waveform at the load bus. Whereas the series inverter enhances the ride-through capability during grid faults, protects the shunt inverter by limiting the current and also controls the power delivered to the grid. The performance...

  19. Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm.

    Science.gov (United States)

    Kyne, Ciara; Crowley, Peter B

    2017-09-19

    Although essential to numerous biotech applications, knowledge of molecular recognition by arginine-rich motifs in live cells remains limited. 1 H, 15 N HSQC and 19 F NMR spectroscopies were used to investigate the effects of C-terminal -GR n (n = 1-5) motifs on GB1 interactions in Escherichia coli cells and cell extracts. While the "biologically inert" GB1 yields high-quality in-cell spectra, the -GR n fusions with n = 4 or 5 were undetectable. This result suggests that a tetra-arginine motif is sufficient to drive interactions between a test protein and macromolecules in the E. coli cytoplasm. The inclusion of a 12 residue flexible linker between GB1 and the -GR 5 motif did not improve detection of the "inert" domain. In contrast, all of the constructs were detectable in cell lysates and extracts, suggesting that the arginine-mediated complexes were weak. Together these data reveal the significance of weak interactions between short arginine-rich motifs and the E. coli cytoplasm and demonstrate the potential of such motifs to modify protein interactions in living cells. These interactions must be considered in the design of (in vivo) nanoscale assemblies that rely on arginine-rich sequences.

  20. Study of Inverted Pendulum Robot Using Fuzzy Servo Control Method

    Directory of Open Access Journals (Sweden)

    Dazhong Wang

    2012-09-01

    Full Text Available The inverted pendulum robot is a classical problem in controls. The inherit instabilities in the setup make it a natural target for a control system. Inverted pendulum robot is suitable to use for investigation and verification of various control methods for dynamic systems. Maintaining an equilibrium position of the pendulum pointing up is a challenge as this equilibrium position is unstable. As the inverted pendulum robot system is nonlinear it is well-suited to be controlled by fuzzy logic. In this paper, Lagrange method has been applied to develop the mathematical model of the system. The objective of the simulation to be shown using the fuzzy control method can stabilize the nonlinear system of inverted pendulum robot.

  1. Anion induced conformational preference of Cα NN motif residues in functional proteins.

    Science.gov (United States)

    Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

    2017-12-01

    Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

  2. Single-stage MPPT control realization for Aalborg inverter in photovoltaic system

    DEFF Research Database (Denmark)

    Zhang, Shuai; Wu, Weimin; Wang, Houqing

    2017-01-01

    In this paper, the single-stage Maximum Power Point Tracking (MPPT) control strategy for the Aalborg photovoltaic inverter is presented. Aalborg inverter has many advantages, such as high efficiency, wide range of input voltage, minimum voltage drop of the filtering inductors, etc. Nevertheless......, it is essentially a “half-bridge” inverter with two input sources, where one source works in MPPT mode, the other is out of control. If without the reasonable parameter design and the proper control, the bus-voltage of this inverter may change greatly, resulting in the serious power oscillation around maximum power...

  3. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

    Science.gov (United States)

    Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

    2018-04-01

    The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

  4. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-25

    Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  5. Evaluation of Resonant Damping Techniques for Z-Source Current-Type Inverter

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Loh, Poh Chiang; Gajanayake, C.J.

    2008-01-01

    For the renewable energy sources whose outputs vary continuously, a Z-source current-type inverter has been proposed as a possible buck-boost alternative for grid-interfacing. With a unique X-shaped LC network connected between its dc power source and inverter topology, Z-source current......-type inverter is however expected to suffer from compounded resonant complications in addition to those associated with its second-order output filter. To improve its damping performance, this paper proposes the careful integration of Posicast or three-step compensators before the inverter pulse-width modulator...... for damping triggered resonant oscillations. In total, two compensators are needed for wave-shaping the inverter boost factor and modulation ratio, and they can conveniently be implemented using first-in first-out stacks and embedded timers of modern digital signal processors widely used in motion control...

  6. Self-balanced modulation and magnetic rebalancing method for parallel multilevel inverters

    Science.gov (United States)

    Li, Hui; Shi, Yanjun

    2017-11-28

    A self-balanced modulation method and a closed-loop magnetic flux rebalancing control method for parallel multilevel inverters. The combination of the two methods provides for balancing of the magnetic flux of the inter-cell transformers (ICTs) of the parallel multilevel inverters without deteriorating the quality of the output voltage. In various embodiments a parallel multi-level inverter modulator is provide including a multi-channel comparator to generate a multiplexed digitized ideal waveform for a parallel multi-level inverter and a finite state machine (FSM) module coupled to the parallel multi-channel comparator, the FSM module to receive the multiplexed digitized ideal waveform and to generate a pulse width modulated gate-drive signal for each switching device of the parallel multi-level inverter. The system and method provides for optimization of the output voltage spectrum without influence the magnetic balancing.

  7. Investigating the role of GXXXG motifs in helical folding and self-association of plasticins, Gly/Leu-rich antimicrobial peptides.

    Science.gov (United States)

    Carlier, Ludovic; Joanne, Pierre; Khemtémourian, Lucie; Lacombe, Claire; Nicolas, Pierre; El Amri, Chahrazade; Lequin, Olivier

    2015-01-01

    Plasticins (PTC) are dermaseptin-related antimicrobial peptides characterized by a large number of leucine and glycine residues arranged in GXXXG motifs that are often described to promote helix association within biological membranes. We report the structure and interaction properties of two plasticins, PTC-B1 from Phyllomedusa bicolor and a cationic analog of PTC-DA1 from Pachymedusa dacnicolor, which exhibit membrane-lytic activities on a broad range of microorganisms. Despite a high number of glycine, CD and NMR spectroscopy show that the two plasticins adopt mainly alpha-helical conformations in a wide variety of environments such as trifluoroethanol, detergent micelles and lipid vesicles. In DPC and SDS, plasticins adopt well-defined helices that lie parallel to the micelle surface, all glycine residues being located on the solvent-exposed face. Spectroscopic data and cross-linking experiments indicate that the GXXXG repeats in these amphipathic helices do not provide a strong oligomerization interface, suggesting a different role from GXXXG motifs found in transmembrane helices. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Reduced-Order Structure-Preserving Model for Parallel-Connected Three-Phase Grid-Tied Inverters: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Brian B [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Purba, Victor [University of Minnesota; Jafarpour, Saber [University of California, Santa Barbara; Bullo, Francesco [University of California, Santa Barbara; Dhople, Sairaj [University of Minnesota

    2017-08-31

    Given that next-generation infrastructures will contain large numbers of grid-connected inverters and these interfaces will be satisfying a growing fraction of system load, it is imperative to analyze the impacts of power electronics on such systems. However, since each inverter model has a relatively large number of dynamic states, it would be impractical to execute complex system models where the full dynamics of each inverter are retained. To address this challenge, we derive a reduced-order structure-preserving model for parallel-connected grid-tied three-phase inverters. Here, each inverter in the system is assumed to have a full-bridge topology, LCL filter at the point of common coupling, and the control architecture for each inverter includes a current controller, a power controller, and a phase-locked loop for grid synchronization. We outline a structure-preserving reduced-order inverter model for the setting where the parallel inverters are each designed such that the filter components and controller gains scale linearly with the power rating. By structure preserving, we mean that the reduced-order three-phase inverter model is also composed of an LCL filter, a power controller, current controller, and PLL. That is, we show that the system of parallel inverters can be modeled exactly as one aggregated inverter unit and this equivalent model has the same number of dynamical states as an individual inverter in the paralleled system. Numerical simulations validate the reduced-order models.

  9. A Transformer-less Single Phase Inverter For photovoltaic Systems

    DEFF Research Database (Denmark)

    Mostaan, Ali; Alizadeh, Ebrahim; Qu, Ying

    2017-01-01

    A single phase transformer-less inverter is introduced in this paper. The negative polarities of the input voltage and output terminal have common ground. Therefore, the leakage current problem that is common in PV systems is eliminated naturally. In addition, the proposed inverter has fewer comp...

  10. CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

    Directory of Open Access Journals (Sweden)

    Hamed Bostan

    2012-01-01

    Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

  11. Voltage resonant inverter as a power source

    OpenAIRE

    Lupenko, Anatoliy; Stakhiv, Petro

    2014-01-01

    The operation mode of a voltage resonant inverter as a power source with variable load is analyzed. In order to reduce load power variations, an approach to development of the inverter’s load power response based on providing similar positive and negative power deviations from its nominal value has been proposed. The design procedure for resonant inverter with open loop structure as a power source has been elaborated. For a high pressure sodium lamp as a load, the power deviation of about 4% ...

  12. Improved Layout of Inverter for EMC Analysis

    OpenAIRE

    Yade , Ousseynou; Martin , Christian; Vollaire , Christian; Bréard , Arnaud; Ali , Marwan; Meuret , Régis; Hervé , Morel

    2017-01-01

    International audience; This paper details EMC (electromagnetic compatibility) analysis on an inverter application. The work deals with the whole power chain (±270Vdc input voltage to 3-phase 115 Vac output voltage). This inverter is composed by modular parts (power module and EMC filters) that supply motors in more electrical aircraft. Through our analysis an approach is defined to design a detailed lumped circuit model of the power module layout by using Q3D extractor and SABER software. Fr...

