Genetic characterization of human herpesvirus type 1: Full-length genome sequence of strain obtained from an encephalitis case from India

Directory of Open Access Journals (Sweden)

Vijay P Bondre

2016-01-01

Interpretation & conclusions: Our results showed that the full-length genome sequence generated from an Indian HSV-1 isolate shared close genetic relationship with the American KOS and Chinese CR38 strains which belonged to the Asian genetic lineage. Recombination analysis of Indian isolate demonstrated multiple recombination crossover points throughout the genome. This full-length genome sequence amplified from the Indian isolate would be helpful to study HSV evolution, genetic basis of differential pathogenesis, host-virus interactions and viral factors contributing towards differential clinical outcome in human infections.

Characterization of full-length sequenced cDNA inserts (FLIcs from Atlantic salmon (Salmo salar

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Lunner Sigbjørn

2009-10-01

Full Text Available Abstract Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP, the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91% of the transcripts were annotated using Gene Ontology (GO terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS. The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS. This

XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

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Giegerich Robert

2005-09-01

Full Text Available Abstract Background Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems. Description Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and ~67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined. Conclusion The results of the analysis have been stored in a publicly available database XenDB http://bibiserv.techfak.uni-bielefeld.de/xendb/. A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches. Supplementary material can be found at http://bibiserv.techfak.uni-bielefeld.de/xendb/.

Full-length Ebola glycoprotein accumulates in the endoplasmic reticulum

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Bhattacharyya Suchita

2011-01-01

Full Text Available Abstract The Filoviridae family comprises of Ebola and Marburg viruses, which are known to cause lethal hemorrhagic fever. However, there is no effective anti-viral therapy or licensed vaccines currently available for these human pathogens. The envelope glycoprotein (GP of Ebola virus, which mediates entry into target cells, is cytotoxic and this effect maps to a highly glycosylated mucin-like region in the surface subunit of GP (GP1. However, the mechanism underlying this cytotoxic property of GP is unknown. To gain insight into the basis of this GP-induced cytotoxicity, HEK293T cells were transiently transfected with full-length and mucin-deleted (Δmucin Ebola GP plasmids and GP localization was examined relative to the nucleus, endoplasmic reticulum (ER, Golgi, early and late endosomes using deconvolution fluorescent microscopy. Full-length Ebola GP was observed to accumulate in the ER. In contrast, GPΔmucin was uniformly expressed throughout the cell and did not localize in the ER. The Ebola major matrix protein VP40 was also co-expressed with GP to investigate its influence on GP localization. GP and VP40 co-expression did not alter GP localization to the ER. Also, when VP40 was co-expressed with the nucleoprotein (NP, it localized to the plasma membrane while NP accumulated in distinct cytoplasmic structures lined with vimentin. These latter structures are consistent with aggresomes and may serve as assembly sites for filoviral nucleocapsids. Collectively, these data suggest that full-length GP, but not GPΔmucin, accumulates in the ER in close proximity to the nuclear membrane, which may underscore its cytotoxic property.

Purification and characterization of recombinant full-length and protease domain of murine MMP-9 expressed in Drosophila S2 cells

DEFF Research Database (Denmark)

Rasch, Morten G; Lund, Ida K; Illemann, Martin

2010-01-01

MMP-9. Constructs encoding zymogens of full-length murine MMP-9 and a version lacking the O-glycosylated linker region and hemopexin domains were therefore generated and expressed in stably transfected Drosophila S2 insect cells. After 7 days of induction the expression levels of the full......-length and truncated versions were 5 mg/l and 2 mg/l, respectively. The products were >95% pure after gelatin Sepharose chromatography and possessed proteolytic activity when analyzed by gelatin zymography. Using the purified full-length murine MMP-9 we raised polyclonal antibodies by immunizations of rabbits......Matrix metalloproteinase-9 (MMP-9) is a 92-kDa soluble pro-enzyme implicated in pathological events including cancer invasion. It is therefore an attractive target for therapeutic intervention studies in mouse models. Development of inhibitors requires sufficient amounts of correctly folded murine...

Near Full-Length Identification of a Novel HIV-1 CRF01_AE/B/C Recombinant in Northern Myanmar.

Science.gov (United States)

Zhou, Yan-Heng; Chen, Xin; Liang, Yue-Bo; Pang, Wei; Qin, Wei-Hong; Zhang, Chiyu; Zheng, Yong-Tang

2015-08-01

The Myanmar-China border appears to be the "hot spot" region for the occurrence of HIV-1 recombination. The majority of the previous analyses of HIV-1 recombination were based on partial genomic sequences, which obviously cannot reflect the reality of the genetic diversity of HIV-1 in this area well. Here, we present a near full-length characterization of a novel HIV-1 CRF01_AE/B/C recombinant isolated from a long-distance truck driver in Northern Myanmar. It is the first description of a near full-length genomic sequence in Myanmar since 2003, and might be one of the most complicated HIV-1 chimeras ever detected in Myanmar, containing four CRF01_AE, six B segments, and five C segments separated by 14 breakpoints throughout its genome. The discovery and characterization of this new CRF01_AE/B/C recombinant indicate that intersubtype recombination is ongoing in Myanmar, continuously generating new forms of HIV-1. More work based on near full-length sequence analyses is urgently needed to better understand the genetic diversity of HIV-1 in these regions.

A comparative phylogenetic analysis of full-length mariner elements

Indian Academy of Sciences (India)

Mariner like elements (MLEs) are widely distributed type II transposons with an open reading frame (ORF) for transposase. We studied comparative phylogenetic evolution and inverted terminal repeat (ITR) conservation of MLEs from Indian saturniid silkmoth, Antheraea mylitta with other full length MLEs submitted in the ...

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

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Carol Soderlund

2009-11-01

Full Text Available Full-length cDNA (FLcDNA sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs, only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org.

Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

Science.gov (United States)

Andreassen, Rune; Lunner, Sigbjørn; Høyheim, Bjørn

2009-01-01

Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining c

Failure Mode and Effects Analysis (FMEA) of the solid state full length rod control system

International Nuclear Information System (INIS)

Shopsky, W.E.

1977-01-01

The Full Length Rod Control System (FLRCS) controls the power to the rod drive mechanisms for rod movement in response to signals received from the Reactor Control System or from signals generated through Reactor Operator action. Rod movement is used to control reactivity of the reactor during plant operation. The Full Length Rod Control System is designed to perform its reactivity control function in conjunction with the Reactor Control and Protection System, to maintain the reactor core within design safety limits. By the use of a Failure Mode and Effects Analysis, it is shown that the FLRCS will perform its reactivity control functions considering the loss of single active components. That is, sufficient fault limiting control circuits are provided which blocks control rod movement and/or indicates presence of a fault condition at the Control Board. Reactor operator action or automatic reactor trip will thus mitigate the consequences of potential failure of the FLRCS. The analysis also qualitatively demonstrates the reliability of the FLRCS to perform its intended function

Irradiation performance of full-length metallic IFR fuels

International Nuclear Information System (INIS)

Tsai, H.; Neimark, L.A.

1992-07-01

An assembly irradiation of 169 full-length U-Pu-Zr metallic fuel pins was successfully completed in FFTF to a goal burnup of 10 at.%. All test fuel pins maintained their cladding integrity during the irradiation. Postirradiation examination showed minimal fuel/cladding mechanical interaction and excellent stability of the fuel column. Fission-gas release was normal and consistent with the existing data base from irradiation testing of shorter metallic fuel pins in EBR-II

The function analysis of full-length cDNA sequence from IRM-2 mouse cDNA library

International Nuclear Information System (INIS)

Wang Qin; Liu Xiaoqiu; Xu Chang; Du Liqing; Sun Zhijuan; Wang Yan; Liu Qiang; Song Li; Li Jin; Fan Feiyue

2013-01-01

Objective: To identify the function of full-length cDNA sequence from IRM-2 mouse cDNA library. Methods: Full-length cDNA products were amplified by PCR from IRM-2 mouse cDNA library according to twenty-one pieces of expressed sequence tag. The expression of full-length cDNAs were detected after mouse embryonic fibroblasts were exposed to 6.5 Gy γ-ray radiation. And the effect on the growth of radiosensitivity cells AT5B1VA transfected with full-length cDNAs was investigated. Results: The expression of No.4, 5 and 2 full-length cDNAs from IRM-2 mouse were higher than that of parental ICR and 615 mouse after mouse embryonic fibroblasts irradiated with γ-ray radiation. And the survival rate of AT5B1VA cells transfected with No.4, 5 and 2 full-length cDNAs was high. Conclusion: No.4, 5 and 2 full-length cDNAs of IRM-2 mouse are of high radioresistance. (authors)

Seismic inference of 57 stars using full-length Kepler data sets

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Creevey Orlagh

2017-01-01

Full Text Available We present stellar properties of 57 stars from a seismic inference using full-length data sets from Kepler (mass, age, radius, distances. These stars comprise active stars, planet-hosts, solar-analogs, and binary systems. We validate the distances derived from the astrometric Gaia-Tycho solution. Ensemble analysis of the stellar properties reveals a trend of mixing-length parameter with the surface gravity and effective temperature. We derive a linear relationship with the seismic quantity ‹r02› to estimate the stellar age. Finally, we define the stellar regimes where the Kjeldsen et al (2008 empirical surface correction for 1D model frequencies is valid.

Full length prototype SSC dipole test results

International Nuclear Information System (INIS)

Strait, J.; Brown, B.C.; Carson, J.

1987-01-01

Results are presented from tests of the first full length prototype SSC dipole magnet. The cryogenic behavior of the magnet during a slow cooldown to 4.5K and a slow warmup to room temperature has been measured. Magnetic field quality was measured at currents up to 2000 A. Averaged over the body field all harmonics with the exception of b 2 and b 8 are at or within the tolerances specified by the SSC Central Design Group. (The values of b 2 and b 8 result from known design and construction defects which will be be corrected in later magnets.) Using an NMR probe the average body field strength is measured to be 10.283 G/A with point to point variations on the order of one part in 1000. Data are presented on quench behavior of the magnet up to 3500 A (approximately 55% of full field) including longitudinal and transverse velocities for the first 250 msec of the quench

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

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Alamar Santiago

2009-09-01

Full Text Available Abstract Background Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation. Results We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis. Conclusion The new

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

Science.gov (United States)

Marques, M Carmen; Alonso-Cantabrana, Hugo; Forment, Javier; Arribas, Raquel; Alamar, Santiago; Conejero, Vicente; Perez-Amador, Miguel A

2009-01-01

Background Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation. Results We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis. Conclusion The new EST collection denotes an

Purification and Fibrillation of Full-Length Recombinant PrP

OpenAIRE

Makarava, Natallia; Baskakov, Ilia V.

2012-01-01

Misfolding and aggregation of prion protein (PrP) is related to several neurodegenerative diseases in humans such as Creutzfeldt–Jacob disease, fatal familial insomnia, and Gerstmann–Straussler–Sheinker disease. Certain applications in prion area require recombinant PrP of high purity and quality. Here, we report an experimental procedure for expression and purification of full-length mammalian PrP. This protocol has been proved to yield PrP of extremely high purity that lac...

Increased circulating full-length betatrophin levels in drug-naïve metabolic syndrome.

Science.gov (United States)

Liu, Dan; Li, Sheyu; He, He; Yu, Chuan; Li, Xiaodan; Liang, Libo; Chen, Yi; Li, Jianwei; Li, Jianshu; Sun, Xin; Tian, Haoming; An, Zhenmei

2017-03-14

Betatrophin is a newly identified circulating adipokine playing a role in the regulation of glucose homeostasis and lipid metabolism. But its role in metabolic syndrome (MetS) remains unknown. Therefore, we aimed to compare the circulating betatrophin concentrations between patients with MetS and healthy controls. We recruited 47 patients with MetS and 47 age and sex matched healthy controls. Anthropometric and biochemical measurements were performed, and serum betatrophin levels were detected by ELISA. Full-length betatrophin levels in patients with MetS were significantly higher than those in controls (694.84 ± 365.51 pg/ml versus 356.64 ± 287.92 pg/ml; P <0.001). While no significant difference of total betatrophin levels was found between the two groups (1.20 ± 0.79 ng/ml versus 1.31 ± 1.08 ng/ml; P = 0.524). Full-length betatrophin level was positively correlated with fasting plasma glucose (FPG) (r = 0.357, P = 0.014) and 2-hour plasma glucose (2hPG) (r = 0.38, P <0.01). Binary logistic regression models indicated that subjects in the tertile of the highest full-length betatrophin level experienced higher odds of having MetS (OR, 8.6; 95% CI 2.8-26.8; P <0.001). Our study showed that full-length betatrophin concentrations were increased in drug-naïve MetS patients.

Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns

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Hayashizaki Yoshihide

2009-06-01

Full Text Available Abstract Background Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs for wheat is becoming particularly important for functional genomics and molecular breeding. We prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues subjected to stress. We also examined their expression profiles in silico. As full-length cDNAs are indispensable to certify the collected ESTs and annotate the genes in the wheat genome, we performed a systematic survey and sequencing of the full-length cDNA clones. This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals. Results As part of the functional genomics and development of genomic wheat resources, we have generated a collection of full-length cDNAs from common wheat. By grouping the ESTs of recombinant clones randomly selected from the full-length cDNA library, we were able to sequence 6,162 independent clones with high accuracy. About 10% of the clones were wheat-unique genes, without any counterparts within the DNA database. Wheat clones that showed high homology to those of rice were selected in order to investigate their expression patterns in various tissues throughout the wheat life cycle and in response to abiotic-stress treatments. To assess the variability of genes that have evolved differently in wheat and rice, we calculated the substitution rate (Ka/Ks of the counterparts in wheat and rice. Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection. Conclusion We have generated a high-quality full-length cDNA resource for common wheat, which is essential for continuation of the

Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

KAUST Repository

Brenner, Sydney

2012-10-08

Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the \\'oligo-capping\\' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5\\'-ESTs and 41,317 3\\'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for

Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

KAUST Repository

Brenner, Sydney; Kodzius, Rimantas; Tan, Yue Ying; Tay, Alice; Tay, Boon-Hui; Venkatesh, Byrappa

2012-01-01

Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the 'oligo-capping' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5'-ESTs and 41,317 3'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole

Impact of Generator Stroke Length on Energy Production for a Direct Drive Wave Energy Converter

Directory of Open Access Journals (Sweden)

Yue Hong

2016-09-01

Full Text Available The Lysekil wave energy converter (WEC, developed by the wave energy research group of Uppsala University, has evolved through a variety of mechanical designs since the first prototype was installed in 2006. The hundreds of engineering decisions made throughout the design processes have been based on a combination of theory, know-how from previous experiments, and educated guesses. One key parameter in the design of the WECs linear generator is the stroke length. A long stroke requires a taller WEC with associated economical and mechanical challenges, but a short stroke limits the power production. The 2-m stroke of the current WECs has been an educated guess for the Swedish wave climate, though the consequences of this choice on energy absorption have not been studied. When the WEC technology is considered for international waters, with larger waves and challenges of energy absorption and survivability, the subject of stroke length becomes even more relevant. This paper studies the impact of generator stroke length on energy absorption for three sites off the coasts of Sweden, Chile and Scotland. 2-m, 4-m, and unlimited stroke are considered. Power matrices for the studied WEC prototype are presented for each of the studied stroke lengths. Presented results quantify the losses incurred by a limited stroke. The results indicate that a 2-m stroke length is likely to be a good choice for Sweden, but 4-m is likely to be necessary in more energetic international waters.

Simulations of The Dalles Dam Proposed Full Length Spillwall

Energy Technology Data Exchange (ETDEWEB)

Rakowski, Cynthia L.; Perkins, William A.; Richmond, Marshall C.; Serkowski, John A.

2008-02-25

This report presents results of a computational fluid dynamics (CFD) modeling study to evaluatethe impacts of a full-length spillwall at The Dalles Dam. The full-length spillwall is being designed and evaluated as a structural means to improve tailrace egress and thus survival of juvenile fish passing through the spillway. During the course of this study, a full-length spillwall at Bays 6/7 and 8/9 were considered. The U.S. Army Corps of Engineers (USACE) has proposed extending the spillwall constructed in the stilling basin between spillway Bays 6 and 7 about 590 ft farther downstream. It is believed that the extension of the spillwall will improve egress conditions for downstream juvenile salmonids by moving them more rapidly into the thalweg of the river hence reducing their exposure to predators. A numerical model was created, validated, and applied the The Dalles Dam tailrace. The models were designed to assess impacts to flow, tailrace egress, navigation, and adult salmon passage of a proposed spill wall extension. The more extensive model validation undertaken in this study greatly improved our confidence in the numerical model to represent the flow conditions in The Dalles tailrace. This study used these validated CFD models to simulate the potential impacts of a spillwall extension for The Dalles Dam tailrace for two locations. We determined the following: (1)The construction of an extended wall (between Bays 6/7) will not adversely impact entering or exiting the navigation lock. Impact should be less if a wall were constructed between Bays 8/9. (2)The construction of a wall between Bays 6/7 will increase the water surface elevation between the wall and the Washington shore. Although the increased water surface elevation would be beneficial to adult upstream migrants in that it decreases velocities on the approach to the adult ladder, the increased flow depth would enhance dissolved gas production, impacting potential operations of the project because of

Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs

Directory of Open Access Journals (Sweden)

Sugano Sumio

2009-07-01

Full Text Available Abstract Background Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six apicomplexa parasites using our full-length oligo-capping cDNA library method. To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites. Results In this study, we used a total of 61,056 5'-end-single-pass cDNA sequences from Plasmodium falciparum, P. vivax, P. yoelii, P. berghei, Cryptosporidium parvum, and Toxoplasma gondii. We compared these partially sequenced cDNA sequences with the currently annotated gene models and observed significant inconsistencies between the two datasets. In particular, we found that on average 14% of the exons in the current gene models were not supported by any cDNA evidence, and that 16% of the current gene models may contain at least one mis-annotation and should be re-evaluated. We also identified a large number of transcripts that had been previously unidentified. For 732 cDNAs in T. gondii, the entire sequences were determined in order to evaluate the annotated gene models at the complete full-length transcript level. We found that 41% of the T. gondii gene models contained at least one inconsistency. We also identified and confirmed by RT-PCR 140 previously unidentified transcripts found in the intergenic regions of the current gene annotations. We show that the majority of these discrepancies are due to questionable predictions of one or two extra exons in the upstream or downstream regions of the genes. Conclusion Our data indicates that the current gene models are likely to still be incomplete and have much room for improvement. Our unique full-length cDNA information is especially useful for further refinement of the annotations for the genomes of

Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Risager, Peter Christian; Fahnøe, Ulrik

2013-01-01

Background Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described....... This strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. Results A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable...

TypeLoader: A fast and efficient automated workflow for the annotation and submission of novel full-length HLA alleles.

Science.gov (United States)

Surendranath, V; Albrecht, V; Hayhurst, J D; Schöne, B; Robinson, J; Marsh, S G E; Schmidt, A H; Lange, V

2017-07-01

Recent years have seen a rapid increase in the discovery of novel allelic variants of the human leukocyte antigen (HLA) genes. Commonly, only the exons encoding the peptide binding domains of novel HLA alleles are submitted. As a result, the IPD-IMGT/HLA Database lacks sequence information outside those regions for the majority of known alleles. This has implications for the application of the new sequencing technologies, which deliver sequence data often covering the complete gene. As these technologies simplify the characterization of the complete gene regions, it is desirable for novel alleles to be submitted as full-length sequences to the database. However, the manual annotation of full-length alleles and the generation of specific formats required by the sequence repositories is prone to error and time consuming. We have developed TypeLoader to address both these facets. With only the full-length sequence as a starting point, Typeloader performs automatic sequence annotation and subsequently handles all steps involved in preparing the specific formats for submission with very little manual intervention. TypeLoader is routinely used at the DKMS Life Science Lab and has aided in the successful submission of more than 900 novel HLA alleles as full-length sequences to the European Nucleotide Archive repository and the IPD-IMGT/HLA Database with a 95% reduction in the time spent on annotation and submission when compared with handling these processes manually. TypeLoader is implemented as a web application and can be easily installed and used on a standalone Linux desktop system or within a Linux client/server architecture. TypeLoader is downloadable from http://www.github.com/DKMS-LSL/typeloader. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Expression of full-length and splice forms of FoxP3 in rheumatoid arthritis

DEFF Research Database (Denmark)

Ryder, L R; Woetmann, A; Madsen, H O

2010-01-01

OBJECTIVE: The aim of our study was to compare the presence of full-length and alternative splice forms of FoxP3 mRNA in CD4 cells from rheumatoid arthritis (RA) patients and healthy controls. METHODS: A quantitative real-time polymerase chain reaction (QRT-PCR) method was used to measure...... the amount of FoxP3 mRNA full-length and splice forms. CD4-positive T cells were isolated from peripheral blood from 50 RA patients by immunomagnetic separation, and the FoxP3 mRNA expression was compared with the results from 10 healthy controls. RESULTS: We observed an increased expression of full......-length FoxP3 mRNA in RA patients when compared to healthy controls, as well as an increase in CD25 mRNA expression, but no corresponding increase in CTLA-4 mRNA expression. The presence of an alternative splice form of FoxP3 lacking exon 2 was confirmed in both RA patients and healthy controls...

Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes

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Jesus F. Salazar-Gonzalez

2016-07-01

Full Text Available Background: Identification of HIV-1 genomes responsible for establishing clinical infection in newly infected individuals is fundamental to prevention and pathogenesis research. Processing, storage, and transportation of the clinical samples required to perform these virologic assays in resource-limited settings requires challenging venipuncture and cold chain logistics. Here, we validate the use of dried-blood spots (DBS as a simple and convenient alternative to collecting and storing frozen plasma. Methods: We performed parallel nucleic acid extraction, single genome amplification (SGA, next generation sequencing (NGS, and phylogenetic analyses on plasma and DBS. Results: We demonstrated the capacity to extract viral RNA from DBS and perform SGA to infer the complete nucleotide sequence of the transmitted/founder (TF HIV-1 envelope gene and full-length genome in two acutely infected individuals. Using both SGA and NGS methodologies, we showed that sequences generated from DBS and plasma display comparable phylogenetic patterns in both acute and chronic infection. SGA was successful on samples with a range of plasma viremia, including samples as low as 1,700 copies/ml and an estimated ~50 viral copies per blood spot. Further, we demonstrated reproducible efficiency in gp160 env sequencing in DBS stored at ambient temperature for up to three weeks or at -20ºC for up to five months. Conclusions: These findings support the use of DBS as a practical and cost-effective alternative to frozen plasma for clinical trials and translational research conducted in resource-limited settings.

Construction experience with Fermilab-built full length 50mm SSC dipoles

International Nuclear Information System (INIS)

Blessing, M.J.; Hoffman, D.E.; Packer, M.D.; Gordon, M.; Higinbotham, W.; Sims, R.

1992-03-01

Fourteen full length SSC dipole magnets are being built and tested at Fermilab. Their purpose is to verify the magnet design as well as transfer the construction technology to industry. Magnet design is summarized. Construction problems and their solutions are discussed. Topics include coil winding, curing and measuring, collaring, instrumentation, end clamp installation, yoking and electrical and mechanical interconnection

A new strategy for full-length Ebola virus glycoprotein expression in E.coli.

Science.gov (United States)

Zai, Junjie; Yi, Yinhua; Xia, Han; Zhang, Bo; Yuan, Zhiming

2016-12-01

Ebola virus (EBOV) causes severe hemorrhagic fever in humans and non-human primates with high rates of fatality. Glycoprotein (GP) is the only envelope protein of EBOV, which may play a critical role in virus attachment and entry as well as stimulating host protective immune responses. However, the lack of expression of full-length GP in Escherichia coli hinders the further study of its function in viral pathogenesis. In this study, the vp40 gene was fused to the full-length gp gene and cloned into a prokaryotic expression vector. We showed that the VP40-GP and GP-VP40 fusion proteins could be expressed in E.coli at 16 °C. In addition, it was shown that the position of vp40 in the fusion proteins affected the yields of the fusion proteins, with a higher level of production of the fusion protein when vp40 was upstream of gp compared to when it was downstream. The results provide a strategy for the expression of a large quantity of EBOV full-length GP, which is of importance for further analyzing the relationship between the structure and function of GP and developing an antibody for the treatment of EBOV infection.

Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L.

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Min Lin

Full Text Available BACKGROUND: Cotton (Gossypium hirsutum L. is one of the world's most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence. METHODOLOGY/PRINCIPAL FINDINGS: In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR, which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves. CONCLUSIONS/SIGNIFICANCE: These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence

An analysis of expressed sequence tags of developing castor endosperm using a full-length cDNA library

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Wallis James G

2007-07-01

Full Text Available Abstract Background Castor seeds are a major source for ricinoleate, an important industrial raw material. Genomics studies of castor plant will provide critical information for understanding seed metabolism, for effectively engineering ricinoleate production in transgenic oilseeds, or for genetically improving castor plants by eliminating toxic and allergic proteins in seeds. Results Full-length cDNAs are useful resources in annotating genes and in providing functional analysis of genes and their products. We constructed a full-length cDNA library from developing castor endosperm, and obtained 4,720 ESTs from 5'-ends of the cDNA clones representing 1,908 unique sequences. The most abundant transcripts are genes encoding storage proteins, ricin, agglutinin and oleosins. Several other sequences are also very numerous, including two acidic triacylglycerol lipases, and the oleate hydroxylase (FAH12 gene that is responsible for ricinoleate biosynthesis. The role(s of the lipases in developing castor seeds are not clear, and co-expressing of a lipase and the FAH12 did not result in significant changes in hydroxy fatty acid accumulation in transgenic Arabidopsis seeds. Only one oleate desaturase (FAD2 gene was identified in our cDNA sequences. Sequence and functional analyses of the castor FAD2 were carried out since it had not been characterized previously. Overexpression of castor FAD2 in a FAH12-expressing Arabidopsis line resulted in decreased accumulation of hydroxy fatty acids in transgenic seeds. Conclusion Our results suggest that transcriptional regulation of FAD2 and FAH12 genes maybe one of the mechanisms that contribute to a high level of ricinoleate accumulation in castor endosperm. The full-length cDNA library will be used to search for additional genes that affect ricinoleate accumulation in seed oils. Our EST sequences will also be useful to annotate the castor genome, which whole sequence is being generated by shotgun sequencing at

Construction of a full-length infectious bacterial artificial chromosome clone of duck enteritis virus vaccine strain

Science.gov (United States)

2013-01-01

Background Duck enteritis virus (DEV) is the causative agent of duck viral enteritis, which causes an acute, contagious and lethal disease of many species of waterfowl within the order Anseriformes. In recent years, two laboratories have reported on the successful construction of DEV infectious clones in viral vectors to express exogenous genes. The clones obtained were either created with deletion of viral genes and based on highly virulent strains or were constructed using a traditional overlapping fosmid DNA system. Here, we report the construction of a full-length infectious clone of DEV vaccine strain that was cloned into a bacterial artificial chromosome (BAC). Methods A mini-F vector as a BAC that allows the maintenance of large circular DNA in E. coli was introduced into the intergenic region between UL15B and UL18 of a DEV vaccine strain by homologous recombination in chicken embryoblasts (CEFs). Then, the full-length DEV clone pDEV-vac was obtained by electroporating circular viral replication intermediates containing the mini-F sequence into E. coli DH10B and identified by enzyme digestion and sequencing. The infectivity of the pDEV-vac was validated by DEV reconstitution from CEFs transfected with pDEV-vac. The reconstructed virus without mini-F vector sequence was also rescued by co-transfecting the Cre recombinase expression plasmid pCAGGS-NLS/Cre and pDEV-vac into CEF cultures. Finally, the in vitro growth properties and immunoprotection capacity in ducks of the reconstructed viruses were also determined and compared with the parental virus. Results The full genome of the DEV vaccine strain was successfully cloned into the BAC, and this BAC clone was infectious. The in vitro growth properties of these reconstructions were very similar to parental DEV, and ducks immunized with these viruses acquired protection against virulent DEV challenge. Conclusions DEV vaccine virus was cloned as an infectious bacterial artificial chromosome maintaining full-length

Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

Energy Technology Data Exchange (ETDEWEB)

Deymier, Martin J., E-mail: mdeymie@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Claiborne, Daniel T., E-mail: dclaibo@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Ende, Zachary, E-mail: zende@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Ratner, Hannah K., E-mail: hannah.ratner@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Kilembe, William, E-mail: wkilembe@rzhrg-mail.org [Zambia-Emory HIV Research Project (ZEHRP), B22/737 Mwembelelo, Emmasdale Post Net 412, P/BagE891, Lusaka (Zambia); Allen, Susan, E-mail: sallen5@emory.edu [Zambia-Emory HIV Research Project (ZEHRP), B22/737 Mwembelelo, Emmasdale Post Net 412, P/BagE891, Lusaka (Zambia); Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States); Hunter, Eric, E-mail: eric.hunter2@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States)

2014-11-15

The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor.

Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

International Nuclear Information System (INIS)

Deymier, Martin J.; Claiborne, Daniel T.; Ende, Zachary; Ratner, Hannah K.; Kilembe, William; Allen, Susan; Hunter, Eric

2014-01-01

The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor

A Note on Non-Generators of Full AFL's

NARCIS (Netherlands)

Asveld, P.R.J.; Engelfriet, Joost

1982-01-01

We compare two definitions of non-generator for full AFL's, leading to two sets of non-generators for each full AFL $K$. The main result gives a necessary and sufficient condition on $K$ such that these sets coincide.

A Note on Non-Generators of Full AFL's

NARCIS (Netherlands)

Asveld, P.R.J.; Engelfriet, Joost

1981-01-01

We compare two definitions of non-generator for full AFL's, leading to two sets of non-generators for each full AFL $K$. The main result gives a necessary and sufficient condition on $K$ such that these sets coincide.

Pulp regeneration in a full-length human tooth root using a hierarchical nanofibrous microsphere system.

Science.gov (United States)

Li, Xiangwei; Ma, Chi; Xie, Xiaohua; Sun, Hongchen; Liu, Xiaohua

2016-04-15

While pulp regeneration using tissue engineering strategy has been explored for over a decade, successful regeneration of pulp tissues in a full-length human root with a one-end seal that truly simulates clinical endodontic treatment has not been achieved. To address this challenge, we designed and synthesized a unique hierarchical growth factor-loaded nanofibrous microsphere scaffolding system. In this system, vascular endothelial growth factor (VEGF) binds with heparin and is encapsulated in heparin-conjugated gelatin nanospheres, which are further immobilized in the nanofibers of an injectable poly(l-lactic acid) (PLLA) microsphere. This hierarchical microsphere system not only protects the VEGF from denaturation and degradation, but also provides excellent control of its sustained release. In addition, the nanofibrous PLLA microsphere integrates the extracellular matrix-mimicking architecture with a highly porous injectable form, efficiently accommodating dental pulp stem cells (DPSCs) and supporting their proliferation and pulp tissue formation. Our in vivo study showed the successful regeneration of pulp-like tissues that fulfilled the entire apical and middle thirds and reached the coronal third of the full-length root canal. In addition, a large number of blood vessels were regenerated throughout the canal. For the first time, our work demonstrates the success of pulp tissue regeneration in a full-length root canal, making it a significant step toward regenerative endodontics. The regeneration of pulp tissues in a full-length tooth root canal has been one of the greatest challenges in the field of regenerative endodontics, and one of the biggest barriers for its clinical application. In this study, we developed a unique approach to tackle this challenge, and for the first time, we successfully regenerated living pulp tissues in a full-length root canal, making it a significant step toward regenerative endodontics. This study will make positive scientific

Rectilinear Full Steiner Tree Generation

DEFF Research Database (Denmark)

Zachariasen, Martin

1999-01-01

The fastest exact algorithm (in practice) for the rectilinear Steiner tree problem in the plane uses a two-phase scheme: First, a small but sufficient set of full Steiner trees (FSTs) is generated and then a Steiner minimum tree is constructed from this set by using simple backtrack search, dynamic...

Full-length genomic characterization and molecular evolution of canine parvovirus in China.

Science.gov (United States)

Zhou, Ling; Tang, Qinghai; Shi, Lijun; Kong, Miaomiao; Liang, Lin; Mao, Qianqian; Bu, Bin; Yao, Lunguang; Zhao, Kai; Cui, Shangjin; Leal, Élcio

2016-06-01

Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. This disease has become one of the most serious infectious diseases of dogs. During 2014 in China, there were many cases of acute infectious diarrhoea in dogs. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. The cytopathic effect on susceptible cells and the results of the immunoperoxidase monolayer assay, PCR, and sequencing indicated that the pathogen was CPV-2. The strain was named CPV-NY-14, and the full-length genome was sequenced and analysed. A maximum likelihood tree was constructed using the full-length genome and all available CPV-2 genomes. New strains have replaced the original strain in Taiwan and Italy, although the CPV-2a strain is still predominant there. However, CPV-2a still causes many cases of acute infectious diarrhoea in dogs in China.

Scalable production in human cells and biochemical characterization of full-length normal and mutant huntingtin.

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Bin Huang

Full Text Available Huntingtin (Htt is a 350 kD intracellular protein, ubiquitously expressed and mainly localized in the cytoplasm. Huntington's disease (HD is caused by a CAG triplet amplification in exon 1 of the corresponding gene resulting in a polyglutamine (polyQ expansion at the N-terminus of Htt. Production of full-length Htt has been difficult in the past and so far a scalable system or process has not been established for recombinant production of Htt in human cells. The ability to produce Htt in milligram quantities would be a prerequisite for many biochemical and biophysical studies aiming in a better understanding of Htt function under physiological conditions and in case of mutation and disease. For scalable production of full-length normal (17Q and mutant (46Q and 128Q Htt we have established two different systems, the first based on doxycycline-inducible Htt expression in stable cell lines, the second on "gutless" adenovirus mediated gene transfer. Purified material has then been used for biochemical characterization of full-length Htt. Posttranslational modifications (PTMs were determined and several new phosphorylation sites were identified. Nearly all PTMs in full-length Htt localized to areas outside of predicted alpha-solenoid protein regions. In all detected N-terminal peptides methionine as the first amino acid was missing and the second, alanine, was found to be acetylated. Differences in secondary structure between normal and mutant Htt, a helix-rich protein, were not observed in our study. Purified Htt tends to form dimers and higher order oligomers, thus resembling the situation observed with N-terminal fragments, although the mechanism of oligomer formation may be different.

Evaluation of full-length, cleaved and nitrosylated serum surfactant protein D as biomarkers for COPD

DEFF Research Database (Denmark)

Duvoix, Annelyse; Miranda, Elena; Perez, Juan

2011-01-01

. Serum levels of SP-D are raised in individuals with COPD but there is no correlation between the serum level of SP-D and the severity of airflow obstruction. Serum SP-D is present in different forms that may have more utility as a biomarker for COPD. We report here the development of new monoclonal...... antibodies to full length and cleaved SP-D. We have assessed these and existing antibodies in 98 individuals with COPD recruited to the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) cohort. Our data show that neither monoclonal antibodies to full length nor cleaved SP...

Insertion of Introns: A Strategy to Facilitate Assembly of Infectious Full Length Clones

DEFF Research Database (Denmark)

Johansen, Ida Elisabeth; Lund, Ole Søgaard

2008-01-01

Some DNA fragments are difficult to clone in Escherichia coli by standard methods. It has been speculated that unintended transcription and translation result in expression of proteins that are toxic to the bacteria. This problem is frequently observed during assembly of infectious full-length vi...

Impaired heat shock response in cells expressing full-length polyglutamine-expanded huntingtin.

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Sidhartha M Chafekar

Full Text Available The molecular mechanisms by which polyglutamine (polyQ-expanded huntingtin (Htt causes neurodegeneration in Huntington's disease (HD remain unclear. The malfunction of cellular proteostasis has been suggested as central in HD pathogenesis and also as a target of therapeutic interventions for the treatment of HD. We present results that offer a previously unexplored perspective regarding impaired proteostasis in HD. We find that, under non-stress conditions, the proteostatic capacity of cells expressing full length polyQ-expanded Htt is adequate. Yet, under stress conditions, the presence of polyQ-expanded Htt impairs the heat shock response, a key component of cellular proteostasis. This impaired heat shock response results in a reduced capacity to withstand the damage caused by cellular stress. We demonstrate that in cells expressing polyQ-expanded Htt the levels of heat shock transcription factor 1 (HSF1 are reduced, and, as a consequence, these cells have an impaired a heat shock response. Also, we found reduced HSF1 and HSP70 levels in the striata of HD knock-in mice when compared to wild-type mice. Our results suggests that full length, non-aggregated polyQ-expanded Htt blocks the effective induction of the heat shock response under stress conditions and may thus trigger the accumulation of cellular damage during the course of HD pathogenesis.

Performance of initial full-length RHIC [Relativistic Heavy Ion Collider] dipoles

International Nuclear Information System (INIS)

Dahl, P.; Cottingham, J.; Garber, M.

1987-01-01

The first four full-length (9.7 m) R and D dipoles for the proposed Relativistic Heavy Ion Collider (RHIC) have been successfully tested. The magnets reached a quench plateau of approximately 4.5 T with very reasonable training - a field level comfortably above the design field of 3.45 T required for operation with beams of 100 GeV/amu gold nuclei. Measured field multipoles are considered to be quite acceptable for this series of R and D magnets

Scored patient-generated Subjective Global Assessment: Length of hospital stay and mortality in cancer patients

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Alexsandro Ferreira dos SANTOS

Full Text Available ABSTRACT Objective To determine the association of a scored patient-generated Subjective Global Assessment with mortality and length of hospital stay in cancer patients. Methods Cross-sectional study carried out between July and September 2014 using secondary data collection using data from 366 medical records of patients admitted to a hospital recognized as a cancer center of excellence. The present study included patients with hospital stay over than or equal three days and minimum age of 20 years. The patient-generated Subjective Global Assessment scores were calculated and compared with the patients’ clinical and anthropometric characteristics and outcomes (death and long length of stay in hospital. Results Of the 366 patients evaluated, 36.0% were malnourished. The presence of malnutrition, according to the scored patient-generated Subjective Global Assessment, was statistically associated with the presence of metastasis (52.4%. On the other hand, malnutrition, according to the body mass index in adults (55.8% and in older elderly patients (54.2%, was associated with death (55.0%. The adjusted logistic regression model showed that the following factors were associated with prolonged hospitalization: early nutritional screening, presence of severe malnutrition, radiotherapy and chemotherapy, and surgical procedures. As for mortality, the associated factors were: male reproductive system tumor, presence of metastasis, clinical treatment, prolonged hospitalization, and the presence of some degree of malnutrition. Conclusion The patient-generated Subjective Global Assessment score is an important risk marker of prolonged hospitalization and mortality rates. It is a useful tool capable of circumventing significant biases in the nutritional evaluation of cancer patients.

Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

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Matt J Cahill

Full Text Available BACKGROUND: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. METHODOLOGY/PRINCIPAL FINDINGS: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. CONCLUSIONS: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length.

Full-length Dysferlin Transfer by the Hyperactive Sleeping Beauty Transposase Restores Dysferlin-deficient Muscle

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Helena Escobar

2016-01-01

Full Text Available Dysferlin-deficient muscular dystrophy is a progressive disease characterized by muscle weakness and wasting for which there is no treatment. It is caused by mutations in DYSF, a large, multiexonic gene that forms a coding sequence of 6.2 kb. Sleeping Beauty (SB transposon is a nonviral gene transfer vector, already used in clinical trials. The hyperactive SB system consists of a transposon DNA sequence and a transposase protein, SB100X, that can integrate DNA over 10 kb into the target genome. We constructed an SB transposon-based vector to deliver full-length human DYSF cDNA into dysferlin-deficient H2K A/J myoblasts. We demonstrate proper dysferlin expression as well as highly efficient engraftment (>1,100 donor-derived fibers of the engineered myoblasts in the skeletal muscle of dysferlin- and immunodeficient B6. Cg-Dysfprmd Prkdcscid/J (Scid/BLA/J mice. Nonviral gene delivery of full-length human dysferlin into muscle cells, along with a successful and efficient transplantation into skeletal muscle are important advances towards successful gene therapy of dysferlin-deficient muscular dystrophy.

Full-Length Fibronectin Drives Fibroblast Accumulation at the Surface of Collagen Microtissues during Cell-Induced Tissue Morphogenesis.

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Jasper Foolen

Full Text Available Generating and maintaining gradients of cell density and extracellular matrix (ECM components is a prerequisite for the development of functionality of healthy tissue. Therefore, gaining insights into the drivers of spatial organization of cells and the role of ECM during tissue morphogenesis is vital. In a 3D model system of tissue morphogenesis, a fibronectin-FRET sensor recently revealed the existence of two separate fibronectin populations with different conformations in microtissues, i.e. 'compact and adsorbed to collagen' versus 'extended and fibrillar' fibronectin that does not colocalize with the collagen scaffold. Here we asked how the presence of fibronectin might drive this cell-induced tissue morphogenesis, more specifically the formation of gradients in cell density and ECM composition. Microtissues were engineered in a high-throughput model system containing rectangular microarrays of 12 posts, which constrained fibroblast-populated collagen gels, remodeled by the contractile cells into trampoline-shaped microtissues. Fibronectin's contribution during the tissue maturation process was assessed using fibronectin-knockout mouse embryonic fibroblasts (Fn-/- MEFs and floxed equivalents (Fnf/f MEFs, in fibronectin-depleted growth medium with and without exogenously added plasma fibronectin (full-length, or various fragments. In the absence of full-length fibronectin, Fn-/- MEFs remained homogenously distributed throughout the cell-contracted collagen gels. In contrast, in the presence of full-length fibronectin, both cell types produced shell-like tissues with a predominantly cell-free compacted collagen core and a peripheral surface layer rich in cells. Single cell assays then revealed that Fn-/- MEFs applied lower total strain energy on nanopillar arrays coated with either fibronectin or vitronectin when compared to Fnf/f MEFs, but that the presence of exogenously added plasma fibronectin rescued their contractility. While collagen

Species-Specific Expression of Full-Length and Alternatively Spliced Variant Forms of CDK5RAP2.

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John S Y Park

Full Text Available CDK5RAP2 is one of the primary microcephaly genes that are associated with reduced brain size and mental retardation. We have previously shown that human CDK5RAP2 exists as a full-length form (hCDK5RAP2 or an alternatively spliced variant form (hCDK5RAP2-V1 that is lacking exon 32. The equivalent of hCDK5RAP2-V1 has been reported in rat and mouse but the presence of full-length equivalent hCDK5RAP2 in rat and mouse has not been examined. Here, we demonstrate that rat expresses both a full length and an alternatively spliced variant form of CDK5RAP2 that are equivalent to our previously reported hCDK5RAP2 and hCDK5RAP2-V1, repectively. However, mouse expresses only one form of CDK5RAP2 that is equivalent to the human and rat alternatively spliced variant forms. Knowledge of this expression of different forms of CDK5RAP2 in human, rat and mouse is essential in selecting the appropriate model for studies of CDK5RAP2 and primary microcephaly but our findings further indicate the evolutionary divergence of mouse from the human and rat species.

Highly efficient full-length hepatitis C virus genotype 1 (strain TN) infectious culture system

DEFF Research Database (Denmark)

Li, Yi-Ping; Ramirez, Santseharay; Jensen, Sanne B

2012-01-01

Chronic infection with hepatitis C virus (HCV) is an important cause of end stage liver disease worldwide. In the United States, most HCV-related disease is associated with genotype 1 infection, which remains difficult to treat. Drug and vaccine development was hampered by inability to culture...... full-length TN infection dose-dependently. Given the unique importance of genotype 1 for pathogenesis, this infectious 1a culture system represents an important advance in HCV research. The approach used and the mutations identified might permit culture development for other HCV isolates, thus......) culture systems in Huh7.5 cells. Here, we developed a highly efficient genotype 1a (strain TN) full-length culture system. We initially found that the LSG substitutions conferred viability to an intergenotypic recombinant composed of TN 5' untranslated region (5'UTR)-NS5A and JFH1 NS5B-3'UTR; recovered...

Temperature-sensitive elastin-mimetic dendrimers: Effect of peptide length and dendrimer generation to temperature sensitivity.

Science.gov (United States)

Kojima, Chie; Irie, Kotaro; Tada, Tomoko; Tanaka, Naoki

2014-06-01

Dendrimers are synthetic macromolecules with unique structure, which are a potential scaffold for peptides. Elastin is one of the main components of extracellular matrix and a temperature-sensitive biomacromolecule. Previously, Val-Pro-Gly-Val-Gly peptides have been conjugated to a dendrimer for designing an elastin-mimetic dendrimer. In this study, various elastin-mimetic dendrimers using different length peptides and different dendrimer generations were synthesized to control the temperature dependency. The elastin-mimetic dendrimers formed β-turn structure by heating, which was similar to the elastin-like peptides. The elastin-mimetic dendrimers exhibited an inverse phase transition, largely depending on the peptide length and slightly depending on the dendrimer generation. The elastin-mimetic dendrimers formed aggregates after the phase transition. The endothermal peak was observed in elastin-mimetic dendrimers with long peptides, but not with short ones. The peptide length and the dendrimer generation are important factors to tune the temperature dependency on the elastin-mimetic dendrimer. Copyright © 2013 Wiley Periodicals, Inc.

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing.

Science.gov (United States)

Anvar, Seyed Yahya; Allard, Guy; Tseng, Elizabeth; Sheynkman, Gloria M; de Klerk, Eleonora; Vermaat, Martijn; Yin, Raymund H; Johansson, Hans E; Ariyurek, Yavuz; den Dunnen, Johan T; Turner, Stephen W; 't Hoen, Peter A C

2018-03-29

The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing.

Single-molecule study of full-length NaChBac by planar lipid bilayer recording.

Directory of Open Access Journals (Sweden)

Andrew Jo

Full Text Available Planar lipid bilayer device, alternatively known as BLM, is a powerful tool to study functional properties of conducting membrane proteins such as ion channels and porins. In this work, we used BLM to study the prokaryotic voltage-gated sodium channel (Nav NaChBac in a well-defined membrane environment. Navs are an essential component for the generation and propagation of electric signals in excitable cells. The successes in the biochemical, biophysical and crystallographic studies on prokaryotic Navs in recent years has greatly promoted the understanding of the molecular mechanism that underlies these proteins and their eukaryotic counterparts. In this work, we investigated the single-molecule conductance and ionic selectivity behavior of NaChBac. Purified NaChBac protein was first reconstituted into lipid vesicles, which is subsequently incorporated into planar lipid bilayer by fusion. At single-molecule level, we were able to observe three distinct long-lived conductance sub-states of NaChBac. Change in the membrane potential switches on the channel mainly by increasing its opening probability. In addition, we found that individual NaChBac has similar permeability for Na+, K+, and Ca2+. The single-molecule behavior of the full-length protein is essentially highly stochastic. Our results show that planar lipid bilayer device can be used to study purified ion channels at single-molecule level in an artificial environment, and such studies can reveal new protein properties that are otherwise not observable in in vivo ensemble studies.

A Novel mouse model of enhanced proteostasis: Full-length human heat shock factor 1 transgenic mice

International Nuclear Information System (INIS)

Pierce, Anson; Wei, Rochelle; Halade, Dipti; Yoo, Si-Eun; Ran, Qitao; Richardson, Arlan

2010-01-01

Research highlights: → Development of mouse overexpressing native human HSF1 in all tissues including CNS. → HSF1 overexpression enhances heat shock response at whole-animal and cellular level. → HSF1 overexpression protects from polyglutamine toxicity and favors aggresomes. → HSF1 overexpression enhances proteostasis at the whole-animal and cellular level. -- Abstract: The heat shock response (HSR) is controlled by the master transcriptional regulator heat shock factor 1 (HSF1). HSF1 maintains proteostasis and resistance to stress through production of heat shock proteins (HSPs). No transgenic model exists that overexpresses HSF1 in tissues of the central nervous system (CNS). We generated a transgenic mouse overexpressing full-length non-mutant HSF1 and observed a 2-4-fold increase in HSF1 mRNA and protein expression in all tissues studied of HSF1 transgenic (HSF1 +/0 ) mice compared to wild type (WT) littermates, including several regions of the CNS. Basal expression of HSP70 and 90 showed only mild tissue-specific changes; however, in response to forced exercise, the skeletal muscle HSR was more elevated in HSF1 +/0 mice compared to WT littermates and in fibroblasts following heat shock, as indicated by levels of inducible HSP70 mRNA and protein. HSF1 +/0 cells elicited a significantly more robust HSR in response to expression of the 82 repeat polyglutamine-YFP fusion construct (Q82YFP) and maintained proteasome-dependent processing of Q82YFP compared to WT fibroblasts. Overexpression of HSF1 was associated with fewer, but larger Q82YFP aggregates resembling aggresomes in HSF1 +/0 cells, and increased viability. Therefore, our data demonstrate that tissues and cells from mice overexpressing full-length non-mutant HSF1 exhibit enhanced proteostasis.

EXPRESSION AND CHARACTERIZATION OF FULL-LENGTH HUMAN HEME OXYGENASE-1: PRESENCE OF INTACT MEMBRANE-BINDING REGION LEADS TO INCREASED BINDING AFFINITY FOR NADPH-CYTOCHROME P450 REDUCTASE

Science.gov (United States)

Huber, Warren J.; Backes, Wayne L.

2009-01-01

Heme oxygenase (HO) is the chief regulatory enzyme in the oxidative degradation of heme to biliverdin. In the process of heme degradation, this NADPH and cytochrome P450 reductase (CPR)-dependent oxidation of heme also releases free iron and carbon monoxide. Much of the recent research involving heme oxygenase is done using a 30-kDa soluble form of the enzyme, which lacks the membrane binding region (C-terminal 23 amino acids). The goal of this study was to express and purify a full-length human HO-1 (hHO-1) protein; however, due to the lability of the full-length form, a rapid purification procedure was required. This was accomplished by use of a GST-tagged hHO-1 construct. Although the procedure permitted the generation of a full-length HO-1, this form was contaminated with a 30-kDa degradation product that could not be eliminated. Therefore, we attempted to remove a putative secondary thrombin cleavage site by a conservative mutation of amino acid 254, which replaces lysine with arginine. This mutation allowed the expression and purification of a full length hHO-1 protein. Unlike wild-type HO-1, the K254R mutant could be purified to a single 32-kDa protein capable of degrading heme at the same rate as the wild-type enzyme. The K254R full-length form had a specific activity of ~200–225 nmol bilirubin hr−1nmol−1 HO-1 as compared to ~140–150 nmol bilirubin hr−1nmol−1 for the WT form, which contains the 30-kDa contaminant. This is a 2–3-fold increase from the previously reported soluble 30-kDa HO-1, suggesting that the C-terminal 23 amino acids are essential for maximal catalytic activity. Because the membrane spanning domain is present, the full-length hHO-1 has the potential to incorporate into phospholipid membranes, which can be reconstituted at known concentrations, in combination with other ER-resident enzymes. PMID:17915953

Non-destructive testing of full-length bonded rock bolts based on HHT signal analysis

Science.gov (United States)

Shi, Z. M.; Liu, L.; Peng, M.; Liu, C. C.; Tao, F. J.; Liu, C. S.

2018-04-01

Full-length bonded rock bolts are commonly used in mining, tunneling and slope engineering because of their simple design and resistance to corrosion. However, the length of a rock bolt and grouting quality do not often meet the required design standards in practice because of the concealment and complexity of bolt construction. Non-destructive testing is preferred when testing a rock bolt's quality because of the convenience, low cost and wide detection range. In this paper, a signal analysis method for the non-destructive sound wave testing of full-length bonded rock bolts is presented, which is based on the Hilbert-Huang transform (HHT). First, we introduce the HHT analysis method to calculate the bolt length and identify defect locations based on sound wave reflection test signals, which includes decomposing the test signal via empirical mode decomposition (EMD), selecting the intrinsic mode functions (IMF) using the Pearson Correlation Index (PCI) and calculating the instantaneous phase and frequency via the Hilbert transform (HT). Second, six model tests are conducted using different grouting defects and bolt protruding lengths to verify the effectiveness of the HHT analysis method. Lastly, the influence of the bolt protruding length on the test signal, identification of multiple reflections from defects, bolt end and protruding end, and mode mixing from EMD are discussed. The HHT analysis method can identify the bolt length and grouting defect locations from signals that contain noise at multiple reflected interfaces. The reflection from the long protruding end creates an irregular test signal with many frequency peaks on the spectrum. The reflections from defects barely change the original signal because they are low energy, which cannot be adequately resolved using existing methods. The HHT analysis method can identify reflections from the long protruding end of the bolt and multiple reflections from grouting defects based on mutations in the instantaneous

Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

Science.gov (United States)

Kuroshu, Reginaldo M; Watanabe, Junichi; Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka; Kasahara, Masahiro

2010-05-07

Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

Science.gov (United States)

Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

2016-11-01

It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum cultivar Micro-Tom, a reference system for the Solanaceae genomics

Directory of Open Access Journals (Sweden)

Kikuchi Mari

2010-03-01

Full Text Available Abstract Background The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. Results To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706 was estimated to be 0.061%. Conclusion The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the

The ability to form full-length intron RNA circles is a general property of nuclear group I introns

DEFF Research Database (Denmark)

Nielsen, Henrik; Fiskaa, Tonje; Birgisdottir, Asa Birna

2003-01-01

at the expense of the host. The circularization pathway has distinct structural requirements that differ from those of splicing and appears to be specifically suppressed in vivo. The ability to form full-length circles is found in all types of nuclear group I introns, including those from the Tetrahymena...... ribosomal DNA. The biological function of the full-length circles is not known, but the fact that the circles contain the entire genetic information of the intron suggests a role in intron mobility....

Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques.

Science.gov (United States)

Semler, Matthew R; Wiseman, Roger W; Karl, Julie A; Graham, Michael E; Gieger, Samantha M; O'Connor, David H

2017-11-13

Pig-tailed macaques (Macaca nemestrina, Mane) are important models for human immunodeficiency virus (HIV) studies. Their infectability with minimally modified HIV makes them a uniquely valuable animal model to mimic human infection with HIV and progression to acquired immunodeficiency syndrome (AIDS). However, variation in the pig-tailed macaque major histocompatibility complex (MHC) and the impact of individual transcripts on the pathogenesis of HIV and other infectious diseases is understudied compared to that of rhesus and cynomolgus macaques. In this study, we used Pacific Biosciences single-molecule real-time circular consensus sequencing to describe full-length MHC class I (MHC-I) transcripts for 194 pig-tailed macaques from three breeding centers. We then used the full-length sequences to infer Mane-A and Mane-B haplotypes containing groups of MHC-I transcripts that co-segregate due to physical linkage. In total, we characterized full-length open reading frames (ORFs) for 313 Mane-A, Mane-B, and Mane-I sequences that defined 86 Mane-A and 106 Mane-B MHC-I haplotypes. Pacific Biosciences technology allows us to resolve these Mane-A and Mane-B haplotypes to the level of synonymous allelic variants. The newly defined haplotypes and transcript sequences containing full-length ORFs provide an important resource for infectious disease researchers as certain MHC haplotypes have been shown to provide exceptional control of simian immunodeficiency virus (SIV) replication and prevention of AIDS-like disease in nonhuman primates. The increased allelic resolution provided by Pacific Biosciences sequencing also benefits transplant research by allowing researchers to more specifically match haplotypes between donors and recipients to the level of nonsynonymous allelic variation, thus reducing the risk of graft-versus-host disease.

