Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains.

Science.gov (United States)

Kurushima, Jun; Ike, Yasuyoshi; Tomita, Haruyoshi

2016-09-01

Bacteriocin 41 (Bac41) is the plasmid-encoded bacteriocin produced by the opportunistic pathogen Enterococcus faecalis Its genetic determinant consists of bacL1 (effector), bacL2 (regulator), bacA (effector), and bacI (immunity). The secreted effectors BacL1 and BacA coordinate to induce the lytic cell death of E. faecalis Meanwhile, the immunity factor BacI provides self-resistance to the Bac41 producer, E. faecalis, against the action of BacL1 and BacA. In this study, we demonstrated that more than half of the 327 clinical strains of E. faecalis screened had functional Bac41 genes. Analysis of the genetic structure of the Bac41 genes in the DNA sequences of the E. faecalis strains revealed that the Bac41-like genes consist of a relatively conserved region and a variable region located downstream from bacA Based on similarities in the variable region, the Bac41-like genes could be classified into type I, type IIa, and type IIb. Interestingly, the distinct Bac41 types had specific immunity factors for self-resistance, BacI1 or BacI2, and did not show cross-immunity to the other type of effector. We also demonstrated experimentally that the specificity of the immunity was determined by the combination of the C-terminal region of BacA and the presence of the unique BacI1 or BacI2 factor. These observations suggested that Bac41-like bacteriocin genes are extensively disseminated among E. faecalis strains in the clinical environment and can be grouped into at least three types. It was also indicated that the partial diversity results in specificity of self-resistance which may offer these strains a competitive advantage. Bacteriocins are antibacterial effectors produced by bacteria. In general, a bacteriocin-coding gene is accompanied by a cognate immunity gene that confers self-resistance on the bacteriocin-producing bacterium itself. We demonstrated that one of the bacteriocins, Bac41, is disseminated among E. faecalis clinical strains and the Bac41 subtypes with

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

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Blackmon Barbara P

2011-07-01

Full Text Available Abstract Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.

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Ragupathy, Raja; Rathinavelu, Rajkumar; Cloutier, Sylvie

2011-05-09

Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be

An efficient approach to BAC based assembly of complex genomes

Czech Academy of Sciences Publication Activity Database

Visendi, P.; Berkman, P.J.; Hayashi, S.; Golicz, A.A.; Bayer, P.E.; Ruperao, P.; Hurgobin, B.; Montenegro, J.; Chan, C.K.K.; Staňková, Helena; Batley, J.; Šimková, Hana; Doležel, Jaroslav; Edwards, D.

2016-01-01

Roč. 12, JAN 20 (2016), s. 2 ISSN 1746-4811 R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GAP501/12/2554 Institutional support: RVO:61389030 Keywords : Next-generation sequencing * SASSY * BAC Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.510, year: 2016

Transposon-mediated BAC transgenesis in zebrafish and mice

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Sumiyama Kenta

2009-10-01

Full Text Available Abstract Background Bacterial artificial chromosomes (BACs are among the most widely used tools for studies of gene regulation and function in model vertebrates, yet methods for predictable delivery of BAC transgenes to the genome are currently limited. This is because BAC transgenes are usually microinjected as naked DNA into fertilized eggs and are known to integrate as multi-copy concatamers in the genome. Although conventional methods for BAC transgenesis have been very fruitful, complementary methods for generating single copy BAC integrations would be desirable for many applications. Results We took advantage of the precise cut-and-paste behavior of a natural transposon, Tol2, to develop a new method for BAC transgenesis. In this new method, the minimal sequences of the Tol2 transposon were used to deliver precisely single copies of a ~70 kb BAC transgene to the zebrafish and mouse genomes. We mapped the BAC insertion sites in the genome by standard PCR methods and confirmed transposase-mediated integrations. Conclusion The Tol2 transposon has a surprisingly large cargo capacity that can be harnessed for BAC transgenesis. The precise delivery of single-copy BAC transgenes by Tol2 represents a useful complement to conventional BAC transgenesis, and could aid greatly in the production of transgenic fish and mice for genomics projects, especially those in which single-copy integrations are desired.

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L. genome

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Cloutier Sylvie

2011-05-01

Full Text Available Abstract Background Flax (Linum usitatissimum L. is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb. The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%, followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable

Construction of BAC Libraries from Flow-Sorted Chromosomes.

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Šafář, Jan; Šimková, Hana; Doležel, Jaroslav

2016-01-01

Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes.

Genetic stability of pestivirus genomes cloned into BACs

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, Ilona; Uttenthal, Åse

pestivirus genomes to demonstrate the suitability of the BAC vector for harbouring pestivirus genomes. Two BAC clones, comprising the complete genomes of BDV Gifhorn (pBeloGif3) and CSFV Paderborn (pBeloPader10) were passaged 15 times in E.coli representing at least 360 bacteria generations. From 15th...

Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

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Shultz Jeffry

2008-07-01

Full Text Available Abstract Background Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS. Here the aim was to use BAC end sequences (BES derived from three minimum tile paths (MTP to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs were single nucleotide polymorphisms (SNPs; 89% and single nucleotide indels (SNIs 10%. Larger indels were rare but present (1%. Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. Conclusion The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de

Features of the organization of bread wheat chromosome 5BS based on physical mapping.

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Salina, Elena A; Nesterov, Mikhail A; Frenkel, Zeev; Kiseleva, Antonina A; Timonova, Ekaterina M; Magni, Federica; Vrána, Jan; Šafář, Jan; Šimková, Hana; Doležel, Jaroslav; Korol, Abraham; Sergeeva, Ekaterina M

2018-02-09

The IWGSC strategy for construction of the reference sequence of the bread wheat genome is based on first obtaining physical maps of the individual chromosomes. Our aim is to develop and use the physical map for analysis of the organization of the short arm of wheat chromosome 5B (5BS) which bears a number of agronomically important genes, including genes conferring resistance to fungal diseases. A physical map of the 5BS arm (290 Mbp) was constructed using restriction fingerprinting and LTC software for contig assembly of 43,776 BAC clones. The resulting physical map covered ~ 99% of the 5BS chromosome arm (111 scaffolds, N50 = 3.078 Mb). SSR, ISBP and zipper markers were employed for anchoring the BAC clones, and from these 722 novel markers were developed based on previously obtained data from partial sequencing of 5BS. The markers were mapped using a set of Chinese Spring (CS) deletion lines, and F2 and RICL populations from a cross of CS and CS-5B dicoccoides. Three approaches have been used for anchoring BAC contigs on the 5BS chromosome, including clone-by-clone screening of BACs, GenomeZipper analysis, and comparison of BAC-fingerprints with in silico fingerprinting of 5B pseudomolecules of T. dicoccoides. These approaches allowed us to reach a high level of BAC contig anchoring: 96% of 5BS BAC contigs were located on 5BS. An interesting pattern was revealed in the distribution of contigs along the chromosome. Short contigs (200-999 kb) containing markers for the regions interrupted by tandem repeats, were mainly localized to the 5BS subtelomeric block; whereas the distribution of larger 1000-3500 kb contigs along the chromosome better correlated with the distribution of the regions syntenic to rice, Brachypodium, and sorghum, as detected by the Zipper approach. The high fingerprinting quality, LTC software and large number of BAC clones selected by the informative markers in screening of the 43,776 clones allowed us to significantly increase the

A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC libraries using High Resolution Melt analysis

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Caligari Peter DS

2010-05-01

Full Text Available Abstract Background The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries is a widely used alternative to high density filter hybridisation of bacterial colonies. To date, concerns over reliability have led most if not all groups engaged in high throughput physical mapping projects to favour BAC DNA isolation prior to amplification by conventional PCR. Results Here, we report the first combined use of Multiplex Tandem PCR (MT-PCR and High Resolution Melt (HRM analysis on bacterial stocks of BAC library superpools as a means of rapidly anchoring markers to BAC colonies and thereby to integrate genetic and physical maps. We exemplify the approach using a BAC library of the model plant Arabidopsis thaliana. Super pools of twenty five 384-well plates and two-dimension matrix pools of the BAC library were prepared for marker screening. The entire procedure only requires around 3 h to anchor one marker. Conclusions A pre-amplification step during MT-PCR allows high multiplexing and increases the sensitivity and reliability of subsequent HRM discrimination. This simple gel-free protocol is more reliable, faster and far less costly than conventional PCR screening. The option to screen in parallel 3 genetic markers in one MT-PCR-HRM reaction using templates from directly pooled bacterial stocks of BAC-containing bacteria further reduces time for anchoring markers in physical maps of species with large genomes.

New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits

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Feltus Frank A

2011-07-01

homoeologous harboring OsBRI1 orthologs present a glimpse into the switchgrass genome structure and complexity. Data obtained demonstrate the feasibility of using HICF fingerprinting to resolve the homoeologous chromosomes of the two distinct genomes in switchgrass, providing a robust and accurate BAC-based physical platform for this species. The genomic resources and sequence data generated will lay the foundation for deciphering the switchgrass genome and lead the way for an accurate genome sequencing strategy.

Giant panda BAC library construction and assembly of a 650-kb contig spanning major histocompatibility complex class II region

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Pan Hui-Juan

2007-09-01

Full Text Available Abstract Background Giant panda is rare and endangered species endemic to China. The low rates of reproductive success and infectious disease resistance have severely hampered the development of captive and wild populations of the giant panda. The major histocompatibility complex (MHC plays important roles in immune response and reproductive system such as mate choice and mother-fetus bio-compatibility. It is thus essential to understand genetic details of the giant panda MHC. Construction of a bacterial artificial chromosome (BAC library will provide a new tool for panda genome physical mapping and thus facilitate understanding of panda MHC genes. Results A giant panda BAC library consisting of 205,800 clones has been constructed. The average insert size was calculated to be 97 kb based on the examination of 174 randomly selected clones, indicating that the giant panda library contained 6.8-fold genome equivalents. Screening of the library with 16 giant panda PCR primer pairs revealed 6.4 positive clones per locus, in good agreement with an expected 6.8-fold genomic coverage of the library. Based on this BAC library, we constructed a contig map of the giant panda MHC class II region from BTNL2 to DAXX spanning about 650 kb by a three-step method: (1 PCR-based screening of the BAC library with primers from homologous MHC class II gene loci, end sequences and BAC clone shotgun sequences, (2 DNA sequencing validation of positive clones, and (3 restriction digest fingerprinting verification of inter-clone overlapping. Conclusion The identifications of genes and genomic regions of interest are greatly favored by the availability of this giant panda BAC library. The giant panda BAC library thus provides a useful platform for physical mapping, genome sequencing or complex analysis of targeted genomic regions. The 650 kb sequence-ready BAC contig map of the giant panda MHC class II region from BTNL2 to DAXX, verified by the three-step method, offers a

Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments.

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Chen, Chao; Zhao, Xinqing; Jin, Yingyu; Zhao, Zongbao Kent; Suh, Joo-Won

2014-11-01

Bacterial artificial chromosomal (BAC) vectors are increasingly being used in cloning large DNA fragments containing complex biosynthetic pathways to facilitate heterologous production of microbial metabolites for drug development. To express inserted genes using Streptomyces species as the production hosts, an integration expression cassette is required to be inserted into the BAC vector, which includes genetic elements encoding a phage-specific attachment site, an integrase, an origin of transfer, a selection marker and a promoter. Due to the large sizes of DNA inserted into the BAC vectors, it is normally inefficient and time-consuming to assemble these fragments by routine PCR amplifications and restriction-ligations. Here we present a rapid method to insert fragments to construct BAC-based expression vectors. A DNA fragment of about 130 bp was designed, which contains upstream and downstream homologous sequences of both BAC vector and pIB139 plasmid carrying the whole integration expression cassette. In-Fusion cloning was performed using the designer DNA fragment to modify pIB139, followed by λ-RED-mediated recombination to obtain the BAC-based expression vector. We demonstrated the effectiveness of this method by rapid construction of a BAC-based expression vector with an insert of about 120 kb that contains the entire gene cluster for biosynthesis of immunosuppressant FK506. The empty BAC-based expression vector constructed in this study can be conveniently used for construction of BAC libraries using either microbial pure culture or environmental DNA, and the selected BAC clones can be directly used for heterologous expression. Alternatively, if a BAC library has already been constructed using a commercial BAC vector, the selected BAC vectors can be manipulated using the method described here to get the BAC-based expression vectors with desired gene clusters for heterologous expression. The rapid construction of a BAC-based expression vector facilitates

Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

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Asamizu, Erika; Shirasawa, Kenta; Hirakawa, Hideki; Sato, Shusei; Tabata, Satoshi; Yano, Kentaro; Ariizumi, Tohru; Shibata, Daisuke; Ezura, Hiroshi

2012-01-01

A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. PMID:23227037

Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

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Wang Jintu

2011-04-01

Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

Science.gov (United States)

2011-01-01

Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

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Hsiao Yu-Yun

2011-01-01

Full Text Available Abstract Background Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC end sequences (BESs can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding. Results We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively, at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6% were predicted to represent protein-encoding regions, whereas 1,272 (23.0% contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively, whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6% of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species. Conclusion Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive

Fight Bac! | Partnership for Food Safety Education

Science.gov (United States)

Fight Bac! Fight Bac! Fight Bac! Partnership for Food Safety Education Supporting consumers to & Symptoms Food Safety Glossary Food Safety Education Food Safety Education Month 2017 Don't Wing Spanish Resources Food Safety Education Food Safety Education Month 2017 Don't Wing It The Story of Your

A controlled comparison of the BacT/ALERT® 3D and VIRTUO™ microbial detection systems.

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Totty, H; Ullery, M; Spontak, J; Viray, J; Adamik, M; Katzin, B; Dunne, W M; Deol, P

2017-10-01

The performance of the next-generation BacT/ALERT® VIRTUO™ Microbial Detection System (VIRTUO™, bioMérieux Inc., Hazelwood, MO) was compared to the BacT/ALERT® 3D Microbial Detection System (3D, bioMérieux Inc., Durham, NC) using BacT/ALERT® FA Plus (FA Plus), BacT/ALERT® PF Plus (PF Plus), BacT/ALERT® FN Plus (FN Plus), BacT/ALERT® Standard Aerobic (SA), and BacT/ALERT® Standard Anaerobic (SN) blood culture bottles (bioMérieux Inc., Durham, NC). A seeded limit of detection (LoD) study was performed for each bottle type in both systems. The LoD studies demonstrated that both systems were capable of detecting organisms at nearly identical levels [detection (TTD) between the systems using a panel of clinically relevant microorganisms inoculated at or near the LoD with 0, 4, or 10 mL of healthy human blood. VIRTUO™ exhibited a faster TTD by an average of 3.5 h, as well as demonstrated a significantly improved detection rate of 99.9% compared to 98.8% with 3D (p-value <0.05).

454 sequencing of pooled BAC clones on chromosome 3H of barley

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Yamaji Nami

2011-05-01

Full Text Available Abstract Background Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp. Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. Results We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. Conclusions We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.

The relationship of normal body temperature, end-expired breath temperature, and BAC/BrAC ratio in 98 physically fit human test subjects.

Science.gov (United States)

Cowan, J Mack; Burris, James M; Hughes, James R; Cunningham, Margaret P

2010-06-01

The relationship between normal body temperature, end-expired breath temperature, and blood alcohol concentration (BAC)/breath alcohol concentration (BrAC) ratio was studied in 98 subjects (84 men, 14 women). Subjects consumed alcohol sufficient to produce a BrAC of at least 0.06 g/210 L 45-75 min after drinking. Breath samples were analyzed using an Intoxilyzer 8000 specially equipped to measure breath temperature. Venous blood samples and body temperatures were then taken. The mean body temperature of the men (36.6 degrees C) was lower than the women (37.0 degrees C); however, their mean breath temperatures were virtually identical (men: 34.5 degrees C; women: 34.6 degrees C). The BAC exceeded the BrAC for every subject. BAC/BrAC ratios were calculated from the BAC and BrAC analytical results. There was no difference in the BAC/BrAC ratios for men (1:2379) and women (1:2385). The correlation between BAC and BrAC was high (r = 0.938, p body temperature and end-expired breath temperature, body temperature and BAC/BrAC ratio, and breath temperature and BAC/BrAC ratio were much lower. Neither normal body temperature nor end-expired breath temperature was strongly associated with BAC/BrAC ratio.

Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization.

Science.gov (United States)

Jiang, Likun; You, Weiwei; Zhang, Xiaojun; Xu, Jian; Jiang, Yanliang; Wang, Kai; Zhao, Zixia; Chen, Baohua; Zhao, Yunfeng; Mahboob, Shahid; Al-Ghanim, Khalid A; Ke, Caihuan; Xu, Peng

2016-02-01

The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.

Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

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King Graham J

2010-10-01

Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies.

Science.gov (United States)

Tulpová, Zuzana; Luo, Ming-Cheng; Toegelová, Helena; Visendi, Paul; Hayashi, Satomi; Vojta, Petr; Paux, Etienne; Kilian, Andrzej; Abrouk, Michaël; Bartoš, Jan; Hajdúch, Marián; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2018-03-08

Bread wheat (Triticum aestivum L.) is a staple food for a significant part of the world's population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere. Copyright © 2018. Published by Elsevier B.V.

A bacterial artificial chromosome-based physical map of Manihot esculenta ssp.flabellifolia

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Yuhua FU; Zhiqiang XIA; Shujuan WANG; Xin CHEN; Cheng LU; Mingcheng LUO; Hongbin ZHANG; Wenquan WANG

2016-01-01

Cassava (Manihot esculenta) is known as the third most important food crop in the tropics and also used for industrial feedstock for biofuels.Two new bacterial artificial chromosome (BAC) libraries were constructed for W14 (M.Esculenta ssp.flabellifolia),a wild ancestor of domesticated cassava.The libraries were constructed with EcoRI and HindⅢ insertion vectors,respectively.The EcoRI library has 29952 clones with an average insert size of 115 kb,while the HindⅢ library consists of 29952 clones with an average insert of 129 kb.The combined libraries contain a total of 59904 clones with an average insert size of 125 kb,representing approximately 10×haploid genome equivalents.A total of 29952 clones were fingerprinted and resulted in a cassava physical map composed of 2485 contigs with an average physical length of 336 kb and 2909 singletons,representing approximately 762 Mb of the cassava genome.5000 clones located at the ends of BAC contigs were selected and sequenced.A total of 6077 SNPs and 231 indels were identified,that covered 459 gene sequences,of which 6 genes were associated with starch and sucrose metabolism.This BAC-based physical map provides valuable tools to understand the genetics and evolution of cassava.

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

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Volckaert Filip AM

2010-01-01

Full Text Available Abstract Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690 were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.

Germ-line transformation of the Queensland fruit fly, Bactrocera tryoni, using a piggyBac vector in the presence of endogenous piggyBac elements

Science.gov (United States)

We report the stable genetic transformation of the Queensland fruit fly Bactrocera tryoni using a piggyBac vector marked with either the fluorescent protein DsRed or EGFP.A transformation frequency of 5–10% was obtained.Inheritance of the transgenes has remained stable over eight generations despite...

A first generation integrated physical and genetic map of the rainbow trout genome

Science.gov (United States)

The rainbow trout physical map was previously constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of ...

BAC-Dkk3-EGFP Transgenic Mouse: An In Vivo Analytical Tool for Dkk3 Expression

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Yuki Muranishi

2012-01-01

Full Text Available Dickkopf (DKK family proteins are secreted modulators of the Wnt signaling pathway and are capable of regulating the development of many organs and tissues. We previously identified Dkk3 to be a molecule predominantly expressed in the mouse embryonic retina. However, which cell expresses Dkk3 in the developing and mature mouse retina remains to be elucidated. To examine the precise expression of the Dkk3 protein, we generated BAC-Dkk3-EGFP transgenic mice that express EGFP integrated into the Dkk3 gene in a BAC plasmid. Expression analysis using the BAC-Dkk3-EGFP transgenic mice revealed that Dkk3 is expressed in retinal progenitor cells (RPCs at embryonic stages and in Müller glial cells in the adult retina. Since Müller glial cells may play a potential role in retinal regeneration, BAC-Dkk3-EGFP mice could be useful for retinal regeneration studies.

End Sequencing and Finger Printing of Human & Mouse BAC Libraries

Energy Technology Data Exchange (ETDEWEB)

Fraser, C

2005-09-27

This project provided for continued end sequencing of existing and new BAC libraries constructed to support human sequencing as well as to initiate BAC end sequencing from the mouse BAC libraries constructed to support mouse sequencing. The clones, the sequences, and the fingerprints are now an available resource for the community at large. Research and development of new metaodologies for BAC end sequencing have reduced costs and increase throughput.

The first insight into the salvia (lamiaceae) genome via bac library construction and high-throughput sequencing of target bac clones

International Nuclear Information System (INIS)

Hao, D.C.; Vautrin, S.; Berges, H.; Chen, S.L.

2015-01-01

Salvia is a representative genus of Lamiaceae, a eudicot family with significant species diversity and population adaptibility. One of the key goals of Salvia genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of medicinal plants to increase their health and productivity. Large-insert genomic libraries are a fundamental tool for achieving this purpose. We report herein the construction, characterization and screening of a gridded BAC library for Salvia officinalis (sage). The S. officinalis BAC library consists of 17,764 clones and the average insert size is 107 Kb, corresponding to 3 haploid genome equivalents. Seventeen positive clones (average insert size 115 Kb) containing five terpene synthase (TPS) genes were screened out by PCR and 12 of them were subject to Illumina HiSeq 2000 sequencing, which yielded 28,097,480 90-bp raw reads (2.53 Gb). Scaffolds containing sabinene synthase (Sab), a Sab homolog, TPS3 (kaurene synthase-like 2), copalyl diphosphate synthase 2 and one cytochrome P450 gene were retrieved via de novo assembly and annotation, which also have flanking noncoding sequences, including predicted promoters and repeat sequences. Among 2,638 repeat sequences, there are 330 amplifiable microsatellites. This BAC library provides a new resource for Lamiaceae genomic studies, including microsatellite marker development, physical mapping, comparative genomics and genome sequencing. Characterization of positive clones provided insights into the structure of the Salvia genome. These sequences will be used in the assembly of a future genome sequence for S. officinalis. (author)

An all-in-one, Tet-On 3G inducible PiggyBac system for human pluripotent stem cells and derivatives.

Science.gov (United States)

Randolph, Lauren N; Bao, Xiaoping; Zhou, Chikai; Lian, Xiaojun

2017-05-08

Human pluripotent stem cells (hPSCs) offer tremendous promise in tissue engineering and cell-based therapies due to their unique combination of two properties: pluripotency and unlimited proliferative capacity. However, directed differentiation of hPSCs to clinically relevant cell lineages is needed to achieve the goal of hPSC-based therapies. This requires a deep understanding of how cell signaling pathways converge on the nucleus to control differentiation and the ability to dissect gene function in a temporal manner. Here, we report the use of the PiggyBac transposon and a Tet-On 3G drug-inducible gene expression system to achieve versatile inducible gene expression in hPSC lines. Our new system, XLone, offers improvement over previous Tet-On systems with significantly reduced background expression and increased sensitivity to doxycycline. Transgene expression in hPSCs is tightly regulated in response to doxycycline treatment. In addition, the PiggyBac elements in our XLone construct provide a rapid and efficient strategy for generating stable transgenic hPSCs. Our inducible gene expression PiggyBac transposon system should facilitate the study of gene function and directed differentiation in human stem cells.

Learning Physics-based Models in Hydrology under the Framework of Generative Adversarial Networks

Science.gov (United States)

Karpatne, A.; Kumar, V.

2017-12-01

Generative adversarial networks (GANs), that have been highly successful in a number of applications involving large volumes of labeled and unlabeled data such as computer vision, offer huge potential for modeling the dynamics of physical processes that have been traditionally studied using simulations of physics-based models. While conventional physics-based models use labeled samples of input/output variables for model calibration (estimating the right parametric forms of relationships between variables) or data assimilation (identifying the most likely sequence of system states in dynamical systems), there is a greater opportunity to explore the full power of machine learning (ML) methods (e.g, GANs) for studying physical processes currently suffering from large knowledge gaps, e.g. ground-water flow. However, success in this endeavor requires a principled way of combining the strengths of ML methods with physics-based numerical models that are founded on a wealth of scientific knowledge. This is especially important in scientific domains like hydrology where the number of data samples is small (relative to Internet-scale applications such as image recognition where machine learning methods has found great success), and the physical relationships are complex (high-dimensional) and non-stationary. We will present a series of methods for guiding the learning of GANs using physics-based models, e.g., by using the outputs of physics-based models as input data to the generator-learner framework, and by using physics-based models as generators trained using validation data in the adversarial learning framework. These methods are being developed under the broad paradigm of theory-guided data science that we are developing to integrate scientific knowledge with data science methods for accelerating scientific discovery.

Comparison of biological activated carbon (BAC) and membrane bioreactor (MBR) for pollutants removal in drinking water treatment.

Science.gov (United States)

Tian, J Y; Chen, Z L; Liang, H; Li, X; Wang, Z Z; Li, G B

2009-01-01

Biological activated carbon (BAC) and membrane bioreactor (MBR) were systematically compared for the drinking water treatment from slightly polluted raw water under the same hydraulic retention time (HRT) of 0.5 h. MBR exhibited excellent turbidity removal capacity due to the separation of the membrane; while only 60% of influent turbidity was intercepted by BAC. Perfect nitrification was achieved by MBR with the 89% reduction in ammonia; by contrast, BAC only eliminated a moderate amount of influent ammonia (by 54.5%). However, BAC was able to remove more dissolved organic matter (DOM, especially for organic molecules of 3,000 approximately 500 Daltons) and corresponding disinfection by-product formation potential (DBPFP) in raw water than MBR. Unfortunately, particulate organic matter (POM) was detected in the BAC effluent. On the other hand, BAC and MBR displayed essentially the same capacity for biodegradable organic matter (BOM) removal. Fractionation of DOM showed that the removal efficiencies of hydrophobic neutrals, hydrophobic acids, weakly hydrophobic acids and hydrophilic organic matter through BAC treatment were 11.7%, 8.8%, 13.9% and 4.8% higher than that through MBR; while MBR achieved 13.8% higher hydrophobic bases removal as compared with BAC.

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

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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.

Bioreactor scale up and protein product quality characterization of piggyBac transposon derived CHO pools.

Science.gov (United States)

Rajendra, Yashas; Balasubramanian, Sowmya; Peery, Robert B; Swartling, James R; McCracken, Neil A; Norris, Dawn L; Frye, Christopher C; Barnard, Gavin C

2017-03-01

Chinese hamster ovary (CHO) cells remain the most popular host for the production of biopharmaceutical drugs, particularly monoclonal antibodies (mAbs), bispecific antibodies, and Fc-fusion proteins. Creating and characterizing the stable CHO clonally-derived cell lines (CDCLs) needed to manufacture these therapeutic proteins is a lengthy and laborious process. Therefore, CHO pools have increasingly been used to rapidly produce protein to support and enable preclinical drug development. We recently described the generation of CHO pools yielding mAb titers as high as 7.6 g/L in a 16 day bioprocess using piggyBac transposon-mediated gene integration. In this study, we wanted to understand why the piggyBac pool titers were significantly higher (2-10 fold) than the control CHO pools. Higher titers were the result of a combination of increased average gene copy number, significantly higher messenger RNA levels and the homogeneity (i.e. less diverse population distribution) of the piggyBac pools, relative to the control pools. In order to validate the use of piggyBac pools to support preclinical drug development, we then performed an in-depth product quality analysis of purified protein. The product quality of protein obtained from the piggyBac pools was very similar to the product quality profile of protein obtained from the control pools. Finally, we demonstrated the scalability of these pools from shake flasks to 36L bioreactors. Overall, these results suggest that gram quantities of therapeutic protein can be rapidly obtained from piggyBac CHO pools without significantly changing product quality attributes. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:534-540, 2017. © 2017 American Institute of Chemical Engineers.

MAS Based Distributed Automatic Generation Control for Cyber-Physical Microgrid System

Institute of Scientific and Technical Information of China (English)

Zhongwen Li; Chuanzhi Zang; Peng Zeng; Haibin Yu; Hepeng Li

2016-01-01

The microgrid is a typical cyber-physical microgrid system(CPMS). The physical unconventional distributed generators(DGs) are intermittent and inverter-interfaced which makes them very different to control. The cyber components,such as the embedded computer and communication network,are equipped with DGs, to process and transmit the necessary information for the controllers. In order to ensure system-wide observability, controllability and stabilization for the microgrid,the cyber and physical component need to be integrated. For the physical component of CPMS, the droop-control method is popular as it can be applied in both modes of operation to improve the grid transient performance. Traditional droop control methods have the drawback of the inherent trade-off between power sharing and voltage and frequency regulation. In this paper, the global information(such as the average voltage and the output active power of the microgrid and so on) are acquired distributedly based on multi-agent system(MAS). Based on the global information from cyber components of CPMS, automatic generation control(AGC) and automatic voltage control(AVC)are proposed to deal with the drawback of traditional droop control. Simulation studies in PSCAD demonstrate the effectiveness of the proposed control methods.

MAS Based Distributed Automatic Generation Control for Cyber-Physical Microgrid System

Institute of Scientific and Technical Information of China (English)

Zhongwen Li; Chuanzhi Zang; Peng Zeng; Haibin Yu; Hepeng Li

2016-01-01

The microgrid is a typical cyber-physical micro grid system (CPMS).The physical unconventional distributed generators (DGs) are intermittent and inverter-interfaced which makes them very different to control.The cyber components,such as the embedded computer and communication network,are equipped with DGs,to process and transmit the necessary information for the controllers.In order to ensure system-wide observability,controllability and stabilization for the microgrid,the cyber and physical component need to be integrated.For the physical component of CPMS,the droop-control method is popular as it can be applied in both modes of operation to improve the grid transient performance.Traditional droop control methods have the drawback of the inherent trade-off between power sharing and voltage and frequency regulation.In this paper,the global information (such as the average voltage and the output active power of the microgrid and so on) are acquired distributedly based on multi-agent system (MAS).Based on the global information from cyber components of CPMS,automatic generation control (AGC) and automatic voltage control (AVC) are proposed to deal with the drawback of traditional droop control.Simulation studies in PSCAD demonstrate the effectiveness of the proposed control methods.

A PiggyBac-mediated approach for muscle gene transfer or cell therapy

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Déborah Ley

2014-11-01

Full Text Available An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies.

The Functionality of Minimal PiggyBac Transposons in Mammalian Cells

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Boris Troyanovsky

2016-01-01

Full Text Available Minimal piggyBac vectors are a modified single-plasmid version of the classical piggyBac delivery system that can be used for stable transgene integration. These vectors have a truncated terminal domain in the delivery cassette and thus, integrate significantly less flanking transposon DNA into host cell chromatin than classical piggyBac vectors. Herein, we test various characteristics of this modified transposon. The integration efficiency of minimal piggyBac vectors was inversely related to the size of both the transposon and the entire plasmid, but inserts as large as 15 kb were efficiently integrated. Open and super-coiled vectors demonstrated the same integration efficiency while DNA methylation decreased the integration efficiency and silenced the expression of previously integrated sequences in some cell types. Importantly, the incidence of plasmid backbone integration was not increased above that seen in nontransposon control vectors. In BALB/c mice, we demonstrated prolonged expression of two transgenes (intracellular mCherry and secretable Gaussia luciferase when delivered by the minimal piggyBac that resulted in a more sustained antibody production against the immunogenic luciferase than when delivered by a transient (nontransposon vector plasmid. We conclude that minimal piggyBac vectors are an effective alternative to other integrative systems for stable DNA delivery in vitro and in vivo.

A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurata L.

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Heiner Kuhl

2011-01-01

Full Text Available This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata, a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp. Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome.

Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus

International Nuclear Information System (INIS)

Jang Songhun; Zhou Fang; Xia Laixin; Zhao Wei; Cheng Hanhua; Zhou Rongjia

2006-01-01

A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes

GenMapDB: a database of mapped human BAC clones

OpenAIRE

Morley, Michael; Arcaro, Melissa; Burdick, Joshua; Yonescu, Raluca; Reid, Thomas; Kirsch, Ilan R.; Cheung, Vivian G.

2001-01-01

GenMapDB (http://genomics.med.upenn.edu/genmapdb) is a repository of human bacterial artificial chromosome (BAC) clones mapped by our laboratory to sequence-tagged site markers. Currently, GenMapDB contains over 3000 mapped clones that span 19 chromosomes, chromosomes 2, 4, 5, 9–22, X and Y. This database provides positional information about human BAC clones from the RPCI-11 human male BAC library. It also contains restriction fragment analysis data and end sequen...

High-throughput physical map anchoring via BAC-pool sequencing

Czech Academy of Sciences Publication Activity Database

Cviková, Kateřina; Cattonaro, F.; Alaux, M.; Stein, N.; Mayer, K.F.X.; Doležel, Jaroslav; Bartoš, Jan

2015-01-01

Roč. 15, APR 11 (2015) ISSN 1471-2229 R&D Projects: GA ČR GA13-08786S; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Physical map * Contig anchoring * Next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.631, year: 2015

De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley

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Scholz Uwe

2009-11-01

Full Text Available Abstract Background De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L. is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable. Results To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes. By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies. Conclusion The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.