  13. Modelling of the modified-LLCL-filter-based single-phase grid-tied Aalborg inverter

    DEFF Research Database (Denmark)

    Liu, Zifa; Wu, Huiyun; Liu, Yuan

    2017-01-01

    Owing to less conduction and switching power losses, the recently proposed Aalborg inverter has high efficiency within a wide range of input DC voltage for single-phase DC/AC power conversion. In theory, the conduction power losses can be further decreased, if an LLCL-filter is adopted instead...... of an LCL-filter for a voltage source inverter, mainly due to the reduced inductance. The Aalborg inverter shows the characteristic of a current source inverter, when working in the `boost' state. Whether the LLCL-filter can meet the control requirement of this type inverter needs to be further explored....... In this study, the small signal analysis for the modified-LLCL-filter-based Aalborg inverter is addressed. Through the modelling, it can be proven that compared with the LCL-filter, the modified-LLCL-filter causes no extra control challenge for the Aalborg inverter, and therefore more inductance in the power...

  14. Reliability Assessment of Transformerless PV Inverters considering Mission Profiles

    Directory of Open Access Journals (Sweden)

    Yongheng Yang

    2015-01-01

    Full Text Available Due to the small volume and high efficiency, transformerless inverters have gained much popularity in grid-connected PV applications, where minimizing leakage current injection is mandatory. This can be achieved by either modifying the modulation schemes or adding extra power switching devices, resulting in an uneven distribution of the power losses on the switching devices. Consequently, the device thermal loading is redistributed and thus may alter the entire inverter reliability performance, especially under a long-term operation. In this consideration, this paper assesses the device reliability of three transformerless inverters under a yearly mission profile (i.e., solar irradiance and ambient temperature. The mission profile is translated to device thermal loading, which is used for lifetime prediction. Comparison results reveal the lifetime mismatches among the power switching devices operating under the same condition, which offers new thoughts for a robust design and a reliable operation of grid-connected transformerless PV inverters with high efficiency.

  15. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  16. Detecting and mitigating battery charger and inverter aging

    International Nuclear Information System (INIS)

    Gunther, W.E.; Lewis, R.; Subudhi, M.

    1988-08-01

    This report constitutes the second of the two-phase approach for assessing the safety and operational aspects of battery charger and inverter aging in nuclear power plants. This work, conducted by Brookhaven National Laboratory (BNL) under the auspices of the US NRC Nuclear Plant Aging Research (NPAR) Program, evaluated operating experience data, nuclear power plant maintenance practices, and plant design information to determine the impact of battery charger and inverter aging on safety, and the methods which should be used to detect aging degradation and mitigate its effects. A naturally aged inverter and battery charger were tested at BNL to evaluate the naturally aged condition, the effectiveness of condition monitoring techniques, and the practicality of implementing selected maintenance and monitoring recommendations. Temperature monitoring, component parameter measurements, and the periodic observation of critical circuit waveforms are viable methods for monitoring aging degradation. A maintenance program for battery chargers and inverters is recommended. As described in this report, the maintenance program incorporates inspection, monitoring, testing and repair activities which should be performed to detect and mitigate aging effects, and thereby assure the operational readiness of this important equipment throughout the plant's operating life. 32 refs., 43 figs., 19 tabs

  17. Mitigation of grid-current distortion for LCL-filtered grid-connected voltage-source inverter with inverter-side current control

    DEFF Research Database (Denmark)

    Xin, Zhen; Mattavelli, Paolo; Yao, WenLi

    2017-01-01

    Due to the low inductance of an LCL-filter, the grid current generated by an LCL-filtered Voltage Source Inverter (VSI) is sensitive to low-order grid-voltage harmonics. This issue is especially tough for the control system with Inverter Current Feedback (ICF), because the grid-current harmonics...... can freely flow into the filter capacitor without control. To cope with this issue, this paper develops an approach for the ICF control system to suppress the grid-current harmonics without adding extra sensors. The proposed method applies harmonic controllers and feedforward scheme simultaneously...

  18. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-09-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  19. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Science.gov (United States)

    Fauteux, François; Strömvik, Martina V

    2009-01-01

    Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

  20. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Directory of Open Access Journals (Sweden)

    Fauteux François

    2009-10-01

    Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

  1. The Sclerotinia sclerotiorum Mating Type Locus (MAT) Contains a 3.6-kb Region That Is Inverted in Every Meiotic Generation

    Science.gov (United States)

    Maruthachalam, Karunakaran; Wu, Bo-Ming; Subbarao, Krishna V.

    2013-01-01

    Sclerotinia sclerotiorum is a fungal plant pathogen and the causal agent of lettuce drop, an economically important disease of California lettuce. The structure of the S. sclerotiorum mating type locus MAT has previously been reported and consists of two idiomorphs that are fused end-to-end as in other homothallics. We investigated the diversity of S. sclerotiorum MAT using a total of 283 isolates from multiple hosts and locations, and identified a novel MAT allele that differed by a 3.6-kb inversion and was designated Inv+, as opposed to the previously known S. sclerotiorum MAT that lacked the inversion and was Inv-. The inversion affected three of the four MAT genes: MAT1-2-1 and MAT1-2-4 were inverted and MAT1-1-1 was truncated at the 3’-end. Expression of MAT genes differed between Inv+ and Inv- isolates. In Inv+ isolates, only one of the three MAT1-2-1 transcript variants of Inv- isolates was detected, and the alpha1 domain of Inv+ MAT1-1-1 transcripts was truncated. Both Inv- and Inv+ isolates were self-fertile, and the inversion segregated in a 1∶1 ratio regardless of whether the parent was Inv- or Inv+. This suggested the involvement of a highly regulated process in maintaining equal proportions of Inv- and Inv+, likely associated with the sexual state. The MAT inversion region, defined as the 3.6-kb MAT inversion in Inv+ isolates and the homologous region of Inv- isolates, was flanked by a 250-bp inverted repeat on either side. The 250-bp inverted repeat was a partial MAT1-1-1 that through mediation of loop formation and crossing over, may be involved in the inversion process. Inv+ isolates were widespread, and in California and Nebraska constituted half of the isolates examined. We speculate that a similar inversion region may be involved in mating type switching in the filamentous ascomycetes Chromocrea spinulosa, Sclerotinia trifoliorum and in certain Ceratocystis species. PMID:23457637

  2. Micro-inverter solar panel mounting

    Science.gov (United States)

    Morris, John; Gilchrist, Phillip Charles

    2016-02-02

    Processes, systems, devices, and articles of manufacture are provided. Each may include adapting micro-inverters initially configured for frame-mounting to mounting on a frameless solar panel. This securement may include using an adaptive clamp or several adaptive clamps secured to a micro-inverter or its components, and using compressive forces applied directly to the solar panel to secure the adaptive clamp and the components to the solar panel. The clamps can also include compressive spacers and safeties for managing the compressive forces exerted on the solar panels. Friction zones may also be used for managing slipping between the clamp and the solar panel during or after installation. Adjustments to the clamps may be carried out through various means and by changing the physical size of the clamps themselves.

  3. Fast Grid Frequency Support from Distributed Inverter-Based Resources

    Energy Technology Data Exchange (ETDEWEB)

    Hoke, Anderson F [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-05-04

    This presentation summarizes power hardware-in-the-loop testing performed to evaluate the ability of distributed inverter-coupled generation to support grid frequency on the fastest time scales. The research found that distributed PV inverters and other DERs can effectively support the grid on sub-second time scales.

  4. Resistance Spot Welding with Middelfrequency-Inverter Weling Gun

    DEFF Research Database (Denmark)

    Rasmussen, Mogens H.

    The paper presents the results of investigations concerning the process stability and weldability lobes for uncoated sheets of 1.0 mm thickness when performing resistance spot welding with a middlefrequency-inverter welding gun......The paper presents the results of investigations concerning the process stability and weldability lobes for uncoated sheets of 1.0 mm thickness when performing resistance spot welding with a middlefrequency-inverter welding gun...

  5. Research on a Compound Control Strategy of Three-Phase Inverter for Unbalanced Loads

    Directory of Open Access Journals (Sweden)

    Yue Gaili

    2017-01-01

    Full Text Available To solve the problem of unbalanced output voltage of inverter under three-phase unbalanced load. In this paper, the main circuit topology using three-phase three-wire inverter topology. Established the mathematical model in several different coordinate system of the three-phase inverter. A compound control method is proposed by combining voltage current dual loop control method and repetitive control method, The control method is realized in three - phase 400 Hz inverter, and can meet the demand of unbalanced load to inverter, the reliability of the inverter circuit is improved. At the end of this paper, Matlab simulation analysis and experimental results are given, it is proved that the composite control method designed in this paper has a strong ability of unbalanced load.

  6. On the origin of distribution patterns of motifs in biological networks

    Directory of Open Access Journals (Sweden)

    Lesk Arthur M

    2008-08-01

    Full Text Available Abstract Background Inventories of small subgraphs in biological networks have identified commonly-recurring patterns, called motifs. The inference that these motifs have been selected for function rests on the idea that their occurrences are significantly more frequent than random. Results Our analysis of several large biological networks suggests, in contrast, that the frequencies of appearance of common subgraphs are similar in natural and corresponding random networks. Conclusion Indeed, certain topological features of biological networks give rise naturally to the common appearance of the motifs. We therefore question whether frequencies of occurrences are reasonable evidence that the structures of motifs have been selected for their functional contribution to the operation of networks.