High yield purification of full-length functional hERG K+ channels produced in Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Molbaek, Karen; Scharff-Poulsen, Peter; Hélix-Nielsen, Claus

2015-01-01

knowledge this is the first reported high-yield production and purification of full length, tetrameric and functional hERG. This significant breakthrough will be paramount in obtaining hERG crystal structures, and in establishment of new high-throughput hERG drug safety screening assays....

Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence

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R.S. Ross

2008-01-01

Full Text Available The genome of the hepatitis C virus (HCV exhibits a high genetic variability. This remarkable heterogeneity is mainly attributed to the gradual accumulation of mutational changes, whereas the contribution of recombination events to the evolution of HCV remains controversial so far. While performing phylogenetic analyses including a large number of sequences deposited in the GenBank, we encountered a full-length HCV sequence (AY651061 that showed evidence for inter-subtype recombination and was, therefore, subjected to a detailed analysis of its molecular structure. The obtained results indicated that AY651061 does not represent a “simple” HCV 1c isolate, but a complex 1a/1c mosaic genome, showing five putative breakpoints in the core to NS3 regions. To our knowledge, this is the first report on a mosaic HCV full- length sequence with multiple breakpoints. The molecular structure of AY651061 is reminiscent of complex homologous recombinant variants occurring among other members of the flaviviridae family, e.g. GB virus C, dengue virus, and Japanese encephalitis virus. Our finding of a mosaic HCV sequence may have important implications for many fields of current HCV research which merit careful consideration.

dsRNA binding characterization of full length recombinant wild type and mutants Zaire ebolavirus VP35.

Science.gov (United States)

Zinzula, Luca; Esposito, Francesca; Pala, Daniela; Tramontano, Enzo

2012-03-01

The Ebola viruses (EBOVs) VP35 protein is a multifunctional major virulence factor involved in EBOVs replication and evasion of the host immune system. EBOV VP35 is an essential component of the viral RNA polymerase, it is a key participant of the nucleocapsid assembly and it inhibits the innate immune response by antagonizing RIG-I like receptors through its dsRNA binding function and, hence, by suppressing the host type I interferon (IFN) production. Insights into the VP35 dsRNA recognition have been recently revealed by structural and functional analysis performed on its C-terminus protein. We report the biochemical characterization of the Zaire ebolavirus (ZEBOV) full-length recombinant VP35 (rVP35)-dsRNA binding function. We established a novel in vitro magnetic dsRNA binding pull down assay, determined the rVP35 optimal dsRNA binding parameters, measured the rVP35 equilibrium dissociation constant for heterologous in vitro transcribed dsRNA of different length and short synthetic dsRNA of 8bp, and validated the assay for compound screening by assessing the inhibitory ability of auryntricarboxylic acid (IC(50) value of 50μg/mL). Furthermore, we compared the dsRNA binding properties of full length wt rVP35 with those of R305A, K309A and R312A rVP35 mutants, which were previously reported to be defective in dsRNA binding-mediated IFN inhibition, showing that the latter have measurably increased K(d) values for dsRNA binding and modified migration patterns in mobility shift assays with respect to wt rVP35. Overall, these results provide the first characterization of the full-length wt and mutants VP35-dsRNA binding functions. Copyright © 2012 Elsevier B.V. All rights reserved.

Quench start localization in full-length SSC R ampersand D dipoles

International Nuclear Information System (INIS)

Devred, A.; Chapman, M.; Cortella, J.; Desportes, A.; Kaugerts, J.; Kirk, T.; Mirk, K.; Schermer, R.; Tompkins, J.C.; Turner, J.; Bleadon, M.; Brown, B.C.; Hanft, R.; Kuchnir, M.; Lamm, M.; Mantsch, P.; Mazur, P.O.; Orris, D.; Peoples, J.; Strait, J.; Tool, G.; Caspi, S.; Gilbert, W.; Meuser, R.; Peters, C.; Rechen, J.; Royet, J.; Scanlan, R.; Taylor, C.; Zbasnik, J.

1989-04-01

Full-length SSC R ampersand D dipole magnets instrumented with four voltage taps on each turn of the inner quarter coils have been tested. These voltage taps enable accurate location of the point at which the quenches start and detailed studies of quench development in the coil. Attention here is focused on localizing the quench source. After recalling the basic mechanism of a quench (why it occurs and how it propagates), the method of quench origin analysis is described: the quench propagation velocity on the turn where the quench occurs is calculated, and the quench location is then verified by reiterating the analysis on the adjacent turns. Last, the velocity value, which appears to be higher than previously measured, is discussed

Generation and biological assessment of recombinant avian metapneumovirus subgroup C (aMPV-C) viruses containing different length of the G gene.

Science.gov (United States)

Yu, Qingzhong; Estevez, Carlos; Song, Minxun; Kapczynski, Darrell; Zsak, Laszlo

2010-02-01

Genetic variation in length of the G gene among different avian metapneumovirus subgroup C (aMPV-C) isolates has been reported. However, its biological significance in virus replication, pathogenicity and immunity is unknown. In this study, we developed a reverse genetics system for aMPV-C and generated two Colorado (CO) strain-based recombinant viruses containing either the full-length G gene derived from a Canadian goose isolate or a C-terminally truncated G gene of the CO strain. The truncated short G (sG) gene encoded 252 amino acids (aa), which is 333 aa shorter than the full-length G (585 aa). The biological properties of these two recombinant G variants were assessed in Vero cells and in specific-pathogen-free (SPF) turkeys. In Vero cells, the short G variant displayed a similar level of growth dynamics and virus titers as the parental aMPV-CO strain, whereas the full-length G variant replicated less efficiently than the sG variant during the first 72 h post-infection. Both of the G variants induced typical cytopathic effects (CPE) that were indistinguishable from those seen with the parental aMPV-CO infection. In SPF turkeys, both of the G variants were attenuated and caused little or no disease signs, but the full-length G variant appeared to grow more readily in tracheal tissue than the sG variant during the first 5 days post-infection. Both G variants were immunogenic and induced a slightly different level of antibody response. These results demonstrated that the large portion (333 aa) of the extracellular domain of the viral attachment protein is not essential for virus viability in vitro and in vivo, but may play a role in enhancing virus attachment specificity and immunity in a natural host. (c) 2009 Elsevier B.V. All rights reserved.

Electrostatic turbulence with finite parallel correlation length and radial electric field generation

International Nuclear Information System (INIS)

Vlad, M.; Spineanu, F.; Misguich, J.H.; Balescu, R.

2001-01-01

Particle diffusion in a given electrostatic turbulence with a finite correlation length along the confining magnetic field is studied in the test particle approach. An anomalous diffusion regime of amplified diffusion coefficients is found in the conditions when particle trapping in the structure of the stochastic potential is effective. The auto-generated radial electric field is calculated. (author)

The full-length form of the Drosophila amyloid precursor protein is involved in memory formation.

Science.gov (United States)

Bourdet, Isabelle; Preat, Thomas; Goguel, Valérie

2015-01-21

The APP plays a central role in AD, a pathology that first manifests as a memory decline. Understanding the role of APP in normal cognition is fundamental in understanding the progression of AD, and mammalian studies have pointed to a role of secreted APPα in memory. In Drosophila, we recently showed that APPL, the fly APP ortholog, is required for associative memory. In the present study, we aimed to characterize which form of APPL is involved in this process. We show that expression of a secreted-APPL form in the mushroom bodies, the center for olfactory memory, is able to rescue the memory deficit caused by APPL partial loss of function. We next assessed the impact on memory of the Drosophila α-secretase kuzbanian (KUZ), the enzyme initiating the nonamyloidogenic pathway that produces secreted APPLα. Strikingly, KUZ overexpression not only failed to rescue the memory deficit caused by APPL loss of function, it exacerbated this deficit. We further show that in addition to an increase in secreted-APPL forms, KUZ overexpression caused a decrease of membrane-bound full-length species that could explain the memory deficit. Indeed, we observed that transient expression of a constitutive membrane-bound mutant APPL form is sufficient to rescue the memory deficit caused by APPL reduction, revealing for the first time a role of full-length APPL in memory formation. Our data demonstrate that, in addition to secreted APPL, the noncleaved form is involved in memory, raising the possibility that secreted and full-length APPL act together in memory processes. Copyright © 2015 the authors 0270-6474/15/351043-09$15.00/0.

Pharmacological efficacy of anti-IL-1β scFv, Fab and full-length antibodies in treatment of rheumatoid arthritis.

Science.gov (United States)

Qi, Jianying; Ye, Xianlong; Ren, Guiping; Kan, Fangming; Zhang, Yu; Guo, Mo; Zhang, Zhiyi; Li, Deshan

2014-02-01

Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease that mainly causes the synovial joint inflammation and cartilage destruction. Interleukin-1β (IL-1β) is an important proinflammatory cytokine involved in the pathogenesis of RA. In this study, we constructed and expressed anti-IL-1β-full-length antibody in CHO-K1-SV, anti-IL-1β-Fab and anti-IL-1β-scFv in Rosetta. We compared the therapeutic efficacy of three anti-IL-1β antibodies for CIA mice. Mice with CIA were subcutaneously injected with humanized anti-IL-1β-scFv, anti-IL-1β-Fab or anti-IL-1β-full-length antibody. The effects of treatment were determined by arthritis severity score, autoreactive humoral, cellular immune responses, histological lesion and cytokines production. Compared with anti-IL-1β-scFv treatments, anti-IL-1β-Fab and anti-IL-1β-full-length antibody therapy resulted in more significant effect in alleviating the severity of arthritis by preventing bone damage and cartilage destruction, reducing humoral and cellular immune responses, and down-regulating the expression of IL-1β, IL-6, IL-2, IFN-γ, TNF-α and MMP-3 in inflammatory tissue. The therapeutic effects of anti-IL-1β-Fab and anti-IL-1β-full-length antibodies on CIA mice had no significant difference. However, production of anti-IL-1β-full-length antibody in eukaryotic system is, in general, time-consuming and more expensive than that of anti-IL-1β-Fab in prokaryotic systems. In conclusion, as a small molecule antibody, anti-IL-1β-Fab is an ideal candidate for RA therapy. Copyright © 2013 Elsevier Ltd. All rights reserved.

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.

Science.gov (United States)

Aoki, Koh; Yano, Kentaro; Suzuki, Ayako; Kawamura, Shingo; Sakurai, Nozomu; Suda, Kunihiro; Kurabayashi, Atsushi; Suzuki, Tatsuya; Tsugane, Taneaki; Watanabe, Manabu; Ooga, Kazuhide; Torii, Maiko; Narita, Takanori; Shin-I, Tadasu; Kohara, Yuji; Yamamoto, Naoki; Takahashi, Hideki; Watanabe, Yuichiro; Egusa, Mayumi; Kodama, Motoichiro; Ichinose, Yuki; Kikuchi, Mari; Fukushima, Sumire; Okabe, Akiko; Arie, Tsutomu; Sato, Yuko; Yazawa, Katsumi; Satoh, Shinobu; Omura, Toshikazu; Ezura, Hiroshi; Shibata, Daisuke

2010-03-30

The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%. The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional

Cocrystallization studies of full-length recombinant butyrylcholinesterase (BChE) with cocaine

Energy Technology Data Exchange (ETDEWEB)

Asojo, Oluwatoyin Ajibola; Asojo, Oluyomi Adebola; Ngamelue, Michelle N.; Homma, Kohei; Lockridge, Oksana (Nebraska-Med)

2011-09-16

Human butyrylcholinesterase (BChE; EC 3.1.1.8) is a 340 kDa tetrameric glycoprotein that is present in human serum at about 5 mg l{sup -1} and has well documented therapeutic effects on cocaine toxicity. BChE holds promise as a therapeutic that reduces and finally eliminates the rewarding effects of cocaine, thus weaning an addict from the drug. There have been extensive computational studies of cocaine hydrolysis by BChE. Since there are no reported structures of BChE with cocaine or any of the hydrolysis products, full-length monomeric recombinant wild-type BChE was cocrystallized with cocaine. The refined 3 {angstrom} resolution structure appears to retain the hydrolysis product benzoic acid in sufficient proximity to form a hydrogen bond to the active-site Ser198.

Expression and characterization of full-length human heme oxygenase-1: the presence of intact membrane-binding region leads to increased binding affinity for NADPH cytochrome P450 reductase.

Science.gov (United States)

Huber, Warren J; Backes, Wayne L

2007-10-30

Heme oxygenase-1 (HO-1) is the chief regulatory enzyme in the oxidative degradation of heme to biliverdin. In the process of heme degradation, HO-1 receives the electrons necessary for catalysis from the flavoprotein NADPH cytochrome P450 reductase (CPR), releasing free iron and carbon monoxide. Much of the recent research involving heme oxygenase has been done using a 30 kDa soluble form of the enzyme, which lacks the membrane binding region (C-terminal 23 amino acids). The goal of this study was to express and purify a full-length human HO-1 (hHO-1) protein; however, due to the lability of the full-length form, a rapid purification procedure was required. This was accomplished by use of a glutathione-s-transferase (GST)-tagged hHO-1 construct. Although the procedure permitted the generation of a full-length HO-1, this form was contaminated with a 30 kDa degradation product that could not be eliminated. Therefore, attempts were made to remove a putative secondary thrombin cleavage site by a conservative mutation of amino acid 254, which replaces arginine with lysine. This mutation allowed the expression and purification of a full-length hHO-1 protein. Unlike wild type (WT) HO-1, the R254K mutant could be purified to a single 32 kDa protein capable of degrading heme at the same rate as the WT enzyme. The R254K full-length form had a specific activity of approximately 200-225 nmol of bilirubin h-1 nmol-1 HO-1 as compared to approximately 140-150 nmol of bilirubin h-1 nmol-1 for the WT form, which contains the 30 kDa contaminant. This is a 2-3-fold increase from the previously reported soluble 30 kDa HO-1, suggesting that the C-terminal 23 amino acids are essential for maximal catalytic activity. Because the membrane-spanning domain is present, the full-length hHO-1 has the potential to incorporate into phospholipid membranes, which can be reconstituted at known concentrations, in combination with other endoplasmic reticulum resident enzymes.

A Novel Strategy to Engineer Pre-Vascularized Full-Length Dental Pulp-like Tissue Constructs.

Science.gov (United States)

Athirasala, Avathamsa; Lins, Fernanda; Tahayeri, Anthony; Hinds, Monica; Smith, Anthony J; Sedgley, Christine; Ferracane, Jack; Bertassoni, Luiz E

2017-06-12

The requirement for immediate vascularization of engineered dental pulp poses a major hurdle towards successful implementation of pulp regeneration as an effective therapeutic strategy for root canal therapy, especially in adult teeth. Here, we demonstrate a novel strategy to engineer pre-vascularized, cell-laden hydrogel pulp-like tissue constructs in full-length root canals for dental pulp regeneration. We utilized gelatin methacryloyl (GelMA) hydrogels with tunable physical and mechanical properties to determine the microenvironmental conditions (microstructure, degradation, swelling and elastic modulus) that enhanced viability, spreading and proliferation of encapsulated odontoblast-like cells (OD21), and the formation of endothelial monolayers by endothelial colony forming cells (ECFCs). GelMA hydrogels with higher polymer concentration (15% w/v) and stiffness enhanced OD21 cell viability, spreading and proliferation, as well as endothelial cell spreading and monolayer formation. We then fabricated pre-vascularized, full-length, dental pulp-like tissue constructs by dispensing OD21 cell-laden GelMA hydrogel prepolymer in root canals of extracted teeth and fabricating 500 µm channels throughout the root canals. ECFCs seeded into the microchannels successfully formed monolayers and underwent angiogenic sprouting within 7 days in culture. In summary, the proposed approach is a simple and effective strategy for engineering of pre-vascularized dental pulp constructs offering potentially beneficial translational outcomes.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Directory of Open Access Journals (Sweden)

Tadashi Imanishi

2004-06-01

Full Text Available The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/. It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs, identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA

Assessment and optimization of theileria parva sporozoite full-length p67 antigen expression in mammalian cells

Science.gov (United States)

Delivery of various forms of recombinant Theileria parva sporozoite antigen (p67) has been shown to elicit antibody responses in cattle capable of providing protection against East Coast fever, the clinical disease caused by T. parva. Previous formulations of full-length and shorter recombinant vers...

A comparative phylogenetic analysis of full-length mariner elements ...

Indian Academy of Sciences (India)

Unknown

recent study showing non-occurance of inter-subfamily excisions because of .... length shown in our figure is greater because of the gaps introduced to maintain an ... to test the feasibility of transforming silkmoths with a foreign gene of ...

Virtually full-length subtype F and F/D recombinant HIV-1 from Africa and South America

NARCIS (Netherlands)

Laukkanen, T.; Carr, J. K.; Janssens, W.; Liitsola, K.; Gotte, D.; McCutchan, F. E.; Op de Coul, E.; Cornelissen, M.; Heyndrickx, L.; van der Groen, G.; Salminen, M. O.

2000-01-01

For reliable classification of HIV-1 strains appropriate reference sequences are needed. The HIV-1 genetic subtype F has a wide geographic spread, causing significant epidemics in South America, Africa, and some regions of Europe. Previously only two full-length sequences of each of the HIV-1

Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

Directory of Open Access Journals (Sweden)

Holt Robert A

2010-04-01

Full Text Available Abstract Background Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar, but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution. Results From existing expressed sequence tag (EST resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (Esox lucius ESTs. Pairwise dN/dS comparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates. Conclusions 9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate.

Fiscal 2000 report on result of the full-length cDNA structure analysis; 2000 nendo kanzen cho cDNA kozo kaiseki seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-03-01

This paper explains the results of research on full-length cDNA structure analysis for the period from April, 2000 to March, 2001. The outline of human genome sequence was published in June, 2000. In Japan, human gene analysis was such that, as the basic technology of the bio industry, a millennium project was decided in the budget of fiscal 2000. The full-length cDNA structure analysis is the core of the project. The libraries of cDNA were prepared using full-length and more than 4-5kbp-long cDNAs by oligo-capping method. It began from determining partial sequence data at end cDNA, and then, with new clones selected therefrom, full-length human cDNA sequence data were determined. The partial sequence data determined by fiscal 2000 were 1,035,000 clones while the full-length sequence data were 12,144 clones. The sequence data obtained were analyzed by homology search and translated into amino acid coding sequences, with predictions conducted on protein functions. A clustering method was examined that selects new clones from partial sequences. Database was constructed on gene expression profiles and disease-related gene sequence data. (NEDO)

Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.

Science.gov (United States)

Paz, Rosalía Cristina; Kozaczek, Melisa Eliana; Rosli, Hernán Guillermo; Andino, Natalia Pilar; Sanchez-Puerta, Maria Virginia

2017-10-01

Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.

Full-Length High-Temperature Severe Fuel Damage Test No. 5: Final safety analysis

International Nuclear Information System (INIS)

Lanning, D.D.; Lombardo, N.J.; Panisko, F.E.

1993-09-01

This report presents the final safety analysis for the preparation, conduct, and post-test discharge operation for the Full-Length High Temperature Experiment-5 (FLHT-5) to be conducted in the L-24 position of the National Research Universal (NRU) Reactor at Chalk River Nuclear Laboratories (CRNL), Ontario, Canada. The test is sponsored by an international group organized by the US Nuclear Regulatory Commission. The test is designed and conducted by staff from Pacific Northwest Laboratory with CRNL staff support. The test will study the consequences of loss-of-coolant and the progression of severe fuel damage

Purification and characterization of recombinant full-length and protease domain of murine MMP-9 expressed in Drosophila S2 cells

DEFF Research Database (Denmark)

Rasch, Morten G; Lund, Ida K.; Illemann, Martin

2010-01-01

-length and truncated versions were 5 mg/l and 2 mg/l, respectively. The products were >95% pure after gelatin Sepharose chromatography and possessed proteolytic activity when analyzed by gelatin zymography. Using the purified full-length murine MMP-9 we raised polyclonal antibodies by immunizations of rabbits...

Functional characterization of a full length pregnane X receptor, expression in vivo, and identification of PXR alleles, in Zebrafish (Danio rerio)

Energy Technology Data Exchange (ETDEWEB)

Bainy, Afonso C.D. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900 (Brazil); Kubota, Akira; Goldstone, Jared V. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Lille-Langøy, Roger [Department of Biology, University of Bergen, N-5020 Bergen (Norway); Karchner, Sibel I. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Celander, Malin C. [Department of Biological and Environmental Sciences, University of Gothenburg, SE 405 30 Göteborg (Sweden); Hahn, Mark E. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Goksøyr, Anders [Department of Biology, University of Bergen, N-5020 Bergen (Norway); Stegeman, John J., E-mail: jstegeman@whoi.edu [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States)

2013-10-15

Highlights: •Full-length pxr has been cloned from zebrafish. •Alleles of pxr were identified in zebrafish. •Full length Pxr was activated less strongly than ligand binding domain in cell-based reporter assays. •High levels of pxr expression were found in eye and brain as well as in liver. •TCPOBOP and PB did not significantly alter expression of pxr in liver. -- Abstract: The pregnane X receptor (PXR) (nuclear receptor NR1I2) is a ligand activated transcription factor, mediating responses to diverse xenobiotic and endogenous chemicals. The properties of PXR in fish are not fully understood. Here we report on cloning and characterization of full-length PXR of zebrafish, Danio rerio, and pxr expression in vivo. Initial efforts gave a cDNA encoding a 430 amino acid protein identified as zebrafish pxr by phylogenetic and synteny analysis. The sequence of the cloned Pxr DNA binding domain (DBD) was highly conserved, with 74% identity to human PXR-DBD, while the ligand-binding domain (LBD) of the cloned sequence was only 44% identical to human PXR-LBD. Sequence variation among clones in the initial effort prompted sequencing of multiple clones from a single fish. There were two prominent variants, one sequence with S183, Y218 and H383 and the other with I183, C218 and N383, which we designate as alleles pxr*1 (nr1i2*1) and pxr*2 (nr1i2*2), respectively. In COS-7 cells co-transfected with a PXR-responsive reporter gene, the full-length Pxr*1 (the more common variant) was activated by known PXR agonists clotrimazole and pregnenolone 16α-carbonitrile but to a lesser extent than the full-length human PXR. Activation of full-length Pxr*1 was only 10% of that with the Pxr*1 LBD. Quantitative real time PCR analysis showed prominent expression of pxr in liver and eye, as well as brain and intestine of adult zebrafish. The pxr was expressed in heart and kidney at levels similar to that in intestine. The expression of pxr in liver was weakly induced by ligands for

Construction of occluded recombinant baculoviruses containing the full-length cry1Ab and cry1Ac genes from Bacillus thuringiensis

Directory of Open Access Journals (Sweden)

B.M. Ribeiro

1998-06-01

Full Text Available The administration of baculoviruses to insects for bioassay purposes is carried out, in most cases, by contamination of food surfaces with a known amount of occlusion bodies (OBs. Since per os infection is the natural route of infection, occluded recombinant viruses containing crystal protein genes (cry1Ab and cry1Ac from Bacillus thuringiensis were constructed for comparison with the baculovirus prototype Autographa californica nucleopolyhedrovirus (AcNPV. The transfer vector pAcUW2B was used for construction of occluded recombinant viruses. The transfer vector containing the crystal protein genes was cotransfected with linearized DNA from a non-occluded recombinant virus. The isolation of recombinant viruses was greatly facilitated by the reduction of background "wild type" virus and the increased proportion of recombinant viruses. Since the recombinant viruses containing full-length and truncated forms of the crystal protein genes did not seem to improve the pathogenicity of the recombinant viruses when compared with the wild type AcNPV, and in order to compare expression levels of the full-length crystal proteins produced by non-occluded and occluded recombinant viruses the full-length cry1Ab and cry1Ac genes were chosen for construction of occluded recombinant viruses. The recombinant viruses containing full-length and truncated forms of the crystal protein genes did not seem to improve its pathogenicity but the size of the larvae infected with the recombinant viruses was significantly smaller than that of larvae infected with the wild type virus.

Effect of heated length on the Critical Heat Flux of subcooled flow boiling. 2. Effective heated length under axially nonuniform heating condition

International Nuclear Information System (INIS)

Kinoshita, Hidetaka; Yoshida, Takuya; Nariai, Hideki; Inasaka, Fujio

1998-01-01

Effect of heated length on the Critical Heat Flux (CHF) of subcooled flow boiling with water was experimentally investigated by using direct current heated tube made of stainless steel a part of whose wall thickness was axially cut for realizing nonuniform heat flux condition. The higher enhancement of the CHF was derived for shorter tube length. The effective heated length was determined for the tube under axially nonuniform heat flux condition. When the lower heat flux part below the Net Vapor Generation (NVG) heat flux exists at the middle of tube length, then the effective heated length becomes the tube length downstream the lower heat flux parts. However, when the lower heat flux part is above the NVG, then the effective heated length is full tube length. (author)

Secretory production of tetrameric native full-length streptavidin with thermostability using Streptomyces lividans as a host.

Science.gov (United States)

Noda, Shuhei; Matsumoto, Takuya; Tanaka, Tsutomu; Kondo, Akihiko

2015-01-13

Streptavidin is a tetrameric protein derived from Streptomyces avidinii, and has tight and specific biotin binding affinity. Applications of the streptavidin-biotin system have been widely studied. Streptavidin is generally produced using protein expression in Escherichia coli. In the present study, the secretory production of streptavidin was carried out using Streptomyces lividans as a host. In this study, we used the gene encoding native full-length streptavidin, whereas the core region is generally used for streptavidin production in E. coli. Tetrameric streptavidin composed of native full-length streptavidin monomers was successfully secreted in the culture supernatant of S. lividans transformants, and had specific biotin binding affinity as strong as streptavidin produced by E. coli. The amount of Sav using S. lividans was about 9 times higher than using E. coli. Surprisingly, streptavidin produced by S. lividans exhibited affinity to biotin after boiling, despite the fact that tetrameric streptavidin is known to lose its biotin binding ability after brief boiling. We successfully produced a large amount of tetrameric streptavidin as a secretory-form protein with unique thermotolerance.

PCR-based isolation and identification of full-length low-molecular-weight glutenin subunit genes in bread wheat (Triticum aestivum L.).

Science.gov (United States)

Zhang, Xiaofei; Liu, Dongcheng; Jiang, Wei; Guo, Xiaoli; Yang, Wenlong; Sun, Jiazhu; Ling, Hongqing; Zhang, Aimin

2011-12-01

Low-molecular-weight glutenin subunits (LMW-GSs) are encoded by a multi-gene family and are essential for determining the quality of wheat flour products, such as bread and noodles. However, the exact role or contribution of individual LMW-GS genes to wheat quality remains unclear. This is, at least in part, due to the difficulty in characterizing complete sequences of all LMW-GS gene family members in bread wheat. To identify full-length LMW-GS genes, a polymerase chain reaction (PCR)-based method was established, consisting of newly designed conserved primers and the previously developed LMW-GS gene molecular marker system. Using the PCR-based method, 17 LMW-GS genes were identified and characterized in Xiaoyan 54, of which 12 contained full-length sequences. Sequence alignments showed that 13 LMW-GS genes were identical to those found in Xiaoyan 54 using the genomic DNA library screening, and the other four full-length LMW-GS genes were first isolated from Xiaoyan 54. In Chinese Spring, 16 unique LMW-GS genes were isolated, and 13 of them contained full-length coding sequences. Additionally, 16 and 17 LMW-GS genes in Dongnong 101 and Lvhan 328 (chosen from the micro-core collections of Chinese germplasm), respectively, were also identified. Sequence alignments revealed that at least 15 LMW-GS genes were common in the four wheat varieties, and allelic variants of each gene shared high sequence identities (>95%) but exhibited length polymorphism in repetitive regions. This study provides a PCR-based method for efficiently identifying LMW-GS genes in bread wheat, which will improve the characterization of complex members of the LMW-GS gene family and facilitate the understanding of their contributions to wheat quality.

Hibiscus latent Fort Pierce virus in Brazil and synthesis of its biologically active full-length cDNA clone.

Science.gov (United States)

Gao, Ruimin; Niu, Shengniao; Dai, Weifang; Kitajima, Elliot; Wong, Sek-Man

2016-10-01

A Brazilian isolate of Hibiscus latent Fort Pierce virus (HLFPV-BR) was firstly found in a hibiscus plant in Limeira, SP, Brazil. RACE PCR was carried out to obtain the full-length sequences of HLFPV-BR which is 6453 nucleotides and has more than 99.15 % of complete genomic RNA nucleotide sequence identity with that of HLFPV Japanese isolate. The genomic structure of HLFPV-BR is similar to other tobamoviruses. It includes a 5' untranslated region (UTR), followed by open reading frames encoding for a 128-kDa protein and a 188-kDa readthrough protein, a 38-kDa movement protein, 18-kDa coat protein, and a 3' UTR. Interestingly, the unique feature of poly(A) tract is also found within its 3'-UTR. Furthermore, from the total RNA extracted from the local lesions of HLFPV-BR-infected Chenopodium quinoa leaves, a biologically active, full-length cDNA clone encompassing the genome of HLFPV-BR was amplified and placed adjacent to a T7 RNA polymerase promoter. The capped in vitro transcripts from the cloned cDNA were infectious when mechanically inoculated into C. quinoa and Nicotiana benthamiana plants. This is the first report of the presence of an isolate of HLFPV in Brazil and the successful synthesis of a biologically active HLFPV-BR full-length cDNA clone.

RT-PCR and sequence analysis of the full-length fusion protein of Canine Distemper Virus from domestic dogs.

Science.gov (United States)

Romanutti, Carina; Gallo Calderón, Marina; Keller, Leticia; Mattion, Nora; La Torre, José

2016-02-01

During 2007-2014, 84 out of 236 (35.6%) samples from domestic dogs submitted to our laboratory for diagnostic purposes were positive for Canine Distemper Virus (CDV), as analyzed by RT-PCR amplification of a fragment of the nucleoprotein gene. Fifty-nine of them (70.2%) were from dogs that had been vaccinated against CDV. The full-length gene encoding the Fusion (F) protein of fifteen isolates was sequenced and compared with that of those of other CDVs, including wild-type and vaccine strains. Phylogenetic analysis using the F gene full-length sequences grouped all the Argentinean CDV strains in the SA2 clade. Sequence identity with the Onderstepoort vaccine strain was 89.0-90.6%, and the highest divergence was found in the 135 amino acids corresponding to the F protein signal-peptide, Fsp (64.4-66.7% identity). In contrast, this region was highly conserved among the local strains (94.1-100% identity). One extra putative N-glycosylation site was identified in the F gene of CDV Argentinean strains with respect to the vaccine strain. The present report is the first to analyze full-length F protein sequences of CDV strains circulating in Argentina, and contributes to the knowledge of molecular epidemiology of CDV, which may help in understanding future disease outbreaks. Copyright © 2015 Elsevier B.V. All rights reserved.

Human microcephaly protein RTTN interacts with STIL and is required to build full-length centrioles.

Science.gov (United States)

Chen, Hsin-Yi; Wu, Chien-Ting; Tang, Chieh-Ju C; Lin, Yi-Nan; Wang, Won-Jing; Tang, Tang K

2017-08-15

Mutations in many centriolar protein-encoding genes cause primary microcephaly. Using super-resolution and electron microscopy, we find that the human microcephaly protein, RTTN, is recruited to the proximal end of the procentriole at early S phase, and is located at the inner luminal walls of centrioles. Further studies demonstrate that RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly. CRISPR/Cas9-mediated RTTN gene knockout in p53-deficient cells induce amplification of primitive procentriole bodies that lack the distal-half centriolar proteins, POC5 and POC1B. Additional analyses show that RTTN serves as an upstream effector of CEP295, which mediates the loading of POC1B and POC5 to the distal-half centrioles. Interestingly, the naturally occurring microcephaly-associated mutant, RTTN (A578P), shows a low affinity for STIL binding and blocks centriole assembly. These findings reveal that RTTN contributes to building full-length centrioles and illuminate the molecular mechanism through which the RTTN (A578P) mutation causes primary microcephaly.Mutations in many centriolar protein-encoding genes cause primary microcephaly. Here the authors show that human microcephaly protein RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly, contributing to building full-length centrioles.

Molecular cloning and expression of full-length DNA copies of the genomic RNAs of cowpea mosaic virus

NARCIS (Netherlands)

Vos, P.

1987-01-01

The experiments described in this thesis were designed to unravel various aspects of the mechanism of gene expression of cowpea mosaic virus (CPMV). For this purpose full-length DNA copies of both genomic RNAs of CPMV were constructed. Using powerful invitro

P-Link: A method for generating multicomponent cytochrome P450 fusions with variable linker length

DEFF Research Database (Denmark)

Belsare, Ketaki D.; Ruff, Anna Joelle; Martinez, Ronny

2014-01-01

Fusion protein construction is a widely employed biochemical technique, especially when it comes to multi-component enzymes such as cytochrome P450s. Here we describe a novel method for generating fusion proteins with variable linker lengths, protein fusion with variable linker insertion (P...

Transformation of Cowpea Vigna unguiculata with a Full-Length DNA Copy of Cowpea Mosaic Virus M-RNA

NARCIS (Netherlands)

Hille, Jacques; Goldbach, Rob

1987-01-01

A full-length DNA copy of the M-RNA of cowpea mosaic virus (CPMV), supplied with either the 35S promoter from cauliflower mosaic virus (CaMV) or the nopaline synthase promoter from Agrobacterium tumefaciens, was introduced into the T-DNA region of a Ti-plasmid-derived gene vector and transferred to

The effect of two different renal denervation strategies on blood pressure in resistant hypertension: Comparison of full-length versus proximal renal artery ablation.

Science.gov (United States)

Chen, Weijie; Ling, Zhiyu; Du, Huaan; Song, Wenxin; Xu, Yanping; Liu, Zengzhang; Su, Li; Xiao, Peilin; Yuan, Yuelong; Lu, Jiayi; Zhang, Jianhong; Li, Zhifeng; Shao, Jiang; Zhong, Bin; Zhou, Bei; Woo, Kamsang; Yin, Yuehui

2016-11-01

Renal denervation (RDN) is used to manage blood pressure (BP) in patients with resistant hypertension (rHT), but effectiveness is still a concern, and key arterial portion for successful RDN is not clear. The aim of this study was to investigate the efficacy and safety of proximal versus full-length renal artery ablation in patients with resistant hypertension (rHT). Forty-seven patients with rHT were randomly assigned to receive full-length ablation (n = 23) or proximal ablation (n = 24) of the renal arteries. All lesions were treated with radiofrequency energy via a saline-irrigated catheter. Office BP was measured during 12 months of follow-up and ambulatory BP at baseline and 6 months (n = 15 in each group). Compared with full-length ablation, proximal ablation reduced the number of ablation points in both the right (6.1 ± 0.7 vs. 3.3 ± 0.6, P renal arteries (6.2 ± 0.7 vs. 3.3 ± 0.8, P  0.5). Similar office BPs was reduced by -39.4 ± 11.5/-20.9 ± 7.1 mm Hg at 6 months and -38.2 ± 10.3/-21.5 ± 5.8 mm Hg at 12 months in the full-length group (P efficacy and safety profile compared with full-length RDN, and propose the proximal artery as the key portion for RDN. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Pseudo-polyprotein translated from the full-length ORF1 of capillovirus is important for pathogenicity, but a truncated ORF1 protein without variable and CP regions is sufficient for replication.

Science.gov (United States)

Hirata, Hisae; Yamaji, Yasuyuki; Komatsu, Ken; Kagiwada, Satoshi; Oshima, Kenro; Okano, Yukari; Takahashi, Shuichiro; Ugaki, Masashi; Namba, Shigetou

2010-09-01

The first open-reading frame (ORF) of the genus Capillovirus encodes an apparently chimeric polyprotein containing conserved regions for replicase (Rep) and coat protein (CP), while other viruses in the family Flexiviridae have separate ORFs encoding these proteins. To investigate the role of the full-length ORF1 polyprotein of capillovirus, we generated truncation mutants of ORF1 of apple stem grooving virus by inserting a termination codon into the variable region located between the putative Rep- and CP-coding regions. These mutants were capable of systemic infection, although their pathogenicity was attenuated. In vitro translation of ORF1 produced both the full-length polyprotein and the smaller Rep protein. The results of in vivo reporter assays suggested that the mechanism of this early termination is a ribosomal -1 frame-shift occurring downstream from the conserved Rep domains. The mechanism of capillovirus gene expression and the very close evolutionary relationship between the genera Capillovirus and Trichovirus are discussed. Copyright (c) 2010. Published by Elsevier B.V.

Genetic deletion of muscle RANK or selective inhibition of RANKL is not as effective as full-length OPG-fc in mitigating muscular dystrophy.

Science.gov (United States)

Dufresne, Sébastien S; Boulanger-Piette, Antoine; Bossé, Sabrina; Argaw, Anteneh; Hamoudi, Dounia; Marcadet, Laetitia; Gamu, Daniel; Fajardo, Val A; Yagita, Hideo; Penninger, Josef M; Russell Tupling, A; Frenette, Jérôme

2018-04-24

Although there is a strong association between osteoporosis and skeletal muscle atrophy/dysfunction, the functional relevance of a particular biological pathway that regulates synchronously bone and skeletal muscle physiopathology is still elusive. Receptor-activator of nuclear factor κB (RANK), its ligand RANKL and the soluble decoy receptor osteoprotegerin (OPG) are the key regulators of osteoclast differentiation and bone remodelling. We thus hypothesized that RANK/RANKL/OPG, which is a key pathway for bone regulation, is involved in Duchenne muscular dystrophy (DMD) physiopathology. Our results show that muscle-specific RANK deletion (mdx-RANK mko ) in dystrophin deficient mdx mice improves significantly specific force [54% gain in force] of EDL muscles with no protective effect against eccentric contraction-induced muscle dysfunction. In contrast, full-length OPG-Fc injections restore the force of dystrophic EDL muscles [162% gain in force], protect against eccentric contraction-induced muscle dysfunction ex vivo and significantly improve functional performance on downhill treadmill and post-exercise physical activity. Since OPG serves a soluble receptor for RANKL and as a decoy receptor for TRAIL, mdx mice were injected with anti-RANKL and anti-TRAIL antibodies to decipher the dual function of OPG. Injections of anti-RANKL and/or anti-TRAIL increase significantly the force of dystrophic EDL muscle [45% and 17% gains in force, respectively]. In agreement, truncated OPG-Fc that contains only RANKL domains produces similar gains, in terms of force production, than anti-RANKL treatments. To corroborate that full-length OPG-Fc also acts independently of RANK/RANKL pathway, dystrophin/RANK double-deficient mice were treated with full-length OPG-Fc for 10 days. Dystrophic EDL muscles exhibited a significant gain in force relative to untreated dystrophin/RANK double-deficient mice, indicating that the effect of full-length OPG-Fc is in part independent of the RANKL

Human uroporphyrinogen III synthase: Molecular cloning, nucleotide sequence, and expression of a full-length cDNA

International Nuclear Information System (INIS)

Tsai, Shihfeng; Bishop, D.F.; Desnick, R.J.

1988-01-01

Uroporphyrinogen III synthase, the fourth enzyme in the heme biosynthetic pathway, is responsible for conversion of the linear tetrapyrrole, hydroxymethylbilane, to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-synthase is the enzymatic defect in the autosomal recessive disorder congenital erythropoietic porphyria. To facilitate the isolation of a full-length cDNA for human URO-synthase, the human erythrocyte enzyme was purified to homogeneity and 81 nonoverlapping amino acids were determined by microsequencing the N terminus and four tryptic peptides. Two synthetic oligonucleotide mixtures were used to screen 1.2 x 10 6 recombinants from a human adult liver cDNA library. Eight clones were positive with both oligonucleotide mixtures. Of these, dideoxy sequencing of the 1.3 kilobase insert from clone pUROS-2 revealed 5' and 3' untranslated sequences of 196 and 284 base pairs, respectively, and an open reading frame of 798 base pairs encoding a protein of 265 amino acids with a predicted molecular mass of 28,607 Da. The isolation and expression of this full-length cDNA for human URO-synthase should facilitate studies of the structure, organization, and chromosomal localization of this heme biosynthetic gene as well as the characterization of the molecular lesions causing congenital erythropoietic porphyria

Full splitting of the first zero-field steps in the I-V curve of Josephson junctions of intermediate length

International Nuclear Information System (INIS)

Hansen, J.B.; Divin, Y.Y.; Mygind, J.

1986-01-01

We report on the observation of full splitting of the first zero-field steps in the I-V curves of Josephson transmission lines of intermediate length Lroughly-equal(3--5)lambda/sub J/, where lambda/sub J/ is the Josephson penetration length. We study in detail how this splitting of the step into two branches depends on the temperature of the junction and on a weak applied magnetic field. We relate the splitting to excitations in the junctions whose behavior is described by the perturbed Sine-Gordon equation

Structure and function of the first full-length murein peptide ligase (Mpl cell wall recycling protein.

Directory of Open Access Journals (Sweden)

Debanu Das

2011-03-01

Full Text Available Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc. MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl, which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl. Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters. Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

Potency of full-length MGF to induce maximal activation of the IGF-I R Is similar to recombinant human IGF-I at high equimolar concentrations

NARCIS (Netherlands)

J.A.M.J.L. Janssen (Joseph); L.J. Hofland (Leo); C.J. Strasburger; E.S.R.D. Van Dungen (Elisabeth S.R. Den); M. Thevis (Mario)

2016-01-01

textabstractAims To compare full-length mechano growth factor (full-length MGF) with human recombinant insulin-like growth factor-I (IGF-I) and human recombinant insulin (HI) in their ability to activate the human IGF-I receptor (IGF-IR), the human insulin receptor (IR-A) and the human insulin

Copper Coordination in the Full-Length, Recombinant Prion Protein†

Science.gov (United States)

Burns, Colin S.; Aronoff-Spencer, Eliah; Legname, Giuseppe; Prusiner, Stanley B.; Antholine, William E.; Gerfen, Gary J.; Peisach, Jack; Millhauser, Glenn L.

2010-01-01

The prion protein (PrP) binds divalent copper at physiologically relevant conditions and is believed to participate in copper regulation or act as a copper-dependent enzyme. Ongoing studies aim at determining the molecular features of the copper binding sites. The emerging consensus is that most copper binds in the octarepeat domain, which is composed of four or more copies of the fundamental sequence PHGGGWGQ. Previous work from our laboratory using PrP-derived peptides, in conjunction with EPR and X-ray crystallography, demonstrated that the HGGGW segment constitutes the fundamental binding unit in the octarepeat domain [Burns et al. (2002) Biochemistry 41, 3991–4001; Aronoff-Spencer et al. (2000) Biochemistry 39, 13760–13771]. Copper coordination arises from the His imidazole and sequential deprotonated glycine amides. In this present work, recombinant, full-length Syrian hamster PrP is investigated using EPR methodologies. Four copper ions are taken up in the octarepeat domain, which supports previous findings. However, quantification studies reveal a fifth binding site in the flexible region between the octarepeats and the PrP globular C-terminal domain. A series of PrP peptide constructs show that this site involves His96 in the PrP(92–96) segment GGGTH. Further examination by X-band EPR, S-band EPR, and electron spin–echo envelope spectroscopy, demonstrates coordination by the His96 imidazole and the glycine preceding the threonine. The copper affinity for this type of binding site is highly pH dependent, and EPR studies here show that recombinant PrP loses its affinity for copper below pH 6.0. These studies seem to provide a complete profile of the copper binding sites in PrP and support the hypothesis that PrP function is related to its ability to bind copper in a pH-dependent fashion. PMID:12779334

Beam test of a full-length prototype of the BESIII drift chamber with the readout electronics

International Nuclear Information System (INIS)

Qin, Z.H.; Chen, Y.B.; Sheng, H.Y.; Wu, L.H.; Liu, J.B.; Zhuang, B.A.; Jiang, X.S.; Zhao, Y.B.; Zhu, K.J.; Yan, Z.K.; Chen, C.; Xu, M.H.; Wang, L.; Ma, X.Y.; Tang, X.; Liu, R.G.; Jin, Y.; Zhu, Q.M.; Zhang, G.F.; Wu, Z.; Li, R.Y.; Zhao, P.P.; Dai, H.L.; Li, X.P.; Li, J.

2007-01-01

A full-length prototype of the BESIII drift chamber together with its readout electronics was built and a beam test was performed. Two different methods, namely 'single-threshold method' and 'double-threshold method' for timing measurement, were studied. Test results show that the BESIII drift chamber and its readout electronics can reach their design specifications. The 'double-threshold method' results in a better timing accuracy and noise suppression capabilities as compared with the 'single-threshold method'

Studies of nontarget-mediated distribution of human full-length IgG1 antibody and its FAb fragment in cardiovascular and metabolic-related tissues.

Science.gov (United States)

Davidsson, Pia; Söderling, Ann-Sofi; Svensson, Lena; Ahnmark, Andrea; Flodin, Christine; Wanag, Ewa; Screpanti-Sundqvist, Valentina; Gennemark, Peter

2015-05-01

Tissue distribution and pharmacokinetics (PK) of full-length nontargeted antibody and its antigen-binding fragment (FAb) were evaluated for a range of tissues primarily of interest for cardiovascular and metabolic diseases. Mice were intravenously injected with a dose of 10 mg/kg of either human IgG1or its FAb fragment; perfused tissues were collected at a range of time points over 3 weeks for the human IgG1 antibody and 1 week for the human FAb antibody. Tissues were homogenized and antibody concentrations were measured by specific immunoassays on the Gyros system. Exposure in terms of maximum concentration (Cmax ) and area under the curve was assessed for all nine tissues. Tissue exposure of full-length antibody relative to plasma exposure was found to be between 1% and 10%, except for brain (0.2%). Relative concentrations of FAb antibody were the same, except for kidney tissue, where the antibody concentration was found to be ten times higher than in plasma. However, the absolute tissue uptake of full-length IgG was significantly higher than the absolute tissue uptake of the FAb antibody. This study provides a reference PK state for full-length whole and FAb antibodies in tissues related to cardiovascular and metabolic diseases that do not include antigen or antibody binding. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Llama immunization with full-length VAR2CSA generates cross-reactive and inhibitory single-domain antibodies against the DBL1X domain.

Science.gov (United States)

Nunes-Silva, Sofia; Gangnard, Stéphane; Vidal, Marta; Vuchelen, Anneleen; Dechavanne, Sebastien; Chan, Sherwin; Pardon, Els; Steyaert, Jan; Ramboarina, Stephanie; Chêne, Arnaud; Gamain, Benoît

2014-12-09

VAR2CSA stands today as the leading vaccine candidate aiming to protect future pregnant women living in malaria endemic areas against the severe clinical outcomes of pregnancy associated malaria (PAM). The rational design of an efficient VAR2CSA-based vaccine relies on a profound understanding of the molecular interactions associated with P. falciparum infected erythrocyte sequestration in the placenta. Following immunization of a llama with the full-length VAR2CSA recombinant protein, we have expressed and characterized a panel of 19 nanobodies able to recognize the recombinant VAR2CSA as well as the surface of erythrocytes infected with parasites originating from different parts of the world. Domain mapping revealed that a large majority of nanobodies targeted DBL1X whereas a few of them were directed towards DBL4ε, DBL5ε and DBL6ε. One nanobody targeting the DBL1X was able to recognize the native VAR2CSA protein of the three parasite lines tested. Furthermore, four nanobodies targeting DBL1X reproducibly inhibited CSA adhesion of erythrocytes infected with the homologous NF54-CSA parasite strain, providing evidences that DBL1X domain is part or close to the CSA binding site. These nanobodies could serve as useful tools to identify conserved epitopes shared between different variants and to characterize the interactions between VAR2CSA and CSA.

Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

KAUST Repository

Cahill, Matt J.

2010-07-12

Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

KAUST Repository

Cahill, Matt J.; Kö ser, Claudio U.; Ross, Nicholas E.; Archer, John A.C.

2010-01-01

Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

Conversion of Chord Length Data into Bubble Size Distribution: Generation of Chord Length Data and the Methodology Comparison

Energy Technology Data Exchange (ETDEWEB)

Hien, Hoang Nhan; Euh, D. J.; Song, C. H. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Yun, B. J. [Pusan National University, Busan (Korea, Republic of)

2012-05-15

Bubble size and its distribution play an important role in thermal hydrodynamic processes in multiphase flow systems. By using the conductivity or optical probe techniques, the size and distribution of bubbles can only be inferred indirectly from a measured chord length data (CLD). Some methods are proposed to convert a CLD into the bubble size distribution (BSD), and they can be classified into parametric, semi-parametric and non-parametric. Most of methods are derived from the following relation of the conditional probability functions that are established under the geometric constraints: P(y) = {infinity}{integral}0 P(R) P(y|R) dR where P(R) is PDF of bubbles of all sizes R pierced by a probe, and P(y|R) is PDF of chord length y corresponding to bubbles of a specified size R. These methods are limited to flows of bubbles having symmetric shapes, i.e. spherical, ellipsoidal, or capspherical. Although the methods were developed from a common relation, there are no physical bases as well as the lack of experimental data to validate them. In this work, the CLD is generated for comparing different conversion methods. The range of bubble size is determined by the Hinze's theory. The CLDs are applied to numerical backward transforms (NBT), analytical backward transform (ABT), and analytical semi-parametric method using Parzen window estimator (ParzenES) to obtain the BSD. A comparison for the obtained results is performed

Conversion of Chord Length Data into Bubble Size Distribution: Generation of Chord Length Data and the Methodology Comparison

International Nuclear Information System (INIS)

Hien, Hoang Nhan; Euh, D. J.; Song, C. H.; Yun, B. J.

2012-01-01

Bubble size and its distribution play an important role in thermal hydrodynamic processes in multiphase flow systems. By using the conductivity or optical probe techniques, the size and distribution of bubbles can only be inferred indirectly from a measured chord length data (CLD). Some methods are proposed to convert a CLD into the bubble size distribution (BSD), and they can be classified into parametric, semi-parametric and non-parametric. Most of methods are derived from the following relation of the conditional probability functions that are established under the geometric constraints: P(y) = ∞∫0 P(R) P(y|R) dR where P(R) is PDF of bubbles of all sizes R pierced by a probe, and P(y|R) is PDF of chord length y corresponding to bubbles of a specified size R. These methods are limited to flows of bubbles having symmetric shapes, i.e. spherical, ellipsoidal, or capspherical. Although the methods were developed from a common relation, there are no physical bases as well as the lack of experimental data to validate them. In this work, the CLD is generated for comparing different conversion methods. The range of bubble size is determined by the Hinze's theory. The CLDs are applied to numerical backward transforms (NBT), analytical backward transform (ABT), and analytical semi-parametric method using Parzen window estimator (ParzenES) to obtain the BSD. A comparison for the obtained results is performed

Full-load converter connected asynchronous generators for MW class wind turbines

Energy Technology Data Exchange (ETDEWEB)

Akhmatov, Vladislav

2005-06-15

Wind turbines equipped with full-load converter-connected asynchronous generators are a known concept. These have rating up to hundreds of kW and are a feasible concept for MW class wind turbines and may have advantages when compared to conventional wind turbines with directly connected generators. The concept requires the use of full-scale frequency converters, but the mechanical gearbox is smaller than in conventional wind turbines of the same rating. Application of smaller gearbox may reduce the no-load losses in the wind turbines, which is why such wind turbines with converter connected generators may start operation at a smaller wind speed. Wind turbines equipped with such converted connected asynchronous generators are pitch-controlled and variable-speed. This allows better performance and control. The converter control may be applied to support the grid voltage at short-circuit faults and to improve the fault-ride-through capability of the wind turbines, which makes the concepts relevant for large wind farms. The Danish transmission system operator Energinet-DK has implemented the general model of wind turbines equipped with converter connected asynchronous generators with the simulation tool Powerfactory (DlgSilent). The article presents Energinet-DK's experience of modeling this feasible wind turbine concept. (Author)

Conformational change in full-length mouse prion: A site-directed spin-labeling study

International Nuclear Information System (INIS)

Inanami, Osamu; Hashida, Shukichi; Iizuka, Daisuke; Horiuchi, Motohiro; Hiraoka, Wakako; Shimoyama, Yuhei; Nakamura, Hideo; Inagaki, Fuyuhiko; Kuwabara, Mikinori

2005-01-01

The structure of the mouse prion (moPrP) was studied using site-directed spin-labeling electron spin resonance (SDSL-ESR). Since a previous NMR study by Hornemanna et al., [Hornemanna, Korthb, Oeschb, Rieka, Widera, Wuethricha, Glockshubera, Recombinant full-length murine prion protein, mPrP (23-231): purification and spectroscopic characterization, FEBS Lett. 413 (1997) 277-281] has indicated that N96, D143, and T189 in moPrP are localized in a Cu 2+ binding region, Helix1 and Helix2, respectively, three recombinant moPrP mutations (N96C, D143C, and T189C) were expressed in an Escherichia coli system, and then refolded by dialysis under low pH and purified by reverse-phase HPLC. By using the preparation, we succeeded in preserving a target cystein residue without alteration of the α-helix structure of moPrP and were able to apply SDSL-ESR with a methane thiosulfonate spin label to the full-length prion protein. The rotational correlation times (τ) of 1.1, 3.3, and 4.8 ns were evaluated from the X-band ESR spectra at pH 7.4 and 20 deg C for N96R1, D143R1, and T189R1, respectively. τ reflects the fact that the Cu 2+ binding region is more flexible than Helix1 or Helix2. ESR spectra recorded at various temperatures revealed two phases together with a transition point at around 20 deg C in D143R1 and T189R1, but not in N96R1. With the variation of pH from 4.0 to 7.8, ESR spectra of T189R1 at 20 deg C showed a gradual increase of τ from 2.9 to 4.8 ns. On the other hand, the pH-dependent conformational changes in N96R1 and D143R1 were negligible. These results indicated that T189 located in Helix2 possessed a structure sensitive to physiological pH changes; simultaneously, N96 in the Cu 2+ binding region and D143 in Helix1 were conserved

Caspase 3 inactivates biologically active full length interleukin-33 as a classical cytokine but does not prohibit nuclear translocation

International Nuclear Information System (INIS)

Ali, Shafaqat; Nguyen, Dang Quan; Falk, Werner; Martin, Michael Uwe

2010-01-01

IL-33 is a member of the IL-1 family of cytokines with dual function which either activates cells via the IL-33 receptor in a paracrine fashion or translocates to the nucleus to regulate gene transcription in an intracrine manner. We show that full length murine IL-33 is active as a cytokine and that it is not processed by caspase 1 to mature IL-33 but instead cleaved by caspase 3 at aa175 to yield two products which are both unable to bind to the IL-33 receptor. Full length IL-33 and its N-terminal caspase 3 breakdown product, however, translocate to the nucleus. Finally, bioactive IL-33 is not released by cells constitutively or after activation. This suggests that IL-33 is not a classical cytokine but exerts its function in the nucleus of intact cells and only activates others cells via its receptor as an alarm mediator after destruction of the producing cell.

Construction and characterization of a full-length cDNA library for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici

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Chen Xianming

2007-06-01

Full Text Available Abstract Background Puccinia striiformis is a plant pathogenic fungus causing stripe rust, one of the most important diseases on cereal crops and grasses worldwide. However, little is know about its genome and genes involved in the biology and pathogenicity of the pathogen. We initiated the functional genomic research of the fungus by constructing a full-length cDNA and determined functions of the first group of genes by sequence comparison of cDNA clones to genes reported in other fungi. Results A full-length cDNA library, consisting of 42,240 clones with an average cDNA insert of 1.9 kb, was constructed using urediniospores of race PST-78 of P. striiformis f. sp. tritici. From 196 sequenced cDNA clones, we determined functions of 73 clones (37.2%. In addition, 36 clones (18.4% had significant homology to hypothetical proteins, 37 clones (18.9% had some homology to genes in other fungi, and the remaining 50 clones (25.5% did not produce any hits. From the 73 clones with functions, we identified 51 different genes encoding protein products that are involved in amino acid metabolism, cell defense, cell cycle, cell signaling, cell structure and growth, energy cycle, lipid and nucleotide metabolism, protein modification, ribosomal protein complex, sugar metabolism, transcription factor, transport metabolism, and virulence/infection. Conclusion The full-length cDNA library is useful in identifying functional genes of P. striiformis.