Construction of a nurse shark (Ginglymostoma cirratum bacterial artificial chromosome (BAC library and a preliminary genome survey

Directory of Open Access Journals (Sweden)

Inoko Hidetoshi

2006-05-01

Full Text Available Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC library for the nurse shark, Ginglymostoma cirratum. Results The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. Conclusion We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey.

Science.gov (United States)

Luo, Meizhong; Kim, Hyeran; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A; Ohta, Yuko

2006-05-03

Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

Insect transformation with piggyBac: getting the number of injections just right

Science.gov (United States)

Morrison, N. I.; Shimeld, S. M.

2016-01-01

Abstract The insertion of exogenous genetic cargo into insects using transposable elements is a powerful research tool with potential applications in meeting food security and public health challenges facing humanity. piggyBac is the transposable element most commonly utilized for insect germline transformation. The described efficiency of this process is variable in the published literature, and a comprehensive review of transformation efficiency in insects is lacking. This study compared and contrasted all available published data with a comprehensive data set provided by a biotechnology group specializing in insect transformation. Based on analysis of these data, with particular focus on the more complete observational data from the biotechnology group, we designed a decision tool to aid researchers' decision‐making when using piggyBac to transform insects by microinjection. A combination of statistical techniques was used to define appropriate summary statistics of piggyBac transformation efficiency by species and insect order. Publication bias was assessed by comparing the data sets. The bias was assessed using strategies co‐opted from the medical literature. The work culminated in building the Goldilocks decision tool, a Markov‐Chain Monte‐Carlo simulation operated via a graphical interface and providing guidance on best practice for those seeking to transform insects using piggyBac. PMID:27027400

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

Directory of Open Access Journals (Sweden)

Kudrna David

2011-03-01

Full Text Available Abstract Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1 digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb to 157 Kb (Eg_Ba, very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×, contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae

Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis; FINAL

International Nuclear Information System (INIS)

Simon, M. I.; Kim, U.-J.

2002-01-01

We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year

Time to Detection with BacT/Alert FA Plus Compared to BacT/Alert FA Blood Culture Media.

Science.gov (United States)

Nutman, A; Fisher Even-Tsur, S; Shapiro, G; Braun, T; Schwartz, D; Carmeli, Y

2016-09-01

Rapid identification of the causative pathogen in patients with bacteremia allows adjustment of antibiotic therapy and improves patient outcomes. We compared in vitro and real-life time to detection (TTD) of two blood culture media, BacT/Alert FA (FA) and BacT/Alert FA Plus (FA Plus), for the nine most common species of bacterial pathogens recovered from blood samples. Experimental data from simulated cultures was compared with microbiology records of TTD for both culture media with growth of the species of interest in clinical blood cultures. In the experimental conditions, median TTD was 3.8 hours (23.9 %) shorter using FA Plus media. The magnitude of reduction differed between species. Similarly, in real life data, FA Plus had shorter TTD than FA media; however, the difference between culture media was smaller, and median TTD was only 1 hour (8.5 %) less. We found shorter TTD with BacT/Alert FA Plus culture media, both experimentally and in real-life conditions and unrelated to antibiotic neutralization, highlighting the importance of appropriate blood culture media selection.

Crystal structures and electronic properties of BaC2 isomers by theoretical study based on DFT

Institute of Scientific and Technical Information of China (English)

2008-01-01

Band structures and electronic properties of two BaC2 isomers were calculated by using density func-tional theory(DFT) properly.The ionic bond features are all typical between cation(Ba) and anion clusters(C2) in both structures of the isomers.However,a much stronger covalent bond exists in anion clusters which can be seen by inspecting the electron distribution contour that has a dull bell like shape between two carbon atoms.The shortest distance between Ba2+ and C22? and the bond length in anion clusters are different in these isomers of BaC2,which are 0.2945 nm and 0.1185 nm for the structure with the I4/mmm space group and 0.2744 and 0.1136 nm with the C2/c type,respectively.Band structures were clarified by combining the DOS to indicate the ionic bonding features more clearly.Population analysis provided further evidence on these ideas.Thermodynamical calculation results reveal that the transition temperature of these two polymorphs of BaC2 locates near 132 K,which is consistent with the recent experimental results.

Toward a molecular cytogenetic map for cultivated sunflower (Helianthus annuus L.) by landed BAC/BIBAC clones.

Science.gov (United States)

Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

2013-01-01

Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (~100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC-fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)-derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources.

Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti.

Science.gov (United States)

Adelman, Zach N; Jasinskiene, Nijole; Vally, K J M; Peek, Corrie; Travanty, Emily A; Olson, Ken E; Brown, Susan E; Stephens, Janice L; Knudson, Dennis L; Coates, Craig J; James, Anthony A

2004-10-01

The Class II transposable element, piggyBac, was used to transform the yellow fever mosquito, Aedes aegypti. In two transformed lines only 15-30% of progeny inherited the transgene, with these individuals displaying mosaic expression of the EGFP marker gene. Southern analyses, gene amplification of genomic DNA, and plasmid rescue experiments provided evidence that these lines contained a high copy number of piggyBac transformation constructs and that much of this DNA consisted of both donor and helper plasmids. A detailed analysis of one line showed that the majority of piggyBac sequences were unit-length donor or helper plasmids arranged in a large tandem array that could be lost en masse in a single generation. Despite the presence of a transposase source and many intact donor elements, no conservative (cut and paste) transposition of piggyBac was observed in these lines. These results reveal one possible outcome of uncontrolled and/or unexpected recombination in this mosquito, and support the conclusion that further investigation is necessary before transposable elements such as piggyBac can be used as genetic drive mechanisms to move pathogen-resistance genes into mosquito populations.

Measuring brain activity cycling (BAC) in long term EEG monitoring of preterm babies

International Nuclear Information System (INIS)

Stevenson, Nathan J; Palmu, Kirsi; Wikström, Sverre; Hellström-Westas, Lena; Vanhatalo, Sampsa

2014-01-01

Measuring fluctuation of vigilance states in early preterm infants undergoing long term intensive care holds promise for monitoring their neurological well-being. There is currently, however, neither objective nor quantitative methods available for this purpose in a research or clinical environment. The aim of this proof-of-concept study was, therefore, to develop quantitative measures of the fluctuation in vigilance states or brain activity cycling (BAC) in early preterm infants. The proposed measures of BAC were summary statistics computed on a frequency domain representation of the proportional duration of spontaneous activity transients (SAT%) calculated from electroencephalograph (EEG) recordings. Eighteen combinations of three statistics and six frequency domain representations were compared to a visual interpretation of cycling in the SAT% signal. Three high performing measures (band energy/periodogram: R = 0.809, relative band energy/nonstationary frequency marginal: R = 0.711, g-statistic/nonstationary frequency marginal: R = 0.638) were then compared to a grading of sleep wake cycling based on the visual interpretation of the amplitude-integrated EEG trend. These measures of BAC are conceptually straightforward, correlate well with the visual scores of BAC and sleep wake cycling, are robust enough to cope with the technically compromised monitoring data available in intensive care units, and are recommended for further validation in prospective studies. (paper)

Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome.

Science.gov (United States)

Santos, Anselmo Azevedo; Penha, Helen Alves; Bellec, Arnaud; Munhoz, Carla de Freitas; Pedrosa-Harand, Andrea; Bergès, Hélène; Vieira, Maria Lucia Carneiro

2014-09-26

The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n=9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome

Applying automatic item generation to create cohesive physics testlets

Science.gov (United States)

Mindyarto, B. N.; Nugroho, S. E.; Linuwih, S.

2018-03-01

Computer-based testing has created the demand for large numbers of items. This paper discusses the production of cohesive physics testlets using an automatic item generation concepts and procedures. The testlets were composed by restructuring physics problems to reveal deeper understanding of the underlying physical concepts by inserting a qualitative question and its scientific reasoning question. A template-based testlet generator was used to generate the testlet variants. Using this methodology, 1248 testlet variants were effectively generated from 25 testlet templates. Some issues related to the effective application of the generated physics testlets in practical assessments were discussed.

Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

Directory of Open Access Journals (Sweden)

Gonser Rusty A

2011-06-01

Full Text Available Abstract Background The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis, which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.

BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

Science.gov (United States)

Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

2012-05-01

Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

A Blumeria graminis f.sp. hordei BAC library - contig building and microsynteny studies

DEFF Research Database (Denmark)

Pedersen, C.; Wu, B.; Giese, H.

2002-01-01

A bacterial artificial chromosome (BAC) library of Blumeria graminis f.sp. hordei, containing 12,000 clones with an average insert size of 41 kb, was constructed. The library represents about three genome equivalents and BAC-end sequencing showed a high content of repetitive sequences, making...... contigs, at or close to avirulence loci, were constructed. Single nucleotide polymorphism (SNP) markers were developed from BAC-end sequences to link the contigs to the genetic maps. Two other BAC contigs were used to study microsynteny between B. graminis and two other ascomycetes, Neurospora crassa...

The complexity of Rhipicephalus (Boophilus microplus genome characterised through detailed analysis of two BAC clones

Directory of Open Access Journals (Sweden)

Valle Manuel

2011-07-01

Full Text Available Abstract Background Rhipicephalus (Boophilus microplus (Rmi a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as Drosophila and Anopheles are too taxonomically distant for a reference in tick genomic sequence analysis. This study focuses on the de-novo assembly of two R. microplus BAC sequences from the understudied R microplus genome. Based on available R. microplus sequenced resources and comparative analysis, tick genomic structure and functional predictions identify complex gene structures and genomic targets expressed during tick-cattle interaction. Results In our BAC analyses we have assembled, using the correct positioning of BAC end sequences and transcript sequences, two challenging genomic regions. Cot DNA fractions compared to the BAC sequences confirmed a highly repetitive BAC sequence BM-012-E08 and a low repetitive BAC sequence BM-005-G14 which was gene rich and contained short interspersed elements (SINEs. Based directly on the BAC and Cot data comparisons, the genome wide frequency of the SINE Ruka element was estimated. Using a conservative approach to the assembly of the highly repetitive BM-012-E08, the sequence was de-convoluted into three repeat units, each unit containing an 18S, 5.8S and 28S ribosomal RNA (rRNA encoding gene sequence (rDNA, related internal transcribed spacer and complex intergenic region. In the low repetitive BM-005-G14, a novel gene complex was found between to 2 genes on the same strand. Nested in the second intron of a large 9 Kb papilin gene was a helicase gene. This helicase overlapped in two exonic regions with the papilin. Both these genes were shown expressed in different tick life stage important in ectoparasite interaction with the host. Tick specific sequence

Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca

Directory of Open Access Journals (Sweden)

Zhang Ying

2006-11-01

Full Text Available Abstract Background The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC library of the giant panda was constructed in this study. Results This BAC library contains 198,844 clones with an average insert size of 108 kb, which represents approximately seven equivalents of the giant panda haploid genome. Screening the library with 15 genes and 8 microsatellite markers demonstrates that it is representative and has good genome coverage. Furthermore, ten BAC clones harbouring AGXT, GHR, FSHR, IRBP, SOX14, TTR, BDNF, NT-4, LH and ZFX1 were mapped to 8 pairs of giant panda chromosomes by fluorescence in situ hybridization (FISH. Conclusion This is the first large-insert genomic DNA library for the giant panda, and will contribute to understanding this endangered species in the areas of genome sequencing, physical mapping, gene cloning and comparative genomic studies. We also identified the physical locations of ten genes on their relative chromosomes by FISH, providing a preliminary framework for further development of a high resolution cytogenetic map of the giant panda.

Bacterial contamination of platelet components not detected by BacT/ALERT®.

Science.gov (United States)

Abela, M A; Fenning, S; Maguire, K A; Morris, K G

2018-02-01

To investigate the possible causes for false negative results in BacT/ALERT ® 3D Signature System despite bacterial contamination of platelet units. The Northern Ireland Blood Transfusion Service (NIBTS) routinely extends platelet component shelf life to 7 days. Components are sampled and screened for bacterial contamination using an automated microbial detection system, the BacT/ALERT ® 3D Signature System. We report on three platelet components with confirmed bacterial contamination, which represent false negative BacT/ALERT ® results and near-miss serious adverse events. NIBTS protocols for risk reduction of bacterial contamination of platelet components are described. The methodology for bacterial detection using BacT/ALERT ® is outlined. Laboratory tests, relevant patient details and relevant follow-up information are analysed. In all three cases, Staphylococcus aureus was isolated from the platelet residue and confirmed on terminal sub-culture using BacT/ALERT ® . In two cases, S. aureus with similar genetic makeup was isolated from the donors. Risk reduction measures for bacterial contamination of platelet components are not always effective. Automated bacterial culture detection does not eliminate the risk of bacterial contamination. Visual inspection of platelet components prior to release, issue and administration remains an important last line of defence. © 2017 British Blood Transfusion Society.

MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes.

Science.gov (United States)

Gradia, Scott D; Ishida, Justin P; Tsai, Miaw-Sheue; Jeans, Chris; Tainer, John A; Fuss, Jill O

2017-01-01

Recombinant expression of large, multiprotein complexes is essential and often rate limiting for determining structural, biophysical, and biochemical properties of DNA repair, replication, transcription, and other key cellular processes. Baculovirus-infected insect cell expression systems are especially well suited for producing large, human proteins recombinantly, and multigene baculovirus systems have facilitated studies of multiprotein complexes. In this chapter, we describe a multigene baculovirus system called MacroBac that uses a Biobricks-type assembly method based on restriction and ligation (Series 11) or ligation-independent cloning (Series 438). MacroBac cloning and assembly is efficient and equally well suited for either single subcloning reactions or high-throughput cloning using 96-well plates and liquid handling robotics. MacroBac vectors are polypromoter with each gene flanked by a strong polyhedrin promoter and an SV40 poly(A) termination signal that minimize gene order expression level effects seen in many polycistronic assemblies. Large assemblies are robustly achievable, and we have successfully assembled as many as 10 genes into a single MacroBac vector. Importantly, we have observed significant increases in expression levels and quality of large, multiprotein complexes using a single, multigene, polypromoter virus rather than coinfection with multiple, single-gene viruses. Given the importance of characterizing functional complexes, we believe that MacroBac provides a critical enabling technology that may change the way that structural, biophysical, and biochemical research is done. © 2017 Elsevier Inc. All rights reserved.

Isolation of Specific Clones from Nonarrayed BAC Libraries through Homologous Recombination

Directory of Open Access Journals (Sweden)

Mikhail Nefedov

2011-01-01

Full Text Available We have developed a new approach to screen bacterial artificial chromosome (BAC libraries by recombination selection. To test this method, we constructed an orangutan BAC library using an E. coli strain (DY380 with temperature inducible homologous recombination (HR capability. We amplified one library segment, induced HR at 42∘C to make it recombination proficient, and prepared electrocompetent cells for transformation with a kanamycin cassette to target sequences in the orangutan genome through terminal recombineering homologies. Kanamycin-resistant colonies were tested for the presence of BACs containing the targeted genes by the use of a PCR-assay to confirm the presence of the kanamycin insertion. The results indicate that this is an effective approach for screening clones. The advantage of recombination screening is that it avoids the high costs associated with the preparation, screening, and archival storage of arrayed BAC libraries. In addition, the screening can be conceivably combined with genetic engineering to create knockout and reporter constructs for functional studies.

Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.

Science.gov (United States)

Reimer, Lorenz C; Söhngen, Carola; Vetcininova, Anna; Overmann, Jörg

2017-11-10

Microbial data and metadata are scattered throughout the scientific literature, databases and unpublished lab notes and thereby often are difficult to access. Hot spots of (meta)data are internal descriptions of culture collections and initial descriptions of novel taxa in primary literature. Here we describe three exemplary mobilization projects which yielded metadata published through the prokaryotic metadatabase BacDive. The Reichenbach collection of myxobacteria includes information on 12,535 typewritten index cards which were digitized. A total of 37,156 data points were extracted by text mining. In the second mobilization project, Analytical Profile Index (API) tests on paper forms were targeted. Overall 6820 API tests were digitized, which provide physiological data of 4524 microbial strains. Thirdly, the extraction of metadata from 523 new species descriptions of the International Journal of Systematic and Evolutionary Microbiology, yielding 35,651 data points, is described. All data sets were integrated and published in BacDive. Thereby these metadata not only became accessible and searchable but were also linked to strain taxonomy, isolation source, cultivation condition, and molecular biology data. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Comparative physical mapping of rice BAC clones linked to resistance genes Glh,Bph-3 and xa-5 in Oryza sativa L.and O.granulata Nees et Am.ex Watt.

Institute of Scientific and Technical Information of China (English)

XIONG Zhiyong; TAN Guangxuan; YOU Aiqing; HE Guangyuan; SHE Chaowen; LI Lijia; SONG Yunchun

2004-01-01

Oryza granulata Nees et Arn. ex Watt. is one of the three wild relatives of rice, which are the most valuable for study and utilization in China. In this study, the homology and physical locations of three rice resistance genes, Glh,Bph-3 and xa-5 are comparatively analyzed between O. sativa and O. granulata by Southern blotting and fluorescence in situ hybridization (FISH). The results of Southern blotting indicate that there exist homologous sequences of the tested RFLP markers in O. granulata. By using three bacterial artificial chromosome (BAC) clones scanned by the tested RFLP as probes, FISH signals are detected on both mitotic and pachytene chromosomes in O. sativa and O. granulata.Dual-color FISH demonstrates that two of the three BAC clones (14E16 and 38J9) are located on the short arm of the same chromosome pair in O. granulata. Additionally, colinearity is shown for the two clones between O. sativa and O.granulata. Another BAC clone 44B4 is located on the end of the short arm of other chromosome pair in these two species.Although the phylogenetic relationship between O. sativa and O. granulata is the most distinct in Oryza and these two species have evidently different biological features and ecological habits, the relative lengths and arm ratios of the detected chromosomes and the relative positions of the tested clone signals on chromosomes in O. granulata are quite similar to those in O. sativa.

Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy

Science.gov (United States)

2011-01-01

Background DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery. Results We have observed that (1) the Tol2 transposase (but not piggyBac) is highly sensitive to molecular engineering; (2) the piggyBac donor with only the 40 bp 3'-and 67 bp 5'-terminal repeat domain is sufficient for effective transposition; and (3) a small amount of piggyBac transposases results in robust transposition suggesting the piggyBac transpospase is highly active. Performing genome-wide target profiling on data sets obtained by retrieving chromosomal targeting sequences from individual clones, we have identified several piggyBac and Tol2 hotspots and observed that (4) piggyBac and Tol2 display a clear difference in targeting preferences in the human genome. Finally, we have observed that (5) only sites with a particular sequence context can be targeted by either piggyBac or Tol2. Conclusions The non-overlapping targeting preference of piggyBac and Tol2 makes them complementary research tools for manipulating mammalian genomes. PiggyBac is the most promising transposon-based vector system for achieving site-specific targeting of therapeutic genes due to the flexibility of its transposase for being molecularly engineered. Insights from this study will provide a basis for engineering piggyBac transposases to achieve site-specific therapeutic gene targeting. PMID:21447194

Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase.

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Guillaume Manat

Full Text Available Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2 catalyze the dephosphorylation of C55-PP molecules on the same (outer side of the plasma membrane.

Aerobic biodegradation of a sulfonated phenylazonaphthol dye by a bacterial community immobilized in a multistage packed-bed BAC reactor.

Science.gov (United States)

Ruiz-Arias, Alfredo; Juárez-Ramírez, Cleotilde; de los Cobos-Vasconcelos, Daniel; Ruiz-Ordaz, Nora; Salmerón-Alcocer, Angélica; Ahuatzi-Chacón, Deifilia; Galíndez-Mayer, Juvencio

2010-11-01

A microbial community able to aerobically degrade the azo dye Acid Orange 7 was selected from riparian or lacustrine sediments collected at sites receiving textile wastewaters. Three bacterial strains, pertaining to the genera Pseudomonas, Arthrobacter, and Rhizobium, constitute the selected community. The biodegradation of AO7 was carried out in batch-suspended cell culture and in a continuously operated multistage packed-bed BAC reactor. The rapid decolorization observed in batch culture, joined to a delay of about 24 h in COD removal and cell growth, suggests that enzymes involved in biodegradation of the aromatic amines generated after AO7 azo-bond cleavage (1-amino-2-naphthol [1-A2N] and 4-aminobenzenesulfonic acid [4-ABS]), are inducible in this microbial consortium. After this presumptive induction period, the accumulated byproducts, measured through COD, were partially metabolized and transformed in cell mass. At all azo dye loading rates used, complete removal of AO7 and 1-A2N was obtained in the multistage packed-bed BAC reactor (PBR).; however, the overall COD (eta ( COD )) and 4-ABS (eta ( ABS )) removal efficiencies obtained in steady state continuous culture were about 90%. Considering the toxicity of 1-A2N, its complete removal has particular relevance. In the first stages of the packed-bed BAC reactor (Fig. 4a-c), major removal was observed. In the last stage, only a slight removal of COD and 4-ABS was obtained. Comparing to several reported studies, the continuously operated multistage packed-bed BAC reactor showed similar or superior results. In addition, the operation of large-packed-bed BAC reactors could be improved by using several shallow BAC bed stages, because the pressure drop caused by bed compaction of a support material constituted by small and fragile particles can be reduced.

Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

A bacterial artificial chromosome (BAC) library containing a large genomic DNA insert is an important tool for genome physical mapping, map-based cloning, and genome sequencing. To isolate genes via a map-based cloning strategy and to perform physical mapping of the cotton genome, a high-quality BAC library containing large cotton DNA inserts is needed. We have developed a BAC library of the restoring line 0-613-2R for isolating the fertility restorer (Rf1) gene and genomic research in cotton (Gossypium hirsutum L.). The BAC library contains 97 825 clones stored in 255 pieces of a 384-well microtiter plate. Random samples of BACs digested with the Notl enzyme indicated that the average insert size is approximately 130 kb, with a range of 80-275 kb,and 95.7% of the BAC clones in the library have an average insert size larger than 100 kb. Based on a cotton genome size of 2 250 Mb, library coverage is 5.7 x haploid genome equivalents. Four clones were selected randomly from the library to determine the stability of the BAC clones. There were no different fingerprints for 0 and 100 generations of each clone digested with Notl and Hindlll enzymes. Thus, the stability of a single BAC clone can be sustained at least for 100 generations. Eight simple sequence repeat (SSR) markers flanking the Rf1 gene were chosen to screen the BAC library by pool using PCR method and 25 positive clones were identified with 3.1 positive clones per SSR marker.

Efficient Expression of Acetylcholine-Binding Protein from Aplysia californica in Bac-to-Bac System

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Bo Lin

2014-01-01

Full Text Available The Bac-to-Bac baculovirus expression system can efficiently produce recombinant proteins, but the system may have to be optimized to achieve high-level expression for different candidate proteins. We reported here the efficient expression of acetylcholine-binding proteins from sea hares Aplysia californica (Ac-AChBP and a convenient method to monitor protein expression level in this expression system. Three key factors affecting expression of Ac-AChBP were optimized for maximizing the yield, which included the cell density, volume of the infecting baculovirus inoculums, and the culturing time of postinfection. We have found it to reach a high yield of ∼5 mg/L, which needs 55 h incubation after infection at the cell density of 2 × 106 cells/mL with an inoculum volume ratio of 1 : 100. The optimized expression system in this study was also applied for expressing another protein Ls-AChBP from Lymnaea stagnalis successfully. Therefore, this established method is helpful to produce high yields of AChBP proteins for X-ray crystallographic structural and functional studies.

Comparison of the chromosome maps around a resistance hot spot on chromosome 5 of potato and tomato using BAC-FISH painting.

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Achenbach, Ute C; Tang, Xiaomin; Ballvora, Agim; de Jong, Hans; Gebhardt, Christiane

2010-02-01

Potato chromosome 5 harbours numerous genes for important qualitative and quantitative traits, such as resistance to the root cyst nematode Globodera pallida and the late blight fungus, Phytophthora infestans. The genes make up part of a "hot spot" for resistances to various pathogens covering a genetic map length of 3 cM between markers GP21 and GP179. We established the physical size and position of this region on chromosome 5 in potato and tomato using fluorescence in situ hybridization (FISH) on pachytene chromosomes. Five potato bacterial artificial chromosome (BAC) clones with the genetically anchored markers GP21, R1-contig (proximal end), CosA, GP179, and StPto were selected, labeled with different fluorophores, and hybridized in a five-colour FISH experiment. Our results showed the location of the BAC clones in the middle of the long arm of chromosome 5 in both potato and tomato. Based on chromosome measurements, we estimate the physical size of the GP21-GP179 interval at 0.85 Mb and 1.2 Mb in potato and tomato, respectively. The GP21-GP179 interval is part of a genome segment known to have inverted map positions between potato and tomato.

Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening

Institute of Scientific and Technical Information of China (English)

SU Ai-guo; LI Shuang-shuang; LIU Guo-zheng; LEI Bin-bin; KANG Ding-ming; LI Zhao-hu; MA Zhi-ying; HUA Jin-ping

2014-01-01

The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artiifcial chromosome (BAC) library. Thirty-ifve primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and veriifed for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be ampliifed, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

Evaluation of chronic lymphocytic leukemia by BAC-based microarray analysis

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McDaniel Lisa D

2011-02-01

Full Text Available Abstract Background Chronic lymphocytic leukemia (CLL is a highly variable disease with life expectancies ranging from months to decades. Cytogenetic findings play an integral role in defining the prognostic significance and treatment for individual patients. Results We have evaluated 25 clinical cases from a tertiary cancer center that have an established diagnosis of CLL and for which there was prior cytogenetic and/or fluorescence in situ hybridization (FISH data. We performed microarray-based comparative genomic hybridization (aCGH using a bacterial artificial chromosome (BAC-based microarray designed for the detection of known constitutional genetic syndromes. In 15 of the 25 cases, aCGH detected all copy number imbalances identified by prior cytogenetic and/or FISH studies. For the majority of those not detected, the aberrations were present at low levels of mosaicism. Furthermore, for 15 of the 25 cases, additional abnormalities were detected. Four of those cases had deletions that mapped to intervals implicated in inherited predisposition to CLL. For most cases, aCGH was able to detect abnormalities present in as few as 10% of cells. Although changes in ploidy are not easily discernable by aCGH, results for two cases illustrate the detection of additional copy gains and losses present within a mosaic tetraploid cell population. Conclusions Our results illustrate the successful evaluation of CLL using a microarray optimized for the interrogation of inherited disorders and the identification of alterations with possible relevance to CLL susceptibility.

A Fine Physical Map of the Rice Chromosome 4

Science.gov (United States)

Zhao, Qiang; Zhang, Yu; Cheng, Zhukuan; Chen, Mingsheng; Wang, Shengyue; Feng, Qi; Huang, Yucheng; Li, Ying; Tang, Yesheng; Zhou, Bo; Chen, Zhehua; Yu, Shuliang; Zhu, Jingjie; Hu, Xin; Mu, Jie; Ying, Kai; Hao, Pei; Zhang, Lei; Lu, Yiqi; Zhang, Lei S.; Liu, Yilei; Yu, Zhen; Fan, Danlin; Weng, Qijun; Chen, Ling; Lu, Tingting; Liu, Xiaohui; Jia, Peixin; Sun, Tongguo; Wu, Yongrui; Zhang, Yujun; Lu, Ying; Li, Can; Wang, Rong; Lei, Haiyan; Li, Tao; Hu, Hao; Wu, Mei; Zhang, Runquan; Guan, Jianping; Zhu, Jia; Fu, Gang; Gu, Minghong; Hong, Guofan; Xue, Yongbiao; Wing, Rod; Jiang, Jiming; Han, Bin

2002-01-01

As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies. [The following individuals and institutions kindly provided reagents, samples, or unpublished information as indicated in the paper: S. McCouch, T. Sasaki, and Monsanto.] PMID:11997348

Effects of nitrogen ion irradiation on endoglucanase activity and gene mutation of Bacillus subtilis Bac01

International Nuclear Information System (INIS)

Lv Jie; Mao Peihong; Jin Xiang; Yu Long; Ying Hanjie

2009-01-01

Bacillus subtilis Bac01 was mutated by 15 keV N + ions of 1.5xl0 16 cm -2 . The mutant strain Bac11 with high yield of endoglucanase was isolated using carboxymethylcellulose sodium and congo red indicative plates. It exhibited higher endoglucanase activity (381.89IU) than the original strain Bac01 (93.33IU). Two 1,500 bp endoglucanase gene fragments were obtained with PCR amplification from B. subtilis Bac01 and mutant strain Bac11. BLAST comparison result indicated that 10 nucleotides mutated. Bioinformatics methods were used to analyze the two predicted amino acid sequences, and it was found that 5 amino acid residues changed, being all in the cellulose-binding domain of endoglucanase. (authors)

Viral Bacterial Artificial Chromosomes: Generation, Mutagenesis, and Removal of Mini-F Sequences

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B. Karsten Tischer

2012-01-01

Full Text Available Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.

Germ line transformation of the yellow fever mosquito, Aedes aegypti, mediated by transpositional insertion of a piggyBac vector.

Science.gov (United States)

Lobo, N F; Hua-Van, A; Li, X; Nolen, B M; Fraser, M J

2002-04-01

Mosquito-vectored diseases such as yellow fever and dengue fever continue to have a substantial impact on human populations world-wide. Novel strategies for control of these mosquito vectored diseases can arise through the development of reliable systems for genetic manipulation of the insect vector. A piggyBac vector marked with the Drosophila melanogaster cinnabar (cn) gene was used to transform the white-eyed khw strain of Aedes aegypti. Microinjection of preblastoderm embryos resulted in four families of cinnabar transformed insects. An overall transformation frequency of 4%, with a range of 0% to as high as 13% for individual experiments, was achieved when using a heat-shock induced transposase providing helper plasmid. Southern hybridizations indicated multiple insertion events in three of four transgenic lines, while the presence of duplicated target TTAA sites at either ends of individual insertions confirmed characteristic piggyBac transposition events in these three transgenic lines. The transgenic phenotype has remained stable for more than twenty generations. The transformations effected using the piggyBac element establish the potential of this element as a germ-line transformation vector for Aedine mosquitoes.

Bac on the Border

OpenAIRE

Umberger, Emily

2007-01-01

Although now on the Tohono O'odom reservation in the modern US Southwest, when the Franciscan church of San Xavier del Bac was built (1780-97), its location was the northern frontier of New Spain. From the outset the church stood out from other northern New Spanish missions in its elaborate decoration, and it still stands out because its contents remain intact, despite changes through time. This essay serves as an introduction to the church as a subject of art historical study. It highlights ...

Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

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Delfina Barabaschi

2015-11-01

Full Text Available The huge size, redundancy, and highly repetitive nature of the bread wheat [ (L.] genome, makes it among the most difficult species to be sequenced. To overcome these limitations, a strategy based on the separation of individual chromosomes or chromosome arms and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium (IWGSC. A total of 95,812 bacterial artificial chromosome (BAC clones of short-arm chromosome 5A (5AS and long-arm chromosome 5A (5AL arm-specific BAC libraries were fingerprinted and assembled into contigs by complementary analytical approaches based on the FingerPrinted Contig (FPC and Linear Topological Contig (LTC tools. Combined anchoring approaches based on polymerase chain reaction (PCR marker screening, microarray, and sequence homology searches applied to several genomic tools (i.e., genetic maps, deletion bin map, neighbor maps, BAC end sequences (BESs, genome zipper, and chromosome survey sequences allowed the development of a high-quality physical map with an anchored physical coverage of 75% for 5AS and 53% for 5AL with high portions (64 and 48%, respectively of contigs ordered along the chromosome. In the genome of grasses, [ (L. Beauv.], rice ( L., and sorghum [ (L. Moench] homologs of genes on wheat chromosome 5A were separated into syntenic blocks on different chromosomes as a result of translocations and inversions during evolution. The physical map presented represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits and a reference for the 5A sequencing projects.

Generating resources for genomics of wheat homoeologous chromosome group 3: 3AS- and 3DS-specific BAC libraries

Czech Academy of Sciences Publication Activity Database

Šafář, Jan; Šimková, Hana; Kubaláková, Marie; Suchánková, Pavla; Čihalíková, Jarmila; Bartoš, Jan; Fiocchetti, F.; Roselli, M.; Gill, B. S.; Doležel, Jaroslav; Lucretti, S.

2009-01-01

Roč. 61, 1-2 (2009), s. 151-160 ISSN 0394-9257 R&D Projects: GA ČR GD521/05/H013; GA ČR GA521/06/1723; GA ČR GA521/07/1573; GA MŠk(CZ) LC06004; GA MŠk OC08025 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC library * Flow sorting * Homoeologous chromosomes Subject RIV: GE - Plant Breeding

Investigation of decolorization of textile wastewater in an anaerobic/aerobic biological activated carbon system (A/A BAC).