  7. New Switched-Dual-Source Multilevel Inverter for Symmetrical and Asymmetrical Operation

    Directory of Open Access Journals (Sweden)

    Kennedy Adinbo Aganah

    2018-04-01

    Full Text Available The increasing integration of large solar PV and wind farms into the power grid has fueled, over the past two decades, growing demands for high-power, high-voltage, utility-scale inverters. Multilevel inverters have emerged as the industry’s choice for megawatt-range inverters because of their reduced voltage stress, capability for generating an almost-sinusoidal voltage, built-in redundancy and other benefits. This paper presents a novel switched-source multilevel inverter (SS MLI architecture. This new inverter shows superior capabilities when compared to existing topologies. It has reduced voltage stress on the semiconductor, uses fewer switches (i.e., reduced size/weight/cost and exhibits increased efficiency. The proposed SS MLI is comprised of two voltage sources ( V 1 , V 2 and six switches. It is capable of generating five-level output voltage in symmetric mode (i.e., V 1 = V 2 and seven-level output voltage in asymmetric mode (i.e., V 1 ≠ V 2 . We present simulations results (using MATLAB®/Simulink® for five- and seven-level output voltages, and they strongly support the validity of the proposed inverter. These positive results are further supported experimentally using a laboratory prototype.

  8. Inverted radiative hierarchy of quark masses

    International Nuclear Information System (INIS)

    Berezhiani, Z.G.; Rattazzi, R.

    1992-01-01

    Inverted radiative hierarchy of quark masses is investigated. The authors suggest that the mass hierarchy is first generated in a sector of heavy isosinglet fermions due to radiative effects and then projected in the inverted way to the usual quarks by means of a universal seesaw. The simple left-right symmetric gauge model is presented with the P- and CP-parities and the exact isotopical symmetry which are softly (or spontaneously) broken in the Higgs potential. This approach naturally explains the observed pattern of quark masses and mixing, providing the quantitatively correct formula for the Cabibbo angle. Top quark is predicted to be in the 90-150 GeV range

  9. Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

    Science.gov (United States)

    König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

    2013-01-01

    G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

  10. Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs.

    Science.gov (United States)

    Iyengar, Bharat Ravi; Pillai, Beena; Venkatesh, K V; Gadgil, Chetan J

    2017-05-30

    We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.

  11. Annotating RNA motifs in sequences and alignments.

    Science.gov (United States)

    Gardner, Paul P; Eldai, Hisham

    2015-01-01

    RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.

    Science.gov (United States)

    Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F; Li, Shuaicheng; Hu, Kailin

    2016-01-07

    The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

  13. Fast social-like learning of complex behaviors based on motor motifs

    Science.gov (United States)

    Calvo Tapia, Carlos; Tyukin, Ivan Y.; Makarov, Valeri A.

    2018-05-01

    Social learning is widely observed in many species. Less experienced agents copy successful behaviors exhibited by more experienced individuals. Nevertheless, the dynamical mechanisms behind this process remain largely unknown. Here we assume that a complex behavior can be decomposed into a sequence of n motor motifs. Then a neural network capable of activating motor motifs in a given sequence can drive an agent. To account for (n -1 )! possible sequences of motifs in a neural network, we employ the winnerless competition approach. We then consider a teacher-learner situation: one agent exhibits a complex movement, while another one aims at mimicking the teacher's behavior. Despite the huge variety of possible motif sequences we show that the learner, equipped with the provided learning model, can rewire "on the fly" its synaptic couplings in no more than (n -1 ) learning cycles and converge exponentially to the durations of the teacher's motifs. We validate the learning model on mobile robots. Experimental results show that the learner is indeed capable of copying the teacher's behavior composed of six motor motifs in a few learning cycles. The reported mechanism of learning is general and can be used for replicating different functions, including, for example, sound patterns or speech.

  14. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...

  15. Inverted Steam Generators for Sodium Cooled Fast Reactors

    International Nuclear Information System (INIS)

    Matal, Oldřich; Šimo, Tomáš; Matal, Oldřich Jr.

    2013-01-01

    Conclusions: Two inverted steam generators of the Czech industry provenience have still been in successful operation with no water into sodium leaks at BOR 60 (RIAR Dimitrovgrad, Russian Federation). Micromodular inverted steam generator (MMISG) since 1981 and modular inverted steam generator (MISG) since 1991. In the framework of the CP ESFR project predesign studies of 100 MW (thermal) ISG modules were performed with the consideration of MMISG and MISG design, operational and safety benefits and experience. Development of material and technology for sodium heated steam generators components reflecting contemporary domestic industrial conditions in the Czech Republic was restarted in the years 2003 to 2004 and supported in the years 2008 to 2011 by the European CP ESFR project and by the Ministry of Industry and Trade of the Czech Republic

  16. Raman mediated all-optical cascadable inverter using silicon-on-insulator waveguides.

    Science.gov (United States)

    Sen, Mrinal; Das, Mukul K

    2013-12-01

    In this Letter, we propose an all-optical circuit for a cascadable and integrable logic inverter based on stimulated Raman scattering. A maximum product criteria for noise margin is taken to analyze the cascadability of the inverter. Variation of noise margin for different model parameters is also studied. Finally, the time domain response of the inverter is analyzed for different widths of input pulses.

  17. Two-motor single-inverter field-oriented induction machine drive ...

    Indian Academy of Sciences (India)

    Multi-machine, single-inverter induction motor drives are attractive in situations in which all machines are of similar ratings, and operate at approximately the same load torques. The advantages include small size compared to multi-inverter system, lower weight and overall cost. However, field oriented control of such drives ...

  18. Investigation of Pseudo-Active State in Z-Source Inverter

    DEFF Research Database (Denmark)

    Schaltz, Erik; Oprea, Octavian; Larsen, Lasse

    2005-01-01

    This paper introduces a new operating state of the Z-source inverter denoted the pseudo-active state. The pseudoactive state is a state that may boost the output voltage of the Zsource inverter to a level higher than expected. The influence of the pseudo-active state is investigated and an equation...

  19. Validation of a screening tool for the rapid and reliable detection of CGG trinucleotide repeat expansions in FMR1.

    Science.gov (United States)

    Basehore, Monica J; Marlowe, Natalia M; Jones, Julie R; Behlendorf, Deborah E; Laver, Thomas A; Friez, Michael J

    2012-06-01

    Most individuals with intellectual disability and/or autism are tested for Fragile X syndrome at some point in their lifetime. Greater than 99% of individuals with Fragile X have an expanded CGG trinucleotide repeat motif in the promoter region of the FMR1 gene, and diagnostic testing involves determining the size of the CGG repeat as well as methylation status when an expansion is present. Using a previously described triplet repeat-primed polymerase chain reaction, we have performed additional validation studies using two cohorts with previous diagnostic testing results available for comparison purposes. The first cohort (n=88) consisted of both males and females and had a high percentage of abnormal samples, while the second cohort (n=624) consisted of only females and was not enriched for expansion mutations. Data from each cohort were completely concordant with the results previously obtained during the course of diagnostic testing. This study further demonstrates the utility of using laboratory-developed triplet repeat-primed FMR1 testing in a clinical setting.

  20. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode

  1. FPGA Based Compensation Method for Correcting Distortion in Voltage Inverters

    National Research Council Canada - National Science Library

    Williamson, Kenya D

    2007-01-01

    ...) voltage source inverters. Blanking time distortion is caused by the delay inserted to prevent the short circuit that would occur if the two transistors in the same inverter leg are both on at the same time...

  2. Lower Side Switching Modification of SHEPWM for Single H-Bridge Unipolar Inverter

    Science.gov (United States)

    Aihsan, M. Z.

    2018-03-01

    Selective Harmonic Elimination Pulse Width Modulation (SHEPWM) is a famous fundamental frequency method for both single stage H-bridge inverter and cascaded multilevel inverters. The main function of SHEPWM is to eliminate the selective lower order of odd harmonic such 3rd, 5th 7th and 9th of the output voltage of the inverter but maintain the fundamental component. In this paper, the 5kHz of the unipolar SHEPWM switching scheme of the inverter is developed and later will be compared to the modified SHEPWM switching scheme. The performance of this inverter is measured through the final total harmonic distortion (THD), the efficiency of the whole system and the natural shape of the output after LC filter.

  3. Motif formation and industry specific topologies in the Japanese business firm network

    Science.gov (United States)

    Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

    2017-05-01

    Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

  4. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  5. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin

    2015-01-01

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  6. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  7. A Coordinate Control Strategy for Circulating Current Suppression in Multiparalleled Three-Phase Inverters

    DEFF Research Database (Denmark)

    Zhang, Xueguang; Wang, Tianyi; Wang, Xiongfei

    2017-01-01

    This paper addresses the zero-sequence circulating current control in the multiparalleled three-phase voltage-source inverters. The model of the zero-sequence circulating current in the N-paralleled (N ≥ 3) inverters is derived. It is shown that the circulating current is not only susceptible...... to the mismatches of circuit parameters, but it is also influenced by the interactions of circulating current controllers used by other paralleled inverters. To eliminate these adverse effects on the circulating current control loop, a coordinate control strategy for the N-paralleled inverter is proposed based...... on the zero-vector feedforward method with the space-vector pulse width modulation. Moreover, a virtual inverter method is introduced to facilitate the implementation of the proposed controller, which decouples the interactions of circulating current controllers in the paralleled inverters. Finally...