Force generation and temperature-jump and length-jump tension transients in muscle fibers.

Science.gov (United States)

Davis, J S; Rodgers, M E

1995-01-01

Muscle tension rises with increasing temperature. The kinetics that govern the tension rise of maximally Ca(2+)-activated, skinned rabbit psoas fibers over a temperature range of 0-30 degrees C was characterized in laser temperature-jump experiments. The kinetic response is simple and can be readily interpreted in terms of a basic three-step mechanism of contraction, which includes a temperature-sensitive rapid preequilibrium(a) linked to a temperature-insensitive rate-limiting step and followed by a temperature-sensitive tension-generating step. These data and mechanism are compared and contrasted with the more complex length-jump Huxley-Simmons phases in which all states that generate tension or bear tension are perturbed. The rate of the Huxley-Simmons phase 4 is temperature sensitive at low temperatures but plateaus at high temperatures, indicating a change in rate-limiting step from a temperature-sensitive (phase 4a) to a temperature-insensitive reaction (phase 4b); the latter appears to correlate with the slow, temperature-insensitive temperature-jump relaxation. Phase 3 is absent in the temperature-jump, which excludes it from tension generation. We confirm that de novo tension generation occurs as an order-disorder transition during phase 2slow and the equivalent, temperature-sensitive temperature-jump relaxation. PMID:7612845

First full length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses.

OpenAIRE

2011-01-01

Abstract An increasing incidence of enteric disorders clinically evocative of the poult enteritis complex has been observed in turkeys in France since 2003. Using a newly designed real-time RT-PCR assay specific for the nucleocapsid (N) gene of infectious bronchitis virus (IBV) and turkey coronaviruses (TCoV), coronaviruses were identified in 37 % of the intestinal samples collected from diseased turkey flocks. The full length Spike (S) gene of these viruses was amplified, cloned a...

Functional PAK-2 knockout and replacement with a caspase cleavage-deficient mutant in mice reveals differential requirements of full-length PAK-2 and caspase-activated PAK-2p34.

Science.gov (United States)

Marlin, Jerry W; Chang, Yu-Wen E; Ober, Margaret; Handy, Amy; Xu, Wenhao; Jakobi, Rolf

2011-06-01

p21-Activated protein kinase 2 (PAK-2) has both anti- and pro-apoptotic functions depending on its mechanism of activation. Activation of full-length PAK-2 by the monomeric GTPases Cdc42 or Rac stimulates cell survival, whereas caspase activation of PAK-2 to the PAK-2p34 fragment is involved in the apoptotic response. In this study we use functional knockout of PAK-2 and gene replacement with the caspase cleavage-deficient PAK-2D212N mutant to differentiate the biological functions of full-length PAK-2 and caspase-activated PAK-2p34. Knockout of PAK-2 results in embryonic lethality at early stages before organ development, whereas replacement with the caspase cleavage-deficient PAK-2D212N results in viable and healthy mice, indicating that early embryonic lethality is caused by deficiency of full-length PAK-2 rather than lack of caspase activation to the PAK-2p34 fragment. However, deficiency of caspase activation of PAK-2 decreased spontaneous cell death of primary mouse embryonic fibroblasts and increased cell growth at high cell density. In contrast, stress-induced cell death by treatment with the anti-cancer drug cisplatin was not reduced by deficiency of caspase activation of PAK-2, but switched from an apoptotic to a nonapoptotic, caspase-independent mechanism. Homozygous PAK-2D212N primary mouse embryonic fibroblasts that lack the ability to generate the proapoptotic PAK-2p34 show less activation of the effector caspase 3, 6, and 7, indicating that caspase activation of PAK-2 amplifies the apoptotic response through a positive feedback loop resulting in more activation of effector caspases.

Normal standards for kidney length as measured with US in premature infants

International Nuclear Information System (INIS)

Schlesinger, A.E.; Hedlund, G.L.; Pierson, W.P.; Null, D.M.

1986-01-01

In order to develop normal standards for kidney length in premature infants, the authors measured kidney length by US imaging in 39 (to date) premature infants less than 72 hours old and without known renal disease. Kidney length was compared with four different parameters of body size, including gestational age, birth weight, birth length, and body surface area. Similar standards have been generated previously for normal renal length as measured by US imaging in full-term infants and older children. These standards have proven utility in cases of congenital and acquired disorders that abnormally increase or decrease renal size. Scatter plots of kidney length versus body weight and kidney length versus body surface area conformed well to a logarithmic distribution, with a high correlation coefficient and close-fitting 95% confidence limits (SEE = 2.05)

Full length articles published in BJOMS during 2010-11--an analysis by sub-specialty and study type.

Science.gov (United States)

Arakeri, Gururaj; Colbert, Serryth; Rosenbaum, Gavin; Brennan, Peter A

2012-12-01

Full length articles such as prospective and retrospective studies, case series, laboratory-based research and reviews form the majority of papers published in the British Journal of Oral and Maxillofacial Surgery (BJOMS). We were interested to evaluate the breakdown of these types of articles both by sub-specialty and the type of study as well as the proportion that are written by UK colleagues compared to overseas authors over a 2 year period (2010-11). A total of 191 full length articles across all sub-specialties of our discipline were published, with 107 papers (56%) coming from UK authors. There were proportionately more oncology papers arising from the UK than overseas (60 and 30% of total respectively) while the opposite was found for cleft/deformity studies (10% and 22%). There was only one laboratory-based study published from the UK compared with 27 papers from overseas. The number of quality papers being submitted to the Journal continues to increase, and the type of article being published between UK and overseas probably reflects different practices and case-loads amongst colleagues. The relatively few UK laboratory based studies published in BJOMS compared to overseas authors are most likely due to authors seeking the most prestigious journals possible for their work. Copyright © 2012 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Telomere Length Reprogramming in Embryos and Stem Cells

Directory of Open Access Journals (Sweden)

Keri Kalmbach

2014-01-01

Full Text Available Telomeres protect and cap linear chromosome ends, yet these genomic buffers erode over an organism’s lifespan. Short telomeres have been associated with many age-related conditions in humans, and genetic mutations resulting in short telomeres in humans manifest as syndromes of precocious aging. In women, telomere length limits a fertilized egg’s capacity to develop into a healthy embryo. Thus, telomere length must be reset with each subsequent generation. Although telomerase is purportedly responsible for restoring telomere DNA, recent studies have elucidated the role of alternative telomeres lengthening mechanisms in the reprogramming of early embryos and stem cells, which we review here.

The full-length microRNA cluster in the intron of large latency transcript is associated with the virulence of pseudorabies virus.

Science.gov (United States)

Wang, Xin; Zhang, Mei-Mei; Yan, Kai; Tang, Qi; Wu, Yi-Quan; He, Wen-Bo; Chen, Huan-Chun; Liu, Zheng-Fei

2018-07-01

Pseudorabies virus (PRV), the etiological pathogen of Aujeszky's disease, belongs to the Alphaherpesvirus subfamily. Large latency transcript (LLT), the most abundant PRV transcript, harbors a ~ 4.6 kb microRNA (miRNA) cluster-encoding intron. To investigate the function of the LLT miRNA cluster during the life cycle of PRV, we generated a miRNA cluster mutation virus (PRV-∆miR cluster) and revertant virus. Analysis of the growth kinetics of PRV-ΔmiR cluster-infected cells revealed significantly smaller plaques and lower titers than the wild-type and revertant viruses. The mutation virus exhibited increased IE180 and decreased EP0 expression. The clinical symptoms observed in mice infected with PRV-ΔmiR cluster revealed that the miRNA cluster is involved in the pathogenesis of PRV. Physical parameters, virus shedding assays, and the SN 50 titers revealed that the miRNA cluster enhances PRV virulence in pigs. Collectively, our findings suggest that the full-length miRNA cluster is involved in PRV replication and virulence. Copyright © 2018 Elsevier Inc. All rights reserved.

Full-color large-scaled computer-generated holograms using RGB color filters.

Science.gov (United States)

Tsuchiyama, Yasuhiro; Matsushima, Kyoji

2017-02-06

A technique using RGB color filters is proposed for creating high-quality full-color computer-generated holograms (CGHs). The fringe of these CGHs is composed of more than a billion pixels. The CGHs reconstruct full-parallax three-dimensional color images with a deep sensation of depth caused by natural motion parallax. The simulation technique as well as the principle and challenges of high-quality full-color reconstruction are presented to address the design of filter properties suitable for large-scaled CGHs. Optical reconstructions of actual fabricated full-color CGHs are demonstrated in order to verify the proposed techniques.

Patient-Specific Instruments Based on Knee Joint Computed Tomography and Full-Length Lower Extremity Radiography in Total Knee Replacement

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Hua Tian

2018-01-01

Conclusions: The use of PSIs based on knee joint CT and standing full-length lower extremity radiography in TKR resulted in acceptable alignment compared with the use of conventional instruments, although the marginal advantage was not statistically different. Surgical time and clinical results were also similar between the two groups. However, the PSI group had less postoperative drainage.

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

Directory of Open Access Journals (Sweden)

Ru Huang

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

An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

Science.gov (United States)

Pollier, Jacob; González-Guzmán, Miguel; Ardiles-Diaz, Wilson; Geelen, Danny; Goossens, Alain

2011-01-01

cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

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Jessica A. Brown

2010-01-01

Full Text Available Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη, a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average than the ground-state binding step (18-fold on average. Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides.

On Sequence Lengths of Some Special External Exclusive OR Type LFSR Structures – Study and Analysis

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A Ahmad

2014-12-01

Full Text Available The study of the length of pseudo-random binary sequences generated by Linear- Feedback Shift Registers (LFSRs plays an important role in the design approaches of built-in selftest, cryptosystems, and other applications. However, certain LFSR structures might not be appropriate in some situations. Given that determining the length of generated pseudo-random binary sequence is a complex task, therefore, before using an LFSR structure, it is essential to investigate the length and the properties of the sequence. This paper investigates some conditions and LFSR’s structures, which restrict the pseudo-random binary sequences’ generation to a certain fixed length. The outcomes of this paper are presented in the form of theorems, simulations, and analyses. We believe that these outcomes are of great importance to the designers of built-in self-test equipment, cryptosystems, and other applications such as radar, CDMA, error correction, and Monte Carlo simulation.

Characterization of near full-length genomes of HIV type 1 strains in Denmark: Basis for a universal therapeutic vaccine

DEFF Research Database (Denmark)

Andresen, Betina S.; Vinner, Lasse; Tang, Sheila Tuyet

2007-01-01

We report here the near full-length sequence characterization of 17 Danish clinical HIV-1 strains isolated from HLA-A02 patients not in need of ART, with relatively low viral loads and normal CD4 cell counts. Sequencing was performed directly on DNA extracted from short-term cocultures of PBMCs...... of a universal immunotherapeutic vaccine construct based on these epitopes....

Binding site analysis of full-length α1a adrenergic receptor using homology modeling and molecular docking

International Nuclear Information System (INIS)

Pedretti, Alessandro; Elena Silva, Maria; Villa, Luigi; Vistoli, Giulio

2004-01-01

The recent availability of crystal structure of bovine rhodopsin offers new opportunities in order to approach the construction of G protein coupled receptors. This study focuses the attention on the modeling of full-length α 1a adrenergic receptor (α 1a -AR) due to its biological role and significant implications in pharmacological treatment of benign prostate hyperplasia. This work could be considered made up by two main steps: (a) the construction of full structure of α 1a -AR, through homology modeling methods; (b) the automated docking of an endogenous agonist, norepinephrine, and of an antagonist, WB-4101, using BioDock program. The obtained results highlight the key residues involved in binding sites of both agonists and antagonists, confirming the mutagenesis data and giving new suggestions for the rational design of selective ligands

Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

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Bhagyashree S Birla

Full Text Available Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

VP1u phospholipase activity is critical for infectivity of full-length parvovirus B19 genomic clones

OpenAIRE

Filippone, Claudia; Zhi, Ning; Wong, Susan; Lu, Jun; Kajigaya, Sachiko; Gallinella, Giorgio; Kakkola, Laura; Söderlund-Venermo, Maria; Young, Neal S.; Brown, Kevin E.

2008-01-01

Three full-length genomic clones (pB19-M20, pB19-FL and pB19-HG1) of parvovirus B19 were produced in different laboratories. pB19-M20 was shown to produce infectious virus. To determine the differences in infectivity, all three plasmids were tested by transfection and infection assays. All three clones were similar in viral DNA replication, RNA transcription, and viral capsid protein production. However, only pB19-M20 and pB19-HG1 produced infectious virus. Comparison of viral sequences showe...

Differing Efficacies of Lead Group A Streptococcal Vaccine Candidates and Full-Length M Protein in Cutaneous and Invasive Disease Models

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Tania Rivera-Hernandez

2016-06-01

Full Text Available Group A Streptococcus (GAS is an important human pathogen responsible for both superficial infections and invasive diseases. Autoimmune sequelae may occur upon repeated infection. For this reason, development of a vaccine against GAS represents a major challenge, since certain GAS components may trigger autoimmunity. We formulated three combination vaccines containing the following: (i streptolysin O (SLO, interleukin 8 (IL-8 protease (Streptococcus pyogenes cell envelope proteinase [SpyCEP], group A streptococcal C5a peptidase (SCPA, arginine deiminase (ADI, and trigger factor (TF; (ii the conserved M-protein-derived J8 peptide conjugated to ADI; and (iii group A carbohydrate lacking the N-acetylglucosamine side chain conjugated to ADI. We compared these combination vaccines to a “gold standard” for immunogenicity, full-length M1 protein. Vaccines were adjuvanted with alum, and mice were immunized on days 0, 21, and 28. On day 42, mice were challenged via cutaneous or subcutaneous routes. High-titer antigen-specific antibody responses with bactericidal activity were detected in mouse serum samples for all vaccine candidates. In comparison with sham-immunized mice, all vaccines afforded protection against cutaneous challenge. However, only full-length M1 protein provided protection in the subcutaneous invasive disease model.

De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.

Science.gov (United States)

Cho, Namjin; Hwang, Byungjin; Yoon, Jung-ki; Park, Sangun; Lee, Joongoo; Seo, Han Na; Lee, Jeewon; Huh, Sunghoon; Chung, Jinsoo; Bang, Duhee

2015-09-21

Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

Construction of a normalized full-length cDNA library of cephalopod Amphioctopus fangsiao and development of microsatellite markers

Science.gov (United States)

Feng, Yanwei; Liu, Wenfen; Xu, Xin; Yang, Jianmin; Wang, Weijun; Wei, Xiumei; Liu, Xiangquan; Sun, Guohua

2017-10-01

Amphioctopus fangsiao is one of the most economically important species and has been considered to be a candidate for aquaculture. In order to facilitate its fine-scale genetic analyses, we constructed a normalized full-length library successfully and developed a set of microsatellite markers in this study. The normalized full-length library had a storage capacity of 6.9×105 independent clones. The recombination efficiency was 95% and the average size of inserted fragments was longer than 1000 bp. A total of 3440 high quality ESTs were obtained, which were assembled into 1803 unigenes. Of these unigenes, 450 (25%) were assigned into 33 Gene Ontology terms, 576 (31.9%) into 153 Kyoto Encyclopedia of Genes and Genomes pathways, and 275 (15.3%) into 22 Clusters of Orthologous Groups. Seventy-six polymorphic microsatellite markers were identified. The number of alleles per locus ranged from 4 to 17, and the observed and expected heterozygosities varied between 0.167 and 0.967 and between 0.326 and 0.944, respectively. Twelve loci were significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no linkage disequilibrium was found between different loci. This study provided not only a useful resource for the isolation of the functional genes, but also a set of informative microsatellites for the assessment of population structure and conservation genetics of A. fangsiao.

Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer

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Mahesh Chandra Patra

2018-03-01

Full Text Available Toll-like receptors (TLRs are a unique category of pattern recognition receptors that recognize distinct pathogenic components, often utilizing the same set of downstream adaptors. Specific molecular features of extracellular, transmembrane (TM, and cytoplasmic domains of TLRs are crucial for coordinating the complex, innate immune signaling pathway. Here, we constructed a full-length structural model of TLR4—a widely studied member of the interleukin-1 receptor/TLR superfamily—using homology modeling, protein–protein docking, and molecular dynamics simulations to understand the differential domain organization of TLR4 in a membrane-aqueous environment. Results showed that each functional domain of the membrane-bound TLR4 displayed several structural transitions that are biophysically essential for plasma membrane integration. Specifically, the extracellular and cytoplasmic domains were partially immersed in the upper and lower leaflets of the membrane bilayer. Meanwhile, TM domains tilted considerably to overcome the hydrophobic mismatch with the bilayer core. Our analysis indicates an alternate dimerization or a potential oligomerization interface of TLR4-TM. Moreover, the helical properties of an isolated TM dimer partly agree with that of the full-length receptor. Furthermore, membrane-absorbed or solvent-exposed surfaces of the toll/interleukin-1 receptor domain are consistent with previous X-ray crystallography and biochemical studies. Collectively, we provided a complete structural model of membrane-bound TLR4 that strengthens our current understanding of the complex mechanism of receptor activation and adaptor recruitment in the innate immune signaling pathway.

Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein.

Science.gov (United States)

Das, Debanu; Hervé, Mireille; Feuerhelm, Julie; Farr, Carol L; Chiu, Hsiu-Ju; Elsliger, Marc-André; Knuth, Mark W; Klock, Heath E; Miller, Mitchell D; Godzik, Adam; Lesley, Scott A; Deacon, Ashley M; Mengin-Lecreulx, Dominique; Wilson, Ian A

2011-03-18

Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

Quench propagation study for the BNL-built, full-length, 50mm aperture SSC model dipoles

International Nuclear Information System (INIS)

Muratore, J.; Anerella, M.; Cottingham, G.

1993-01-01

As part of the program to build and test SSC 50mm aperture prototype dipole magnets, a series of seven full-length dipoles were built and tested at BNL. Important part of the testing program was the study of quench propagation velocity and hot spot temperature over a range of experimental conditions in order to characterize the safety of the conductor during quenches experienced under different circumstances. Such studies are important tools in design, implementation, and verification of quench protection strategies in superconducting accelerator magnets. This investigation was facilitated by artificially inducing quenches under controlled experimental conditions with spot heaters placed at carefully chosen locations on the magnet coils. Such studies were done as part of the 15m-long magnet test program and were performed on five of the magnets in the series. All were equipped with spot heaters on an inner coil, and two of these also had spot heaters on an outer coil. Therefore, in addition to the studies in the inner coils, it was also possible to study quench propagation in the outer coils, where slower quench velocities and higher conductor temperatures are expected, in comparison to that in the inner coils. In spontaneous quenches, where there may be no voltage taps, it is not possible to measure the conductor hot spot temperature. It is straightforward to measure the number of MIITs generated, since only the magnet current and voltage need be measured. The concept of MIITs then becomes a valuable diagnostic tool which can characterize the temperature behavior of a conductor during quench and can be used to determine limits for safe operation of the coil. With spot heaters placed at known locations and closely bracketed by voltage taps, hot spot temperature can be measured. Research such as is described in this paper is therefore important in order to determine the validity of the MIITs approach and to establish a correlation between temperature and MIITs

Octave-spanning supercontinuum generation at telecommunications wavelengths in a precisely dispersion- and length-controlled silicon-wire waveguide with a double taper structure

Science.gov (United States)

Ishizawa, Atsushi; Goto, Takahiro; Kou, Rai; Tsuchizawa, Tai; Matsuda, Nobuyuki; Hitachi, Kenichi; Nishikawa, Tadashi; Yamada, Koji; Sogawa, Tetsuomi; Gotoh, Hideki

2017-07-01

We demonstrate on-chip octave-spanning supercontinuum (SC) generation with a Si-wire waveguide (SWG). We precisely controlled the SWG width so that the group velocity becomes flat over a wide wavelength range. By adjusting the SWG length, we could reduce the optical losses due to two-photon absorption and pulse propagation. In addition, for efficient coupling between the laser pulse and waveguide, we fabricated a two-step inverse taper at both ends of the SWG. Using a 600-nm-wide SWG, we were able to generate a broadband SC spectrum at wavelengths from 1060 to 2200 nm at a -40 dB level with only 50-pJ laser energy from an Er-doped fiber laser oscillator. We found that we can generate an on-chip broadband SC spectrum with an SWG with a length even as small as 1.7 mm.

High avidity antibodies to full-length VAR2CSA correlate with absence of placental malaria

DEFF Research Database (Denmark)

Tutterrow, Yeung Lo; Salanti, Ali; Avril, Marion

2012-01-01

VAR2CSA mediates sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, increasing the risk of poor pregnancy outcomes. Naturally acquired antibodies (Ab) to placental parasites at delivery have been associated with improved pregnancy outcomes, but Ab levels and how early...... in pregnancy Ab must be present in order to eliminate placental parasites before delivery remains unknown. Antibodies to individual Duffy-binding like domains of VAR2CSA have been studied, but the domains lack many of the conformational epitopes present in full-length VAR2CSA (FV2). Thus, the purpose...... of this study was to describe the acquisition of Ab to FV2 in women residing in high and low transmission areas and determine how Ab levels during pregnancy correlate with clearance of placental parasites. Plasma samples collected monthly throughout pregnancy from pregnant women living in high and low...

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

DEFF Research Database (Denmark)

Karst, Søren Michael; Dueholm, Morten Simonsen; McIlroy, Simon Jon

2018-01-01

Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied e...

Molecular comparisons of full length metapneumovirus (MPV genomes, including newly determined French AMPV-C and -D isolates, further supports possible subclassification within the MPV Genus.

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Paul A Brown

Full Text Available Four avian metapneumovirus (AMPV subgroups (A-D have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus "clusters" HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II.

Ultrashort electron bunch length measurement with diffraction radiation deflector

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Dao Xiang

2007-01-01

Full Text Available In this paper, we propose a novel method to measure electron bunch length with a diffraction radiation (DR deflector which is composed of a DR radiator and three beam position monitors (BPMs. When an electron beam passes through a metallic aperture which is tilted by 45 degrees with respect to its trajectory, backward DR that propagates perpendicular to the beam’s trajectory is generated which adds a transverse deflection to the beam as a result of momentum conservation. The deflection is found to be largely dependent on the bunch length and could be easily observed with a downstream BPM. Detailed investigations show that this method has wide applicability, high temporal resolution, and great simplicity.

Upper bound for the length of commutative algebras

International Nuclear Information System (INIS)

Markova, Ol'ga V

2009-01-01

By the length of a finite system of generators for a finite-dimensional associative algebra over an arbitrary field one means the least positive integer k such that the words of length not exceeding k span this algebra (as a vector space). The maximum length for the systems of generators of an algebra is referred to as the length of the algebra. In the present paper, an upper bound for the length of a commutative algebra in terms of a function of two invariants of the algebra, the dimension and the maximal degree of the minimal polynomial for the elements of the algebra, is obtained. As a corollary, a formula for the length of the algebra of diagonal matrices over an arbitrary field is obtained. Bibliography: 8 titles.

RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function.

Science.gov (United States)

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

2011-02-01

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named 'RiceFOX'. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/.

Intersubunit distances in full-length, dimeric, bacterial phytochrome Agp1, as measured by pulsed electron-electron double resonance (PELDOR) between different spin label positions, remain unchanged upon photoconversion.

Science.gov (United States)

Kacprzak, Sylwia; Njimona, Ibrahim; Renz, Anja; Feng, Juan; Reijerse, Edward; Lubitz, Wolfgang; Krauss, Norbert; Scheerer, Patrick; Nagano, Soshichiro; Lamparter, Tilman; Weber, Stefan

2017-05-05

Bacterial phytochromes are dimeric light-regulated histidine kinases that convert red light into signaling events. Light absorption by the N-terminal photosensory core module (PCM) causes the proteins to switch between two spectrally distinct forms, Pr and Pfr, thus resulting in a conformational change that modulates the C-terminal histidine kinase region. To provide further insights into structural details of photoactivation, we investigated the full-length Agp1 bacteriophytochrome from the soil bacterium Agrobacterium fabrum using a combined spectroscopic and modeling approach. We generated seven mutants suitable for spin labeling to enable application of pulsed EPR techniques. The distances between attached spin labels were measured using pulsed electron-electron double resonance spectroscopy to probe the arrangement of the subunits within the dimer. We found very good agreement of experimental and calculated distances for the histidine-kinase region when both subunits are in a parallel orientation. However, experimental distance distributions surprisingly showed only limited agreement with either parallel- or antiparallel-arranged dimer structures when spin labels were placed into the PCM region. This observation indicates that the arrangements of the PCM subunits in the full-length protein dimer in solution differ significantly from that in the PCM crystals. The pulsed electron-electron double resonance data presented here revealed either no or only minor changes of distance distributions upon Pr-to-Pfr photoconversion. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Entangled photon pair generation by spontaneous parametric down-conversion in finite-length one-dimensional photonic crystals

International Nuclear Information System (INIS)

Centini, M.; Sciscione, L.; Sibilia, C.; Bertolotti, M.; Perina, J. Jr.; Scalora, M.; Bloemer, M.J.

2005-01-01

A description of spontaneous parametric down-conversion in finite-length one-dimensional nonlinear photonic crystals is developed using semiclassical and quantum approaches. It is shown that if a suitable averaging is added to the semiclassical model, its results are in very good agreement with the quantum approach. We propose two structures made with GaN/AlN that generate both degenerate and nondegenerate entangled photon pairs. Both structures are designed so as to achieve a high efficiency of the nonlinear process

The effects of session length on demand functions generated using FR schedules.

Science.gov (United States)

Foster, T Mary; Kinloch, Jennifer; Poling, Alan

2011-05-01

In comparing open and closed economies, researchers often arrange shorter sessions under the former condition than under the latter. Several studies indicate that session length per se can affect performance and there are some data that indicate that this variable can influence demand functions. To provide further data, the present study exposed domestic hens to series of increasing fixed-ratio schedules with the length of the open-economy sessions varied over 10, 40, 60, and 120 min. Session time affected the total-session response rates and pause lengths. The shortest session gave the greatest response rates and shortest pauses and the longest gave the lowest response rates and longest pauses. The total-session demand functions also changed with session length: The shortest session gave steeper initial slopes (i.e., the functions were more elastic at small ratios) and smaller rates of change of elasticity than the longest session. Response rates, pauses, and demand functions were, however, similar for equivalent periods of responding taken from within sessions of different overall lengths (e.g., total-session data for 10-min sessions and the data for the first 10 min of 120-min sessions). These findings suggest that differences in session length can confound the results of studies comparing open and closed economies when those economies are arranged in sessions that differ substantially in length, hence data for equivalent-length periods of responding, rather than total-session data, should be of primary interest under these conditions.

The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics.

Science.gov (United States)

Dorfman, Kevin D

2018-02-01

The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

Calculation of evolutionary correlation between individual genes and full-length genome: a method useful for choosing phylogenetic markers for molecular epidemiology.

Directory of Open Access Journals (Sweden)

Shuai Wang

Full Text Available Individual genes or regions are still commonly used to estimate the phylogenetic relationships among viral isolates. The genomic regions that can faithfully provide assessments consistent with those predicted with full-length genome sequences would be preferable to serve as good candidates of the phylogenetic markers for molecular epidemiological studies of many viruses. Here we employed a statistical method to evaluate the evolutionary relationships between individual viral genes and full-length genomes without tree construction as a way to determine which gene can match the genome well in phylogenetic analyses. This method was performed by calculation of linear correlations between the genetic distance matrices of aligned individual gene sequences and aligned genome sequences. We applied this method to the phylogenetic analyses of porcine circovirus 2 (PCV2, measles virus (MV, hepatitis E virus (HEV and Japanese encephalitis virus (JEV. Phylogenetic trees were constructed for comparisons and the possible factors affecting the method accuracy were also discussed in the calculations. The results revealed that this method could produce results consistent with those of previous studies about the proper consensus sequences that could be successfully used as phylogenetic markers. And our results also suggested that these evolutionary correlations could provide useful information for identifying genes that could be used effectively to infer the genetic relationships.

Experience with vacuum distillation cleaning of a full-size steam generator

Energy Technology Data Exchange (ETDEWEB)

Smit, C C

1975-07-01

In the 50 MW Sodium Component Test Facility at Hengelo tests are conducted on several types of full size prototype steam generators and an intermediate heat exchanger. The necessary post-test examination of these prototype components requires a complete removal of all sodium. Since in some cases the endurance test has to be continued after internal inspection, the cleaning-method should be such that no damage occurs to the component. After partial disassembly and internal inspection the component will be reassembled and must be acceptable for further use. The qualification tests of the Neratoom straight tube steam generator were concluded in June 1974. The evaporator module was decided to be partially disassembled in order to meet the requirement of a thorough examination before fabrication of the SNR-generators is started. In preparation for the most suitable cleaning procedure, several methods of sodium removal were considered.

Experience with vacuum distillation cleaning of a full-size steam generator

International Nuclear Information System (INIS)

Smit, C.C.

1975-01-01

In the 50 MW Sodium Component Test Facility at Hengelo tests are conducted on several types of full size prototype steam generators and an intermediate heat exchanger. The necessary post-test examination of these prototype components requires a complete removal of all sodium. Since in some cases the endurance test has to be continued after internal inspection, the cleaning-method should be such that no damage occurs to the component. After partial disassembly and internal inspection the component will be reassembled and must be acceptable for further use. The qualification tests of the Neratoom straight tube steam generator were concluded in June 1974. The evaporator module was decided to be partially disassembled in order to meet the requirement of a thorough examination before fabrication of the SNR-generators is started. In preparation for the most suitable cleaning procedure, several methods of sodium removal were considered

Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

Science.gov (United States)

Birla, Bhagyashree S; Chou, Hui-Hsien

2015-01-01

Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

Single-dose monomeric HA subunit vaccine generates full protection from influenza challenge

CSIR Research Space (South Africa)

Mallajosyula, JK

2014-03-01

Full Text Available 50% survival, or 100% survival with adjuvant, compared with 10% survival after vaccination with a commercially available H 1 N 1 vaccine. TMV-HA is an effective dose-sparing influenza vaccine, using a single-step process to rapidly generate large...

The length-weight and length-length relationships of bluefish, Pomatomus saltatrix (Linnaeus, 1766 from Samsun, middle Black Sea region

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Melek Özpiçak

2017-10-01

Full Text Available In this study, length-weight relationship (LWR and length-length relationship (LLR of bluefish, Pomatomus saltatrix were determined. A total of 125 specimens were sampled from Samsun, the middle Black Sea in 2014 fishing season. Bluefish specimens were monthly collected from commercial fishing boats from October to December 2014. All captured individuals (N=125 were measured to the nearest 0.1 cm for total, fork and standard lengths. The weight of each fish (W was recorded to the nearest 0.01 g. According to results of analyses, there were no statistically significant differences between sexes in term of length and weight (P˃0.05. The minimum and maximum total, fork and standard lengths of bluefish ranged between 13.5-23.6 cm, 12.50-21.80 cm and 10.60-20.10 cm, respectively. The equation of length-weight relationship were calculated as W=0.008TL3.12 (r2>0.962. Positive allometric growth was observed for bluefish (b>3. Length-length relationship was also highly significant (P<0.001 with coefficient of determination (r2 ranging from 0.916 to 0.988.

A Rapid and Improved Method to Generate Recombinant Dengue Virus Vaccine Candidates.

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Dhanasekaran Govindarajan

Full Text Available Dengue is one of the most important mosquito-borne infections accounting for severe morbidity and mortality worldwide. Recently, the tetravalent chimeric live attenuated Dengue vaccine Dengvaxia® was approved for use in several dengue endemic countries. In general, live attenuated vaccines (LAV are very efficacious and offer long-lasting immunity against virus-induced disease. Rationally designed LAVs can be generated through reverse genetics technology, a method of generating infectious recombinant viruses from full length cDNA contained in bacterial plasmids. In vitro transcribed (IVT viral RNA from these infectious clones is transfected into susceptible cells to generate recombinant virus. However, the generation of full-length dengue virus cDNA clones can be difficult due to the genetic instability of viral sequences in bacterial plasmids. To circumvent the need for a single plasmid containing a full length cDNA, in vitro ligation of two or three cDNA fragments contained in separate plasmids can be used to generate a full-length dengue viral cDNA template. However, in vitro ligation of multiple fragments often yields low quality template for IVT reactions, resulting in inconsistent low yield RNA. These technical difficulties make recombinant virus recovery less efficient. In this study, we describe a simple, rapid and efficient method of using LONG-PCR to recover recombinant chimeric Yellow fever dengue (CYD viruses as potential dengue vaccine candidates. Using this method, we were able to efficiently generate several viable recombinant viruses without introducing any artificial mutations into the viral genomes. We believe that the techniques reported here will enable rapid and efficient recovery of recombinant flaviviruses for evaluation as vaccine candidates and, be applicable to the recovery of other RNA viruses.

A Rapid and Improved Method to Generate Recombinant Dengue Virus Vaccine Candidates.

Science.gov (United States)

Govindarajan, Dhanasekaran; Guan, Liming; Meschino, Steven; Fridman, Arthur; Bagchi, Ansu; Pak, Irene; ter Meulen, Jan; Casimiro, Danilo R; Bett, Andrew J

2016-01-01

Dengue is one of the most important mosquito-borne infections accounting for severe morbidity and mortality worldwide. Recently, the tetravalent chimeric live attenuated Dengue vaccine Dengvaxia® was approved for use in several dengue endemic countries. In general, live attenuated vaccines (LAV) are very efficacious and offer long-lasting immunity against virus-induced disease. Rationally designed LAVs can be generated through reverse genetics technology, a method of generating infectious recombinant viruses from full length cDNA contained in bacterial plasmids. In vitro transcribed (IVT) viral RNA from these infectious clones is transfected into susceptible cells to generate recombinant virus. However, the generation of full-length dengue virus cDNA clones can be difficult due to the genetic instability of viral sequences in bacterial plasmids. To circumvent the need for a single plasmid containing a full length cDNA, in vitro ligation of two or three cDNA fragments contained in separate plasmids can be used to generate a full-length dengue viral cDNA template. However, in vitro ligation of multiple fragments often yields low quality template for IVT reactions, resulting in inconsistent low yield RNA. These technical difficulties make recombinant virus recovery less efficient. In this study, we describe a simple, rapid and efficient method of using LONG-PCR to recover recombinant chimeric Yellow fever dengue (CYD) viruses as potential dengue vaccine candidates. Using this method, we were able to efficiently generate several viable recombinant viruses without introducing any artificial mutations into the viral genomes. We believe that the techniques reported here will enable rapid and efficient recovery of recombinant flaviviruses for evaluation as vaccine candidates and, be applicable to the recovery of other RNA viruses.

Full C-band Tunable MEMS-VCSEL for Next Generation G.metro Mobile Front- and Backhauling

DEFF Research Database (Denmark)

Wagner, Christoph; Zou, Shihuan Jim; Ortsiefer, Markus

2017-01-01

We report full C-band tunable, 10 Gbit/s capability, directly modulated MEMS-VCSEL for next generation converged mobile fronthaul and backhaul applications. Bit error rates below 10(-9) were achieved over up to 40 km SSMF.......We report full C-band tunable, 10 Gbit/s capability, directly modulated MEMS-VCSEL for next generation converged mobile fronthaul and backhaul applications. Bit error rates below 10(-9) were achieved over up to 40 km SSMF....

Significance of urinary full-length megalin in patients with IgA nephropathy.

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Takuto Seki

Full Text Available BACKGROUND AND OBJECTIVES: Megalin is highly expressed at the apical membranes of proximal tubular epithelial cells. A urinary full-length megalin (C-megalin assay is linked to the severity of diabetic nephropathy in type 2 diabetes. This study examined the relationship between levels of urinary C-megalin and histological findings in adult patients with IgA nephropathy (IgAN. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Urine samples voided in the morning on the day of renal biopsy were obtained from 73 patients with IgAN (29 men and 44 women; mean age, 33 years and 5 patients with membranous nephropathy (MN. Renal pathologic variables were analyzed using the Oxford classification of IgAN, the Shigematsu classification and the Clinical Guidelines of IgAN in Japan. The levels of urinary C-megalin were measured by sandwich ELISA. RESULTS: Histological analysis based on the Oxford classification revealed that the levels of urinary C-megalin were correlated with mesangial hypercellularity in IgAN patients (OR = 1.76, 95% CI: 1.04-3.27, P<0.05. There was a significant correlation between the levels of urinary C-megalin and the severity of chronic extracapillary abnormalities according to the Shigematsu classification in IgAN patients (β = 0.33, P = 0.008. The levels of urinary C-megalin were significantly higher in all risk levels of IgAN patients requiring dialysis using the Clinical Guidelines of IgAN in Japan than in the control group. The levels of urinary C-megalin were significantly higher in the high risk and very high risk grades than in the low risk grade (P<0.05. The levels of urinary C-megalin were significantly higher in MN patients compared to the control group. CONCLUSIONS: The levels of urinary C-megalin are associated with histological abnormalities in adult IgAN patients. There is a possibility that urinary C-megalin is an independent predictor of disease progression of IgAN. In addition, our results suggest that

Cloning and sequencing of full-length cDNAs of RNA1 and RNA2 of a Tomato black ring virus isolate from Poland.

Science.gov (United States)

Jończyk, M; Le Gall, O; Pałucha, A; Borodynko, N; Pospieszny, H

2004-04-01

Full-length cDNA clones corresponding to the RNA1 and RNA2 of the Polish isolate MJ of Tomato black ring virus (TBRV, genus Nepovirus) were obtained using a direct recombination strategy in yeast, and their complete nucleotide sequences were established. RNA1 is 7358 nucleotides and RNA2 is 4633 nucleotides in length, excluding the poly(A) tails. Both RNAs contain a single open reading frame encoding polyproteins of 254 kDa and 149 kDa for RNA1 and RNA2 respectively. Putative cleavage sites were identified, and the relationships between TBRV and related nepoviruses were studied by sequence comparison.

Multiple Word-Length High-Level Synthesis

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Coussy Philippe

2008-01-01

Full Text Available Abstract Digital signal processing (DSP applications are nowadays widely used and their complexity is ever growing. The design of dedicated hardware accelerators is thus still needed in system-on-chip and embedded systems. Realistic hardware implementation requires first to convert the floating-point data of the initial specification into arbitrary length data (finite-precision while keeping an acceptable computation accuracy. Next, an optimized hardware architecture has to be designed. Considering uniform bit-width specification allows to use traditional automated design flow. However, it leads to oversized design. On the other hand, considering non uniform bit-width specification allows to get a smaller circuit but requires complex design tasks. In this paper, we propose an approach that inputs a C/C++ specification. The design flow, based on high-level synthesis (HLS techniques, automatically generates a potentially pipeline RTL architecture described in VHDL. Both bitaccurate integer and fixed-point data types can be used in the input specification. The generated architecture uses components (operator, register, etc. that have different widths. The design constraints are the clock period and the throughput of the application. The proposed approach considers data word-length information in all the synthesis steps by using dedicated algorithms. We show in this paper the effectiveness of the proposed approach through several design experiments in the DSP domain.

Multiple Word-Length High-Level Synthesis

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Dominique Heller

2008-09-01

Full Text Available Digital signal processing (DSP applications are nowadays widely used and their complexity is ever growing. The design of dedicated hardware accelerators is thus still needed in system-on-chip and embedded systems. Realistic hardware implementation requires first to convert the floating-point data of the initial specification into arbitrary length data (finite-precision while keeping an acceptable computation accuracy. Next, an optimized hardware architecture has to be designed. Considering uniform bit-width specification allows to use traditional automated design flow. However, it leads to oversized design. On the other hand, considering non uniform bit-width specification allows to get a smaller circuit but requires complex design tasks. In this paper, we propose an approach that inputs a C/C++ specification. The design flow, based on high-level synthesis (HLS techniques, automatically generates a potentially pipeline RTL architecture described in VHDL. Both bitaccurate integer and fixed-point data types can be used in the input specification. The generated architecture uses components (operator, register, etc. that have different widths. The design constraints are the clock period and the throughput of the application. The proposed approach considers data word-length information in all the synthesis steps by using dedicated algorithms. We show in this paper the effectiveness of the proposed approach through several design experiments in the DSP domain.

Effect of Full-Length Carbon Fiber Insoles on Lower Limb Kinetics in Patients With Midfoot Osteoarthritis: A Pilot Study.

Science.gov (United States)

Yi, Taeim; Kim, Jung Hyun; Oh-Park, Mooyeon; Hwang, Ji Hye

2018-03-01

We investigated the effects of full-length carbon fiber (FCF) insoles on gait, muscle activity, kinetics, and pain in patients with midfoot osteoarthritis (OA). We enrolled 13 patients with unilateral midfoot OA (mild: Visual Analog Scale [VAS] range, 1-3; moderate, VAS range, 4-7) and healthy controls. All participants were asked to walk under two conditions: with and without FCF insole. The outcome measures were ground reaction force, quantitative gait parameters, electromyography activities and pain severity (VAS). In the patients with moderate midfoot OA, significantly longer gait cycle and higher muscle activity of lower limb during loading-response phase were observed while walking without FCF insoles. In the mild midfoot OA group, there was no significant difference in VAS score (without, 2.0 ± 1.0 vs. with, 2.0 ± 0.5) with FCF insole use. However, significantly reduced VAS score (without, 5.5 ± 1.4 vs. with, 2.0 ± 0.5) and muscle activity of the tibialis anterior and increased muscle activity of gastrocnemius were observed in the moderate midfoot OA group by using an FCF insole (P < 0.05). Full-length carbon fiber insoles can improve pain in individuals with moderate midfoot OA, which might be associated with changes in the kinetics and muscle activities of the lower limb. Taken together, the results of the present study suggest that FCF insoles may be used as a helpful option for midfoot OA.

Chord length distribution for a compound capsule

International Nuclear Information System (INIS)

Pitřík, Pavel

2017-01-01

Chord length distribution is a factor important in the calculation of ionisation chamber responses. This article describes Monte Carlo calculations of the chord length distribution for a non-convex compound capsule. A Monte Carlo code was set up for generation of random chords and calculation of their lengths based on the input number of generations and cavity dimensions. The code was written in JavaScript and can be executed in the majority of HTML viewers. The plot of occurrence of cords of different lengths has 3 peaks. It was found that the compound capsule cavity cannot be simply replaced with a spherical cavity of a triangular design. Furthermore, the compound capsule cavity is directionally dependent, which must be taken into account in calculations involving non-isotropic fields of primary particles in the beam, unless equilibrium of the secondary charged particles is attained. (orig.)

A full-length Plasmodium falciparum recombinant circumsporozoite protein expressed by Pseudomonas fluorescens platform as a malaria vaccine candidate.

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Amy R Noe

Full Text Available The circumsporozoite protein (CSP of Plasmodium falciparum is a major surface protein, which forms a dense coat on the sporozoite's surface. Preclinical research on CSP and clinical evaluation of a CSP fragment-based RTS, S/AS01 vaccine have demonstrated a modest degree of protection against P. falciparum, mediated in part by humoral immunity and in part by cell-mediated immunity. Given the partial protective efficacy of the RTS, S/AS01 vaccine in a recent Phase 3 trial, further improvement of CSP-based vaccines is crucial. In this report, we describe the preclinical development of a full-length, recombinant CSP (rCSP-based vaccine candidate against P. falciparum malaria suitable for current Good Manufacturing Practice (cGMP production. Utilizing a novel high-throughput Pseudomonas fluorescens expression platform, we demonstrated greater efficacy of full-length rCSP as compared to N-terminally truncated versions, rapidly down-selected a promising lead vaccine candidate, and developed a high-yield purification process to express immunologically active, intact antigen for clinical trial material production. The rCSP, when formulated with various adjuvants, induced antigen-specific antibody responses as measured by enzyme-linked immunosorbent assay (ELISA and immunofluorescence assay (IFA, as well as CD4+ T-cell responses as determined by ELISpot. The adjuvanted rCSP vaccine conferred protection in mice when challenged with transgenic P. berghei sporozoites containing the P. falciparum repeat region of CSP. Furthermore, heterologous prime/boost regimens with adjuvanted rCSP and an adenovirus type 35-vectored CSP (Ad35CS showed modest improvements in eliciting CSP-specific T-cell responses and anti-malarial protection, depending on the order of vaccine delivery. Collectively, these data support the importance of further clinical development of adjuvanted rCSP, either as a stand-alone product or as one of the components in a heterologous prime

Construction of a Full-Length Enriched cDNA Library and Preliminary Analysis of Expressed Sequence Tags from Bengal Tiger Panthera tigris tigris

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Changqing Liu

2013-05-01

Full Text Available In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers.

The Effect of Casting Ring Liner Length and Prewetting on the Marginal Adaptation and Dimensional Accuracy of Full Crown Castings.

Science.gov (United States)

Haralur, Satheesh B; Hamdi, Osama A; Al-Shahrani, Abdulaziz A; Alhasaniah, Sultan

2017-01-01

To evaluate the effect of varying cellulose casting ring liner length and its prewetting on the marginal adaptation and dimensional accuracy of full veneer metal castings. The master die was milled in stainless steel to fabricate the wax pattern. Sixty wax patterns were fabricated with a uniform thickness of 1.5 mm at an occlusal surface and 1 mm axial surface, cervical width at 13.5 mm, and 10 mm cuspal height. The samples were divided into six groups ( n = 10). Groups I and II samples had the full-length cellulose prewet and dry ring liner, respectively. The groups III and IV had 2 mm short prewet and dry cellulose ring liner, respectively, whereas groups V and VI were invested in 6 mm short ring liner. The wax patterns were immediately invested in phosphate bonded investment, and casting procedure was completed with nickel-chrome alloy. The castings were cleaned and mean score of measurements at four reference points for marginal adaption, casting height, and cervical width was calculated. The marginal adaption was calculated with Imaje J software, whereas the casting height and cervical width was determined using a digital scale. The data was subjected to one-way analysis of varaince and Tukey post hoc statistical analysis with Statistical Package for the Social Sciences version 20 software. The group II had the best marginal adaption with a gap of 63.786 μm followed by group I (65.185 μm), group IV (87.740 μm), and group III (101.455 μm). A large marginal gap was observed in group V at 188.871 μm. Cuspal height was more accurate with group V (10.428 mm), group VI (10.421 mm), and group II (10.488 mm). The cervical width was approximately similar in group I, group III, and group V. Statistically significant difference was observed in Tukey post hoc analysis between group V and group VI with all the other groups with regards to marginal adaptation. The dry cellulose ring liners provided better marginal adaptation in comparison to prewet cellulose ring

Tula hantavirus isolate with the full-length ORF for nonstructural protein NSs survives for more consequent passages in interferon-competent cells than the isolate having truncated NSs ORF.

Science.gov (United States)

Jääskeläinen, Kirsi M; Plyusnina, Angelina; Lundkvist, Ake; Vaheri, Antti; Plyusnin, Alexander

2008-01-11

The competitiveness of two Tula hantavirus (TULV) isolates, TULV/Lodz and TULV/Moravia, was evaluated in interferon (IFN) -competent and IFN-deficient cells. The two isolates differ in the length of the open reading frame (ORF) encoding the nonstructural protein NSs, which has previously been shown to inhibit IFN response in infected cells. In IFN-deficient Vero E6 cells both TULV isolates survived equally well. In contrast, in IFN-competent MRC5 cells TULV/Lodz isolate, that possesses the NSs ORF for the full-length protein of 90 aa, survived for more consequent passages than TULV/Moravia isolate, which contains the ORF for truncated NSs protein (66-67 aa). Our data show that expression of a full-length NSs protein is beneficial for the virus survival and competitiveness in IFN-competent cells and not essential in IFN-deficient cells. These results suggest that the N-terminal aa residues are important for the full activity of the NSs protein.

Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection▿

OpenAIRE

Humphreys, Isla; Fleming, Vicki; Fabris, Paolo; Parker, Joe; Schulenberg, Bodo; Brown, Anthony; Demetriou, Charis; Gaudieri, Silvana; Pfafferott, Katja; Lucas, Michaela; Collier, Jane; Huang, Kuan-Hsiang Gary; Pybus, Oliver G.; Klenerman, Paul; Barnes, Eleanor

2009-01-01

Hepatitis C virus subtype 3a is a highly prevalent and globally distributed strain that is often associated with infection via injection drug use. This subtype exhibits particular phenotypic characteristics. In spite of this, detailed genetic analysis of this subtype has rarely been performed. We performed full-length viral sequence analysis in 18 patients with chronic HCV subtype 3a infection and assessed genomic viral variability in comparison to other HCV subtypes. Two novel regions of int...

Construction and evaluation of normalized cDNA libraries enriched with full-length sequences for rapid discovery of new genes from Sisal (Agave sisalana Perr.) different developmental stages.

Science.gov (United States)

Zhou, Wen-Zhao; Zhang, Yan-Mei; Lu, Jun-Ying; Li, Jun-Feng

2012-10-12

To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing.

Milligram quantities of homogeneous recombinant full-length mouse Munc18c from Escherichia coli cultures.

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Asma Rehman

Full Text Available Vesicle fusion is an indispensable cellular process required for eukaryotic cargo delivery. The Sec/Munc18 protein Munc18c is essential for insulin-regulated trafficking of glucose transporter4 (GLUT4 vesicles to the cell surface in muscle and adipose tissue. Previously, our biophysical and structural studies have used Munc18c expressed in SF9 insect cells. However to maximize efficiency, minimize cost and negate any possible effects of post-translational modifications of Munc18c, we investigated the use of Escherichia coli as an expression host for Munc18c. We were encouraged by previous reports describing Munc18c production in E. coli cultures for use in in vitro fusion assay, pulldown assays and immunoprecipitations. Our approach differs from the previously reported method in that it uses a codon-optimized gene, lower temperature expression and autoinduction media. Three N-terminal His-tagged constructs were engineered, two with a tobacco etch virus (TEV or thrombin protease cleavage site to enable removal of the fusion tag. The optimized protocol generated 1-2 mg of purified Munc18c per L of culture at much reduced cost compared to Munc18c generated using insect cell culture. The purified recombinant Munc18c protein expressed in bacteria was monodisperse, monomeric, and functional. In summary, we developed methods that decrease the cost and time required to generate functional Munc18c compared with previous insect cell protocols, and which generates sufficient purified protein for structural and biophysical studies.

The full-length E1-circumflexE4 protein of human papillomavirus type 18 modulates differentiation-dependent viral DNA amplification and late gene expression

International Nuclear Information System (INIS)

Wilson, Regina; Ryan, Gordon B.; Knight, Gillian L.; Laimins, Laimonis A.; Roberts, Sally

2007-01-01

Activation of the productive phase of the human papillomavirus (HPV) life cycle in differentiated keratinocytes is coincident with high-level expression of E1-circumflexE4 protein. To determine the role of E1-circumflexE4 in the HPV replication cycle, we constructed HPV18 mutant genomes in which expression of the full-length E1-circumflexE4 protein was abrogated. Undifferentiated keratinocytes containing mutant genomes showed enhanced proliferation when compared to cells containing wildtype genomes, but there were no differences in maintenance of viral episomes. Following differentiation, cells with mutant genomes exhibited reduced levels of viral DNA amplification and late gene expression, compared to wildtype genome-containing cells. This indicates that HPV18 E1-circumflexE4 plays an important role in regulating HPV late functions, and it may also function in the early phase of the replication cycle. Our finding that full-length HPV18 E1-circumflexE4 protein plays a significant role in promoting viral genome amplification concurs with a similar report with HPV31, but is in contrast to an HPV11 study where viral DNA amplification was not dependent on full-length E1-circumflexE4 expression, and to HPV16 where only C-terminal truncations in E1-circumflexE4 abrogated vegetative genome replication. This suggests that type-specific differences exist between various E1-circumflexE4 proteins

Inheritance of spike length in F3, F4 and F5 wheat hybrids obtained by different selection methods

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Janković Snežana

2012-01-01

Full Text Available This study analyses the mode of inheritance of spike length in F3, F4 and F5 wheat hybrids obtained by pedigree, bulk and modified pedigree method of selection. Wheat hybrids were produced after crossing five varieties by M x N method. Three varieties were used as a female parent (Briscard, Carifen 12 and Rescler and two as a male component (Francuska and PKB-Prelivka. Descendents in F2 generation were produced from 6 F1 hybrids (3 x 2. Selection after F2 generation were undertaken from 1996 to 1999, while in 2000 the field experiments with complete breeding material were set up at the Institute 'PKB INI Agroekonomik' in Padinska Skela near Belgrade. Spike length was measured in progeny generations, from F3 to F5. It was observed that progenies had higher values for spike length than better parent (BP, with longer spikes in 5 out of 6 analyzed hybrids: Briscard x PKB-Prelivka, Carifen 12 x Francuska, Carifen 12 x PKB-Prelivka, Rescler x Francuska, and Rescler x PKB-Prelivka. From the above mentioned hybrid combinations, only Rescler x Francuska descendents in F5 generation obtained by pedigree and bulk selection inherited the spike length from the parent with lower value. High significant interaction was observed for spike length between genotype and generation of progenies in each of the applied selection methods.

Production of a full-length infectious GFP-tagged cDNA clone of Beet mild yellowing virus for the study of plant-polerovirus interactions.

Science.gov (United States)

Stevens, Mark; Viganó, Felicita

2007-04-01

The full-length cDNA of Beet mild yellowing virus (Broom's Barn isolate) was sequenced and cloned into the vector pLitmus 29 (pBMYV-BBfl). The sequence of BMYV-BBfl (5721 bases) shared 96% and 98% nucleotide identity with the other complete sequences of BMYV (BMYV-2ITB, France and BMYV-IPP, Germany respectively). Full-length capped RNA transcripts of pBMYV-BBfl were synthesised and found to be biologically active in Arabidopsis thaliana protoplasts following electroporation or PEG inoculation when the protoplasts were subsequently analysed using serological and molecular methods. The BMYV sequence was modified by inserting DNA that encoded the jellyfish green fluorescent protein (GFP) into the P5 gene close to its 3' end. A. thaliana protoplasts electroporated with these RNA transcripts were biologically active and up to 2% of transfected protoplasts showed GFP-specific fluorescence. The exploitation of these cDNA clones for the study of the biology of beet poleroviruses is discussed.

Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes

Science.gov (United States)

Li, Xiaofang; Zhu, Yong-Guan; Shaban, Babak; Bruxner, Timothy J. C.; Bond, Philip L.; Huang, Longbin

2015-01-01

Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses. PMID:26286020

Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

Science.gov (United States)

Brown, Jessica A.; Zhang, Likui; Sherrer, Shanen M.; Taylor, John-Stephen; Burgers, Peter M. J.; Suo, Zucai

2010-01-01

Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη), a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers) in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average) than the ground-state binding step (18-fold on average). Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides. PMID:20798853

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.