Science.gov (United States)

Pasukphun, N; Vinitnantharat, S; Gheewala, S

2010-04-01

The aim of this study is to investigate the decolorization in anaerobic/aerobic biological activated carbon (A/A BAC) system. The experiment was divided into 2 stages; stage I is batch test for preliminary study of dye removal equilibrium time. The preliminary experiment (stage I) provided the optimal data for experimental design of A/A BAC system in SBR (stage II). Stage II is A/A BAC system imitated Sequencing Batch Reactor (SBR) which consist of 5 main periods; fill, react, settle, draw and idle. React period include anaerobic phase followed by aerobic phase. The BAC main media; Granular Activated Carbon (GAC), Mixed Cultures (MC) and Biological Activated Carbon (BAC) were used for dye and organic substances removal in three different solutions; Desizing Agent Solution (DAS), dye Solution (DS) and Synthetic Textile Wastewater (STW). Results indicate that GAC adsorption plays role in dye removal followed by BAC and MC activities, respectively. In the presence desizing agent, decolorization by MC was improved because desizing agent acts as co-substrates for microorganisms. It was found that 50% of dye removal efficiency was achieved in Fill period by MC. GC/MS analysis was used to identify dye intermediate from decolorization. Dye intermediate containing amine group was found in the solution and on BAC surfaces. The results demonstrated that combination of MC and BAC in the system promotes decolorization and dye intermediate removal. In order to improve dye removal efficiency in an A/A BAC system, replacement of virgin GAC, sufficient co-substrates supply and the appropriate anaerobic: aerobic period should be considered.

Application of EDTA-functionalized bamboo activated carbon (BAC) for Pb(II) and Cu(II) removal from aqueous solutions

Science.gov (United States)

Lv, Dan; Liu, Yu; Zhou, Jiasheng; Yang, Kunlun; Lou, Zimo; Baig, Shams Ali; Xu, Xinhua

2018-01-01

In this study, a novel bamboo activated carbon (BAC) with ethylene diamine tetraacetic acid (EDTA) functionality was prepared by direct grafting in the presence of tetraethyl orthosilicate (TEOS) as a crosslinking agent. The BAC@SiO2-EDTA was characterized by SEM, TEM, TGA, FTIR, XPS and its adsorption property for removal of Pb(II) and Cu(II) under various experimental conditions was also investigated. The characterization results reflected that EDTA was successfully assembled on the surface of the BAC and average pore size increased from 4.10 to 4.83 nm as BAC grafted with EDTA. Adsorption data fitted very well in Langmuir isotherm model and pseudo-second-order kinetic model. As compared with the raw BAC, the maximum adsorption capacities of BAC@SiO2-EDTA for the Pb(II) and Cu(II) increased from 45.45 to 123.45 mg g-1 and from 6.85 to 42.19 mg g-1, since the existence of EDTA on modified BAC promoted the formation of chemical complex. The removal of heavy metal ions mainly depended on the complexation with EDTA and the electrostatic attractions with negatively charged surface of BAC@SiO2-EDTA. The adsorption of Pb(II)/Cu(II) on the BAC@SiO2-EDTA was pH dependent and pH 5-6 was considered an optimum. However, lower temperature favored the adsorption and the maximum adsorption was recorded at 20 °C. In addition, BAC@SiO2-EDTA had an excellent reusability with about 40% decline in the adsorption capacity for Pb(II) after fifth reuse. Insignificant influences of co-existing cations and natural organic matter (NOM) were found on the adsorption of Pb(II) and Cu(II). All the results demonstrate that BAC@SiO2-EDTA is a potential adsorbent for metal ions in wastewater.

Sensitivity and applicability of the Brazilian version of the Brief Assessment of Cognition in Schizophrenia (BACS

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João Vinícius Salgado

Full Text Available Abstract Cognitive assessment in schizophrenia has traditionally used batteries that are long and complex or differ widely in their content. The Brief Assessment of Cognition in Schizophrenia (BACS has been developed to cover the main cognitive deficits of schizophrenia as well as to be easily and briefly administered, portable, sensitive and reliable. Objectives: To investigate the applicability and sensitivity of the Brazilian Version of the BACS (Brazilian-BACS. Methods: Performance of 20 stable patients with schizophrenia on the Brazilian-BACS was compared to 20 matched healthy controls. Results: Applying the Brazilian-BACS required 43.4±8.4 minutes for patients and 40.5±5.7 minutes for controls (p=0.17. All tests demonstrated significant differences between controls and patients (P<0.01. Pearson's correlation analysis and Cronbach's a evidenced a high internal consistency for patient performance. The cognitive deficit in the patients was approximately 1.5 standard deviations below controls. These results were consistent with those reported in the validation of the original version and in meta-analyses of similar studies. Conclusions: The Brazilian-BACS displayed good applicability and sensitivity in assessing the major cognitive constructs that are impaired in schizophrenia. Thus, the Brazilian-BACS seems to be a promising tool for assessing cognition in patients with schizophrenia in Brazil.

The host antimicrobial peptide Bac71-35 binds to bacterial ribosomal proteins and inhibits protein synthesis.

Science.gov (United States)

Mardirossian, Mario; Grzela, Renata; Giglione, Carmela; Meinnel, Thierry; Gennaro, Renato; Mergaert, Peter; Scocchi, Marco

2014-12-18

Antimicrobial peptides (AMPs) are molecules from innate immunity with high potential as novel anti-infective agents. Most of them inactivate bacteria through pore formation or membrane barrier disruption, but others cross the membrane without damages and act inside the cells, affecting vital processes. However, little is known about their intracellular bacterial targets. Here we report that Bac71-35, a proline-rich AMP belonging to the cathelicidin family, can reach high concentrations (up to 340 μM) inside the E. coli cytoplasm. The peptide specifically and completely inhibits in vitro translation in the micromolar concentration range. Experiments of incorporation of radioactive precursors in macromolecules with E. coli cells confirmed that Bac71-35 affects specifically protein synthesis. Ribosome coprecipitation and crosslinking assays showed that the peptide interacts with ribosomes, binding to a limited subset of ribosomal proteins. Overall, these results indicate that the killing mechanism of Bac71-35 is based on a specific block of protein synthesis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Defining “Binge” Drinking as Five Drinks per Occasion or Drinking to a 0.08% BAC: Which is More Sensitive to Risk?

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Fillmore, Mark T.; Jude, Rebecca

2011-01-01

Heavy episodic or “binge” drinking is commonly defined as drinking 4–5 drinks per occasion (5/4 definition) or drinking that results in a blood alcohol concentration (BAC) of 0.08%. The present study compared the validity of each binge definition as an indicator of at-risk, problem drinking. 251 college students were classified as non-binge drinkers or as binge drinkers based on the 5/4 definition or the 0.08% BAC definition. The two definitions of binge drinking were examined in terms of their sensitivity and specificity as indicators of alcohol-related problems as determined by scores on the Alcohol Use Disorders Identification Test (AUDIT). Over half the sample (56%) were at-risk drinkers according to the AUDIT. The 0.08% definition detected only one-half of these individuals. Gender differences were also evident. Female binge drinkers actually achieved significantly higher estimated BACs per episode than their male binge drinking counterparts. The findings suggest that drinking to a sub-threshold BAC (i.e., risk independent of the BAC achieved during drinking episodes. The findings also highlight the importance of considering frequency of consumption in determining risky drinking versus relying solely on quantity measures. PMID:21838847

BAC and Beer: Operationalizing Drunk Driving Laws in a Research Methods Course Exercise.

Science.gov (United States)

Taylor, Ralph B.; McConnell, Patrick

2001-01-01

Focuses on an exercise utilized in a research methods class and based on social problems that invites student interest. Explains the exercise has students determine their blood alcohol level (BAC) by asking them to estimate the number of beers it would take to have them just reach driving under the influence (DUI) status. (CMK)

Differential CT features of infectious pneumonia versus bronchioloalveolar carcinoma (BAC) mimicking pneumonia

International Nuclear Information System (INIS)

Kim, Tae Hoon; Kim, Sang Jin; Ryu, Young Hoon; Chung, Soo Yoon; Seo, Jae Seung; Kim, Young Jin; Choi, Byoung Wook; Lee, Sun Hwa; Cho, Sang Ho

2006-01-01

The purpose of this study was to evaluate retrospectively the differential CT features of bronchioloalveolar carcinoma (BAC) mimicking pneumonia and infectious pneumonia at the lung periphery. CT images were reviewed in 47 patients with focal areas of parenchymal opacification at the lung periphery. We evaluated the presence of ground-glass attenuation, marginal conspicuity of the lesion, CT angiogram sign, air-bronchogram sign, a bubble-like low-attenuation area within the lesion, presence of pleural thickening and retraction associated with the lesion, presence of pleural effusion and extra-pleural fatty hypertrophy, presence of bronchial wall thickening proximal to the lesion, and air-trapping in the normal lung near the lesion. BAC (n=18) depicted the presence of a bubble-like low-attenuation area within the lesion, whereas infectious pneumonia (n=29) represented the pleural thickening associated with the lesion and bronchial wall thickening proximal to the lesion (P 0.05). The focal areas of the parenchymal opacification on the CT images may suggest infectious pneumonia rather than BAC when they show bronchial wall thickening proximal to the lesion and pleural thickening associated with the lesion, whereas BAC is characterized as the presence of a bubble-like low attenuation area within the tumor. (orig.)

Differential CT features of infectious pneumonia versus bronchioloalveolar carcinoma (BAC) mimicking pneumonia

Energy Technology Data Exchange (ETDEWEB)

Kim, Tae Hoon [Yonsei University College of Medicine, Department of Radiology, Seoul (Korea); Yongdong Severance Hospital, Department of Radiology, Seoul (Korea); Kim, Sang Jin; Ryu, Young Hoon; Chung, Soo Yoon; Seo, Jae Seung; Kim, Young Jin; Choi, Byoung Wook [Yonsei University College of Medicine, Department of Radiology, Seoul (Korea); Lee, Sun Hwa [NeoDin Medical Institute, Department of Clinical Pathology, Seoul (Korea); Cho, Sang Ho [Yonsei University College of Medicine, Department of Pathology, Seoul (Korea)

2006-08-15

The purpose of this study was to evaluate retrospectively the differential CT features of bronchioloalveolar carcinoma (BAC) mimicking pneumonia and infectious pneumonia at the lung periphery. CT images were reviewed in 47 patients with focal areas of parenchymal opacification at the lung periphery. We evaluated the presence of ground-glass attenuation, marginal conspicuity of the lesion, CT angiogram sign, air-bronchogram sign, a bubble-like low-attenuation area within the lesion, presence of pleural thickening and retraction associated with the lesion, presence of pleural effusion and extra-pleural fatty hypertrophy, presence of bronchial wall thickening proximal to the lesion, and air-trapping in the normal lung near the lesion. BAC (n=18) depicted the presence of a bubble-like low-attenuation area within the lesion, whereas infectious pneumonia (n=29) represented the pleural thickening associated with the lesion and bronchial wall thickening proximal to the lesion (P<0.05). The other CT findings showed no significant differences (P>0.05). The focal areas of the parenchymal opacification on the CT images may suggest infectious pneumonia rather than BAC when they show bronchial wall thickening proximal to the lesion and pleural thickening associated with the lesion, whereas BAC is characterized as the presence of a bubble-like low attenuation area within the tumor. (orig.)

BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper (Capsicum annuum L.).

Science.gov (United States)

Kim, Hyoun-Joung; Nahm, Seok-Hyeon; Lee, Heung-Ryul; Yoon, Gi-Bo; Kim, Ki-Taek; Kang, Byoung-Cheorl; Choi, Doil; Kweon, Oh Yeol; Cho, Myeong-Cheoul; Kwon, Jin-Kyung; Han, Jung-Heon; Kim, Jeong-Ho; Park, Minkyu; Ahn, Jong Hwa; Choi, Soon Ho; Her, Nam Han; Sung, Joo-Hee; Kim, Byung-Dong

2008-12-01

Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F(2) individuals from a cross between Capsicum annuum 'CM334' and C. annuum 'Chilsungcho'. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F(2:3) originated from a cross between resistant Mexican landrace C. annuum 'CM334' and susceptible Korean landrace C. annuum 'Chilsungcho' using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum 'CM334' was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.

Event generators in particle physics

International Nuclear Information System (INIS)

Sjostrand, Torbjorn

1994-01-01

This presentation gives an introduction to the topic of event generators in particle physics . The emphasis is on the physics aspects that have to be considered in the construction of a generator, and what lessons we have learned from comparisons with data. A brief survey of existing generators is also included. As illustration, a few topics of current interest are covered in a bit more detail: QCD uncertainties in W mass determinations and γp/γγ physics. (author)

Insulated piggyBac vectors for insect transgenesis

Directory of Open Access Journals (Sweden)

Horn Carsten

2006-06-01

Full Text Available Abstract Background Germ-line transformation of insects is now a widely used method for analyzing gene function and for the development of genetically modified strains suitable for pest control programs. The most widely used transposable element for the germ-line transformation of insects is piggyBac. The site of integration of the transgene can influence gene expression due to the effects of nearby transcription enhancers or silent heterochromatic regions. Position effects can be minimized by flanking a transgene with insulator elements. The scs/scs' and gypsy insulators from Drosophila melanogaster as well as the chicken β-globin HS4 insulator function in both Drosophila and mammalian cells. Results To minimize position effects we have created a set of piggyBac transformation vectors that contain either the scs/scs', gypsy or chicken β-globin HS4 insulators. The vectors contain either fluorescent protein or eye color marker genes and have been successfully used for germ-line transformation of Drosophila melanogaster. A set of the scs/scs' vectors contains the coral reef fluorescent protein marker genes AmCyan, ZsGreen and DsRed that have not been optimized for translation in human cells. These marker genes are controlled by a combined GMR-3xP3 enhancer/promoter that gives particularly strong expression in the eyes. This is also the first report of the use of the ZsGreen and AmCyan reef fluorescent proteins as transformation markers in insects. Conclusion The insulated piggyBac vectors should protect transgenes against position effects and thus facilitate fine control of gene expression in a wide spectrum of insect species. These vectors may also be used for transgenesis in other invertebrate species.

Spatial attributes of the four-helix bundle group of bacteriocins – The high-resolution structure of BacSp222 in solution

KAUST Repository

Nowakowski, Michał

2017-11-01

BacSp222 is a multifunctional bacteriocin produced by Staphylococcus pseudintermedius strain 222, an opportunistic pathogen of domestic animals. At micromolar concentrations, BacSp222 kills Gram-positive bacteria and is cytotoxic toward mammalian cells, while at nanomolar doses, it acts as an immunomodulatory factor, enhancing nitric oxide release in macrophage-like cell lines. The bacteriocin is a cationic, N-terminally formylated, 50-amino-acid-long linear peptide that is rich in tryptophan residues.In this study, the solution structure of BacSp222 was determined and compared to the currently known structures of similar bacteriocins. BacSp222 was isolated from a liquid culture medium in a uniformly 13C- and 15N-labeled form, and NMR data were collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns.Although the amino acid sequence of BacSp222 has no significant similarity to any known peptide or protein, a 3D structure similarity search indicates a close relation to other four-helix bundle-motif bacteriocins, such as aureocin A53, lacticin Q and enterocins 7A/7B. Assuming similar functions, biology, structure and physicochemical properties, we propose to distinguish the four-helix bundle bacteriocins as a new Type A in subclass IId of bacteriocins, containing linear, non-pediocin-like peptides.

General-purpose event generators for LHC physics

CERN Document Server

Buckley, Andy; Gieseke, Stefan; Grellscheid, David; Hoche, Stefan; Hoeth, Hendrik; Krauss, Frank; Lonnblad, Leif; Nurse, Emily; Richardson, Peter; Schumann, Steffen; Seymour, Michael H.; Sjostrand, Torbjorn; Skands, Peter; Webber, Bryan

2011-01-01

We review the physics basis, main features and use of general-purpose Monte Carlo event generators for the simulation of proton-proton collisions at the Large Hadron Collider. Topics included are: the generation of hard-scattering matrix elements for processes of interest, at both leading and next-to-leading QCD perturbative order; their matching to approximate treatments of higher orders based on the showering approximation; the parton and dipole shower formulations; parton distribution functions for event generators; non-perturbative aspects such as soft QCD collisions, the underlying event and diffractive processes; the string and cluster models for hadron formation; the treatment of hadron and tau decays; the inclusion of QED radiation and beyond-Standard-Model processes. We describe the principal features of the ARIADNE, Herwig++, PYTHIA 8 and SHERPA generators, together with the Rivet and Professor validation and tuning tools, and discuss the physics philosophy behind the proper use of these generators ...

Physical Principle for Generation of Randomness

Science.gov (United States)

Zak, Michail

2009-01-01

A physical principle (more precisely, a principle that incorporates mathematical models used in physics) has been conceived as the basis of a method of generating randomness in Monte Carlo simulations. The principle eliminates the need for conventional random-number generators. The Monte Carlo simulation method is among the most powerful computational methods for solving high-dimensional problems in physics, chemistry, economics, and information processing. The Monte Carlo simulation method is especially effective for solving problems in which computational complexity increases exponentially with dimensionality. The main advantage of the Monte Carlo simulation method over other methods is that the demand on computational resources becomes independent of dimensionality. As augmented by the present principle, the Monte Carlo simulation method becomes an even more powerful computational method that is especially useful for solving problems associated with dynamics of fluids, planning, scheduling, and combinatorial optimization. The present principle is based on coupling of dynamical equations with the corresponding Liouville equation. The randomness is generated by non-Lipschitz instability of dynamics triggered and controlled by feedback from the Liouville equation. (In non-Lipschitz dynamics, the derivatives of solutions of the dynamical equations are not required to be bounded.)

Validation of the French version of the BACS (the brief assessment of cognition in schizophrenia) among 50 French schizophrenic patients.

Science.gov (United States)

Bralet, Marie-Cécile; Falissard, Bruno; Neveu, Xavier; Lucas-Ross, Margaret; Eskenazi, Anne-Marie; Keefe, Richard S E

2007-09-01

Schizophrenic patients demonstrate impairments in several key dimensions of cognition. These impairments are correlated with important aspects of functional outcome. While assessment of these cognition disorders is increasingly becoming a part of clinical and research practice in schizophrenia, there is no standard and easily administered test battery. The BACS (Brief Assessment of Cognition in Schizophrenia) has been validated in English language [Keefe RSE, Golberg TE, Harvey PD, Gold JM, Poe MP, Coughenour L. The Brief Assessment of Cognition in Schizophrenia: reliability, sensibility, and comparison with a standard neurocognitive battery. Schizophr. Res 2004;68:283-97], and was found to be as sensitive to cognitive dysfunction as a standard battery of tests, with the advantage of requiring less than 35 min to complete. We developed a French adaptation of the BACS and this study tested its ease of administration and concurrent validity. Correlation analyses between the BACS (version A) and a standard battery were performed. A sample of 50 stable schizophrenic patients received the French Version A of the BACS in a first session, and in a second session a standard battery. All the patients completed each of the subtests of the French BACS . The mean duration of completion for the BACS French version was 36 min (S.D.=5.56). A correlation analysis between the BACS (version A) global score and the standard battery global score showed a significant result (r=0.81, p<0.0001). The correlation analysis between the BACS (version A) sub-scores and the standard battery sub-scores showed significant results for verbal memory, working memory, verbal fluency, attention and speed of information processing and executive functions (p<0.001) and for motor speed (p<0.05). The French Version of the BACS is easier to use in French schizophrenic patients compared to a standard battery (administration shorter and completion rate better) and its good psychometric properties suggest

Conversion of BAC Clones into Binary BAC (BIBAC) Vectors and Their Delivery into Basidiomycete Fungal Cells Using Agrobacterium tumefaciens

KAUST Repository

Ali, Shawkat

2014-09-19

The genetic transformation of certain organisms, required for gene function analysis or complementation, is often not very efficient, especially when dealing with large gene constructs or genomic fragments. We have adapted the natural DNA transfer mechanism from the soil pathogenic bacterium Agrobacterium tumefaciens, to deliver intact large DNA constructs to basidiomycete fungi of the genus Ustilago where they stably integrated into their genome. To this end, Bacterial Artificial Chromosome (BAC) clones containing large fungal genomic DNA fragments were converted via a Lambda phage-based recombineering step to Agrobacterium transfer-competent binary vectors (BIBACs) with a Ustilago-specific selection marker. The fungal genomic DNA fragment was subsequently successfully delivered as T-DNA through Agrobacterium-mediated transformation into Ustilago species where an intact copy stably integrated into the genome. By modifying the recombineering vector, this method can theoretically be adapted for many different fungi.

The need for blood alcohol concentration (BAC) legislation in Nigeria

African Journals Online (AJOL)

Dr Patrick O Erah

Tropical Journal of Pharmaceutical Research, June 2004; 3 (1): 319-327. © Pharmacotherapy Group, ... 1Department of Restorative Dentistry, Clinical therapeutic Unit, University of Benin, Benin City, .... An international survey of BAC is quite.

Development of a testlet generator in re-engineering the Indonesian physics national-exams

Science.gov (United States)

Mindyarto, Budi Naini; Mardapi, Djemari; Bastari

2017-08-01

The Indonesian Physics national-exams are end-of-course summative assessments that could be utilized to support the assessment for learning in physics educations. This paper discusses the development and evaluation of a testlet generator based on a re-engineering of Indonesian physics national exams. The exam problems were dissected and decomposed into testlets revealing the deeper understanding of the underlying physical concepts by inserting a qualitative question and its scientific reasoning question. A template-based generator was built to facilitate teachers in generating testlet variants that would be more conform to students' scientific attitude development than their original simple multiple-choice formats. The testlet generator was built using open source software technologies and was evaluated focusing on the black-box testing by exploring the generator's execution, inputs and outputs. The results showed the correctly-performed functionalities of the developed testlet generator in validating inputs, generating testlet variants, and accommodating polytomous item characteristics.

EVENT GENERATOR FOR RHIC SPIN PHYSICS

International Nuclear Information System (INIS)

SAITO, N.; SCHAEFER, A.

1999-01-01

This volume archives the reports from the RIKEN BNL Research Center workshop on ''Event Generator for RHIC Spin Physics II'' held during the week March 15, 1999 at Brookhaven National Laboratory. It was the second meeting on the subject following a first one in last September. This workshop has been initiated to establish a firm collaboration between theorists and experimentalists involved in RHIC spin physics with the aim of developing a reliable, high-precision event generator for RHIC spin physics. Needless to say, adequate event generators are indispensable tools for high energy physics programs in general, especially in the process of: planning the experimental programs; developing algorithms to extract the physics signals of interest; estimating the background in the extracted results, and connecting the final particle kinematics to the fundamental i.e. partonic level processes. Since RHIC is the first polarized collider, dedicated efforts are required to obtain a full-fledged event generator which describes spin dependent reactions in great detail

General-purpose event generators for LHC physics

International Nuclear Information System (INIS)

Buckley, Andy; Butterworth, Jonathan; Gieseke, Stefan; Grellscheid, David; Hoeche, Stefan; Hoeth, Hendrik; Krauss, Frank; Loennblad, Leif; Nurse, Emily; Richardson, Peter; Schumann, Steffen; Seymour, Michael H.; Sjoestrand, Torbjoern; Skands, Peter; Webber, Bryan

2011-01-01

We review the physics basis, main features and use of general-purpose Monte Carlo event generators for the simulation of proton-proton collisions at the Large Hadron Collider. Topics included are: the generation of hard scattering matrix elements for processes of interest, at both leading and next-to-leading QCD perturbative order; their matching to approximate treatments of higher orders based on the showering approximation; the parton and dipole shower formulations; parton distribution functions for event generators; non-perturbative aspects such as soft QCD collisions, the underlying event and diffractive processes; the string and cluster models for hadron formation; the treatment of hadron and tau decays; the inclusion of QED radiation and beyond Standard Model processes. We describe the principal features of the ARIADNE, Herwig++, PYTHIA 8 and SHERPA generators, together with the Rivet and Professor validation and tuning tools, and discuss the physics philosophy behind the proper use of these generators and tools. This review is aimed at phenomenologists wishing to understand better how parton-level predictions are translated into hadron-level events as well as experimentalists seeking a deeper insight into the tools available for signal and background simulation at the LHC.

General-purpose event generators for LHC physics

Energy Technology Data Exchange (ETDEWEB)

Buckley, Andy [PPE Group, School of Physics and Astronomy, University of Edinburgh, EH25 9PN (United Kingdom); Butterworth, Jonathan [Department of Physics and Astronomy, University College London, WC1E 6BT (United Kingdom); Gieseke, Stefan [Institute for Theoretical Physics, Karlsruhe Institute of Technology, D-76128 Karlsruhe (Germany); Grellscheid, David [Institute for Particle Physics Phenomenology, Durham University, DH1 3LE (United Kingdom); Hoeche, Stefan [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Hoeth, Hendrik; Krauss, Frank [Institute for Particle Physics Phenomenology, Durham University, DH1 3LE (United Kingdom); Loennblad, Leif [Department of Astronomy and Theoretical Physics, Lund University (Sweden); PH Department, TH Unit, CERN, CH-1211 Geneva 23 (Switzerland); Nurse, Emily [Department of Physics and Astronomy, University College London, WC1E 6BT (United Kingdom); Richardson, Peter [Institute for Particle Physics Phenomenology, Durham University, DH1 3LE (United Kingdom); Schumann, Steffen [Institute for Theoretical Physics, University of Heidelberg, 69120 Heidelberg (Germany); Seymour, Michael H. [School of Physics and Astronomy, University of Manchester, M13 9PL (United Kingdom); Sjoestrand, Torbjoern [Department of Astronomy and Theoretical Physics, Lund University (Sweden); Skands, Peter [PH Department, TH Unit, CERN, CH-1211 Geneva 23 (Switzerland); Webber, Bryan, E-mail: webber@hep.phy.cam.ac.uk [Cavendish Laboratory, J.J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom)

2011-07-15

We review the physics basis, main features and use of general-purpose Monte Carlo event generators for the simulation of proton-proton collisions at the Large Hadron Collider. Topics included are: the generation of hard scattering matrix elements for processes of interest, at both leading and next-to-leading QCD perturbative order; their matching to approximate treatments of higher orders based on the showering approximation; the parton and dipole shower formulations; parton distribution functions for event generators; non-perturbative aspects such as soft QCD collisions, the underlying event and diffractive processes; the string and cluster models for hadron formation; the treatment of hadron and tau decays; the inclusion of QED radiation and beyond Standard Model processes. We describe the principal features of the ARIADNE, Herwig++, PYTHIA 8 and SHERPA generators, together with the Rivet and Professor validation and tuning tools, and discuss the physics philosophy behind the proper use of these generators and tools. This review is aimed at phenomenologists wishing to understand better how parton-level predictions are translated into hadron-level events as well as experimentalists seeking a deeper insight into the tools available for signal and background simulation at the LHC.

General-purpose event generators for LHC physics

Energy Technology Data Exchange (ETDEWEB)

Buckley, Andy; /Edinburgh U.; Butterworth, Jonathan; /University Coll. London; Gieseke, Stefan; /Karlsruhe U., ITP; Grellscheid, David; /Durham U., IPPP; Hoche, Stefan; /SLAC; Hoeth, Hendrik; Krauss, Frank; /Durham U., IPPP; Lonnblad, Leif; /Lund U., Dept. Theor. Phys. /CERN; Nurse, Emily; /University Coll. London; Richardson, Peter; /Durham U., IPPP; Schumann, Steffen; /Heidelberg U.; Seymour, Michael H.; /Manchester U.; Sjostrand, Torbjorn; /Lund U., Dept. Theor. Phys.; Skands, Peter; /CERN; Webber, Bryan; /Cambridge U.

2011-03-03

We review the physics basis, main features and use of general-purpose Monte Carlo event generators for the simulation of proton-proton collisions at the Large Hadron Collider. Topics included are: the generation of hard-scattering matrix elements for processes of interest, at both leading and next-to-leading QCD perturbative order; their matching to approximate treatments of higher orders based on the showering approximation; the parton and dipole shower formulations; parton distribution functions for event generators; non-perturbative aspects such as soft QCD collisions, the underlying event and diffractive processes; the string and cluster models for hadron formation; the treatment of hadron and tau decays; the inclusion of QED radiation and beyond-Standard-Model processes. We describe the principal features of the Ariadne, Herwig++, Pythia 8 and Sherpa generators, together with the Rivet and Professor validation and tuning tools, and discuss the physics philosophy behind the proper use of these generators and tools. This review is aimed at phenomenologists wishing to understand better how parton-level predictions are translated into hadron-level events as well as experimentalists wanting a deeper insight into the tools available for signal and background simulation at the LHC.

Construction of an American mink Bacterial Artificial Chromosome (BAC library and sequencing candidate genes important for the fur industry

Directory of Open Access Journals (Sweden)

Christensen Knud

2011-07-01

Full Text Available Abstract Background Bacterial artificial chromosome (BAC libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. Results Here, we report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison. The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs, representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library. These included candidate genes for coat coloring, hair growth and length, coarseness, and some receptors potentially involved in viral diseases in mink. The extensive screening yielded positive results for 19 of these genes. Thirty-five clones corresponding to 19 genes were sequenced using 454 Roche, and large contigs (184 kb in average were assembled. Knowing the complete sequences of these candidate genes will enable confirmation of the association with a phenotype and the finding of causative mutations for the targeted phenotypes. Additionally, 1577 BAC clones were end sequenced; 2505 BAC end sequences (80% of BACs were obtained. An excess of 2 Mb has been analyzed, thus giving a snapshot of the mink genome. Conclusions The availability of the CHORI-321 American mink BAC library will aid in identification of genes and genomic regions of interest. We have demonstrated how the library can be used to identify specific genes of interest, develop genetic markers, and for BAC end sequencing and deep sequencing of selected clones. To our knowledge, this is the

Generation of soluble microbial products by bio-activated carbon filter during drinking water advanced treatment and its influence on spectral characteristics

Energy Technology Data Exchange (ETDEWEB)

Shen, Hong, E-mail: song.wei0326@163.com [National Engineering Research Center for Urban Pollution Control, College of Environmental Science and Engineering, Tongji University, Shanghai 200092 (China); Chen, Xin, E-mail: 742702437@qq.com [National Engineering Research Center for Urban Pollution Control, College of Environmental Science and Engineering, Tongji University, Shanghai 200092 (China); Zhang, Dong, E-mail: zhdongtj7021@sina.com [National Engineering Research Center of Urban Water Resources, Shanghai National Engineering Research Center of Urban Water Resources Co. Ltd, Shanghai 200082 (China); Chen, Hong-bin, E-mail: hbctxc@tongji.edu.cn [National Engineering Research Center for Urban Pollution Control, College of Environmental Science and Engineering, Tongji University, Shanghai 200092 (China)

2016-11-01

In order to improve our understanding of bio-activated carbon (BAC) filter, the water quality of influent and effluent treated with BAC in a drinking water treatment plant (DWTP) of Shanghai during 2015 was valued. Combining the results from UV{sub 254}, SUVA{sub 254}, dissolved organic carbon (DOC) and scanning electron microscopic (SEM), it is found that performance of BAC treatment will be affected by characteristics of activated carbon (AC), which is relevant to the type of activated carbon (including shape and operating time) in this study. Fluorescence excitation–emission matrix (FEEM) shows that the humification index (HIX) and index of recent autochthonous contribution (BIX) is a reliable indicator to descript the variation of dissolved organic matter (DOM) during BAC process. The pattern of variation in BIX and HIX implies that soluble microbial products (SMPs) are formed and humic-like substances are removed during BAC treatment, which is also confirmed by the change of peaks of FEEM in BAC effluent. Large, positive correlations between SUVA{sub 254} and disinfection by-products formation potential yield (DBPFP yield) demonstrate that UV-absorbing DOM is directly related to the generation of DBPs. Poor correlations of HIX with DBPFP suggest that non-humic substances with UV-absorbing properties play an important role in the generation of DBPs in water with low SUVA{sub 254}. Finally, strong but negative correlations between BIX and DBPFP suggest that vigorous microbial metabolism of BAC results in a decrease in DBPFP. However, the DBPFP yield will be enhanced for the generation of SMPs by BAC, especially in summer. - Highlights: • SMPs can be produced by BAC during drinking water advanced treatment. • BAC can reduce DBPFP, while there are risks associated with increasing DBPFP yield. • SUVA{sub 254} is strongly correlated with the DBPFP yields. • BIX is strongly correlated with DBPFP and THMFP, but weakly with HAAFP.

The physical and genetic framework of the maize B73 genome.

Directory of Open Access Journals (Sweden)

Fusheng Wei

2009-11-01

Full Text Available Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP of 16,910 bacterial artificial chromosome (BAC and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93% of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map. More importantly, 336 contigs, comprising 94.0% of the physical map ( approximately 1,993 Mb, were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1.

Physics of frequency-modulated comb generation in quantum-well diode lasers

Science.gov (United States)

Dong, Mark; Cundiff, Steven T.; Winful, Herbert G.

2018-05-01

We investigate the physical origin of frequency-modulated combs generated from single-section semiconductor diode lasers based on quantum wells, isolating the essential physics necessary for comb generation. We find that the two effects necessary for comb generation—spatial hole burning (leading to multimode operation) and four-wave mixing (leading to phase locking)—are indeed present in some quantum-well systems. The physics of comb generation in quantum wells is similar to that in quantum dot and quantum cascade lasers. We discuss the nature of the spectral phase and some important material parameters of these diode lasers.

The Magnetohydrodynamic Generator A Physics Olympiad Problem

Indian Academy of Sciences (India)

The Magnetohydrodynamic Generator A Physics Olympiad Problem (2001). Vijay A Singh ... Magnetohydrodynamics; generator; power; efficiency; Faraday's law; Physics Olympiad . Author Affiliations. Vijay A Singh1 Manish Kapoor2. Physics Department Indian Institute of Technology Kanpur 208016, India. MPE College ...

BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins

Directory of Open Access Journals (Sweden)

MuthuKrishnan Selvaraj

2016-01-01

Full Text Available The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Support vector machine (SVM models were developed for predicting HbL proteins based upon amino acid composition (AC, dipeptide composition (DC, hybrid method (AC + DC, and position specific scoring matrix (PSSM. In addition, we introduce for the first time a new prediction method based on max to min amino acid residue (MM profiles. The average accuracy, standard deviation (SD, false positive rate (FPR, confusion matrix, and receiver operating characteristic (ROC were analyzed. We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques. Prediction accuracy was further investigated through confusion matrix and ROC curve analysis. All experimental results indicate that the proposed BacHbpred can be a perspective predictor for determination of HbL related proteins. BacHbpred, a web tool, has been developed for HbL prediction.

Comparison of 'time to detection' values between BacT/ALERT VIRTUO and BacT/ALERT 3D instruments for clinical blood culture samples.

Science.gov (United States)

Congestrì, Francesco; Pedna, Maria Federica; Fantini, Michela; Samuelli, Michela; Schiavone, Pasqua; Torri, Arianna; Bertini, Stefania; Sambri, Vittorio

2017-09-01

The early detection of bacteraemia and fungemia is of paramount importance to guide antimicrobial therapy in septic patients. In this study the 'time to detection' (TTD) value for the new blood culture system BacT/ALERT VIRTUO (VIRTUO) was evaluated in 1462 positive clinical bottles and compared with the TTD for 1601 positive clinical bottles incubated in the BacT/ALERT 3D system (BTA-3D). The most representative microorganisms isolated from bottles incubated in both blood culture systems were divided into eight categories (in order of frequency): coagulase-negative staphylococci (CoNS), Escherichia coli, Enterobacteriaceae (other than E. coli), Staphylococcus aureus, Enterococcus spp, viridans group streptococci, Pseudomonas aeruginosa, and Candida spp. The comparison of TTD values for the two blood culture systems strongly indicated that growth of the first five groups listed above was detected earlier with VIRTUO than with BTA-3D (p culture system can reduce the TTD for more than 75% of isolated microorganisms. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The need for blood alcohol concentration (BAC) legislation in Nigeria

African Journals Online (AJOL)

The pharmacology, clinical and sports implications of indulgence in alcohol and the debate on its legal status are highlighted in this article. The information presented could offer both clinical and safety benefits to psychomotor tasks executors and road safety professionals. Keywords: Blood alcohol concentration (BAC), ...

Generation of soluble microbial products by bio-activated carbon filter during drinking water advanced treatment and its influence on spectral characteristics

International Nuclear Information System (INIS)

Shen, Hong; Chen, Xin; Zhang, Dong; Chen, Hong-bin

2016-01-01

In order to improve our understanding of bio-activated carbon (BAC) filter, the water quality of influent and effluent treated with BAC in a drinking water treatment plant (DWTP) of Shanghai during 2015 was valued. Combining the results from UV_2_5_4, SUVA_2_5_4, dissolved organic carbon (DOC) and scanning electron microscopic (SEM), it is found that performance of BAC treatment will be affected by characteristics of activated carbon (AC), which is relevant to the type of activated carbon (including shape and operating time) in this study. Fluorescence excitation–emission matrix (FEEM) shows that the humification index (HIX) and index of recent autochthonous contribution (BIX) is a reliable indicator to descript the variation of dissolved organic matter (DOM) during BAC process. The pattern of variation in BIX and HIX implies that soluble microbial products (SMPs) are formed and humic-like substances are removed during BAC treatment, which is also confirmed by the change of peaks of FEEM in BAC effluent. Large, positive correlations between SUVA_2_5_4 and disinfection by-products formation potential yield (DBPFP yield) demonstrate that UV-absorbing DOM is directly related to the generation of DBPs. Poor correlations of HIX with DBPFP suggest that non-humic substances with UV-absorbing properties play an important role in the generation of DBPs in water with low SUVA_2_5_4. Finally, strong but negative correlations between BIX and DBPFP suggest that vigorous microbial metabolism of BAC results in a decrease in DBPFP. However, the DBPFP yield will be enhanced for the generation of SMPs by BAC, especially in summer. - Highlights: • SMPs can be produced by BAC during drinking water advanced treatment. • BAC can reduce DBPFP, while there are risks associated with increasing DBPFP yield. • SUVA_2_5_4 is strongly correlated with the DBPFP yields. • BIX is strongly correlated with DBPFP and THMFP, but weakly with HAAFP.

Genome-wide BAC-end sequencing of Musa acuminata DH Pahang reveals further insights into the genome organization of banana

NARCIS (Netherlands)

Arnago, R.E.; Togawa, R.C.; Carpentier, S.C.; Lintel Hekkert, te B.; Kema, G.H.J.; Souza, M.T.

2011-01-01

Banana and plantain (Musa spp.) are grown in more than 120 countries in tropical and subtropical regions and constitute an important staple food for millions of people. A Musa acuminata ssp. malaccencis DH Pahang bacterial artificial chromosome (BAC) library (MAMB) was submitted for BAC-end

Characterization of Extracellular Penicilin G Acylase Produced by A New Local Strain of Bacillus subtilis BAC4

Directory of Open Access Journals (Sweden)

SUPARTONO

2008-06-01

Full Text Available Penicillin G acylase (PGA which catalyses penicillin G hydrolysis reaction is a key enzyme for the industrial production of penicilin G derivatives used in therapeutics. A new local strain of Bacillus subtilis BAC4 was found capable of producing extracellular PGA. However, characteristics of this extracellular PGA are not known. The goal of this research was to characterize the extracellular PGA produced by B. subtilis BAC4. Enzyme production was carried out by batch fermentation, followed by enzyme purification and characterization of the PGA. The PGA activity was determined by the Kornfeld method, with optimal activity for hydrolysing penicillin G observed at 43 °C and pH 8.5. The activation energy of penicillin G hydrolysis by the PGA of B. subtilis BAC4 was determined as 4.9 kcal.mol−1 and Vmax and Km values were found to be 0.7 μmole.min−1.mg−1 and 3.5 mM respectively. PGA catalytic activity was competitively inhibited by phenylacetic acid with an inhibition constant, Ki(PAA, of 347.2 mM. It was concluded that the extracellular PGA of B. subtilis BAC4 can hydrolyse penicillin G efficiently.

Characterization of Extracellular Penicilin G Acylase Produced by A New Local Strain of Bacillus subtilis BAC4

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SUPARTONO

2008-06-01

Full Text Available Penicillin G acylase (PGA which catalyses penicillin G hydrolysis reaction is a key enzyme for the industrial production of penicilin G derivatives used in therapeutics. A new local strain of Bacillus subtilis BAC4 was found capable of producing extracellular PGA. However, characteristics of this extracellular PGA are not known. The goal of this research was to characterize the extracellular PGA produced by B. subtilis BAC4. Enzyme production was carried out by batch fermentation, followed by enzyme purification and characterization of the PGA. The PGA activity was determined by the Kornfeld method, with optimal activity for hydrolysing penicillin G observed at 43 oC and pH 8.5. The activation energy of penicillin G hydrolysis by the PGA of B. subtilis BAC4 was determined as 4.9 kcal.mol-1 and Vmax and Km values were found to be 0.7 µmole.min-1.mg-1 and 3.5 mM respectively. PGA catalytic activity was competitively inhibited by phenylacetic acid with an inhibition constant, Ki(PAA, of 347.2 mM. It was concluded that the extracellular PGA of B. subtilis BAC4 can hydrolyse penicillin G efficiently.

Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L. Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic–Physical Map Integration

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Juana M. Córdoba

2010-11-01

Full Text Available Microsatellite markers or simple sequence repeat (SSR loci are useful for diversity characterization and genetic–physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs from the G19833 common bean ( L. library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]. Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-, and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.

A Bac Library and Paired-PCR Approach to Mapping and Completing the Genome Sequence of Sulfolobus Solfataricus P2

DEFF Research Database (Denmark)

She, Qunxin; Confalonieri, F.; Zivanovic, Y.

2000-01-01

The original strategy used in the Sulfolobus solfatnricus genome project was to sequence non overlapping, or minimally overlapping, cosmid or lambda inserts without constructing a physical map. However, after only about two thirds of the genome sequence was completed, this approach became counter......-productive because there was a high sequence bias in the cosmid and lambda libraries. Therefore, a new approach was devised for linking the sequenced regions which may be generally applicable. BAC libraries were constructed and terminal sequences of the clones were determined and used for both end mapping and PCR...

Spatial attributes of the four-helix bundle group of bacteriocins – The high-resolution structure of BacSp222 in solution

KAUST Repository

Nowakowski, Michał; Jaremko, Łukasz; Wladyka, Benedykt; Dubin, Grzegorz; Ejchart, Andrzej; Mak, Paweł

2017-01-01

collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns.Although the amino acid sequence of BacSp222 has no significant

Wave Generation in Physical Models

DEFF Research Database (Denmark)

Andersen, Thomas Lykke; Frigaard, Peter

The present book describes the most important aspects of wave generation techniques in physical models. Moreover, the book serves as technical documentation for the wave generation software AwaSys 6, cf. Aalborg University (2012). In addition to the two main authors also Tue Hald and Michael...

Physical Analysis of the Complex Rye (Secale cereale L.) Alt4 Aluminium (Aluminum) Tolerance Locus Using a Whole-Genome BAC Library of Rye cv. Blanco

Science.gov (United States)

Rye is a diploid crop species with many outstanding qualities, and is also important as a source of new traits for wheat and triticale improvement. Here we describe a BAC library of rye cv. Blanco, representing a valuable resource for rye molecular genetic studies. The library provides a 6 × genome ...

BACs-on-Beads Technology: A Reliable Test for Rapid Detection of Aneuploidies and Microdeletions in Prenatal Diagnosis

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Sandra García-Herrero

2014-01-01

Full Text Available The risk of fetal aneuploidies is usually estimated based on high resolution ultrasound combined with biochemical determination of criterion in maternal blood, with invasive procedures offered to the population at risk. The purpose of this study was to investigate the effectiveness of a new rapid aneuploidy screening test on amniotic fluid (AF or chorionic villus (CV samples based on BACs-on-Beads (BoBs technology and to compare the results with classical karyotyping by Giemsa banding (G-banding of cultured cells in metaphase as the gold standard technique. The prenatal-BoBs kit was used to study aneuploidies involving chromosomes 13, 18, 21, X, and Y as well as nine microdeletion syndromes in 321 AF and 43 CV samples. G-banding of metaphase cultured cells was performed concomitantly for all prenatal samples. A microarray-based comparative genomic hybridization (aCGH was also carried out in a subset of samples. Prenatal-BoBs results were widely confirmed by classical karyotyping. Only six karyotype findings were not identified by Prenatal-BoBs, all of them due to the known limitations of the technique. In summary, the BACs-on-Beads technology was an accurate, robust, and efficient method for the rapid diagnosis of common aneuploidies and microdeletion syndromes in prenatal samples.

Effect of mercaptoethylamine on DNA degradation in thermophilic bacteria Bac. stearothermophilus exposed to. gamma. -, UV-radiation or methylnitrosourea

Energy Technology Data Exchange (ETDEWEB)

Fomenko, L A; Kuznetsovea, E A; Gaziev, A I

1984-07-01

The effect of mercaptoethylamine (MEA) on degradation of DNA in thermophilic bacteria Bac. stear. exposed to ..gamma..-, UV-rays or methylnitrosourea (MNU) was studied. Using centrifugation on alkaline and neutral sucrose gradients, it was shown that MEA inhibits the accumulation of breaks in the DNA of Bac. stear. It also lowers the level of DNA degradation in toluene-treated cells of Bac. stear. under the action of the intrinsic nuclease, reduces the activity of the endonuclease specific for apurinic DNA, as well as that of S/sub 1/-nuclease and DNase-I in vitro. The inhibition in the accumulation of DNA breaks is assumed to be due to a decrease of the endonuclease activity in the cells of thermophilic bacteria.

Effect of mercaptoethylamine on DNA degradation in thermophilic bacteria Bac. stearothermophilus exposed to γ-, UV-radiation or methylnitrosourea

International Nuclear Information System (INIS)

Fomenko, L.A.; Kuznetsovea, E.A.; Gaziev, A.I.

1984-01-01

The effect of mercaptoethylamine (MEA) on degradation of DNA in thermophilic bacteria Bac. stear. exposed to γ-, UV-rays or methylnitrosourea (MNU) was studied. Using centrifugation on alkaline and neutral sucrose gradients, it was shown that MEA inhibits the accumulation of breaks in the DNA of Bac. stear. It also lowers the level of DNA degradation in toluene-treated cells of Bac. stear. under the action of the intrinsic nuclease, reduces the activity of the endonuclease specific for apurinic DNA, as well as that of S 1 -nuclease and DNase-I in vitro. The inhibition in the accumulation of DNA breaks is assumed to be due to a decrease of the endonuclease activity in the cells of thermophilic bacteria. (orig.)

Physical-depth architectural requirements for generating universal photonic cluster states

Science.gov (United States)

Morley-Short, Sam; Bartolucci, Sara; Gimeno-Segovia, Mercedes; Shadbolt, Pete; Cable, Hugo; Rudolph, Terry

2018-01-01

Most leading proposals for linear-optical quantum computing (LOQC) use cluster states, which act as a universal resource for measurement-based (one-way) quantum computation. In ballistic approaches to LOQC, cluster states are generated passively from small entangled resource states using so-called fusion operations. Results from percolation theory have previously been used to argue that universal cluster states can be generated in the ballistic approach using schemes which exceed the critical threshold for percolation, but these results consider cluster states with unbounded size. Here we consider how successful percolation can be maintained using a physical architecture with fixed physical depth, assuming that the cluster state is continuously generated and measured, and therefore that only a finite portion of it is visible at any one point in time. We show that universal LOQC can be implemented using a constant-size device with modest physical depth, and that percolation can be exploited using simple pathfinding strategies without the need for high-complexity algorithms.

Enhanced Expression of Anti-CD19 Chimeric Antigen Receptor in piggyBac Transposon-Engineered T Cells

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Daisuke Morita

2018-03-01

Full Text Available Adoptive T cell therapy using chimeric antigen receptor (CAR-modified T cells is a promising cancer immunotherapy. We previously developed a non-viral method of gene transfer into T cells using a piggyBac transposon system to improve the cost-effectiveness of CAR-T cell therapy. Here, we have further improved our technology by a novel culture strategy to increase the transfection efficiency and to reduce the time of T cell manufacturing. Using a CH2CH3-free CD19-specific CAR transposon vector and combining irradiated activated T cells (ATCs as feeder cells and virus-specific T cell receptor (TCR stimulation, we achieved 51.4% ± 14% CAR+ T cells and 2.8-fold expansion after 14 culture days. Expanded CD19.CAR-T cells maintained a significant fraction of CD45RA+CCR7+ T cells and demonstrated potent antitumor activity against CD19+ leukemic cells both in vitro and in vivo. Therefore, piggyBac-based gene transfer may provide an alternative to viral gene transfer for CAR-T cell therapy.

State Blood Alcohol Concentration (BAC) Testing and Reporting for Drivers Involved in Fatal Crashes : Current Practices, Results, and Strategies, 1997-2009

Science.gov (United States)

2012-08-01

This report documents current State blood alcohol concentration (BAC) testing and reporting practices and results for drivers involved in fatal crashes. It summarizes known BAC results by State for the years 1997 to 2009 for both fatally injured and ...

Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes.

Science.gov (United States)

Kukekova, Anna V; Vorobieva, Nadegda V; Beklemisheva, Violetta R; Johnson, Jennifer L; Temnykh, Svetlana V; Yudkin, Dmitry V; Trut, Lyudmila N; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D; Acland, Gregory M; Graphodatsky, Alexander S

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.

The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood

Science.gov (United States)

Rothman, Richard E.; Peterson, Stephen; Carroll, Karen C.; Zhang, Sean X.; Avornu, Gideon D.; Rounds, Megan A.; Carolan, Heather E.; Toleno, Donna M.; Moore, David; Hall, Thomas A.; Massire, Christian; Richmond, Gregory S.; Gutierrez, Jose R.; Sampath, Rangarajan; Ecker, David J.; Blyn, Lawrence B.

2016-01-01

Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States. PMID:27384540

Fast physical random bit generation with chaotic semiconductor lasers

Science.gov (United States)

Uchida, Atsushi; Amano, Kazuya; Inoue, Masaki; Hirano, Kunihito; Naito, Sunao; Someya, Hiroyuki; Oowada, Isao; Kurashige, Takayuki; Shiki, Masaru; Yoshimori, Shigeru; Yoshimura, Kazuyuki; Davis, Peter

2008-12-01

Random number generators in digital information systems make use of physical entropy sources such as electronic and photonic noise to add unpredictability to deterministically generated pseudo-random sequences. However, there is a large gap between the generation rates achieved with existing physical sources and the high data rates of many computation and communication systems; this is a fundamental weakness of these systems. Here we show that good quality random bit sequences can be generated at very fast bit rates using physical chaos in semiconductor lasers. Streams of bits that pass standard statistical tests for randomness have been generated at rates of up to 1.7 Gbps by sampling the fluctuating optical output of two chaotic lasers. This rate is an order of magnitude faster than that of previously reported devices for physical random bit generators with verified randomness. This means that the performance of random number generators can be greatly improved by using chaotic laser devices as physical entropy sources.

Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

Science.gov (United States)

Seoane-Zonjic, Pedro; Cañas, Rafael A; Bautista, Rocío; Gómez-Maldonado, Josefa; Arrillaga, Isabel; Fernández-Pozo, Noé; Claros, M Gonzalo; Cánovas, Francisco M; Ávila, Concepción

2016-02-27

In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82% of the gene structures, and a high proportion (85%) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members. The experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a

Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies.

Science.gov (United States)

Wang, Gang; Yang, Luhan; Grishin, Dennis; Rios, Xavier; Ye, Lillian Y; Hu, Yong; Li, Kai; Zhang, Donghui; Church, George M; Pu, William T

2017-01-01

Genome editing of human induced pluripotent stem cells (hiPSCs) offers unprecedented opportunities for in vitro disease modeling and personalized cell replacement therapy. The introduction of Cas9-directed genome editing has expanded adoption of this approach. However, marker-free genome editing using standard protocols remains inefficient, yielding desired targeted alleles at a rate of ∼1-5%. We developed a protocol based on a doxycycline-inducible Cas9 transgene carried on a piggyBac transposon to enable robust and highly efficient Cas9-directed genome editing, so that a parental line can be expeditiously engineered to harbor many separate mutations. Treatment with doxycycline and transfection with guide RNA (gRNA), donor DNA and piggyBac transposase resulted in efficient, targeted genome editing and concurrent scarless transgene excision. Using this approach, in 7 weeks it is possible to efficiently obtain genome-edited clones with minimal off-target mutagenesis and with indel mutation frequencies of 40-50% and homology-directed repair (HDR) frequencies of 10-20%.

Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant.

Directory of Open Access Journals (Sweden)

Qing Ye

Full Text Available The bacterial artificial chromosome (BAC system is widely used in isolation of large genomic fragments of interest. Construction of a routine BAC library requires several months for picking clones and arraying BACs into superpools in order to employ 4D-PCR to screen positive BACs, which might be time-consuming and laborious. The major histocompatibility complex (MHC is a cluster of genes involved in the vertebrate immune system, and the classical avian MHC-B locus is a minimal essential one, occupying a 100-kb genomic region. In this study, we constructed a more effective reverse-4D BAC library for the golden pheasant, which first creates sub-libraries and then only picks clones of positive sub-libraries, and identified several MHC clones within thirty days. The full sequencing of a 97-kb reverse-4D BAC demonstrated that the golden pheasant MHC-B locus contained 20 genes and showed good synteny with that of the chicken. The notable differences between these two species were the numbers of class II B loci and NK genes and the inversions of the TAPBP gene and the TAP1-TAP2 region. Furthermore, the inverse TAP2-TAP1 was unique in the golden pheasant in comparison with that of chicken, turkey, and quail. The newly defined genomic structure of the golden pheasant MHC will give an insight into the evolutionary history of the avian MHC.

Enhanced biodegradation of petrochemical wastewater using ozonation and BAC advanced treatment system

Energy Technology Data Exchange (ETDEWEB)

Lin, Chi-Kang; Tsai, Tsung-Yueh; Liu, Jiunn-Ching; Chen, Mei-Chen [Energy and Resources Labs., ITRI, Hsinchu (Taiwan)

2001-07-01

The characteristics of degradation/conversion of bio-refractory and the growth of a biofilm are investigated in laboratory-scale pre-ozonation and lifted moving-bed biological activated carbon (BAC) advanced treatment processes treating phenol, benzoic acid, aminobenzoic acid and petrochemical industry wastewater which contains acrylonitrile butadiene styrene (ABS). The optimal reaction time and ozone dosage of pre-ozonation for bio-refractory conversion were determined to be 30 min and 100-200mg O{sub 3}/hr, respectively. After pre-ozonation of 30 min treatment, BOD{sub 5}/COD ratio of influent and effluent increased apparently from 20 to 35%, approximately. However, the change of pH in pre-ozonation was inconspicuous. The optimal flow rate of influent and air were controlled at 1.6 1/h and 120-l50nl/min in lifted moving-bed BAC advanced treatment reactor. A COD removal efficiency of 85-95% and 70-90% may be maintained by using an organic loading of 3.2-6.3kg COD/m{sup 3} day and 0.6-1.6 kg-COD/m{sup 3} day with an HRT of 6.0 h as secondary and advanced treatment system, respectively. The time required for the BAC bed to be regenerated by a thermal regeneration is prolonged 4-5 times more than that of GAC system. It can be estimated that the enhanced COD removal capability of the biofilm was not only due to the increase in the COD removal capability of acclimated bacteria, but also due to species succession of bacteria in bio-film ecosystem. (Author)

The canine sarcoglycan delta gene: BAC clone contig assembly, chromosome assignment and interrogation as a candidate gene for dilated cardiomyopathy in Dobermann dogs.

Science.gov (United States)

Stabej, P; Leegwater, P A J; Imholz, S; Versteeg, S A; Zijlstra, C; Stokhof, A A; Domanjko-Petriè, A; van Oost, B A

2005-01-01

Dilated cardiomyopathy (DCM) is a common disease of the myocardium recognized in human, dog and experimental animals. Genetic factors are responsible for a large proportion of cases in humans, and 17 genes with DCM causing mutations have been identified. The genetic origin of DCM in the Dobermann dogs has been suggested, but no disease genes have been identified to date. In this paper, we describe the characterization and evaluation of the canine sarcoglycan delta (SGCD), a gene implicated in DCM in human and hamster. Bacterial artificial chromosomes (BACs) containing the canine SGCD gene were isolated with probes for exon 3 and exons 4-8 and were characterized by Southern blot analysis. BAC end sequences were obtained for four BACs. Three of the BACs overlapped and could be ordered relative to each other and the end sequences of all four BACs could be anchored on the preliminary assembly of the dog genome sequence (www. ensembl.org). One of the BACs of the partial contig was localized by fluorescent in situ hybridization to canine chromosome 4q22, in agreement with the dog genome sequence. Two highly informative polymorphic microsatellite markers in intron 7 of the SGCD gene were identified. In 25 DCM-affected and 13 non DCM-affected dogs seven different haplotypes could be distinguished. However, no association between any of the SGCD variants and the disease locus was apparent.

Construction of an Americn mink Bacterial Artificial Chromosome (BAC) library and sequencing candidate genes important for the fur industry

DEFF Research Database (Denmark)

Anistoroaei, Razvan Marian; Hallers, Boudewijn ten; Nefedov, Michael

2011-01-01

BACKGROUND: Bacterial artificial chromosome (BAC) libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. RESULTS: Here, we...... report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison). The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each...... consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs), representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library...

Direct conversion of human pluripotent stem cells into cranial motor neurons using a piggyBac vector

Directory of Open Access Journals (Sweden)

Riccardo De Santis

2018-05-01

Full Text Available Human pluripotent stem cells (PSCs are widely used for in vitro disease modeling. One of the challenges in the field is represented by the ability of converting human PSCs into specific disease-relevant cell types. The nervous system is composed of a wide variety of neuronal types with selective vulnerability in neurodegenerative diseases. This is particularly relevant for motor neuron diseases, in which different motor neurons populations show a different susceptibility to degeneration. Here we developed a fast and efficient method to convert human induced Pluripotent Stem Cells into cranial motor neurons of the branchiomotor and visceral motor subtype. These populations represent the motor neuron subgroup that is primarily affected by a severe form of amyotrophic lateral sclerosis with bulbar onset and worst prognosis. This goal was achieved by stable integration of an inducible vector, based on the piggyBac transposon, allowing controlled activation of Ngn2, Isl1 and Phox2a (NIP. The NIP module effectively produced electrophysiologically active cranial motor neurons. Our method can be easily extended to PSCs carrying disease-associated mutations, thus providing a useful tool to shed light on the cellular and molecular bases of selective motor neuron vulnerability in pathological conditions. Keywords: Spinal motor neuron, Cranial motor neuron, Induced pluripotent stem cells, Amyotrophic lateral sclerosis, Phox2a, piggyBac

A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance

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Scalabrin Simone

2008-06-01

Full Text Available Abstract Background Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. Results The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32% were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. Conclusion Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and

PLE-wu, a new member of piggyBac transposon family from insect, is active in mammalian cells.

Science.gov (United States)

Wu, Chunxiao; Wang, Shu

2014-10-01

piggyBac, a highly active transposon in insect and mammalian cells, is a very useful tool in genome manipulation. A new piggyBac-like element (PLE), named PLE-wu, was identified from a mutant baculovirus cultured in sf9 insect cells. This new transposon is 2931 bp in length and encodes two active forms of transposase, a 708-amino acid-long transposase and a short 576-residue-long transposase translated from a downstream in-frame initiation codon. PLE-wu has asymmetric terminal structures, containing 6-bp inverted terminal repeats, 32-bp imperfect inverted and direct sub-terminal repeats. Similar to piggyBac, PLE-wu exhibits traceless excision activity in both insect and mammalian cells, restoring the original TTAA target sequence upon excision. It also retains the insertion activity in mammalian cells with a plasmid to chromosome transposition rate about 10-fold higher than random integration. Plasmid rescue assays revealed that the TTAA target sequence was duplicated at the junctions of the insertion site. Deletion of the terminal sequences including the sub-terminal repeats decreased the transposition activity of the 708-residue-long transposase, while the transposition activity of the short form of transposase was not affected. With its low sequence similarity to piggyBac, PLE-wu will contribute to the understanding the mechanism of PLE transposition, as well as design of new transposon systems with higher activity. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Heterogeneous transgene expression in the retinas of the TH-RFP, TH-Cre, TH-BAC-Cre and DAT-Cre mouse lines.

Science.gov (United States)

Vuong, H E; Pérez de Sevilla Müller, L; Hardi, C N; McMahon, D G; Brecha, N C

2015-10-29

Transgenic mouse lines are essential tools for understanding the connectivity, physiology and function of neuronal circuits, including those in the retina. This report compares transgene expression in the retina of a tyrosine hydroxylase (TH)-red fluorescent protein (RFP) mouse line with three catecholamine-related Cre recombinase mouse lines [TH-bacterial artificial chromosome (BAC)-, TH-, and dopamine transporter (DAT)-Cre] that were crossed with a ROSA26-tdTomato reporter line. Retinas were evaluated and immunostained with commonly used antibodies including those directed to TH, GABA and glycine to characterize the RFP or tdTomato fluorescent-labeled amacrine cells, and an antibody directed to RNA-binding protein with multiple splicing to identify ganglion cells. In TH-RFP retinas, types 1 and 2 dopamine (DA) amacrine cells were identified by their characteristic cellular morphology and type 1 DA cells by their expression of TH immunoreactivity. In the TH-BAC-, TH-, and DAT-tdTomato retinas, less than 1%, ∼ 6%, and 0%, respectively, of the fluorescent cells were the expected type 1 DA amacrine cells. Instead, in the TH-BAC-tdTomato retinas, fluorescently labeled AII amacrine cells were predominant, with some medium diameter ganglion cells. In TH-tdTomato retinas, fluorescence was in multiple neurochemical amacrine cell types, including four types of polyaxonal amacrine cells. In DAT-tdTomato retinas, fluorescence was in GABA immunoreactive amacrine cells, including two types of bistratified and two types of monostratified amacrine cells. Although each of the Cre lines was generated with the intent to specifically label DA cells, our findings show a cellular diversity in Cre expression in the adult retina and indicate the importance of careful characterization of transgene labeling patterns. These mouse lines with their distinctive cellular labeling patterns will be useful tools for future studies of retinal function and visual processing. Published by Elsevier

A highly redundant BAC library of Atlantic salmon (Salmo salar: an important tool for salmon projects

Directory of Open Access Journals (Sweden)

Koop Ben F

2005-04-01

Full Text Available Abstract Background As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Traits of importance might be related to growth, disease resistance, food conversion efficiency, color or taste. To identify genomic regions responsible for specific traits, genomic large insert libraries have previously proven to be of crucial importance. These large insert libraries can be screened using gene or genetic markers in order to identify and map regions of interest. Furthermore, large-scale mapping can utilize highly redundant libraries in genome projects, and hence provide valuable data on the genome structure. Results Here we report the construction and characterization of a highly redundant bacterial artificial chromosome (BAC library constructed from a Norwegian aquaculture strain male of Atlantic salmon (Salmo salar. The library consists of a total number of 305 557 clones, in which approximately 299 000 are recombinants. The average insert size of the library is 188 kbp, representing 18-fold genome coverage. High-density filters each consisting of 18 432 clones spotted in duplicates have been produced for hybridization screening, and are publicly available 1. To characterize the library, 15 expressed sequence tags (ESTs derived overgos and 12 oligo sequences derived from microsatellite markers were used in hybridization screening of the complete BAC library. Secondary hybridizations with individual probes were performed for the clones detected. The BACs positive for the EST probes were fingerprinted and mapped into contigs, yielding an average of 3 contigs for each probe. Clones identified using genomic probes were PCR verified using microsatellite specific primers. Conclusion Identification of genes and genomic regions of interest is greatly aided by the availability of the CHORI-214 Atlantic salmon BAC

Sur la filabilité d'une laine teinte en bac-ouvert et d'une laine teinte à la continue

NARCIS (Netherlands)

Werker, W.; Mulder, D.; Stomph, J.; Schartman, A.F.

1966-01-01

Afin de constater, si la teinture selon le procédé à la continue ou selon le procédé en bac-ouvert influence les résultats dans Ia filature, on a teint deux lots homogènes à 18OO kg par lot en quatre parties: 450 kg, procédé à la continue, teints en rouge, 450 kg, procédé bac-ouvert, teints en

Promoting Plasma Physics as a Career: A Generational Approach

Science.gov (United States)

Morgan, James

2005-10-01

A paradigm shift is occurring in education physics programs. Educators are shifting from the traditional teaching focus to concentrate on student learning. Students are unaware of physics as a career, plasma physics or the job opportunities afforded to them with a physics degree. The physics profession needs to promote itself to the younger generations, or specifically the millennial generation (Born in the 1980's-2000's). Learning styles preferred by ``Millennials'' include a technological environment that promotes learning through active task performance rather than passive attendance at lectures. Millennials respond well to anything experiential and will be motivated by opportunities for creativity and challenging learning environments. The open-ended access to information, the ability to tailor learning paths, and continuous and instantaneous performance assessment offer flexibility in the design of curricula as well as in the method of delivery. Educators need to understand the millennial generation, appeal to their motivations and offer a learning environment designed for their learning style. This poster suggests promoting a physics career by focusing on generational learning styles and preferences.

Proceso para transferir el conocimiento en la adquisición de software en la Gerencia de Tecnologías de Información del BAC San José

OpenAIRE

Castillo Rivera, Roberto

2016-01-01

Proyecto final de graduación, Maestría profesional El presente proyecto es el resultado de la aplicación de las mejores prácticas tomando como base la metodología de ITIL en su versión 3 para la liberación final de productos de software, específicamente en cuanto a la transferencia del conocimiento obtenido durante el proceso de adquisición de software aplicativo en la Gerencia de Tecnologías de Información del Banco BAC San José. El Banco BAC San José es una entidad financiera privada,...

Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca)

OpenAIRE

Liu, Wei; Zhao, Yonghui; Liu, Zhaoliang; Zhang, Ying; Lian, Zhengxing; Li, Ning

2006-01-01

Abstract Background The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda was constructed in this study. Results This BAC library contains 198,844 clones with an average insert size of 108 kb, which represents approximately seven equivalents o...

Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat

Czech Academy of Sciences Publication Activity Database

Šafář, Jan; Šimková, Hana; Kubaláková, Marie; Čihalíková, Jarmila; Suchánková, Pavla; Bartoš, Jan; Doležel, Jaroslav

2010-01-01

Roč. 129, 1-3 (2010), s. 211-223 ISSN 1424-8581 R&D Projects: GA ČR GA521/07/1573; GA MŠk(CZ) LC06004 Grant - others:European Community’s Seventh Framework Programme(XE) FP7/2007–2013 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC library * Chromosome * DNA markers Subject RIV: GE - Plant Breeding Impact factor: 1.783, year: 2010

Development of diagnostic prediction tools for bacteraemia caused by third-generation cephalosporin-resistant enterobacteria in suspected bacterial infections: a nested case-control study.