  8. Comparative Evaluation of Pulsewidth Modulation Strategies for Z-Source Neutral-Point-Clamped Inverter

    DEFF Research Database (Denmark)

    Loh, P.C.; Blaabjerg, Frede; Wong, C.P.

    2007-01-01

    modulation (PWM) strategies for controlling the Z-source NPC inverter. While developing the PWM techniques, attention has been devoted to carefully derive them from a common generic basis for improved portability, easier implementation, and most importantly, assisting readers in understanding all concepts......Z-source neutral-point-clamped (NPC) inverter has recently been proposed as an alternative three-level buck-boost power conversion solution with an improved output waveform quality. In principle, the designed Z-source inverter functions by selectively "shooting through" its power sources, coupled...... to the inverter using two unique Z-source impedance networks, to boost the inverter three-level output waveform. Proper modulation of the new inverter would therefore require careful integration of the selective shoot-through process to the basic switching concepts to achieve maximal voltage-boost, minimal...

  9. Glycomic Analysis of Life Stages of the Human Parasite Schistosoma mansoni Reveals Developmental Expression Profiles of Functional and Antigenic Glycan Motifs.

    Science.gov (United States)

    Smit, Cornelis H; van Diepen, Angela; Nguyen, D Linh; Wuhrer, Manfred; Hoffmann, Karl F; Deelder, André M; Hokke, Cornelis H

    2015-07-01

    Glycans present on glycoproteins and glycolipids of the major human parasite Schistosoma mansoni induce innate as well as adaptive immune responses in the host. To be able to study the molecular characteristics of schistosome infections it is therefore required to determine the expression profiles of glycans and antigenic glycan-motifs during a range of critical stages of the complex schistosome lifecycle. We performed a longitudinal profiling study covering schistosome glycosylation throughout worm- and egg-development using a mass spectrometry-based glycomics approach. Our study revealed that during worm development N-glycans with Galβ1-4(Fucα1-3)GlcNAc (LeX) and core-xylose motifs were rapidly lost after cercariae to schistosomula transformation, whereas GalNAcβ1-4GlcNAc (LDN)-motifs gradually became abundant and predominated in adult worms. LeX-motifs were present on glycolipids up to 2 weeks of schistosomula development, whereas glycolipids with mono- and multifucosylated LDN-motifs remained present up to the adult worm stage. In contrast, expression of complex O-glycans diminished to undetectable levels within days after transformation. During egg development, a rich diversity of N-glycans with fucosylated motifs was expressed, but with α3-core fucose and a high degree of multifucosylated antennae only in mature eggs and miracidia. N-glycan antennae were exclusively LDN-based in miracidia. O-glycans in the mature eggs were also diverse and contained LeX- and multifucosylated LDN, but none of these were associated with miracidia in which we detected only the Galβ1-3(Galβ1-6)GalNAc core glycan. Immature eggs also exhibited short O-glycan core structures only, suggesting that complex fucosylated O-glycans of schistosome eggs are derived primarily from glycoproteins produced by the subshell envelope in the developed egg. Lipid glycans with multifucosylated GlcNAc repeats were present throughout egg development, but with the longer highly fucosylated

  10. Sine-wave three phase resonance inverter for operation of ...

    African Journals Online (AJOL)

    naeema

    conventional and simple solution to this requirement are in the following [8]. Using conventional H-bridge inverter beside of a step-up transformer. Using a renewable energy source with sufficiently large output voltage, which may be realized by a string of series connected modules followed by an H-bridge inverter [12], [13].

  11. Frequency scanning-based stability analysis method for grid-connected inverter system

    DEFF Research Database (Denmark)

    Wang, Yanbo; Wang, Xiongfei; Blaabjerg, Frede

    2017-01-01

    This paper proposes a frequency scanning-based impedance analysis for stability assessment of grid-connected inverter system, which is able to perform stability assessment without using system mathematical models and inherit the superior feature of impedance-based stability criterion with conside......This paper proposes a frequency scanning-based impedance analysis for stability assessment of grid-connected inverter system, which is able to perform stability assessment without using system mathematical models and inherit the superior feature of impedance-based stability criterion...... with consideration of the inverter nonlinearities. Small current disturbance is injected into grid-connected inverter system in a particular frequency range, and the impedance is computed according to the harmonic-frequency response using Fourier analysis, and then the stability is predicted on the basis...... of the impedance stability criterion. The stability issues of grid-connected inverters with grid-current feedback and the converter-current feedback are addressed using the proposed method. The results obtained from simulation and experiments validate the effectiveness of the method. The frequency scanning...

  12. Experimental study of inverted-annular-flow hydrodynamics utilizing an adiabatic simulation

    International Nuclear Information System (INIS)

    De Jarlais, G.

    1983-03-01

    In experiments, inverted annular flow was simulated adiabatically with turbulent water jets, issuing downward from long aspect nozzles, enclosed in gas annuli. Velocities, diameters, and gas species were varied, and core jet length, shape, break-up mode, and dispersed-core droplet sizes were recorded at approximately 750 data points. Inverted annular flow was observed to develop into inverted slug flow at low relative velocities, and into dispersed droplet flow at high relative velocities. For both of the above transitions from inverted annular flow, correlations for core jet length were developed by extending work done on free liquid jets to include this new, coaxial, jet disintegration phenomenon. Jet break-up length is correlated as a function of jet diameter, jet Reynolds number, jet Weber number, void fraction, and gas Weber number. Correlations for core shape, break-up mechanisms and dispersed core droplet size for the case of transition to inverted slug flow were developed

  13. Transnasal endoscopic medial maxillectomy in recurrent maxillary sinus inverted papilloma.

    Science.gov (United States)

    Kamel, Reda H; Abdel Fattah, Ahmed F; Awad, Ayman G

    2014-12-01

    Maxillary sinus inverted papilloma entails medial maxillectomy and is associated with high incidence of recurrence. To study the impact of prior surgery on recurrence rate after transnasal endoscopic medial maxillectomy. Eighteen patients with primary and 33 with recurrent maxillary sinus inverted papilloma underwent transnasal endoscopic medial maxillectomy. Caldwell-Luc operation was the primary surgery in 12 patients, transnasal endoscopic resection in 20, and midfacial degloving technique in one. The follow-up period ranged between 2 to 19.5 years with an average of 8.8 years. Recurrence was detected in 8/51 maxillary sinus inverted papilloma patients (15.7 %), 1/18 of primary cases (5.5 %), 7/33 of recurrent cases (21.2 %); 3/20 of the transnasal endoscopic resection group (15%) and 4/12 of the Caldwell-Luc group (33.3%). Redo transnasal endoscopic medial maxillectomy was followed by a single recurrence in the Caldwell-Luc group (25%), and no recurrence in the other groups. Recurrence is more common in recurrent maxillary sinus inverted papilloma than primary lesions. Recurrent maxillary sinus inverted papilloma after Caldwell-Luc operation has higher incidence of recurrence than after transnasal endoscopic resection.

  14. Efficient sequential and parallel algorithms for finding edit distance based motifs.

    Science.gov (United States)

    Pal, Soumitra; Xiao, Peng; Rajasekaran, Sanguthevar

    2016-08-18

    Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approximation algorithms to solve this problem. In this paper, we present several novel, exact, sequential and parallel algorithms for solving the (l,d) Edit-distance-based Motif Search (EMS) problem: given two integers l,d and n biological strings, find all strings of length l that appear in each input string with atmost d errors of types substitution, insertion and deletion. One popular technique to solve the problem is to explore for each input string the set of all possible l-mers that belong to the d-neighborhood of any substring of the input string and output those which are common for all input strings. We introduce a novel and provably efficient neighborhood exploration technique. We show that it is enough to consider the candidates in neighborhood which are at a distance exactly d. We compactly represent these candidate motifs using wildcard characters and efficiently explore them with very few repetitions. Our sequential algorithm uses a trie based data structure to efficiently store and sort the candidate motifs. Our parallel algorithm in a multi-core shared memory setting uses arrays for storing and a novel modification of radix-sort for sorting the candidate motifs. The algorithms for EMS are customarily evaluated on several challenging instances such as (8,1), (12,2), (16,3), (20,4), and so on. The best previously known algorithm, EMS1, is sequential and in estimated 3 days solves up to instance (16,3). Our sequential algorithms are more than 20 times faster on (16,3). On other hard instances such as (9,2), (11,3), (13,4), our algorithms are much faster. Our parallel algorithm has more than 600 % scaling performance while using 16 threads. Our algorithms have pushed up the state-of-the-art of EMS solvers and we believe that the techniques introduced in

  15. Physical-chemical property based sequence motifs and methods regarding same

    Science.gov (United States)

    Braun, Werner [Friendswood, TX; Mathura, Venkatarajan S [Sarasota, FL; Schein, Catherine H [Friendswood, TX

    2008-09-09

    A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.