Science.gov (United States)

Tudor, Catalina O; Ross, Karen E; Li, Gang; Vijay-Shanker, K; Wu, Cathy H; Arighi, Cecilia N

2015-01-01

Protein phosphorylation is a reversible post-translational modification where a protein kinase adds a phosphate group to a protein, potentially regulating its function, localization and/or activity. Phosphorylation can affect protein-protein interactions (PPIs), abolishing interaction with previous binding partners or enabling new interactions. Extracting phosphorylation information coupled with PPI information from the scientific literature will facilitate the creation of phosphorylation interaction networks of kinases, substrates and interacting partners, toward knowledge discovery of functional outcomes of protein phosphorylation. Increasingly, PPI databases are interested in capturing the phosphorylation state of interacting partners. We have previously developed the eFIP (Extracting Functional Impact of Phosphorylation) text mining system, which identifies phosphorylated proteins and phosphorylation-dependent PPIs. In this work, we present several enhancements for the eFIP system: (i) text mining for full-length articles from the PubMed Central open-access collection; (ii) the integration of the RLIMS-P 2.0 system for the extraction of phosphorylation events with kinase, substrate and site information; (iii) the extension of the PPI module with new trigger words/phrases describing interactions and (iv) the addition of the iSimp tool for sentence simplification to aid in the matching of syntactic patterns. We enhance the website functionality to: (i) support searches based on protein roles (kinases, substrates, interacting partners) or using keywords; (ii) link protein entities to their corresponding UniProt identifiers if mapped and (iii) support visual exploration of phosphorylation interaction networks using Cytoscape. The evaluation of eFIP on full-length articles achieved 92.4% precision, 76.5% recall and 83.7% F-measure on 100 article sections. To demonstrate eFIP for knowledge extraction and discovery, we constructed phosphorylation-dependent interaction

Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and –D Isolates, Further Supports Possible Subclassification within the MPV Genus

Science.gov (United States)

Brown, Paul A.; Lemaitre, Evelyne; Briand, François-Xavier; Courtillon, Céline; Guionie, Olivier; Allée, Chantal; Toquin, Didier; Bayon-Auboyer, Marie-Hélène; Jestin, Véronique; Eterradossi, Nicolas

2014-01-01

Four avian metapneumovirus (AMPV) subgroups (A–D) have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively) have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV) sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus “clusters” HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II. PMID:25036224

Drug resistance is conferred on the model yeast Saccharomyces cerevisiae by expression of full-length melanoma-associated human ATP-binding cassette transporter ABCB5.

Science.gov (United States)

Keniya, Mikhail V; Holmes, Ann R; Niimi, Masakazu; Lamping, Erwin; Gillet, Jean-Pierre; Gottesman, Michael M; Cannon, Richard D

2014-10-06

ABCB5, an ATP-binding cassette (ABC) transporter, is highly expressed in melanoma cells, and may contribute to the extreme resistance of melanomas to chemotherapy by efflux of anti-cancer drugs. Our goal was to determine whether we could functionally express human ABCB5 in the model yeast Saccharomyces cerevisiae, in order to demonstrate an efflux function for ABCB5 in the absence of background pump activity from other human transporters. Heterologous expression would also facilitate drug discovery for this important target. DNAs encoding ABCB5 sequences were cloned into the chromosomal PDR5 locus of a S. cerevisiae strain in which seven endogenous ABC transporters have been deleted. Protein expression in the yeast cells was monitored by immunodetection using both a specific anti-ABCB5 antibody and a cross-reactive anti-ABCB1 antibody. ABCB5 function in recombinant yeast cells was measured by determining whether the cells possessed increased resistance to known pump substrates, compared to the host yeast strain, in assays of yeast growth. Three ABCB5 constructs were made in yeast. One was derived from the ABCB5-β mRNA, which is highly expressed in human tissues but is a truncation of a canonical full-size ABC transporter. Two constructs contained full-length ABCB5 sequences: either a native sequence from cDNA or a synthetic sequence codon-harmonized for S. cerevisiae. Expression of all three constructs in yeast was confirmed by immunodetection. Expression of the codon-harmonized full-length ABCB5 DNA conferred increased resistance, relative to the host yeast strain, to the putative substrates rhodamine 123, daunorubicin, tetramethylrhodamine, FK506, or clorgyline. We conclude that full-length ABCB5 can be functionally expressed in S. cerevisiae and confers drug resistance.

Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant.

Science.gov (United States)

Lu, Ling; Li, Chunhua; Yuan, Jie; Lu, Teng; Okamoto, Hiroaki; Murphy, Donald G

2013-03-01

We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.

Correlated evolution of sternal keel length and ilium length in birds

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Tao Zhao

2017-07-01

Full Text Available The interplay between the pectoral module (the pectoral girdle and limbs and the pelvic module (the pelvic girdle and limbs plays a key role in shaping avian evolution, but prior empirical studies on trait covariation between the two modules are limited. Here we empirically test whether (size-corrected sternal keel length and ilium length are correlated during avian evolution using phylogenetic comparative methods. Our analyses on extant birds and Mesozoic birds both recover a significantly positive correlation. The results provide new evidence regarding the integration between the pelvic and pectoral modules. The correlated evolution of sternal keel length and ilium length may serve as a mechanism to cope with the effect on performance caused by a tradeoff in muscle mass between the pectoral and pelvic modules, via changing moment arms of muscles that function in flight and in terrestrial locomotion.

Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication

Science.gov (United States)

Rustiguel, Joane K.; Soares, Ricardo O. S.; Meisburger, Steve P.; Davis, Katherine M.; Malzbender, Kristina L.; Ando, Nozomi; Dias-Baruffi, Marcelo; Nonato, Maria Cristina

2016-09-01

Galectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations, and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.

First full-length genome sequence of the polerovirus luffa aphid-borne yellows virus (LABYV) reveals the presence of at least two consensus sequences in an isolate from Thailand.

Science.gov (United States)

Knierim, Dennis; Maiss, Edgar; Kenyon, Lawrence; Winter, Stephan; Menzel, Wulf

2015-10-01

Luffa aphid-borne yellows virus (LABYV) was proposed as the name for a previously undescribed polerovirus based on partial genome sequences obtained from samples of cucurbit plants collected in Thailand between 2008 and 2013. In this study, we determined the first full-length genome sequence of LABYV. Based on phylogenetic analysis and genome properties, it is clear that this virus represents a distinct species in the genus Polerovirus. Analysis of sequences from sample TH24, which was collected in 2010 from a luffa plant in Thailand, reveals the presence of two different full-length genome consensus sequences.

Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds

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Sugantham Priyanka Annabel

2010-10-01

Full Text Available Abstract Background Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs. Results A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 106 clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes. Conclusions The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding

Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal β-Hairpin in the Absence of N-Terminal Proline

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Christelle Folio

2017-11-01

Full Text Available Feline immunodeficiency virus (FIV is a member of the Retroviridae family. It is the causative agent of an acquired immunodeficiency syndrome (AIDS in cats and wild felines. Its capsid protein (CA drives the assembly of the viral particle, which is a critical step in the viral replication cycle. Here, the first atomic structure of full-length FIV CA to 1.67 Å resolution is determined. The crystallized protein exhibits an original tetrameric assembly, composed of dimers which are stabilized by an intermolecular disulfide bridge induced by the crystallogenesis conditions. The FIV CA displays a standard α-helical CA topology with two domains, separated by a linker shorter than other retroviral CAs. The β-hairpin motif at its amino terminal end, which interacts with nucleotides in HIV-1, is unusually long in FIV CA. Interestingly, this functional β-motif is formed in this construct in the absence of the conserved N-terminal proline. The FIV CA exhibits a cis Arg–Pro bond in the CypA-binding loop, which is absent in known structures of lentiviral CAs. This structure represents the first tri-dimensional structure of a functional, full-length FIV CA.

From the Generation Memory to the Group Identity: The Film "A Throat Full of Strawberries"

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Nataša Delač

2015-09-01

Full Text Available In the work entitled “From the generation memory to the group identity: the film "A Throat Full of Strawberries", the influence of personal and collective memory on generation identity is analyzed. The work is based on Jan Assmann and Aleida Assmann’s theory of memory, with a special review of the books “Cultural Memory” (Jan Assmann, and “Work on the National Memory” and “The Long Shadow of the Past” (Aleida Assmann. Firstly, the analysis includes the mapping, then the explanation of the memory figures which appear in the movie. Also, the thesis which I covered in the work refers to the difference between Halbwachs’s  term “the images of memory”, and “the figure of memory” introduced by Assmann: the figures of memory are complementary to the first term “because they include not only pictorial, but narrative forms as well.” (Assmann. In this paper, the relation between personal and collective memory is examined, as well as how individual memory influences the establishment of one’s group memory, and how memory and remembrance affect what we call generation identity. The Film “A Throat Full of Strawberries” (by Srdjan Karanovic, 1985 was chosen as my case study. This movie is a sequel to the series “The Unpicked Strawberries” (Srdjan Karanovic, 1976. It tells about a reunion of the group of people of the particular generation, who evoke the memories about the events during the 60’s (the time of their youth, so the topic this film is focused on represents the starting point for the study of the generation memory and its function. The aim of this paper is to prove that generation memory has the crucial role when it comes to the creation of one’s group identity

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan

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Shotland Lawrence I

2004-09-01

Full Text Available Abstract Background Mutant alleles of TMPRSS3 are associated with nonsyndromic recessive deafness (DFNB8/B10. TMPRSS3 encodes a predicted secreted serine protease, although the deduced amino acid sequence has no signal peptide. In this study, we searched for mutant alleles of TMPRSS3 in families from Pakistan and Newfoundland with recessive deafness co-segregating with DFNB8/B10 linked haplotypes and also more thoroughly characterized the genomic structure of TMPRSS3. Methods We enrolled families segregating recessive hearing loss from Pakistan and Newfoundland. Microsatellite markers flanking the TMPRSS3 locus were used for linkage analysis. DNA samples from participating individuals were sequenced for TMPRSS3. The structure of TMPRSS3 was characterized bioinformatically and experimentally by sequencing novel cDNA clones of TMPRSS3. Results We identified mutations in TMPRSS3 in four Pakistani families with recessive, nonsyndromic congenital deafness. We also identified two recessive mutations, one of which is novel, of TMPRSS3 segregating in a six-generation extended family from Newfoundland. The spectrum of TMPRSS3 mutations is reviewed in the context of a genotype-phenotype correlation. Our study also revealed a longer isoform of TMPRSS3 with a hitherto unidentified exon encoding a signal peptide, which is expressed in several tissues. Conclusion Mutations of TMPRSS3 contribute to hearing loss in many communities worldwide and account for 1.8% (8 of 449 of Pakistani families segregating congenital deafness as an autosomal recessive trait. The newly identified TMPRSS3 isoform e will be helpful in the functional characterization of the full length protein.

Full-energy-chain analysis of greenhouse gas emissions for solar thermal electric power generation systems

International Nuclear Information System (INIS)

Norton, B.; Lawson, W.R.

1997-01-01

Technical attributes and environmental impacts of solar thermal options for centralized electricity generation are discussed. In particular, the full-energy-chain, including embodied energy and energy production, is considered in relation to greenhouse gas emission arising from solar thermal electricity generation. Central receiver, parabolic dish, parabolic trough and solar pond systems are considered. (author)

Alternatives Generation Analysis Long Length Contaminated Equipment Removal System Storage

International Nuclear Information System (INIS)

BOGER, R.M.

1999-01-01

Major pieces of Characterization sampling equipment are currently stored outdoors. This includes the Long Length Contaminated Equipment receiver trailer and transportation trailer. A decision is required to determine the preferred alternative for facilities to store and maintain this equipment. The Long Length Contaminated Equipment Removal System (LLCERS) consists of many tools, mechanisms, and controllers currently stored in various locations. Much of this equipment should be protected from the elements while being stored. Some of the LLCERS equipment should be protected with some kind of roof cover. This decision analysis is to determine the best alternative for weather protection for the large equipment requiring a cover. Additional details are included in Sections 2.0 and 5.0. Key assumptions used in this analysis are detailed in Section 3.2

Length dependence of force generation exhibit similarities between rat cardiac myocytes and skeletal muscle fibres.

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Hanft, Laurin M; McDonald, Kerry S

2010-08-01

According to the Frank-Starling relationship, increased ventricular volume increases cardiac output, which helps match cardiac output to peripheral circulatory demand. The cellular basis for this relationship is in large part the myofilament length-tension relationship. Length-tension relationships in maximally calcium activated preparations are relatively shallow and similar between cardiac myocytes and skeletal muscle fibres. During twitch activations length-tension relationships become steeper in both cardiac and skeletal muscle; however, it remains unclear whether length dependence of tension differs between striated muscle cell types during submaximal activations. The purpose of this study was to compare sarcomere length-tension relationships and the sarcomere length dependence of force development between rat skinned left ventricular cardiac myocytes and fast-twitch and slow-twitch skeletal muscle fibres. Muscle cell preparations were calcium activated to yield 50% maximal force, after which isometric force and rate constants (k(tr)) of force development were measured over a range of sarcomere lengths. Myofilament length-tension relationships were considerably steeper in fast-twitch fibres compared to slow-twitch fibres. Interestingly, cardiac myocyte preparations exhibited two populations of length-tension relationships, one steeper than fast-twitch fibres and the other similar to slow-twitch fibres. Moreover, myocytes with shallow length-tension relationships were converted to steeper length-tension relationships by protein kinase A (PKA)-induced myofilament phosphorylation. Sarcomere length-k(tr) relationships were distinct between all three cell types and exhibited patterns markedly different from Ca(2+) activation-dependent k(tr) relationships. Overall, these findings indicate cardiac myocytes exhibit varied length-tension relationships and sarcomere length appears a dominant modulator of force development rates. Importantly, cardiac myocyte length

Production of full length and splicing form of chymosin using pETexpression system in E-coli and investigation its enzyme activity and preplasmic secretion

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M. Ahmadi Zeydabadi

2008-05-01

Full Text Available Introduction: Chymosin (Rennin EC 3.4.23.4 is an aspartyl proteinas (the major proteolyticenzyme in the fourth stomach of the unweaned calf that is formed by proteolytic activation fromzymogene prochymosin. The aim of his study was to produce the full length and splicing form ofchymosin using pETexpression system in E-coli and to assay the activity of expressed enzyme andpreplasmic secretion.Materials and Methods: The sense primer F-prochy(+ (5´-ggggccatgGCTGAGATCACCAGGAincluding NCOI restriction site. The anti sense R-prochy(- (5´-gggcggccgcGATGGCTTTGGCCAGC -3´ hybridizing to the C-terminal end of calf preprocymosincDNA and contains an additional NotI restriction site at its 5´-end . The cells were disrupted bysonication and proteins were purified by using Ni-NTA beads from Qiagen under native conditional.The preprochymosin and AS6 preprochymosin were activated at pH 4.7. The enzyme solutions werediluted 20-fold with 50 mM phosphate buffer .Results: Sequencing data analysis showed that the exon six has been spliced out and, therefore thegene product is 114 bp shorter in length, both chymosin forms were expressed together in E.coli.Under the same expression conditions, at least AS6 preprochymosin was produced 7-fold highexpression in comparison to a full-length recombinant chymosin. Following acid activation andneutralization, the purified fractions were tested in a qualitative milk clotting assay. The clottingactivity of preprochymosin and exon6-less preprochymosin were comparable.Conclusion: High expression of this alternatively expressed transcript in bacteria, and properfolding of the AS6 chymosin protein molecule in the absence of exon six are the two most importantaspects distinguished in this research.

Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme

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Bezem, Maria T.; Baumann, Anne; Skjærven, Lars; Meyer, Romain; Kursula, Petri; Martinez, Aurora; Flydal, Marte I.

2016-01-01

Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of catecholamine neurotransmitters. TH is a highly complex enzyme at mechanistic, structural, and regulatory levels, and the preparation of kinetically and conformationally stable enzyme for structural characterization has been challenging. Here, we report on improved protocols for purification of recombinant human TH isoform 1 (TH1), which provide large amounts of pure, stable, active TH1 with an intact N-terminus. TH1 purified through fusion with a His-tagged maltose-binding protein on amylose resin was representative of the iron-bound functional enzyme, showing high activity and stabilization by the natural feedback inhibitor dopamine. TH1 purified through fusion with a His-tagged ZZ domain on TALON is remarkably stable, as it was partially inhibited by resin-derived cobalt. This more stable enzyme preparation provided high-quality small-angle X-ray scattering (SAXS) data and reliable structural models of full-length tetrameric TH1. The SAXS-derived model reveals an elongated conformation (Dmax = 20 nm) for TH1, different arrangement of the catalytic domains compared with the crystal structure of truncated forms, and an N-terminal region with an unstructured tail that hosts the phosphorylation sites and a separated Ala-rich helical motif that may have a role in regulation of TH by interacting with binding partners. PMID:27462005

Preparation of a differentially expressed, full-length cDNA expression library by RecA-mediated triple-strand formation with subtractively enriched cDNA fragments

NARCIS (Netherlands)

Hakvoort, T. B.; Spijkers, J. A.; Vermeulen, J. L.; Lamers, W. H.

1996-01-01

We have developed a fast and general method to obtain an enriched, full-length cDNA expression library with subtractively enriched cDNA fragments. The procedure relies on RecA-mediated triple-helix formation of single-stranded cDNA fragments with a double-stranded cDNA plasmid library. The complexes

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Dr Ahmed

other areas of business administration. ... mathematics, real estate, insurance, actuarial science and business administration (McCutcheon & Scott, 1989). Most textbooks written in these ..... Mathematics of Finance; Heinemann; Oxford. Murray ...

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ABSTRACT. This paper considered contamination of aquifer resulting from petroleum spillage, which is a common phenomenal in the. Niger Delta area of Nigeria. We used the model given by. Bestman (1987) and assumed that some endogenous variables are built into the system. To achieve a level of desirable state, we ...

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Mbah & Amao (SWJ):11-14. Natural Foods and Feeding Habits Of The African Honey bee ... Keywords: natural food, nectar, pollen, african honeybee, Apis mellifera adansonii ..... Crailsheim, K. (1990). The Protein balance of the honeybee.

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... Solarin (SWJ):1-6. On Existence Of Control For A Class Of Uncertain Dynamical Systems ... .m We apply the Conjugate Gradient Method. (C.G.M) in ...... Numerical Technique .... Some of its Applications; Journal of Mathematical Analysis and.

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providing energy storage and metabolic fuel, acting as functional and structural ... zoonotic and non-zoonotic diseases are been imported and exported in and out ..... rabbits infected with T. brucie and Gow et al., (2007) in which dog naturally ...

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In recent years, a new technique was introduced that combines both hydrolysis and ... Cassava Starch Preparation: The cassava starch used for this investigation was prepared ... One normal HCl and one normal NaOH were used to adjust the ...

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Administrator

chemical oxidation and reduction, electro-chemical treatment and ion-pair extraction were extensively used ... The present study is an effort to develop a fungal-based treatment system for the cleaning of dye industrial ..... Biochemical and Biophysical Research Communications 178:1056-. 1063. Raju, N. S., Venkataramana ...

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SPECKLED PIGEON (Columba guinea HARTLAUB AND. FINSCH ... area of the Nigerian northern guinea savanna (Fry, 1965). The habit of the .... defined by Margolis et al., (1982). Chi-square ..... Southern Africa, Academic Press, London.. 4 ...

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Marcos

2012-08-21

Aug 21, 2012 ... Cut flowers have a very limited life after they have been cut off from the mother plant, as survival on their own reserves is ... One of the techniques used for the removal ... and vegetables (Pellegrini and Belle, 2008). There are ...

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inorganic, synthetic organic polymer and naturally occurring coagulants .... Flash fast mixing was done for 2 mins at a speed of 100rpm, followed by slow mixing for ..... Moringa leaves from germplasm to plant, to food, to health. Symposium on ...

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The isotope techniques used in hydrology may be classified into three groups: environmental ..... In that case a solution may be found in measurements of 14C content of groundwaters. ... Applied Isotope Hydrogeology. Elsevier, New. York.

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some rural communities of Zaria, Nigeria for microbial index of water quality in relation to ... These factors, together with the inadequate waste treatment facilities and ..... The Need for an Integrated Approach to Water Supply and. Sanitation in ...

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Marcos

2012-08-21

Aug 21, 2012 ... 1Universidade Estadual Paulista, Faculdade de Ciências Agronômicas, CEP: 18601-060, Botucatu, SP, Brasil. 2Universidade Federal de Alagoas, Centro de Ciências Agrárias-CECA, Maceio, AL, Brasil. 3Universidade Federal Rural do Semi-Árido, Departamento de Ciências Vegetais, Mossoró, RN, Brasil ...

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MEMUNA

markovian process could be reduced to a markovian chain with the homogenous .... x and y respectively. n= the value of the strategy i.e. number of dummies/virtual ..... Groove, CA. Feinberg, E. A. & Shwartz, A. (2002), Handbook of Markov.

Molecular Cloning and Characterization of Full-Length cDNA of Calmodulin Gene from Pacific Oyster Crassostrea gigas

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Xing-Xia Li

2016-01-01

Full Text Available The shell of the pearl oyster (Pinctada fucata mainly comprises aragonite whereas that of the Pacific oyster (Crassostrea gigas is mainly calcite, thereby suggesting the different mechanisms of shell formation between above two mollusks. Calmodulin (CaM is an important gene for regulating the uptake, transport, and secretion of calcium during the process of shell formation in pearl oyster. It is interesting to characterize the CaM in oysters, which could facilitate the understanding of the different shell formation mechanisms among mollusks. We cloned the full-length cDNA of Pacific oyster CaM (cgCaM and found that the cgCaM ORF encoded a peptide of 113 amino acids containing three EF-hand calcium-binding domains, its expression level was highest in the mantle, hinting that the cgCaM gene is probably involved in shell formation of Pacific oyster, and the common ancestor of Gastropoda and Bivalvia may possess at least three CaM genes. We also found that the numbers of some EF hand family members in highly calcified species were higher than those in lowly calcified species and the numbers of these motifs in oyster genome were the highest among the mollusk species with whole genome sequence, further hinting the correlation between CaM and biomineralization.

Characterization of a Full-Length Endogenous Beta-Retrovirus, EqERV-Beta1, in the Genome of the Horse (Equus caballus

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Antoinette C. van der Kuyl

2011-06-01

Full Text Available Information on endogenous retroviruses fixed in the horse (Equus caballus genome is scarce. The recent availability of a draft sequence of the horse genome enables the detection of such integrated viruses by similarity search. Using translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for initial searches, a full-length beta-retrovirus genome was retrieved from a horse chromosome 5 contig. The provirus, tentatively named EqERV-beta1 (for the first equine endogenous beta-retrovirus, was 10434 nucleotide (nt in length with the usual retroviral genome structure of 5’LTR-gag-pro-pol-env-3’LTR. The LTRs were 1361 nt long, and differed approximately 1% from each other, suggestive of a relatively recent integration. Coding sequences for gag, pro and pol were present in three different reading-frames, as common for beta-retroviruses, and the reading frames were completely open, except that the env gene was interrupted by a single stopcodon. No reading frame was apparent downstream of the env gene, suggesting that EqERV-beta1 does not encode a superantigen like mouse mammary tumor virus (MMTV. A second proviral genome of EqERV-beta1, with no stopcodon in env, is additionally integrated on chromosome 5 downstream of the first virus. Single EqERV-beta1 LTRs were abundantly present on all chromosomes except chromosome 24. Phylogenetically, EqERV-beta1 most closely resembles an unclassified retroviral sequence from cattle (Bos taurus, and the murine beta-retrovirus MMTV.

Study of canine parvovirus evolution: comparative analysis of full-length VP2 gene sequences from Argentina and international field strains.

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Gallo Calderón, Marina; Wilda, Maximiliano; Boado, Lorena; Keller, Leticia; Malirat, Viviana; Iglesias, Marcela; Mattion, Nora; La Torre, Jose

2012-02-01

The continuous emergence of new strains of canine parvovirus (CPV), poorly protected by current vaccination, is a concern among breeders, veterinarians, and dog owners around the world. Therefore, the understanding of the genetic variation in emerging CPV strains is crucial for the design of disease control strategies, including vaccines. In this paper, we obtained the sequences of the full-length gene encoding for the main capsid protein (VP2) of 11 canine parvovirus type 2 (CPV-2) Argentine representative field strains, selected from a total of 75 positive samples studied in our laboratory in the last 9 years. A comparative sequence analysis was performed on 9 CPV-2c, one CPV-2a, and one CPV-2b Argentine strains with respect to international strains reported in the GenBank database. In agreement with previous reports, a high degree of identity was found among CPV-2c Argentine strains (99.6-100% and 99.7-100% at nucleotide and amino acid levels, respectively). However, the appearance of a new substitution in the 440 position (T440A) in four CPV-2c Argentine strains obtained after the year 2009 gives support to the variability observed for this position located within the VP2, three-fold spike. This is the first report on the genetic characterization of the full-length VP2 gene of emerging CPV strains in South America and shows that all the Argentine CPV-2c isolates cluster together with European and North American CPV-2c strains.

Generating potentially nilpotent full sign patterns

NARCIS (Netherlands)

Kim, I.J.; Olesky, D.D.; Shader, B.L.; Driessche, van den P.; Holst, van der H.; Vander Meulen, K.N.

2009-01-01

A sign pattern is a matrix with entries in {+,-, 0}. A full sign pattern has no zero entries. The refined inertia of a matrix pattern is defined and techniques are developed for constructing potentially nilpotent full sign patterns. Such patterns are spectrally arbitrary. These techniques can also

Development of three full-length infectious cDNA clones of distinct brassica yellows virus genotypes for agrobacterium-mediated inoculation.

Science.gov (United States)

Zhang, Xiao-Yan; Dong, Shu-Wei; Xiang, Hai-Ying; Chen, Xiang-Ru; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

2015-02-02

Brassica yellows virus is a newly identified species in the genus of Polerovirus within the family Luteoviridae. Brassica yellows virus (BrYV) is prevalently distributed throughout Mainland China and South Korea, is an important virus infecting cruciferous crops. Based on six BrYV genomic sequences of isolates from oilseed rape, rutabaga, radish, and cabbage, three genotypes, BrYV-A, BrYV-B, and BrYV-C, exist, which mainly differ in the 5' terminal half of the genome. BrYV is an aphid-transmitted and phloem-limited virus. The use of infectious cDNA clones is an alternative means of infecting plants that allows reverse genetic studies to be performed. In this study, full-length cDNA clones of BrYV-A, recombinant BrYV5B3A, and BrYV-C were constructed under control of the cauliflower mosaic virus 35S promoter. An agrobacterium-mediated inoculation system of Nicotiana benthamiana was developed using these cDNA clones. Three days after infiltration with full-length BrYV cDNA clones, necrotic symptoms were observed in the inoculated leaves of N. benthamiana; however, no obvious symptoms appeared in the upper leaves. Reverse transcription-PCR (RT-PCR) and western blot detection of samples from the upper leaves showed that the maximum infection efficiency of BrYVs could reach 100%. The infectivity of the BrYV-A, BrYV-5B3A, and BrYV-C cDNA clones was further confirmed by northern hybridization. The system developed here will be useful for further studies of BrYV, such as host range, pathogenicity, viral gene functions, and plant-virus-vector interactions, and especially for discerning the differences among the three genotypes. Copyright © 2014 Elsevier B.V. All rights reserved.

Construction of a Full-Length Enriched cDNA Library and Preliminary Analysis of Expressed Sequence Tags from Bengal Tiger Panthera tigris tigris

Science.gov (United States)

Liu, Changqing; Liu, Dan; Guo, Yu; Lu, Taofeng; Li, Xiangchen; Zhang, Minghai; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

2013-01-01

In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers. PMID:23708105

Experimental validation of 3D reconstructed pin-power distributions in full-scale BWR fuel assemblies with partial length rods

Energy Technology Data Exchange (ETDEWEB)

Giust, F. D. [Axpo Kernenergie, Parkstrasse 23, CH-5401 Baden (Switzerland); Swiss Federal Inst. of Technology EPFL, CH-1015 Lausanne (Switzerland); Grimm, P. [Paul Scherrer Inst., CH-5232 Villigen (Switzerland); Chawla, R. [Paul Scherrer Inst., CH-5232 Villigen (Switzerland); Swiss Federal Inst. of Technology (EPFL), CH-1015 Lausanne (Switzerland)

2012-07-01

Total fission rate measurements have been performed on full-size BWR fuel assemblies of type SVEA-96 Optima2 in the framework of Phase III of the LWR-PROTEUS experimental program at the Paul Scherrer Inst.. This paper presents comparisons of calculated, nodal reconstructed, pin-wise total-fission rate distributions with experimental results. Radial comparisons have been performed for the three sections of the assembly (96, 92 and 84 fuel pins), while three-dimensional effects have been investigated at pellet-level for the two transition regions, i.e. the tips of the short (1/3) and long (2/3) partial length rods. The test zone has been modeled using two different code systems: HELIOS/PRESTO-2 and CASMO-5/SIMULATE-5. The first is presently used for core monitoring and design at the Leibstadt Nuclear Power Plant (KKL). The second represents the most recent generation of the widely applied CASMO/SIMULATE system. For representing the PROTEUS test-zone boundaries, Partial Current Ratios (PCRs) - derived from a 3D MCNPX model of the entire reactor - have been applied to the PRESTO-2 and SIMULATE-5 models in the form of 2- and 5-group diagonal albedo matrices, respectively. The MCNPX results have also served as a reference, high-order transport solution in the calculation/experiment comparisons. It is shown that the performance of the nodal methodologies in predicting the global distribution of the total-fission rate is very satisfactory. Considering the various radial comparisons, the standard deviations of the calculated/experimental (C/E) distributions do not exceed 1.9% for any of the three methodologies - PRESTO-2, SIMULATE-5 and MCNPX. For the three-dimensional comparisons at pellet-level, the corresponding standard deviations are 2.7%, 2.0% and 2.1%, respectively. (authors)

Full-turn symplectic map from a generator in a Fourier-spline basis

International Nuclear Information System (INIS)

Berg, J.S.; Warnock, R.L.; Ruth, R.D.; Forest, E.

1993-04-01

Given an arbitrary symplectic tracking code, one can construct a full-turn symplectic map that approximates the result of the code to high accuracy. The map is defined implicitly by a mixed-variable generating function. The implicit definition is no great drawback in practice, thanks to an efficient use of Newton's method to solve for the explicit map at each iteration. The generator is represented by a Fourier series in angle variables, with coefficients given as B-spline functions of action variables. It is constructed by using results of single-turn tracking from many initial conditions. The method has been appliedto a realistic model of the SSC in three degrees of freedom. Orbits can be mapped symplectically for 10 7 turns on an IBM RS6000 model 320 workstation, in a run of about one day

Construction of a full-length prototype of the BESIII drift chamber and on-detector test for the BESIII drift chamber electronics

International Nuclear Information System (INIS)

Qin Zhonghua; Wu Linghui; Liu Jianbei; Chinese Academy of Sciences, Beijing; Yan Zhikang; Hunan Univ., Changsha; Chen Yuanbo; Chen Chang; Xu Meihang; Wang Lan; Ma Xiaoyan; Jin Yan; Liu Rongguang; Tang Xiao; Zhang Guifang; Zhu Qiming; Sheng Huayi; Zhu Kejun

2007-01-01

A full-length prototype of the BESIII drift chamber was built. The experience gained on gas sealing, high voltage supply and front-end electronics installation should be greatly beneficial to the successful construction of the BESIII drift chamber. An on-detector test of the BESIII drift chamber electronics was carried out with the constructed prototype chamber. The noise performance, drift time and charge measurements, and electronics gains were examined specifically. The final test results indicate that the electronics have a good performance and can satisfy their design requirements. (authors)

A Heuristic T-S Fuzzy Model for the Pumped-Storage Generator-Motor Using Variable-Length Tree-Seed Algorithm-Based Competitive Agglomeration

Directory of Open Access Journals (Sweden)

Jianzhong Zhou

2018-04-01

Full Text Available With the fast development of artificial intelligence techniques, data-driven modeling approaches are becoming hotspots in both academic research and engineering practice. This paper proposes a novel data-driven T-S fuzzy model to precisely describe the complicated dynamic behaviors of pumped storage generator motor (PSGM. In premise fuzzy partition of the proposed T-S fuzzy model, a novel variable-length tree-seed algorithm based competitive agglomeration (VTSA-CA algorithm is presented to determine the optimal number of clusters automatically and improve the fuzzy clustering performances. Besides, in order to promote modeling accuracy of PSGM, the input and output formats in the T-S fuzzy model are selected by an economical parameter controlled auto-regressive (CAR model derived from a high-order transfer function of PSGM considering the distributed components in the water diversion system of the power plant. The effectiveness and superiority of the T-S fuzzy model for PSGM under different working conditions are validated by performing comparative studies with both practical data and the conventional mechanistic model.

Generating Approximative Minimum Length Paths in 3D for UAVs

DEFF Research Database (Denmark)

Schøler, Flemming; la Cour-Harbo, Anders; Bisgaard, Morten

2012-01-01

We consider the challenge of planning a minimum length path from an initial position to a desired position for a rotorcraft. The path is found in a 3-dimensional Euclidean space containing a geometric obstacle. We base our approach on visibility graphs which have been used extensively for path pl...

NANOG priming before full reprogramming may generate germ cell tumours

Directory of Open Access Journals (Sweden)

I Grad

2011-11-01

Full Text Available Reprogramming somatic cells into a pluripotent state brings patient-tailored, ethical controversy-free cellular therapy closer to reality. However, stem cells and cancer cells share many common characteristics; therefore, it is crucial to be able to discriminate between them. We generated two induced pluripotent stem cell (iPSC lines, with NANOG pre-transduction followed by OCT3/4, SOX2, and LIN28 overexpression. One of the cell lines, CHiPS W, showed normal pluripotent stem cell characteristics, while the other, CHiPS A, though expressing pluripotency markers, failed to differentiate and gave rise to germ cell-like tumours in vivo. Comparative genomic hybridisation analysis of the generated iPS lines revealed that they were genetically more stable than human embryonic stem cell counterparts. This analysis proved to be predictive for the differentiation potential of analysed cells. Moreover, the CHiPS A line expressed a lower ratio of p53/p21 when compared to CHiPS W. NANOG pre-induction followed by OCT3/4, SOX2, MYC, and KLF4 induction resulted in the same tumour-inducing phenotype. These results underline the importance of a re-examination of the role of NANOG during reprogramming. Moreover, this reprogramming method may provide insights into primordial cell tumour formation and cancer stem cell transformation.

The small FOXP1 isoform predominantly expressed in activated B cell-like diffuse large B-cell lymphoma and full-length FOXP1 exert similar oncogenic and transcriptional activity in human B cells.

Science.gov (United States)

van Keimpema, Martine; Grüneberg, Leonie J; Schilder-Tol, Esther J M; Oud, Monique E C M; Beuling, Esther A; Hensbergen, Paul J; de Jong, Johann; Pals, Steven T; Spaargaren, Marcel

2017-03-01

The forkhead transcription factor FOXP1 is generally regarded as an oncogene in activated B cell-like diffuse large B-cell lymphoma. Previous studies have suggested that a small isoform of FOXP1 rather than full-length FOXP1, may possess this oncogenic activity. Corroborating those studies, we herein show that activated B cell-like diffuse large B-cell lymphoma cell lines and primary activated B cell-like diffuse large B-cell lymphoma cells predominantly express a small FOXP1 isoform, and that the 5'-end of the Foxp1 gene is a common insertion site in murine lymphomas in leukemia virus- and transposon-mediated insertional mutagenesis screens. By combined mass spectrometry, (quantative) reverse transcription polymerase chain reaction/sequencing, and small interfering ribonucleic acid-mediated gene silencing, we determined that the small FOXP1 isoform predominantly expressed in activated B cell-like diffuse large B-cell lymphoma lacks the N-terminal 100 amino acids of full-length FOXP1. Aberrant overexpression of this FOXP1 isoform (ΔN100) in primary human B cells revealed its oncogenic capacity; it repressed apoptosis and plasma cell differentiation. However, no difference in potency was found between this small FOXP1 isoform and full-length FOXP1. Furthermore, overexpression of full-length FOXP1 or this small FOXP1 isoform in primary B cells and diffuse large B-cell lymphoma cell lines resulted in similar gene regulation. Taken together, our data indicate that this small FOXP1 isoform and full-length FOXP1 have comparable oncogenic and transcriptional activity in human B cells, suggesting that aberrant expression or overexpression of FOXP1, irrespective of the specific isoform, contributes to lymphomagenesis. These novel insights further enhance the value of FOXP1 for the diagnostics, prognostics, and treatment of diffuse large B-cell lymphoma patients. Copyright© Ferrata Storti Foundation.

Method for Generating Pseudorandom Sequences with the Assured Period Based on R-blocks

Directory of Open Access Journals (Sweden)

M. A. Ivanov

2011-03-01

Full Text Available The article describes the characteristics of a new class of fast-acting pseudorandom number generators, based on the use of stochastic adders or R-blocks. A new method for generating pseudorandom sequences with the assured length of period is offered.

Automatic Determination of Fiber-Length Distribution in Composite Material Using 3D CT Data

Directory of Open Access Journals (Sweden)

Günther Greiner

2010-01-01

Full Text Available Determining fiber length distribution in fiber reinforced polymer components is a crucial step in quality assurance, since fiber length has a strong influence on overall strength, stiffness, and stability of the material. The approximate fiber length distribution is usually determined early in the development process, as conventional methods require a destruction of the sample component. In this paper, a novel, automatic, and nondestructive approach for the determination of fiber length distribution in fiber reinforced polymers is presented. For this purpose, high-resolution computed tomography is used as imaging method together with subsequent image analysis for evaluation. The image analysis consists of an iterative process where single fibers are detected automatically in each iteration step after having applied image enhancement algorithms. Subsequently, a model-based approach is used together with a priori information in order to guide a fiber tracing and segmentation process. Thereby, the length of the segmented fibers can be calculated and a length distribution can be deduced. The performance and the robustness of the segmentation method is demonstrated by applying it to artificially generated test data and selected real components.

Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Boniotti, Maria Beatrice; Papetti, Alice

2018-01-01

Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine...... the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence...... the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies....

Estimation Issues and Generational Changes in Modeling Criminal Career Length

Science.gov (United States)

Francis, Brian; Soothill, Keith; Piquero, Alex R.

2007-01-01

This article seeks to model criminal career length using data from six different birth cohorts born between 1953 and 1978, totaling more than 58,000 males and females from England and Wales. A secondary aim of this article is to consider whether information available at the first court appearance leading to a conviction is associated with the…

Digitization and simulation realization of full range control system for steam generator water level

International Nuclear Information System (INIS)

Qian Hong; Ye Jianhua; Qian Fei; Li Chao

2010-01-01

In this paper, a full range digital control system for the steam generator water level is designed by a control scheme of single element control and three-element cascade feed-forward control, and the method to use the software module configuration is proposed to realize the water level control strategy. This control strategy is then applied in the operation of the nuclear power simulation machine. The simulation result curves indicate that the steam generator water level maintains constant at the stable operation condition, and when the load changes, the water level changes but finally maintains the constant. (authors)

IFF, Full-Screen Input Menu Generator for FORTRAN Program

International Nuclear Information System (INIS)

Seidl, Albert

1991-01-01

1 - Description of program or function: The IFF-package contains input modules for use within FORTRAN programs. This package enables the programmer to easily include interactive menu-directed data input (module VTMEN1) and command-word processing (module INPCOM) into a FORTRAN program. 2 - Method of solution: No mathematical operations are performed. 3 - Restrictions on the complexity of the problem: Certain restrictions of use may arise from the dimensioning of arrays. Field lengths are defined via PARAMETER-statements

Nonlinear dispersion-based incoherent photonic processing for microwave pulse generation with full reconfigurability.

Science.gov (United States)

Bolea, Mario; Mora, José; Ortega, Beatriz; Capmany, José

2012-03-12

A novel all-optical technique based on the incoherent processing of optical signals using high-order dispersive elements is analyzed for microwave arbitrary pulse generation. We show an approach which allows a full reconfigurability of a pulse in terms of chirp, envelope and central frequency by the proper control of the second-order dispersion and the incoherent optical source power distribution, achieving large values of time-bandwidth product.

Velocity and texture of a plasma jet created in a plasma torch with fixed minimal arc length

International Nuclear Information System (INIS)

Vilotijevic, M; Dacic, B; Bozic, D

2009-01-01

A new plasma jet (PJ-100) plasma spraying torch with a fixed minimal arc length was tested and the basic working parameters were measured and evaluated. The velocity of the plasma exiting both the cylindrical and the conical anode nozzles was assessed by measuring the thrust generated by the plasma jet and by photographing the translation of plasma clouds (parts with different brightnesses) in the last third of the length of the plasma plume. The basic characteristics of the argon/hydrogen plasma jets (enthalpy, mean temperature, mean plasma velocity and effective exhaust thrust velocity) were determined for different working regimes, for both the cylindrical and the conical nozzles. The thermal efficiency of the new plasma torch is between 70% and 74% for the plasma generation power up to 90 kW. The plasma plume generated in the cylindrical nozzle has a homogeneous radial temperature (and velocity) distribution with a full laminar flow.

Pulse length of ultracold electron bunches extracted from a laser cooled gas

Directory of Open Access Journals (Sweden)

J. G. H. Franssen

2017-07-01

Full Text Available We present measurements of the pulse length of ultracold electron bunches generated by near-threshold two-photon photoionization of a laser-cooled gas. The pulse length has been measured using a resonant 3 GHz deflecting cavity in TM110 mode. We have measured the pulse length in three ionization regimes. The first is direct two-photon photoionization using only a 480 nm femtosecond laser pulse, which results in short (∼15 ps but hot (∼104 K electron bunches. The second regime is just-above-threshold femtosecond photoionization employing the combination of a continuous-wave 780 nm excitation laser and a tunable 480 nm femtosecond ionization laser which results in both ultracold (∼10 K and ultrafast (∼25 ps electron bunches. These pulses typically contain ∼103 electrons and have a root-mean-square normalized transverse beam emittance of 1.5 ± 0.1 nm rad. The measured pulse lengths are limited by the energy spread associated with the longitudinal size of the ionization volume, as expected. The third regime is just-below-threshold ionization which produces Rydberg states which slowly ionize on microsecond time scales.

Comparison between length and velocity gauges in quantum simulations of high-order harmonic generation

DEFF Research Database (Denmark)

Han, Yong-Chang; Madsen, Lars Bojer

2010-01-01

, and acceleration forms, and two gauges, the length and velocity gauges. The relationships among the harmonic phases obtained from the Fourier transform of the three forms are discussed in detail. Although quantum mechanics is gauge invariant and the length and velocity gauges should give identical results, the two...... gauges present different computation efficiencies, which reflects the different behavior in terms of characteristics of the physical couplings acting in the two gauges. In order to obtain convergence, more angular momentum states are required in the length gauge, while more grid points are required...

Dither Cavity Length Controller with Iodine Locking

Directory of Open Access Journals (Sweden)

Lawson Marty

2016-01-01

Full Text Available A cavity length controller for a seeded Q-switched frequency doubled Nd:YAG laser is constructed. The cavity length controller uses a piezo-mirror dither voltage to find the optimum length for the seeded cavity. The piezo-mirror dither also dithers the optical frequency of the output pulse. [1]. This dither in optical frequency is then used to lock to an Iodine absorption line.

High avidity antibodies to full-length VAR2CSA correlate with absence of placental malaria.

Directory of Open Access Journals (Sweden)

Yeung Lo Tutterrow

Full Text Available VAR2CSA mediates sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, increasing the risk of poor pregnancy outcomes. Naturally acquired antibodies (Ab to placental parasites at delivery have been associated with improved pregnancy outcomes, but Ab levels and how early in pregnancy Ab must be present in order to eliminate placental parasites before delivery remains unknown. Antibodies to individual Duffy-binding like domains of VAR2CSA have been studied, but the domains lack many of the conformational epitopes present in full-length VAR2CSA (FV2. Thus, the purpose of this study was to describe the acquisition of Ab to FV2 in women residing in high and low transmission areas and determine how Ab levels during pregnancy correlate with clearance of placental parasites. Plasma samples collected monthly throughout pregnancy from pregnant women living in high and low transmission areas in Cameroon were evaluated for Ab to FV2 and the proportion of high avidity Ab (i.e., Ab that remain bound in the presence of 3M NH(4SCN was assessed. Ab levels and proportion of high avidity Ab were compared between women with placental malaria (PM(+ and those without (PM(- at delivery. Results showed that PM(- women had significantly higher Ab levels (p = 0.0047 and proportion of high avidity Ab (p = 0.0009 than PM(+ women throughout pregnancy. Specifically, women with moderate to high Ab levels (>5,000 MFI and those with ≥ 35% high avidity Ab at 5-6 months were found to have 2.3 (95% CI, 1.0-4.9 and 7.6-fold (p = 0.0013, 95% CI: 1.2-50.0 reduced risk of placental malaria, respectively. These data show that high levels of Ab to FV2, particularly those with high avidity for FV2, produced by mid-pregnancy are important in clearing parasites from the placenta. Both high Ab levels and proportion of high avidity Ab to FV2 may serve as correlates of protection for assessing immunity against placental malaria.

Calibration and validation of a phenomenological influent pollutant disturbance scenario generator using full-scale data

DEFF Research Database (Denmark)

Flores Alsina, Xavier; Saagi, Ramesh; Lindblom, Erik Ulfson

2014-01-01

The objective of this paper is to demonstrate the full-scale feasibility of the phenomenological dynamic influent pollutant disturbance scenario generator (DIPDSG) that was originally used to create the influent data of the International Water Association (IWA) Benchmark Simulation Model No. 2 (BSM...... rainfall patterns (climate change) or influent biodegradability (process uncertainty) on the generated time series; 2) a demonstration of how to reduce the cost/workload of measuring campaigns by filling the gaps due to missing data in the influent profiles; and, 3) a critical discussion of the presented...

Full-length VP2 gene analysis of canine parvovirus reveals emergence of newer variants in India.

Science.gov (United States)

Nookala, Mangadevi; Mukhopadhyay, Hirak Kumar; Sivaprakasam, Amsaveni; Balasubramanian, Brindhalakshmi; Antony, Prabhakar Xavier; Thanislass, Jacob; Srinivas, Mouttou Vivek; Pillai, Raghavan Madhusoodanan

2016-12-01

The canine parvovirus (CPV) infection is a highly contagious and serious enteric disease of dogs with high fatality rate. The present study was taken up to characterize the full-length viral polypeptide 2 (VP2) gene of CPV of Indian origin along with the commercially available vaccines. The faecal samples from parvovirus suspected dogs were collected from various states of India for screening by PCR assay and 66.29% of samples were found positive. Six CPV-2a, three CPV-2b, and one CPV-2c types were identified by sequence analysis. Several unique and existing mutations have been noticed in CPV types analyzed indicating emergence of newer variants of CPV in India. The phylogenetic analysis revealed that all the field CPV types were grouped in different subclades within two main clades, but away from the commercial vaccine strains. CPV-2b and CPV-2c types with unique mutations were found to be establishing in India apart from the prevailing CPV-2a type. Mutations and the positive selection of the mutants were found to be the major mechanism of emergence and evolution of parvovirus. Therefore, the incorporation of local strain in the vaccine formulation may be considered for effective control of CPV infections in India.

Generation and Analysis of Full-length cDNA Sequences from Elephant Shark (Callorhinchus milii)

KAUST Repository

Kodzius, Rimantas; Tay, Boon-Hui; Tan, Yue Ying; Brenner, Sydney; Venkatesh, Byrappa

2009-01-01

Cartilaginous fishes are the oldest living group of jawed vertebrates and therefore is an important group for understanding the evolution of vertebrate genomes including the human genome. Our laboratory has proposed elephant shark (C. milii) as a

Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains

DEFF Research Database (Denmark)

Crowther, P J; Doherty, J P; Linsenmeyer, M E

1991-01-01

preferentially from L1 members which have accumulated mutations that have removed sites of methylation. We present a revised consensus from the 5' presumptive control region of these elements. This revised consensus contains a consensus RNA polymerase III promoter which would permit the synthesis of transcripts......Efficient recovery of clones from the 5' end of the human L1 dispersed repetitive elements necessitates the use of deletion mcr- host strains since this region contains a CpG island which is hypermethylated in vivo. Clones recovered with conventional mcr+ hosts seem to have been derived...... from the 5' end of full length L1 elements. Such potential transcripts are likely to exhibit a high degree of secondary structure. In addition, we have determined the flanking sequences for 6 full length L1 elements. The majority of full length L1 clones show no convincing evidence for target site...

Diagnostic value of newborn foot length to predict gestational age

Directory of Open Access Journals (Sweden)

Mutia Farah Fawziah

2017-08-01

Full Text Available Background  Identification of gestational age, especially within 48 hours of birth, is crucial for newborns, as the earlier preterm status is detected, the earlier the child can receive optimal management. Newborn foot length is an anthropometric measurement which is easy to perform, inexpensive, and potentially efficient for predicting gestational age. Objective  To analyze the diagnostic value of newborn foot length in predicting gestational age. Methods  This diagnostic study was performed between October 2016 and February 2017 in the High Care Unit of Neonates at Dr. Moewardi General Hospital, Surakarta. A total of 152 newborns were consecutively selected and underwent right foot length measurements before 96 hours of age. The correlation between newborn foot length to classify as full term and gestational age was analyzed with Spearman’s correlation test because of non-normal data distribution. The cut-off point of newborn foot length was calculated by receiver operating characteristic (ROC curve and diagnostic values of newborn foot length were analyzed by 2 x 2 table with SPSS 21.0 software. Results There were no significant differences between male and female newborns in terms of gestational age, birth weight, choronological age, and newborn foot length (P>0.05. Newborn foot length and gestational age had a significant correlation (r=0.53; P=0.000. The optimal cut-off newborn foot length to predict full term status was 7.1 cm. Newborn foot length below 7.1 cm had sensitivity 75%, specificity 98%, positive predictive value 94.3%, negative predictive value 90.6%, positive likelihood ratio 40.5, negative likelihood ratio 0.25, and post-test probability 94.29%, to predict preterm status in newborns. Conclusion  Newborn foot length can be used to predict gestational age, especially for the purpose of differentiating between preterm and full term newborns.

The benefits of longer fuel cycle lengths

International Nuclear Information System (INIS)

Kesler, D.C.

1986-01-01

Longer fuel cycle lengths have been found to increase generation and improve outage management. A study at Duke Power Company has shown that longer fuel cycles offer both increased scheduling flexibility and increased capacity factors

Characterization and long term operation of a novel superconducting undulator with 15 mm period length in a synchrotron light source

Directory of Open Access Journals (Sweden)

S. Casalbuoni

2016-11-01

Full Text Available A new cryogen-free full scale (1.5 m long superconducting undulator with a period length of 15 mm (SCU15 has been successfully tested in the ANKA storage ring. This represents a very important milestone in the development of superconducting undulators for third and fourth generation light sources carried on by the collaboration between the Karlsruhe Institute of Technology and the industrial partner Babcock Noell GmbH. SCU15 is the first full length device worldwide that with beam reaches a higher peak field than what expected with the same geometry (vacuum gap and period length with an ideal cryogenic permanent magnet undulator built with the best material available PrFeB. After a summary on the design and main parameters of the device, we present here the characterization in terms of spectral properties and the long term operation of the SCU15 in the ANKA storage ring.

Cutting Whole Length or Partial Length of Internal Anal Sphincter in Managementof Fissure in Ano

Directory of Open Access Journals (Sweden)

Furat Shani Aoda

2017-12-01

Full Text Available A chronic anal fissure is a common painful perianal condition.The main operative procedure to treat this painful condition is a lateral internal sphincteretomy (LIS.The aim of study is to compare the outcome and complications of closed LIS up to the dentate line (whole length of internal sphincter or up to the fissure apex (partial length of internal sphincter in the treatment of anal fissure.It is a prospective comparativestudy including 100 patients with chronic fissure in ano. All patients assigned to undergo closed LIS. Those patients were randomly divided into two groups: 50 patients underwent LIS to the level of dentate line (whole length and other 50 patients underwent LIS to the level of fissure apex (partial length. Patients were followed up weekly in the 1st month, twice monthly in the second month then monthly   for next 2 months and finally after 1 year. There was satisfactory relief of pain in all patients in both groups & complete healing of the fissure occurred. Regarding post operative incontinence no major degree of incontinence occur in both group but minor degree of incontinence persists In 7 patients after whole length LIS after one year. In conclusion, both whole length & partial length LIS associated with improvement of pain, good chance of healing but whole length LIS associated with more chance of long term  flatus incontinence. Hence,we recommend partial length LIS as treatment forchronic anal fissure.

FULL LENGTH RESEARCH ARTICLE Yoriyo et al.(2008) SWJ:35 ...

African Journals Online (AJOL)

Dr. Ahmed

poultry industry to its full capacity. These factors include poor management systems and diseases. Poultry diseases are the major cause of financial loss in poultry production (Oluyemi & Rober, 1979). Intestinal parasitism is a common problem in poultry especially those reared under extensive systems. Ajayi & Ajayi (1983) ...

The algorithm of random length sequences synthesis for frame synchronization of digital television systems

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Аndriy V. Sadchenko

2015-12-01

Full Text Available Digital television systems need to ensure that all digital signals processing operations are performed simultaneously and consistently. Frame synchronization dictated by the need to match phases of transmitter and receiver so that it would be possible to identify the start of a frame. As a frame synchronization signals are often used long length binary sequence with good aperiodic autocorrelation function. Aim: This work is dedicated to the development of the algorithm of random length sequences synthesis. Materials and Methods: The paper provides a comparative analysis of the known sequences, which can be used at present as synchronization ones, revealed their advantages and disadvantages. This work proposes the algorithm for the synthesis of binary synchronization sequences of random length with good autocorrelation properties based on noise generator with a uniform distribution law of probabilities. A "white noise" semiconductor generator is proposed to use as the initial material for the synthesis of binary sequences with desired properties. Results: The statistical analysis of the initial implementations of the "white noise" and synthesized sequences for frame synchronization of digital television is conducted. The comparative analysis of the synthesized sequences with known ones was carried out. The results show the benefits of obtained sequences in compare with known ones. The performed simulations confirm the obtained results. Conclusions: Thus, the search algorithm of binary synchronization sequences with desired autocorrelation properties received. According to this algorithm, the sequence can be longer in length and without length limitations. The received sync sequence can be used for frame synchronization in modern digital communication systems that will increase their efficiency and noise immunity.

Identification of the full-length β-actin sequence and expression profiles in the tree shrew (Tupaia belangeri).

Science.gov (United States)

Zheng, Yu; Yun, Chenxia; Wang, Qihui; Smith, Wanli W; Leng, Jing

2015-02-01

The tree shrew (Tupaia belangeri) diverges from the primate order (Primates) and is classified as a separate taxonomic group of mammals - Scandentia. It has been suggested that the tree shrew can be used as an animal model for studying human diseases; however, the genomic sequence of the tree shrew is largely unidentified. In the present study, we reported the full-length cDNA sequence of the housekeeping gene, β-actin, in the tree shrew. The amino acid sequence of β-actin in the tree shrew was compared to that of humans and other species; a simple phylogenetic relationship was discovered. Quantitative polymerase chain reaction (qPCR) and western blot analysis further demonstrated that the expression profiles of β-actin, as a general conservative housekeeping gene, in the tree shrew were similar to those in humans, although the expression levels varied among different types of tissue in the tree shrew. Our data provide evidence that the tree shrew has a close phylogenetic association with humans. These findings further enhance the potential that the tree shrew, as a species, may be used as an animal model for studying human disorders.