Science.gov (United States)

Rottier, W C; van Werkhoven, C H; Bamberg, Y R P; Dorigo-Zetsma, J W; van de Garde, E M; van Hees, B C; Kluytmans, J A J W; Kuck, E M; van der Linden, P D; Prins, J M; Thijsen, S F T; Verbon, A; Vlaminckx, B J M; Ammerlaan, H S M; Bonten, M J M

2018-03-23

Current guidelines for the empirical antibiotic treatment predict the presence of third-generation cephalosporin-resistant enterobacterial bacteraemia (3GCR-E-Bac) in case of infection only poorly, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems which can better predict the presence of 3GCR-E-Bac. A retrospective nested case-control study was performed that included patients ≥18 years of age from eight Dutch hospitals in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GCR-E-Bac was matched to four control infection episodes within the same hospital, based on blood-culture date and onset location (community or hospital). Starting from 32 commonly described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GCR-E-Bac. 3GCR-E-Bac occurred in 90 of 22 506 (0.4%) community-onset infections and in 82 of 8110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes. The derived community-onset and hospital-onset scoring systems consisted of six and nine predictors, respectively. With selected score cut-offs, the models identified 3GCR-E-Bac with sensitivity equal to existing guidelines (community-onset: 54.3%; hospital-onset: 81.5%). However, they reduced the proportion of patients classified as at risk for 3GCR-E-Bac (i.e. eligible for empirical carbapenem therapy) with 40% (95%CI 21-56%) and 49% (95%CI 39-58%) in, respectively, community-onset and hospital-onset infections. These prediction scores for 3GCR-E-Bac, specifically geared towards the initiation of empirical antibiotic treatment, may improve the balance between inappropriate antibiotics and carbapenem overuse. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

A nucleolus-predominant piggyBac transposase, NP-mPB, mediates elevated transposition efficiency in mammalian cells.

Science.gov (United States)

Hong, Jin-Bon; Chou, Fu-Ju; Ku, Amy T; Fan, Hsiang-Hsuan; Lee, Tung-Lung; Huang, Yung-Hsin; Yang, Tsung-Lin; Su, I-Chang; Yu, I-Shing; Lin, Shu-Wha; Chien, Chung-Liang; Ho, Hong-Nerng; Chen, You-Tzung

2014-01-01

PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase) codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP) signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB). Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3-4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells.

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

Science.gov (United States)

Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.

2013-01-01

For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960

Combinatorial pooling enables selective sequencing of the barley gene space.

Directory of Open Access Journals (Sweden)

Stefano Lonardi

2013-04-01

Full Text Available For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

Combinatorial pooling enables selective sequencing of the barley gene space.

Science.gov (United States)

Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J

2013-04-01

For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

BacHBerry:: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

DEFF Research Database (Denmark)

Dudnik, Alexey; Almeida, A. Filipa; Andrade, Ricardo

2017-01-01

BACterial Hosts for production of Bioactive phenolics from bERRY fruits (BacHBerry) was a 3-year project funded by the Seventh Framework Programme (FP7) of the European Union that ran between November 2013 and October 2016. The overall aim of the project was to establish a sustainable and economi...

Generation of Quasi-Gaussian Pulses Based on Correlation Techniques

Directory of Open Access Journals (Sweden)

POHOATA, S.

2012-02-01

Full Text Available The Gaussian pulses have been mostly used within communications, where some applications can be emphasized: mobile telephony (GSM, where GMSK signals are used, as well as the UWB communications, where short-period pulses based on Gaussian waveform are generated. Since the Gaussian function signifies a theoretical concept, which cannot be accomplished from the physical point of view, this should be expressed by using various functions, able to determine physical implementations. New techniques of generating the Gaussian pulse responses of good precision are approached, proposed and researched in this paper. The second and third order derivatives with regard to the Gaussian pulse response are accurately generated. The third order derivates is composed of four individual rectangular pulses of fixed amplitudes, being easily to be generated by standard techniques. In order to generate pulses able to satisfy the spectral mask requirements, an adequate filter is necessary to be applied. This paper emphasizes a comparative analysis based on the relative error and the energy spectra of the proposed pulses.

nanos-Driven expression of piggyBac transposase induces mobilization of a synthetic autonomous transposon in the malaria vector mosquito, Anopheles stephensi.

Science.gov (United States)

Macias, Vanessa M; Jimenez, Alyssa J; Burini-Kojin, Bianca; Pledger, David; Jasinskiene, Nijole; Phong, Celine Hien; Chu, Karen; Fazekas, Aniko; Martin, Kelcie; Marinotti, Osvaldo; James, Anthony A

2017-08-01

Transposons are a class of selfish DNA elements that can mobilize within a genome. If mobilization is accompanied by an increase in copy number (replicative transposition), the transposon may sweep through a population until it is fixed in all of its interbreeding members. This introgression has been proposed as the basis for drive systems to move genes with desirable phenotypes into target species. One such application would be to use them to move a gene conferring resistance to malaria parasites throughout a population of vector mosquitos. We assessed the feasibility of using the piggyBac transposon as a gene-drive mechanism to distribute anti-malarial transgenes in populations of the malaria vector, Anopheles stephensi. We designed synthetic gene constructs that express the piggyBac transposase in the female germline using the control DNA of the An. stephensi nanos orthologous gene linked to marker genes to monitor inheritance. Two remobilization events were observed with a frequency of one every 23 generations, a rate far below what would be useful to drive anti-pathogen transgenes into wild mosquito populations. We discuss the possibility of optimizing this system and the impetus to do so. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Efficient Strategy to Generate a Vectored Duck Enteritis Virus Delivering Envelope of Duck Tembusu Virus

Directory of Open Access Journals (Sweden)

Zhong Zou

2014-06-01

Full Text Available Duck Tembusu virus (DTMUV is a recently emerging pathogenic flavivirus that has resulted in a huge economic loss in the duck industry. However, no vaccine is currently available to control this pathogen. Consequently, a practical strategy to construct a vaccine against this pathogen should be determined. In this study, duck enteritis virus (DEV was examined as a candidate vaccine vector to deliver the envelope (E of DTMUV. A modified mini-F vector was inserted into the SORF3 and US2 gene junctions of the attenuated DEV vaccine strain C-KCE genome to generate an infectious bacterial artificial chromosome (BAC of C-KCE (vBAC-C-KCE. The envelope (E gene of DTMUV was inserted into the C-KCE genome through the mating-assisted genetically integrated cloning (MAGIC strategy, resulting in the recombinant vector, pBAC-C-KCE-E. A bivalent vaccine C-KCE-E was generated by eliminating the BAC backbone. Immunofluorescence and western blot analysis results indicated that the E proteins were vigorously expressed in C-KCE-E-infected chicken embryo fibroblasts (CEFs. Duck experiments demonstrated that the insertion of the E gene did not alter the protective efficacy of C-KCE. Moreover, C-KCE-E-immunized ducks induced neutralization antibodies against DTMUV. These results demonstrated, for the first time, that recombinant C-KCE-E can serve as a potential bivalent vaccine against DEV and DTMUV.

The GENIE Neutrino Monte Carlo Generator: Physics and User Manual

Energy Technology Data Exchange (ETDEWEB)

Andreopoulos, Costas [Univ. of Liverpool (United Kingdom). Dept. of Physics; Science and Technology Facilities Council (STFC), Oxford (United Kingdom). Rutherford Appleton Lab. (RAL). Particle Physics Dept.; Barry, Christopher [Univ. of Liverpool (United Kingdom). Dept. of Physics; Dytman, Steve [Univ. of Pittsburgh, PA (United States). Dept. of Physics and Astronomy; Gallagher, Hugh [Tufts Univ., Medford, MA (United States). Dept. of Physics and Astronomy; Golan, Tomasz [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Univ. of Rochester, NY (United States). Dept. of Physics and Astronomy; Hatcher, Robert [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Perdue, Gabriel [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Yarba, Julia [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States)

2015-10-20

GENIE is a suite of products for the experimental neutrino physics community. This suite includes i) a modern software framework for implementing neutrino event generators, a state-of-the-art comprehensive physics model and tools to support neutrino interaction simulation for realistic experimental setups (the Generator product), ii) extensive archives of neutrino, charged-lepton and hadron scattering data and software to produce a comprehensive set of data/MC comparisons (the Comparisons product), and iii) a generator tuning framework and fitting applications (the Tuning product). This book provides the definite guide for the GENIE Generator: It presents the software architecture and a detailed description of its physics model and official tunes. In addition, it provides a rich set of data/MC comparisons that characterise the physics performance of GENIE. Detailed step-by-step instructions on how to install and configure the Generator, run its applications and analyze its outputs are also included.

Rapid generation of markerless recombinant MVA vaccines by en passant recombineering of a self-excising bacterial artificial chromosome.

Science.gov (United States)

Cottingham, Matthew G; Gilbert, Sarah C

2010-09-01

The non-replicating poxviral vector modified vaccinia virus Ankara (MVA) is currently a leading candidate for development of novel recombinant vaccines against globally important diseases. The 1980s technology for making recombinant MVA (and other poxviruses) is powerful and robust, but relies on rare recombination events in poxviral-infected cells. In the 21st century, it has become possible to apply bacterial artificial chromosome (BAC) technology to poxviruses, as first demonstrated by B. Moss' lab in 2002 for vaccinia virus. A similar BAC clone of MVA was subsequently derived, but while recombination-mediated genetic engineering for rapid production was used of deletion mutants, an alternative method was required for efficient insertion of transgenes. Furthermore "markerless" viruses, which carry no trace of the selectable marker used for their isolation, are increasingly required for clinical trials, and the viruses derived via the new method contained the BAC sequence in their genomic DNA. Two methods are adapted to MVA-BAC to provide more rapid generation of markerless recombinants in weeks rather than months. "En passant" recombineering is applied to the insertion of a transgene expression cassette and the removal of the selectable marker in bacteria; and a self-excising variant of MVA-BAC is constructed, in which the BAC cassette region is rapidly and efficiently lost from the viral genome following rescue of the BAC into infectious virus. These methods greatly facilitate and accelerate production of recombinant MVA, including markerless constructs. Copyright 2010 Elsevier B.V. All rights reserved.

Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

Energy Technology Data Exchange (ETDEWEB)

Venken, Koen J.T.; Carlson, Joseph W.; Schulze, Karen L.; Pan, Hongling; He, Yuchun; Spokony, Rebecca; Wan, Kenneth H.; Koriabine, Maxim; de Jong, Pieter J.; White, Kevin P.; Bellen, Hugo J.; Hoskins, Roger A.

2009-04-21

We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95percent of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using Phi C31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.

Driving performance on the descending limb of blood alcohol concentration (BAC) in undergraduate students: a pilot study.

Science.gov (United States)

Tremblay, Mathieu; Gallant, François; Lavallière, Martin; Chiasson, Martine; Silvey, Dustin; Behm, David; Albert, Wayne J; Johnson, Michel J

2015-01-01

Young drivers are overrepresented in collisions resulting in fatalities. It is not uncommon for young drivers to socially binge drink and decide to drive a vehicle a few hours after consumption. To better understand the risks that may be associated with this behaviour, the present study has examined the effects of a social drinking bout followed by a simulated drive in undergraduate students on the descending limb of their BAC (blood alcohol concentration) curve. Two groups of eight undergraduate students (n = 16) took part in this study. Participants in the alcohol group were assessed before drinking, then at moderate and low BAC as well as 24 hours post-acute consumption. This group consumed an average of 5.3 ± 1.4 (mean ± SD) drinks in an hour in a social context and were then submitted to a driving and a predicted crash risk assessment. The control group was assessed at the same time points without alcohol intake or social context.; at 8 a.m., noon, 3 p.m. and 8 a.m. the next morning. These multiple time points were used to measure any potential learning effects from the assessment tools (i.e. driving simulator and useful field of view test (UFOV)). Diminished driving performance at moderate BAC was observed with no increases in predicted crash risk. Moderate correlations between driving variables were observed. No association exists between driving variables and UFOV variables. The control group improved measures of selective attention after the third assessment. No learning effect was observed from multiple sessions with the driving simulator. Our results show that a moderate BAC, although legal, increases the risky behaviour. Effects of alcohol expectancy could have been displayed by the experimental group. UFOV measures and predicted crash risk categories were not sensitive enough to predict crash risk for young drivers, even when intoxicated.

The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.)

Czech Academy of Sciences Publication Activity Database

Kasprzak, A.; Šafář, Jan; Janda, Jaroslav; Doležel, Jaroslav; Wolko, B.; Naganowska, B.

2006-01-01

Roč. 11, - (2006), s. 396-407 ISSN 1425-8153 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC * genomic DNA library * Lupinus angustifolius L. Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.238, year: 2006

[Use of the recombinant baculovirus BacVP6C for the construction of an internal positive control of rotavirus C].

Science.gov (United States)

Abid-Ayadi, I; Guix, S; Pintó, R M; Bosch, A

2011-06-01

Unlike group A, a few studies have interested other groups of the rotavirus, especially in Tunisia. The role of rotavirus C (RVC) infection is underestimated because of its sporadic nature. The aim of our study was to develop rapid diagnostic procedures of RVC by using an internal positive control of reverse transcription PCR (RT-PCR). The internal positive control (386pb) was designed from the recombinant baculovirus BacVP6C containing the full length cDNA of the Cowden strain gene 5 (1353pb). A fragment of 596pb was amplified by PCR using the BacVP6C DNA ds as template. Then, a central part of 210pb was deleted and the remaining fragment (386pb) was cloned into pGEM-3Zf(+) plasmid between SP6 and T7 RNA polymerase promoters. The obtained recombinant plasmid "pIAM1" was then used for the generation of the internal positive control by in vitro transcription. The sensibility of the RT-PCR was about 3.66×10(5) molecules of RNA/μl. The use of a shorter positive control, as compared to the wild type, allows increased specificity of the RT-PCR reaction, and could be used for efficient diagnostic and surveillance of RVC-caused diseases. Copyright © 2009 Elsevier Masson SAS. All rights reserved.

Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library

Directory of Open Access Journals (Sweden)

Cribiu Edmond-Paul

2000-07-01

Full Text Available Abstract In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57. This study allowed us, (i, to anchor all linkage groups on sheep chromosomes, (ii, to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii, to contradict the previous orientation of the ovine × linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.

Construction of physical maps for the sex-specific regions of papaya sex chromosomes

Directory of Open Access Journals (Sweden)

Na Jong-Kuk

2012-05-01

Full Text Available Abstract Background Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Yh for hermaphrodite. The sex chromosome genotypes are XY (male, XYh (hermaphrodite, and XX (female. The papaya hermaphrodite-specific Yh chromosome region (HSY is pericentromeric and heterochromatic. Physical mapping of HSY and its X counterpart is essential for sequencing these regions and uncovering the early events of sex chromosome evolution and to identify the sex determination genes for crop improvement. Results A reiterate chromosome walking strategy was applied to construct the two physical maps with three bacterial artificial chromosome (BAC libraries. The HSY physical map consists of 68 overlapped BACs on the minimum tiling path, and covers all four HSY-specific Knobs. One gap remained in the region of Knob 1, the only knob structure shared between HSY and X, due to the lack of HSY-specific sequences. This gap was filled on the physical map of the HSY corresponding region in the X chromosome. The X physical map consists of 44 BACs on the minimum tiling path with one gap remaining in the middle, due to the nature of highly repetitive sequences. This gap was filled on the HSY physical map. The borders of the non-recombining HSY were defined genetically by fine mapping using 1460 F2 individuals. The genetically defined HSY spanned approximately 8.5 Mb, whereas its X counterpart extended about 5.4 Mb including a 900 Kb region containing the Knob 1 shared by the HSY and X. The 8.5 Mb HSY corresponds to 4.5 Mb of its X counterpart, showing 4 Mb (89% DNA sequence expansion. Conclusion The 89% increase of DNA sequence in HSY indicates rapid expansion of the Yh chromosome after genetic recombination was suppressed 2–3 million years ago. The

Inducible targeting of CNS astrocytes in Aldh1l1-CreERT2 BAC transgenic mice.

Science.gov (United States)

Winchenbach, Jan; Düking, Tim; Berghoff, Stefan A; Stumpf, Sina K; Hülsmann, Swen; Nave, Klaus-Armin; Saher, Gesine

2016-01-01

Background: Studying astrocytes in higher brain functions has been hampered by the lack of genetic tools for the efficient expression of inducible Cre recombinase throughout the CNS, including the neocortex. Methods: Therefore, we generated BAC transgenic mice, in which CreERT2 is expressed under control of the Aldh1l1 regulatory region. Results: When crossbred to Cre reporter mice, adult Aldh1l1-CreERT2 mice show efficient gene targeting in astrocytes. No such Cre-mediated recombination was detectable in CNS neurons, oligodendrocytes, and microglia. As expected, Aldh1l1-CreERT2 expression was evident in several peripheral organs, including liver and kidney. Conclusions: Taken together, Aldh1l1-CreERT2 mice are a useful tool for studying astrocytes in neurovascular coupling, brain metabolism, synaptic plasticity and other aspects of neuron-glia interactions.

Expression of Human CAR Splicing Variants in BAC-Transgenic Mice

OpenAIRE

Zhang, Yu-Kun Jennifer; Lu, Hong; Klaassen, Curtis D.

2012-01-01

The nuclear receptor constitutive androstane receptor (CAR) is a key regulator for drug metabolism in liver. Human CAR (hCAR) transcripts are subjected to alternative splicing. Some hCAR splicing variants (SVs) have been shown to encode functional proteins by reporter assays. However, in vivo research on the activity of these hCAR SVs has been impeded by the absence of a valid model. This study engineered an hCAR-BAC-transgenic (hCAR-TG) mouse model by integrating the 8.5-kbp hCAR gene as wel...

Graphical interface for the physics-based generation of inputs to 3D MEEC SGEMP and SREMP simulations

International Nuclear Information System (INIS)

Bland, M; Walters, D; Wondra, J

1999-01-01

A graphical user interface (GUI) is under development for the MEEC family of SGEMP and SREMP simulation codes [1,2]. These codes are ''workhorse'' legacy codes that have been in use for nearly two decades, with modifications and enhanced physics models added throughout the years. The MEEC codes are currently being evaluated for use by the DOE in the Dual Revalidation Program and experiments at NIF. The new GUI makes the codes more accessible and less prone to input errors by automatically generating the parameters and grids that previously had to be designed ''by hand''. Physics-based algorithms define the simulation volume with expanding meshes. Users are able to specify objects, materials, and emission surfaces through dialogs and input boxes. 3D and orthographic views are available to view objects in the volume. Zone slice views are available for stepping through the overlay of objects on the mesh in planes aligned with the primary axes

Super fast physical-random number generation using laser diode frequency noises

Science.gov (United States)

Ushiki, Tetsuro; Doi, Kohei; Maehara, Shinya; Sato, Takashi; Ohkawa, Masashi; Ohdaira, Yasuo

2011-02-01

Random numbers can be classified as either pseudo- or physical-random in character. Pseudo-random numbers' periodicity renders them inappropriate for use in cryptographic applications, but naturally-generated physical-random numbers have no calculable periodicity, thereby making them ideally-suited to the task. The laser diode naturally produces a wideband "noise" signal that is believed to have tremendous capacity and great promise, for the rapid generation of physical-random numbers for use in cryptographic applications. We measured a laser diode's output, at a fast photo detector and generated physical-random numbers from frequency noises. We then identified and evaluated the binary-number-line's statistical properties. The result shows that physical-random number generation, at speeds as high as 40Gbps, is obtainable, using the laser diode's frequency noise characteristic.

Generation of quantum logic operations from physical Hamiltonians

International Nuclear Information System (INIS)

Zhang Jun; Whaley, K. Birgitta

2005-01-01

We provide a systematic analysis of the physical generation of single- and two-qubit quantum operations from Hamiltonians available in various quantum systems for scalable quantum information processing. We show that generation of single-qubit operations can be transformed into a steering problem on the Bloch sphere, which represents all R z -equivalence classes of single-qubit operations, whereas the two-qubit problem can be generally transformed into a steering problem in a tetrahedron representing all the local-equivalence classes of two-qubit operations (the Weyl chamber). We use this approach to investigate several physical examples for the generation of two-qubit operations. The steering approach provides useful guidance for the realization of various quantum computation schemes

Development of a Set of Chromosome-Specific Cytogenetic DNA Markers in Sunflower Using BAC-FISH

Science.gov (United States)

In diploid sunflower (2n=34), conventional karyotypes and various genetic linkage maps have been established. However, the relationship between genetic linkage groups and individual chromosomes of sunflower remains unknown. Recently, a set of linkage group-specific BAC and BIBAC clones were identifi...

Uncertainty of Blood Alcohol Concentration (BAC Results as Related to Instrumental Conditions: Optimization and Robustness of BAC Analysis Headspace Parameters

Directory of Open Access Journals (Sweden)

Haleigh A. Boswell

2015-12-01

Full Text Available Analysis of blood alcohol concentration is a routine analysis performed in many forensic laboratories. This analysis commonly utilizes static headspace sampling, followed by gas chromatography combined with flame ionization detection (GC-FID. Studies have shown several “optimal” methods for instrumental operating conditions, which are intended to yield accurate and precise data. Given that different instruments, sampling methods, application specific columns and parameters are often utilized, it is much less common to find information on the robustness of these reported conditions. A major problem can arise when these “optimal” conditions may not also be robust, thus producing data with higher than desired uncertainty or potentially inaccurate results. The goal of this research was to incorporate the principles of quality by design (QBD in the adjustment and determination of BAC (blood alcohol concentration instrumental headspace parameters, thereby ensuring that minor instrumental variations, which occur as a matter of normal work, do not appreciably affect the final results of this analysis. This study discusses both the QBD principles as well as the results of the experiments, which allow for determination of more favorable instrumental headspace conditions. Additionally, method detection limits will also be reported in order to determine a reporting threshold and the degree of uncertainty at the common threshold value of 0.08 g/dL. Furthermore, the comparison of two internal standards, n-propanol and t-butanol, will be investigated. The study showed that an altered parameter of 85 °C headspace oven temperature and 15 psi headspace vial pressurization produces the lowest percent relative standard deviation of 1.3% when t-butanol is implemented as an internal standard, at least for one very common platform. The study also showed that an altered parameter of 100 °C headspace oven temperature and 15-psi headspace vial pressurization

Expression Analysis of CB2-GFP BAC Transgenic Mice.

Science.gov (United States)

Schmöle, Anne-Caroline; Lundt, Ramona; Gennequin, Benjamin; Schrage, Hanna; Beins, Eva; Krämer, Alexandra; Zimmer, Till; Limmer, Andreas; Zimmer, Andreas; Otte, David-Marian

2015-01-01

The endocannabinoid system (ECS) is a retrograde messenger system, consisting of lipid signaling molecules that bind to at least two G-protein-coupled receptors, Cannabinoid receptor 1 and 2 (CB1 and 2). As CB2 is primarily expressed on immune cells such as B cells, T cells, macrophages, dendritic cells, and microglia, it is of great interest how CB2 contributes to immune cell development and function in health and disease. Here, understanding the mechanisms of CB2 involvement in immune-cell function as well as the trafficking and regulation of CB2 expressing cells are crucial issues. Up to now, CB2 antibodies produce unclear results, especially those targeting the murine protein. Therefore, we have generated BAC transgenic GFP reporter mice (CB2-GFPTg) to trace CB2 expression in vitro and in situ. Those mice express GFP under the CB2 promoter and display GFP expression paralleling CB2 expression on the transcript level in spleen, thymus and brain tissue. Furthermore, by using fluorescence techniques we show that the major sources for GFP-CB2 expression are B cells in spleen and blood and microglia in the brain. This novel CB2-GFP transgenic reporter mouse line represents a powerful resource to study CB2 expression in different cell types. Furthermore, it could be used for analyzing CB2-mediated mobilization and trafficking of immune cells as well as studying the fate of recruited immune cells in models of acute and chronic inflammation.

A web delivered intervention for depression combining Behavioural Activation with physical activity promotion: study protocol for a pilot randomised controlled trial

Directory of Open Access Journals (Sweden)

Jeffrey David Lambert

2015-10-01

Full Text Available Background: Physical activity (PA yields moderate effect sizes for treating depression (Cooney et al., 2013. PA may also help reduce depressive relapse, providing additional psychological benefits such as positive self-regard and a sense of competence (Babyak et al., 2000. Behavioural Activation (BA is an evidence-based psychological therapy for depression, which aims to get people more engaged with activities that provide positive reinforcement for non-depressed behaviours (Hopko, Lejuez, LePage, Hopko, & McNeil, 2003. The structured nature of BA is consistent with the use of good behaviour change techniques (specific goal-setting, self-regulation offering a potential platform for promoting PA alongside depression treatment. BA may also be useful for gradually increasing PA in people who are more sedentary than the general population. Aims: This pilot randomised controlled trial aims to assess the feasibility, acceptability, and fidelity of a web-delivered intervention combining BA and PA (eBAcPAc to enhance mental and physical health, and assess the trial methods. Method: A community sample of 120 people exhibiting symptoms of depression and who are participating in less than 150 minutes of moderate to vigorous physical activity per week will be randomized to receive eBAcPAc or be put on a wait list control group. eBAcPAc is informed by previous work (Farrand et al., 2014; Pentecost et al., 2015 and further developed using the Centre for eHealth Research and Disease management Roadmap (CeHReS (van Gemert-Pijnen et al., 2011 in order to be applied in an web-based setting. A platform hosted by the University of Glasgow which has been used to deliver a wide range of successful web-delivered interventions for mental health, will be used to deliver eBAcPAc. Feasibility measures will include data on recruitment, attrition and acceptability. Pre-post outcome measures will include the PHQ-9, and self-reported and accelerometer measured PA. Process and

Sequencing of 15622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Czech Academy of Sciences Publication Activity Database

Munoz-Amatriain, M.; Lonardi, S.; Luo, M.C.; Madishetty, K.; Svensson, J.T.; Moscou, M. J.; Wanamaker, S.; Kudrna, D.; Zheng, J.; Šimková, Hana; Doležel, Jaroslav; Grimwood, J.; Mammadov, J.; Close, T.J.

2015-01-01

Roč. 84, č. 1 (2015), s. 216-227 ISSN 0960-7412 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Barley * Hordeum vulgare L * BAC sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.468, year: 2015

[Interest of a new instrument to assess cognition in schizophrenia: The Brief Assessment of Cognition in Schizophrenia (BACS)].

Science.gov (United States)

Bralet, M C; Navarre, M; Eskenazi, A M; Lucas-Ross, M; Falissard, B

2008-12-01

SCHIZOPHRENIA: It is therefore of great interest to create an available and easily used battery of validated tests. This would enable one to measure the different cognitive deficits and to repeat the tests, and assess evolution through longitudinal follow up of the patients. The BACS is a new instrument developed by Keefe et al. in the Department of Psychiatry and Behavioural Sciences at the University of Duke Medical Centre. It evaluates the cognitive dimensions specifically altered in schizophrenia and correlated with the evolution of the disease. This test is simple to use, requiring only paper, pencils and a stopwatch. It can be administered by different carers. The duration of the test session is approximately 35min. This battery of tests was validated on a sample of 150 patients compared with a sample of 50 controls, matched for age, parent education and ethnic groups. This aim of this study is to create a French adaptation of the BACS (translation and back translation approved by the Department of Psychiatry and Behavioural Sciences at the University of Duke Medical Centre) and then to test its easiness of administration and its sensitivity, performing correlation analysis between the French Version of the BACS (version A) and a standard battery. Its adaptation and validation in French would at first be useful for the French-speaking areas and then would add some new data for the pertinence of using the BACS. 35 French stabilized schizophrenic patients were recruited from the inpatient and outpatient facilities at the Clermont-de-L'Oise Mental Health Hospital (Picardie area, France) in Dr Boitard's Psychiatric Department (FJ 5.) Patients were required to meet DSM-IV criteria for schizophrenia or schizoaffective illness. The patients were tested on two separate days by two independent clinicians with less than two weeks between the two assessments. During the first test session, subjects received the French A version of the BACS and during the second session, they were

Feasibility of a novel positive feedback effect of 131I-promoted Bac-Egr1-hNIS expression in malignant glioma via baculovirus

International Nuclear Information System (INIS)

Guo Rui; Tian Lipeng; Han Bing; Xu Haoping; Zhang Miao; Li Biao

2011-01-01

Purpose: As intracellular iodine is released rapidly, increased expression of sodium/iodide symporter (NIS) is required for effective radioiodine treatment of tumor. As Egr1 promoter is activated by 131 I and may promote human NIS (hNIS) expression, hNIS also induces 131 I uptake and activates Egr1, so the existence of a positive feedback effect of 131 I-promoted Egr1-hNIS expression is possible. Our purpose was to investigate the possible existence of this positive feedback effect through a series of in vitro pioneer studies. Method: Recombinant baculovirus (Bac-Egr1-hNIS) encoding the hNIS gene under the control of a radiation-inducible Egrl promoter was constructed. To test 131 I-promoted hNIS expression, human malignant glioma U87 cells were transfected with Bac-Egr1-hNIS, stimulated with or without 131 I; the expression of hNIS protein was detected by immunofluorescence and flow cytometry test. In addition, the uptake and efflux of 131 I were determined after the incubation of Bac-Egr1-hNIS-transfected U87 cells with or without 131 I. Results: Immunocytochemical staining and flow cytometry test showed a higher hNIS protein expression in Bac-Egr1-hNIS-transfected U87 cells with 131 I stimulation than in cells without stimulation. Bac-Egr1-hNIS-transfected U87 cells accumulated up to about 4.05 times of 131 I after 131 I stimulation. The amount of 131 I uptake in both groups showed a baculovirus dose-dependent manner. However, rapid efflux of radioactivity was observed in both groups, with 50% lost during the first 2 min after the 131 I-containing medium had been replaced by a nonradioactive medium. Conclusion: Our results indicated that an improved transgene expression of 131 I-stimulated hNIS in U87 cells using a baculovirus vector containing the Egr1 promoter is possible, and the increased expression of hNIS is responsible for a higher 131 I uptake. It might provide a reference for the existence of a positive feedback effect in 131 I-promoted Bac-Egr1-h

BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

International Nuclear Information System (INIS)

Samuelson, Emma; Karlsson, Sara; Partheen, Karolina; Nilsson, Staffan; Szpirer, Claude; Behboudi, Afrouz

2012-01-01

Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform. Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic

Cross-species BAC-FISH painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements

NARCIS (Netherlands)

Tang, X.; Szinay, D.; Ramanna, M.S.; Vossen, van der E.A.G.; Datema, E.; Klein Lankhorst, R.M.; Boer, de J.M.; Peters, S.A.; Bachem, C.W.B.; Stiekema, W.J.; Visser, R.G.F.; Jong, de J.H.; Bai, Y.

2008-01-01

Ongoing genomics projects of tomato (Solanum lycopersicum ) and potato (Solanum tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, BACs can be positioned on pachytene comple-ments by fluorescent in situ hybridization (FISH) on homoeologous

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

Science.gov (United States)

Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2016-07-01

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Generation and Active Absorption of 2- and 3-Dimensional Linear Water Waves in Physical Models

DEFF Research Database (Denmark)

Christensen, Morten

in the wave channel in front of the wave generator. The results of physical model tests performed with an absorbing wave maker based on this principle show that the problem of rereflection is reduced significantly when active absorption is performed. Finally, an absorbing directional wave generator for 3-D...... generator is capable of of reducing the problem of rereflection in multidirectional, irregular wave fields significantly....

Sequence finishing and mapping of Drosophila melanogasterheterochromatin

Energy Technology Data Exchange (ETDEWEB)

Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

2007-06-15

Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

Physics-based deformable organisms for medical image analysis

Science.gov (United States)

Hamarneh, Ghassan; McIntosh, Chris

2005-04-01

Previously, "Deformable organisms" were introduced as a novel paradigm for medical image analysis that uses artificial life modelling concepts. Deformable organisms were designed to complement the classical bottom-up deformable models methodologies (geometrical and physical layers), with top-down intelligent deformation control mechanisms (behavioral and cognitive layers). However, a true physical layer was absent and in order to complete medical image segmentation tasks, deformable organisms relied on pure geometry-based shape deformations guided by sensory data, prior structural knowledge, and expert-generated schedules of behaviors. In this paper we introduce the use of physics-based shape deformations within the deformable organisms framework yielding additional robustness by allowing intuitive real-time user guidance and interaction when necessary. We present the results of applying our physics-based deformable organisms, with an underlying dynamic spring-mass mesh model, to segmenting and labelling the corpus callosum in 2D midsagittal magnetic resonance images.

Waypoint Generation Based on Sensor Aimpoint

Science.gov (United States)

2009-03-01

United States Government . AFIT/GAE/ENV/09-M01 WAYPOINT GENERATION BASED ON SENSOR AIMPOINT THESIS Presented to the Faculty Department of Aeronautical...BATCAM. Aviones physics parameters for the Procerus testbed, the Unicorn UAV, were provided by Procerus, which allowed another simulated MAV to 48 be...flown in the HIL tests. The AFIT Advanced Navigation Technologies (ANT) Center did not own a Unicorn UAV, so it could not be flown in flight tests

The sensitivity of direct identification from positive BacT/ALERT™ (bioMérieux) blood culture bottles by matrix-assisted laser desorption ionization time-of-flight mass spectrometry is low.