  16. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2011-06-20

    One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  17. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2011-06-01

    Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  18. Repeat interruptions in spinocerebellar ataxia type 10 expansions are strongly associated with epileptic seizures

    Science.gov (United States)

    McFarland, Karen N.; Liu, Jilin; Landrian, Ivette; Zeng, Desmond; Raskin, Salmo; Moscovich, Mariana; Gatto, Emilia M.; Ochoa, Adriana; Teive, Hélio A. G.; Rasmussen, Astrid; Ashizawa, Tetsuo

    2014-01-01

    Spinocerebellar ataxia type 10 (SCA10), an autosomal dominant neurodegenerative disorder, is the result of a non-coding, pentanucleotide repeat expansion within intron 9 of the Ataxin 10 gene. SCA10 patients present with pure cerebellar ataxia; yet, some families also have a high incidence of epilepsy. SCA10 expansions containing penta- and heptanucleotide interruption motifs, termed “ATCCT interruptions,” experience large contractions during germline transmission, particularly in paternal lineages. At the same time, these alleles confer an earlier age at onset which contradicts traditional rules of genetic anticipation in repeat expansions. Previously, ATCCT interruptions have been associated with a higher prevalence of epileptic seizures in one Mexican-American SCA10 family. In a large cohort of SCA10 families, we analyzed whether ATCCT interruptions confers a greater risk for developing seizures in these families. Notably, we find that the presence of repeat interruptions within the SCA10 expansion confers a 6.3-fold increase in the risk of an SCA10 patient developing epilepsy (6.2-fold when considering patients of Mexican ancestry only) and a 13.7-fold increase in having a positive family history of epilepsy (10.5-fold when considering patients of Mexican ancestry only). We conclude that the presence of repeat interruptions in SCA10 repeat expansion indicates a significant risk for the epilepsy phenotype and should be considered during genetic counseling. PMID:24318420

  19. New model of inverting substation for DC traction with regenerative braking system

    Science.gov (United States)

    Omar, Abdul Malek Saidina; Samat, Ahmad Asri Abd; Isa, Siti Sarah Mat; Shamsuddin, Sarah Addyani; Jamaludin, Nur Fadhilah; Khyasudeen, Muhammad Farris

    2017-08-01

    This paper presents a power electronic devices application focus on modeling, analysis, and control of switching power converter in the inverting DC substation with regenerative braking system which is used to recycle the surplus regenerative power by feed it back to the main AC grid. The main objective of this research is to improve the switching power electronic converter of the railway inverting substation and optimize the maximum kinetic energy recovery together with minimum power losses from the railway braking system. Assess performance including efficiency and robustness will be evaluated in order to get the best solution for the design configuration. Research methodology included mathematical calculation, simulation, and detail analysis on modeling of switching power converter on inverting substation. The design stage separates to four main areas include rectification mode, regenerative mode, control inverter mode and filtering mode. The simulation result has shown that the regenerative inverter has a capability to accept a maximum recovery power on the regeneration mode. Total energy recovery has increase and power losses have decreases because inverter abilities to transfer the surplus energy back to the main AC supply. An Inverter controller with PWM Generator and PI Voltage Regulator has been designed to control voltage magnitude and frequency of the DC traction system.

  20. Shunt Active-Power-Filter Topology Based on Parallel Interleaved Inverters

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Asiminoaei, Lucian; Aeloiza, E.

    2008-01-01

    In this paper, an interleaved active-power-filter concept with reduced size of passive components is discussed. The topology is composed of two pulsewidth-modulation interleaved voltage-source inverters connected together on the ac line and sharing the same dc-link capacitor. The advantages......, because the power sharing allows one to use a higher switching frequency in each inverter. This paper analyzes the design of the passive components and gives a practical and low-cost solution for the minimization of the circulation currents between the inverters, by using common-mode coils. Several...

  1. State of the Art analysis for the 'SolcelleInverter' project. Optimised design and control of inverter for photovoltaic systems: the AC-module

    Energy Technology Data Exchange (ETDEWEB)

    Baekhoej Kjaer, S.

    2002-02-01

    The 'SolcelleInverter' project starts with this state-of-the-art analysis of 27 different inverter topologies for use in photovoltaic applications. The main concern is the present status for inverters for single solar modules. Technologies for larger clusters of modules are also investigated. The possibility of combining a small decentralised and a big centralised unit is as well investigated. A series of topologies are discovered and this paper will present them. That includes solutions with and without transformers, systems for one or multiple modules, commercial solutions and solutions found in scientific papers and patents. (au)

  2. Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

    Science.gov (United States)

    Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

    2018-03-01

    Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

  3. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

    Science.gov (United States)

    Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2017-07-27

    Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Power inverter design for ASDEX Upgrade saddle coils

    Energy Technology Data Exchange (ETDEWEB)

    Teschke, M., E-mail: teschke@ipp.mpg.de [Max Planck Institute for Plasma Physics, EURATOM Association, Boltzmannstr. 2, 85748 Garching (Germany); Suttrop, W.; Rott, M. [Max Planck Institute for Plasma Physics, EURATOM Association, Boltzmannstr. 2, 85748 Garching (Germany)

    2013-10-15

    Highlights: ► A cost effective inverter topology for AUG's 16 in-vessel saddle coils has been found. ► Use of commercially available power modules is possible. ► Exchange of reactive power between multiple inverters is possible. ► Influence of electromagnetic noise to AUG's diagnostics was measured. ► Gas insulation of electric feed through significantly depends on magnetic fields. It is protected by fast turn-off circuit. -- Abstract: A set of 16 in-vessel saddle coils has been installed in the ASDEX Upgrade (AUG) experiment since the end of 2011 [1]. To achieve full performance, it is necessary to operate them with alternating current (AC) of arbitrary waveforms. To generate spatially resolved magnetic fields, it is required to allocate separate power inverters to every single coil. Therefore, different topologies are analyzed and compared. Studies of the commutation behavior of power stages, different pulse width modulation (PWM) schemes and single-phase-to-earth fault detection are executed. Experiments to evaluate the electromagnetic interference (EMI) of possible inverter topologies on the AUG diagnostics are done as well. A special focus is put on the feasibility of analyzed topologies using industrially available and fully assembled “power modules” to minimize development effort and costs.

  5. Electron-nuclear magnetic resonance in the inverted state

    International Nuclear Information System (INIS)

    Ignatchenko, V.A.; Tsifrinovich, V.I.

    1975-01-01

    The paper considers the susceptibility of the electron-nucleus system of a ferromagnet when nuclear magnetization is inverted with respect to the hyperfine field direction. The inverted state is a situation in which nuclear magnetization is turned through π relative to its equilibrium orientation, whereas electron magnetization is in an equilibrium state with respect to an external magnetic field. The consideration is carried out for a thin plate magnetized in its plane. Amplification of a weak radiofrequency signal can be attained under the fulfilment of an additional inequality relating the interaction frequency with electron and nuclear relaxation parameters. The gain may exceed the gain for an inverted nuclear system in magnetically disordered substances. In the range of strong interaction between the frequencies of ferromagnetic (FMR) and nuclear magnetic (NMR) resonances the electron-nuclear magnetic resonance (ENMR) spectrum possesses a fine structure which is inverse to that obtained for the ENMR spectrum in a normal state. The inverted state ENMR line shape is analysed in detail for the case of so weak HF fields that the relaxation conditions may be regarded as stationary. The initial (linear) stages of a forced transient process arising in an electron-nuclear system under the effect of a strong HF field are briefly analysed

  6. Does human papilloma virus play a role in sinonasal inverted papilloma?

    Science.gov (United States)

    Govindaraj, Satish; Wang, Hailun

    2014-02-01

    Inverted papillomas are a benign sinonasal tumor with a propensity for recurrence and malignant transformation. Although many investigations have been made into the nature of this disease, its etiology and causes for malignant transformation have yet to be fully elucidated. It is the authors' objective to present a review on management of the disease and evaluate the present relationship between human papilloma virus (HPV) and inverted papilloma. A causal relationship between HPV and the pathogenesis and progression of inverted papilloma has been posited since the 1980s. Although widely varied HPV detection rates have been reported, recent studies have noted a substantial increase in both recurrence and malignant transformation in HPV-infected inverted papillomas. However, exact cellular mechanisms by which infection leads to subsequent recurrence and development of carcinoma have yet to be elucidated. Evidence exists suggesting that HPV infection plays a role in the progression of inverted papilloma and confers an increased risk for recurrence and malignant transformation. PCR is the preferred detection method, and fresh or frozen specimens are the ideal source of tissue for evaluation. Although multiple studies have detected an association between HPV and inverted papilloma (both recurrent and malignant transformation), further studies are necessary to elucidate the underlying molecular pathways before an association can be changed to causation.

  7. Review of PV Inverter Technology Cost and Performance Projections

    Energy Technology Data Exchange (ETDEWEB)

    Navigant Consulting Inc.

    2006-01-01

    The National Renewable Energy Laboratory (NREL) has a major responsibility in the implementation of the U.S. Department of Energy's (DOE's) Solar Energy Technologies Program. Sandia National Laboratories (SNL) has a major role in supporting inverter development, characterization, standards, certifications, and verifications. The Solar Energy Technologies Program recently published a Multiyear Technical Plan, which establishes a goal of reducing the Levelized Energy Cost (LEC) for photovoltaic (PV) systems to $0.06/kWh by 2020. The Multiyear Technical Plan estimates that, in order to meet the PV system goal, PV inverter prices will need to decline to $0.25-0.30 Wp by 2020. DOE determined the need to conduct a rigorous review of the PV Program's technical and economic targets, including the target set for PV inverters. NREL requested that Navigant Consulting Inc.(NCI) conduct a review of historical and projected cost and performance improvements for PV inverters, including identification of critical barriers identified and the approaches government might use to address them.