New Algorithm of Automatic Complex Password Generator Employing Genetic Algorithm

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Sura Jasim Mohammed

2018-01-01

Full Text Available Due to the occurred increasing in information sharing, internet popularization, E-commerce transactions, and data transferring, security and authenticity become an important and necessary subject. In this paper an automated schema was proposed to generate a strong and complex password which is based on entering initial data such as text (meaningful and simple information or not, with the concept of encoding it, then employing the Genetic Algorithm by using its operations crossover and mutation to generated different data from the entered one. The generated password is non-guessable and can be used in many and different applications and internet services like social networks, secured system, distributed systems, and online services. The proposed password generator achieved diffusion, randomness, and confusions, which are very necessary, required and targeted in the resulted password, in addition to the notice that the length of the generated password differs from the length of initial data, and any simple changing and modification in the initial data produces more and clear modification in the generated password. The proposed work was done using visual basic programing language.

Permutations avoiding an increasing number of length-increasing forbidden subsequences

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Elena Barcucci

2000-12-01

Full Text Available A permutation π is said to be τ-avoiding if it does not contain any subsequence having all the same pairwise comparisons as τ. This paper concerns the characterization and enumeration of permutations which avoid a set F j of subsequences increasing both in number and in length at the same time. Let F j be the set of subsequences of the form σ(j+1(j+2, σ being any permutation on {1,...,j}. For j=1 the only subsequence in F 1 is 123 and the 123-avoiding permutations are enumerated by the Catalan numbers; for j=2 the subsequences in F 2 are 1234 2134 and the (1234,2134 avoiding permutations are enumerated by the Schröder numbers; for each other value of j greater than 2 the subsequences in F j are j! and their length is (j+2 the permutations avoiding these j! subsequences are enumerated by a number sequence {a n } such that C n ≤ a n ≤ n!, C n being the n th Catalan number. For each j we determine the generating function of permutations avoiding the subsequences in F j according to the length, to the number of left minima and of non-inversions.

Impedance of finite length resistive cylinder

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S. Krinsky

2004-11-01

Full Text Available We determine the impedance of a cylindrical metal tube (resistor of radius a, length g, and conductivity σ attached at each end to perfect conductors of semi-infinite length. Our main interest is in the asymptotic behavior of the impedance at high frequency (k≫1/a. In the equilibrium regime, ka^{2}≪g, the impedance per unit length is accurately described by the well-known result for an infinite length tube with conductivity σ. In the transient regime, ka^{2}≫g, where the contribution of transition radiation arising from the discontinuity in conductivity is important, we derive an analytic expression for the impedance and compute the short-range wakefield. The analytic results are shown to agree with numerical evaluation of the impedance.

A study on the Stress Corrosion Cracking reduction method of Steam Generator secondary side of KSNP

International Nuclear Information System (INIS)

Kim, June Hoon; Lee, Goune Jin

2014-01-01

In order to avoid sludge accumulation affecting the life of the steam generator, the best way is to prevent the sludge inflow in advance by optimization of water quality management through chemical concentration and pH control etc. However it is very difficult to prevent sludge accumulation under the weak condition of corrosion, such as condensation, boiling and high temperature of feed-water in NPPs. Particularly stress corrosion cracking occurs in a top-of-tube sheet area of steam generator with an increase in number of operation years of Korea Standard Nuclear Plant(KSNP)... The purpose of this study is to improve suppression of stress corrosion cracking and life extension for steam generator and improve plant efficiency by performing full length bulk high chemical cleaning in order to remove iron oxide of steam generator secondary side in KSNP Hanbit Unit 6. This study analyzed the Free EDTA and Fe concentrations and sludge removal after performed full length bulk high temperature chemical cleaning for removing the iron oxide of steam generator secondary side, which of Hanbit unit 6 of KSNP. 1) It showed a typical pattern that Fe concentration increased in accordance with to decrease Free EDTA(Ethylene Diamine Tetea acetic Acid) concentration. 2) Sludge removal based on iron oxide after performing the full length bulk high temperature chemical cleaning was 3001kg and sludge removal by lancing additionally was 200.1kg

Isolation of full-length putative rat lysophospholipase cDNA using improved methods for mRNA isolation and cDNA cloning

International Nuclear Information System (INIS)

Han, J.H.; Stratowa, C.; Rutter, W.J.

1987-01-01

The authors have cloned a full-length putative rat pancreatic lysophospholipase cDNA by an improved mRNA isolation method and cDNA cloning strategy using [ 32 P]-labelled nucleotides. These new methods allow the construction of a cDNA library from the adult rat pancreas in which the majority of recombinant clones contained complete sequences for the corresponding mRNAs. A previously recognized but unidentified long and relatively rare cDNA clone containing the entire sequence from the cap site at the 5' end to the poly(A) tail at the 3' end of the mRNA was isolated by single-step screening of the library. The size, amino acid composition, and the activity of the protein expressed in heterologous cells strongly suggest this mRNA codes for lysophospholipase

Hybrid System Modeling and Full Cycle Operation Analysis of a Two-Stroke Free-Piston Linear Generator

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Peng Sun

2017-02-01

Full Text Available Free-piston linear generators (FPLGs have attractive application prospects for hybrid electric vehicles (HEVs owing to their high-efficiency, low-emissions and multi-fuel flexibility. In order to achieve long-term stable operation, the hybrid system design and full-cycle operation strategy are essential factors that should be considered. A 25 kW FPLG consisting of an internal combustion engine (ICE, a linear electric machine (LEM and a gas spring (GS is designed. To improve the power density and generating efficiency, the LEM is assembled with two modular flat-type double-sided PM LEM units, which sandwich a common moving-magnet plate supported by a middle keel beam and bilateral slide guide rails to enhance the stiffness of the moving plate. For the convenience of operation processes analysis, the coupling hybrid system is modeled mathematically and a full cycle simulation model is established. Top-level systemic control strategies including the starting, stable operating, fault recovering and stopping strategies are analyzed and discussed. The analysis results validate that the system can run stably and robustly with the proposed full cycle operation strategy. The effective electric output power can reach 26.36 kW with an overall system efficiency of 36.32%.

Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.

Science.gov (United States)

Otsuki, Tetsuji; Ota, Toshio; Nishikawa, Tetsuo; Hayashi, Koji; Suzuki, Yutaka; Yamamoto, Jun-ichi; Wakamatsu, Ai; Kimura, Kouichi; Sakamoto, Katsuhiko; Hatano, Naoto; Kawai, Yuri; Ishii, Shizuko; Saito, Kaoru; Kojima, Shin-ichi; Sugiyama, Tomoyasu; Ono, Tetsuyoshi; Okano, Kazunori; Yoshikawa, Yoko; Aotsuka, Satoshi; Sasaki, Naokazu; Hattori, Atsushi; Okumura, Koji; Nagai, Keiichi; Sugano, Sumio; Isogai, Takao

2005-01-01

We have developed an in silico method of selection of human full-length cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Fullness rates were increased to about 80% by combination of the oligo-capping method and ATGpr, software for prediction of translation start point and the coding potential. Then, using 5'-end single-pass sequences, cDNAs having the signal sequence were selected by PSORT ('signal sequence trap'). We also applied 'secretion or membrane protein-related keyword trap' based on the result of BLAST search against the SWISS-PROT database for the cDNAs which could not be selected by PSORT. Using the above procedures, 789 cDNAs were primarily selected and subjected to full-length sequencing, and 334 of these cDNAs were finally selected as novel. Most of the cDNAs (295 cDNAs: 88.3%) were predicted to encode secretion or membrane proteins. In particular, 165(80.5%) of the 205 cDNAs selected by PSORT were predicted to have signal sequences, while 70 (54.2%) of the 129 cDNAs selected by 'keyword trap' preserved the secretion or membrane protein-related keywords. Many important cDNAs were obtained, including transporters, receptors, and ligands, involved in significant cellular functions. Thus, an efficient method of selecting secretion or membrane protein-encoding cDNAs was developed by combining the above four procedures.

The comparison between the length of vertical dimension of occlusion and the length of thumb on undergraduate Mongoloid students

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Goh Li Teng

2011-03-01

Full Text Available The Thumb Rule of Leonardo da Vinci states that many proportions of the face show relationship with the length of thumb which is measured from the proximal tip of the proximal phalanx to the distal tip of the distal phalanx. Previous studies have shown that the length of the vertical dimension of occlusion (VDO is similar to the length of thumb of the Caucasoid race. The purpose of this study is to determine whether the length of VDO have correlations with the length of thumb among those of the Mongoloid race. This study took a survey method with the analytical cross-sectional approach. A total of 80 students of Faculty of Dentistry who have fulfilled all population criteria were randomly chosen to measure the length of VDO and the length of the thumb. Results analyzed with Student's t-test statistic revealed that there was a significant difference between males and females in the length of VDO and the length of the thumb, however, there was no significant difference between the length of VDO and the length of the thumb. There were very strong correlations (P<0.05 between the length of VDO and the length of the thumb. As a conclusion, the length of thumb can be suggested as an objective method to determine the length of VDO in this population.

Full-Length Sequence of Mouse Acupuncture-Induced 1-L (Aig1l Gene Including Its Transcriptional Start Site

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Mika Ohta

2011-01-01

Full Text Available We have been investigating the molecular efficacy of electroacupuncture (EA, which is one type of acupuncture therapy. In our previous molecular biological study of acupuncture, we found an EA-induced gene, named acupuncture-induced 1-L (Aig1l, in mouse skeletal muscle. The aims of this study consisted of identification of the full-length cDNA sequence of Aig1l including the transcriptional start site, determination of the tissue distribution of Aig1l and analysis of the effect of EA on Aig1l gene expression. We determined the complete cDNA sequence including the transcriptional start site via cDNA cloning with the cap site hunting method. We then analyzed the tissue distribution of Aig1l by means of northern blot analysis and real-time quantitative polymerase chain reaction. We used the semiquantitative reverse transcriptase-polymerase chain reaction to examine the effect of EA on Aig1l gene expression. Our results showed that the complete cDNA sequence of Aig1l was 6073 bp long, and the putative protein consisted of 962 amino acids. All seven tissues that we analyzed expressed the Aig1l gene. In skeletal muscle, EA induced expression of the Aig1l gene, with high expression observed after 3 hours of EA. Our findings thus suggest that the Aig1l gene may play a key role in the molecular mechanisms of EA efficacy.

The giant protein titin regulates the length of the striated muscle thick filament.

Science.gov (United States)

Tonino, Paola; Kiss, Balazs; Strom, Josh; Methawasin, Mei; Smith, John E; Kolb, Justin; Labeit, Siegfried; Granzier, Henk

2017-10-19

The contractile machinery of heart and skeletal muscles has as an essential component the thick filament, comprised of the molecular motor myosin. The thick filament is of a precisely controlled length, defining thereby the force level that muscles generate and how this force varies with muscle length. It has been speculated that the mechanism by which thick filament length is controlled involves the giant protein titin, but no conclusive support for this hypothesis exists. Here we show that in a mouse model in which we deleted two of titin's C-zone super-repeats, thick filament length is reduced in cardiac and skeletal muscles. In addition, functional studies reveal reduced force generation and a dilated cardiomyopathy (DCM) phenotype. Thus, regulation of thick filament length depends on titin and is critical for maintaining muscle health.

A Full-size High Temperature Superconducting Coil Employed in a Wind Turbine Generator Set-up

DEFF Research Database (Denmark)

Song, Xiaowei (Andy); Mijatovic, Nenad; Kellers, Jürgen

2016-01-01

A full-size stationary experimental set-up, which is a pole pair segment of a 2 MW high temperature superconducting (HTS) wind turbine generator, has been built and tested under the HTS-GEN project in Denmark. The performance of the HTS coil is crucial to the set-up, and further to the development...... is tested in LN2 first, and then tested in the set-up so that the magnetic environment in a real generator is reflected. The experimental results are reported, followed by a finite element simulation and a discussion on the deviation of the results. The tested and estimated Ic in LN2 are 148 A and 143 A...

The length of the male urethra

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Tobias. S. Kohler

2008-08-01

Full Text Available PURPOSE: Catheter-based medical devices are an important component of the urologic armamentarium. To our knowledge, there is no population-based data regarding normal male urethral length. We evaluated the length of the urethra in men with normal genitourinary anatomy undergoing either Foley catheter removal or standard cystoscopy. MATERIALS AND METHODS: Male urethral length was obtained in 109 men. After study permission was obtained, the subject's penis was placed on a gentle stretch and the catheter was marked at the tip of the penis. The catheter was then removed and the distance from the mark to the beginning of the re-inflated balloon was measured. Alternatively, urethral length was measured at the time of cystoscopy, on removal of the cystoscope. Data on age, weight, and height was obtained in patients when possible. RESULTS: The mean urethral length was 22.3 cm with a standard deviation of 2.4 cm. Urethral length varied between 15 cm and 29 cm. No statistically significant correlation was found between urethral length and height, weight, body mass index (BMI, or age. CONCLUSIONS: Literature documenting the length of the normal male adult urethra is scarce. Our data adds to basic anatomic information of the male urethra and may be used to optimize genitourinary device design.

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

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Peipei Zhang

2017-09-01

Full Text Available To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV (most likely pathogens using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV. The full genome of WLYaV corresponds to 5,772 nucleotides (nt, with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV, but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90% in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

FULL LENGTH RESEARCH ARTICLE Gnut

African Journals Online (AJOL)

Dr Ahmed

. Peanuts, Groundnuts microflora and pathogenesis of peanut pod. Root Phytopathology, 55(4):359-367. Halima, A. S. 2000. Isolation and preliminary Identification of fungi in stored groundnut. HND project. Department of Science Laboratory.

Mutation-specific effects on thin filament length in thin filament myopathy.

Science.gov (United States)

Winter, Josine M de; Joureau, Barbara; Lee, Eun-Jeong; Kiss, Balázs; Yuen, Michaela; Gupta, Vandana A; Pappas, Christopher T; Gregorio, Carol C; Stienen, Ger J M; Edvardson, Simon; Wallgren-Pettersson, Carina; Lehtokari, Vilma-Lotta; Pelin, Katarina; Malfatti, Edoardo; Romero, Norma B; Engelen, Baziel G van; Voermans, Nicol C; Donkervoort, Sandra; Bönnemann, C G; Clarke, Nigel F; Beggs, Alan H; Granzier, Henk; Ottenheijm, Coen A C

2016-06-01

Thin filament myopathies are among the most common nondystrophic congenital muscular disorders, and are caused by mutations in genes encoding proteins that are associated with the skeletal muscle thin filament. Mechanisms underlying muscle weakness are poorly understood, but might involve the length of the thin filament, an important determinant of force generation. We investigated the sarcomere length-dependence of force, a functional assay that provides insights into the contractile strength of muscle fibers as well as the length of the thin filaments, in muscle fibers from 51 patients with thin filament myopathy caused by mutations in NEB, ACTA1, TPM2, TPM3, TNNT1, KBTBD13, KLHL40, and KLHL41. Lower force generation was observed in muscle fibers from patients of all genotypes. In a subset of patients who harbor mutations in NEB and ACTA1, the lower force was associated with downward shifted force-sarcomere length relations, indicative of shorter thin filaments. Confocal microscopy confirmed shorter thin filaments in muscle fibers of these patients. A conditional Neb knockout mouse model, which recapitulates thin filament myopathy, revealed a compensatory mechanism; the lower force generation that was associated with shorter thin filaments was compensated for by increasing the number of sarcomeres in series. This allowed muscle fibers to operate at a shorter sarcomere length and maintain optimal thin-thick filament overlap. These findings might provide a novel direction for the development of therapeutic strategies for thin filament myopathy patients with shortened thin filament lengths. Ann Neurol 2016;79:959-969. © 2016 American Neurological Association.

Economic issues of broiler production length

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Szőllősi László

2014-01-01

Full Text Available The length of broiler production cycle is also an important factor when profitability is measured. This paper is to determine the effects of different market ages and down-time period, overall broiler production cycle length on performance and economic parameters based on Hungarian production and financial circumstances. A deterministic model was constructed to manage the function-like correlations of age-related daily weight gain, daily feed intake and daily mortality data. The results show that broiler production cycle length has a significant effect on production and economic performance. Cycle length is determined by the length of down-time and grow-out periods. If down-time period is reduced by one day, an average net income of EUR 0.55 per m2 is realizable. However, the production period is not directly proportional either with emerging costs or obtainable revenues. Profit maximization is attainable if the production period is 41-42 days.

Walking on inclines: how do desert ants monitor slope and step length

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Seidl Tobias

2008-06-01

Full Text Available Abstract Background During long-distance foraging in almost featureless habitats desert ants of the genus Cataglyphis employ path-integrating mechanisms (vector navigation. This navigational strategy requires an egocentric monitoring of the foraging path by incrementally integrating direction, distance, and inclination of the path. Monitoring the latter two parameters involves idiothetic cues and hence is tightly coupled to the ant's locomotor behavior. Results In a kinematic study of desert ant locomotion performed on differently inclined surfaces we aimed at pinpointing the relevant mechanisms of estimating step length and inclination. In a behavioral experiment with ants foraging on slippery surfaces we broke the otherwise tightly coupled relationship between stepping frequency and step length and examined the animals' ability to monitor distances covered even under those adverse conditions. We show that the ants' locomotor system is not influenced by inclined paths. After removing the effect of speed, slope had only marginal influence on kinematic parameters. Conclusion From the obtained data we infer that the previously proposed monitoring of angles of the thorax-coxa joint is not involved in inclinometry. Due to the tiny variations in cycle period, we also argue that an efference copy of the central pattern generator coding the step length in its output frequency will most likely not suffice for estimating step length and complementing the pedometer. Finally we propose that sensing forces acting on the ant's legs could provide the desired neuronal correlate employed in monitoring inclination and step length.

Characteristic length of the knotting probability revisited

International Nuclear Information System (INIS)

Uehara, Erica; Deguchi, Tetsuo

2015-01-01

We present a self-avoiding polygon (SAP) model for circular DNA in which the radius of impermeable cylindrical segments corresponds to the screening length of double-stranded DNA surrounded by counter ions. For the model we evaluate the probability for a generated SAP with N segments having a given knot K through simulation. We call it the knotting probability of a knot K with N segments for the SAP model. We show that when N is large the most significant factor in the knotting probability is given by the exponentially decaying part exp(−N/N K ), where the estimates of parameter N K are consistent with the same value for all the different knots we investigated. We thus call it the characteristic length of the knotting probability. We give formulae expressing the characteristic length as a function of the cylindrical radius r ex , i.e. the screening length of double-stranded DNA. (paper)

Relativistic length agony continued

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Redžić D.V.

2014-01-01

Full Text Available We made an attempt to remedy recent confusing treatments of some basic relativistic concepts and results. Following the argument presented in an earlier paper (Redžić 2008b, we discussed the misconceptions that are recurrent points in the literature devoted to teaching relativity such as: there is no change in the object in Special Relativity, illusory character of relativistic length contraction, stresses and strains induced by Lorentz contraction, and related issues. We gave several examples of the traps of everyday language that lurk in Special Relativity. To remove a possible conceptual and terminological muddle, we made a distinction between the relativistic length reduction and relativistic FitzGerald-Lorentz contraction, corresponding to a passive and an active aspect of length contraction, respectively; we pointed out that both aspects have fundamental dynamical contents. As an illustration of our considerations, we discussed briefly the Dewan-Beran-Bell spaceship paradox and the ‘pole in a barn’ paradox. [Projekat Ministarstva nauke Republike Srbije, br. 171028

ESTIMATION OF BURSTS LENGTH AND DESIGN OF A FIBER DELAY LINE BASED OBS ROUTER

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RICHA AWASTHI

2017-03-01

Full Text Available The demand for higher bandwidth is increasing day by day and this ever growing demand cannot be catered to with current electronic technology. Thus new communication technology like optical communication needs to be used. In the similar context OBS (optical burst switching is considered as next generation data transfer technology. In OBS information is transmitted in forms of optical bursts of variable lengths. However, contention among the bursts is a major problem in OBS system, and for contention resolution defection routing is mostly preferred. However, deflection routing increases delay. In this paper, it is shown that the arrival of very large bursts is rare event, and for moderate burst length the buffering of contending burst can provide very effective solution. However, in case of arrival of large bursts deflection can be used.

Molecular Cloning and Characterization of Full-Length cDNA of Calmodulin Gene from Pacific Oyster Crassostrea gigas.

Science.gov (United States)

Li, Xing-Xia; Yu, Wen-Chao; Cai, Zhong-Qiang; He, Cheng; Wei, Na; Wang, Xiao-Tong; Yue, Xi-Qing

2016-01-01

The shell of the pearl oyster ( Pinctada fucata ) mainly comprises aragonite whereas that of the Pacific oyster ( Crassostrea gigas ) is mainly calcite, thereby suggesting the different mechanisms of shell formation between above two mollusks. Calmodulin (CaM) is an important gene for regulating the uptake, transport, and secretion of calcium during the process of shell formation in pearl oyster. It is interesting to characterize the CaM in oysters, which could facilitate the understanding of the different shell formation mechanisms among mollusks. We cloned the full-length cDNA of Pacific oyster CaM (cgCaM) and found that the cgCaM ORF encoded a peptide of 113 amino acids containing three EF-hand calcium-binding domains, its expression level was highest in the mantle, hinting that the cgCaM gene is probably involved in shell formation of Pacific oyster, and the common ancestor of Gastropoda and Bivalvia may possess at least three CaM genes. We also found that the numbers of some EF hand family members in highly calcified species were higher than those in lowly calcified species and the numbers of these motifs in oyster genome were the highest among the mollusk species with whole genome sequence, further hinting the correlation between CaM and biomineralization.

VP1u phospholipase activity is critical for infectivity of full-length parvovirus B19 genomic clones.

Science.gov (United States)

Filippone, Claudia; Zhi, Ning; Wong, Susan; Lu, Jun; Kajigaya, Sachiko; Gallinella, Giorgio; Kakkola, Laura; Söderlund-Venermo, Maria; Young, Neal S; Brown, Kevin E

2008-05-10

Three full-length genomic clones (pB19-M20, pB19-FL and pB19-HG1) of parvovirus B19 were produced in different laboratories. pB19-M20 was shown to produce infectious virus. To determine the differences in infectivity, all three plasmids were tested by transfection and infection assays. All three clones were similar in viral DNA replication, RNA transcription, and viral capsid protein production. However, only pB19-M20 and pB19-HG1 produced infectious virus. Comparison of viral sequences showed no significant differences in ITR or NS regions. In the capsid region, there was a nucleotide sequence difference conferring an amino acid substitution (E176K) in the phospholipase A2-like motif of the VP1-unique (VP1u) region. The recombinant VP1u with the E176K mutation had no catalytic activity as compared with the wild-type. When this mutation was introduced into pB19-M20, infectivity was significantly attenuated, confirming the critical role of this motif. Investigation of the original serum from which pB19-FL was cloned confirmed that the phospholipase mutation was present in the native B19 virus.

VP1u phospholipase activity is critical for infectivity of full-length parvovirus B19 genomic clones✰

Science.gov (United States)

Filippone, Claudia; Zhi, Ning; Wong, Susan; Lu, Jun; Kajigaya, Sachiko; Gallinella, Giorgio; Kakkola, Laura; Venermo, Maria S Söderlund; Young, Neal S.; Brown, Kevin E.

2008-01-01

Three full-length genomic clones (pB19-M20, pB19-FL and pB19-HG1) of parvovirus B19 were produced in different laboratories. pB19-M20 was shown to produce infectious virus. To determine the differences in infectivity, all three plasmids were tested by transfection and infection assays. All three clones were similar in viral DNA replication, RNA transcription, and viral capsid protein production. However, only pB19-M20 and pB19-HG1 produced infectious virus. Comparison of viral sequences showed no significant differences in ITR or NS regions. In the capsid region, there was a nucleotide sequence difference conferring an amino acid substitution (E176K) in the phospholipase A2-like motif of the VP1-unique (VP1u) region. The recombinant VP1u with the E176K mutation had no catalytic activity as compared with the wild-type. When this mutation was introduced into pB19-M20, infectivity was significantly attenuated, confirming the critical role of this motif. Investigation of the original serum from which pB19-FL was cloned confirmed that the phospholipase mutation was present in the native B19 virus. PMID:18252260

Fundamental length and relativistic length

International Nuclear Information System (INIS)

Strel'tsov, V.N.

1988-01-01

It si noted that the introduction of fundamental length contradicts the conventional representations concerning the contraction of the longitudinal size of fast-moving objects. The use of the concept of relativistic length and the following ''elongation formula'' permits one to solve this problem

Design and Optimization of Tube Type Interior Permanent Magnets Generator for Free Piston Applications

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Serdal ARSLAN

2017-05-01

Full Text Available In this study a design and optimization of a generator to be used in free piston applications was made. In order to supply required initial force, an IPM (interior permanent magnets cavity tube type linear generator was selected. By using analytical equations’ basic dimensioning of generator was made. By using Ansys-Maxwell dimensioning, analysis and optimization of the generator was realized. Also, the effects of design basic variables (pole step ratio, cavity step ratio, inner diameter - outer diameter ratio, primary final length, air interval on pinking force were examined by using parametric analyses. Among these variables, cavity step ratio, inner diameter - outer diameter ratio, primary final length were optimally determined by algorithm and sequential nonlinear programming. The two methods were compared in terms of pinking force calculation problem. Preliminary application of the linear generator was performed for free piston application.

Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.

Directory of Open Access Journals (Sweden)

Kouji Satoh

Full Text Available Rice (Oryza sativa L. is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE genes, 33K annotated non-expressed (ANE genes, and 5.5K non-annotated expressed (NAE genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.

Effects of Conjugate Gradient Methods and Step-Length Formulas on the Multiscale Full Waveform Inversion in Time Domain: Numerical Experiments

Science.gov (United States)

Liu, Youshan; Teng, Jiwen; Xu, Tao; Badal, José; Liu, Qinya; Zhou, Bing

2017-05-01

We carry out full waveform inversion (FWI) in time domain based on an alternative frequency-band selection strategy that allows us to implement the method with success. This strategy aims at decomposing the seismic data within partially overlapped frequency intervals by carrying out a concatenated treatment of the wavelet to largely avoid redundant frequency information to adapt to wavelength or wavenumber coverage. A pertinent numerical test proves the effectiveness of this strategy. Based on this strategy, we comparatively analyze the effects of update parameters for the nonlinear conjugate gradient (CG) method and step-length formulas on the multiscale FWI through several numerical tests. The investigations of up to eight versions of the nonlinear CG method with and without Gaussian white noise make clear that the HS (Hestenes and Stiefel in J Res Natl Bur Stand Sect 5:409-436, 1952), CD (Fletcher in Practical methods of optimization vol. 1: unconstrained optimization, Wiley, New York, 1987), and PRP (Polak and Ribière in Revue Francaise Informat Recherche Opertionelle, 3e Année 16:35-43, 1969; Polyak in USSR Comput Math Math Phys 9:94-112, 1969) versions are more efficient among the eight versions, while the DY (Dai and Yuan in SIAM J Optim 10:177-182, 1999) version always yields inaccurate result, because it overestimates the deeper parts of the model. The application of FWI algorithms using distinct step-length formulas, such as the direct method ( Direct), the parabolic search method ( Search), and the two-point quadratic interpolation method ( Interp), proves that the Interp is more efficient for noise-free data, while the Direct is more efficient for Gaussian white noise data. In contrast, the Search is less efficient because of its slow convergence. In general, the three step-length formulas are robust or partly insensitive to Gaussian white noise and the complexity of the model. When the initial velocity model deviates far from the real model or the

A novel copper(II) coordination at His186 in full-length murine prion protein

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Yasuko [Laboratory of Radiation Biology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan); Hiraoka, Wakako [Laboratory of Biophysics, School of Science and Technology, Meiji University, Kawasaki 214-8571 (Japan); Igarashi, Manabu; Ito, Kimihito [Department of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020 (Japan); Shimoyama, Yuhei [Soft-Matter Physics Laboratory, Graduate School of Emergent Science, Muroran Institute of Technology, Muroran 050-8585 (Japan); Horiuchi, Motohiro [Laboratory of Prion Diseases, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan); Yamamori, Tohru; Yasui, Hironobu; Kuwabara, Mikinori [Laboratory of Radiation Biology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan); Inagaki, Fuyuhiko [Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 (Japan); Inanami, Osamu, E-mail: inanami@vetmed.hokudai.ac.jp [Laboratory of Radiation Biology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan)

2010-04-09

To explore Cu(II) ion coordination by His{sup 186} in the C-terminal domain of full-length prion protein (moPrP), we utilized the magnetic dipolar interaction between a paramagnetic metal, Cu(II) ion, and a spin probe introduced in the neighborhood of the postulated binding site by the spin labeling technique (SDSL technique). Six moPrP mutants, moPrP(D143C), moPrP(Y148C), moPrP(E151C), moPrP(Y156C), moPrP(T189C), and moPrP(Y156C,H186A), were reacted with a methane thiosulfonate spin probe and a nitroxide residue (R1) was created in the binding site of each one. Line broadening of the ESR spectra was induced in the presence of Cu(II) ions in moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) but not moPrP(D143R1). This line broadening indicated the presence of electron-electron dipolar interaction between Cu(II) and the nitroxide spin probe, suggesting that each interspin distance was within 20 A. The interspin distance ranges between Cu(II) and the spin probes of moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) were estimated to be 12.1 A, 18.1 A, 10.7 A, and 8.4 A, respectively. In moPrP(Y156R1,H186A), line broadening between Cu(II) and the spin probe was not observed. These results suggest that a novel Cu(II) binding site is involved in His186 in the Helix2 region of the C-terminal domain of moPrP{sup C}.

A novel copper(II) coordination at His186 in full-length murine prion protein

International Nuclear Information System (INIS)

Watanabe, Yasuko; Hiraoka, Wakako; Igarashi, Manabu; Ito, Kimihito; Shimoyama, Yuhei; Horiuchi, Motohiro; Yamamori, Tohru; Yasui, Hironobu; Kuwabara, Mikinori; Inagaki, Fuyuhiko; Inanami, Osamu

2010-01-01

To explore Cu(II) ion coordination by His 186 in the C-terminal domain of full-length prion protein (moPrP), we utilized the magnetic dipolar interaction between a paramagnetic metal, Cu(II) ion, and a spin probe introduced in the neighborhood of the postulated binding site by the spin labeling technique (SDSL technique). Six moPrP mutants, moPrP(D143C), moPrP(Y148C), moPrP(E151C), moPrP(Y156C), moPrP(T189C), and moPrP(Y156C,H186A), were reacted with a methane thiosulfonate spin probe and a nitroxide residue (R1) was created in the binding site of each one. Line broadening of the ESR spectra was induced in the presence of Cu(II) ions in moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) but not moPrP(D143R1). This line broadening indicated the presence of electron-electron dipolar interaction between Cu(II) and the nitroxide spin probe, suggesting that each interspin distance was within 20 A. The interspin distance ranges between Cu(II) and the spin probes of moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) were estimated to be 12.1 A, 18.1 A, 10.7 A, and 8.4 A, respectively. In moPrP(Y156R1,H186A), line broadening between Cu(II) and the spin probe was not observed. These results suggest that a novel Cu(II) binding site is involved in His186 in the Helix2 region of the C-terminal domain of moPrP C .

Blind sequence-length estimation of low-SNR cyclostationary sequences

CSIR Research Space (South Africa)

Vlok, JD

2014-06-01

Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

Stochastic Simulation of a Full-Chain Reptation Model with Constraint Release, Chain-Length Fluctuations and Chain Stretching

DEFF Research Database (Denmark)

Neergaard, Jesper; Schieber, Jay D.

1999-01-01

A self-consistent reptation model that includes chain stretching, chain-length fluctuations, segment connectivity and constraint release is used to predict transient and steady flows. Quantitative comparisons are made with entangledsolution data. The model is able to capture quantitatively all...

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

Science.gov (United States)

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-07-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.

Laser interferometric method for determining the carrier diffusion length in semiconductors

Energy Technology Data Exchange (ETDEWEB)

Manukhov, V. V. [Saint Petersburg State University (Russian Federation); Fedortsov, A. B.; Ivanov, A. S., E-mail: ivaleks58@gmail.com [Saint Petersburg Mining University (Russian Federation)

2015-09-15

A new laser interferometric method for measuring the carrier diffusion length in semiconductors is proposed. The method is based on the interference–absorption interaction of two laser radiations in a semiconductor. Injected radiation generates additional carriers in a semiconductor, which causes a change in the material’s optical constants and modulation of the probing radiation passed through the sample. When changing the distance between carrier generation and probing points, a decrease in the carrier concentration, which depends on the diffusion length, is recorded. The diffusion length is determined by comparing the experimental and theoretical dependences of the probe signal on the divergence of the injector and probe beams. The method is successfully tested on semiconductor samples with different thicknesses and surface states and can be used in scientific research and the electronics industry.

Security analysis of the decoy method with the Bennett–Brassard 1984 protocol for finite key lengths

International Nuclear Information System (INIS)

Hayashi, Masahito; Nakayama, Ryota

2014-01-01

This paper provides a formula for the sacrifice bit-length for privacy amplification with the Bennett–Brassard 1984 protocol for finite key lengths, when we employ the decoy method. Using the formula, we can guarantee the security parameter for a realizable quantum key distribution system. The key generation rates with finite key lengths are numerically evaluated. The proposed method improves the existing key generation rate even in the asymptotic setting. (paper)

Extending electronic length frequency analysis in R

DEFF Research Database (Denmark)

Taylor, M. H.; Mildenberger, Tobias K.

2017-01-01

VBGF (soVBGF) requires a more intensive search due to two additional parameters. This work describes the implementation of two optimisation approaches ("simulated annealing" and "genetic algorithm") for growth function fitting using the open-source software "R." Using a generated LFQ data set......Electronic length frequency analysis (ELEFAN) is a system of stock assessment methods using length-frequency (LFQ) data. One step is the estimation of growth from the progression of LFQ modes through time using the von Bertalanffy growth function (VBGF). The option to fit a seasonally oscillating...... of the asymptotic length parameter (L-infinity) are found to have significant effects on parameter estimation error. An outlook provides context as to the significance of the R-based implementation for further testing and development, as well as the general relevance of the method for data-limited stock assessment....

Zero-point length from string fluctuations

International Nuclear Information System (INIS)

Fontanini, Michele; Spallucci, Euro; Padmanabhan, T.

2006-01-01

One of the leading candidates for quantum gravity, viz. string theory, has the following features incorporated in it. (i) The full spacetime is higher-dimensional, with (possibly) compact extra-dimensions; (ii) there is a natural minimal length below which the concept of continuum spacetime needs to be modified by some deeper concept. On the other hand, the existence of a minimal length (zero-point length) in four-dimensional spacetime, with obvious implications as UV regulator, has been often conjectured as a natural aftermath of any correct quantum theory of gravity. We show that one can incorporate the apparently unrelated pieces of information-zero-point length, extra-dimensions, string T-duality-in a consistent framework. This is done in terms of a modified Kaluza-Klein theory that interpolates between (high-energy) string theory and (low-energy) quantum field theory. In this model, the zero-point length in four dimensions is a 'virtual memory' of the length scale of compact extra-dimensions. Such a scale turns out to be determined by T-duality inherited from the underlying fundamental string theory. From a low energy perspective short distance infinities are cutoff by a minimal length which is proportional to the square root of the string slope, i.e., α ' . Thus, we bridge the gap between the string theory domain and the low energy arena of point-particle quantum field theory

Full length SSC R and D dipole magnet test results

International Nuclear Information System (INIS)

Strait, J.; Bleadon, M.; Brown, B.C.

1989-03-01

Four full scale SSC development dipole magnets have been tested for mechanical and quench behavior. Two are of a design similar to previous magnets but contain a number of improvements, including more uniform coil size, higher pre-stress and a redesigned inner-outer coil splice. One exceeds the SSC operating current on the second quench but the other appears to be limited by damaged superconductor to a lower current. The other two magnets are of alternate designs. One trains erratically and fails to reach a plateau and the other reaches plateau after four quenches. 12 refs., 4 figs

Lyso-myristoyl phosphatidylcholine micelles sustain the activity of Dengue non-structural (NS) protein 3 protease domain fused with the full-length NS2B.

Science.gov (United States)

Huang, Qiwei; Li, Qingxin; Joy, Joma; Chen, Angela Shuyi; Ruiz-Carrillo, David; Hill, Jeffrey; Lescar, Julien; Kang, Congbao

2013-12-01

Dengue virus (DENV), a member of the flavivirus genus, affects 50-100 million people in tropical and sub-tropical regions. The DENV protease domain is located at the N-terminus of the NS3 protease and requires for its enzymatic activity a hydrophilic segment of the NS2B that acts as a cofactor. The protease is an important antiviral drug target because it plays a crucial role in virus replication by cleaving the genome-coded polypeptide into mature functional proteins. Currently, there are no drugs to inhibit DENV protease activity. Most structural and functional studies have been conducted using protein constructs containing the NS3 protease domain connected to a soluble segment of the NS2B membrane protein via a nine-residue linker. For in vitro structural and functional studies, it would be useful to produce a natural form of the DENV protease containing the NS3 protease domain and the full-length NS2B protein. Herein, we describe the expression and purification of a natural form of DENV protease (NS2BFL-NS3pro) containing the full-length NS2B protein and the protease domain of NS3 (NS3pro). The protease was expressed and purified in detergent micelles necessary for its folding. Our results show that this purified protein was active in detergent micelles such as lyso-myristoyl phosphatidylcholine (LMPC). These findings should facilitate further structural and functional studies of the protease and will facilitate drug discovery targeting DENV. Copyright © 2013 Elsevier Inc. All rights reserved.

Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

DEFF Research Database (Denmark)

Einer-Jensen, Katja; Winton, J.; Lorenzen, Niels

2005-01-01

The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt....... Experimental evaluation of the method consisted of three steps: (i) RT-PCR amplification of the G-gene of VHSV isolates using purified viral RNA as template, (ii) digestion of the PCR products with a panel of restriction endonucleases and (iii) interpretation of the resulting RFLP profiles. The RFLP analysis...

Analysis of ureteral length in adult cadavers

Directory of Open Access Journals (Sweden)

Hugo F. F. Novaes

2013-04-01

Full Text Available Introduction In some occasions, correlations between human structures can help planning surgical intra-abdominal interventions. The previous determination of ureteral length helps pre-operatory planning of surgeries, reduces costs of auxiliary exams, the correct choice of double-J catheter with low morbidity and fewer symptoms, and an adequate adhesion to treatment. Objective To evaluate ureteral length in adult cadavers and to analyze its correlation with anthropometric measures. Materials and Methods: From April 2009 to January 2012 we determined ureteral length of adult cadavers submitted to necropsy and obtained the following measures: height, distance from shoulder to wrist, elbow-wrist, xiphoid appendix-umbilicus, umbilicus-pubis, xiphoid appendix-pubis and between iliac spines. We analyzed the correlations between ureteral length and those anthropometric measures. Results We dissected 115 ureters from 115 adult corpses from April 2009 to January 2012. Median ureteral length didn't vary between sexes or according to height. It was observed no correlation among ureteral length and all considered anthropometric measures in all analyzed subgroups and in general population. There were no significant differences between right and left ureteral measures. Conclusions There is no difference of ureteral length in relation to height or gender (male or female. There is no significant correlation among ureteral length and the considered anthropometric measures.

Fabrication of a Scaled MgB2 Racetrack Demonstrator Pole for a 10-MW Direct-Drive Wind Turbine Generator

DEFF Research Database (Denmark)

Magnusson, Niklas; Eliassen, Jan Christian; Abrahamsen, Asger Bech

2018-01-01

Field windings made of MgB2 wires or tapes are considered for their potential to reduce volume, weight, and cost of large offshore wind turbine generators. To gain experience of how to use this relatively new material in full-scale generators, tests of different winding methodologies and techniques...... are needed. In this paper, we describe in detail the steps used to wind a racetrack coil with a length of 1 m and a width of 0.5 m out of 4.5 km of MgB2 superconducting tape. The width corresponds to a full-scale pole of a 10-MW generator, whereas the length of the straight section is shorter than...... the corresponding full-scale pole. The coil was built up of ten double pancake coils. Each double pancake coil was wet wound using a semiautomatic winding process, where Stycast 2850 was applied directly to the MgB2 tape without any other dedicated electrical insulation. The strengths and weaknesses of the winding...

Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.

Directory of Open Access Journals (Sweden)

Carole F S Koning-Boucoiran

2015-04-01

Full Text Available In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array.Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L. genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.

Molecular markers. Amplified fragment length polymorphism

Directory of Open Access Journals (Sweden)

Pržulj Novo

2005-01-01

Full Text Available Amplified Fragment Length Polymorphism molecular markers (AFLPs has been developed combining procedures of RFLPs and RAPDs molekular markers, i.e. the first step is restriction digestion of the genomic DNA that is followed by selective amplification of the restricted fragments. The advantage of the AFLP technique is that it allows rapid generation of a large number of reproducible markers. The reproducibility of AFLPs markers is assured by the use of restriction site-specific adapters and adapter-specific primers for PCR reaction. Only fragments containing the restriction site sequence plus the additional nucleotides will be amplified and the more selected nucleotides added on the primer sequence the fewer the number of fragments amplified by PCR. The amplified products are normally separated on a sequencing gel and visualized after exposure to X-ray film or by using fluorescent labeled primers. AFLP shave proven to be extremely proficient in revealing diversity at below the species level. A disadvantage of AFLP technique is that AFLPs are essentially a dominant marker system and not able to identify heterozygotes.

Divergence of host range and biological properties between natural isolate and full-length infectious cDNA clone of the Beet mild yellowing virus 2ITB.

Science.gov (United States)

Klein, Elodie; Brault, Véronique; Klein, Delphine; Weyens, Guy; Lefèbvre, Marc; Ziegler-Graff, Véronique; Gilmer, David

2014-01-01

Plant infection by poleroviruses is restricted to phloem tissues, preventing any classical leaf rub inoculation with viral RNA or virions. Efficient virus inoculation to plants is achieved by viruliferous aphids that acquire the virus by feeding on infected plants. The use of promoter-driven infectious cDNA is an alternative means to infect plants and allows reverse genetic studies to be performed. Using Beet mild yellowing virus isolate 2ITB (BMYV-2ITB), we produced a full-length infectious cDNA clone of the virus (named BMYV-EK) placed under the control of the T7 RNA polymerase and the Cauliflower mosaic virus 35S promoters. Infectivity of the engineered BMYV-EK virus was assayed in different plant species and compared with that of the original virus. We showed that in vitro- or in planta-derived transcripts were infectious in protoplasts and in whole plants. Importantly, the natural aphid vector Myzus persicae efficiently transmitted the viral progeny produced in infected plants. By comparing agroinoculation and aphid infection in a host range assay, we showed that the engineered BMYV-EK virus displayed a similar host range to BMYV-2ITB, except for Nicotiana benthamiana, which proved to be resistant to systemic infection with BMYV-EK. Finally, both the BMYV-EK P0 and the full-length clone were able to strongly interfere with post-transcriptional gene silencing. © 2013 BSPP AND JOHN WILEY & SONS LTD.

Extreme telomere length dimorphism in the Tasmanian devil and related marsupials suggests parental control of telomere length.

Directory of Open Access Journals (Sweden)

Hannah S Bender

Full Text Available Telomeres, specialised structures that protect chromosome ends, play a critical role in preserving chromosome integrity. Telomere dynamics in the Tasmanian devil (Sarcophilus harrisii are of particular interest in light of the emergence of devil facial tumour disease (DFTD, a transmissible malignancy that causes rapid mortality and threatens the species with extinction. We used fluorescent in situ hybridisation to investigate telomere length in DFTD cells, in healthy Tasmanian devils and in four closely related marsupial species. Here we report that animals in the Order Dasyuromorphia have chromosomes characterised by striking telomere length dimorphism between homologues. Findings in sex chromosomes suggest that telomere length dimorphism may be regulated by events in the parental germlines. Long telomeres on the Y chromosome imply that telomere lengthening occurs during spermatogenesis, whereas telomere diminution occurs during oogenesis. Although found in several somatic cell tissue types, telomere length dimorphism was not found in DFTD cancer cells, which are characterised by uniformly short telomeres. This is, to our knowledge, the first report of naturally occurring telomere length dimorphism in any species and suggests a novel strategy of telomere length control. Comparative studies in five distantly related marsupials and a monotreme indicate that telomere dimorphism evolved at least 50 million years ago.

Importance of length and sequence order on magnesium binding to surface-bound oligonucleotides studied by second harmonic generation and atomic force microscopy.

Science.gov (United States)

Holland, Joseph G; Geiger, Franz M

2012-06-07

The binding of magnesium ions to surface-bound single-stranded oligonucleotides was studied under aqueous conditions using second harmonic generation (SHG) and atomic force microscopy (AFM). The effect of strand length on the number of Mg(II) ions bound and their free binding energy was examined for 5-, 10-, 15-, and 20-mers of adenine and guanine at pH 7, 298 K, and 10 mM NaCl. The binding free energies for adenine and guanine sequences were calculated to be -32.1(4) and -35.6(2) kJ/mol, respectively, and invariant with strand length. Furthermore, the ion density for adenine oligonucleotides did not change as strand length increased, with an average value of 2(1) ions/strand. In sharp contrast, guanine oligonucleotides displayed a linear relationship between strand length and ion density, suggesting that cooperativity is important. This data gives predictive capabilities for mixed strands of various lengths, which we exploit for 20-mers of adenines and guanines. In addition, the role sequence order plays in strands of hetero-oligonucleotides was examined for 5'-A(10)G(10)-3', 5'-(AG)(10)-3', and 5'-G(10)A(10)-3' (here the -3' end is chemically modified to bind to the surface). Although the free energy of binding is the same for these three strands (averaged to be -33.3(4) kJ/mol), the total ion density increases when several guanine residues are close to the 3' end (and thus close to the solid support substrate). To further understand these results, we analyzed the height profiles of the functionalized surfaces with tapping-mode atomic force microscopy (AFM). When comparing the average surface height profiles of the oligonucleotide surfaces pre- and post- Mg(II) binding, a positive correlation was found between ion density and the subsequent height decrease following Mg(II) binding, which we attribute to reductions in Coulomb repulsion and strand collapse once a critical number of Mg(II) ions are bound to the strand.

The MX/G/1 queue with queue length dependent service times

Directory of Open Access Journals (Sweden)

Bong Dae Choi

2001-01-01

Full Text Available We deal with the MX/G/1 queue where service times depend on the queue length at the service initiation. By using Markov renewal theory, we derive the queue length distribution at departure epochs. We also obtain the transient queue length distribution at time t and its limiting distribution and the virtual waiting time distribution. The numerical results for transient mean queue length and queue length distributions are given.

Full-length characterization of A1/D intersubtype recombinant genomes from a therapy-induced HIV type 1 controller during acute infection and his noncontrolling partner

DEFF Research Database (Denmark)

Fomsgaard, A.; Vinner, L.; Therrien, D.

2008-01-01

To increase the understanding of mechanisms of HIV control we have genetically and immunologically characterized a full-length HIV-1 isolated from an acute infection in a rare case of undetectable viremia. The subject, a 43-year-old Danish white male (DK1), was diagnosed with acute HIV-1 infection...... and phylogenic trees were constructed and diversity and evolutionary distances were calculated. Intracellular IFN-gamma in CD8(+)CD3(+) T-lymphocyte reactions was investigated by intracellular flow cytometry (IC-FACS). Virus isolates from both patients were A1D intersubtype recombinants showing 98% sequence...

Association of murine lupus and thymic full-length endogenous retroviral expression maps to a bone marrow stem cell

International Nuclear Information System (INIS)

Krieg, A.M.; Gourley, M.F.; Steinberg, A.D.

1991-01-01

Recent studies of thymic gene expression in murine lupus have demonstrated 8.4-kb (full-length size) modified polytropic (Mpmv) endogenous retroviral RNA. In contrast, normal control mouse strains do not produce detectable amounts of such RNA in their thymuses. Prior studies have attributed a defect in experimental tolerance in murine lupus to a bone marrow stem cell rather than to the thymic epithelium; in contrast, infectious retroviral expression has been associated with the thymic epithelium, rather than with the bone marrow stem cell. The present study was designed to determine whether the abnormal Mpmv expression associated with murine lupus mapped to thymic epithelium or to a marrow precursor. Lethally irradiated control and lupus-prone mice were reconstituted with T cell depleted bone marrow; one month later their thymuses were studied for endogenous retroviral RNA and protein expression. Recipients of bone marrow from nonautoimmune donors expressed neither 8.4-kb Mpmv RNA nor surface MCF gp70 in their thymuses. In contrast, recipients of bone marrow from autoimmune NZB or BXSB donors expressed thymic 8.4-kb Mpmv RNA and mink cell focus-forming gp70. These studies demonstrate that lupus-associated 8.4-kb Mpmv endogenous retroviral expression is determined by bone marrow stem cells

Depletion length and space charge layer capacitance in doped semiconductor nanoshpere

International Nuclear Information System (INIS)

Nersesyan, S R; Petrosyan, S G

2012-01-01

The depletion length in a semiconductor nanosphere depends not only on the material parameters but on the nanosphere radius as well. For this reason, the depletion length does not present a universal characteristic length for all spherical interfaces. The difference from the standard flat model caused by the surface curvature is significant for a structure with the depletion length comparable to the radius of a nanosphere. We show that the depletion layer capacitance in a nanosphere becomes quite sensitive to the light intensity when, as a result of increasing optical generation rate, the surface potential barrier height is decreased and becomes very small. (paper)

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease.

Science.gov (United States)

Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

2017-01-01

To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae . Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae . Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

Comparison of Newly Assembled Full Length HIV-1 Integrase With Prototype Foamy Virus Integrase: Structure-Function Prospective.

Science.gov (United States)

Dayer, Mohammad Reza

2016-05-01

Drug design against human immunodeficiency virus type 1 (HIV-1) integrase through its mechanistic study is of great interest in the area in biological research. The main obstacle in this area is the absence of the full-length crystal structure for HIV-1 integrase to be used as a model. A complete structure, similar to HIV-1 of a prototype foamy virus integrase in complex with DNA, including all conservative residues, is available and has been extensively used in recent investigations. The aim of this study was to determine whether the above model is precisely representative of HIV-1 integrase. This would critically determine the success of any designed drug using the model in deactivation of integrase and AIDS treatment. Primarily, a new structure for HIV-1 was constructed, using a crystal structure of prototype foamy virus as the starting structure. The constructed structure of HIV-1 integrase was simultaneously simulated with a prototype foamy virus integrase on a separate occasion. Our results indicate that the HIV-1 system behaves differently from the prototype foamy virus in terms of folding, hydration, hydrophobicity of binding site and stability. Based on our findings, we can conclude that HIV-1 integrase is vastly different from the prototype foamy virus integrase and does not resemble it, and the modeling output of the prototype foamy virus simulations could not be simply generalized to HIV-1 integrase. Therefore, our HIV-1 model seems to be more representative and more useful for future research.

Sexual Dimorphism and Estimation of Height from Body Length Anthropometric Parameters among the Hausa Ethnic Group of Nigeria

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Jaafar Aliyu

2018-01-01

Full Text Available The study was carried out to investigate the sexual dimorphism in length and other anthropometric parameters. To also generate formulae for height estimation using anthropometric measurements of some length parameters among Hausa ethnic group of Kaduna State, Nigeria. A cross sectional study was conducted and a total of 500 subjects participated in this study which was mainly secondary school students between the age ranges of 16-27 years, anthropometric measurements were obtained using standard protocols. It was observed that there was significant sexual dimorphism in all the parameters except for body mass index. In all the parameters males tend to have significantly (P < 0.05 higher mean values except biaxillary distances. Height showed positive and strongest correlations with demispan length, followed by knee height, thigh length, sitting height, hand length, foot length, humeral length, forearm length and weight respectively. There were weak and positive correlations between height and neck length as well as biaxillary length. The demi span length showed the strongest correlation coefficient and low standard error of estimate indicating the strong estimation ability than other parameters. The combination of two parameters tends to give better estimations and low standard error of estimates, so also combining the three parameters gives better estimations with a lower standard error of estimates. The better correlation coefficient was also observed with the double and triple parameters respectively. Male Hausa tend to have larger body proportion compared to female. Height showed positive and strongest correlations with demispan length. Body length anthropometric proved to be useful in estimation of stature among Hausa ethnic group of Kaduna state Nigeria.

Distance and Cable Length Measurement System

Science.gov (United States)

Hernández, Sergio Elias; Acosta, Leopoldo; Toledo, Jonay

2009-01-01

A simple, economic and successful design for distance and cable length detection is presented. The measurement system is based on the continuous repetition of a pulse that endlessly travels along the distance to be detected. There is a pulse repeater at both ends of the distance or cable to be measured. The endless repetition of the pulse generates a frequency that varies almost inversely with the distance to be measured. The resolution and distance or cable length range could be adjusted by varying the repetition time delay introduced at both ends and the measurement time. With this design a distance can be measured with centimeter resolution using electronic system with microsecond resolution, simplifying classical time of flight designs which require electronics with picosecond resolution. This design was also applied to position measurement. PMID:22303169

The relationship of protein conservation and sequence length

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Panchenko Anna R

2002-11-01

Full Text Available Abstract Background In general, the length of a protein sequence is determined by its function and the wide variance in the lengths of an organism's proteins reflects the diversity of specific functional roles for these proteins. However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints. Results We performed sequence comparisons to distinguish highly conserved and poorly conserved proteins from the bacterium Escherichia coli, the archaeon Archaeoglobus fulgidus, and the eukaryotes Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. For all organisms studied, the conserved and nonconserved proteins have strikingly different length distributions. The conserved proteins are, on average, longer than the poorly conserved ones, and the length distributions for the poorly conserved proteins have a relatively narrow peak, in contrast to the conserved proteins whose lengths spread over a wider range of values. For the two prokaryotes studied, the poorly conserved proteins approximate the minimal length distribution expected for a diverse range of structural folds. Conclusions There is a relationship between protein conservation and sequence length. For all the organisms studied, there seems to be a significant evolutionary trend favoring shorter proteins in the absence of other, more specific functional constraints.

Influence of repair length on residual stress in the repair weld of a clad plate

International Nuclear Information System (INIS)

Jiang Wenchun; Xu, X.P.; Gong, J.M.; Tu, S.T.

2012-01-01

Highlights: ► Residual stress in the repair weld of a stainless steel clad plate is investigated. ► The effect of repair length on residual stress has been studied. ► Large tensile residual stress is generated in the repair weld and heat affected zone. ► With the increase of repair length, transverse stress is decreased. ► Repair length has little effect on longitudinal stress. - Abstract: A 3-D sequential coupling finite element simulation is performed to investigate the temperature field and residual stress in the repair weld of a stainless steel clad plate. The effect of repair length on residual stress has been studied, aiming to provide a reference for repairing the cracked clad plate. The results show that large tensile residual stresses are generated in the repair weld and heat affected zone (HAZ), and then decrease gradually away from the weld and HAZ. The residual stresses through thickness in the clad layer are relative uniform, while they are non-uniform in the base metal. A discontinuous stress distribution is generated across the interface between weld metal and base metal. The repair length has a great effect on transverse stress. With the increase of repair length, the transverse stress is decreased. When the repair length is increased to 14 cm, the peak of transverse stress has been decreased below yield strength, and the transverse stress in the weld and HAZ has also been greatly decreased. But the repair length has little effect on longitudinal stress.