Science.gov (United States)

Szabados, F; Michels, M; Kaase, M; Gatermann, S

2011-02-01

Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been presented as a novel method for the direct identification of bacteria from positive blood culture bottles. The rate of the MALDI TOF MS-based identification in the present study from positive BacT/ALERT (bioMérieux, Marcy l'Etoile, France) blood culture bottles was 30%, which is far below the previously reported sensitivities using the BACTEC (Becton Dickinson, Franklin Lakes, NJ, USA) system. We also found evidence that the Biotyper algorithm did not identify a second pathogen in cases of positive BacT/ALERT blood culture bottles containing two different species. © 2010 The Authors. Journal Compilation © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Expression Analysis of CB2-GFP BAC Transgenic Mice.

Directory of Open Access Journals (Sweden)

Anne-Caroline Schmöle

Full Text Available The endocannabinoid system (ECS is a retrograde messenger system, consisting of lipid signaling molecules that bind to at least two G-protein-coupled receptors, Cannabinoid receptor 1 and 2 (CB1 and 2. As CB2 is primarily expressed on immune cells such as B cells, T cells, macrophages, dendritic cells, and microglia, it is of great interest how CB2 contributes to immune cell development and function in health and disease. Here, understanding the mechanisms of CB2 involvement in immune-cell function as well as the trafficking and regulation of CB2 expressing cells are crucial issues. Up to now, CB2 antibodies produce unclear results, especially those targeting the murine protein. Therefore, we have generated BAC transgenic GFP reporter mice (CB2-GFPTg to trace CB2 expression in vitro and in situ. Those mice express GFP under the CB2 promoter and display GFP expression paralleling CB2 expression on the transcript level in spleen, thymus and brain tissue. Furthermore, by using fluorescence techniques we show that the major sources for GFP-CB2 expression are B cells in spleen and blood and microglia in the brain. This novel CB2-GFP transgenic reporter mouse line represents a powerful resource to study CB2 expression in different cell types. Furthermore, it could be used for analyzing CB2-mediated mobilization and trafficking of immune cells as well as studying the fate of recruited immune cells in models of acute and chronic inflammation.

A new normalizing algorithm for BAC CGH arrays with quality control metrics.

Science.gov (United States)

Miecznikowski, Jeffrey C; Gaile, Daniel P; Liu, Song; Shepherd, Lori; Nowak, Norma

2011-01-01

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose "SmoothArray", a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package "aCGHplus," this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

Directory of Open Access Journals (Sweden)

Jeffrey C. Miecznikowski

2011-01-01

Full Text Available The main focus in pin-tip (or print-tip microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose “SmoothArray”, a new method to preprocess comparative genomic hybridization (CGH bacterial artificial chromosome (BAC arrays and we show the effects on a cancer dataset. As part of our R software package “aCGHplus,” this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

A PiggyBac mediated approach for lactoferricin gene transfer in bovine mammary epithelial stem cells for management of bovine mastitis.

Science.gov (United States)

Sharma, Neelesh; Huynh, Do Luong; Kim, Sung Woo; Ghosh, Mrinmoy; Sodhi, Simrinder Singh; Singh, Amit Kumar; Kim, Nam Eun; Lee, Sung Jin; Hussain, Kafil; Oh, Sung Jong; Jeong, Dong Kee

2017-11-28

The antibacterial and anti-inflammatory properties of lactoferricin have been ascribed to its ability to sequester essential iron. The objective of the study was to clone bovine lactoferricin ( LFcinB ) gene into PiggyBac Transposon vector, expression study in the bovine mammary epithelial stem cells (bMESCs) and also to determine the antimicrobial property of recombinant LFcinB against bovine mastitis-causing organisms. The PiggyBac-LFcinB was transfected into bMESCs by electroporation and a three fold of LFcinB secretion was observed in the transfected bMESCs medium by ELISA assay. Furthermore, the assessment of antimicrobial activity against mastitis causing pathogens Staphylococcus aureus and Escherichia coli demonstrated convincing evidence to prove strong antibacterial activity of LFcinB with 14.0±1.0 mm and 18.0±1.5 mm zone of inhibition against both organisms, respectively. The present study provides the convincing evidence to suggest the potential of PiggyBac transposon system to transfer antibacterial peptide into bMESCs or cow mammary gland and also pave the way to use bovine mammary gland as the bioreactors. Simultaneously, it also suggest toward commercial utilization of LFcinB bioreactor system in pharmaceutical industry.

A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method.

Science.gov (United States)

Cao, Yiping; Sivaganesan, Mano; Kelty, Catherine A; Wang, Dan; Boehm, Alexandria B; Griffith, John F; Weisberg, Stephen B; Shanks, Orin C

2018-01-01

Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and management. However, there are currently no standardized approaches for field implementation and interpretation of qPCR data. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and a novel Bayesian weighted average approach to establish a human fecal contamination score (HFS) that can be used to prioritize sampling sites for remediation based on measured human waste levels. The HFS was then used to investigate 975 study design scenarios utilizing different combinations of sites with varying sampling intensities (daily to once per week) and number of qPCR replicates per sample (2-14 replicates). Findings demonstrate that site prioritization with HFS is feasible and that both sampling intensity and number of qPCR replicates influence reliability of HFS estimates. The novel data analysis strategy presented here provides a prescribed approach for the implementation and interpretation of human-associated HF183/BacR287 qPCR data with the goal of site prioritization based on human fecal pollution levels. In addition, information is provided for future users to customize study designs for optimal HFS performance. Published by Elsevier Ltd.

Contributions of Bacău to the economic literature and culture – The life and work of Professor Vasile Pătruţ

OpenAIRE

Mihai Deju

2012-01-01

The economic culture and accounting theory in Bacău area has its beginnings in the setting up of the first practical school of agriculture, by Ion Ionescu de la Brad, who included in the curriculum an accounting course, as well. Over the years, the economic education of Bacău area education has evolved from “The School of Accounting and Co-operative Education” (1919) to the modern economic higher education, in our days. During an important period of the evolution of education and culture in B...

Modern particle physics event generation with WHIZARD

International Nuclear Information System (INIS)

Reuter, J.; Bach, F.; Chokoufe, B.; Kilian, W.; Sekulla, M.; Ohl, T.; Weiss, C.; Siegen Univ.

2014-01-01

We describe the multi-purpose Monte-Carlo event generator WHIZARD for the simulation of high-energy particle physics experiments. Besides the presentation of the general features of the program like SM physics, BSM physics, and QCD effects, special emphasis is given to the support of the most accurate simulation of the collider environments at hadron colliders and especially at future linear lepton colliders. On the more technical side, the very recent code refactoring towards a completely object-oriented software package to improve maintainability, flexibility and code development are discussed. Finally, we present ongoing work and future plans regarding higher-order corrections, more general model support including the setup to search for new physics in vector boson scattering at the LHC, as well as several lines of performance improvements.

Modern Particle Physics Event Generation with WHIZARD

Science.gov (United States)

Reuter, J.; Bach, F.; Chokoufé, B.; Kilian, W.; Ohl, T.; Sekulla, M.; Weiss, C.

2015-05-01

We describe the multi-purpose Monte-Carlo event generator WHIZARD for the simulation of high-energy particle physics experiments. Besides the presentation of the general features of the program like SM physics, BSM physics, and QCD effects, special emphasis will be given to the support of the most accurate simulation of the collider environments at hadron colliders and especially at future linear lepton colliders. On the more technical side, the very recent code refactoring towards a completely object-oriented software package to improve maintainability, flexibility and code development will be discussed. Finally, we present ongoing work and future plans regarding higher-order corrections, more general model support including the setup to search for new physics in vector boson scattering at the LHC, as well as several lines of performance improvements.

Modern Particle Physics Event Generation with WHIZARD

International Nuclear Information System (INIS)

Reuter, J; Bach, F; Chokoufé, B; Weiss, C; Kilian, W; Sekulla, M; Ohl, T

2015-01-01

We describe the multi-purpose Monte-Carlo event generator WHIZARD for the simulation of high-energy particle physics experiments. Besides the presentation of the general features of the program like SM physics, BSM physics, and QCD effects, special emphasis will be given to the support of the most accurate simulation of the collider environments at hadron colliders and especially at future linear lepton colliders. On the more technical side, the very recent code refactoring towards a completely object-oriented software package to improve maintainability, flexibility and code development will be discussed. Finally, we present ongoing work and future plans regarding higher-order corrections, more general model support including the setup to search for new physics in vector boson scattering at the LHC, as well as several lines of performance improvements. (paper)

Functional characterization of Kaposi's sarcoma-associated herpesvirus small capsid protein by bacterial artificial chromosome-based mutagenesis

International Nuclear Information System (INIS)

Sathish, Narayanan; Yuan Yan

2010-01-01

A systematic investigation of interactions amongst KSHV capsid proteins was undertaken in this study to comprehend lesser known KSHV capsid assembly mechanisms. Interestingly the interaction patterns of the KSHV small capsid protein, ORF65 suggested its plausible role in viral capsid assembly pathways. Towards further understanding this, ORF65-null recombinant mutants (BAC-Δ65 and BAC-stop65) employing a bacterial artificial chromosome (BAC) system were generated. No significant difference was found in both overall viral gene expression and lytic DNA replication between stable monolayers of 293T-BAC36 (wild-type) and 293T-BAC-ORF65-null upon induction with 12-O-tetradecanoylphorbol-13-acetate, though the latter released 30-fold fewer virions to the medium than 293T-BAC36 cells. Sedimentation profiles of capsid proteins of ORF65-null recombinant mutants were non-reflective of their organization into the KSHV capsids and were also undetectable in cytoplasmic extracts compared to noticeable levels in nuclear extracts. These observations collectively suggested the pivotal role of ORF65 in the KSHV capsid assembly processes.

Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs

Science.gov (United States)

M.N. lslam-Faridi; C.D. Nelson; S.P. DiFazio; L.E. Gunter; G.A. Tuskan

2009-01-01

The 185-285 rDNA and 55 rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 185-285 rDNA sites and one 55 rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis-type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones...

Dynamic Frames Based Generation of 3D Scenes and Applications

Directory of Open Access Journals (Sweden)

Danijel Radošević

2015-05-01

Full Text Available Modern graphic/programming tools like Unity enables the possibility of creating 3D scenes as well as making 3D scene based program applications, including full physical model, motion, sounds, lightning effects etc. This paper deals with the usage of dynamic frames based generator in the automatic generation of 3D scene and related source code. The suggested model enables the possibility to specify features of the 3D scene in a form of textual specification, as well as exporting such features from a 3D tool. This approach enables higher level of code generation flexibility and the reusability of the main code and scene artifacts in a form of textual templates. An example of the generated application is presented and discussed.

Advanced Machine Learning for Classification, Regression, and Generation in Jet Physics

CERN Multimedia

CERN. Geneva

2017-01-01

There is a deep connection between machine learning and jet physics - after all, jets are defined by unsupervised learning algorithms. Jet physics has been a driving force for studying modern machine learning in high energy physics. Domain specific challenges require new techniques to make full use of the algorithms. A key focus is on understanding how and what the algorithms learn. Modern machine learning techniques for jet physics are demonstrated for classification, regression, and generation. In addition to providing powerful baseline performance, we show how to train complex models directly on data and to generate sparse stacked images with non-uniform granularity.

Performance of two resin-containing blood culture media in detection of bloodstream infections and in direct matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) broth assays for isolate identification: clinical comparison of the BacT/Alert Plus and Bactec Plus systems.

Science.gov (United States)

Fiori, Barbara; D'Inzeo, Tiziana; Di Florio, Viviana; De Maio, Flavio; De Angelis, Giulia; Giaquinto, Alessia; Campana, Lara; Tanzarella, Eloisa; Tumbarello, Mario; Antonelli, Massimo; Sanguinetti, Maurizio; Spanu, Teresa

2014-10-01

We compared the clinical performances of the BacT/Alert Plus (bioMérieux) and Bactec Plus (Becton Dickinson) aerobic and anaerobic blood culture (BC) media with adsorbent polymeric beads. Patients ≥ 16 years old with suspected bloodstream infections (BSIs) were enrolled in intensive care units and infectious disease wards. A single 40-ml blood sample was collected from each and used to inoculate (10 ml/bottle) one set of BacT/Alert Plus cultures and one set of Bactec Plus cultures, each set consisting of one aerobic and one anaerobic bottle. Cultures were incubated ≤ 5 days in the BacT/Alert 3D and Bactec FX instruments, respectively. A total of 128 unique BSI episodes were identified based on the recovery of clinically significant growth in 212 aerobic cultures (106 BacT/Alert and 106 Bactec) and 151 anaerobic cultures (82 BacT/Alert and 69 Bactec). The BacT/Alert aerobic medium had higher recovery rates for Gram-positive cocci (P = 0.024), whereas the Bactec aerobic medium was superior for recovery of Gram-negative bacilli (P = 0.006). BacT/Alert anaerobic medium recovery rates exceeded those of the Bactec anaerobic medium for total organisms (P = 0.003), Gram-positive cocci (P = 0.013), and Escherichia coli (P = 0.030). In terms of capacity for diagnosing the 128 septic episodes, the BacT/Alert and Bactec sets were comparable, although the former sets diagnosed more BSIs caused by Gram-positive cocci (P = 0.008). They also allowed earlier identification of coagulase-negative staphylococcal growth (mean, 2.8 h; P = 0.003) and growth in samples from patients not on antimicrobial therapy that yielded positive results (mean, 1.3 h; P direct matrix-assisted laser desorption ionization-time of flight mass spectrometry assay of BC broths. The BacT/Alert Plus media line appears to be a reliable, timesaving tool for routine detection of BSIs in the population we studied, although further studies are needed to evaluate their performance in other settings. Copyright �

Development of Health Education Learning Module in Bac.TSE-LDPE Programme in TTI: Needs Analysis Study

Science.gov (United States)

Ujang, Alijah; Alias, Norlidah; Siraj, Saedah

2015-01-01

This study is to explore the need to develop learning modules of health education for trainee teachers in the Bachelor Of Teaching (Hons)(Special Education-Learning Disabilities For Primary Education) Programme (Bac.TSE-LDPE) in the Teacher Training Institute (TTI). The questionnaire uses the Likert scale with the close ended questions analysed by…

Event generator for RHIC spin physics. Proceedings of RIKEN BNL Research Center workshop: Volume 11

International Nuclear Information System (INIS)

1998-01-01

A major objective of the workshop was to establish a firm collaboration to develop suitable event generators for the spin physics program at RHIC. With the completion of the Relativistic Heavy Ion Collider (RHIC) as a polarized collider a completely new domain of high-energy spin physics will be opened. The planned studies address the spin structure of the nucleon, tests of the standard model, and transverse spin effects in initial and final states. RHIC offers the unique opportunity to pursue these studies because of its high and variable energy, 50 ≤ √s ≤ 500 GeV, high polarization, 70%, and high luminosity, 2 x 10 32 cm -2 sec -1 or more at 500 GeV. To maximize the output from the spin program at RHIC, the understanding of both experimental and theoretical systematic errors is crucial. It will require full-fledged event generators, to simulate the processes of interest in great detail. The history of event generators shows that their development and improvement are ongoing processes taking place in parallel to the physics analysis by various experimental groups. The number of processes included in the generators has been increasing and the precision of their predictions is being improved continuously. This workshop aims at getting this process well under way for the spin physics program at RHIC, based on the first development in this direction, SPHINX

The 5th Generation model of Particle Physics

Science.gov (United States)

Lach, Theodore

2009-05-01

The Standard model of Particle Physics is able to account for all known HEP phenomenon, yet it is not able to predict the masses of the quarks or leptons nor can it explain why they have their respective values. The Checker Board Model (CBM) predicts that there are 5 generation of quarks and leptons and shows a pattern to those masses, namely each three quarks or leptons (within adjacent generations or within a generation) are related to each other by a geometric mean relationship. A 2D structure of the nucleus can be imaged as 2D plate spinning on its axis, it would for all practical circumstances appear to be a 3D object. The masses of the hypothesized ``up'' and ``dn'' quarks determined by the CBM are 237.31 MeV and 42.392 MeV respectively. These new quarks in addition to a lepton of 7.4 MeV make up one of the missing generations. The details of this new particle physics model can be found at the web site: checkerboard.dnsalias.net. The only areas were this theory conflicts with existing dogma is in the value of the mass of the Top quark. The particle found at Fermi Lab must be some sort of composite particle containing Top quarks.

Cattle mammary bioreactor generated by a novel procedure of transgenic cloning for large-scale production of functional human lactoferrin.

Directory of Open Access Journals (Sweden)

Penghua Yang

Full Text Available Large-scale production of biopharmaceuticals by current bioreactor techniques is limited by low transgenic efficiency and low expression of foreign proteins. In general, a bacterial artificial chromosome (BAC harboring most regulatory elements is capable of overcoming the limitations, but transferring BAC into donor cells is difficult. We describe here the use of cattle mammary bioreactor to produce functional recombinant human lactoferrin (rhLF by a novel procedure of transgenic cloning, which employs microinjection to generate transgenic somatic cells as donor cells. Bovine fibroblast cells were co-microinjected for the first time with a 150-kb BAC carrying the human lactoferrin gene and a marker gene. The resulting transfection efficiency of up to 15.79 x 10(-2 percent was notably higher than that of electroporation and lipofection. Following somatic cell nuclear transfer, we obtained two transgenic cows that secreted rhLF at high levels, 2.5 g/l and 3.4 g/l, respectively. The rhLF had a similar pattern of glycosylation and proteolytic susceptibility as the natural human counterpart. Biochemical analysis revealed that the iron-binding and releasing properties of rhLF were identical to that of native hLF. Importantly, an antibacterial experiment further demonstrated that rhLF was functional. Our results indicate that co-microinjection with a BAC and a marker gene into donor cells for somatic cell cloning indeed improves transgenic efficiency. Moreover, the cattle mammary bioreactors generated with this novel procedure produce functional rhLF on an industrial scale.

Creation of a BAC resource to study the structure and evolution of the banana (Musa balbisiana) genome

Czech Academy of Sciences Publication Activity Database

Šafář, Jan; Noa-Carrazana, J. C.; Vrána, Jan; Bartoš, Jan; Alkhimova, Olena; Lheureux, F.; Šimková, Hana; Caruana, M. L.; Doležel, Jaroslav; Piffanelli, P.

2004-01-01

Roč. 47, - (2004), 1182ů1191 E-ISSN 1480-3321 R&D Projects: GA AV ČR IAA6038201 Grant - others:research contract IAEA(FR) 12230/RBF Institutional research plan: CEZ:AV0Z5038910 Keywords : bacterial artificial chromosome library * banana * BAC-FISH Subject RIV: EB - Genetics ; Molecular Biology

Time-to-detection of bacteria and yeast with the BACTEC FX versus BacT/Alert Virtuo blood culture systems.

Science.gov (United States)

Somily, Ali Mohammed; Habib, Hanan Ahmed; Torchyan, Armen Albert; Sayyed, Samina B; Absar, Muhammed; Al-Aqeel, Rima; Binkhamis, A Khalifa

2018-01-01

Bloodstream infections are associated with high rates of morbidity and mortality. Rapid detection of bloodstream infections is important in achieving better patient outcomes. Compare the time-to-detection (TTD) of the new BacT/Alert Virtuo and the BACTEC FX automated blood culture systems. Prospective simulated comparison of two instruments using seeded samples. Medical microbiology laboratory. Blood culture bottles were seeded in triplicate with each of the standard ATCC strains of aerobes, anaerobes and yeast. TTD was calculated as the length of time from the beginning of culture incubation to the detection of bacterial growth. TTD for the various tested organisms on the two microbial detection systems. The 99 bottles of seeded blood cultures incubated in each of the blood culture systems included 21 anaerobic, 39 aerobic and 39 pediatric bottles. The BacT/Alert Virtuo system exhibited significantly shorter TTD for 72.7 % of the tested organisms compared to BACTEC FX system with a median difference in mean TTD of 2.1 hours (interquartile range: 1.5-3.5 hours). The BACTEC FX system was faster in 15.2% (5/33) of microorganisms, with a median difference in mean TTD of 25.9 hours (IQR: 9.1-29.2 hours). TTD was significantly shorter for most of the microorganisms tested on the new BacT/Alert Virtuo system compared to the BACTEC FX system. Use of simulated cultures to assess TTD may not precisely represent clinical blood cultures. None.

Parallel octree-based hexahedral mesh generation for eulerian to lagrangian conversion.

Energy Technology Data Exchange (ETDEWEB)

Staten, Matthew L.; Owen, Steven James

2010-09-01

Computational simulation must often be performed on domains where materials are represented as scalar quantities or volume fractions at cell centers of an octree-based grid. Common examples include bio-medical, geotechnical or shock physics calculations where interface boundaries are represented only as discrete statistical approximations. In this work, we introduce new methods for generating Lagrangian computational meshes from Eulerian-based data. We focus specifically on shock physics problems that are relevant to ASC codes such as CTH and Alegra. New procedures for generating all-hexahedral finite element meshes from volume fraction data are introduced. A new primal-contouring approach is introduced for defining a geometric domain. New methods for refinement, node smoothing, resolving non-manifold conditions and defining geometry are also introduced as well as an extension of the algorithm to handle tetrahedral meshes. We also describe new scalable MPI-based implementations of these procedures. We describe a new software module, Sculptor, which has been developed for use as an embedded component of CTH. We also describe its interface and its use within the mesh generation code, CUBIT. Several examples are shown to illustrate the capabilities of Sculptor.

WE-G-207-06: 3D Fluoroscopic Image Generation From Patient-Specific 4DCBCT-Based Motion Models Derived From Physical Phantom and Clinical Patient Images

International Nuclear Information System (INIS)

Dhou, S; Cai, W; Hurwitz, M; Rottmann, J; Myronakis, M; Cifter, F; Berbeco, R; Lewis, J; Williams, C; Mishra, P; Ionascu, D

2015-01-01

Purpose: Respiratory-correlated cone-beam CT (4DCBCT) images acquired immediately prior to treatment have the potential to represent patient motion patterns and anatomy during treatment, including both intra- and inter-fractional changes. We develop a method to generate patient-specific motion models based on 4DCBCT images acquired with existing clinical equipment and used to generate time varying volumetric images (3D fluoroscopic images) representing motion during treatment delivery. Methods: Motion models are derived by deformably registering each 4DCBCT phase to a reference phase, and performing principal component analysis (PCA) on the resulting displacement vector fields. 3D fluoroscopic images are estimated by optimizing the resulting PCA coefficients iteratively through comparison of the cone-beam projections simulating kV treatment imaging and digitally reconstructed radiographs generated from the motion model. Patient and physical phantom datasets are used to evaluate the method in terms of tumor localization error compared to manually defined ground truth positions. Results: 4DCBCT-based motion models were derived and used to generate 3D fluoroscopic images at treatment time. For the patient datasets, the average tumor localization error and the 95th percentile were 1.57 and 3.13 respectively in subsets of four patient datasets. For the physical phantom datasets, the average tumor localization error and the 95th percentile were 1.14 and 2.78 respectively in two datasets. 4DCBCT motion models are shown to perform well in the context of generating 3D fluoroscopic images due to their ability to reproduce anatomical changes at treatment time. Conclusion: This study showed the feasibility of deriving 4DCBCT-based motion models and using them to generate 3D fluoroscopic images at treatment time in real clinical settings. 4DCBCT-based motion models were found to account for the 3D non-rigid motion of the patient anatomy during treatment and have the potential

Genome Sequencing

DEFF Research Database (Denmark)

Sato, Shusei; Andersen, Stig Uggerhøj

2014-01-01

The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

Random number generators in support of Monte Carlo problems in physics

International Nuclear Information System (INIS)

Dyadkin, I.G.

1993-01-01

The ability to support a modern users' expectations of random number generators to solve problems in physics is analyzed. The capabilities of the newest concepts and the old pseudo-random algorithms are compared. The author is in favor of multiplicative generators. Due to the 64-bit arithmetic of a modern PC, multiplicative generators have a sufficient number of periods (up to 2 62 ) and are quicker to generate and to govern independent sequences for parallel processing. In addition they are able to replicate sub-sequences (without storing their seeds) for each standard trial in any code and to simulate spatial and planar directions and EXP(-x) distributions often needed as ''bricks'' for simulating events in physics. Hundreds of multipliers for multiplicative generators have been tabulated and tested, and the required speeds have been obtained. (author)

The comparative effectiveness of a team-based versus group-based physical activity intervention for cancer survivors.

Science.gov (United States)

Carter, Cindy L; Onicescu, Georgiana; Cartmell, Kathleen B; Sterba, Katherine R; Tomsic, James; Alberg, Anthony J

2012-08-01

Physical activity benefits cancer survivors, but the comparative effectiveness of a team-based delivery approach remains unexplored. The hypothesis tested was that a team-based physical activity intervention delivery approach has added physical and psychological benefits compared to a group-based approach. A team-based sport accessible to survivors is dragon boating, which requires no previous experience and allows for diverse skill levels. In a non-randomized trial, cancer survivors chose between two similarly structured 8-week programs, a dragon boat paddling team (n = 68) or group-based walking program (n = 52). Three separate intervention rounds were carried out in 2007-2008. Pre-post testing measured physical and psychosocial outcomes. Compared to walkers, paddlers had significantly greater (all p team cohesion, program adherence/attendance, and increased upper-body strength. For quality-of-life outcomes, both interventions were associated with pre-post improvements, but with no clear-cut pattern of between-intervention differences. These hypothesis-generating findings suggest that a short-term, team-based physical activity program (dragon boat paddling) was associated with increased cohesion and adherence/attendance. Improvements in physical fitness and psychosocial benefits were comparable to a traditional, group-based walking program. Compared to a group-based intervention delivery format, the team-based intervention delivery format holds promise for promoting physical activity program adherence/attendance in cancer survivors.

A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

DEFF Research Database (Denmark)

Benkel, Bernhard F.; Smith, Amanda; Christensen, Knud

2012-01-01

In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000th of the mink genome, suggests that simple sequence repeats (SSRs...

Generating physical symptoms from visual cues: An experimental study.

Science.gov (United States)

Ogden, Jane; Zoukas, Serafim

2009-12-01

This experimental study explored whether the physical symptoms of cold, pain and itchiness could be generated by visual cues, whether they varied in the ease with which they could be generated and whether they were related to negative affect. Participants were randomly allocated by group to watch one of three videos relating to cold (e.g. ice, snow, wind), pain (e.g. sporting injuries, tattoos) or itchiness (e.g. head lice, scratching). They then rated their self-reported symptoms of cold, pain and itchiness as well as their negative affect (depression and anxiety). The researcher recorded their observed behaviour relating to these symptoms. The results showed that the interventions were successful and that all three symptoms could be generated by the visual cues in terms of both self-report and observed behaviour. In addition, the pain video generated higher levels of anxiety and depression than the other two videos. Further, the degree of itchiness was related to the degree of anxiety. This symptom onset process also showed variability between symptoms with self-reported cold symptoms being greater than either pain or itchy symptoms. The results show that physical symptoms can be generated by visual cues indicating that psychological factors are not only involved in symptom perception but also in symptom onset.

Multicenter Clinical Evaluation of BacT/Alert Virtuo Blood Culture System.

Science.gov (United States)

Jacobs, Michael R; Mazzulli, Tony; Hazen, Kevin C; Good, Caryn E; Abdelhamed, Ayman M; Lo, Pauline; Shum, Bianche; Roman, Katharine P; Robinson, Danielle C

2017-08-01

BacT/Alert Virtuo is an advanced, automated blood culture system incorporating improved automation and an enhanced detection algorithm to shorten time to detection. A multicenter study of the investigational Virtuo system (bioMérieux, Inc., Durham, NC) compared to BacT/Alert 3D (BTA3D) for detection of bacteremia/fungemia in four bottle types, SA and FA Plus (aerobic) and SN and FN Plus (anaerobic), was performed in a clinical setting with patient samples in a matched system design clinical trial. Blood was added to paired aerobic or anaerobic bottles, with the volume in each bottle in each pair required to be ≤10 ml and with the volumes required to be within 30% of each other. Of 5,709 bottle sets (52.5% aerobic pairs and 47.5% anaerobic pairs), 430 (7.5%) were positive for bacterial or fungal growth, with 342 (6.0%) clinically significant and 83 (1.5%) contaminated. A total of 3,539 sets (62.0%) were volume compliant, with 203 sets (5.7%) clinically significant. The positivity rates for volume-compliant bottle pairs determined by the two systems were comparable, with 68.7% of clinically significant isolates detected by both instruments, 15.7% by Virtuo only, and 15.7% by BTA3D only. Virtuo detected microbial growth nearly 2 h sooner overall than BTA3D (mean, 15.9 h versus 17.7 h). Shorter time to detection by Virtuo was related to organism group, with the time to detection being significantly shorter for enteric Gram-negative bacilli and enterococci (means, 3.6 h and 2.3 h shorter, respectively). This large clinical study demonstrated that the Virtuo blood culture system produced results comparable to those seen with the long-established BTA3D system, with significantly shorter time to detection. Copyright © 2017 Jacobs et al.

Toward forward genetic screens in malaria-causing parasites using the piggyBac transposon

Directory of Open Access Journals (Sweden)

de Koning-Ward Tania F

2011-03-01

Full Text Available Abstract The ability to analyze gene function in malaria-causing Plasmodium parasites has received a boost with a recent paper in BMC Genomics that describes a genome-wide mutagenesis system in the rodent malaria species Plasmodium berghei using the transposon piggyBac. This advance holds promise for identifying and validating new targets for intervention against malaria. But further improvements are still needed for the full power of genome-wide molecular genetic screens to be utilized in this organism. See research article: http://www.biomedcentral.com/1471-2164/12/155

Characterization of pig farms in Hung Yen, Hai Duong and Bac Ninh provinces

OpenAIRE

Nguyen Van Duy; Vu Dinh; Dang Vu, Binh; Vo Trong, Thanh; Nguyen Cong, oanh; Phan Van, Chung

2007-01-01

In order to characterization of pig farms in the Red River Delta, a study was conducted on 90 pig farms in Hung Yen, Hai Duong and Bac Ninh provinces from June to December 2006. Results show that most of the pig farms had been built for five years with a small size (0.5 hectare per farm). The invested capital was about 300-400 millions VND per farm. Four main sow groups used in the farms included crossbred exotic sows (51.1%), crossbred sow between local and exotic breeds (14.4%), purebred La...

The DKIST Data Center: Meeting the Data Challenges for Next-Generation, Ground-Based Solar Physics

Science.gov (United States)

Davey, A. R.; Reardon, K.; Berukoff, S. J.; Hays, T.; Spiess, D.; Watson, F. T.; Wiant, S.

2016-12-01

The Daniel K. Inouye Solar Telescope (DKIST) is under construction on the summit of Haleakalā in Maui, and scheduled to start science operations in 2020. The DKIST design includes a four-meter primary mirror coupled to an adaptive optics system, and a flexible instrumentation suite capable of delivering high-resolution optical and infrared observations of the solar chromosphere, photosphere, and corona. Through investigator-driven science proposals, the facility will generate an average of 8 TB of data daily, comprised of millions of images and hundreds of millions of metadata elements. The DKIST Data Center is responsible for the long-term curation and calibration of data received from the DKIST, and for distributing it to the user community for scientific use. Two key elements necessary to meet the inherent big data challenge are the development of flexible public/private cloud computing and coupled relational and non-relational data storage mechanisms. We discuss how this infrastructure is being designed to meet the significant expectation of automatic and manual calibration of ground-based solar physics data, and the maximization the data's utility through efficient, long-term data management practices implemented with prudent process definition and technology exploitation.

A review of reagents for fluorescence microscopy of cellular compartments and structures, part I: BacMam labeling and reagents for vesicular structures.

Science.gov (United States)

Dolman, Nick J; Kilgore, Jason A; Davidson, Michael W

2013-07-01

Fluorescent labeling of vesicular structures in cultured cells, particularly for live cells, can be challenging for a number of reasons. The first challenge is to identify a reagent that will be specific enough where some structures have a number of potential reagents and others very few options. The emergence of BacMam constructs has allowed more easy-to-use choices. Presented here is a discussion of BacMam constructs as well as a review of commercially-available reagents for labeling vesicular structures in cells, including endosomes, peroxisomes, lysosomes, and autophagosomes, complete with a featured reagent for each structure, recommended protocol, troubleshooting guide, and example image. © 2013 by John Wiley & Sons, Inc.

The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS.

Directory of Open Access Journals (Sweden)

Mohammed Almuhayawi

Full Text Available Detection and identification of anaerobic bacteria in blood cultures (BC is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux, BACTEC-Plus and -Lytic (Becton Dickinson BioSciences BC bottles in detection and time to detection (TTD of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94% than BacT/ALERT FN Plus (80/100, 80% (p<0.01 in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001. The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h, BACTEC Plus (27 h and finally BacT/ALERT FN Plus (38 h bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76% BacT/ALERT FN, 51/67 (76% BacT/ALERT FN Plus, 53/67 (79% BACTEC Plus and 50/67 (75% BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.