  8. A Family of Cost-Effective Magnetically-Coupled Impedance Source Inverters

    DEFF Research Database (Denmark)

    Li, Kerui; Yang, Yongheng; Qin, Zian

    2017-01-01

    of required semiconductor switches is reduced. More important, the elimination of leakage currents makes it particularly suitable for high-efficiency photovoltaic (PV) applications. A comparison among prior-art PV inverters is then performed. The Performances of the inverters are evaluated analytically...

  9. CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds.

    Science.gov (United States)

    Yan, Fan; Di, Shaokang; Takahashi, Ryoji

    2015-08-01

    The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-2040, a Clark 63 NIL with the r-m allele. Clark 63 is a NIL of Clark with the rxp and Rps1 alleles. A DNA fragment of 13 060 bp was inserted in the intron of Glyma.09G235100 in L72-2040. The fragment had the CACTA motif at both ends, imperfect terminal inverted repeats (TIR), inverse repetition of short sequence motifs close to the 5' and 3' ends, and a duplication of three nucleotides at the site of integration, indicating that it belongs to a CACTA-superfamily transposable element. We designated the element as Tgm11. Overall nucleotide sequence, motifs of TIR, and subterminal repeats were similar to those of Tgm1 and Tgs1, suggesting that these elements comprise a family.

  10. A solution process for inverted tandem solar cells

    DEFF Research Database (Denmark)

    Larsen-Olsen, Thue Trofod; Bundgaard, Eva; Sylvester-Hvid, Kristian O.

    2011-01-01

    Tandem solar cells with normal and inverted device geometries were prepared by a solution process. Both device types were based on the use of zinc(II)oxide as the electron transporting layer (ETL). The hole transporting layer (HTL) was either PEDOT:PSS for normal geometry tandem solar cells...... or vanadium(V)oxide in the case of inverted tandem cells. It was found that the inverted tandem solar cells performed comparable or better than the normal geometry devices, showing that the connection structure of vanadium(V)oxide, Ag nanoparticles and zinc(II)oxide functions both as a good recombination...... layer, ensuring serial connection, and as a solvent barrier, protecting the first photoactive layer from processing of the second layer. This successfully demonstrates a tandem solar cell fabrication process fully compatible with state-of-the-art solution based automated production procedures....

  11. Analysis of Voltage Forming Methods for Multiphase Inverters

    Directory of Open Access Journals (Sweden)

    Tadas Lipinskis

    2013-05-01

    Full Text Available The article discusses advantages of the multiphase AC induction motor over three or less phase motors. It presents possible stator winding configurations for a multiphase induction motor. Various fault control strategies were reviewed for phases feeding the motor. The authors propose a method for quality evaluation of voltage forming algorithm in the inverter. Simulation of a six-phase voltage source inverter, voltage in which is formed using a simple SPWM control algorithm, was performed in Matlab Simulink. Simulation results were evaluated using the proposed method. Inverter’s power stage was powered by 400 V DC source. The spectrum of output currents was analysed and the magnitude of the main frequency component was at least 12 times greater than the next biggest-magnitude component. The value of rectified inverter voltage was 373 V.Article in Lithuanian

  12. Behandling af invert papillom med endonasal endoskopisk sinuskirurgi

    DEFF Research Database (Denmark)

    Andersen, Pia Juul; Kjeldsen, Anette Drøhse; Pedersen, Arne Toft

    2002-01-01

    INTRODUCTION: Inverted papilloma is a benign sinonasal tumour and has a marked tendency to recur after surgical excision. The tumour may be associated with malignancy and during growth it may destroy surrounding tissue. The treatment is either lateral rhinotomy or endoscopic sinus surgery. The aim...... of the study was to describe the course of all patients treated with endoscopic sinus surgery at the ENT Department at Vejle County Hospital during the period 1 January to 31 December 1999. MATERIAL AND METHODS: Twenty-eight journals of patients diagnosed with inverted nasal papillomas were reviewed...... with carcinoma. We did not see any serious side effects to the treatment. DISCUSSION: Endoscopic sinus surgery in combination with Caldwell-Luc can be recommended as an alternative treatment to lateral rhinotomy in patients with inverted papillomas. Preoperative staging with CT or MR-scanning, experienced...

  13. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  14. PeakSeeker: a program for interpreting genotypes of mononucleotide repeats

    Directory of Open Access Journals (Sweden)

    Salipante Stephen J

    2009-02-01

    Full Text Available Abstract Background Mononucleotide repeat microsatellites are abundant, highly polymorphic DNA sequences, having the potential to serve as valuable genetic markers. Use of mononucleotide microsatellites has been limited by their tendency to produce "stutter", confounding signals from insertions and deletions within the mononucleotide tract that occur during PCR, which complicates interpretation of genotypes by masking the true position of alleles. Consequently, microsatellites with larger repeating subunits (dinucleotide and trinucleotide motifs are used, which produce less stutter but are less genetically heterogeneous and less informative. A method to interpret the genotypes of mononucleotide repeats would permit the widespread use of those highly informative microsatellites in genetic research. Findings We have developed an approach to interpret genotypes of mononucleotide repeats using a software program, named PeakSeeker. PeakSeeker interprets experimental electropherograms as the most likely product of signals from individual alleles. Because mononucleotide tracts demonstrate locus-specific patterns of stutter peaks, this approach requires that the genotype pattern from a single allele is defined for each marker, which can be approximated by genotyping single DNA molecules or homozygotes. We have evaluated the program's ability to discriminate various types of homozygous and heterozygous mononucleotide loci using simulated and experimental data. Conclusion Mononucleotide tracts offer significant advantages over di- and tri-nucleotide microsatellite markers traditionally employed in genetic research. The PeakSeeker algorithm provides a high-throughput means to type mononucleotide tracts using conventional and widely implemented fragment length polymorphism genotyping. Furthermore, the PeakSeeker algorithm could potentially be adapted to improve, and perhaps to standardize, the analysis of conventional microsatellite genotypes.

  15. Modeling and analysis of energy quantization effects on single electron inverter performance

    Science.gov (United States)

    Dan, Surya Shankar; Mahapatra, Santanu

    2009-08-01

    In this paper, for the first time, the effects of energy quantization on single electron transistor (SET) inverter performance are analyzed through analytical modeling and Monte Carlo simulations. It is shown that energy quantization mainly changes the Coulomb blockade region and drain current of SET devices and thus affects the noise margin, power dissipation, and the propagation delay of SET inverter. A new analytical model for the noise margin of SET inverter is proposed which includes the energy quantization effects. Using the noise margin as a metric, the robustness of SET inverter is studied against the effects of energy quantization. A compact expression is developed for a novel parameter quantization threshold which is introduced for the first time in this paper. Quantization threshold explicitly defines the maximum energy quantization that an SET inverter logic circuit can withstand before its noise margin falls below a specified tolerance level. It is found that SET inverter designed with CT:CG=1/3 (where CT and CG are tunnel junction and gate capacitances, respectively) offers maximum robustness against energy quantization.

  16. An Enhanced Inverter Controller for PV Applications Using the dSPACE Platform

    Directory of Open Access Journals (Sweden)

    M. A. Hannan

    2010-01-01

    Full Text Available This paper presents the simulation modeling and prototype development of an inverter controller for photovoltaic (PV applications using the dSPACE DS1104 controller platform. The controller platform can link the simulation model developed in the MATLAB/SIMULINK environment to its prototype hardware. In the dSPACE controller, the voltage regulator controls the inverter by employing a proportional integral (PI controller and the Park transformation method to generate sinusoidal pulse-width modulation (SPWM signals. The SPWM signals switch the insulated gate bipolar transistor (IGBT to stabilize the 50-Hz sinusoidal AC output voltages of the inverter. The simulation was performed with a DC power supply that acts as the PV generator to supply the power to the inverter. The simulation model was then translated into the inverter prototype using the dSPACE platform and tested in the laboratory to prove the efficacy of the proposed controller. The experimental results for the inverter system demonstrated the feasibility of the proposed control strategy by maintaining the THD of the output voltage at 4.6%.

  17. Optimal Design of Modern Transformerless PV Inverter Topologies

    OpenAIRE

    Saridakis, Stefanos; Koutroulis, Eftichios; Blaabjerg, Frede

    2013-01-01

    The design optimization of H5, H6, neutral point clamped, active-neutral point clamped, and conergy-NPC transformerless photovoltaic (PV) inverters is presented in this paper. The components reliability in terms of the corresponding malfunctions, affecting the PV inverter maintenance cost during the operational lifetime period of the PV installation, is also considered in the optimization process. According to the results of the proposed design method, different optimal values of the PV inver...