The Length-Weight, Length-Length Relationship and Condition Factor of Angora Loach, Oxynoemacheilus angorae (Steindachner, 1897 Inhabiting Kılıçözü Stream in Kızılırmak River Basin (Central Anatolia-Turkey

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Okan Yazıcıoğlu

2016-12-01

Full Text Available In this study, length-weight relationship (LWR, length- length relationship (LLR and condition factor (K of Angora loach, Oxynoemacheilus angorae were determined. A total of 103 specimens were sampled from Kılıçözü Stream in 2014. The length and weight of specimens were ranged 3.5-9.8 cm and 0.38-6.58 g, respectively. Length-weight relationships for female, male and all samples were found as W= 0.01056.TL2.896 (r²= 0.923, W= 0.00963.TL2.940 (r²= 0.978 and W= 0.00987.TL2.929 (r²= 0.963, respectively. LWRs indicated an isometric growth in female, male and all samples. The values of Fulton’s condition factor (K ranged from 0.699 to 1.246 for females and from 0.654 to 1.072 for males. All length-length relationships were statistically significant.

CURVES AND AESTHETIC SURFACES GENERATED BY THE R-R-RTR MECHANISM

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Liliana LUCA

2013-05-01

Full Text Available Let’s consider a mechanism having two driving elements with revolving movements and a RTR dyad, with elements of null length and aesthetic tracks of a point are determined on a rod, for various linear movement laws of driving elements. The generated curves revolve around x and y axes and aesthetic surfaces result.

SURVIVAL ANALYSIS AND LENGTH-BIASED SAMPLING

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Masoud Asgharian

2010-12-01

Full Text Available When survival data are colleted as part of a prevalent cohort study, the recruited cases have already experienced their initiating event. These prevalent cases are then followed for a fixed period of time at the end of which the subjects will either have failed or have been censored. When interests lies in estimating the survival distribution, from onset, of subjects with the disease, one must take into account that the survival times of the cases in a prevalent cohort study are left truncated. When it is possible to assume that there has not been any epidemic of the disease over the past period of time that covers the onset times of the subjects, one may assume that the underlying incidence process that generates the initiating event times is a stationary Poisson process. Under such assumption, the survival times of the recruited subjects are called “lengthbiased”. I discuss the challenges one is faced with in analyzing these type of data. To address the theoretical aspects of the work, I present asymptotic results for the NPMLE of the length-biased as well as the unbiased survival distribution. I also discuss estimating the unbiased survival function using only the follow-up time. This addresses the case that the onset times are either unknown or known with uncertainty. Some of our most recent work and open questions will be presented. These include some aspects of analysis of covariates, strong approximation, functional LIL and density estimation under length-biased sampling with right censoring. The results will be illustrated with survival data from patients with dementia, collected as part of the Canadian Study of Health and Aging (CSHA.

Nonthermal Argon Plasma Generator and Some Potential Applications

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Bunoiu M.

2015-12-01

Full Text Available A laboratory - made nonthermal plasma generator is presented. It has a diameter of 0.020 m and length of 0.155 m and contains two electrodes. The first electrode is a 2% Th-W alloy, 0.002 m in diameter bar, centred inside the generator’s body by means of a four channel teflon piece; the other three channels, 0.003 m in diameter, are used for Ar supply. The second electrode is a nozzle of 0.002 m - 0.008 m diameter and 0.005m length. A ~500 kV/m electric field is generated between the two electrodes by a high frequency source (13.56 MHz ±5%, equipped with a OT-1000 (Tungsram power triode. For Ar flows ranging from 0.00008 m3/s to 0.00056 m3/s, a plasma jet of length not exceeding 0.015 m and temperature below 315 K is obtained. Anthurium andraeanumis sample , blood matrix, human hair and textile fibers may be introduced in the plasma jet. For time periods of 30 s and 60 s, various effects like, cell detexturization, fast blood coagulation or textile fiber or hair cleaning and smoothing are obtained. These effects are presented and discussed in the paper.

Low risk of inhibitor formation in haemophilia A patients following en masse switch in treatment to a third generation full length plasma and albumin-free recombinant factor VIII product (ADVATE®).

LENUS (Irish Health Repository)

Bacon, C L

2011-05-01

Previous studies have suggested that development of inhibitors in previously treated patients (PTPs) may be attributable to a switch in factor VIII (FVIII) therapeutic product. Consequently, it is widely recognized that inhibitor development must be assessed in PTPs following the introduction of any new FVIII product. Following a national tender process in 2006, all patients with haemophilia A in Ireland changed their FVIII treatment product en masse to a plasma and albumin-free recombinant full-length FVIII product (ADVATE(®)). In this study, we retrospectively reviewed the case records of Irish PTPs to evaluate risk of inhibitor formation following this treatment switch. One hundred and thirteen patients participated in the study. Most patients (89%) had severe haemophilia. Only one of 96 patients with no inhibitor history developed an inhibitor. Prior to the switch in his recombinant FVIII (rFVIII) treatment of choice, this child had only experienced three exposure days (EDs). Consequently, in total he had only received 6 EDs when his inhibitor was first diagnosed. In keeping with this lack of de novo inhibitor development, we observed no evidence of any recurrent inhibitor formation in any of 16 patients with previously documented inhibitors. Similarly, following a previous en masse switch, we have previously reported that changing from a Chinese hamster ovary cell-produced to a baby hamster kidney cell-produced rFVIII was also associated with a low risk of inhibitor formation in PTPs. Our cumulative findings from these two studies clearly emphasizes that the risk of inhibitor development for PTPs following changes in commercial rFVIII product is low, at least in the Irish population.

Transgenic Parasites Stably Expressing Full-Length Plasmodium falciparum Circumsporozoite Protein as a Model for Vaccine Down-Selection in Mice Using Sterile Protection as an Endpoint

Science.gov (United States)

Porter, Michael D.; Nicki, Jennifer; Pool, Christopher D.; DeBot, Margot; Illam, Ratish M.; Brando, Clara; Bozick, Brooke; De La Vega, Patricia; Angra, Divya; Spaccapelo, Roberta; Crisanti, Andrea; Murphy, Jittawadee R.; Bennett, Jason W.; Schwenk, Robert J.; Ockenhouse, Christian F.

2013-01-01

Circumsporozoite protein (CSP) of Plasmodium falciparum is a protective human malaria vaccine candidate. There is an urgent need for models that can rapidly down-select novel CSP-based vaccine candidates. In the present study, the mouse-mosquito transmission cycle of a transgenic Plasmodium berghei malaria parasite stably expressing a functional full-length P. falciparum CSP was optimized to consistently produce infective sporozoites for protection studies. A minimal sporozoite challenge dose was established, and protection was defined as the absence of blood-stage parasites 14 days after intravenous challenge. The specificity of protection was confirmed by vaccinating mice with multiple CSP constructs of differing lengths and compositions. Constructs that induced high NANP repeat-specific antibody titers in enzyme-linked immunosorbent assays were protective, and the degree of protection was dependent on the antigen dose. There was a positive correlation between antibody avidity and protection. The antibodies in the protected mice recognized the native CSP on the parasites and showed sporozoite invasion inhibitory activity. Passive transfer of anti-CSP antibodies into naive mice also induced protection. Thus, we have demonstrated the utility of a mouse efficacy model to down-select human CSP-based vaccine formulations. PMID:23536694

Potts ferromagnet correlation length in hypercubic lattices: Renormalization - group approach

International Nuclear Information System (INIS)

Curado, E.M.F.; Hauser, P.R.

1984-01-01

Through a real space renormalization group approach, the q-state Potts ferromagnet correlation length on hierarchical lattices is calculated. These hierarchical lattices are build in order to simulate hypercubic lattices. The high-and-low temperature correlation length asymptotic behaviours tend (in the Ising case) to the Bravais lattice correlation length ones when the size of the hierarchical lattice cells tends to infinity. It is conjectured that the asymptotic behaviours several values of q and d (dimensionality) so obtained are correct. Numerical results are obtained for the full temperature range of the correlation length. (Author) [pt

Body Weight Determination from Foot Outline Length among the Iban Population in Malaysia

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Hairunnisa Bt Mohd Anas K

2017-12-01

Full Text Available Foot impressions form a valuable physical evidence to solve crime. Foot impression measurements provide valuable information in estimating stature, weight, gender and age in crime scene investigation. In Asian countries, many people living in rural places walk without footwear. The aim of this research is to generate regression equations to determine living body weight from foot outline length among the Iban population of Malaysia. The study involved 200 (100 males, 100 females adult Ibans, mostly living in Sarawak, a state in   Malaysia. Following the standard procedure, the foot outlines were collected followed by body weight measurements and were recorded for analysis. The collected data were analysed with PASW 20 computer software. The correlation coefficient (R between the foot outline lengths and body weight was determined for males, females and pooled sample. Based on the foot outline and body weight, 30 regression equations were generated, 10 for males, 10 for females and 10 for pooled samples/unknown gender. The correlation coefficient (R values were positive and statistically significant. It is concluded that the present investigation provided regression equations to determine body weight from foot outline anthropometry. These equations can be used to determine body weight even when partial foot impressions are available at crime scenes.   Keywords: Forensic Science, Body Weight, Foot Outline, Iban Population, Malaysia

Domain-specific modeling enabling full code generation

CERN Document Server

Kelly, Steven

2007-01-01

Domain-Specific Modeling (DSM) is the latest approach tosoftware development, promising to greatly increase the speed andease of software creation. Early adopters of DSM have been enjoyingproductivity increases of 500–1000% in production for over adecade. This book introduces DSM and offers examples from variousfields to illustrate to experienced developers how DSM can improvesoftware development in their teams. Two authorities in the field explain what DSM is, why it works,and how to successfully create and use a DSM solution to improveproductivity and quality. Divided into four parts, the book covers:background and motivation; fundamentals; in-depth examples; andcreating DSM solutions. There is an emphasis throughout the book onpractical guidelines for implementing DSM, including how toidentify the nece sary language constructs, how to generate fullcode from models, and how to provide tool support for a new DSMlanguage. The example cases described in the book are available thebook's Website, www.dsmbook....

Telomere Length – a New Biomarker in Medicine

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Agnieszka Kozłowska

2015-12-01

Full Text Available A number of xenobiotics in the environment and workplace influences on our health and life. Biomarkers are tools for measuring such exposures and their effects in the organism. Nowadays, telomere length, epigenetic changes, mutations and changes in gene expression pattern have become new molecular biomarkers. Telomeres play the role of molecular clock, which influences on expectancy of cell life and thus aging, the formation of damages, development diseases and carcinogenesis. The telomere length depends on mechanisms of replication and the activity of telomerase. Telomere length is currently used as a biomarker of susceptibility and/or exposure. This paper describes the role of telomere length as a biomarker of aging cells, oxidative stress, a marker of many diseases including cancer, and as a marker of environmental and occupational exposure.

The X-ray Crystal Structure of Full-Length Human Plasminogen

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Ruby H.P. Law

2012-03-01

Full Text Available Plasminogen is the proenzyme precursor of the primary fibrinolytic protease plasmin. Circulating plasminogen, which comprises a Pan-apple (PAp domain, five kringle domains (KR1-5, and a serine protease (SP domain, adopts a closed, activation-resistant conformation. The kringle domains mediate interactions with fibrin clots and cell-surface receptors. These interactions trigger plasminogen to adopt an open form that can be cleaved and converted to plasmin by tissue-type and urokinase-type plasminogen activators. Here, the structure of closed plasminogen reveals that the PAp and SP domains, together with chloride ions, maintain the closed conformation through interactions with the kringle array. Differences in glycosylation alter the position of KR3, although in all structures the loop cleaved by plasminogen activators is inaccessible. The ligand-binding site of KR1 is exposed and likely governs proenzyme recruitment to targets. Furthermore, analysis of our structure suggests that KR5 peeling away from the PAp domain may initiate plasminogen conformational change.

Full scale demonstration of air-purifying pavement

NARCIS (Netherlands)

Ballari, M.; Brouwers, H.J.H.

2013-01-01

Experiments concerning a full-scale demonstration of air purifying pavement in Hengelo, The Netherlands, are reported. The full width of the street was provided with concrete pavement containing TiO2 over a length of 150 m ("DeNOx street"). Another part of the street, about 100 m, was paved with

Joint source-channel coding using variable length codes

NARCIS (Netherlands)

Balakirsky, V.B.

2001-01-01

We address the problem of joint source-channel coding when variable-length codes are used for information transmission over a discrete memoryless channel. Data transmitted over the channel are interpreted as pairs (m k ,t k ), where m k is a message generated by the source and t k is a time instant

Full Length R esearch A rticle

African Journals Online (AJOL)

Germ tube tests were performed for identification of the isolates. Susceptibility ... agents for the treatment of genitourinary tract infections caused by Candida species. Keywords: ..... contraceptives, drug abuse or even due to sexual promiscuity.

A Fault-Tolerant Parallel Structure of Single-Phase Full-Bridge Rectifiers for a Wound-Field Doubly Salient Generator

DEFF Research Database (Denmark)

Chen, Zhihui; Chen, Ran; Chen, Zhe

2013-01-01

The fault-tolerance design is widely adopted for high-reliability applications. In this paper, a parallel structure of single-phase full-bridge rectifiers (FBRs) (PS-SPFBR) is proposed for a wound-field doubly salient generator. The analysis shows the potential fault-tolerance capability of the PS...

Blue light-excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis.

Science.gov (United States)

Oide, Mao; Okajima, Koji; Nakagami, Hirofumi; Kato, Takayuki; Sekiguchi, Yuki; Oroguchi, Tomotaka; Hikima, Takaaki; Yamamoto, Masaki; Nakasako, Masayoshi

2018-01-19

Phototropin2 (phot2) is a blue-light (BL) receptor that regulates BL-dependent activities for efficient photosynthesis in plants. phot2 comprises two BL-receiving light-oxygen-voltage-sensing domains (LOV1 and LOV2) and a kinase domain. BL-excited LOV2 is thought to be primarily responsible for the BL-dependent activation of the kinase. However, the molecular mechanisms by which small BL-induced conformational changes in the LOV2 domain are transmitted to the kinase remain unclear. Here, we used full-length wild-type and mutant phot2 proteins from Arabidopsis to study their molecular properties in the dark and under BL irradiation. Phosphorylation assays and absorption measurements indicated that the LOV1 domain assists the thermal relaxation of BL-excited LOV2 and vice versa. Using small-angle X-ray scattering and electron microscopy, we observed that phot2 forms a dimer and has a rod shape with a maximum length of 188 Å and a radius of gyration of 44 Å. Under BL, phot2 displayed large conformational changes that bent the rod shape. By superimposing the crystal structures of the LOV1 dimer, LOV2, and a homology model of the kinase to the observed changes, we inferred that the BL-dependent change consisted of positional shifts of both LOV2 and the kinase relative to LOV1. Furthermore, phot2 mutants lacking the photocycle in LOV1 or LOV2 still exhibited conformational changes under BL, suggesting that LOV1 and LOV2 cooperatively contribute to the conformational changes that activate the kinase. These results suggest that BL-activated LOV1 contributes to the kinase activity of phot2. We discuss the possible intramolecular interactions and signaling mechanisms in phot2. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Tube Length and Water Flow

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Ben Ruktantichoke

2011-06-01

Full Text Available In this study water flowed through a straight horizontal plastic tube placed at the bottom of a large tank of water. The effect of changing the length of tubing on the velocity of flow was investigated. It was found that the Hagen-Poiseuille Equation is valid when the effect of water entering the tube is accounted for.

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

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Kedzierska Anna M

2012-08-01

Full Text Available Abstract Background A number of software packages are available to generate DNA multiple sequence alignments (MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages. Results We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site, the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. Conclusion The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.

ASC-J9 Suppresses Castration-Resistant Prostate Cancer Growth through Degradation of Full-length and Splice Variant Androgen Receptors

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Shinichi Yamashita

2012-01-01

Full Text Available Early studies suggested androgen receptor (AR splice variants might contribute to the progression of prostate cancer (PCa into castration resistance. However, the therapeutic strategy to target these AR splice variants still remains unresolved. Through tissue survey of tumors from the same patients before and after castration resistance, we found that the expression of AR3, a major AR splice variant that lacks the AR ligand-binding domain, was substantially increased after castration resistance development. The currently used antiandrogen, Casodex, showed little growth suppression in CWR22Rv1 cells. Importantly, we found that AR degradation enhancer ASC-J9 could degrade both full-length (fAR and AR3 in CWR22Rv1 cells as well as in C4-2 and C81 cells with addition of AR3. The consequences of such degradation of both fAR and AR3 might then result in the inhibition of AR transcriptional activity and cell growth in vitro. More importantly, suppression of AR3 specifically by short-hairpin AR3 or degradation of AR3 by ASC-J9 resulted in suppression of AR transcriptional activity and cell growth in CWR22Rv1-fARKD (fAR knockdown cells in which DHT failed to induce, suggesting the importance of targeting AR3. Finally, we demonstrated the in vivo therapeutic effects of ASC-J9 by showing the inhibition of PCa growth using the xenografted model of CWR22Rv1 cells orthotopically implanted into castrated nude mice with undetectable serum testosterone. These results suggested that targeting both fAR- and AR3-mediated PCa growth by ASC-J9 may represent the novel therapeutic approach to suppress castration-resistant PCa. Successful clinical trials targeting both fAR and AR3 may help us to battle castration-resistant PCa in the future.

Estimation of genetic variability and selection response for clutch length in dwarf brown-egg layers carrying or not the naked neck gene

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Tixier-Boichard Michèle

2003-03-01

Full Text Available Abstract In order to investigate the possibility of using the dwarf gene for egg production, two dwarf brown-egg laying lines were selected for 16 generations on average clutch length; one line (L1 was normally feathered and the other (L2 was homozygous for the naked neck gene NA. A control line from the same base population, dwarf and segregating for the NA gene, was maintained during the selection experiment under random mating. The average clutch length was normalized using a Box-Cox transformation. Genetic variability and selection response were estimated either with the mixed model methodology, or with the classical methods for calculating genetic gain, as the deviation from the control line, and the realized heritability, as the ratio of the selection response on cumulative selection differentials. Heritability of average clutch length was estimated to be 0.42 ± 0.02, with a multiple trait animal model, whereas the estimates of the realized heritability were lower, being 0.28 and 0.22 in lines L1 and L2, respectively. REML estimates of heritability were found to decline with generations of selection, suggesting a departure from the infinitesimal model, either because a limited number of genes was involved, or their frequencies were changed. The yearly genetic gains in average clutch length, after normalization, were estimated to be 0.37 ± 0.02 and 0.33 ± 0.04 with the classical methods, 0.46 ± 0.02 and 0.43 ± 0.01 with animal model methodology, for lines L1 and L2 respectively, which represented about 30% of the genetic standard deviation on the transformed scale. Selection response appeared to be faster in line L2, homozygous for the NA gene, but the final cumulated selection response for clutch length was not different between the L1 and L2 lines at generation 16.

Length of a Hanging Cable

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Eric Costello

2011-01-01

Full Text Available The shape of a cable hanging under its own weight and uniform horizontal tension between two power poles is a catenary. The catenary is a curve which has an equation defined by a hyperbolic cosine function and a scaling factor. The scaling factor for power cables hanging under their own weight is equal to the horizontal tension on the cable divided by the weight of the cable. Both of these values are unknown for this problem. Newton's method was used to approximate the scaling factor and the arc length function to determine the length of the cable. A script was written using the Python programming language in order to quickly perform several iterations of Newton's method to get a good approximation for the scaling factor.

Paediatric renal length measurements from ultrasound and DMSA scans: does clinical practice reflect theoretical normal values?

International Nuclear Information System (INIS)

Que, L.; Rutland, M.D.; Hassan, I.M.

1999-01-01

Full text: Renal length measurement is a routine part of ultrasound examination in children and those results are plotted on a normogram style graph, so that each child's results are compared to a normal range (mean ± 2 S.D.). Renal length measurements from the posterior oblique views of dimercaptosuccinic acid (DMSA) scans in our department have not always correlated well with the ultrasound measurements on the same patients. Renal lengths from the DMSA scans of 120 patients with apparently normal kidneys were recorded and used to generate a normogram of renal length at different ages (0.5-7 years). This DMSA normogram was compared to the ultrasound (US) normogram used in the Paediatric Radiology Department, and it showed slight differences in renal lengths (3-8 mm), but that the US normogram had smaller coefficients of variation (US = 6.6%, NM 8.3%), implying a 'tighter' normal range. 39 of these patients had DMSA and ultrasound measurements of renal length within 3 months, and these were studied first by calculating the mean and CV values for different age groups, and then by plotting individual renal lengths on the appropriate normograms. The measured data produced much greater variability in the ultrasound measurements than the DTPA measurements, and the individual points produced 4/78 (5.1%) abnormal results for DMSA, but 21/78 (26.9%) abnormal results for ultrasound. Thus, in routine clinical use, using patients with apparently normal kidneys, ultrasound was unable to match the 'normal range' set by their current normogram, but the nuclear medicine showed 5.1% of values outside the normal (DMSA) range, which was completely appropriate for a range of ± 2 standard deviations

Progress in Long Scale Length Laser-Plasma Interactions

International Nuclear Information System (INIS)

Glenzer, S H; Arnold, P; Bardsley, G; Berger, R L; Bonanno, G; Borger, T; Bower, D E; Bowers, M; Bryant, R; Buckman, S.; Burkhart, S C; Campbell, K; Chrisp, M P; Cohen, B I; Constantin, G; Cooper, F; Cox, J; Dewald, E; Divol, L; Dixit, S; Duncan, J; Eder, D; Edwards, J; Erbert, G; Felker, B; Fornes, J; Frieders, G; Froula, D H; Gardner, S D; Gates, C; Gonzalez, M; Grace, S; Gregori, G; Greenwood, A; Griffith, R; Hall, T; Hammel, B A; Haynam, C; Heestand, G; Henesian, M; Hermes, G; Hinkel, D; Holder, J; Holdner, F; Holtmeier, G; Hsing, W; Huber, S; James, T; Johnson, S; Jones, O S; Kalantar, D; Kamperschroer, J H; Kauffman, R; Kelleher, T; Knight, J; Kirkwood, R K; Kruer, W L; Labiak, W; Landen, O L; Langdon, A B; Langer, S; Latray, D; Lee, A; Lee, F D; Lund, D; MacGowan, B; Marshall, S; McBride, J; McCarville, T; McGrew, L; Mackinnon, A J; Mahavandi, S; Manes, K; Marshall, C; Mertens, E; Meezan, N; Miller, G; Montelongo, S; Moody, J D; Moses, E; Munro, D; Murray, J; Neumann, J; Newton, M; Ng, E; Niemann, C; Nikitin, A; Opsahl, P; Padilla, E; Parham, T; Parrish, G; Petty, C; Polk, M; Powell, C; Reinbachs, I; Rekow, V; Rinnert, R; Riordan, B; Rhodes, M.

2003-01-01

The first experiments on the National Ignition Facility (NIF) have employed the first four beams to measure propagation and laser backscattering losses in large ignition-size plasmas. Gas-filled targets between 2 mm and 7 mm length have been heated from one side by overlapping the focal spots of the four beams from one quad operated at 351 nm (3ω) with a total intensity of 2 x 10 15 W cm -2 . The targets were filled with 1 atm of CO 2 producing of up to 7 mm long homogeneously heated plasmas with densities of n e = 6 x 10 20 cm -3 and temperatures of T e = 2 keV. The high energy in a NIF quad of beams of 16kJ, illuminating the target from one direction, creates unique conditions for the study of laser plasma interactions at scale lengths not previously accessible. The propagation through the large-scale plasma was measured with a gated x-ray imager that was filtered for 3.5 keV x rays. These data indicate that the beams interact with the full length of this ignition-scale plasma during the last ∼1 ns of the experiment. During that time, the full aperture measurements of the stimulated Brillouin scattering and stimulated Raman scattering show scattering into the four focusing lenses of 6% for the smallest length (∼2 mm). increasing to 12% for ∼7 mm. These results demonstrate the NIF experimental capabilities and further provide a benchmark for three-dimensional modeling of the laser-plasma interactions at ignition-size scale lengths

CEPF Western Ghats Special Series: Length-weight and length-length relationship of three species of snakehead fish, Channa diplogramma, C. marulius and C. striata from the riverine reaches of Lake Vembanad, Kerala, India.

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A. Ali

2013-09-01

Full Text Available The length-weight relationship (LWR and length-length relationships (LLR of three snakehead fishes, Channa diplogramma, C. marulius and C. striata, exploited by small-scale fishers in the riverine reaches of Lake Vembanad, Kerala were studied using the allometric growth equation Y = aXb. Our analysis shows that the LWR of C. diplogramma and C. marulius is nonisometric with exponents much smaller than the cubic value (b = 3, while that of C. striata is isometric. Channa marulius showed a definite change in LWR with size, with smaller fish growing with positive allometric exponents (b greater than 3 and larger individuals having negative allometric relationship (b less than 3, indicating a possible age-related change in growth pattern. In the case of LLR, all three snakehead species showed non-isometric growth patterns. The caudal fin did not grow substantially with increasing fish length.

Cycle length maximization in PWRs using empirical core models

International Nuclear Information System (INIS)

Okafor, K.C.; Aldemir, T.

1987-01-01

The problem of maximizing cycle length in nuclear reactors through optimal fuel and poison management has been addressed by many investigators. An often-used neutronic modeling technique is to find correlations between the state and control variables to describe the response of the core to changes in the control variables. In this study, a set of linear correlations, generated by two-dimensional diffusion-depletion calculations, is used to find the enrichment distribution that maximizes cycle length for the initial core of a pressurized water reactor (PWR). These correlations (a) incorporate the effect of composition changes in all the control zones on a given fuel assembly and (b) are valid for a given range of control variables. The advantage of using such correlations is that the cycle length maximization problem can be reduced to a linear programming problem

PRIMITIVE MATRICES AND GENERATORS OF PSEUDO RANDOM SEQUENCES OF GALOIS

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A. Beletsky

2014-04-01

Full Text Available In theory and practice of information cryptographic protection one of the key problems is the forming a binary pseudo-random sequences (PRS with a maximum length with acceptable statistical characteristics. PRS generators are usually implemented by linear shift register (LSR of maximum period with linear feedback [1]. In this paper we extend the concept of LSR, assuming that each of its rank (memory cell can be in one of the following condition. Let’s call such registers “generalized linear shift register.” The research goal is to develop algorithms for constructing Galois and Fibonacci generalized matrix of n-order over the field , which uniquely determined both the structure of corresponding generalized of n-order LSR maximal period, and formed on their basis Galois PRS generators of maximum length. Thus the article presents the questions of formation the primitive generalized Fibonacci and Galois arbitrary order matrix over the prime field . The synthesis of matrices is based on the use of irreducible polynomials of degree and primitive elements of the extended field generated by polynomial. The constructing methods of Galois and Fibonacci conjugated primitive matrices are suggested. The using possibilities of such matrices in solving the problem of constructing generalized generators of Galois pseudo-random sequences are discussed.

discouraged by queue length

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P. R. Parthasarathy

2001-01-01

Full Text Available The transient solution is obtained analytically using continued fractions for a state-dependent birth-death queue in which potential customers are discouraged by the queue length. This queueing system is then compared with the well-known infinite server queueing system which has the same steady state solution as the model under consideration, whereas their transient solutions are different. A natural measure of speed of convergence of the mean number in the system to its stationarity is also computed.

A New Concept of Full Employment

NARCIS (Netherlands)

Delsen, L.W.M.

1997-01-01

The target of full employment depends upon the goals regarding labour force participation rates, the length of the work week and frictional unemployment. Although nearly all social groups agree that stronger economic growth would contribute most to solving the unemployment problem, the prospects for

pEVL: A Linear Plasmid for Generating mRNA IVT Templates With Extended Encoded Poly(A Sequences

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Alexandra E Grier

2016-01-01

Full Text Available Increasing demand for large-scale synthesis of in vitro transcribed (IVT mRNA is being driven by the increasing use of mRNA for transient gene expression in cell engineering and therapeutic applications. An important determinant of IVT mRNA potency is the 3′ polyadenosine (poly(A tail, the length of which correlates with translational efficiency. However, present methods for generation of IVT mRNA rely on templates derived from circular plasmids or PCR products, in which homopolymeric tracts are unstable, thus limiting encoded poly(A tail lengths to ≃120 base pairs (bp. Here, we have developed a novel method for generation of extended poly(A tracts using a previously described linear plasmid system, pJazz. We find that linear plasmids can successfully propagate poly(A tracts up to ≃500 bp in length for IVT mRNA production. We then modified pJazz by removing extraneous restriction sites, adding a T7 promoter sequence upstream from an extended multiple cloning site, and adding a unique type-IIS restriction site downstream from the encoded poly(A tract to facilitate generation of IVT mRNA with precisely defined encoded poly(A tracts and 3′ termini. The resulting plasmid, designated pEVL, can be used to generate IVT mRNA with consistent defined lengths and terminal residue(s.

Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.).

Science.gov (United States)

Koning-Boucoiran, Carole F S; Esselink, G Danny; Vukosavljev, Mirjana; van 't Westende, Wendy P C; Gitonga, Virginia W; Krens, Frans A; Voorrips, Roeland E; van de Weg, W Eric; Schulz, Dietmar; Debener, Thomas; Maliepaard, Chris; Arens, Paul; Smulders, Marinus J M

2015-01-01

In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.

Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale

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Liu He

2017-10-01

Full Text Available Dendrobium officinale is an extremely valuable orchid used in traditional Chinese medicine, so sought after that it has a higher market value than gold. Although the expression profiles of some genes involved in the polysaccharide synthesis have previously been investigated, little research has been carried out on their alternatively spliced isoforms in D. officinale. In addition, information regarding the translocation of sugars from leaves to stems in D. officinale also remains limited. We analyzed the polysaccharide content of D. officinale leaves and stems, and completed in-depth transcriptome sequencing of these two diverse tissue types using second-generation sequencing (SGS and single-molecule real-time (SMRT sequencing technology. The results of this study yielded a digital inventory of gene and mRNA isoform expressions. A comparative analysis of both transcriptomes uncovered a total of 1414 differentially expressed genes, including 844 that were up-regulated and 570 that were down-regulated in stems. Of these genes, one sugars will eventually be exported transporter (SWEET and one sucrose transporter (SUT are expressed to a greater extent in D. officinale stems than in leaves. Two glycosyltransferase (GT and four cellulose synthase (Ces genes undergo a distinct degree of alternative splicing. In the stems, the content of polysaccharides is twice as much as that in the leaves. The differentially expressed GT and transcription factor (TF genes will be the focus of further study. The genes DoSWEET4 and DoSUT1 are significantly expressed in the stem, and are likely to be involved in sugar loading in the phloem.

Minimal Length Scale Scenarios for Quantum Gravity

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Sabine Hossenfelder

2013-01-01

Full Text Available We review the question of whether the fundamental laws of nature limit our ability to probe arbitrarily short distances. First, we examine what insights can be gained from thought experiments for probes of shortest distances, and summarize what can be learned from different approaches to a theory of quantum gravity. Then we discuss some models that have been developed to implement a minimal length scale in quantum mechanics and quantum field theory. These models have entered the literature as the generalized uncertainty principle or the modified dispersion relation, and have allowed the study of the effects of a minimal length scale in quantum mechanics, quantum electrodynamics, thermodynamics, black-hole physics and cosmology. Finally, we touch upon the question of ways to circumvent the manifestation of a minimal length scale in short-distance physics.

The Length of Maternity Leave and Family Health

OpenAIRE

Beuchert, Louise Voldby; Humlum, Maria Knoth; Vejlin, Rune Majlund

2014-01-01

We study the relationship between the length of maternity leave and the physical and psychological health of the family. Using a reform of the parental leave scheme in Denmark that increased the number of weeks of leave with full benefit compensation,we estimate the effect of the length of maternity leave on a range of health indicators including the number of hospital admissions for both mother and child and the probability of the mother receiving antidepressants. The reform led to an increa...

Full-duplex radio-over-fiber system with tunable millimeter-wave signal generation and wavelength reuse for upstream signal.

Science.gov (United States)

Wang, Yiqun; Pei, Li; Li, Jing; Li, Yueqin

2017-06-10

A full-duplex radio-over-fiber system is proposed, which provides both the generation of a millimeter-wave (mm-wave) signal with tunable frequency multiplication factors (FMFs) and wavelength reuse for uplink data. A dual-driving Mach-Zehnder modulator and a phase modulator are cascaded to form an optical frequency comb. An acousto-optic tunable filter based on a uniform fiber Bragg grating (FBG-AOTF) is employed to select three target optical sidebands. Two symmetrical sidebands are chosen to generate mm waves with tunable FMFs up to 16, which can be adjusted by changing the frequency of the applied acoustic wave. The optical carrier is reused at the base station for uplink connection. FBG-AOTFs driven by two acoustic wave signals are experimentally fabricated and further applied in the proposed scheme. Results of the research indicate that the 2-Gbit/s data can be successfully transmitted over a 25-km single-mode fiber for bidirectional full-duplex channels with power penalty of less than 2.6 dB. The feasibility of the proposed scheme is verified by detailed simulations and partial experiments.

On the calculation of length scales for turbulent heat transfer correlation

Energy Technology Data Exchange (ETDEWEB)

Barrett, M.J.; Hollingsworth, D.K.

1999-07-01

Turbulence length scale calculation methods were critically reviewed for their usefulness in boundary layer heat transfer correlations. Merits and deficiencies in each calculation method were presented. A rigorous method for calculating an energy-based integral scale was introduced. The method uses the variance of the streamwise velocity and a measured dissipation spectrum to calculate the length scale. Advantages and disadvantages of the new method were discussed. A principal advantage is the capability to decisively calculate length scales in a low-Reynolds-number turbulent boundary layer. The calculation method was tested with data from grid-generated, free-shear-layer, and wall-bounded turbulence. In each case, the method proved successful. The length scale is well behaved in turbulent boundary layers with momentum thickness Reynolds numbers from 400 to 2,100 and in flows with turbulent Reynolds numbers as low as 90.

The additive congruential random number generator--A special case of a multiple recursive generator

Science.gov (United States)

Wikramaratna, Roy S.

2008-07-01

This paper considers an approach to generating uniformly distributed pseudo-random numbers which works well in serial applications but which also appears particularly well-suited for application on parallel processing systems. Additive Congruential Random Number (ACORN) generators are straightforward to implement for arbitrarily large order and modulus; if implemented using integer arithmetic, it becomes possible to generate identical sequences on any machine. Previously published theoretical analysis has demonstrated that a kth order ACORN sequence approximates to being uniformly distributed in up to k dimensions, for any given k. ACORN generators can be constructed to give period lengths exceeding any given number (for example, with period length in excess of 230p, for any given p). Results of empirical tests have demonstrated that, if p is greater than or equal to 2, then the ACORN generator can be used successfully for generating double precision uniform random variates. This paper demonstrates that an ACORN generator is a particular case of a multiple recursive generator (and, therefore, also a special case of a matrix generator). Both these latter approaches have been widely studied, and it is to be hoped that the results given in the present paper will lead to greater confidence in using the ACORN generators.

Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains.

Science.gov (United States)

Trémeaux, P; Caporossi, A; Ramière, C; Santoni, E; Tarbouriech, N; Thélu, M-A; Fusillier, K; Geneletti, L; François, O; Leroy, V; Burmeister, W P; André, P; Morand, P; Larrat, S

2016-05-01

Directly acting antiviral drugs have contributed considerable progress to hepatitis C virus (HCV) treatment, but they show variable activity depending on virus genotypes and subtypes. Therefore, accurate genotyping including recombinant form detection is still of major importance, as is the detection of resistance-associated mutations in case of therapeutic failure. To meet these goals, an approach to amplify the HCV near-complete genome with a single long-range PCR and sequence it with Roche GS Junior was developed. After optimization, the overall amplification success rate was 73% for usual genotypes (i.e. HCV 1a, 1b, 3a and 4a, 16/22) and 45% for recombinant forms RF_2k/1b (5/11). After pyrosequencing and subsequent de novo assembly, a near-full-length genomic consensus sequence was obtained for 19 of 21 samples. The genotype and subtype were confirmed by phylogenetic analysis for every sample, including the suspected recombinant forms. Resistance-associated mutations were detected in seven of 13 samples at baseline, in the NS3 (n = 3) or NS5A (n = 4) region. Of these samples, the treatment of one patient included daclatasvir, and that patient experienced a relapse. Virus sequences from pre- and posttreatment samples of four patients who experienced relapse after sofosbuvir-based therapy were compared: the selected variants seem too far from the NS5B catalytic site to be held responsible. Although tested on a limited set of samples and with technical improvements still necessary, this assay has proven to be successful for both genotyping and resistance-associated variant detection on several HCV types. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

FULL-LENGTH PEPTIDE ASSAY OF ANTIGENIC PROFILE OF ENVELOPE PROTEINS FROM SIBERIAN ISOLATES OF HEPATITIS C VIRUS

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A. A. Grazhdantseva

2010-01-01

Full Text Available Antigenic profiles of envelope glycoproteins of hepatitis C virus presented by three genotypes 1b, 2a/2c and 3a, which are most widespread in the territory of Russia and, in particular, in Novosibirsk, were studied using a panel of overlapping synthetic peptides. It was shown that highly immunogenic peptide epitopes of Е1 and Е2 proteins common for all HCV genotypes, are located in amino acid positions 250-260, 315-325 (Е1 protein, 390-400 (hypervariable region 1, 430-440, and 680-690 (Е2 protein. The greatest inter-genotypic differences were recorded in positions 280-290, 410-430 and 520-540. A novel antigenic determinant was detected in the region of aa 280-290 of the Е1 protein which was typical only for HCV 2a/2c genotype. A broad variation in the boundaries for the most epitopes suggests a high variability of the Е1 and Е2 viral proteins; however, a similar repertoire of antibodies induced by different HCV genotypes indicates to an opportunity of designing a new generation of cross-reactive HCV vaccines based on mapping of the E1 and E2 antigenic regions.

CFD prediction of mixing in a steam generator mock-up: Comparison between full geometry and porous medium approaches

International Nuclear Information System (INIS)

Dehbi, A.; Badreddine, H.

2013-01-01

Highlights: • CFD is used to simulate single phase mixing in a model steam generator. • Motive of the work is to compare porous media approach with full geometry representation of tubes. • Porous media approach is found to compare favorably with full representation in steady states. - Abstract: In CFD simulations of single phase flow mixing in a steam generator (SG) during a station blackout severe accident, one is faced with the problem of representing the thousands of SG U-tubes. Typically simplifications are made to render the problem computationally tractable. In particular, one or a number of tubes are lumped in one volume that is treated as a single porous medium which replicates the pressure loss and heat transfer characteristics of the real tube. This approach significantly reduces the computational size of the problem and hence simulation time. In this work, we endeavor to investigate the adequacy of this approach by performing a series of simulations. We first validate the porous medium approach against results of the 1/7th scale Westinghouse SG-S3 test. In a second step, we make two separate simulations of flow in the PSI SG mock-up, i.e. one in which the porous medium model is used for the tube bundle, and another in which the full geometry is represented. In all simulations, the Reynolds Stress (RSM) model of turbulence is used. We show that in steady state conditions, the porous medium treatment yields results which are comparable to those of the full geometry representation (temperature distribution, recirculation ratio, hot plume spread, etc.). Hence, the porous medium approach can be extended with a good degree of confidence to model single phase mixing in the full scale SG

Use of Full-Length Recombinant Calflagin and Its C Fragment for Improvement of Diagnosis of Trypanosoma cruzi Infection†

Science.gov (United States)

Marcipar, Iván S.; Roodveldt, Cintia; Corradi, Gerardo; Cabeza, María L.; Brito, Maria Edileuza F.; Winter, Lucile M. Floeter; Marcipar, Alberto J.; Silber, Ariel M.

2005-01-01

Serological diagnosis of Trypanosoma cruzi infection is hampered by issues related to test specificity due to the cross-reactivity of most antigens with proteins of related parasites such as Leishmania spp. The recombinant calflagins are considered relevant antigens for the diagnosis of infection by Trypanosoma cruzi. In the present work, we describe two genes coding for putative calflagins in Leishmania major with the N-terminal moieties presenting high similarity with T. cruzi genes. This fact raised questions about their role in some cross-recognition of this antigen by sera from Leishmania spp.-infected individuals. The complete T. cruzi calflagin and two fragments of the protein, consisting of 146 amino acids of the N-terminal and 65 amino acids of the C-terminal regions, were expressed and evaluated against a panel of sera, which included well-characterized samples from T. cruzi, and Leishmania-infected patients. We were able to show that sera from Leishmania (Viannia) braziliensis-infected individuals recognized the recombinant full-length calflagin. Both the N-terminal and the complete protein presented the same high sensitivity (98.5% of sera from T. cruzi-infected patients was detected) but different specificities (94% and 98%, respectively, when evaluated against sera from people not infected by T. cruzi, including 15 sera from people infected with L. braziliensis). The C-terminal fragment presented low sensitivity (70%) but 100% specificity. We propose the use of these antigens in two sequential assays to optimize the serological diagnosis of T. cruzi infection in humans in geographic areas where Leishmania spp. infection is coendemic. PMID:16272476

A simple strategy for the purification of native recombinant full-length human RPL10 protein from inclusion bodies.

Science.gov (United States)

Pereira, Larissa M; Silva, Luana R; Alves, Joseane F; Marin, Nélida; Silva, Flavio Sousa; Morganti, Ligia; Silva, Ismael D C G; Affonso, Regina

2014-09-01

The L10 ribosomal protein (RPL10) plays a role in the binding of the 60 S and 40 S ribosomal subunits and in mRNA translation. The evidence indicates that RPL10 also has multiple extra-ribosomal functions, including tumor suppression. Recently, the presence of RPL10 in prostate and ovarian cancers was evaluated, and it was demonstrated to be associated with autistic disorders and premature ovarian failure. In the present work, we successfully cloned and expressed full-length human RPL10 (hRPL10) protein and isolated inclusion bodies containing this protein that had formed under mild growth conditions. The culture produced 376mg of hRPL10 protein per liter of induced bacterial culture, of which 102.4mg was present in the soluble fraction, and 25.6mg was recovered at approximately 94% purity. These results were obtained using a two-step process of non-denaturing protein extraction from pelleted inclusion bodies. We studied the characteristics of this protein using circular dichroism spectroscopy and by monitoring the changes induced by the presence or absence of zinc ions using fluorescence spectrometry. The results demonstrated that the protein obtained using these non-conventional methods retained its secondary and tertiary structure. The conformational changes induced by the incorporation of zinc suggested that this protein could interact with Jun or the SH3 domain of c-yes. The results suggested that the strategy used to obtain hRPL10 is simple and could be applied to obtaining other proteins that are susceptible to degradation. Copyright © 2014 Elsevier Inc. All rights reserved.

Generation of Recombinant Ebola Viruses Using Reverse Genetics.

Science.gov (United States)

Groseth, Allison

2017-01-01

Reverse genetics systems encompass a wide array of tools aimed at recapitulating some or all of the virus life cycle. In their most complete form, full-length clone systems allow us to use plasmid-encoded versions of the ribonucleoprotein (RNP) components to initiate the transcription and replication of a plasmid-encoded version of the complete viral genome, thereby initiating the complete virus life cycle and resulting in infectious virus. As such this approach is ideal for the generation of tailor-made recombinant filoviruses, which can be used to study virus biology. In addition, the generation of tagged and particularly fluorescent or luminescent viruses can be applied as tools for both diagnostic applications and for screening to identify novel countermeasures. Here we describe the generation and basic characterization of recombinant Ebola viruses rescued from cloned cDNA using a T7-driven system.

Itinerary planning: Modelling cruise lines’ lengths of stay in ports

NARCIS (Netherlands)

Chen, Jamie M.; Nijkamp, Peter

Cruise tourism is a fast-growing segment of the tourism industry that generates substantial benefits to port cities. This study explores strategic aspects of cruise lines’ itinerary planning, and models the determinants of their lengths of stay in ports, based on extensive observations of network

Short fetal leukocyte telomere length and preterm prelabor rupture of the membranes.

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Ramkumar Menon

Full Text Available BACKGROUND: Rupture of the fetal membranes is a common harbinger of imminent labor and delivery. Telomere shortening is a surrogate for oxidative stress (OS and senescence. Fetal leukocyte and placental membrane DNA telomere lengths were evaluated to determine their association with preterm prelabor rupture of the membranes (pPROM or spontaneous preterm births with intact membranes (PTB, compared to term birth. METHODS: Telomere lengths were quantified in cord blood leukocytes (n = 133 from three major groups: 1 pPROM (n = 28, 2 PTB (n = 69 and 3 uncomplicated full term births (controls, n = 35, using real-time quantitative PCR. Placental membrane specimens (n = 18 were used to correlate fetal leukocyte and placental telomere lengths. Telomere length differences among the groups were analyzed by ANOVA. Pearson correlation coefficients determined relationships between leukocyte and placental membrane telomere lengths. RESULTS: In pregnancies with intact membranes, fetal leukocyte telomere length was inversely proportional to gestational age. The mean telomere length decreased as gestation progressed, with the shortest at term. pPROM had telomere lengths (9962 ± 3124 bp that were significantly shorter than gestational age-matched PTB (11546 ± 4348 bp, p = 0.04, but comparable to term births (9011 ± 2497 bp, p = 0.31. Secondary analyses revealed no effects of race (African American vs. Caucasian or intraamniotic infection on telomere length. A strong Pearson's correlation was noted between fetal leukocyte and placental membrane telomere lengths (ρ = 0.77; p<0.01. CONCLUSIONS: Fetal leukocyte telomere length is reduced in pPROM compared to PTB but is similar to term births. pPROM represents a placental membrane disease likely mediated by OS-induced senescence.

Minimal Length Effects on Tunnelling from Spherically Symmetric Black Holes

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Benrong Mu

2015-01-01

Full Text Available We investigate effects of the minimal length on quantum tunnelling from spherically symmetric black holes using the Hamilton-Jacobi method incorporating the minimal length. We first derive the deformed Hamilton-Jacobi equations for scalars and fermions, both of which have the same expressions. The minimal length correction to the Hawking temperature is found to depend on the black hole’s mass and the mass and angular momentum of emitted particles. Finally, we calculate a Schwarzschild black hole's luminosity and find the black hole evaporates to zero mass in infinite time.

Utility of telomere length measurements for age determination of humpback whales

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Morten Tange Olsen

2014-12-01

Full Text Available This study examines the applicability of telomere length measurements by quantitative PCR as a tool for minimally invasive age determination of free-ranging cetaceans. We analysed telomere length in skin samples from 28 North Atlantic humpback whales (Megaptera novaeangliae, ranging from 0 to 26 years of age. The results suggested a significant correlation between telomere length and age in humpback whales. However, telomere length was highly variable among individuals of similar age, suggesting that telomere length measured by quantitative PCR is an imprecise determinant of age in humpback whales. The observed variation in individual telomere length was found to be a function of both experimental and biological variability, with the latter perhaps reflecting patterns of inheritance, resource allocation trade-offs, and stochasticity of the marine environment.

Heat generation and cooling of SSC magnets at high ramp rates

International Nuclear Information System (INIS)

Snitchler, G.; Capone, D.; Kovachev, V.; Schermer, R.

1992-01-01

This presentation will address a summary of AC loss calculations (SSCL), experimental results on cable samples (Westinghouse STC), short model magnets test results (FNAL, KEK-Japan), and recent full length magnets test data on AC losses and quench current ramp rate sensitivity (FNAL, BNL). Possible sources of the observed enhanced heat generation and quench sensitivity for some magnets will be discussed. A model for cooling conditions of magnet coils considering heat generation distribution and specific anisotropy of the heat transfer will be presented. The crossover contact resistance in cables and curing procedure influence on resistivity, currently under study, will be briefly discussed. (author)

Short Rayleigh length free electron lasers

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W. B. Colson

2006-03-01

Full Text Available Conventional free electron laser (FEL oscillators minimize the optical mode volume around the electron beam in the undulator by making the resonator Rayleigh length about one third to one half of the undulator length. This maximizes gain and beam-mode coupling. In compact configurations of high-power infrared FELs or moderate power UV FELs, the resulting optical intensity can damage the resonator mirrors. To increase the spot size and thereby reduce the optical intensity at the mirrors below the damage threshold, a shorter Rayleigh length can be used, but the FEL interaction is significantly altered. We model this interaction using a coordinate system that expands with the rapidly diffracting optical mode from the ends of the undulator to the mirrors. Simulations show that the interaction of the strongly focused optical mode with a narrow electron beam inside the undulator distorts the optical wave front so it is no longer in the fundamental Gaussian mode. The simulations are used to study how mode distortion affects the single-pass gain in weak fields, and the steady-state extraction in strong fields.

Stopping potential and ion beamlet control for micro-resistive patterning through sub-Debye length plasma apertures

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Abhishek Chowdhury

2014-12-01

Full Text Available Focused multiple ion beamlets from a microwave plasma source is investigated for localized micron-scale modification of substrates in a patterned manner. Plasma electrodes (PE with an array of through apertures having aperture diameters of the order of plasma Debye length are investigated for generating the beamlets. Extraction through sub-Debye length apertures becomes possible when the PE is kept at floating potential. It is found that the current – voltage characteristics of the extracted beamlets exhibits interesting features such as a space-charge-limited region that has a different behaviour than the conventional Child-Langmuir’s law and an extraction-voltage-limited region that does not undergo saturation but exhibits a Schottky-like behaviour similar to that of a vacuum diode. A switching technique to control the motion of individual beamlets is developed and the stopping potential determined. The beamlets are thereafter used to create localized micro-resistive patterns. The experimental results are compared with simulations and reasonably good agreement is obtained.

Minimal Length, Measurability and Gravity

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Alexander Shalyt-Margolin

2016-03-01

Full Text Available The present work is a continuation of the previous papers written by the author on the subject. In terms of the measurability (or measurable quantities notion introduced in a minimal length theory, first the consideration is given to a quantum theory in the momentum representation. The same terms are used to consider the Markov gravity model that here illustrates the general approach to studies of gravity in terms of measurable quantities.

Production of enzymatically active recombinant full-length barley high pI alpha-glucosidase of glycoside family 31 by high cell-density fermentation of Pichia pastoris and affinity purification

DEFF Research Database (Denmark)

Næsted, Henrik; Kramhøft, Birte; Lok, F.

2006-01-01

Recombinant barley high pI alpha-glucosidase was produced by high cell-density fermentation of Pichia pastoris expressing the cloned full-length gene. The gene was amplified from a genomic clone and exons (coding regions) were assembled by overlap PCR. The resulting cDNA was expressed under contr...... nM x s(-1), and 85 s(-1) using maltose as substrate. This work presents the first production of fully active recombinant alpha-glucosidase of glycoside hydrolase family 31 from higher plants. (c) 2005 Elsevier Inc. All rights reserved....

Photoconductivity, pH Sensitivity, Noise, and Channel Length Effects in Si Nanowire FET Sensors

Science.gov (United States)

Gasparyan, Ferdinand; Zadorozhnyi, Ihor; Khondkaryan, Hrant; Arakelyan, Armen; Vitusevich, Svetlana

2018-03-01

Silicon nanowire (NW) field-effect transistor (FET) sensors of various lengths were fabricated. Transport properties of Si NW FET sensors were investigated involving noise spectroscopy and current-voltage (I-V) characterization. The static I-V dependencies demonstrate the high quality of fabricated silicon FETs without leakage current. Transport and noise properties of NW FET structures were investigated under different light illumination conditions, as well as in sensor configuration in an aqueous solution with different pH values. Furthermore, we studied channel length effects on the photoconductivity, noise, and pH sensitivity. The magnitude of the channel current is approximately inversely proportional to the length of the current channel, and the pH sensitivity increases with the increase of channel length approaching the Nernst limit value of 59.5 mV/pH. We demonstrate that dominant 1/f-noise can be screened by the generation-recombination plateau at certain pH of the solution or external optical excitation. The characteristic frequency of the generation-recombination noise component decreases with increasing of illumination power. Moreover, it is shown that the measured value of the slope of 1/f-noise spectral density dependence on the current channel length is 2.7 which is close to the theoretically predicted value of 3.

Nanosecond neutron generator

International Nuclear Information System (INIS)

Lobov, S.I.; Pavlovskaya, N.G.; Pukhov, S.P.

1991-01-01

High-voltage nanosecond neutron generator for obtaining neutrons in D-T reaction is described. Yield of 6x10 6 neutron/pulse was generated in a sealed gas-filled diode with a target on the cathode by accelerating pulse voltage of approximately 0.5 MV and length at half-height of 0.5 ns and deuterium pressure of 6x10 -2 Torr. Ways of increasing neutron yield and possibilities of creating generators of nanosecond neutron pulses with great service life are considered

Tapered fluorotellurite microstructured fibers for broadband supercontinuum generation.

Science.gov (United States)

Wang, Fang; Wang, Kangkang; Yao, Chuanfei; Jia, Zhixu; Wang, Shunbin; Wu, Changfeng; Qin, Guanshi; Ohishi, Yasutake; Qin, Weiping

2016-02-01

Fluorotellurite microstructured fibers (MFs) based on TeO2-BaF2-Y2O3 glasses are fabricated by using a rod-in-tube method. Tapered fluorotellurite MFs with varied transition region lengths are prepared by employing an elongation machine. By using a tapered fluorotellurite MF with a transition region length of ∼3.3  cm as the nonlinear medium and a 1560 nm femtosecond fiber laser as the pump source, broadband supercontinuum generation covering from 470 to 2770 nm is obtained. The effects of the transition region length of the tapered fluorotellurite MF on supercontinuum generation are also investigated. Our results show that tapered fluorotellurite MFs are promising nonlinear media for generating broadband supercontinuum light expanding from visible to mid-infrared spectral region.

Maximum length scale in density based topology optimization

DEFF Research Database (Denmark)

Lazarov, Boyan Stefanov; Wang, Fengwen

2017-01-01

The focus of this work is on two new techniques for imposing maximum length scale in topology optimization. Restrictions on the maximum length scale provide designers with full control over the optimized structure and open possibilities to tailor the optimized design for broader range...... of manufacturing processes by fulfilling the associated technological constraints. One of the proposed methods is based on combination of several filters and builds on top of the classical density filtering which can be viewed as a low pass filter applied to the design parametrization. The main idea...

The length-weight and length-length relationships of bluefish, Pomatomus saltatrix (Linnaeus, 1766) from Samsun, middle Black Sea region

OpenAIRE

Özpiçak, Melek; Saygın, Semra; Polat, Nazmi

2017-01-01

In this study, length-weight relationship (LWR) and length-length relationship (LLR) of bluefish,Pomatomus saltatrix were determined. A total of 125 specimens were sampled from Samsun, themiddle Black Sea in 2014 fishing season. Bluefish specimens were monthly collected fromcommercial fishing boats from October to December 2014. All captured individuals (N=125) weremeasured to the nearest 0.1 cm for total, fork and standard lengths. The weight of each fish (W)was recorded to the nearest 0.01 ...

Generation of artificial FASTQ files to evaluate the performance of next-generation sequencing pipelines.

Directory of Open Access Journals (Sweden)

Matthew Frampton

Full Text Available Pipelines for the analysis of Next-Generation Sequencing (NGS data are generally composed of a set of different publicly available software, configured together in order to map short reads of a genome and call variants. The fidelity of pipelines is variable. We have developed ArtificialFastqGenerator, which takes a reference genome sequence as input and outputs artificial paired-end FASTQ files containing Phred quality scores. Since these artificial FASTQs are derived from the reference genome, it provides a gold-standard for read-alignment and variant-calling, thereby enabling the performance of any NGS pipeline to be evaluated. The user can customise DNA template/read length, the modelling of coverage based on GC content, whether to use real Phred base quality scores taken from existing FASTQ files, and whether to simulate sequencing errors. Detailed coverage and error summary statistics are outputted. Here we describe ArtificialFastqGenerator and illustrate its implementation in evaluating a typical bespoke NGS analysis pipeline under different experimental conditions. ArtificialFastqGenerator was released in January 2012. Source code, example files and binaries are freely available under the terms of the GNU General Public License v3.0. from https://sourceforge.net/projects/artfastqgen/.