MBBR evaluation for oil refinery wastewater treatment, with post-ozonation and BAC, for wastewater reuse.

Science.gov (United States)

Schneider, E E; Cerqueira, A C F P; Dezotti, M

2011-01-01

This work evaluated the performance of a Moving Bed Biofilm Reactor (MBBR) in the treatment of an oil refinery wastewater. Also, it investigated the possibility of reuse of the MBBR effluent, after ozonation in series with a biological activated carbon (BAC) column. The best performance of the MBBR was achieved with a hydraulic retention time (HRT) of 6 hours, employing a bed to bioreactor volume ratio (V(B)/V(R)) of 0.6. COD and N-NH₄(+) MBBR effluent concentrations ranged from 40 to 75 mg L⁻¹ (removal efficiency of 69-89%) and 2 to 6 mg L⁻¹ (removal efficiency of 45-86%), respectively. Ozonation carried out for 15 min with an ozone concentration of 5 mg L⁻¹ was able to improve the treated wastewater biodegradability. The treatment performance of the BAC columns was practically the same for ozonated and non ozonated MBBR effluents. The dissolved organic carbon (DOC) content of the columns of the activated carbon columns (CAG) was in the range of 2.1-3.8 mg L⁻¹, and the corresponding DOC removal efficiencies were comprised between 52 and 75%. The effluent obtained at the end of the proposed treatment presented a quality, which meet the requirements for water reuse in the oil refinery.

MUTATION ON Bacillus subtilis BAC4 USING ACRIDINE ORANGE AS AN EFFORT FOR INCREASING ANTIBIOTIC PRODUCTION

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Supartono Supartono

2010-06-01

Full Text Available The efforts to get a new antibiotic require to be done continuously, because infection diseases still become the main health problems in Indonesia. A new local strain of Bacillus subtilis BAC4 has been known producing an antibiotic that inhibites Serratia marcescens ATCC 27117 growth. Nevertheless, the optimum conditions have not been studied seriously. The objective of this research was to conduct mutation on B. subtilis BAC4 in order to obtain a mutant cell that overproduct in producing antibiotic. The mutation process was performed by using acridine orange of 1 g.L-1 randomly at various volumes. The production of antibiotic was conducted using batch fermentation and antibiotic assay was performed with agar absorption method using S.  marcescens ATCC 27117 as bacteria assay. Research result provided a B. subtilis M10 mutant with overproduction of antibiotic. Characterization of B. subtilis M10 mutant showed that the mutant cell has size of (0.5-1.0 µm x (1.85-2.5 µm; spore has the form of ellipse with thick wavy wall, positive reaction for catalase, and forming acid from glucose and xylose.   Keywords: mutant, Bacillus, acridin, and antibiotics

MEMS-Based Power Generation Techniques for Implantable Biosensing Applications

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Jonathan Lueke

2011-01-01

Full Text Available Implantable biosensing is attractive for both medical monitoring and diagnostic applications. It is possible to monitor phenomena such as physical loads on joints or implants, vital signs, or osseointegration in vivo and in real time. Microelectromechanical (MEMS-based generation techniques can allow for the autonomous operation of implantable biosensors by generating electrical power to replace or supplement existing battery-based power systems. By supplementing existing battery-based power systems for implantable biosensors, the operational lifetime of the sensor is increased. In addition, the potential for a greater amount of available power allows additional components to be added to the biosensing module, such as computational and wireless and components, improving functionality and performance of the biosensor. Photovoltaic, thermovoltaic, micro fuel cell, electrostatic, electromagnetic, and piezoelectric based generation schemes are evaluated in this paper for applicability for implantable biosensing. MEMS-based generation techniques that harvest ambient energy, such as vibration, are much better suited for implantable biosensing applications than fuel-based approaches, producing up to milliwatts of electrical power. High power density MEMS-based approaches, such as piezoelectric and electromagnetic schemes, allow for supplemental and replacement power schemes for biosensing applications to improve device capabilities and performance. In addition, this may allow for the biosensor to be further miniaturized, reducing the need for relatively large batteries with respect to device size. This would cause the implanted biosensor to be less invasive, increasing the quality of care received by the patient.

MEMS-based power generation techniques for implantable biosensing applications.

Science.gov (United States)

Lueke, Jonathan; Moussa, Walied A

2011-01-01

Implantable biosensing is attractive for both medical monitoring and diagnostic applications. It is possible to monitor phenomena such as physical loads on joints or implants, vital signs, or osseointegration in vivo and in real time. Microelectromechanical (MEMS)-based generation techniques can allow for the autonomous operation of implantable biosensors by generating electrical power to replace or supplement existing battery-based power systems. By supplementing existing battery-based power systems for implantable biosensors, the operational lifetime of the sensor is increased. In addition, the potential for a greater amount of available power allows additional components to be added to the biosensing module, such as computational and wireless and components, improving functionality and performance of the biosensor. Photovoltaic, thermovoltaic, micro fuel cell, electrostatic, electromagnetic, and piezoelectric based generation schemes are evaluated in this paper for applicability for implantable biosensing. MEMS-based generation techniques that harvest ambient energy, such as vibration, are much better suited for implantable biosensing applications than fuel-based approaches, producing up to milliwatts of electrical power. High power density MEMS-based approaches, such as piezoelectric and electromagnetic schemes, allow for supplemental and replacement power schemes for biosensing applications to improve device capabilities and performance. In addition, this may allow for the biosensor to be further miniaturized, reducing the need for relatively large batteries with respect to device size. This would cause the implanted biosensor to be less invasive, increasing the quality of care received by the patient.

INTERACTION BETWEEN DIFFERENT MOLECULAR FORMS OF IMMUNOGLOBULIN A AND RECOMBINANT DERIVATIVES POLYPEPTIDES OF BAC RECEPTOR PROTEINS FROM GROUP B STREPTOCOCCI

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A. S. Korzhueva

2008-01-01

Full Text Available Abstract. The article concerns interactions between immunoglobulin A and recombinant P6, P7, P8 polypeptides, designed on the basis of externally localized Bac protein of the Group B streptococci, possessing IgA-binding activity.There is a current demand for immunochemical reagents that are strictly specific for IgA, in order to develop antigenic standards for detection of IgA levels in biological fluids, as well as for affinity purification of IgA and its fragments.To analyze an opportunity of the abovementioned application ways for these proteins, a special study was performed to assay an interaction capability of recombinant P6, P7, P8 polypeptides binding to Fc regions of different IgA forms (serum IgA, secretory IgA, subclasses of serum IgA – IgA1, IgA2. Selectivity of ligand binding was specially confirmed.It was found out that, among three presented polypeptides, the structure of recombinant P6 derivative proved to be optimal for IgA-binding ability of Bac protein.Structural features of IgA-binding fragments of Bac protein, i.e., binding site position on the IgA molecule (proximity to epitopes for three monoclonal antibodies, variability of the site structure, as well as resistance of binding site for P6, P7, P8 in IgA molecule against partial disulfide bonds reduction. (Med. Immunol., vol. 10, N 4-5, pp 327-336.

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

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Ritland Carol

2009-08-01

Full Text Available Abstract Background Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs and full-length (FLcDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. Results We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR and a cytochrome P450 (CYP720B4 from a non-arrayed genomic BAC library of white spruce (Picea glauca. Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR and 94 kbp (CYP720B4 long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs, high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. Conclusion We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome.

Science.gov (United States)

Hamberger, Björn; Hall, Dawn; Yuen, Mack; Oddy, Claire; Hamberger, Britta; Keeling, Christopher I; Ritland, Carol; Ritland, Kermit; Bohlmann, Jörg

2009-08-06

Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR) and a cytochrome P450 (CYP720B4) from a non-arrayed genomic BAC library of white spruce (Picea glauca). Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR) and 94 kbp (CYP720B4) long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs), high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene families can be isolated in a gene-specific fashion. The

A Physically Based Analytical Model to Describe Effective Excess Charge for Streaming Potential Generation in Water Saturated Porous Media

Science.gov (United States)

Guarracino, L.; Jougnot, D.

2018-01-01

Among the different contributions generating self-potential, the streaming potential is of particular interest in hydrogeology for its sensitivity to water flow. Estimating water flux in porous media using streaming potential data relies on our capacity to understand, model, and upscale the electrokinetic coupling at the mineral-solution interface. Different approaches have been proposed to predict streaming potential generation in porous media. One of these approaches is the flux averaging which is based on determining the excess charge which is effectively dragged in the medium by water flow. In this study, we develop a physically based analytical model to predict the effective excess charge in saturated porous media using a flux-averaging approach in a bundle of capillary tubes with a fractal pore size distribution. The proposed model allows the determination of the effective excess charge as a function of pore water ionic concentration and hydrogeological parameters like porosity, permeability, and tortuosity. The new model has been successfully tested against different set of experimental data from the literature. One of the main findings of this study is the mechanistic explanation to the empirical dependence between the effective excess charge and the permeability that has been found by several researchers. The proposed model also highlights the link to other lithological properties, and it is able to reproduce the evolution of effective excess charge with electrolyte concentrations.

Vector modifications to eliminate transposase expression following piggyBac-mediated transgenesis

Science.gov (United States)

Chakraborty, Syandan; Ji, HaYeun; Chen, Jack; Gersbach, Charles A.; Leong, Kam W.

2014-01-01

Transgene insertion plays an important role in gene therapy and in biological studies. Transposon-based systems that integrate transgenes by transposase-catalyzed “cut-and-paste” mechanism have emerged as an attractive system for transgenesis. Hyperactive piggyBac transposon is particularly promising due to its ability to integrate large transgenes with high efficiency. However, prolonged expression of transposase can become a potential source of genotoxic effects due to uncontrolled transposition of the integrated transgene from one chromosomal locus to another. In this study we propose a vector design to decrease post-transposition expression of transposase and to eliminate the cells that have residual transposase expression. We design a single plasmid construct that combines the transposase and the transpositioning transgene element to share a single polyA sequence for termination. Consequently, the separation of the transposase element from the polyA sequence after transposition leads to its deactivation. We also co-express Herpes Simplex Virus thymidine kinase (HSV-tk) with the transposase. Therefore, cells having residual transposase expression can be eliminated by the administration of ganciclovir. We demonstrate the utility of this combination transposon system by integrating and expressing a model therapeutic gene, human coagulation Factor IX, in HEK293T cells. PMID:25492703

A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii

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Patel Hardip R

2011-08-01

Full Text Available Abstract Background The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH, (b End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby

A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii).

Science.gov (United States)

Wang, Chenwei; Webley, Lee; Wei, Ke-jun; Wakefield, Matthew J; Patel, Hardip R; Deakin, Janine E; Alsop, Amber; Marshall Graves, Jennifer A; Cooper, Desmond W; Nicholas, Frank W; Zenger, Kyall R

2011-08-19

The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6.

Science.gov (United States)

Saski, Christopher A; Feltus, Frank A; Staton, Margaret E; Blackmon, Barbara P; Ficklin, Stephen P; Kuhn, David N; Schnell, Raymond J; Shapiro, Howard; Motamayor, Juan Carlos

2011-08-16

The fermented dried seeds of Theobroma cacao (cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected. Here, we describe the construction of a BAC-based integrated genetic-physical map of the T. cacao cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the two T. cacao

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6

Directory of Open Access Journals (Sweden)

Kuhn David N

2011-08-01

Full Text Available Abstract Background The fermented dried seeds of Theobroma cacao (cacao tree are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected. Results Here, we describe the construction of a BAC-based integrated genetic-physical map of the T. cacao cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105 span 67.4 Mbp and therefore the estimated genome size of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map

Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae

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Gonthier Lucy

2010-08-01

Full Text Available Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L. constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This

Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae).

Science.gov (United States)

Gonthier, Lucy; Bellec, Arnaud; Blassiau, Christelle; Prat, Elisa; Helmstetter, Nicolas; Rambaud, Caroline; Huss, Brigitte; Hendriks, Theo; Bergès, Hélène; Quillet, Marie-Christine

2010-08-11

The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. This indicated that both BAC libraries are valuable tools for molecular

Radiative corrections and Monte Carlo generators for physics at flavor factories

Directory of Open Access Journals (Sweden)

Montagna Guido

2016-01-01

Full Text Available I review the state of the art of precision calculations and related Monte Carlo generators used in physics at flavor factories. The review describes the tools relevant for the measurement of the hadron production cross section (via radiative return, energy scan and in γγ scattering, luminosity monitoring, searches for new physics and physics of the τ lepton.

Spin-torque generation in topological insulator based heterostructures

KAUST Repository

Fischer, Mark H.

2016-03-11

Heterostructures utilizing topological insulators exhibit a remarkable spin-torque efficiency. However, the exact origin of the strong torque, in particular whether it stems from the spin-momentum locking of the topological surface states or rather from spin-Hall physics of the topological-insulator bulk, remains unclear. Here, we explore a mechanism of spin-torque generation purely based on the topological surface states. We consider topological-insulator-based bilayers involving ferromagnetic metal (TI/FM) and magnetically doped topological insulators (TI/mdTI), respectively. By ascribing the key theoretical differences between the two setups to location and number of active surface states, we describe both setups within the same framework of spin diffusion of the nonequilibrium spin density of the topological surface states. For the TI/FM bilayer, we find large spin-torque efficiencies of roughly equal magnitude for both in-plane and out-of-plane spin torques. For the TI/mdTI bilayer, we elucidate the dominance of the spin-transfer-like torque. However, we cannot explain the orders of magnitude enhancement reported. Nevertheless, our model gives an intuitive picture of spin-torque generation in topological-insulator-based bilayers and provides theoretical constraints on spin-torque generation due to topological surface states.

ARIMA-Based Time Series Model of Stochastic Wind Power Generation

DEFF Research Database (Denmark)

Chen, Peiyuan; Pedersen, Troels; Bak-Jensen, Birgitte

2010-01-01

This paper proposes a stochastic wind power model based on an autoregressive integrated moving average (ARIMA) process. The model takes into account the nonstationarity and physical limits of stochastic wind power generation. The model is constructed based on wind power measurement of one year from...... the Nysted offshore wind farm in Denmark. The proposed limited-ARIMA (LARIMA) model introduces a limiter and characterizes the stochastic wind power generation by mean level, temporal correlation and driving noise. The model is validated against the measurement in terms of temporal correlation...... and probability distribution. The LARIMA model outperforms a first-order transition matrix based discrete Markov model in terms of temporal correlation, probability distribution and model parameter number. The proposed LARIMA model is further extended to include the monthly variation of the stochastic wind power...

[Intel random number generator-based true random number generator].

Science.gov (United States)

Huang, Feng; Shen, Hong

2004-09-01

To establish a true random number generator on the basis of certain Intel chips. The random numbers were acquired by programming using Microsoft Visual C++ 6.0 via register reading from the random number generator (RNG) unit of an Intel 815 chipset-based computer with Intel Security Driver (ISD). We tested the generator with 500 random numbers in NIST FIPS 140-1 and X(2) R-Squared test, and the result showed that the random number it generated satisfied the demand of independence and uniform distribution. We also compared the random numbers generated by Intel RNG-based true random number generator and those from the random number table statistically, by using the same amount of 7500 random numbers in the same value domain, which showed that the SD, SE and CV of Intel RNG-based random number generator were less than those of the random number table. The result of u test of two CVs revealed no significant difference between the two methods. Intel RNG-based random number generator can produce high-quality random numbers with good independence and uniform distribution, and solves some problems with random number table in acquisition of the random numbers.

Expression of the Azotobacter vinelandii Poly-β-Hydroxybutyrate Biosynthetic phbBAC Operon Is Driven by Two Overlapping Promoters and Is Dependent on the Transcriptional Activator PhbR

OpenAIRE

Peralta-Gil, Martín; Segura, Daniel; Guzmán, Josefina; Servín-González, Luis; Espín, Guadalupe

2002-01-01

The Azotobacter vinelandii phbBAC genes encode the enzymes for poly-β-hydroxybutyrate (PHB) synthesis. The phbR gene, which is located upstream of and in the opposite direction of phbBAC, encodes PhbR, a transcriptional activator which is a member of the AraC family of activators. Here we report that a mutation in phbR reduced PHB accumulation and transcription of a phbB-lacZ fusion. We also report that phbB is transcribed from two overlapping promoters, pB1 and pB2. The region corresponding ...

Improving Phrap-based assembly of the rat using "reliable" overlaps.

Directory of Open Access Journals (Sweden)

Michael Roberts

2008-03-01

Full Text Available The assembly methods used for whole-genome shotgun (WGS data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our "reliable-overlap" algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.

Trophic effects of adipose-tissue-derived and bone-marrow-derived mesenchymal stem cells enhance cartilage generation by chondrocytes in co-culture.

Science.gov (United States)

Pleumeekers, M M; Nimeskern, L; Koevoet, J L M; Karperien, M; Stok, K S; van Osch, G J V M

2018-01-01

Combining mesenchymal stem cells (MSCs) and chondrocytes has great potential for cell-based cartilage repair. However, there is much debate regarding the mechanisms behind this concept. We aimed to clarify the mechanisms that lead to chondrogenesis (chondrocyte driven MSC-differentiation versus MSC driven chondroinduction) and whether their effect was dependent on MSC-origin. Therefore, chondrogenesis of human adipose-tissue-derived MSCs (hAMSCs) and bone-marrow-derived MSCs (hBMSCs) combined with bovine articular chondrocytes (bACs) was compared. hAMSCs or hBMSCs were combined with bACs in alginate and cultured in vitro or implanted subcutaneously in mice. Cartilage formation was evaluated with biochemical, histological and biomechanical analyses. To further investigate the interactions between bACs and hMSCs, (1) co-culture, (2) pellet, (3) Transwell® and (4) conditioned media studies were conducted. The presence of hMSCs-either hAMSCs or hBMSCs-increased chondrogenesis in culture; deposition of GAG was most evidently enhanced in hBMSC/bACs. This effect was similar when hMSCs and bAC were combined in pellet culture, in alginate culture or when conditioned media of hMSCs were used on bAC. Species-specific gene-expression analyses demonstrated that aggrecan was expressed by bACs only, indicating a predominantly trophic role for hMSCs. Collagen-10-gene expression of bACs was not affected by hBMSCs, but slightly enhanced by hAMSCs. After in-vivo implantation, hAMSC/bACs and hBMSC/bACs had similar cartilage matrix production, both appeared stable and did not calcify. This study demonstrates that replacing 80% of bACs by either hAMSCs or hBMSCs does not influence cartilage matrix production or stability. The remaining chondrocytes produce more matrix due to trophic factors produced by hMSCs.

Inducible targeting of CNS astrocytes in Aldh1l1-CreERT2 BAC transgenic mice [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Jan Winchenbach

2016-12-01

Full Text Available Background: Studying astrocytes in higher brain functions has been hampered by the lack of genetic tools for the efficient expression of inducible Cre recombinase throughout the CNS, including the neocortex. Methods: Therefore, we generated BAC transgenic mice, in which CreERT2 is expressed under control of the Aldh1l1 regulatory region. Results: When crossbred to Cre reporter mice, adult Aldh1l1-CreERT2 mice show efficient gene targeting in astrocytes. No such Cre-mediated recombination was detectable in CNS neurons, oligodendrocytes, and microglia. As expected, Aldh1l1-CreERT2 expression was evident in several peripheral organs, including liver and kidney. Conclusions: Taken together, Aldh1l1-CreERT2 mice are a useful tool for studying astrocytes in neurovascular coupling, brain metabolism, synaptic plasticity and other aspects of neuron-glia interactions.

Clustered regulatory interspaced short palindromic repeats (CRISPR)-mediated mutagenesis and phenotype rescue by piggyBac transgenesis in a nonmodel Drosophila species.

Science.gov (United States)

Tanaka, R; Murakami, H; Ote, M; Yamamoto, D

2016-08-01

How behavioural diversity emerged in evolution is an unexplored subject in biology. To tackle this problem, genes and circuits for a behaviour need to be determined in different species for phylogenetic comparisons. The recently developed clustered regulatory interspaced short palindromic repeats/CRISPR associated protein9 (CRISPR/Cas9) system made such a challenge possible by providing the means to induce mutations in a gene of interest in any organism. Aiming at elucidating diversification in genetic and neural networks for courtship behaviour, we attempted to generate a genetic tool kit in Drosophila subobscura, a nonmodel species distantly related to the genetic model Drosophila melanogaster. Here we report the generation of yellow (y) and white mutations with the aid of the CRISPR/Cas9 system, and the rescue of the y mutant phenotype by germline transformation of the newly established y mutant fly line with a y(+) -marked piggyBac vector. This successful mutagenesis and transformation in D. subobscura open up an avenue for comprehensive genetic analyses of higher functions in this and other nonmodel Drosophila species, representing a key step toward systematic comparisons of genes and circuitries underlying behaviour amongst species. © 2016 The Royal Entomological Society.

The physics data base

International Nuclear Information System (INIS)

Gault, F.D.

1984-01-01

The physics data base is introduced along with its associated data base management system. The emphasis is on data and their use and a classification of data and of data bases is developed to distinguish compilation organizations. The characteristics of these organizations are examined briefly and the long term consequences of the physics data base discussed. (orig.)

Evaluation of BacT/Alert 3D Liquid Culture System for Recovery of Mycobacteria from Clinical Specimens Using Sodium Dodecyl (Lauryl) Sulfate-NaOH Decontamination

Science.gov (United States)

Carricajo, A.; Fonsale, N.; Vautrin, A. C.; Aubert, G.

2001-01-01

A total of 52 mycobacterial isolates were recovered from 1,197 clinical specimens decontaminated by a sodium dodecyl (lauryl) sulfate (SDS)-NaOH protocol. Of these, 94% were recovered with the BacT/Alert 3D system (Organon Teknika, Durham, N.C.) and 79% were recovered on Löwenstein-Jensen (LJ) medium. Mean times to detection of organisms of the Mycobacterium tuberculosis complex (n = 47) were 22.8 days with LJ medium and 16.2 days with the system. The BacT/Alert 3D system is a rapid and efficient detection system which can be used with an SDS-NaOH decontamination procedure. PMID:11574623

Synchronization of random bit generators based on coupled chaotic lasers and application to cryptography.

Science.gov (United States)

Kanter, Ido; Butkovski, Maria; Peleg, Yitzhak; Zigzag, Meital; Aviad, Yaara; Reidler, Igor; Rosenbluh, Michael; Kinzel, Wolfgang

2010-08-16

Random bit generators (RBGs) constitute an important tool in cryptography, stochastic simulations and secure communications. The later in particular has some difficult requirements: high generation rate of unpredictable bit strings and secure key-exchange protocols over public channels. Deterministic algorithms generate pseudo-random number sequences at high rates, however, their unpredictability is limited by the very nature of their deterministic origin. Recently, physical RBGs based on chaotic semiconductor lasers were shown to exceed Gbit/s rates. Whether secure synchronization of two high rate physical RBGs is possible remains an open question. Here we propose a method, whereby two fast RBGs based on mutually coupled chaotic lasers, are synchronized. Using information theoretic analysis we demonstrate security against a powerful computational eavesdropper, capable of noiseless amplification, where all parameters are publicly known. The method is also extended to secure synchronization of a small network of three RBGs.

Generating physical symptoms from visual cues: An experimental study

OpenAIRE

Ogden, J; Zoukas, S

2010-01-01

This experimental study explored whether the physical symptoms of cold, pain and itchiness could be generated by visual cues, whether they varied in the ease with which they could be generated and whether they were related to negative affect. Participants were randomly allocated by group to watch one of three videos relating to cold (e.g. ice, snow, wind), pain (e.g. sporting injuries, tattoos) or itchiness (e.g. head lice, scratching). They then rated their self-reported symptoms of cold, pa...

Physical model for the generation of ideal resources in multipartite quantum networking

International Nuclear Information System (INIS)

Ciccarello, F.; Zarcone, M.; Paternostro, M.; Bose, S.; Browne, D. E.; Palma, G. M.

2010-01-01

We propose a physical model for generating multipartite entangled states of spin-s particles that have important applications in distributed quantum information processing. Our protocol is based on a process where mobile spins induce the interaction among remote scattering centers. As such, a major advantage lies in the management of stationary and well-separated spins. Among the generable states, there is a class of N-qubit singlets allowing for optimal quantum telecloning in a scalable and controllable way. We also show how to prepare Aharonov, W, and Greenberger-Horne-Zeilinger states.

Relationship between neural rhythm generation disorders and physical disabilities in Parkinson's disease patients' walking.

Science.gov (United States)

Ota, Leo; Uchitomi, Hirotaka; Ogawa, Ken-ichiro; Orimo, Satoshi; Miyake, Yoshihiro

2014-01-01

Walking is generated by the interaction between neural rhythmic and physical activities. In fact, Parkinson's disease (PD), which is an example of disease, causes not only neural rhythm generation disorders but also physical disabilities. However, the relationship between neural rhythm generation disorders and physical disabilities has not been determined. The aim of this study was to identify the mechanism of gait rhythm generation. In former research, neural rhythm generation disorders in PD patients' walking were characterized by stride intervals, which are more variable and fluctuate randomly. The variability and fluctuation property were quantified using the coefficient of variation (CV) and scaling exponent α. Conversely, because walking is a dynamic process, postural reflex disorder (PRD) is considered the best way to estimate physical disabilities in walking. Therefore, we classified the severity of PRD using CV and α. Specifically, PD patients and healthy elderly were classified into three groups: no-PRD, mild-PRD, and obvious-PRD. We compared the contributions of CV and α to the accuracy of this classification. In this study, 45 PD patients and 17 healthy elderly people walked 200 m. The severity of PRD was determined using the modified Hoehn-Yahr scale (mH-Y). People with mH-Y scores of 2.5 and 3 had mild-PRD and obvious-PRD, respectively. As a result, CV differentiated no-PRD from PRD, indicating the correlation between CV and PRD. Considering that PRD is independent of neural rhythm generation, this result suggests the existence of feedback process from physical activities to neural rhythmic activities. Moreover, α differentiated obvious-PRD from mild-PRD. Considering α reflects the intensity of interaction between factors, this result suggests the change of the interaction. Therefore, the interaction between neural rhythmic and physical activities is thought to plays an important role for gait rhythm generation. These characteristics have

BACS: The Brussels Artificial Character Sets for studies in cognitive psychology and neuroscience.

Science.gov (United States)

Vidal, Camille; Content, Alain; Chetail, Fabienne

2017-12-01

Written symbols such as letters have been used extensively in cognitive psychology, whether to understand their contributions to written word recognition or to examine the processes involved in other mental functions. Sometimes, however, researchers want to manipulate letters while removing their associated characteristics. A powerful solution to do so is to use new characters, devised to be highly similar to letters, but without the associated sound or name. Given the growing use of artificial characters in experimental paradigms, the aim of the present study was to make available the Brussels Artificial Character Sets (BACS): two full, strictly controlled, and portable sets of artificial characters for a broad range of experimental situations.

Physical Modeling of microtubule force generation and self-organization

NARCIS (Netherlands)

Tanase, C.

2004-01-01

Biological systems are complex heterogeneous and far from equilibrium systems. The fundamental questions posed by the physics of such systems are what the force generation mechanisms are, and how energy is processed and distributed among the components inside them. In answering these questions we

A novel image encryption algorithm based on synchronized random bit generated in cascade-coupled chaotic semiconductor ring lasers

Science.gov (United States)

Li, Jiafu; Xiang, Shuiying; Wang, Haoning; Gong, Junkai; Wen, Aijun

2018-03-01

In this paper, a novel image encryption algorithm based on synchronization of physical random bit generated in a cascade-coupled semiconductor ring lasers (CCSRL) system is proposed, and the security analysis is performed. In both transmitter and receiver parts, the CCSRL system is a master-slave configuration consisting of a master semiconductor ring laser (M-SRL) with cross-feedback and a solitary SRL (S-SRL). The proposed image encryption algorithm includes image preprocessing based on conventional chaotic maps, pixel confusion based on control matrix extracted from physical random bit, and pixel diffusion based on random bit stream extracted from physical random bit. Firstly, the preprocessing method is used to eliminate the correlation between adjacent pixels. Secondly, physical random bit with verified randomness is generated based on chaos in the CCSRL system, and is used to simultaneously generate the control matrix and random bit stream. Finally, the control matrix and random bit stream are used for the encryption algorithm in order to change the position and the values of pixels, respectively. Simulation results and security analysis demonstrate that the proposed algorithm is effective and able to resist various typical attacks, and thus is an excellent candidate for secure image communication application.

Enabling full field physics based OPC via dynamic model generation

Science.gov (United States)

Lam, Michael; Clifford, Chris; Raghunathan, Ananthan; Fenger, Germain; Adam, Kostas

2017-03-01

As EUV lithography marches closer to reality for high volume production, its peculiar modeling challenges related to both inter- and intra- field effects has necessitated building OPC infrastructure that operates with field position dependency. Previous state of the art approaches to modeling field dependency used piecewise constant models where static input models are assigned to specific x/y-positions within the field. OPC and simulation could assign the proper static model based on simulation-level placement. However, in the realm of 7nm and 5nm feature sizes, small discontinuities in OPC from piecewise constant model changes can cause unacceptable levels of EPE errors. The introduction of Dynamic Model Generation (DMG) can be shown to effectively avoid these dislocations by providing unique mask and optical models per simulation region, allowing a near continuum of models through field. DMG allows unique models for EMF, apodization, aberrations, etc to vary through the entire field and provides a capability to precisely and accurately model systematic field signatures.

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

OpenAIRE

Luo, Meizhong; Kim, HyeRan; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A

2006-01-01

Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) ...

Steam generators clogging diagnosis through physical and statistical modelling

International Nuclear Information System (INIS)

Girard, S.

2012-01-01

Steam generators are massive heat exchangers feeding the turbines of pressurised water nuclear power plants. Internal parts of steam generators foul up with iron oxides which gradually close some holes aimed for the passing of the fluid. This phenomenon called clogging causes safety issues and means to assess it are needed to optimise the maintenance strategy. The approach investigated in this thesis is the analysis of steam generators dynamic behaviour during power transients with a mono dimensional physical model. Two improvements to the model have been implemented. One was taking into account flows orthogonal to the modelling axis, the other was introducing a slip between phases accounting for velocity difference between liquid water and steam. These two elements increased the model's degrees of freedom and improved the adequacy of the simulation to plant data. A new calibration and validation methodology has been proposed to assess the robustness of the model. The initial inverse problem was ill posed: different clogging spatial configurations can produce identical responses. The relative importance of clogging, depending on its localisation, has been estimated by sensitivity analysis with the Sobol' method. The dimension of the model functional output had been previously reduced by principal components analysis. Finally, the input dimension has been reduced by a technique called sliced inverse regression. Based on this new framework, a new diagnosis methodology, more robust and better understood than the existing one, has been proposed. (author)

Ontology-Based Generation of Dynamic Feedback on Physical Activity

NARCIS (Netherlands)

Wieringa, Wilko; op den Akker, Harm; Jones, Valerie M.; Hermens, Hermanus J.; op den Akker, Hendrikus J.A.

2011-01-01

This article describes a new, AI-inspired telemedicine system for providing feedback on daily activity. Optimising daily levels of physical activity is an important focus in the treatment of chronic illnesses. An ambulatory monitoring and feedback system has been developed to monitor activity and

Toxicity and genotoxicity of the quaternary ammonium compound benzalkonium chloride (BAC) using Daphnia magna and Ceriodaphnia dubia as model systems

International Nuclear Information System (INIS)

Lavorgna, Margherita; Russo, Chiara; D'Abrosca, Brigida; Parrella, Alfredo; Isidori, Marina

2016-01-01

The toxicity and genotoxicity of the cationic surfactant benzalkonium chloride (BAC) were studied using Daphnia magna and Ceriodaphnia dubia as model systems. Acute and chronic toxicity testing were performed according to the international standard guidelines and the genotoxicity was detected through the comet assay on cells from whole organisms in vivo exposed. Acute effects occurred at concentrations in the order of tens of μg/L in D. magna and hundreds of μg/L in C. dubia. Chronic effects were found at one order of magnitude less than short-term effects maintaining the same difference in sensitivity between D. magna and C. dubia. BAC induced relevant DNA damage, in both cladocerans; the lowest adverse effect levels were 0.4 and 4 ng/L for D. magna and C. dubia, respectively. As these effective concentrations are far lower than BAC occurrence in surface waters (units of μg/L) a concerning environmental risk cannot be excluded. The findings of this study showed that D. magna and C. dubia, could be used as model organisms to detect acute and chronic toxicity as well as genotoxicity at the whole organism level. - Highlights: • Benzalkonium chloride chronic effect in C. dubia was found at dozens of μg/L. • The LOAEC detected by comet assay in D. magna is in the order of hundreds of pg/L. • D. magna and C. dubia are useful model organisms to detect toxicity and genotoxicity. - Benzalkonium chloride showed chronic toxicity and genotoxicity in Daphnia magna and Ceriodaphnia dubia at concentrations of environmental concern. Daphnids are useful model organisms.