  18. Grid-connected to/from off-grid transference for micro-grid inverters

    OpenAIRE

    Heredero Peris, Daniel; Chillón Antón, Cristian; Pages Gimenez, Marc; Gross, Gabriel Igor; Montesinos Miracle, Daniel

    2013-01-01

    This paper compares two methods for controlling the on-line transference from connected to stand-alone mode and vice versa in converters for micro-grids. The first proposes a method where the converter changes from CSI (Current Source Inverter) in grid-connected mode to VSI (Voltage Source Inverter) in off-grid. In the second method, the inverter always works as a non-ideal voltage source, acting as VSI, using AC droop control strategy.

  19. [Cover motifs of the Tidsskrift. A 14-year cavalcade].

    Science.gov (United States)

    Nylenna, M

    1998-12-10

    In 1985 the Journal of the Norwegian Medical Association changed its cover policy, moving the table of contents inside the Journal and introducing cover illustrations. This article provides an analysis of all cover illustrations published over this 14-year period, 420 covers in all. There is a great variation in cover motifs and designs and a development towards more general motifs. The initial emphasis on historical and medical aspects is now less pronounced, while the use of works of art and nature motifs has increased, and the cover now more often has a direct bearing on the specific contents of the issue. Professor of medical history Oivind Larsen has photographed two thirds of the covers and contributed 95% of the inside essay-style reflections on the cover motif. Over the years, he has expanded the role of the historian of medicine disseminating knowledge to include that of the raconteur with a personal tone of voice. The Journal's covers are now one of its most characteristic features, emblematic of the Journal's ambition of standing for quality and timelessness vis-à-vis the news media, and of its aim of bridging the gap between medicine and the humanities.

  20. Insights into the motif preference of APOBEC3 enzymes.

    Directory of Open Access Journals (Sweden)

    Diako Ebrahimi

    Full Text Available We used a multivariate data analysis approach to identify motifs associated with HIV hypermutation by different APOBEC3 enzymes. The analysis showed that APOBEC3G targets G mainly within GG, TG, TGG, GGG, TGGG and also GGGT. The G nucleotides flanked by a C at the 3' end (in +1 and +2 positions were indicated as disfavoured targets by APOBEC3G. The G nucleotides within GGGG were found to be targeted at a frequency much less than what is expected. We found that the infrequent G-to-A mutation within GGGG is not limited to the inaccessibility, to APOBEC3, of poly Gs in the central and 3'polypurine tracts (PPTs which remain double stranded during the HIV reverse transcription. GGGG motifs outside the PPTs were also disfavoured. The motifs GGAG and GAGG were also found to be disfavoured targets for APOBEC3. The motif-dependent mutation of G within the HIV genome by members of the APOBEC3 family other than APOBEC3G was limited to GA→AA changes. The results did not show evidence of other types of context dependent G-to-A changes in the HIV genome.

  1. I-motif DNA structures are formed in the nuclei of human cells

    Science.gov (United States)

    Zeraati, Mahdi; Langley, David B.; Schofield, Peter; Moye, Aaron L.; Rouet, Romain; Hughes, William E.; Bryan, Tracy M.; Dinger, Marcel E.; Christ, Daniel

    2018-06-01

    Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

  2. A modified two-level three-phase quasi-soft-switching inverter

    DEFF Research Database (Denmark)

    Liu, Yusheng; Wu, Weimin; Blaabjerg, Frede

    2014-01-01

    A traditional Voltage Source Inverter (VSI) has higher efficiency than a Current Voltage Source (CSI) due to the less conduction power loss. However, the reverse recovery of the free-wheeling diode limits the efficiency improvement for the silicon devices based hard-switching VSI. The traditional...... quasi-soft-switching inverter can alternate between VSI and CSI by using a proper control scheme and thereby reduce the power losses caused by the reverse recovery of the free-wheeling diode. Nevertheless, slightly extra conduction power loss of the auxiliary switch is also introduced. In order...... to reduce the extra conduction power loss and the voltage stress across the DC-link capacitor, a modified two-level three-phase quasi-soft-switching inverter is proposed by using a SiC MOSFET instead of an IGBT. The principle of the modified two-level three-phase quasi-soft-switching inverter is analyzed...

  3. An LLCL Power Filter for Single-Phase Grid-Tied Inverter

    DEFF Research Database (Denmark)

    Wu, Weimin; He, Yuanbin; Blaabjerg, Frede

    2012-01-01

    This paper presents a new topology of higher order power filter for grid-tied voltage-source inverters, named the LLCL filter, which inserts a small inductor in the branch loop of the capacitor in the traditional LCL filter to compose a series resonant circuit at the switching frequency. Particul......This paper presents a new topology of higher order power filter for grid-tied voltage-source inverters, named the LLCL filter, which inserts a small inductor in the branch loop of the capacitor in the traditional LCL filter to compose a series resonant circuit at the switching frequency...... to the inverter system control. The parameter design criteria of the proposed LLCL filter is also introduced. The comparative analysis and discussions regarding the traditional LCL filter and the proposed LLCL filter have been presented and evaluated through experiment on a 1.8-kW-single-phase grid-tied inverter...

  4. Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

    KAUST Repository

    Alam, Tanvir

    2018-03-11

    Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

  5. Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

    Directory of Open Access Journals (Sweden)

    Pupko Tal

    2008-10-01

    Full Text Available Abstract Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif. Reviewers This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers' Reports section.

  6. Argonne inverted sputter source

    International Nuclear Information System (INIS)

    Yntema, J.L.; Billquist, P.J.

    1983-01-01

    The emittance of the inverted sputter source with immersion lenses was measured to be about 5π mm mrad MeV/sup 1/2/ at the 75% level over a wide range of beam intensities. The use of the source in experiments with radioactive sputter targets and hydrogen loaded targets is described. Self contamination of the source is discussed

  7. Single DV-DXCCII Based Voltage Controlled First Order All-pass Filter with Inverting and Non-inverting responses

    Directory of Open Access Journals (Sweden)

    B Chaturvedi

    2015-12-01

    Full Text Available In this paper, a new voltage controlled first order all-pass filter is presented. The proposed circuit employs a single differential voltage dual-X second generation current conveyor (DV-DXCCII and a grounded capacitor only. The proposed all-pass filter provides both inverting and non inverting voltage-mode outputs from the same configuration simultaneously without any matching condition. Non-ideal analysis along with sensitivity analysis is also investigated. The proposed circuit has low active and passive sensitivities. As an application the proposed all-pass filter is connected in cascade to get higher order filter. The theoretical results are validated thorough PSPICE simulations using TSMC 0.18µm CMOS process parameters.

  8. Hawaiian Electric Advanced Inverter Grid Support Function Laboratory Validation and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Austin [National Renewable Energy Lab. (NREL), Golden, CO (United States); Nagarajan, Adarsh [National Renewable Energy Lab. (NREL), Golden, CO (United States); Prabakar, Kumar [National Renewable Energy Lab. (NREL), Golden, CO (United States); Gevorgian, Vahan [National Renewable Energy Lab. (NREL), Golden, CO (United States); Lundstrom, Blake [National Renewable Energy Lab. (NREL), Golden, CO (United States); Nepal, Shaili [National Renewable Energy Lab. (NREL), Golden, CO (United States); Hoke, Anderson [National Renewable Energy Lab. (NREL), Golden, CO (United States); Asano, Marc [Hawaiian Electric Company, Honolulu, HI (United States); Ueda, Reid [Hawaiian Electric Company, Honolulu, HI (United States); Shindo, Jon [Hawaiian Electric Company, Honolulu, HI (United States); Kubojiri, Kandice [Hawaiian Electric Company, Honolulu, HI (United States); Ceria, Riley [Hawaiian Electric Company, Honolulu, HI (United States); Ifuku, Earle [Hawaiian Electric Company, Honolulu, HI (United States)

    2016-12-01

    The objective for this test plan was to better understand how to utilize the performance capabilities of advanced inverter functions to allow the interconnection of distributed energy resource (DER) systems to support the new Customer Self-Supply, Customer Grid-Supply, and other future DER programs. The purpose of this project was: 1) to characterize how the tested grid supportive inverters performed the functions of interest, 2) to evaluate the grid supportive inverters in an environment that emulates the dynamics of O'ahu's electrical distribution system, and 3) to gain insight into the benefits of the grid support functions on selected O'ahu island distribution feeders. These goals were achieved through laboratory testing of photovoltaic inverters, including power hardware-in-the-loop testing.

  9. High Quality Model Predictive Control for Single Phase Grid Connected Photovoltaic Inverters

    DEFF Research Database (Denmark)

    Zangeneh Bighash, Esmaeil; Sadeghzadeh, Seyed Mohammad; Ebrahimzadeh, Esmaeil

    2018-01-01

    Single phase grid-connected inverters with LCL filter are widely used to connect the photovoltaic systems to the utility grid. Among the presented control schemes, predictive control methods are faster and more accurate but are more complex to implement. Recently, the model-predictive control...... algorithm for single-phase inverter has been presented, where the algorithm implementation is straightforward. In the proposed approach, all switching states are tested in each switching period to achieve the control objectives. However, since the number of the switching states in single-phase inverter...... is low, the inverter output current has a high total harmonic distortions. In order to reduce the total harmonic distortions of the injected current, this paper presents a high-quality model-predictive control for one of the newest structure of the grid connected photovoltaic inverter, i.e., HERIC...