A novel method for length of chirped fiber Bragg grating sensor

Science.gov (United States)

Li, Zhenwei; Wei, Peng; Liu, Taolin

2018-03-01

Length of chirped fiber Bragg grating sensor is very important for detonation velocity. Different from other ways, we proposed a novel method based on the optical frequency domain reflection theory to measure the length of chirped fiber grating sensor in non-contact condition. This method adopts a tunable laser source to provide wavelength scanning laser, which covers the Full Width at Half Maximum of spectrum of the chirped fiber Bragg grating sensor. A Michelson interferometer is used to produce optical interference signal. Finally, the grating's length is attainable by distance domain signal. In theory, length resolution of chirped fiber Bragg grating sensor could be 0.02 mm. We perform a series of length measurement experiments for chirped fiber grating sensor, including comparison experiments with hot-tip method. And the experiment results show that the novel method could accurately measure the length of chirped fiber Bragg grating sensors, and the length differences between the optical frequency domain reflection method and the hot-tip probe method are very small.

Cross-dimensional mapping of number, length and brightness by preschool children.

Directory of Open Access Journals (Sweden)

Maria Dolores de Hevia

Full Text Available Human adults in diverse cultures, children, infants, and non-human primates relate number to space, but it is not clear whether this ability reflects a specific and privileged number-space mapping. To investigate this possibility, we tested preschool children in matching tasks where the dimensions of number and length were mapped both to one another and to a third dimension, brightness. Children detected variation on all three dimensions, and they reliably performed mappings between number and length, and partially between brightness and length, but not between number and brightness. Moreover, children showed reliably better mapping of number onto the dimension of length than onto the dimension of brightness. These findings suggest that number establishes a privileged mapping with the dimension of length, and that other dimensions, including brightness, can be mapped onto length, although less efficiently. Children's adeptness at number-length mappings suggests that these two dimensions are intuitively related by the end of the preschool years.

Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice

Science.gov (United States)

Badoni, Saurabh; Das, Sweta; Sayal, Yogesh K.; Gopalakrishnan, S.; Singh, Ashok K.; Rao, Atmakuri R.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

2016-01-01

We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17–79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9–21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, “Oryza ISM-ILP marker” database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice. PMID:27032371

Ultrashort electron bunch length measurement with diffraction radiation deflector

Science.gov (United States)

Xiang, Dao; Huang, Wen-Hui

2007-01-01

In this paper, we propose a novel method to measure electron bunch length with a diffraction radiation (DR) deflector which is composed of a DR radiator and three beam position monitors (BPMs). When an electron beam passes through a metallic aperture which is tilted by 45 degrees with respect to its trajectory, backward DR that propagates perpendicular to the beam’s trajectory is generated which adds a transverse deflection to the beam as a result of momentum conservation. The deflection is found to be largely dependent on the bunch length and could be easily observed with a downstream BPM. Detailed investigations show that this method has wide applicability, high temporal resolution, and great simplicity.

Electroless Nickel-Based Catalyst for Diffusion Limited Hydrogen Generation through Hydrolysis of Borohydride

Directory of Open Access Journals (Sweden)

Shannon P. Anderson

2013-07-01

Full Text Available Catalysts based on electroless nickel and bi-metallic nickel-molybdenum nanoparticles were synthesized for the hydrolysis of sodium borohydride for hydrogen generation. The catalysts were synthesized by polymer-stabilized Pd nanoparticle-catalyzation and activation of Al2O3 substrate and electroless Ni or Ni-Mo plating of the substrate for selected time lengths. Catalytic activity of the synthesized catalysts was tested for the hydrolyzation of alkaline-stabilized NaBH4 solution for hydrogen generation. The effects of electroless plating time lengths, temperature and NaBH4 concentration on hydrogen generation rates were analyzed and discussed. Compositional analysis and surface morphology were carried out for nano-metallized Al2O3 using Scanning Electron Micrographs (SEM and Energy Dispersive X-Ray Microanalysis (EDAX. The as-plated polymer-stabilized electroless nickel catalyst plated for 10 min and unstirred in the hydrolysis reaction exhibited appreciable catalytic activity for hydrolysis of NaBH4. For a zero-order reaction assumption, activation energy of hydrogen generation using the catalyst was estimated at 104.6 kJ/mol. Suggestions are provided for further work needed prior to using the catalyst for portable hydrogen generation from aqueous alkaline-stabilized NaBH4 solution for fuel cells.

Telomere length analysis.

Science.gov (United States)

Canela, Andrés; Klatt, Peter; Blasco, María A

2007-01-01

Most somatic cells of long-lived species undergo telomere shortening throughout life. Critically short telomeres trigger loss of cell viability in tissues, which has been related to alteration of tissue function and loss of regenerative capabilities in aging and aging-related diseases. Hence, telomere length is an important biomarker for aging and can be used in the prognosis of aging diseases. These facts highlight the importance of developing methods for telomere length determination that can be employed to evaluate telomere length during the human aging process. Telomere length quantification methods have improved greatly in accuracy and sensitivity since the development of the conventional telomeric Southern blot. Here, we describe the different methodologies recently developed for telomere length quantification, as well as their potential applications for human aging studies.

BACHD rats expressing full-length mutant huntingtin exhibit differences in social behavior compared to wild-type littermates.

Directory of Open Access Journals (Sweden)

Giuseppe Manfré

Full Text Available Huntington disease (HD is a devastating inherited neurodegenerative disorder characterized by progressive motor, cognitive, and psychiatric symptoms without any cure to slow down or stop the progress of the disease. The BACHD rat model for HD carrying the human full-length mutant huntingtin protein (mHTT with 97 polyQ repeats has been recently established as a promising model which reproduces several HD-like features. While motor and cognitive functions have been characterized in BACHD rats, little is known about their social phenotype.This study focuses especially on social behavior since evidence for social disturbances exists in human patients. Our objective was to compare social behavior in BACHD and wild-type (WT rats at different ages, using two different measures of sociability.Animals were tested longitudinally at the age of 2, 4 and 8 months in the social interaction test to examine different parameters of sociability. A separate cohort of 7 month old rats was tested in the three chamber social test to measure both sociability and social novelty. Gene expression analyses in 8 months old animals were performed by real time qRT-PCR to evaluate a potential involvement of D1 and D2 dopaminergic receptors and the contribution of Brain-derived neurotrophic factor (BDNF to the observed behavioral alterations.In the social interaction test, BACHD rats showed age-dependent changes in behaviour when they were-re introduced to their cagemate after a 24 hours-period of individual housing. The time spent on nape attacks increased with aging. Furthermore, a significant higher level of pinning at 2 months of age was shown in the BACHD rats compared to wild-types, followed by a reduction at 4 and 8 months. On the other hand, BACHD rats exhibited a decreased active social behaviour compared to wild-types, reflected by genotype-effects on approaching, following and social nose contact. In the three chamber social test, BACHD rats seemed to show a mild

Detailed study of spontaneous rotation generation in diverted H-mode plasma using the full-f gyrokinetic code XGC1

Science.gov (United States)

Seo, Janghoon; Chang, C. S.; Ku, S.; Kwon, J. M.; Yoon, E. S.

2013-10-01

The Full-f gyrokinetic code XGC1 is used to study the details of toroidal momentum generation in H-mode plasma. Diverted DIII-D geometry is used, with Monte Carlo neutral particles that are recycled at the limiter wall. Nonlinear Coulomb collisions conserve particle, momentum, and energy. Gyrokinetic ions and adiabatic electrons are used in the present simulation to include the effects from ion gyrokinetic turbulence and neoclassical physics, under self-consistent radial electric field generation. Ion orbit loss physics is automatically included. Simulations show a strong co-Ip flow in the H-mode layer at outside midplane, similarly to the experimental observation from DIII-D and ASDEX-U. The co-Ip flow in the edge propagates inward into core. It is found that the strong co-Ip flow generation is mostly from neoclassical physics. On the other hand, the inward momentum transport is from turbulence physics, consistently with the theory of residual stress from symmetry breaking. Therefore, interaction between the neoclassical and turbulence physics is a key factor in the spontaneous momentum generation.

Evaluation of full-strength paper mill effluent for electricity generation ...

African Journals Online (AJOL)

In the search for renewable, sustainable and affordable energy sources, microbial fuel cells (MFCs) offer the advantage of a biological oxidation of pollutants to the direct generation of electricity by microorganisms. We thus examined the biodegradability and suitability of unamended paper mill effluent for power production ...

Wood Quality of Acacia Hybrid and Second-Generation Acacia mangium

Directory of Open Access Journals (Sweden)

Ismail Jusoh

2013-11-01

Full Text Available Two new tree variants, namely Acacia hybrid and second-generation Acacia mangium, have been introduced in plantation forests in Sarawak, Malaysia, and their wood qualities were examined. The mean basic density of Acacia hybrid was comparable with Acacia mangium. However basic density and strength properties of second-generation A. mangium were significantly lower compared to Acacia hybrid. The mean fibre length and fibre wall thickness in the hybrid were found to be greater than that of second-generation A. mangium. Fibre diameter and fibre lumen diameter of Acacia hybrid were smaller compared to second-generation A. mangium. Runkel and slenderness ratios of Acacia hybrid and second-generation A. mangium fibres showed that they were suitable for pulp and paper production. Acacia hybrid was more resistant to Coptotermes curvignathus attack than second-generation A. mangium. A laboratory soil block test showed that Acacia hybrid and second-generation A. mangium were moderately durable timbers. In summary, marked differences in wood properties and qualities were observed between Acacia hybrid and second-generation A. mangium.

A comparative evaluation of working length with digital radiography and third generation apex locator (ProPex in the presence of various intracanal irrigants: An in vivo/ex vivo study

Directory of Open Access Journals (Sweden)

Irfana Khursheed

2014-01-01

Full Text Available Background: Accurate working length determination is a pre-requisite for a successful endodontic treatment. Even with improved systems of working length measurement, different readings may be recorded in different electrolytes present in the canal. The purpose of this in vivo/ex vivo comparative study was to determine the accuracy in measuring the working length of root canal using Direct Digital Radiographic Method (Radiovisiography or RVG and ProPex electronic apex locator in the presence of three different irrigating solutions: 0.9% normal saline, 2% chlorhexidine, 3% NaOCl solutions. Materials and Methods: Forty single-rooted human teeth scheduled for extraction with mature apices were selected for this study. Measurements were performed by using RVG and ProPex in the presence of irrigating solutions. After extraction of the teeth, light microscope was used to confirm visually the relationship of the tip of the endodontic file to the apical foramen, and actual lengths were determined by reducing 0.5 mm from this length. The statistical analysis was performed by one-way ANOVA test and Tukey-HSD post hoc procedure. P < 0.05 was considered as significant. Results: No significant difference was found between overall mean electronic working length and digital radiographic length; however, prediction error (P < 0.05 was significant with respect to different irrigants. Among the irrigating solutions, chlorhexidine gluconate had the smallest distance to the actual lengths, whereas NaOCl had the greatest. Conclusion: Electronic apex locator ProPex yielded best result in the presence of chlorhexidine, whereas the largest error was demonstrated with NaOCl indicating that higher electroconductive irrigating solutions affect the precision of multi-frequency apex locators.

Length of urethra in the Indian adult male population

Directory of Open Access Journals (Sweden)

Venkatesh Krishnamoorthy

2012-01-01

Full Text Available Objective: The urethral length has not been measured in the Indian population. Even the international literature in this arena is very sparse. This paper is an attempt to develop a simple anatomical database for urethral length. Materials and Methods: Between January 2010 and April 2011, the urethral lengths of 422 adult male patients who required catheterization as part of regular treatment at our hospital, were recorded after obtaining consent from the patients and from the scientific and ethics review boards of the institution. Patients with history of prostatic or urethral abnormalities were excluded. The balloon of a sterile Foley′s catheter was inflated using 10 cc of saline. The length from the junction of the balloon to the ′Y′ junction of the Foley was measured. The catheter was then passed into the bladder and re-inflated to same volume. The penis was gently straightened and the length of the catheter outside the penis was measured till the premarked point at the ′Y′ junction. Subtracting this from the original length gave the length of the urethra. Results: The mean length of the urethra was 17.55 + 1.42 cm with a range between 14 and 22.5 cm. Conclusions: Literature in which the length of the normal adult male urethra is recorded for a significant sample size is very scarce. Our data adds to basic anatomic information of the male urethra specific to the Indian population. Statistical Methods: Descriptive statistical analysis was performed. The non-linear regression analysis was employed to find the normative values of urethral length according to age class.

Accelerated one-step generation of full-color holographic videos using a color-tunable novel-look-up-table method for holographic three-dimensional television broadcasting

Science.gov (United States)

Kim, Seung-Cheol; Dong, Xiao-Bin; Kim, Eun-Soo

2015-09-01

A color-tunable novel-look-up-table (CT-NLUT) for fast one-step calculation of full-color computer-generated holograms is proposed. The proposed method is composed of four principal fringe patterns (PFPs) such as a baseline, a depth-compensating and two color-compensating PFPs. CGH patterns for one color are calculated by combined use of baseline-PFP and depth-compensating-PFP and from them, those for two other colors are generated by being multiplied by the corresponding color-compensating-PFPs. color-compensating-PFPs compensate for differences in the wavelength between two colors based on their unique achromatic thin-lens properties, enabling transformation of one-color CGH pattern into those for other colors. This color-conversion property of the proposed method enables simultaneous generation of full color-CGH patterns, resulting in a significant reduction of the full color-CGH calculation time. Experimental results with test scenario show that the full color-CGH calculation time of the proposed CT-NLUT has been reduced by 45.10%, compared to the conventional NLUT. It has been further reduced by 96.01% when a data compression algorithm, called temporal redundancy-based NLUT, was used together, which means 25-fold reduction of its full color-CGH calculation time. Successful computational and optical reconstructions of full color-CGH patterns confirm the feasibility of the proposed method.

Slack length reduces the contractile phenotype of the Swine carotid artery.

Science.gov (United States)

Rembold, Christopher M; Garvey, Sean M; Tejani, Ankit D

2013-01-01

Contraction is the primary function of adult arterial smooth muscle. However, in response to vessel injury or inflammation, arterial smooth muscle is able to phenotypically modulate from the contractile state to several 'synthetic' states characterized by proliferation, migration and/or increased cytokine secretion. We examined the effect of tissue length (L) on the phenotype of intact, isometrically held, initially contractile swine carotid artery tissues. Tissues were studied (1) without prolonged incubation at the optimal length for force generation (1.0 Lo, control), (2) with prolonged incubation for 17 h at 1.0 Lo, or (3) with prolonged incubation at slack length (0.6 Lo) for 16 h and then restoration to 1.0 Lo for 1 h. Prolonged incubation at 1.0 Lo minimally reduced the contractile force without substantially altering the mediators of contraction (crossbridge phosphorylation, shortening velocity or stimulated actin polymerization). Prolonged incubation of tissues at slack length (0.6 Lo), despite return of length to 1.0 Lo, substantially reduced contractile force, reduced crossbridge phosphorylation, nearly abolished crossbridge cycling (shortening velocity) and abolished stimulated actin polymerization. These data suggest that (1) slack length treatment significantly alters the contractile phenotype of arterial tissue, and (2) slack length treatment is a model to study acute phenotypic modulation of intact arterial smooth muscle. Copyright © 2013 S. Karger AG, Basel.

History-dependence of muscle slack length following contraction and stretch in the human vastus lateralis.

Science.gov (United States)

Stubbs, Peter W; Walsh, Lee D; D'Souza, Arkiev; Héroux, Martin E; Bolsterlee, Bart; Gandevia, Simon C; Herbert, Robert D

2018-06-01

In reduced muscle preparations, the slack length and passive stiffness of muscle fibres have been shown to be influenced by previous muscle contraction or stretch. In human muscles, such behaviours have been inferred from measures of muscle force, joint stiffness and reflex magnitudes and latencies. Using ultrasound imaging, we directly observed that isometric contraction of the vastus lateralis muscle at short lengths reduces the slack lengths of the muscle-tendon unit and muscle fascicles. The effect is apparent 60 s after the contraction. These observations imply that muscle contraction at short lengths causes the formation of bonds which reduce the effective length of structures that generate passive tension in muscles. In reduced muscle preparations, stretch and muscle contraction change the properties of relaxed muscle fibres. In humans, effects of stretch and contraction on properties of relaxed muscles have been inferred from measurements of time taken to develop force, joint stiffness and reflex latencies. The current study used ultrasound imaging to directly observe the effects of stretch and contraction on muscle-tendon slack length and fascicle slack length of the human vastus lateralis muscle in vivo. The muscle was conditioned by (a) strong isometric contractions at long muscle-tendon lengths, (b) strong isometric contractions at short muscle-tendon lengths, (c) weak isometric contractions at long muscle-tendon lengths and (d) slow stretches. One minute after conditioning, ultrasound images were acquired from the relaxed muscle as it was slowly lengthened through its physiological range. The ultrasound image sequences were used to identify muscle-tendon slack angles and fascicle slack lengths. Contraction at short muscle-tendon lengths caused a mean 13.5 degree (95% CI 11.8-15.0 degree) shift in the muscle-tendon slack angle towards shorter muscle-tendon lengths, and a mean 5 mm (95% CI 2-8 mm) reduction in fascicle slack length, compared to the

An improved steam generator model for the SASSYS code

International Nuclear Information System (INIS)

Pizzica, P.A.

1989-01-01

A new steam generator model has been developed for the SASSYS computer code, which analyzes accident conditions in a liquid-metal-cooled fast reactor. It has been incorporated into the new SASSYS balance-of-plant model, but it can also function as a stand-alone model. The model provides a full solution of the steady-state condition before the transient calculation begins for given sodium and water flow rates, inlet and outlet sodium temperatures, and inlet enthalpy and region lengths on the water side

Channel length scaling and the impact of metal gate work function ...

Indian Academy of Sciences (India)

As the channel length is reduced from one transistor generation to the next, ... As CMOS technology continues to scale, metal gate electrodes need to be intro .... in the z-direction, q is the electron charge, h is the Planck's constant, Ψ(x, z) is the.

Frequency Characteristics of Double-Walled Carbon Nanotube Resonator with Different Length

Directory of Open Access Journals (Sweden)

Jun-Ha LEE

2016-05-01

Full Text Available In this paper, we have conducted classical molecular dynamics simulations for DWCNTs of various wall lengths to investigate their use as ultrahigh frequency nano-mechanical resonators. We sought to determine the variations in the frequency of these resonators according to changes in the DWCNT wall lengths. For a double-walled carbon nanotube resonator with a shorter inner nanotube, the shorter inner nanotube can be considered to be a flexible core, and thus, the length influences the fundamental frequency. In this paper, we analyze the variation in frequency of ultra-high frequency nano-mechnical resonators constructed from DWCNTs with different wall lengths.DOI: http://dx.doi.org/10.5755/j01.ms.22.2.12951

Relationships of body lengths with mouth opening and prey length of nemipterid fishes (Regan, 1913 in the Gulf of Thailand

Directory of Open Access Journals (Sweden)

Mithun Paul

2017-12-01

Full Text Available This study aims to investigate the relationship among total length (TL of fish with mouth opening namely horizontal opening (MH, vertical opening (VH, mouth area (MA and fork length (FL of seven sympatric nemipterid fish species and to know the relationship between total length and consumed prey length of five sympatric species sampled from the Gulf of Thailand in 2015. A total 883 fish were investigated collected from both cruise surveys and fishing port survey. TL was linearly and log-linearly related with both MV and MH for three and four species, respectively. MA’s were always the log linear relation of TL and shapes were nearly oval for all species. FL in all TL-FL relationships were proportional to the TL’s in all species (r2 = 0.94, P  .5 and in invertebrate prey items for N. tambuloides (P > .5. So, this study clearly confirms that nemipterid fishes of different sizes feed on all different specific prey items according to its own body size and feed according to size class for prey items available nearby.

Construction of cold mass assembly for full-length dipoles for the SSC [Superconducting Super Collider] accelerator

International Nuclear Information System (INIS)

Dahl, P.; Cottingham, J.; Garber, M.

1986-10-01

Four of the initial six 17m long demonstration dipole magnets for the proposed Superconducting Super Collider have been constructed, and the first one is now being tested. This paper describes the magnet design and construction of the cold mass assembly. The magnets are cold iron (and cold bore) 1-in-1 dipoles, wound with partially keystoned current density-graded high homogeneity NbTi cable in a two-layer cos θ coil of 40 mm inner diameter. The magnetic length is 16.6 m. The coil is prestressed by 15 mm wide stainless steel collars, and mounted in a circular, split iron yoke of 267 mm outer diameter, supported by a cylindrical yoke (and helium) containment vessel of stainless steel. The magnet bore tube assembly incorporates superconducting sextupole trim coils produced by an industrial, automatic process akin to printed circuit fabrication

Stroma-induced Jagged1 expression drives PC3 prostate cancer cell migration; disparate effects of RIP-generated proteolytic fragments on cell behaviour and Notch signaling

Energy Technology Data Exchange (ETDEWEB)

Delury, Craig, E-mail: c.delury@lancaster.ac.uk [Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YQ (United Kingdom); Hart, Claire, E-mail: claire.hart@manchester.ac.uk [Genito Urinary Cancer Research Group, Institute of Cancer Sciences, Paterson Building, The University of Manchester, Manchester Academic Health Science Centre, Wilmslow Road, Manchester, M20 4BX (United Kingdom); Brown, Mick, E-mail: michael.brown@ics.manchester.ac.uk [Genito Urinary Cancer Research Group, Institute of Cancer Sciences, Paterson Building, The University of Manchester, Manchester Academic Health Science Centre, Wilmslow Road, Manchester, M20 4BX (United Kingdom); Clarke, Noel, E-mail: noel.clarke@christie.nhs.uk [Genito Urinary Cancer Research Group, Institute of Cancer Sciences, Paterson Building, The University of Manchester, Manchester Academic Health Science Centre, Wilmslow Road, Manchester, M20 4BX (United Kingdom); Parkin, Edward, E-mail: e.parkin@lancaster.ac.uk [Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YQ (United Kingdom)

2016-03-25

The Notch ligand Jagged1 is subject to regulated intramembrane proteolysis (RIP) which yields a soluble ectodomain (sJag) and a soluble Jagged1 intracellular domain (JICD). The full-length Jagged1 protein enhances prostate cancer (PCa) cell proliferation and is highly expressed in metastatic cells. However, little is known regarding the mechanisms by which Jagged1 or its RIP-generated fragments might promote PCa bone metastasis. In the current study we show that bone marrow stroma (BMS) induces Jagged1 expression in bone metastatic prostate cancer PC3 cells and that this enhanced expression is mechanistically linked to the promotion of cell migration. We also show that RIP-generated Jagged1 fragments exert disparate effects on PC3 cell behaviour and Notch signaling. In conclusion, the expression of both the full-length ligand and its RIP-generated fragments must be considered in tandem when attempting to regulate Jagged1 as a possible PCa therapy. - Highlights: • Bone marrow stroma induces Jagged1 expression in prostate cancer (PCa) PC3 cells. • This enhanced expression of full-length Jagged1 is required for PC3 cell migration. • Proteolytic fragments of Jagged1 exert disparate effects on PC3 cell behaviour. • Effects of fragments on cell behaviour do not correlate with Notch signaling. • Effects of Jagged1 and its fragments on PCa metastasis likely to be complex.

An Imaging System for Automated Characteristic Length Measurement of Debrisat Fragments

Science.gov (United States)

Moraguez, Mathew; Patankar, Kunal; Fitz-Coy, Norman; Liou, J.-C.; Sorge, Marlon; Cowardin, Heather; Opiela, John; Krisko, Paula H.

2015-01-01

The debris fragments generated by DebriSat's hypervelocity impact test are currently being processed and characterized through an effort of NASA and USAF. The debris characteristics will be used to update satellite breakup models. In particular, the physical dimensions of the debris fragments must be measured to provide characteristic lengths for use in these models. Calipers and commercial 3D scanners were considered as measurement options, but an automated imaging system was ultimately developed to measure debris fragments. By automating the entire process, the measurement results are made repeatable and the human factor associated with calipers and 3D scanning is eliminated. Unlike using calipers to measure, the imaging system obtains non-contact measurements to avoid damaging delicate fragments. Furthermore, this fully automated measurement system minimizes fragment handling, which reduces the potential for fragment damage during the characterization process. In addition, the imaging system reduces the time required to determine the characteristic length of the debris fragment. In this way, the imaging system can measure the tens of thousands of DebriSat fragments at a rate of about six minutes per fragment, compared to hours per fragment in NASA's current 3D scanning measurement approach. The imaging system utilizes a space carving algorithm to generate a 3D point cloud of the article being measured and a custom developed algorithm then extracts the characteristic length from the point cloud. This paper describes the measurement process, results, challenges, and future work of the imaging system used for automated characteristic length measurement of DebriSat fragments.

Length-weight and length-length relationships of common carp (Cyprinus carpio L.) in the middle and southern Iraq provinces

Science.gov (United States)

Al-jebory, Taymaa A.; Das, Simon K.; Usup, Gires; Bakar, Y.; Al-saadi, Ali H.

2018-04-01

In this study, length-weight and length-length relationships of common carp (Cyprinus carpio L.) in the middle and southern Iraq provinces were determined. Fish specimens were procured from seven provinces from July to December, 2015. A negative and positive allometric growth pattern was obtained, where the total length (TL) ranged from 25.60 cm to 33.53 cm, and body weight (BW) ranged from 700 g to 1423 g. Meanwhile, the lowest of 1.03 and highest of 3.54 in "b" value was recorded in group F and group C, respectively. Therefore, Fulton condition factor (K) range from 2.57 to 4.94. While, relative condition factor (Kn) was in the ranged of 0.95 to 1.01. A linear relationship between total length (TL) and standard length (SL) among the provinces for fish groups was obtained. The variances in "b" value ranged from 0.10 to 0.93 with correlation coefficient (r2) of 0.02 to 0.97. This research could be used as a guide to study the ecology and biology of common Carp (Cyprinus carpio L.) in the middle and southern Iraq provinces.

[Clinic-internal and -external factors of length of hospital stay].

Science.gov (United States)

Schariatzadeh, R; Imoberdorf, R; Ballmer, P E

2011-01-19

In the context of forthcoming initiation of Diagnosis Related Groups (DRG) in Switzerland, the objective of the study was to find factors having an impact on the inpatient's length of hospital stay. The study was performed on two general-medical wards of the Kantonsspital Winterthur, where all admitted patients were included in the study over two months. The various periods of diagnostic and therapeutic management of the patients and all diagnostic and therapeutic measures plus the arrangements after hospitalization were recorded. The determinants influencing the length of hospital stay were classified in clinic-internal or -external. 124 inpatients entered the study. 91 (73.4%) had a length of hospital stay without delay, whereas 33 (26.6%) patients had an extended length of hospital stay. The cumulative length of hospital stay of all patients was 1314 days, whereof 216 days (16.4%) were caused by delays. 67 days were caused by clinic-internal (5.1%) and 149 days by clinic-external factors (11.3%). Delays were substantially more generated by clinic-internal than -external factors. Clinic-internal factors were mainly weekends with interruption of the diagnostic and therapeutic procedures, dead times waiting for diagnostic results and waiting times for consultations. Clinic-external factors were caused by delayed transfer in nursing homes or rehabilitation institutions, waiting for family members for the backhaul and by indetermination of the patient. Also factors relating to the patients' characteristics had an influence on the length of hospital stay. Summing up, a substantial part of the length of hospital stay was caused by delays. However, the many different clinic-internal factors complicate solutions to lower the length of hospital stay. Moreover, factors that cannot be influenced such as waiting for microbiological results, contribute to extended length of hospital stay. Early scheduling of post-hospital arrangements may lower length of hospital stay

Do climate variables and human density affect Achatina fulica (Bowditch (Gastropoda: Pulmonata shell length, total weight and condition factor?

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FS. Albuquerque

Full Text Available The length-weight relationship and condition factor have been broadly investigated in snails to obtain the index of physical condition of populations and evaluate habitat quality. Herein, our goal was to describe the best predictors that explain Achatina fulica biometrical parameters and well being in a recently introduced population. From November 2001 to November 2002, monthly snail samples were collected in Lauro de Freitas City, Bahia, Brazil. Shell length and total weight were measured in the laboratory and the potential curve and condition factor were calculated. Five environmental variables were considered: temperature range, mean temperature, humidity, precipitation and human density. Multiple regressions were used to generate models including multiple predictors, via model selection approach, and then ranked with AIC criteria. Partial regressions were used to obtain the separated coefficients of determination of climate and human density models. A total of 1.460 individuals were collected, presenting a shell length range between 4.8 to 102.5 mm (mean: 42.18 mm. The relationship between total length and total weight revealed that Achatina fulica presented a negative allometric growth. Simple regression indicated that humidity has a significant influence on A. fulica total length and weight. Temperature range was the main variable that influenced the condition factor. Multiple regressions showed that climatic and human variables explain a small proportion of the variance in shell length and total weight, but may explain up to 55.7% of the condition factor variance. Consequently, we believe that the well being and biometric parameters of A. fulica can be influenced by climatic and human density factors.

Inelastic analysis of finite length and depth cracked tubes

International Nuclear Information System (INIS)

Reich, M.; Prachuktam, S.; Gardner, D.

1977-01-01

Steam generator tube failure can at times result in reactor safety problems and subsequent premature reactor shutdowns. Typical PWR steam generator units contain thousands of long straight tubes with U-bend sections. These tubes are primarily made from alloy 600 and their sizes vary between 3 / 4 '' and 7 / 8 '' (1.905 cm and 2.223 cm) in diameter with nominal thicknesses of 0.043'' to 0.053'' (0.109 cm to 0.135 cm). Since alloy 600 (and the previously used 304-SS tubes) are ductile, high toughness materials LEFM (linear elastic fracture mechanics) criteria do not apply. This paper concerns itself with the prediction of the failure pressures for typical PWR steam generator tubes with longitudinal finite length and finite depth cracks. Only local plastic overload failure is considered

Modelling length of hospital stay in motor victims

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Mercedes Ayuso-Gutiérrez

2015-03-01

Full Text Available Objective. To analyze which socio-demographic and other factors related to motor injuries affect the length of hospital recovery stay. Materials and methods. In the study a sample of 17 932 motor accidents was used. All the crashes occurred in Spain between 2000 and 2007. Different regression models were fitted to data to identify and measure the impact of a set of explanatory regressors. Results. Time of hospital stay for men is on average 41% larger than for women. When the victim has a fracture as a consequence of the accident, the mean time of hospital stay is multiplied by five. Injuries located in lower extremities, the head and abdomen are associated with greater hospitalization lengths. Conclusions. Gender, age and type of victim, as well as the location and nature of injuries, are found to be factors that have significant impact on the expected length of hospital stay.

Evaluation of Efficient Line Lengths for Better Readability

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Zahid Hussain

2012-01-01

Full Text Available In this paper the major findings of a formal experiment about onscreen text line lengths are presented. The experiment examined the effects of four different line lengths on the reading speed and the reading efficiency. Efficiency is defined as a combination of reading speed and accuracy. Sixteen people between the age of 24 and 36 participated at the experiment. The subjects had to read four different texts with an average line length around 2000 characters. The texts contained substitution words, which had to be detected by the subjects to measure reading accuracy. Besides objective measures like reading speed and accuracy, the subjects were asked to subjectively vote on their reading experience. The results from our objective measures show strong similarities to those of the work done previously by different researchers. The absolute reading speed grows when the line length grows from CPL (Characters Per Line 30-120. The measured reading efficiency, however, doesn\\\\\\'t grow steadily, although a growing trend can be seen. This is due to the fact, that the test persons found in average more substitution words from the 60 CPL text than they did from the 30 and 90 CPL texts. The reading speed seems to increase while the line length increases but the overall comprehension seems to peak at medium line lengths. As in the previous studies, our test persons also prefer the medium (60 and 90 CPL line lengths, although they perform better when reading longer lines. In the overall subjective opinion 13 out of 16 test persons selected the 60 or 90 CPL line length as their favorite. The literature doesn\\\\\\'t truly provide a scientific explanation for the difference between the objective performance and the subjective preference. A natural hypothesis would be that the line length that is the fastest to read would also feel most comfortable to the readers but in the light of this and the earlier research it seems like this is not the case.

Musculoskeletal pain and posture decrease step length in young adults

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Maria Regina Rachmawati

2009-08-01

Full Text Available Pain of the musculoskeletal system, especially low back pain, is one of the most frequent problems with a high risk of disability. The aim of this research study was to determine the existence of an association between low back pain on one hand, posture and step length on the other. This cross-sectional study was conducted on 77 healthy young adult subjects. Step length was measured with the Biodex Gait Trainer 2 (230 VAC. The study results indicate that 62.3% of the young adult subjects had suffered from low back pain. There was no significant association between gender and pain. In male subjects no significant association was found between pain on one hand and mean difference in step length and posture on the other. However, in female subjects with abnormal posture, there was a highly significant difference in left step length between subjects with back pain and those without (p=0.007. The results of a multiple regression analysis indicate that posture has the greatest influence on left step length (B=4.135; 95% Confidence Interval 0.292-7.977. It is recommended that in the examination of low back pain an assessment be made of posture, step length and difference in step lengths.

Musculoskeletal pain and posture decrease step length in young adults

Directory of Open Access Journals (Sweden)

Maria Regina Rachmawati

2016-02-01

Full Text Available Pain of the musculoskeletal system, especially low back pain, is one of the most frequent problems with a high risk of disability. The aim of this research study was to determine the existence of an association between low back pain on one hand,  posture and step length on the other. This cross-sectional study was conducted on 77 healthy young adult subjects. Step length was measured with the Biodex Gait Trainer 2 (230 VAC. The study results indicate that 62.3% of the young adult subjects had suffered from low back pain. There was no significant association between gender and pain. In male subjects no significant association was found between pain on one hand and mean difference in step length and posture on the other. However, in female subjects with abnormal posture, there was a highly significant difference in left step length between subjects with back pain and those without (p=0.007.  The results of a multiple regression analysis indicate that posture has the greatest influence on left step length (B=4.135; 95% Confidence Interval 0.292-7.977. It is recommended that in the examination of low back pain an assessment be made of posture, step length and difference in step lengths.

Relation of Stump Length with Various Gait Parameters in Trans-tibial Amputee

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Koyel Majumdar

2008-07-01

Full Text Available The purpose of this paper is evaluating the impact of stump length of unilateral below knee amputees (BKA on different gait parameters. Nine unilateral BKA were chosen and divided into three groups comprising patients with short, medium, and long stump length. Each of them underwent gait analysis test by Computer Dynography (CDG system to measure the gait parameters. It was found that the ground reaction force is higher in the patients with medium stump length whereas the velocity, step length both for the prosthetic and sound limb and cadence were high in longer stump length. Statistical analysis shows a significant difference (p<0.05 between the gait parameters of BKA with medium and longer stump length. The patients with longer stump length were more efficient than medium and short stump patients as they consumed comparatively lesser energy while walking with self-selected velocity and conventional (Solid ankle cushioned heel SACH foot.

Anatomic and functional leg-length inequality: A review and recommendation for clinical decision-making. Part I, anatomic leg-length inequality: prevalence, magnitude, effects and clinical significance

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Knutson Gary A

2005-07-01

Full Text Available Abstract Background Leg-length inequality is most often divided into two groups: anatomic and functional. Part I of this review analyses data collected on anatomic leg-length inequality relative to prevalence, magnitude, effects and clinical significance. Part II examines the functional "short leg" including anatomic-functional relationships, and provides an outline for clinical decision-making. Methods Online database – Medline, CINAHL and MANTIS – and library searches for the time frame of 1970–2005 were done using the term "leg-length inequality". Results and Discussion Using data on leg-length inequality obtained by accurate and reliable x-ray methods, the prevalence of anatomic inequality was found to be 90%, the mean magnitude of anatomic inequality was 5.2 mm (SD 4.1. The evidence suggests that, for most people, anatomic leg-length inequality does not appear to be clinically significant until the magnitude reaches ~ 20 mm (~3/4". Conclusion Anatomic leg-length inequality is near universal, but the average magnitude is small and not likely to be clinically significant.

RESEARCH ARTICLE Full length sequencing and novel ...

Indian Academy of Sciences (India)

Navya

2016-12-16

Dec 16, 2016 ... TOLONE, ANNA MARIA SUTERA, MARIA TERESA SARDINA, BALDASSARE ... finding of novel SNPs that might be important in future studies and laid the .... power, precision and quality to assess the relationship between ...

FULL LENGTH RESEARCH ARTICLE Adamu & Babatunde (2008 ...

African Journals Online (AJOL)

Dr. Ahmed

standards which now appear in BS 1006 (standard method 1978). These properties are fundamental in the ... to increase its affinity for disperse colours and make it possible to dye the fibre easily. Determination of dye ... Colour fastness to washing test results are shown in Table 4. The procedure was also repeated for dye ...

FULL LENGTH RESEARCH ARTICLE Onuh & Ohazurike (2008 ...

African Journals Online (AJOL)

Dr. Ahmed

flasks containing 50 ml of Reese and Levinson's solution, consisting of Sodium Polypectate (NaPP) as carbon source, and incubated for 7 days at 38oC. ... containing 50ml of Reese and Levinson's medium with Carboxylmethyl. Cellulose (CMC) as the .... from the brown rot fungus Postia placenta. Applied Microbiology and.

The Length of the Day: A Cosmological Perspective

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Arbab A. I.

2009-01-01

Full Text Available We have found an empirical law for the variation of the length of the Earth’s day with geologic time employing Wells’s data. We attribute the lengthening of the Earth’s day to the present cosmic expansion of the Universe. The prediction of law has been found to be in agreement with the astronomical and geological data. The day increases at a present rate of 0.002 sec / century. The length of the day is found to be 6 hours when the Earth formed. We have also found a new limit for the value of the Hubble constant and the age of the Universe.

Does Reproductive Investment Decrease Telomere Length in Menidia menidia?

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Jin Gao

Full Text Available Given finite resources, intense investment in one life history trait is expected to reduce investment in others. Although telomere length appears to be strongly tied to age in many taxa, telomere maintenance requires energy. We therefore hypothesize that telomere maintenance may trade off against other life history characters. We used natural variation in laboratory populations of Atlantic silversides (Menidia menidia to study the relationship between growth, fecundity, life expectancy, and relative telomere length. In keeping with several other studies on fishes, we found no clear dependence of telomere length on age. However, we did find that more fecund fish tended to have both reduced life expectancy and shorter telomeres. This result is consistent with the hypothesis that there is a trade-off between telomere maintenance and reproductive output.

A Design of Finite Memory Residual Generation Filter for Sensor Fault Detection

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Kim Pyung Soo

2017-04-01

Full Text Available In the current paper, a residual generation filter with finite memory structure is proposed for sensor fault detection. The proposed finite memory residual generation filter provides the residual by real-time filtering of fault vector using only the most recent finite measurements and inputs on the window. It is shown that the residual given by the proposed residual generation filter provides the exact fault for noisefree systems. The proposed residual generation filter is specified to the digital filter structure for the amenability to hardware implementation. Finally, to illustrate the capability of the proposed residual generation filter, extensive simulations are performed for the discretized DC motor system with two types of sensor faults, incipient soft bias-type fault and abrupt bias-type fault. In particular, according to diverse noise levels and windows lengths, meaningful simulation results are given for the abrupt bias-type fault.

Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5

Energy Technology Data Exchange (ETDEWEB)

Upadhyay, Anup K.; Cyr, Matthew; Longenecker, Kenton; Tripathi, Rakesh; Sun, Chaohong; Kempf, Dale J. (AbbVie)

2017-02-21

The rapid spread of the recentZika virus(ZIKV) epidemic across various countries in the American continent poses a major health hazard for the unborn fetuses of pregnant women. To date, there is no effective medical intervention. The nonstructural protein 5 ofZika virus(ZIKV-NS5) is critical for ZIKV replication through the 5'-RNA capping and RNA polymerase activities present in its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains, respectively. The crystal structure of the full-length ZIKV-NS5 protein has been determined at 3.05 Å resolution from a crystal belonging to space groupP2₁2₁2 and containing two protein molecules in the asymmetric unit. The structure is similar to that reported for the NS5 protein fromJapanese encephalitis virusand suggests opportunities for structure-based drug design targeting either its MTase or RdRp domain.

The queue-length in GI/G/s queues

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Le Gall Pierre

2000-01-01

Full Text Available The distribution of the queue-length in the stationary symmetrical GI/G/s queue is given with an application to the M/G/s queue, particularly in the case of the combination of several packet traffics, with various constant service times, to dimension the buffer capacity.

Telomere Length and Mortality

DEFF Research Database (Denmark)

Kimura, Masayuki; Hjelmborg, Jacob V B; Gardner, Jeffrey P

2008-01-01

Leukocyte telomere length, representing the mean length of all telomeres in leukocytes, is ostensibly a bioindicator of human aging. The authors hypothesized that shorter telomeres might forecast imminent mortality in elderly people better than leukocyte telomere length. They performed mortality...

LPV Control for the Full Region Operation of a Wind Turbine Integrated with Synchronous Generator

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Guoyan Cao

2015-01-01

Full Text Available Wind turbine conversion systems require feedback control to achieve reliable wind turbine operation and stable current supply. A robust linear parameter varying (LPV controller is proposed to reduce the structural loads and improve the power extraction of a horizontal axis wind turbine operating in both the partial load and the full load regions. The LPV model is derived from the wind turbine state space models extracted by FAST (fatigue, aerodynamics, structural, and turbulence code linearization at different operating points. In order to assure a smooth transition between the two regions, appropriate frequency-dependent varying scaling parametric weighting functions are designed in the LPV control structure. The solution of a set of linear matrix inequalities (LMIs leads to the LPV controller. A synchronous generator model is connected with the closed LPV control loop for examining the electrical subsystem performance obtained by an inner speed control loop. Simulation results of a 1.5 MW horizontal axis wind turbine model on the FAST platform illustrates the benefit of the LPV control and demonstrates the advantages of this proposed LPV controller, when compared with a traditional gain scheduling PI control and prior LPV control configurations. Enhanced structural load mitigation, improved power extraction, and good current performance were obtained from the proposed LPV control.

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

Science.gov (United States)

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

2015-05-01

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

Inertial Effects on Finite Length Pipe Seismic Response

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Virginia Corrado

2012-01-01

Full Text Available A seismic analysis for soil-pipe interaction which accounts for length and constraining conditions at the ends of a continuous pipe is developed. The Winkler model is used to schematize the soil-structure interaction. The approach is focused on axial strains, since bending strains in a buried pipe due to the wave propagation are typically a second-order effect. Unlike many works, the inertial terms are considered in solving equations. Accurate numerical simulations are carried out to show the influence of pipe length and constraint conditions on the pipe seismic strain. The obtained results are compared with results inferred from other models present in the literature. For free-end pipelines, inertial effects have significant influence only for short length. On the contrary, their influence is always important for pinned pipes. Numerical simulations show that a simple rigid model can be used for free-end pipes, whereas pinned pipes need more accurate models.

A new generation all-optical Cs BEC

International Nuclear Information System (INIS)

Gustavsson, M.; Haller, E.; Flir, A.; Rojas Kopeinig, G.; Naegerl, H.C.

2006-01-01

Full text: We have recently produced a Cs BEC in a new generation setup. The condensate is formed in a glass cell, allowing maximum optical access and rapid switching of magnetic fields compared to our first Cs BEC experiment. After a pre-cooling stage consisting of a MOT and 3D Raman sideband cooling, we load 10 7 atoms at a temperature of 1.5 μK in a large-volume crossed optical dipole trap, generated by a high power laser diode stack. To reach degeneracy the atoms are transferred to a focused 'dimple' trap where the density is high enough to allow for efficient evaporation. We report on the progress of loading the BEC in an optical lattice, which together with tunable s-wave scattering length and several Feshbach resonances at low magnetic fields will offer many possibilities for exciting experiments towards the complete control of all degrees of freedom for ultracold molecules. The regime of zero scattering length is another interesting area of study. A BEC without perturbing mean-field shifts is ideally suited for a detailed study of Bloch oscillations in the noninteracting regime. It will also be possible to extend and improve previous BEC based experiments to determine the fine structure constant via a measurement of the photon recoil in an atom interferometer. (author)

Focal Length Affects Depicted Shape and Perception of Facial Images.

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Vít Třebický

Full Text Available Static photographs are currently the most often employed stimuli in research on social perception. The method of photograph acquisition might affect the depicted subject's facial appearance and thus also the impression of such stimuli. An important factor influencing the resulting photograph is focal length, as different focal lengths produce various levels of image distortion. Here we tested whether different focal lengths (50, 85, 105 mm affect depicted shape and perception of female and male faces. We collected three portrait photographs of 45 (22 females, 23 males participants under standardized conditions and camera setting varying only in the focal length. Subsequently, the three photographs from each individual were shown on screen in a randomized order using a 3-alternative forced-choice paradigm. The images were judged for attractiveness, dominance, and femininity/masculinity by 369 raters (193 females, 176 males. Facial width-to-height ratio (fWHR was measured from each photograph and overall facial shape was analysed employing geometric morphometric methods (GMM. Our results showed that photographs taken with 50 mm focal length were rated as significantly less feminine/masculine, attractive, and dominant compared to the images taken with longer focal lengths. Further, shorter focal lengths produced faces with smaller fWHR. Subsequent GMM revealed focal length significantly affected overall facial shape of the photographed subjects. Thus methodology of photograph acquisition, focal length in this case, can significantly affect results of studies using photographic stimuli perhaps due to different levels of perspective distortion that influence shapes and proportions of morphological traits.

Application of Displacement Height and Surface Roughness Length to Determination Boundary Layer Development Length over Stepped Spillway

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Xiangju Cheng

2014-12-01

Full Text Available One of the most uncertain parameters in stepped spillway design is the length (from the crest of boundary layer development. The normal velocity profiles responding to the steps as bed roughness are investigated in the developing non-aerated flow region. A detailed analysis of the logarithmic vertical velocity profiles on stepped spillways is conducted through experimental data to verify the computational code and numerical experiments to expand the data available. To determine development length, the hydraulic roughness and displacement thickness, along with the shear velocity, are needed. This includes determining displacement height d and surface roughness length z0 and the relationship of d and z0 to the step geometry. The results show that the hydraulic roughness height ks is the primary factor on which d and z0 depend. In different step height, step width, discharge and intake Froude number, the relations d/ks = 0.22–0.27, z0/ks = 0.06–0.1 and d/z0 = 2.2–4 result in a good estimate. Using the computational code and numerical experiments, air inception will occur over stepped spillway flow as long as the Bauer-defined boundary layer thickness is between 0.72 and 0.79.

Sonographic Measurement of Fetal Ear Length in Turkish Women with a Normal Pregnancy

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Mucize Eriç Özdemir

2014-12-01

Full Text Available Background: Abnormal fetal ear length is a feature of chromosomal disorders. Fetal ear length measurement is a simple measurement that can be obtained during ultrasonographic examinations. Aims: To develop a nomogram for fetal ear length measurements in our population and investigate the correlation between fetal ear length, gestational age, and other standard fetal biometric measurements. Study Design: Cohort study. Methods: Ear lengths of the fetuses were measured in normal singleton pregnancies. The relationship between gestational age and fetal ear length in millimetres was analysed by simple linear regression. In addition, the correlation of fetal ear length measurements with biparietal diameter, head circumference, abdominal circumference, and femur length were evaluated.Ear length measurements were obtained from fetuses in 389 normal singleton pregnancies ranging between 16 and 28 weeks of gestation. Results: A nomogram was developed by linear regression analysis of the parameters ear length and gestational age. Fetal ear length (mm = y = (1.348 X gestational age-12.265, where gestational ages is in weeks. A high correlation was found between fetal ear length and gestational age, and a significant correlation was also found between fetal ear length and the biparietal diameter (r=0.962; p<0.001. Similar correlations were found between fetal ear length and head circumference, and fetal ear length and femur length. Conclusion: The results of this study provide a nomogram for fetal ear length. The study also demonstrates the relationship between ear length and other biometric measurements.

Full scale wind turbine test of vortex generators mounted on the entire blade

DEFF Research Database (Denmark)

Bak, Christian; Skrzypinski, Witold Robert; Gaunaa, Mac

2016-01-01

Measurements on a heavily instrumented pitch regulated variable speed Vestas V52 850 kW wind turbine situated at the DTU Risø Campus are carried out, where the effect of vortex generators mounted on almost the entire blade is tested with and without leading edge roughness. The measurements...... are compared to the predictions carried out by a developed design tool, where the effect of vortex generators and leading edge roughness is simulated using engineering models. The measurements showed that if vortex generators are mounted there is an increase in flapwise blade moments if the blades are clean...

Static correlation lengths in QCD at high temperatures and finite densities

CERN Document Server

Hart, A; Philipsen, O

2000-01-01

We use a perturbatively derived effective field theory and three-dimensional lattice simulations to determine the longest static correlation lengths in the deconfined QCD plasma phase at high temperatures (T\\gsim 2 Tc) and finite densities (\\mu\\lsim 4 T). For vanishing chemical potential, we refine a previous determination of the Debye screening length, and determine the dependence of different correlation lengths on the number of massless flavours as well as on the number of colours. For non-vanishing but small chemical potential, the existence of Debye screening allows us to carry out simulations corresponding to the full QCD with two (or three) massless dynamical flavours, in spite of a complex action. We investigate how the correlation lengths in the different quantum number channels change as the chemical potential is switched on.

Telomere length is highly inherited and associated with hyperactivity-impulsivity in children with attention deficit/hyperactivity disorder

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Danielle Souza Costa

2015-07-01

Full Text Available Telomere length (TL is highly heritable, and a shorter telomere at birth may increase the risk of age-related problems. Telomere length (TL is highly heritable, and a shorter telomere at birth may increase the risk of age-related problems. Additionally, a shorter TL may represent a biomarker of chronic stress and has been associated with psychiatric disorders. However, no study has explored whether there is an association between TL and the symptoms of one of the most common neurodevelopmental disorders in childhood: Attention Deficit/Hyperactive Disorder (ADHD. We evaluated 61 (range, 6-16 years ADHD children and their parents between 2012 and 2014. Telomere length was measured with a quantitative polymerase chain reaction method with telomere signal normalized to the signal from a single copy gene (36B4 to generate a T/S ratio. Family data was processed through a GEE model to determine the effect of parental TL on children TL. Inattentive and hyperactive-impulsive symptoms were also evaluated in relation to TL. For the first time, we found general heritability to be the major mechanism explaining interindividual telomere length variation in ADHD (father-child: 95%CI=0.35/0.91, p0.05. The ADHD inattentive dimension was not significant associated with TL in this study (p>0.05. TL was shown to be a potential biomarker of the ADHD symptoms burden in families affected by this neurodevelopmental disorder. However, it is crucial that future studies investigating the rate of telomere attrition in relation to psychiatric problems to consider the strong determination of telomere length at birth by inheritance.

Dividing the Force Concept Inventory into two equivalent half-length tests

Directory of Open Access Journals (Sweden)

Jing Han

2015-05-01

Full Text Available The Force Concept Inventory (FCI is a 30-question multiple-choice assessment that has been a building block for much of the physics education research done today. In practice, there are often concerns regarding the length of the test and possible test-retest effects. Since many studies in the literature use the mean score of the FCI as the primary variable, it would be useful then to have different shorter tests that can produce FCI-equivalent scores while providing the benefits of being quicker to administer and overcoming the test-retest effects. In this study, we divide the 1995 version of the FCI into two half-length tests; each contains a different subset of the original FCI questions. The two new tests are shorter, still cover the same set of concepts, and produce mean scores equivalent to those of the FCI. Using a large quantitative data set collected at a large midwestern university, we statistically compare the assessment features of the two half-length tests and the full-length FCI. The results show that the mean error of equivalent scores between any two of the three tests is within 3%. Scores from all tests are well correlated. Based on the analysis, it appears that the two half-length tests can be a viable option for score based assessment that need to administer tests quickly or need to measure short-term gains where using identical pre- and post-test questions is a concern.

Probiotics supplementation and length of hospital stay in neonates with gastrointestinal surgery

Directory of Open Access Journals (Sweden)

Veronica Mugarab-Samedi

Full Text Available Any manipulation on open bowel causes interventional impact on gut microbiome, and surgical stress triggers bacterial translocation; thus, it will be fundamental to determine gut microbiome after surgery. Monitoring dynamic changes in microbiome of post-surgical infants who received probiotics and placebo could provide with important information about gut colonization and potential bacterial overgrowth.The purpose of this study is to assess the effect of probiotics supplementation on length of hospital stay, duration of parenteral nutrition, and feed tolerance in neonates after gastrointestinal surgery. Keywords: Neonates, Surgery, Probiotics, Microbiome, Length of hospital stay, Full enteral feeds

Foot length measurements of newborns of high and low risk pregnancies

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Ana Karina Marques Salge

Full Text Available Abstract OBJECTIVE Comparing foot length measurements of newborns in high and low risk pregnancies at a public hospital in Goiânia, GO, Brazil. METHOD A cross-sectional study carried out between April, 2013 and May, 2015, with a sample consisting of 180 newborns; 106 infants of women from high-risk pregnancies and 74 of women from low-risk pregnancies. Data were descriptively analyzed. Foot length measurement was performed using a stiff transparent plastic ruler, graduated in millimeters. The length of both feet was measured from the tip of the hallux (big toe to the end of the heel. RESULTS A statistically significant relationship was found between the foot length and newborn’s weight, between the cephalic and thoracic perimeters in the high-risk group and between the cephalic perimeter in the control group. CONCLUSION There is a need for creating cut-off points to identify newborns with intrauterine growth disorders using foot length.

Why the Length of a Quantum String Cannot Be Lorentz Contracted

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Antonio Aurilia

2013-01-01

Full Text Available We propose a quantum gravity-extended form of the classical length contraction law obtained in special relativity. More specifically, the framework of our discussion is the UV self-complete theory of quantum gravity. We show how our results are consistent with (i the generalized form of the uncertainty principle (GUP, (ii the so-called hoop-conjecture, and (iii the intriguing notion of “classicalization” of trans-Planckian physics. We argue that there is a physical limit to the Lorentz contraction rule in the form of some minimal universal length determined by quantum gravity, say the Planck Length, or any of its current embodiments such as the string length, or the TeV quantum gravity length scale. In the latter case, we determine the critical boost that separates the ordinary “particle phase,” characterized by the Compton wavelength, from the “black hole phase,” characterized by the effective Schwarzschild radius of the colliding system.

Determination of Onramp Weaving Length for Resolving Merging Dilemma

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Chiu Liu

2012-03-01

Full Text Available It is physically known that onramp merging may turn out to be difficult if the onramp (weaving/merging length is too short because a driver under certain driving circumstances may find that either merging ahead or merging behind a neighboring vehicle on the adjacent highway lane cannot be completed. Various existing guidelines or design manuals provide no clear physical understanding and explanations to the design onramp weaving length but often based on evolved empirical experiences. By integrating human factors, vehicle dynamic characteristics, roadway surface condition, and the onramp weaving design into a single unified analytic framework, the onramp length required for a driver to merge into the highway traffic successfully is determined exactly with formulas and physical solutions to avoid the merging dilemma and enhance driving safety at highway interchanges. The design onramp weaving length is examined and evaluated with various foreseeable merging scenarios and physical examples. This analytic framework sheds light on the understanding of the onramp weaving the first time strictly on a physical human-vehicle-roadway interaction setting. Practitioners can easily apply these user friendly formulae and equations derived from the unified framework to calculate the onramp weaving length to resolve the merging dilemma and enhance driving safety for any highway interchanges.

Evaluation of materials' corrosion and chemistry issues for advanced gas cooled reactor steam generators using full scale plant simulations

International Nuclear Information System (INIS)

Woolsey, I.S.; Rudge, A.J.; Vincent, D.J.

1998-01-01

Advanced Gas Cooled Reactors (AGRS) employ once-through steam Generators of unique design to provide steam at approximately 530 degrees C and 155 bar to steam turbines of similar design to those of fossil plants. The steam generators are highly compact, and have either a serpentine or helical tube geometry. The tubes are heated on the outside by hot C0 2 gas, and steam is generated on the inside of the tubes. Each individual steam generator tube consists of a carbon steel feed and primary economiser section, a 9%Cr steel secondary economiser, evaporator and primary superheater, and a Type 316L austenitic stainless steel secondary superheater, all within a single tube pass. The multi-material nature of the individual tube passes, the need to maintain specific thermohydraulic conditions within the different material sections, and the difficulties of steam generator inspection and repair, have required extensive corrosion-chemistry test programmes to ensure waterside corrosion does not present a challenge to their integrity. A major part of these programmes has been the use of a full scale steam generator test facility capable of simulating all aspects of the waterside conditions which exist in the plant. This facility has been used to address a wide variety of possible plant drainage/degradation processes. These include; single- and two-phase flow accelerated corrosion of carbon steel, superheat margins requirements and the stress-corrosion behaviour of the austenitic superheaters, on-load corrosion of the evaporator materials, and iron transport and oxide deposition behaviour. The paper outlines a number of these, and indicates how they have been of value in helping to maintain reliable operation of the plant. (author)

Superconducting super collider second generation dipole magnet cryostat design

International Nuclear Information System (INIS)

Niemann, R.C.; Bossert, R.C.; Carson, J.A.; Engler, N.H.; Gonczy, J.D.; Larson, E.T.; Nicol, T.H.; Ohmori, T.

1988-12-01

The Superconducting Super Collider, a planned colliding beam particle physics research facility, requires /approximately/10,000 superconducting devices for the control of high energy particle beams. The /approximately/7,500 collider ring superconducting dipole magnets require cryostats that are functional, cryogenically efficient, mass producible and cost effective. A second generation cryostat design has been developed utilizing the experiences gained during the construction, installation and operation of several full length first generation dipole magnet models. The nature of the cryostat improvements is presented. Considered are the connections between the magnet cold mass and its supports, cryogenic supports, cold mass axial anchor, thermal shields, insulation, vacuum vessel and interconnections. The details of the improvements are enumerated and the abstracted results of available component and system evaluations are presented. 8 refs., 11 figs

Automatic Determination of Fiber-Length Distribution in Composite Material Using 3D CT Data

Science.gov (United States)

Teßmann, Matthias; Mohr, Stephan; Gayetskyy, Svitlana; Haßler, Ulf; Hanke, Randolf; Greiner, Günther

2010-12-01

Determining fiber length distribution in fiber reinforced polymer components is a crucial step in quality assurance, since fiber length has a strong influence on overall strength, stiffness, and stability of the material. The approximate fiber length distribution is usually determined early in the development process, as conventional methods require a destruction of the sample component. In this paper, a novel, automatic, and nondestructive approach for the determination of fiber length distribution in fiber reinforced polymers is presented. For this purpose, high-resolution computed tomography is used as imaging method together with subsequent image analysis for evaluation. The image analysis consists of an iterative process where single fibers are detected automatically in each iteration step after having applied image enhancement algorithms. Subsequently, a model-based approach is used together with a priori information in order to guide a fiber tracing and segmentation process. Thereby, the length of the segmented fibers can be calculated and a length distribution can be deduced. The performance and the robustness of the segmentation method is demonstrated by applying it to artificially generated test data and selected real components.

Full Len gth Res earc h Arti cle Full Length Research Article

African Journals Online (AJOL)

functioning of adults as well as children, often with significant ... learning disability particularly in children (Albert,. 1999 ... Signs and Symptoms of this infection include, mild to ..... Isolation and Antimicrobial ... Bayesian Statistics for Social.

Does length or neighborhood size cause the word length effect?

Science.gov (United States)

Jalbert, Annie; Neath, Ian; Surprenant, Aimée M

2011-10-01

Jalbert, Neath, Bireta, and Surprenant (2011) suggested that past demonstrations of the word length effect, the finding that words with fewer syllables are recalled better than words with more syllables, included a confound: The short words had more orthographic neighbors than the long words. The experiments reported here test two predictions that would follow if neighborhood size is a more important factor than word length. In Experiment 1, we found that concurrent articulation removed the effect of neighborhood size, just as it removes the effect of word length. Experiment 2 demonstrated that this pattern is also found with nonwords. For Experiment 3, we factorially manipulated length and neighborhood size, and found only effects of the latter. These results are problematic for any theory of memory that includes decay offset by rehearsal, but they are consistent with accounts that include a redintegrative stage that is susceptible to disruption by noise. The results also confirm the importance of lexical and linguistic factors on memory tasks thought to tap short-term memory.

Field programmable gate array (FPGA implementation of novel complex PN-code-generator- based data scrambler and descrambler

Directory of Open Access Journals (Sweden)

Shabir A. Parah

2010-04-01

Full Text Available A novel technique for the generation of complex and lengthy code sequences using low- length linear feedback shift registers (LFSRs for data scrambling and descrambling is proposed. The scheme has been implemented using VHSIC hardware description language (VHDL approach which allows the reconfigurability of the proposed system such that the length of the generated sequences can be changed as per the security requirements. In the present design consideration the power consumption and chip area requirements are small and the operating speed is high compared to conventional discrete I.C. design, which is a pre-requisite for any system designer. The design has been synthesised on device EP2S15F484C3 of Straitx II FPGA family, using Quarts Altera version 8.1. The simulation results have been found satisfactory and are in conformity with the theoretical observations.

Fundamental length

International Nuclear Information System (INIS)

Pradhan, T.

1975-01-01

The concept of fundamental length was first put forward by Heisenberg from purely dimensional reasons. From a study of the observed masses of the elementary particles known at that time, it is sumrised that this length should be of the order of magnitude 1 approximately 10 -13 cm. It was Heisenberg's belief that introduction of such a fundamental length would eliminate the divergence difficulties from relativistic quantum field theory by cutting off the high energy regions of the 'proper fields'. Since the divergence difficulties arise primarily due to infinite number of degrees of freedom, one simple remedy would be the introduction of a principle that limits these degrees of freedom by removing the effectiveness of the waves with a frequency exceeding a certain limit without destroying the relativistic invariance of the theory. The principle can be stated as follows: It is in principle impossible to invent an experiment of any kind that will permit a distintion between the positions of two particles at rest, the distance between which is below a certain limit. A more elegant way of introducing fundamental length into quantum theory is through commutation relations between two position operators. In quantum field theory such as quantum electrodynamics, it can be introduced through the commutation relation between two interpolating photon fields (vector potentials). (K.B.)

A cryogenic test stand for full length SSC magnets with superfluid capability

International Nuclear Information System (INIS)

Peterson, T.J.; Mazur, P.O.

1989-02-01

The Fermilab Magnet Test Facility performs testing of the full scale SSC magnets on test stands capable of simulating the cryogenic environment of the SSC main ring. One of these test stands, Stand 5, also has the ability to operate the magnet under test at temperatures from 1.8K to 4.5K with either supercritical helium or subcooled liquid, providing at least 25 Watts of refrigeration. At least 50 g/s flow is available from 2.3K to 4.5K, whereas superfluid operation occurs with zero flow. Cooldown time from 4.5K to 1.8K is 1.5 hours. A maximum current capability of 10,000 amps is provided, as is instrumentation to monitor and control the cryogenic conditions. This paper describes the cryogenic design of this test stand. 8 refs., 6 figs

Diffusion length in nanoporous TiO2 films under above-band-gap illumination

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J. D. Park

2014-06-01

Full Text Available We determined the carrier diffusion lengths in TiO2 nanoporous layers of dye-sensitized solar cells by using scanning photocurrent microscopy using an ultraviolet laser. Here, we excited the carrier directly in the nanoporous layers where the diffusion lengths were found to 140 μm as compared to that of visible illumination measured at 90 μm. The diffusion length decreased with increasing laser modulation frequency, in which we determined the electron lifetimes and the diffusion coefficients for both visible and UV illuminations. The diffusion lengths have been studied in terms of the sintering temperatures for both cells with and without binding molecules. We found a strong correlation between the diffusion length and the overall light-to-current conversion efficiency, proving that improving the diffusion length and hence the interparticle connections, is key to improving cell efficiency.

Efficient Statistical Extraction of the Per-Unit-Length Capacitance and Inductance Matrices of Cables with Random Parameters

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P. Manfredi

2015-05-01

Full Text Available Cable bundles often exhibit random parameter variations due to uncertain or uncontrollable physical properties and wire positioning. Efficient tools, based on the so-called polynomial chaos, exist to rapidly assess the impact of such variations on the per-unit-length capacitance and inductance matrices, and on the pertinent cable response. Nevertheless, the state-of-the-art method for the statistical extraction of the per-unit-length capacitance and inductance matrices of cables suffers from several inefficiencies that hinder its applicability to large problems, in terms of number of random parameters and/or conductors. This paper presents an improved methodology that overcomes the aforementioned limitations by exploiting a recently-published, alternative approach to generate the pertinent polynomial chaos system of equations. A sparse and decoupled system is obtained that provides remarkable benefits in terms of speed, memory consumption and problem size that can be dealt with. The technique is thoroughly validated through the statistical analysis of two canonical structures, i.e. a ribbon cable and a shielded cable with random geometry and position.

Prediction of Separation Length of Turbulent Multiphase Flow Using Radiotracer and Computational Fluid Dynamics Simulation

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S. Sugiharto1

2013-04-01

Full Text Available Multiphase flow modeling presents great challenges due to its extreme importance in various industrial and environmental applications. In the present study, prediction of separation length of multiphase flow is examined experimentally by injection of two kinds of iodine-based radiotracer solutions into a hydrocarbon transport pipeline (HCT having an inner diameter of 24 in (60,96 m. The main components of fluids in the pipeline are water 95%, crude oil 3% and gas 2%. A radiotracing experiment was carried out at the segment of pipe which is located far from branch points with assumptions that stratified flows in such segment were achieved. Two radiation detectors located at 80 and 100 m from injection point were used to generate residence time distribution (RTD curve resulting from injection of radiotracer solutions. Multiphase computational fluid dynamics (CFD simulations using Eulerian-Eulerian control volume and commercial CFD package Fluent 6.2 were employed to simulate separation length of multiphase flow. The results of study shows that the flow velocity of water is higher than the flow rate of crude oil in water-dominated system despite the higher density of water than the density of the crude oil. The separation length in multiphase flow predicted by Fluent mixture model is approximately 20 m, measured from injection point. This result confirms that the placement of the first radiation detector at the distance 80 m from the injection point was correct

Dorsal Phalloplasty to Preserve Penis Length after Penile Prosthesis Implantation

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Osama Shaeer

2017-03-01

Full Text Available Objectives: Following penile prosthesis implantation (PPI, patients may complain of a decrease in visible penis length. A dorsal phalloplasty defines the penopubic junction by tacking pubic skin to the pubis, revealing the base of the penis. This study aimed to evaluate the efficacy of a dorsal phalloplasty in increasing the visible penis length following PPI. Methods: An inflatable penile prosthesis was implanted in 13 patients with severe erectile dysfunction (ED at the Kamal Shaeer Hospital, Cairo, Egypt, from January 2013 to May 2014. During the surgery, nonabsorbable tacking sutures were used to pin the pubic skin to the pubis through the same penoscrotal incision. Intraoperative penis length was measured before and after the dorsal phalloplasty. Overall patient satisfaction was measured on a 5-point rating scale and patients were requested to subjectively compare their postoperative penis length with memories of their penis length before the onset of ED. Results: Intraoperatively, the dorsal phalloplasty increased the visible length of the erect penis by an average of 25.6%. The average length before and after tacking was 10.2 ± 2.9 cm and 13.7 ± 2.8 cm, respectively (P <0.002. Postoperatively, seven patients (53.8% reported a longer penis, five patients (38.5% reported no change in length and one patient (7.7% reported a slightly shorter penis. The mean overall patient satisfaction score was 4.9 ± 0.3. None of the patients developed postoperative complications. Conclusion: A dorsal phalloplasty during PPI is an effective method of increasing visible penis length, therefore minimising the impression of a shorter penis after implantation.

Electron heating, magnetic field amplification, and cosmic-ray precursor length at supernova remnant shocks

Energy Technology Data Exchange (ETDEWEB)

Laming, J. Martin [Space Science Division, Naval Research Laboratory, Code 7684, Washington, DC 20375 (United States); Hwang, Una [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Ghavamian, Parviz [Department of Physics, Astronomy and Geosciences, Towson University, Towson, MD 21252 (United States); Rakowski, Cara, E-mail: laming@nrl.navy.mil, E-mail: Una.Hwang-1@nasa.gov, E-mail: pghavamian@towson.edu

2014-07-20

We investigate the observability, by direct and indirect means, of a shock precursor arising from magnetic field amplification by cosmic rays. We estimate the depth of such a precursor under conditions of nonresonant amplification, which can provide magnetic field strengths comparable to those inferred for supernova remnants. Magnetic field generation occurs as the streaming cosmic rays induce a plasma return current, and it may be quenched by either nonresonant or resonant channels. In the case of nonresonant saturation, the cosmic rays become magnetized and amplification saturates at higher magnetic fields. The precursor can extend out to 10{sup 17}-10{sup 18} cm and is potentially detectable. If resonant saturation occurs, the cosmic rays are scattered by turbulence and the precursor length will likely be much smaller. The dependence of precursor length on shock velocity has implications for electron heating. In the case of resonant saturation, this dependence is similar to that in the more familiar resonantly generated shock precursor, which when expressed in terms of the cosmic-ray diffusion coefficient kappav and shock velocity v{sub s} is kappav/v{sub s} . In the nonresonantly saturated case, the precursor length declines less quickly with increasing v{sub s} . Where precursor length proportional to 1/v{sub s} gives constant electron heating, this increased precursor length could be expected to lead to higher electron temperatures for nonresonant amplification. This should be expected at faster supernova remnant shocks than studied by previous works. Existing results and new data analysis of SN 1006 and Cas A suggest some observational support for this idea.

Investigation of Vortex Clouds and Droplet Sizes in Heated Water Spray Patterns Generated by Axisymmetric Full Cone Nozzles

Directory of Open Access Journals (Sweden)

M. Y. Naz

2013-01-01

Full Text Available The hot water sprays are an important part of many industrial processes, where the detailed knowledge of physical phenomena involved in jet transportation, interaction, secondary breakup, evaporation, and coalescence of droplets is important to reach more efficient processes. The objective of the work was to study the water spray jet breakup dynamics, vortex cloud formation, and droplet size distribution under varying temperature and load pressure. Using a high speed camera, the spray patterns generated by axisymmetric full cone nozzles were visualized as a function water temperature and load pressure. The image analysis confirmed that the spray cone angle and width do not vary significantly with increasing Reynolds and Weber numbers at early injection phases leading to increased macroscopic spray propagation. The formation and decay of semitorus like vortex clouds were also noticed in spray structures generated at near water boiling point temperature. For the nozzle with smallest orifice diameter (1.19 mm, these vortex clouds were very clear at 90°C heating temperature and 1 bar water load pressure. In addition, the sauter mean diameter (SMD of the spray droplets was also measured by using Phase Doppler Anemometry (PDA at different locations downstream of the nozzle exit. It was noticed that SMD varies slightly w.r.t. position when measured at room temperature whereas at higher temperature values, it became almost constant at distance of 55 mm downstream of the nozzle exit.

Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome.

Science.gov (United States)

Chen, Meili; Hu, Yibo; Liu, Jingxing; Wu, Qi; Zhang, Chenglin; Yu, Jun; Xiao, Jingfa; Wei, Fuwen; Wu, Jiayan

2015-12-11

High-quality and complete gene models are the basis of whole genome analyses. The giant panda (Ailuropoda melanoleuca) genome was the first genome sequenced on the basis of solely short reads, but the genome annotation had lacked the support of transcriptomic evidence. In this study, we applied RNA-seq to globally improve the genome assembly completeness and to detect novel expressed transcripts in 12 tissues from giant pandas, by using a transcriptome reconstruction strategy that combined reference-based and de novo methods. Several aspects of genome assembly completeness in the transcribed regions were effectively improved by the de novo assembled transcripts, including genome scaffolding, the detection of small-size assembly errors, the extension of scaffold/contig boundaries, and gap closure. Through expression and homology validation, we detected three groups of novel full-length protein-coding genes. A total of 12.62% of the novel protein-coding genes were validated by proteomic data. GO annotation analysis showed that some of the novel protein-coding genes were involved in pigmentation, anatomical structure formation and reproduction, which might be related to the development and evolution of the black-white pelage, pseudo-thumb and delayed embryonic implantation of giant pandas. The updated genome annotation will help further giant panda studies from both structural and functional perspectives.

Full parallax three-dimensional computer generated hologram with occlusion effect using ray casting technique

International Nuclear Information System (INIS)

Zhang, Hao; Tan, Qiaofeng; Jin, Guofan

2013-01-01

Holographic display is capable of reconstructing the whole optical wave field of a three-dimensional (3D) scene. It is the only one among all the 3D display techniques that can produce all the depth cues. With the development of computing technology and spatial light modulators, computer generated holograms (CGHs) can now be used to produce dynamic 3D images of synthetic objects. Computation holography becomes highly complicated and demanding when it is employed to produce real 3D images. Here we present a novel algorithm for generating a full parallax 3D CGH with occlusion effect, which is an important property of 3D perception, but has often been neglected in fully computed hologram synthesis. The ray casting technique, which is widely used in computer graphics, is introduced to handle the occlusion issue of CGH computation. Horizontally and vertically distributed rays are projected from each hologram sample to the 3D objects to obtain the complex amplitude distribution. The occlusion issue is handled by performing ray casting calculations to all the hologram samples. The proposed algorithm has no restriction on or approximation to the 3D objects, and hence it can produce reconstructed images with correct shading effect and no visible artifacts. Programmable graphics processing unit (GPU) is used to perform parallel calculation. This is made possible because each hologram sample belongs to an independent operation. To demonstrate the performance of our proposed algorithm, an optical experiment is performed to reconstruct the 3D scene by using a phase-only spatial light modulator. We can easily perceive the accommodation cue by focusing our eyes on different depths of the scene and the motion parallax cue with occlusion effect by moving our eyes around. The experiment result confirms that the CGHs produced by our algorithm can successfully reconstruct 3D images with all the depth cues.

Second generation superconducting super collider dipole magnet cryostat design

International Nuclear Information System (INIS)

Niemann, R.C.; Bossert, R.C.; Carson, J.A.; Engler, N.H.; Gonczy, J.D.; Larson, E.T.; Nicol, T.H.; Ohmori, T.

1988-12-01

The SSC Magnet Development Program is developing accelerator dipole magnets in successive iterations. The initial iteration is complete with six full length model magnets and a thermal model having been built and tested. This initial experience along with the evolving SSC Magnet System Requirements have resulted in the second generation magnet cryostat design. It is this configuration that will be employed for the near term ongoing magnetic, thermal, string and accelerated life testing and will be the design considered for Phase I; i.e., Technology Orientation, of the SSC Magnet Industrialization Program. 5 refs., 7 figs., 1 tab

Emergency Department Length of Stay for Critical Care Admissions. A Population-based Study.

Science.gov (United States)

Rose, Louise; Scales, Damon C; Atzema, Clare; Burns, Karen E A; Gray, Sara; Doing, Christina; Kiss, Alex; Rubenfeld, Gordon; Lee, Jacques S

2016-08-01

Hospital emergency department (ED) strain is common in North America. Excessive strain may result in prolonged ED length of stay and may lead to worse outcomes for patients admitted to intensive care units (ICUs). To describe patient, ED, and hospital characteristics associated with prolonged ED length of stay for adult patients admitted from EDs to ICUs. We conducted a population-based cohort study in the Province of Ontario, Canada, including patients admitted to an adult ICU from an ED and excluding only interhospital transfers and scheduled visits. Using regression modeling, we examined associations between patient- and hospital-level characteristics and two ED performance measures: length of stay in the ED of more than 6 hours and 90-day mortality. From April 2007 to March 2012, 261,274 adults presented to 118 EDs in Ontario, generating 314,836 ICU admissions. This activity represented 4.1% of all adult ED visits (incidence, 1,374 ICU admissions/100,000 ED visits). Median (interquartile range) ED length of stay was 7 (4-13) hours. Less than half (41.4%; 95% confidence interval [CI], 41.2-41.5) of these patients had an ED length of stay of 6 hours or less, whereas 10.5% (95% CI, 10.4-10.6) stayed 24 hours or longer. Hospital characteristics associated with ED length of stay more than 6 hours included shift-level ED crowding (mean length of stay of patients of similar acuity registering during same 8 h epoch) (odds ratio [OR], 1.19/h; 95% CI, 1.19-1.19), ED annual visit volume (OR, 1.01/1,000 patients; 95% CI, 1.01-1.01), time of ED presentation (00:00-07:59) (OR, 1.41; 95% CI, 1.38-1.45), and ICU functioning at greater than 20% above the average annual census (OR, 1.10; 95% CI, 1.08-1.12). ED length of stay more than 6 hours was not associated with 90-day mortality after adjustment for selected confounders (OR, 0.99; 95% CI, 0.97-1.02). In this population-based study, less than half of adult ED patients were admitted to an ICU 6 hours or less after arrival to

Heritable circadian period length in a wild bird population

NARCIS (Netherlands)

Helm, B.; Visser, M.E.

2010-01-01

Timing is essential, but circadian clocks, which play a crucial role in timekeeping, are almost unaddressed in evolutionary ecology. A key property of circadian clocks is their free-running period length (τ), i.e. the time taken for a full cycle under constant conditions. Under laboratory

Characterising the large coherence length at diamond’s beamline I13L

Energy Technology Data Exchange (ETDEWEB)

Wagner, U. H., E-mail: ulrich.wagner@diamond.ac.uk; Parsons, A. [Diamond Light Source Ltd, Didcot, UK, OX11 0DE (United Kingdom); Rahomaki, J.; Vogt, U. [KTH Royal Institute of Technology, Stockholm, Sweden, SE-100 44 (Sweden); Rau, C. [Diamond Light Source Ltd, Didcot, UK, OX11 0DE (United Kingdom); Northwestern University, Chicago, IL 60611-3008 (United States)

2016-07-27

I13 is a 250 m long hard x-ray beamline (6 keV to 35 keV) at the Diamond Light Source. The beamline comprises of two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques [1]. An outstanding feature of the coherence branch, due to its length and a new generation of ultra-stable beamline instrumentation [2], is its capability of delivering a very large coherence length well beyond 200 μm, providing opportunities for unique x-ray optical experiments. In this paper we discuss the challenges of measuring a large coherence length and present quantitative measurement based on analyzing diffraction patterns from a boron fiber [3]. We also discuss the limitations of this classical method in respect to detector performance, very short and long coherence lengths. Furthermore we demonstrate how a Ronchi grating setup [4] can be used to quickly establish if the beam is coherent over a large area.

Characterising the large coherence length at diamond’s beamline I13L

International Nuclear Information System (INIS)

Wagner, U. H.; Parsons, A.; Rahomaki, J.; Vogt, U.; Rau, C.

2016-01-01

I13 is a 250 m long hard x-ray beamline (6 keV to 35 keV) at the Diamond Light Source. The beamline comprises of two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques [1]. An outstanding feature of the coherence branch, due to its length and a new generation of ultra-stable beamline instrumentation [2], is its capability of delivering a very large coherence length well beyond 200 μm, providing opportunities for unique x-ray optical experiments. In this paper we discuss the challenges of measuring a large coherence length and present quantitative measurement based on analyzing diffraction patterns from a boron fiber [3]. We also discuss the limitations of this classical method in respect to detector performance, very short and long coherence lengths. Furthermore we demonstrate how a Ronchi grating setup [4] can be used to quickly establish if the beam is coherent over a large area.

Increasing average period lengths by switching of robust chaos maps in finite precision

Science.gov (United States)

Nagaraj, N.; Shastry, M. C.; Vaidya, P. G.

2008-12-01

Grebogi, Ott and Yorke (Phys. Rev. A 38, 1988) have investigated the effect of finite precision on average period length of chaotic maps. They showed that the average length of periodic orbits (T) of a dynamical system scales as a function of computer precision (ɛ) and the correlation dimension (d) of the chaotic attractor: T ˜ɛ-d/2. In this work, we are concerned with increasing the average period length which is desirable for chaotic cryptography applications. Our experiments reveal that random and chaotic switching of deterministic chaotic dynamical systems yield higher average length of periodic orbits as compared to simple sequential switching or absence of switching. To illustrate the application of switching, a novel generalization of the Logistic map that exhibits Robust Chaos (absence of attracting periodic orbits) is first introduced. We then propose a pseudo-random number generator based on chaotic switching between Robust Chaos maps which is found to successfully pass stringent statistical tests of randomness.

Direct Numerical Simulations of a Full Stationary Wind-Turbine Blade

Science.gov (United States)

Qamar, Adnan; Zhang, Wei; Gao, Wei; Samtaney, Ravi

2014-11-01

Direct numerical simulation of flow past a full stationary wind-turbine blade is carried out at Reynolds number, Re = 10,000 placed at 0 and 5 (degree) angle of attack. The study is targeted to create a DNS database for verification of solvers and turbulent models that are utilized in wind-turbine modeling applications. The full blade comprises of a circular cylinder base that is attached to a spanwise varying airfoil cross-section profile (without twist). An overlapping composite grid technique is utilized to perform these DNS computations, which permits block structure in the mapped computational space. Different flow shedding regimes are observed along the blade length. Von-Karman shedding is observed in the cylinder shaft region of the turbine blade. Along the airfoil cross-section of the blade, near body shear layer breakdown is observed. A long tip vortex originates from the blade tip region, which exits the computational plane without being perturbed. Laminar to turbulent flow transition is observed along the blade length. The turbulent fluctuations amplitude decreases along the blade length and the flow remains laminar regime in the vicinity of the blade tip. The Strouhal number is found to decrease monotonously along the blade length. Average lift and drag coefficients are also reported for the cases investigated. Supported by funding under a KAUST OCRF-CRG grant.

Progress on next generation linear colliders

International Nuclear Information System (INIS)

Ruth, R.D.

1989-01-01

In this paper, I focus on reviewing the issues and progress on a next generation linear collider with the general parameters of energy, luminosity, length, power, technology. The energy range is dictated by physics with a mass reach well beyond LEP, although somewhat short of SSC. The luminosity is that required to obtain 10 3 /minus/ 10 4 units of R 0 per year. The length is consistent with a site on Stanford land with collisions occurring on the SLAC site. The power was determined by economic considerations. Finally, the technology was limited by the desire to have a next generation linear collider before the next century. 25 refs., 3 figs., 6 tabs

Test results on the long models and full scale prototypes of the second generation LHC arc dipoles

CERN Document Server

Billan, J; Bottura, L; Leroy, D; Pagano, O; Perin, R; Perini, D; Savary, F; Siemko, A; Sievers, P; Spigo, G; Vlogaert, J; Walckiers, L; Wyss, C; Rossi, L

1999-01-01

With the test of the first full scale prototype in June-July 1998, the R&D on the long superconducting dipoles based on the LHC design of 1993-95 has come to an end. This second generation of long magnets has a 56 mm coil aperture, is wound with 15 mm wide cable arranged in a 5 coil block layout. The series includes four 10 m long model dipoles, whose coils have been wound and collared in industry and the cold mass assembled and cryostated at CERN, as well as one 15 m long dipole prototype, manufactured totally in industry in the framework of a CERN-INFN collaboration for the LHC. After a brief description of particular features of the design and of the manufacturing, test results are reported and compared with the expectations. One magnet reached the record field for long model dipoles of 9.8 T but results have not been well reproducible from magnet to magnet. Guidelines for modifications that will appear in the next generation of long magnets, based on a six block coil design, are indicated in the concl...

NDT developments in the CEGB [Central Electricity Generating Board] for turbine and generator rotor shafts

International Nuclear Information System (INIS)

Denby, D.

1990-01-01

In common with many utilities world-wide, the Central Electricity Generating Board (CEGB) has suffered problems of cracking in turbine and generator rotors, in a wide range of Units. The type of cracking that has stimulated most NDT development work is transverse cracking initiating at the outside of shafts, though axial cracking at turbine disc keyways has also required considerable effort. This paper describes current and recent developments of NDT techniques and equipment designed to provide early warning and assessment of service-induced cracks which could propagate to failure. The following developments are included: in-situ inspection of LP turbine rotor shafts by means of low-angle ultrasonic beams fired along the length of the shaft; techniques for detecting and measuring cracking in shrunk-on turbine disc keyways; a remote, in-situ technique for cracking initiating in the pole teeth of large generator rotors, aimed at detecting cracks while they are small enough for the rotor to be repaired; an in-situ technique for rapidly inspecting these same generator rotors for the presence of larger cracks, by an ultrasonic beam fired along the length of the shaft; ultrasonic in-situ inspection of generator rotor teeth directly under the shrunk-on end (retaining) rings

The cosmic microwave background radiation power spectrum as a random bit generator for symmetric- and asymmetric-key cryptography

Directory of Open Access Journals (Sweden)

Jeffrey S. Lee

2017-10-01

Full Text Available In this note, the Cosmic Microwave Background (CMB Radiation is shown to be capable of functioning as a Random Bit Generator, and constitutes an effectively infinite supply of truly random one-time pad values of arbitrary length. It is further argued that the CMB power spectrum potentially conforms to the FIPS 140-2 standard. Additionally, its applicability to the generation of a (n × n random key matrix for a Vernam cipher is established. Keywords: Particle physics, Computer science, Mathematics, Astrophysics

Identifying Scientific Project-generated Data Citation from Full-text Articles: An Investigation of TCGA Data Citation

Directory of Open Access Journals (Sweden)

Jiao Li

2016-06-01

Full Text Available Purpose: In the open science era, it is typical to share project-generated scientific data by depositing it in an open and accessible database. Moreover, scientific publications are preserved in a digital library archive. It is challenging to identify the data usage that is mentioned in literature and associate it with its source. Here, we investigated the data usage of a government-funded cancer genomics project, The Cancer Genome Atlas (TCGA, via a full-text literature analysis. Design/methodology/approach: We focused on identifying articles using the TCGA dataset and constructing linkages between the articles and the specific TCGA dataset. First, we collected 5,372 TCGA-related articles from PubMed Central (PMC. Second, we constructed a benchmark set with 25 full-text articles that truly used the TCGA data in their studies, and we summarized the key features of the benchmark set. Third, the key features were applied to the remaining PMC full-text articles that were collected from PMC. Findings: The amount of publications that use TCGA data has increased significantly since 2011, although the TCGA project was launched in 2005. Additionally, we found that the critical areas of focus in the studies that use the TCGA data were glioblastoma multiforme, lung cancer, and breast cancer; meanwhile, data from the RNA-sequencing (RNA-seq platform is the most preferable for use. Research limitations: The current workflow to identify articles that truly used TCGA data is labor-intensive. An automatic method is expected to improve the performance. Practical implications: This study will help cancer genomics researchers determine the latest advancements in cancer molecular therapy, and it will promote data sharing and data-intensive scientific discovery. Originality/value: Few studies have been conducted to investigate data usage by government-funded projects/programs since their launch. In this preliminary study, we extracted articles that use TCGA data

Electron bunch length measurement with a wakefield radiation decelerator

Directory of Open Access Journals (Sweden)

Weiwei Li

2014-03-01

Full Text Available In this paper, we propose a novel method to measure the electron bunch length with a dielectric wakefield radiation (DWR decelerator which is composed of two dielectric-lined waveguides (DLWs and an electron spectrometer. When an electron beam passes through a DLW, the DWR is excited which leads to an energy loss of the electron beam. The energy loss is found to be largely dependent on the electron bunch length and can be easily measured by an electron spectrometer which is essential for a normal accelerator facility. Our study shows that this method has a high resolution and a great simplicity.

The determinants of IPO firm prospectus length in Africa

Directory of Open Access Journals (Sweden)

Bruce Hearn

2013-04-01

Full Text Available This paper studies the differential impact on IPO firm listing prospectus length from increasing proportions of foreign directors from civil as opposed to common law societies and social elites. Using a unique hand-collected and comprehensive sample of 165 IPO firms from across 18 African countries the evidence suggests that increasing proportions of directors from civil code law countries is associated with shorter prospectuses while the opposite is true for their common law counterparts. Furthermore increasing proportions of directors drawn from elevated social positions in indigenous society is related to increasing prospectus length in North Africa while being insignificant in SSA.

The structure of carbosilane dendrimers of higher generations

International Nuclear Information System (INIS)

Rogachev, A.V.; Kuklin, A.I.; Chernyj, A.Yu.; Ozerin, A.N.; Muzafarov, A.M.; Tatarinova, E.A.; Gordelij, V.I.

2008-01-01

Using small-angle neutron scattering method, we investigate the structure of carbosilane dendrimers of the ninth generation with a four-function core and butyl terminal groups. It is shown that the dendrimers in question are monodispersive objects having anisometric form. The values of the partial volume and the mean scattering length density are determined with the contrast variation method. The studied dendrimers exhibit the same size and distribution of the scattering length density. It is found that about 20% of the interior dendrimer volume is permeable to a solvent. Performing a Monte Carlo simulation, we reconstruct the spatial distribution of scattering length density over the dendrimers and reveal changing of the excluded volume for different contrasts. The spatial structure features of carbosilane dendrimers of higher generations are discussed

Determination of carrier diffusion length in GaN

Science.gov (United States)

Hafiz, Shopan; Zhang, Fan; Monavarian, Morteza; Avrutin, Vitaliy; Morkoç, Hadis; Özgür, Ümit; Metzner, Sebastian; Bertram, Frank; Christen, Jürgen; Gil, Bernard

2015-01-01

Diffusion lengths of photo-excited carriers along the c-direction were determined from photoluminescence (PL) and cross-sectional cathodoluminescence (CL) measurements in p- and n-type GaN epitaxial layers grown on c-plane sapphire by metal-organic chemical vapor deposition. The investigated samples incorporate a 6 nm thick In0.15Ga0.85N active layer capped with either 500 nm p-GaN or 1500 nm n-GaN. The top GaN layers were etched in steps and PL from the InGaN active region and the underlying layers was monitored as a function of the top GaN thickness upon photo-generation near the surface region by above bandgap excitation. Taking into consideration the absorption in the top GaN layer as well as active and underlying layers, the diffusion lengths at 295 K and at 15 K were measured to be 93 ± 7 nm and 70 ± 7 nm for Mg-doped p-type GaN and 432 ± 30 nm and 316 ± 30 nm for unintentionally doped n-type GaN, respectively, at photogenerated carrier densities of 4.2 × 1018 cm-3 using PL spectroscopy. CL measurements of the unintentionally doped n-type GaN layer at much lower carrier densities of 1017 cm-3 revealed a longer diffusion length of 525 ± 11 nm at 6 K.

The influence of the edge effect on the skyrmion generation in a magnetic nanotrack

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N. Ran

2017-02-01

Full Text Available Magnetic skyrmions might be used for building next-generation nanomagnetic and spintronic devices, as they have several perspective properties, such as topologically protected stability, nanoscale size, and ultra-low depinning current density. Here we study the influence of the edge effect on the current-induced generation of a magnetic skyrmion in a finite-length thin-film ferromagnetic nanotrack with interface-induced Dzyaloshinskii-Moriya interaction. It shows that a stable skyrmion or a bunch of skyrmions can be successfully generated as long as the distance between the current injection region and the nanotrack terminal is larger than a certain threshold. We investigate the failed skyrmion generation caused by the edge effect, which will lead to an error writing event. We also present the phase diagrams of the skyrmion generation obtained for different material and geometric parameters. Our results could be useful for designing skyrmion-based information storage devices.

Optimizing x-ray mirror thermal performance using variable length cooling for second generation FELs

Science.gov (United States)

Hardin, Corey L.; Srinivasan, Venkat N.; Amores, Lope; Kelez, Nicholas M.; Morton, Daniel S.; Stefan, Peter M.; Nicolas, Josep; Zhang, Lin; Cocco, Daniele

2016-09-01

The success of the LCLS led to an interest across a number of disciplines in the scientific community including physics, chemistry, biology, and material science. Fueled by this success, SLAC National Accelerator Laboratory is developing a new high repetition rate free electron laser, LCLS-II, a superconducting linear accelerator capable of a repetition rate up to 1 MHz. Undulators will be optimized for 200 to 1300 eV soft X-rays, and for 1000 to 5000 eV hard X-rays. To absorb spontaneous radiation, higher harmonic energies and deflect the x-ray beam to various end stations, the transport and diagnostics system includes grazing incidence plane mirrors on both the soft and Hard X-ray beamline. To deliver the FEL beam with minimal power loss and wavefront distortion, we need mirrors of height errors below 1nm rms in operational conditions. We need to mitigate the thermal load effects due to the high repetition rate. The absorbed thermal profile is highly dependent on the beam divergence, and this is a function of the photon energy. To address this complexity, we developed a mirror cradle with variable length cooling and first order curve correction. Mirror figure error is minimized using variable length water-cooling through a gallium-indium eutectic bath. Curve correction is achieved with an off-axis bender that will be described in details. We present the design features, mechanical analysis and results from optical and mechanical tests of a prototype assembly, with particular regards to the figure sensitivity to bender corrections.

Association of Telomere Length with Breast Cancer Prognostic Factors.

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Kaoutar Ennour-Idrissi

Full Text Available Telomere length, a marker of cell aging, seems to be affected by the same factors thought to be associated with breast cancer prognosis.To examine associations of peripheral blood cell-measured telomere length with traditional and potential prognostic factors in breast cancer patients.We conducted a cross-sectional analysis of data collected before surgery from 162 breast cancer patients recruited consecutively between 01/2011 and 05/2012, at a breast cancer reference center. Data on the main lifestyle factors (smoking, alcohol consumption, physical activity were collected using standardized questionnaires. Anthropometric factors were measured. Tumor biological characteristics were extracted from pathology reports. Telomere length was measured using a highly reproducible quantitative PCR method in peripheral white blood cells. Spearman partial rank-order correlations and multivariate general linear models were used to evaluate relationships between telomere length and prognostic factors.Telomere length was positively associated with total physical activity (rs = 0.17, P = 0.033; Ptrend = 0.069, occupational physical activity (rs = 0.15, P = 0.054; Ptrend = 0.054 and transportation-related physical activity (rs = 0.19, P = 0.019; P = 0.005. Among post-menopausal women, telomere length remained positively associated with total physical activity (rs = 0.27, P = 0.016; Ptrend = 0.054 and occupational physical activity (rs = 0.26, P = 0.021; Ptrend = 0.056 and was only associated with transportation-related physical activity among pre-menopausal women (rs = 0.27, P = 0.015; P = 0.004. No association was observed between telomere length and recreational or household activities, other lifestyle factors or traditional prognostic factors.Telomeres are longer in more active breast cancer patients. Since white blood cells are involved in anticancer immune responses, these findings suggest that even regular low-intensity physical activity, such as that

Porosity effects in flame length of the porous burners

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Fatemeh Bahadori

2014-10-01

Full Text Available Furnaces are the devices for providing heat to the industrial systems like boilers, gas turbines and etc. The main challenge of furnaces is emission of huge air pollutants. However, porous burners produce less contaminant compared to others. The quality of the combustion process in the porous burners depends on the length of flame in the porous medium. In this paper, the computational fluid dynamic (CFD is used to investigate the porosity effects on the flame length of the combustion process in porous burner. The simulation results demonstrate that increasing the porosity increases the flame length and the combustion zone extends forward. So, combustion quality increases and production of carbon monoxide decrease. It is possible to conclude that temperature distribution in low porosity burner is lower and more uniform than high porosity one. Therefore, by increasing the porosity of the burner, the production of nitrogen oxides increases. So, using an intermediate porosity in the burner appears to be reasonable.

Measurement of Telomere Length in Colorectal Cancers for Improved Molecular Diagnosis

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Eric Le Balc’h

2017-08-01

Full Text Available All tumors have in common to reactivate a telomere maintenance mechanism to allow for unlimited proliferation. On the other hand, genetic instability found in some tumors can result from the loss of telomeres. Here, we measured telomere length in colorectal cancers (CRCs using TRF (Telomere Restriction Fragment analysis. Telomeric DNA content was also quantified as the ratio of total telomeric (TTAGGG sequences over that of the invariable Alu sequences. In most of the 125 CRCs analyzed, there was a significant diminution in telomere length compared with that in control healthy tissue. Only 34 tumors exhibited no telomere erosion and, in some cases, a slight telomere lengthening. Telomere length did not correlate with age, gender, tumor stage, tumor localization or stage of tumor differentiation. In addition, while telomere length did not correlate with the presence of a mutation in BRAF (V-raf murine sarcoma viral oncogene homolog B, PIK3CA (phosphatidylinositol 3-kinase catalytic subunit, or MSI status, it was significantly associated with the occurrence of a mutation in KRAS. Interestingly, we found that the shorter the telomeres in healthy tissue of a patient, the larger an increase in telomere length in the tumor. Our study points to the existence of two types of CRCs based on telomere length and reveals that telomere length in healthy tissue might influence telomere maintenance mechanisms in the tumor.

Measurements of Turbulent Flame Speed and Integral Length Scales in a Lean Stationary Premixed Flame

OpenAIRE

Klingmann, Jens; Johansson, Bengt

1998-01-01

Turbulent premixed natural gas - air flame velocities have been measured in a stationary axi-symmetric burner using LDA. The flame was stabilized by letting the flow retard toward a stagnation plate downstream of the burner exit. Turbulence was generated by letting the flow pass through a plate with drilled holes. Three different hole diameters were used, 3, 6 and 10 mm, in order to achieve different turbulent length scales. Turbulent integral length scales were measured using two-point LD...

Source-Independent Quantum Random Number Generation

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Zhu Cao

2016-02-01

Full Text Available Quantum random number generators can provide genuine randomness by appealing to the fundamental principles of quantum mechanics. In general, a physical generator contains two parts—a randomness source and its readout. The source is essential to the quality of the resulting random numbers; hence, it needs to be carefully calibrated and modeled to achieve information-theoretical provable randomness. However, in practice, the source is a complicated physical system, such as a light source or an atomic ensemble, and any deviations in the real-life implementation from the theoretical model may affect the randomness of the output. To close this gap, we propose a source-independent scheme for quantum random number generation in which output randomness can be certified, even when the source is uncharacterized and untrusted. In our randomness analysis, we make no assumptions about the dimension of the source. For instance, multiphoton emissions are allowed in optical implementations. Our analysis takes into account the finite-key effect with the composable security definition. In the limit of large data size, the length of the input random seed is exponentially small compared to that of the output random bit. In addition, by modifying a quantum key distribution system, we experimentally demonstrate our scheme and achieve a randomness generation rate of over 5×10^{3}  bit/s.

A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

Science.gov (United States)

Frampton, Dan; Gallo Cassarino, Tiziano; Raffle, Jade; Hubb, Jonathan; Ferns, R. Bridget; Waters, Laura; Tong, C. Y. William; Kozlakidis, Zisis; Hayward, Andrew; Kellam, Paul; Pillay, Deenan; Clark, Duncan; Nastouli, Eleni; Leigh Brown, Andrew J.

2018-01-01

Background & methods The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. Results The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. Conclusions

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

Energy Technology Data Exchange (ETDEWEB)

Wang, Bin; Xu, Bingqian, E-mail: bxu@engr.uga.edu [Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605 (United States); Lou, Zhichao [Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605 (United States); College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016 (China); Zhang, Haiqian [College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016 (China)

2016-03-21

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

International Nuclear Information System (INIS)

Wang, Bin; Xu, Bingqian; Lou, Zhichao; Zhang, Haiqian

2016-01-01

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

Science.gov (United States)

Wang, Bin; Lou, Zhichao; Zhang, Haiqian; Xu, Bingqian

2016-03-01

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

Word length, set size, and lexical factors: Re-examining what causes the word length effect.

Science.gov (United States)

Guitard, Dominic; Gabel, Andrew J; Saint-Aubin, Jean; Surprenant, Aimée M; Neath, Ian

2018-04-19

The word length effect, better recall of lists of short (fewer syllables) than long (more syllables) words has been termed a benchmark effect of working memory. Despite this, experiments on the word length effect can yield quite different results depending on set size and stimulus properties. Seven experiments are reported that address these 2 issues. Experiment 1 replicated the finding of a preserved word length effect under concurrent articulation for large stimulus sets, which contrasts with the abolition of the word length effect by concurrent articulation for small stimulus sets. Experiment 2, however, demonstrated that when the short and long words are equated on more dimensions, concurrent articulation abolishes the word length effect for large stimulus sets. Experiment 3 shows a standard word length effect when output time is equated, but Experiments 4-6 show no word length effect when short and long words are equated on increasingly more dimensions that previous demonstrations have overlooked. Finally, Experiment 7 compared recall of a small and large neighborhood words that were equated on all the dimensions used in Experiment 6 (except for those directly related to neighborhood size) and a neighborhood size effect was still observed. We conclude that lexical factors, rather than word length per se, are better predictors of when the word length effect will occur. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

THE NETWORK OF CITY PUBLIC TRANSPORT AS THE BASE FOR TRIP LENGTH DISTRIBUTION DETERMINING

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P. Horbachov

2015-07-01

Full Text Available The up-to-date methods of modelling the demand for public transport services require an objective estimation and improvement. Such an improvement can be achieved by taking into account the trip length distribution during trip matrix calculation that requires determining the reasons of regularities occurance in city population trip lengths.

Determination of the Pt spin diffusion length by spin-pumping and spin Hall effect

Energy Technology Data Exchange (ETDEWEB)

Zhang, Wei; Pearson, John E.; Hoffmann, Axel [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Vlaminck, Vincent [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Colegio de Ciencias e Ingenería, Universidad San Fransciso de Quito, Quito (Ecuador); Divan, Ralu [Center for Nanoscale Materials, Argonne National Laboratory, Illinois 60439 (United States); Bader, Samuel D. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Center for Nanoscale Materials, Argonne National Laboratory, Illinois 60439 (United States)

2013-12-09

The spin diffusion length of Pt at room temperature and at 8 K is experimentally determined via spin pumping and spin Hall effect in permalloy/Pt bilayers. Voltages generated during excitation of ferromagnetic resonance from the inverse spin Hall effect and anisotropic magnetoresistance effect were investigated with a broadband approach. Varying the Pt layer thickness gives rise to an evolution of the voltage line shape due to the superposition of the above two effects. By studying the ratio of the two voltage components with the Pt layer thickness, the spin diffusion length of Pt can be directly extracted. We obtain a spin diffusion length of ∼1.2 nm at room temperature and ∼1.6 nm at 8 K.

Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors

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Tatiana Tatarinova

2015-01-01

Full Text Available Proteins of the same functional family (for example, kinases may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3 content tend to have longer genes than species with low GC3 content.

Optimization of the Heat Exchangers of a Thermoelectric Generation System

Science.gov (United States)

Martínez, A.; Vián, J. G.; Astrain, D.; Rodríguez, A.; Berrio, I.

2010-09-01

The thermal resistances of the heat exchangers have a strong influence on the electric power produced by a thermoelectric generator. In this work, the heat exchangers of a thermoelectric generator have been optimized in order to maximize the electric power generated. This thermoelectric generator harnesses heat from the exhaust gas of a domestic gas boiler. Statistical design of experiments was used to assess the influence of five factors on both the electric power generated and the pressure drop in the chimney: height of the generator, number of modules per meter of generator height, length of the fins of the hot-side heat exchanger (HSHE), length of the gap between fins of the HSHE, and base thickness of the HSHE. The electric power has been calculated using a computational model, whereas Fluent computational fluid dynamics (CFD) has been used to obtain the thermal resistances of the heat exchangers and the pressure drop. Finally, the thermoelectric generator has been optimized, taking into account the restrictions on the pressure drop.

Oblique-Length Contraction Factor in the Special Theory of Relativity

Directory of Open Access Journals (Sweden)

Smarandache F.

2013-01-01

Full Text Available In this paper one generalizes the Lorentz Contraction Factor for the case when the lengths are moving at an oblique angle with respect to the motion direction. One shows that the angles of the moving relativistic objects are distorted.

Gap length distributions by PEPR

International Nuclear Information System (INIS)

Warszawer, T.N.

1980-01-01

Conditions guaranteeing exponential gap length distributions are formulated and discussed. Exponential gap length distributions of bubble chamber tracks first obtained on a CRT device are presented. Distributions of resulting average gap lengths and their velocity dependence are discussed. (orig.)

Targeting the Full Length of the Motor End Plate Regions in the Mouse Forelimb Increases the Uptake of Fluoro-Gold into Corresponding Spinal Cord Motor Neurons

Directory of Open Access Journals (Sweden)

Andrew Paul Tosolini

2013-05-01

Full Text Available Lower motor neuron dysfunction is one of the most debilitating motor conditions. In this regard, transgenic mouse models of various lower motor neuron dysfunctions provide insight into the mechanisms underlying these pathologies and can also aid the development of new therapies. Viral-mediated gene therapy can take advantage of the muscle-motor neuron topographical relationship to shuttle therapeutic genes into specific populations of motor neurons in these mouse models. In this context, motor end plates (MEPs are highly specialised regions on the skeletal musculature that offer direct access to the pre-synaptic nerve terminals, henceforth to the spinal cord motor neurons. The aim of this study was two-folded. First it was to characterise the exact position of the MEP regions for several muscles of the mouse forelimb using acetylcholinesterase histochemistry. This MEP-muscle map was then used to guide a series of intramuscular injections of Fluoro-Gold (FG in order to characterise the distribution of the innervating motor neurons. This analysis revealed that the MEPs are typically organised in an orthogonal fashion across the muscle fibres and extending throughout the full width of each muscle. Furthermore, targeting the full length of the MEP regions gave rise to a seemingly greater number of labelled motor neurons that are organised into columns spanning through more spinal cord segments than previously reported. The present analysis suggests that targeting the full width of the muscles’ MEP regions with FG increases the somatic availability of the tracer. This process ensures a greater uptake of the tracer by the pre-synaptic nerve terminals, hence maximising the labelling in spinal cord motor neurons. This investigation should have positive implications for future studies involving the somatic delivery of therapeutic genes into motor neurons for the treatment of various motor dysfunctions.

Research on determine the absolute neutron output of distributed pulse generators

International Nuclear Information System (INIS)

Li Bojun; Tang Zhangkui; Wang Dong; Yang Gaozhao; Peng Taiping

2009-01-01

In order to determine the absolute neutron output of distributed pulse generators, we deduced equivalent length to deal with experimental data, according to the different layout and weighting of multiple pulse generators. The deposited energy in scintillation crystal and the integral flux which drilling through crystal interface was simulated by MCNP code. The result shows the simulated proportion of different distributed pulse generators is approximately agreed with experimental data. The validity of the equivalent length model was proved by the consistent results between calculation and experimental data. (authors)

Probing cooperative force generation in collective cancer invasion

Science.gov (United States)

Alobaidi, Amani A.; Xu, Yaopengxiao; Chen, Shaohua; Jiao, Yang; Sun, Bo

2017-08-01

Collective cellular dynamics in the three-dimensional extracellular matrix (ECM) plays a crucial role in many physiological processes such as cancer invasion. Both chemical and mechanical signaling support cell-cell communications on a variety of length scales, leading to collective migratory behaviors. Here we conduct experiments using 3D in vitro tumor models and develop a phenomenological model in order to probe the cooperativity of force generation in the collective invasion of breast cancer cells. In our model, cell-cell communication is characterized by a single parameter that quantifies the correlation length of cellular migration cycles. We devise a stochastic reconstruction method to generate realizations of cell colonies with specific contraction phase correlation functions and correlation length a. We find that as a increases, the characteristic size of regions containing cells with similar contraction phases grows. For small a values, the large fluctuations in individual cell contraction phases smooth out the temporal fluctuations in the time-dependent deformation field in the ECM. For large a values, the periodicity of an individual cell contraction cycle is clearly manifested in the temporal variation of the overall deformation field in the ECM. Through quantitative comparisons of the simulated and experimentally measured deformation fields, we find that the correlation length for collective force generation in the breast cancer diskoid in geometrically micropatterned ECM (DIGME) system is a≈ 25~μ \\text{m} , which is roughly twice the linear size of a single cell. One possible mechanism for this intermediate cell correlation length is the fiber-mediated stress propagation in the 3D ECM network in the DIGME system.

Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers

Directory of Open Access Journals (Sweden)

Phillip R. Myer

2016-09-01

Full Text Available Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided. For more information, see “Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers” P.R. Myer, M. Kim, H.C. Freetly, T.P.L. Smith (2016 [1]. Keywords: 16S rRNA gene, MiSeq, Pacific Biosciences, Rumen microbiome

Identification of a truncated nucleoprotein in avian metapneumovirus-infected cells encoded by a second AUG, in-frame to the full-length gene

Directory of Open Access Journals (Sweden)

Alvarez Rene

2005-04-01

Full Text Available Abstract Background Avian metapneumoviruses (aMPV cause an upper respiratory disease with low mortality, but high morbidity primarily in commercial turkeys. There are three types of aMPV (A, B, C of which the C type is found only in the United States. Viruses related to aMPV include human, bovine, ovine, and caprine respiratory syncytial viruses and pneumonia virus of mice, as well as the recently identified human metapneumovirus (hMPV. The aMPV and hMPV have become the type viruses of a new genus within the Metapneumovirus. The aMPV nucleoprotein (N amino acid sequences of serotypes A, B, and C were aligned for comparative analysis. Based on predicted antigenicity of consensus protein sequences, five aMPV-specific N peptides were synthesized for development of peptide-antigens and antisera. Results The presence of two aMPV nucleoprotein (N gene encoded polypeptides was detected in aMPV/C/US/Co and aMPV/A/UK/3b infected Vero cells. Nucleoprotein 1 (N1 encoded from the first open reading frame (ORF was predicted to be 394 amino acids in length for aMPV/C/US/Co and 391 amino acids in length for aMPV/A/UK/3b with approximate molecular weights of 43.3 kilodaltons and 42.7 kilodaltons, respectively. Nucleoprotein 2 (N2 was hypothesized to be encoded by a second downstream ORF in-frame with ORF1 and encoded a protein predicted to contain 328 amino acids for aMPV/C/US/Co or 259 amino acids for aMPV/A/UK/3b with approximate molecular weights of 36 kilodaltons and 28.3 kilodaltons, respectively. Peptide antibodies to the N-terminal and C-terminal portions of the aMPV N protein confirmed presence of these products in both aMPV/C/US/Co- and aMPV/A/UK/3b-infected Vero cells. N1 and N2 for aMPV/C/US/Co ORFs were molecularly cloned and expressed in Vero cells utilizing eukaryotic expression vectors to confirm identity of the aMPV encoded proteins. Conclusion This is the first reported identification of potential, accessory in-frame N2 ORF gene products among