  10. A Novel Model Predictive Control for Single-Phase Grid-Connected Photovoltaic Inverters

    DEFF Research Database (Denmark)

    Zangeneh Bighash, Esmaeil; Sadeghzadeh, Seyed Mohammad; Ebrahimzadeh, Esmaeil

    2017-01-01

    Single-phase grid-connected inverters with LCL filter are widely used to connect photovoltaic systems to the utility grid. Among the existing control schemes, predictive control methods are faster and more accurate but also more complicated to implement. Recently, the Model Predictive Control (MPC......) algorithm for single-phase inverter has been presented, where the algorithm implementation is straightforward. In the MPC approach, all switching states are considered in each switching period to achieve the control objectives. However, since the number of switching states in single-phase inverters is small......, the inverter output current has a high Total Harmonic Distortions (THD). In order to reduce this, this paper presents an improved MPC for single-phase grid-connected inverters. In the proposed approach, the switching algorithm is changed and the number of the switching states is increased by means of virtual...

  11. Lifetime Evaluation of PV Inverters considering Panel Degradation Rates and Installation Sites

    DEFF Research Database (Denmark)

    Sangwongwanich, Ariya; Yang, Yongheng; Sera, Dezso

    2017-01-01

    The PV inverter lifetime is affected by the installed sites related to different solar irradiance and ambient temperature profiles. In fact, the installation site also affects the PV panel degradation rate, and thus the long-term power production. Prior-art lifetime analysis in PV inverters has...... not yet investigated the impact of panel degradation. This paper thus evaluates the lifetime of PV inverters considering panel degradation rates and installation sites. Evaluations have been carried out on PV systems installed in Denmark and Arizona. The results reveal that the PV panel degradation rate...... has a considerable impact on the PV inverter lifetime, especially in the hot climate (e.g., Arizona), where the panel degrades at a faster rate. In that case, the PV inverter lifetime estimation can be deviated by 54%, if the impact of PV panel degradation is not taken into account....

  12. Identification of a putative nuclear export signal motif in human NANOG homeobox domain

    International Nuclear Information System (INIS)

    Park, Sung-Won; Do, Hyun-Jin; Huh, Sun-Hyung; Sung, Boreum; Uhm, Sang-Jun; Song, Hyuk; Kim, Nam-Hyung; Kim, Jae-Hwan

    2012-01-01

    Highlights: ► We found the putative nuclear export signal motif within human NANOG homeodomain. ► Leucine-rich residues are important for human NANOG homeodomain nuclear export. ► CRM1-specific inhibitor LMB blocked the potent human NANOG NES-mediated nuclear export. -- Abstract: NANOG is a homeobox-containing transcription factor that plays an important role in pluripotent stem cells and tumorigenic cells. To understand how nuclear localization of human NANOG is regulated, the NANOG sequence was examined and a leucine-rich nuclear export signal (NES) motif ( 125 MQELSNILNL 134 ) was found in the homeodomain (HD). To functionally validate the putative NES motif, deletion and site-directed mutants were fused to an EGFP expression vector and transfected into COS-7 cells, and the localization of the proteins was examined. While hNANOG HD exclusively localized to the nucleus, a mutant with both NLSs deleted and only the putative NES motif contained (hNANOG HD-ΔNLSs) was predominantly cytoplasmic, as observed by nucleo/cytoplasmic fractionation and Western blot analysis as well as confocal microscopy. Furthermore, site-directed mutagenesis of the putative NES motif in a partial hNANOG HD only containing either one of the two NLS motifs led to localization in the nucleus, suggesting that the NES motif may play a functional role in nuclear export. Furthermore, CRM1-specific nuclear export inhibitor LMB blocked the hNANOG potent NES-mediated export, suggesting that the leucine-rich motif may function in CRM1-mediated nuclear export of hNANOG. Collectively, a NES motif is present in the hNANOG HD and may be functionally involved in CRM1-mediated nuclear export pathway.

  13. Reliability consideration of low-power-grid-tied inverter for photovoltaic application

    OpenAIRE

    Liu, J.; Henze, N.

    2009-01-01

    In recent years PV modules have been improved evidently. An excellent reliability has been validated corresponding to Mean Time between Failure (MTBF) between 500 and 6000 years respectively in commercial utility power systems. Manufactures can provide performance guarantees for PV modules at least for 20 years. If an average inverter lifetime of 5 years is assumed, it is evident that the overall reliability of PV systems [PVSs] with integrated inverter is determined chiefly by the inverter i...

  14. Methods for the Optimal Design of Grid-Connected PV Inverters

    DEFF Research Database (Denmark)

    Koutroulis, Eftichios; Blaabjerg, Frede

    2011-01-01

    and the efficient processing of this power by the DC/AC inverter. In this paper two new methods are presented for the optimal design of a PV inverter power section, output filter and MPPT control strategy. The influences of the electric grid regulations and standards as well as the PV array operational......The DC/AC inverters are used in grid-connected PV energy production systems as the power processing interface between the PV energy source and the electric grid. The energy injected into the electric grid by the PV installation depends on the amount of power extracted from the PV power source...

  15. Analysis and Design of Solar Photo voltaic Grid Connected Inverter

    Directory of Open Access Journals (Sweden)

    Muddasani Satyanarayana

    2015-08-01

    Full Text Available This paper presents common mode voltage analysis of single phase grid connected photovoltaic inverter. Many researchers proposed different grid tie inverters for applications like domestic powering, street lighting, water pumping, cooling and heating applications, however traditional grid tie PV inverter uses either a line frequency or a high frequency transformer between the inverter and grid but losses will increase in the network leading to reduced efficiency of the system. In order to increase the efficiency, with reduced size and cost of the system, the effective solution is to remove the isolation transformer. But common mode (CM ground leakage current due to parasitic capacitance between the PV panels and the ground making the system unreliable. The common mode current reduces the efficiency of power conversion stage, affects the quality of grid current, deteriorate the electric magnetic compatibility and give rise to the safety threats. In order to eliminate the common mode leakage current in Transformerless PV systm two control algorithms of multi-carrier pwm are implemented and compared for performance analysis.The shoot-through issue that is encountered by traditional voltage source inverter is analyzed for enhanced system reliability. These control algorithms are compared for common mode voltage and THD comparisons. The proposed system is designed using MATLAB/SIMULINK software for analysis.

  16. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L

    1998-01-01

    Many integral membrane proteins contain leucine-based motifs within their cytoplasmic domains that mediate internalization and intracellular sorting. Two types of leucine-based motifs have been identified. One type is dependent on phosphorylation, whereas the other type, which includes an acidic...... amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane...... and the phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic...

  17. Dead-Time Generation in Six-Phase Frequency Inverter

    Directory of Open Access Journals (Sweden)

    Aurelijus Pitrėnas

    2016-06-01

    Full Text Available In this paper control of multi-phase induction drives is discussed. Structure of six-phase frequency inverter is examined. The article deals with dead-time generation circuits in six-phase frequency inverter for transistor control signals. Computer models of dead-time circuits is created using LTspice software package. Simulation results are compared with experimental results of the tested dead-time circuits. Parameters obtained in simulation results are close to the parameters obtained in experimental results.

  18. Active control of flying capacitor currents in multilevel voltage-source inverters

    Czech Academy of Sciences Publication Activity Database

    Kokeš, Petr; Semerád, Radko

    2013-01-01

    Roč. 58, č. 4 (2013), s. 393-410 ISSN 0001-7043 Institutional support: RVO:61388998 Keywords : voltage source inverter (VSI) * multilevel inverter * flying capacitor Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  19. Inverted opal luminescent Ce-doped silica glasses

    Directory of Open Access Journals (Sweden)

    R. Scotti

    2006-01-01

    Full Text Available Inverted opal Ce-doped silica glasses (Ce : Si molar ratio 1 ⋅ 10−3 were prepared by a sol-gel method using opals of latex microspheres as templates. The rare earth is homogeneously dispersed in silica host matrix, as evidenced by the absence of segregated CeO2, instead present in monolithic Ce-doped SG with the same cerium content. This suggests that the nanometric dimensions of bridges and junctions of the host matrix in the inverted opal structures favor the RE distribution avoiding the possible segregation of CeO2.

  20. An Improved Fuzzy Logic Controller Design for PV Inverters Utilizing Differential Search Optimization

    Directory of Open Access Journals (Sweden)

    Ammar Hussein Mutlag

    2014-01-01

    Full Text Available This paper presents an adaptive fuzzy logic controller (FLC design technique for photovoltaic (PV inverters using differential search algorithm (DSA. This technique avoids the exhaustive traditional trial and error procedure in obtaining membership functions (MFs used in conventional FLCs. This technique is implemented during the inverter design phase by generating adaptive MFs based on the evaluation results of the objective function formulated by the DSA. In this work, the mean square error (MSE of the inverter output voltage is used as an objective function. The DSA optimizes the MFs such that the inverter provides the lowest MSE for output voltage and improves the performance of the PV inverter output in terms of amplitude and frequency. The design procedure and accuracy of the optimum FLC are illustrated and investigated using simulations conducted for a 3 kW three-phase inverter in a MATLAB/Simulink environment. Results show that the proposed controller can successfully obtain the desired output when different linear and nonlinear loads are connected to the system. Furthermore, the inverter has reasonably low steady state error and fast response to reference variation.