Identification of an extensive gene cluster among a family of PPOs in Trifolium pratense L. (red clover using a large insert BAC library

Directory of Open Access Journals (Sweden)

Thomas Ann

2009-07-01

Full Text Available Abstract Background Polyphenol oxidase (PPO activity in plants is a trait with potential economic, agricultural and environmental impact. In relation to the food industry, PPO-induced browning causes unacceptable discolouration in fruit and vegetables: from an agriculture perspective, PPO can protect plants against pathogens and environmental stress, improve ruminant growth by increasing nitrogen absorption and decreasing nitrogen loss to the environment through the animal's urine. The high PPO legume, red clover, has a significant economic and environmental role in sustaining low-input organic and conventional farms. Molecular markers for a range of important agricultural traits are being developed for red clover and improved knowledge of PPO genes and their structure will facilitate molecular breeding. Results A bacterial artificial chromosome (BAC library comprising 26,016 BAC clones with an average 135 Kb insert size, was constructed from Trifolium pratense L. (red clover, a diploid legume with a haploid genome size of 440–637 Mb. Library coverage of 6–8 genome equivalents ensured good representation of genes: the library was screened for polyphenol oxidase (PPO genes. Two single copy PPO genes, PPO4 and PPO5, were identified to add to a family of three, previously reported, paralogous genes (PPO1–PPO3. Multiple PPO1 copies were identified and characterised revealing a subfamily comprising three variants PPO1/2, PPO1/4 and PPO1/5. Six PPO genes clustered within the genome: four separate BAC clones could be assembled onto a predicted 190–510 Kb single BAC contig. Conclusion A PPO gene family in red clover resides as a cluster of at least 6 genes. Three of these genes have high homology, suggesting a more recent evolutionary event. This PPO cluster covers a longer region of the genome than clusters detected in rice or previously reported in tomato. Full-length coding sequences from PPO4, PPO5, PPO1/5 and PPO1/4 will facilitate

Estimation of methane generation based on anaerobic digestion ...

African Journals Online (AJOL)

Drake

Technology ... generation of methane from waste at Kiteezi landfill was measured using .... estimate methane gas generation by the anaerobic decomposition ..... Z (2007). Climate Change 2007. The Physical Science Basis. Contribution of ...

Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

Science.gov (United States)

Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

2012-05-01

The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

Micromotor-based energy generation.

Science.gov (United States)

Singh, Virendra V; Soto, Fernando; Kaufmann, Kevin; Wang, Joseph

2015-06-01

A micromotor-based strategy for energy generation, utilizing the conversion of liquid-phase hydrogen to usable hydrogen gas (H2), is described. The new motion-based H2-generation concept relies on the movement of Pt-black/Ti Janus microparticle motors in a solution of sodium borohydride (NaBH4) fuel. This is the first report of using NaBH4 for powering micromotors. The autonomous motion of these catalytic micromotors, as well as their bubble generation, leads to enhanced mixing and transport of NaBH4 towards the Pt-black catalytic surface (compared to static microparticles or films), and hence to a substantially faster rate of H2 production. The practical utility of these micromotors is illustrated by powering a hydrogen-oxygen fuel cell car by an on-board motion-based hydrogen and oxygen generation. The new micromotor approach paves the way for the development of efficient on-site energy generation for powering external devices or meeting growing demands on the energy grid. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Desarrollo de un modelo de evaluación financiera de proyectos para BAC Credomatic Network

OpenAIRE

Sandí Piedra, Allan Adolfo

2016-01-01

Universidad de Costa Rica. Posgrado en Administración y Dirección de Empresas. Maestría Profesional en Administración y Dirección de Empresas con énfasis en Finanzas, 2016 El presente trabajo final de investigación contiene los aspectos que fundamentan un modelo de Evaluación Financiera de Proyectos que permite solventar la problemática identificada en BAC Credomatic Network respecto al limitado valor agregado del proceso existente de valoración financiera de los proyectos de la empresa. P...

The generator coordinate method in nuclear physics

International Nuclear Information System (INIS)

Giraud, B.G.

1981-01-01

The generator coordinate method is introduced as a physical description of a N-body system in a subspace of a reduced number of degrees of freedom. Special attention is placed on the identification of these special, 'collective' degrees of freedom. It is shown in particular that the method has close links with the Born-Oppenheimer approximation and also that considerations of differential geometry are useful in the theory. A set of applications is discussed and in particular the case of nuclear collisions is considered. (Author) [pt

Computer soundcard as an AC signal generator and oscilloscope for the physics laboratory

Science.gov (United States)

Sinlapanuntakul, Jinda; Kijamnajsuk, Puchong; Jetjamnong, Chanthawut; Chotikaprakhan, Sutharat

2018-01-01

The purpose of this paper is to develop both an AC signal generator and a dual-channel oscilloscope based on standard personal computer equipped with sound card as parts of the laboratory of the fundamental physics and the introduction to electronics classes. The setup turns the computer into the two channel measured device which can provides sample rate, simultaneous sampling, frequency range, filters and others essential capabilities required to perform amplitude, phase and frequency measurements of AC signal. The AC signal also generate from the same computer sound card output simultaneously in any waveform such as sine, square, triangle, saw-toothed pulsed, swept sine and white noise etc. These can convert an inexpensive PC sound card into powerful device, which allows the students to measure physical phenomena with their own PCs either at home or at university attendance. A graphic user interface software was developed for control and analysis, including facilities for data recording, signal processing and real time measurement display. The result is expanded utility of self-learning for the students in the field of electronics both AC and DC circuits, including the sound and vibration experiments.

Physics of thermo-acoustic sound generation

Science.gov (United States)

Daschewski, M.; Boehm, R.; Prager, J.; Kreutzbruck, M.; Harrer, A.

2013-09-01

We present a generalized analytical model of thermo-acoustic sound generation based on the analysis of thermally induced energy density fluctuations and their propagation into the adjacent matter. The model provides exact analytical prediction of the sound pressure generated in fluids and solids; consequently, it can be applied to arbitrary thermal power sources such as thermophones, plasma firings, laser beams, and chemical reactions. Unlike existing approaches, our description also includes acoustic near-field effects and sound-field attenuation. Analytical results are compared with measurements of sound pressures generated by thermo-acoustic transducers in air for frequencies up to 1 MHz. The tested transducers consist of titanium and indium tin oxide coatings on quartz glass and polycarbonate substrates. The model reveals that thermo-acoustic efficiency increases linearly with the supplied thermal power and quadratically with thermal excitation frequency. Comparison of the efficiency of our thermo-acoustic transducers with those of piezoelectric-based airborne ultrasound transducers using impulse excitation showed comparable sound pressure values. The present results show that thermo-acoustic transducers can be applied as broadband, non-resonant, high-performance ultrasound sources.

MCPLOTS: a particle physics resource based on volunteer computing

CERN Document Server

Karneyeu, A; Prestel, S; Skands, P Z

2014-01-01

The mcplots.cern.ch web site (MCPLOTS) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the HEPDATA online database of experimental results and on the RIVET Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the LHC@HOME platform.

Real-time physics-based 3D biped character animation using an inverted pendulum model.

Science.gov (United States)

Tsai, Yao-Yang; Lin, Wen-Chieh; Cheng, Kuangyou B; Lee, Jehee; Lee, Tong-Yee

2010-01-01

We present a physics-based approach to generate 3D biped character animation that can react to dynamical environments in real time. Our approach utilizes an inverted pendulum model to online adjust the desired motion trajectory from the input motion capture data. This online adjustment produces a physically plausible motion trajectory adapted to dynamic environments, which is then used as the desired motion for the motion controllers to track in dynamics simulation. Rather than using Proportional-Derivative controllers whose parameters usually cannot be easily set, our motion tracking adopts a velocity-driven method which computes joint torques based on the desired joint angular velocities. Physically correct full-body motion of the 3D character is computed in dynamics simulation using the computed torques and dynamical model of the character. Our experiments demonstrate that tracking motion capture data with real-time response animation can be achieved easily. In addition, physically plausible motion style editing, automatic motion transition, and motion adaptation to different limb sizes can also be generated without difficulty.

Amélioration de la politique de sécurité des systèmes DRM introduction des notions du modèle Or-BAC dans le langage MPEG-21 REL

Directory of Open Access Journals (Sweden)

Morad Rafi

2013-12-01

Full Text Available Digital Rights Management (DRM allows controlling the access, the use and the diffusion of digital contents produced by the rights holders. With this intention, a right expression language is necessary. The MPEG-21 REL is a standardized language used to express the licenses. In this paper, we propose an improvement of the security policy and expressivity of MPEG-21 REL by introducing concepts based on the Or-BAC (Organization Based Access Control data model. This improvement will be illustrated by some use cases

Generation of BAC Transgenic Epithelial Organoids

NARCIS (Netherlands)

Schwank, G.; Andersson-Rolf, A.; Koo, B.K.; Sasaki, N.; Clevers, H.

2013-01-01

Under previously developed culture conditions, mouse and human intestinal epithelia can be cultured and expanded over long periods. These so-called organoids recapitulate the three-dimensional architecture of the gut epithelium, and consist of all major intestinal cell types. One key advantage of

Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum race 3 in cowpea [Vigna unguiculata (L.) Walp].

Science.gov (United States)

Pottorff, Marti; Wanamaker, Steve; Ma, Yaqin Q; Ehlers, Jeffrey D; Roberts, Philip A; Close, Timothy J

2012-01-01

Fusarium oxysporum f.sp. tracheiphilum (Fot) is a soil-borne fungal pathogen that causes vascular wilt disease in cowpea. Fot race 3 is one of the major pathogens affecting cowpea production in California. Identification of Fot race 3 resistance determinants will expedite delivery of improved cultivars by replacing time-consuming phenotypic screening with selection based on perfect markers, thereby generating successful cultivars in a shorter time period. Resistance to Fot race 3 was studied in the RIL population California Blackeye 27 (resistant) x 24-125B-1 (susceptible). Biparental mapping identified a Fot race 3 resistance locus, Fot3-1, which spanned 3.56 cM on linkage group one of the CB27 x 24-125B-1 genetic map. A marker-trait association narrowed the resistance locus to a 1.2 cM region and identified SNP marker 1_1107 as co-segregating with Fot3-1 resistance. Macro and microsynteny was observed for the Fot3-1 locus region in Glycine max where six disease resistance genes were observed in the two syntenic regions of soybean chromosomes 9 and 15. Fot3-1 was identified on the cowpea physical map on BAC clone CH093L18, spanning approximately 208,868 bp on BAC contig250. The Fot3-1 locus was narrowed to 0.5 cM distance on the cowpea genetic map linkage group 6, flanked by SNP markers 1_0860 and 1_1107. BAC clone CH093L18 was sequenced and four cowpea sequences with similarity to leucine-rich repeat serine/threonine protein kinases were identified and are cowpea candidate genes for the Fot3-1 locus. This study has shown how readily candidate genes can be identified for simply inherited agronomic traits when appropriate genetic stocks and integrated genomic resources are available. High co-linearity between cowpea and soybean genomes illustrated that utilizing synteny can transfer knowledge from a reference legume to legumes with less complete genomic resources. Identification of Fot race 3 resistance genes will enable transfer into high yielding cowpea varieties

An Idea for Generating Diversity Conversations: Physics Jeopardy and the Future Faces of Physics Kit

Science.gov (United States)

Rand, Kendra; White, Gary

2008-10-01

Is there a way to engage typical physics undergraduates in a conversation about under-represented groups in physics that doesn't result in rolled-eyes or fingers-in-the-ears? The Society of Physics Students (SPS) has begun an experiment using a jeopardy-like game at physics meetings in an attempt to generate conversations about diversity. The physics jeopardy game is part of a "Future Faces of Physics" kit that includes a variety of materials that are of interest to those wanting to address under-represented audiences in physics, such as video clips exhibiting common physics words in sign language, tactile representations of the lunar surface for blind students, guidelines regarding lab procedures for the wheel-chair bound, and the book, Einstein on Race and Racism with a challenge letter directed at SPS chapters from the authors. While attempts to assess the impact of the game are modest, we report anecdotally some of the qualitative features seen in the discussions when the game is played. We also strive to indulge in a few physics jeopardy game moments to give a sense of how the game works. If you are hosting a meeting, large or small, and would like to receive this kit for use at your meeting, notify Kendra Rand, SPS Program Coordinator at krand@aip.org.

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

Science.gov (United States)

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing. Here, we evaluated ten of these methods (BacH, BacHum-UCD, B. thetaiotaomic...

Deletion of the budBAC operon in Klebsiella pneumoniae to understand the physiological role of 2,3-butanediol biosynthesis.

Science.gov (United States)

Jeong, Daun; Yang, Jeongmo; Lee, Soojin; Kim, Borim; Um, Youngsoon; Kim, Youngrok; Ha, Kyoung-Su; Lee, Jinwon

2016-05-18

Klebsiella pneumoniae is known to produce 2,3-butanediol (2,3-BDO), a valuable chemical. In K. pneumoniae, the 2,3-BDO operon (budBAC) is involved in the production of 2,3-BDO. To observe the physiological role of the 2,3-BDO operon in a mixed acid fermentation, we constructed a budBAC-deleted strain (SGSB109). The production of extracellular metabolites, CO2 emission, carbon distribution, and NADH/NAD(+) balance of SGSB109 were compared with the parent strain (SGSB100). When comparing the carbon distribution at 15 hr, four significant differences were observed: in 2,3-BDO biosynthesis, lactate and acetate production (lactate and acetate production increased 2.3-fold and 4.1-fold in SGSB109 compared to SGSB100), CO2 emission (higher in SGSB100), and carbon substrate uptake (higher in SGSB100). Previous studies on the inactivation of the 2,3-BDO operon were focused on the increase of 1,3-propanediol production. Few studies have been done observing the role of 2,3-BDO biosynthesis. This study provides a prime insight into the role of 2,3-BDO biosynthesis of K. pneumoniae.

Deep Learning-Based Data Forgery Detection in Automatic Generation Control

Energy Technology Data Exchange (ETDEWEB)

Zhang, Fengli [Univ. of Arkansas, Fayetteville, AR (United States); Li, Qinghua [Univ. of Arkansas, Fayetteville, AR (United States)

2017-10-09

Automatic Generation Control (AGC) is a key control system in the power grid. It is used to calculate the Area Control Error (ACE) based on frequency and tie-line power flow between balancing areas, and then adjust power generation to maintain the power system frequency in an acceptable range. However, attackers might inject malicious frequency or tie-line power flow measurements to mislead AGC to do false generation correction which will harm the power grid operation. Such attacks are hard to be detected since they do not violate physical power system models. In this work, we propose algorithms based on Neural Network and Fourier Transform to detect data forgery attacks in AGC. Different from the few previous work that rely on accurate load prediction to detect data forgery, our solution only uses the ACE data already available in existing AGC systems. In particular, our solution learns the normal patterns of ACE time series and detects abnormal patterns caused by artificial attacks. Evaluations on the real ACE dataset show that our methods have high detection accuracy.

MCPLOTS: a particle physics resource based on volunteer computing

International Nuclear Information System (INIS)

Karneyeu, A.; Mijovic, L.; Prestel, S.; Skands, P.Z.

2014-01-01

The mcplots.cern.ch web site (mcplots) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the hepdata online database of experimental results and on the rivet Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the lhc rate at home 2.0 platform. (orig.)

MCPLOTS. A particle physics resource based on volunteer computing

Energy Technology Data Exchange (ETDEWEB)

Karneyeu, A. [Joint Inst. for Nuclear Research, Moscow (Russian Federation); Mijovic, L. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Irfu/SPP, CEA-Saclay, Gif-sur-Yvette (France); Prestel, S. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Lund Univ. (Sweden). Dept. of Astronomy and Theoretical Physics; Skands, P.Z. [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

2013-07-15

The mcplots.cern.ch web site (MCPLOTS) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the HEPDATA online database of experimental results and on the RIVET Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the LHC rate at HOME 2.0 platform.

MCPLOTS. A particle physics resource based on volunteer computing

International Nuclear Information System (INIS)

Karneyeu, A.; Mijovic, L.; Prestel, S.

2013-07-01

The mcplots.cern.ch web site (MCPLOTS) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the HEPDATA online database of experimental results and on the RIVET Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the LHC rate at HOME 2.0 platform.

A rule-based software test data generator

Science.gov (United States)

Deason, William H.; Brown, David B.; Chang, Kai-Hsiung; Cross, James H., II

1991-01-01

Rule-based software test data generation is proposed as an alternative to either path/predicate analysis or random data generation. A prototype rule-based test data generator for Ada programs is constructed and compared to a random test data generator. Four Ada procedures are used in the comparison. Approximately 2000 rule-based test cases and 100,000 randomly generated test cases are automatically generated and executed. The success of the two methods is compared using standard coverage metrics. Simple statistical tests showing that even the primitive rule-based test data generation prototype is significantly better than random data generation are performed. This result demonstrates that rule-based test data generation is feasible and shows great promise in assisting test engineers, especially when the rule base is developed further.

Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

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You Frank M

2010-06-01

Full Text Available Abstract Background Physical maps employing libraries of bacterial artificial chromosome (BAC clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum, Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete

Reactors physics. Bases of nuclear physics

International Nuclear Information System (INIS)

Diop, Ch.M.

2006-01-01

The aim of nuclear reactor physics is to quantify the relevant macroscopic data for the characterization of the neutronic state of a reactor core and to evaluate the effects of radiations (neutrons and gamma radiations) on organic matter and on inorganic materials. This first article presents the bases of nuclear physics in the context of nuclear reactors: 1 - reactor physics and nuclear physics; 2 - atomic nucleus - basic definitions: nucleus constituents, dimensions and mass of the atomic nucleus, mass defect, binding energy and stability of the nucleus, strong interaction, nuclear momentums of nucleons and nucleus; 3 - nucleus stability and radioactivity: equation of evolution with time - radioactive decay law; alpha decay, stability limit of spontaneous fission, beta decay, electronic capture, gamma emission, internal conversion, radioactivity, two-body problem and notion of radioactive equilibrium. (J.S.)

Transposon Invasion of the Paramecium Germline Genome Countered by a Domesticated PiggyBac Transposase and the NHEJ Pathway

Science.gov (United States)

Dubois, Emeline; Bischerour, Julien; Marmignon, Antoine; Mathy, Nathalie; Régnier, Vinciane; Bétermier, Mireille

2012-01-01

Sequences related to transposons constitute a large fraction of extant genomes, but insertions within coding sequences have generally not been tolerated during evolution. Thanks to their unique nuclear dimorphism and to their original mechanism of programmed DNA elimination from their somatic nucleus (macronucleus), ciliates are emerging model organisms for the study of the impact of transposable elements on genomes. The germline genome of the ciliate Paramecium, located in its micronucleus, contains thousands of short intervening sequences, the IESs, which interrupt 47% of genes. Recent data provided support to the hypothesis that an evolutionary link exists between Paramecium IESs and Tc1/mariner transposons. During development of the macronucleus, IESs are excised precisely thanks to the coordinated action of PiggyMac, a domesticated piggyBac transposase, and of the NHEJ double-strand break repair pathway. A PiggyMac homolog is also required for developmentally programmed DNA elimination in another ciliate, Tetrahymena. Here, we present an overview of the life cycle of these unicellular eukaryotes and of the developmentally programmed genome rearrangements that take place at each sexual cycle. We discuss how ancient domestication of a piggyBac transposase might have allowed Tc1/mariner elements to spread throughout the germline genome of Paramecium, without strong counterselection against insertion within genes. PMID:22888464

Minimal-post-processing 320-Gbps true random bit generation using physical white chaos.

Science.gov (United States)

Wang, Anbang; Wang, Longsheng; Li, Pu; Wang, Yuncai

2017-02-20

Chaotic external-cavity semiconductor laser (ECL) is a promising entropy source for generation of high-speed physical random bits or digital keys. The rate and randomness is unfortunately limited by laser relaxation oscillation and external-cavity resonance, and is usually improved by complicated post processing. Here, we propose using a physical broadband white chaos generated by optical heterodyning of two ECLs as entropy source to construct high-speed random bit generation (RBG) with minimal post processing. The optical heterodyne chaos not only has a white spectrum without signature of relaxation oscillation and external-cavity resonance but also has a symmetric amplitude distribution. Thus, after quantization with a multi-bit analog-digital-convertor (ADC), random bits can be obtained by extracting several least significant bits (LSBs) without any other processing. In experiments, a white chaos with a 3-dB bandwidth of 16.7 GHz is generated. Its entropy rate is estimated as 16 Gbps by single-bit quantization which means a spectrum efficiency of 96%. With quantization using an 8-bit ADC, 320-Gbps physical RBG is achieved by directly extracting 4 LSBs at 80-GHz sampling rate.

Physical degradation assessment of generator station cables

International Nuclear Information System (INIS)

Stonkus, D.J.

1988-01-01

Preliminary studies of fossil-fired and nuclear generator station cables indicate that the low voltage PVC insulated cables are in relatively good condition. The insulation is flexible and in the case of nuclear cables can withstand a design basis event after nearly 15 years of service. Cables insulated with styrene butadiene rubber have been found embrittled and cables insulated with SBR should be closely inspected in any plant assurance program. Thermal analysis using oxidative induction technique shows promise to indicate cable insulation degradation. Long term reliability assurance and plant life extension studies are being actively pursued at Ontario Hydro. A major study is currently underway to extend the life of the oldest operating fossil-fuel station, the 8-unit, 2400 MW Lakeview TGS in operation since the 1960s. Plant life assurance programs have been initiated at the 2000 MW Lambton TGS in operation since 1969, and for the oldest operating nuclear plant, Pickering NGS A in operation since the early 1970s. As cables are considered one of the critical components in a generator station due to the extreme difficulty and cost of cable replacement, test programs have been initiated to evaluate the physical degradation of the cables and relate the results to electrical diagnostic tests and to chemical changes. The decommissioning of two small nuclear stations, the 20 MW Nuclear Power Demonstration (NPD) and the 200 MW Douglas Point NGS, which were placed in service in 1962 and 1967 respectively, will provide an opportunity to perform destructive electrical and physical evaluation on field aged cables

Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

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Sahu Binod B

2012-01-01

Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

Study of physical properties, gas generation and gas retention in simulated Hanford waste

International Nuclear Information System (INIS)

Bryan, S.A.; Pederson, L.R.; Scheele, R.D.

1993-04-01

The purpose of this study was to establish the chemical and physical processes responsible for the generation and retention of gases within high-level waste from Tank 101-SY on the Hanford Site. This research, conducted using simulated waste on a laboratory scale, supports the development of mitigation/remediation strategies for Tank 101-SY. Simulated waste formulations are based on actual waste compositions. Selected physical properties of the simulated waste are compared to properties of actual Tank 101-SY waste samples. Laboratory studies using aged simulated waste show that significant gas generation occurs thermally at current tank temperatures (∼60 degrees C). Gas compositions include the same gases produced in actual tank waste, primarily N 2 , N 2 O, and H 2 . Gas stoichiometries have been shown to be greatly influenced by several organic and inorganic constituents within the simulated waste. Retention of gases in the simulated waste is in the form of bubble attachment to solid particles. This attachment phenomenon is related to the presence of organic constituents (HEDTA, EDTA, and citrate) of the simulated waste. A mechanism is discussed that relates the gas bubble/particle interactions to the partially hydrophobic surface produced on the solids by the organic constituents

Comparison of BacT/Alert FAN and FAN Plus Bottles with Conventional Medium for Culturing Cerebrospinal Fluid.

Science.gov (United States)

Yoo, In Young; Chun, Sejong; Song, Dong Joon; Huh, Hee Jae; Lee, Nam Yong

2016-11-01

We compared the BacT/Alert system FAN and FAN Plus media to conventional media for culturing cerebrospinal fluid (CSF) with 2,545 samples. FAN/FAN Plus bottles showed better performance for isolating microorganisms in CSF than conventional media (positive rate, 7.2% [182/2,545] versus 3.1% [80/2,545]). The incremental recovery rate of Cryptococcus neoformans from FAN Plus bottles was higher than that from FAN bottles. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus.

Science.gov (United States)

Telgmann-Rauber, Alexa; Jamsari, Ari; Kinney, Michael S; Pires, J Chris; Jung, Christian

2007-09-01

Asparagus officinalis L. is a dioecious plant. A region called the M-locus located on a pair of homomorphic sex chromosomes controls the sexual dimorphism in asparagus. The aim of this work was to clone the region determining sex in asparagus from its position in the genome. The structure of the region encompassing M should be investigated and compared to the sex-determining regions in other dioecious model species. To establish an improved basis for physical mapping, a high-resolution genetic map was enriched with AFLP markers closely linked to the target locus by carrying out a bulked segregant analysis. By screening a BAC library with AFLP- and STS-markers followed by chromosome walking, a physical map with eight contigs could be established. However, the gaps between the contigs could not be closed due to a plethora of repetitive elements. Surprisingly, two of the contigs on one side of the M-locus did not overlap although they have been established with two markers, which mapped in a distance as low as 0.25 cM flanking the sex locus. Thus, the clustering of the markers indicates a reduced recombination frequency within the M-region. On the opposite side of the M-locus, a contig was mapped in a distance of 0.38 cM. Four closely linked BAC clones were partially sequenced and 64 putative ORFs were identified. Interestingly, only 25% of the ORFs showed sequence similarity to known proteins and ESTs. In addition, an accumulation of repetitive sequences and a low gene density was revealed in the sex-determining region of asparagus. Molecular cytogenetic and sequence analysis of BACs flanking the M-locus indicate that the BACs contain highly repetitive sequences that localize to centromeric and pericentromeric locations on all asparagus chromosomes, which hindered the localization of the M-locus to the single pair of sex chromosomes. We speculate that dioecious Silene, papaya and Asparagus species may represent three stages in the evolution of XX, XY sex

Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides.

Directory of Open Access Journals (Sweden)

Shuhong Ouyang

Full Text Available Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90 via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.

Generative Representations for the Automated Design of Modular Physical Robots

Science.gov (United States)

Hornby, Gregory S.; Lipson, Hod; Pollack, Jordan B.

2003-01-01

We will begin with a brief background of evolutionary robotics and related work, and demonstrate the scaling problem with our own prior results. Next we propose the use of an evolved generative representation as opposed to a non-generative representation. We describe this representation in detail as well as the evolutionary process that uses it. We then compare progress of evolved robots with and without the use of the grammar, and quantify the obtained advantage. Working two- dimensional and three-dimensional physical robots produced by the system are shown.

Construction of an infectious clone of canine herpesvirus genome as a bacterial artificial chromosome.

Science.gov (United States)

Arii, Jun; Hushur, Orkash; Kato, Kentaro; Kawaguchi, Yasushi; Tohya, Yukinobu; Akashi, Hiroomi

2006-04-01

Canine herpesvirus (CHV) is an attractive candidate not only for use as a recombinant vaccine to protect dogs from a variety of canine pathogens but also as a viral vector for gene therapy in domestic animals. However, developments in this area have been impeded by the complicated techniques used for eukaryotic homologous recombination. To overcome these problems, we used bacterial artificial chromosomes (BACs) to generate infectious BACs. Our findings may be summarized as follows: (i) the CHV genome (pCHV/BAC), in which a BAC flanked by loxP sites was inserted into the thymidine kinase gene, was maintained in Escherichia coli; (ii) transfection of pCHV/BAC into A-72 cells resulted in the production of infectious virus; (iii) the BAC vector sequence was almost perfectly excisable from the genome of the reconstituted virus CHV/BAC by co-infection with CHV/BAC and a recombinant adenovirus that expressed the Cre recombinase; and (iv) a recombinant virus in which the glycoprotein C gene was deleted was generated by lambda recombination followed by Flp recombination, which resulted in a reduction in viral titer compared with that of the wild-type virus. The infectious clone pCHV/BAC is useful for the modification of the CHV genome using bacterial genetics, and CHV/BAC should have multiple applications in the rapid generation of genetically engineered CHV recombinants and the development of CHV vectors for vaccination and gene therapy in domestic animals.

160 Gb/s OFDM transmission utilizing an all-optical symbol generator based on PLC

Science.gov (United States)

Liang, Xiaojun; Qiao, Yaojun; Li, Wei; Mei, Junyao; Qin, Yi

2009-11-01

We demonstrate a 160 Gb/s orthogonal frequency division multiplexing (OFDM) system using an all-optical symbol generator based on planar light circuit (PLC) technology. Excellent bit error rate (BER) is observed after long-distance transmission. The proposed symbol generator fundamentally eliminates the processing speed limits introduced by electronics and is suitable for high integration, making it physically realizable to build high-speed all-optical OFDM systems with a large number of subcarriers.

Generation of Mouse Haploid Somatic Cells by Small Molecules for Genome-wide Genetic Screening

Directory of Open Access Journals (Sweden)

Zheng-Quan He

2017-08-01

Full Text Available The recent success of derivation of mammalian haploid embryonic stem cells (haESCs has provided a powerful tool for large-scale functional analysis of the mammalian genome. However, haESCs rapidly become diploidized after differentiation, posing challenges for genetic analysis. Here, we show that the spontaneous diploidization of haESCs happens in metaphase due to mitotic slippage. Diploidization can be suppressed by small-molecule-mediated inhibition of CDK1 and ROCK. Through ROCK inhibition, we can generate haploid somatic cells of all three germ layers from haESCs, including terminally differentiated neurons. Using piggyBac transposon-based insertional mutagenesis, we generated a haploid neural cell library harboring genome-wide mutations for genetic screening. As a proof of concept, we screened for Mn2+-mediated toxicity and identified the Park2 gene. Our findings expand the applications of mouse haploid cell technology to somatic cell types and may also shed light on the mechanisms of ploidy maintenance.

BacMam Virus Transduced Cardiomyoblasts Can Be Used for Myocardial Transplantation Using AP-PEG-A Microcapsules: Molecular Cloning, Preparation, and In Vitro Analysis

Directory of Open Access Journals (Sweden)

Arghya Paul

2010-01-01

Full Text Available The potential of genetically modified cardiomyoblasts in treating damaged myocardium is well known. However, efficient delivery of these cells is of major concern during treatment. The limiting factors are the massive cell death that occurs soon after their intramyocardial transplantation into the beating heart. To address these problems, we generated recombinant baculoviruses (BacMam viruses which efficiently transduced cardiomyoblast cells under optimized conditions. These genetically modified cells were then protected in a new polymeric microcapsule using poly-ethylene-glycol (PEG, alginate, and poly-L-lysine (PLL polymers for efficient delivery. Results showed that microcapsules maintain cell viability and support cell proliferation for at least 30 days. The capsules exhibit strong immunoprotective potential and have high mechanical and osmotic stability with more than 70% intact capsules. The encased transduced cells showed a rapid transgene expression inside the capsule for at least 15 days. However, preclinical studies are needed to further explore its long-term functional benefits.

BacMam virus transduced cardiomyoblasts can be used for myocardial transplantation using AP-PEG-A microcapsules: molecular cloning, preparation, and in vitro analysis.

Science.gov (United States)

Paul, Arghya; Khan, Afshan Afsar; Shum-Tim, Dominique; Prakash, Satya

2010-01-01

The potential of genetically modified cardiomyoblasts in treating damaged myocardium is well known. However, efficient delivery of these cells is of major concern during treatment. The limiting factors are the massive cell death that occurs soon after their intramyocardial transplantation into the beating heart. To address these problems, we generated recombinant baculoviruses (BacMam viruses) which efficiently transduced cardiomyoblast cells under optimized conditions. These genetically modified cells were then protected in a new polymeric microcapsule using poly-ethylene-glycol (PEG), alginate, and poly-L-lysine (PLL) polymers for efficient delivery. Results showed that microcapsules maintain cell viability and support cell proliferation for at least 30 days. The capsules exhibit strong immunoprotective potential and have high mechanical and osmotic stability with more than 70% intact capsules. The encased transduced cells showed a rapid transgene expression inside the capsule for at least 15 days. However, preclinical studies are needed to further explore its long-term functional benefits.

Interactive physically-based sound simulation

Science.gov (United States)

Raghuvanshi, Nikunj

The realization of interactive, immersive virtual worlds requires the ability to present a realistic audio experience that convincingly compliments their visual rendering. Physical simulation is a natural way to achieve such realism, enabling deeply immersive virtual worlds. However, physically-based sound simulation is very computationally expensive owing to the high-frequency, transient oscillations underlying audible sounds. The increasing computational power of desktop computers has served to reduce the gap between required and available computation, and it has become possible to bridge this gap further by using a combination of algorithmic improvements that exploit the physical, as well as perceptual properties of audible sounds. My thesis is a step in this direction. My dissertation concentrates on developing real-time techniques for both sub-problems of sound simulation: synthesis and propagation. Sound synthesis is concerned with generating the sounds produced by objects due to elastic surface vibrations upon interaction with the environment, such as collisions. I present novel techniques that exploit human auditory perception to simulate scenes with hundreds of sounding objects undergoing impact and rolling in real time. Sound propagation is the complementary problem of modeling the high-order scattering and diffraction of sound in an environment as it travels from source to listener. I discuss my work on a novel numerical acoustic simulator (ARD) that is hundred times faster and consumes ten times less memory than a high-accuracy finite-difference technique, allowing acoustic simulations on previously-intractable spaces, such as a cathedral, on a desktop computer. Lastly, I present my work on interactive sound propagation that leverages my ARD simulator to render the acoustics of arbitrary static scenes for multiple moving sources and listener in real time, while accounting for scene-dependent effects such as low-pass filtering and smooth attenuation

Synthesis and Examination of Nanocomposites Based on Poly(2-hydroxyethyl methacrylate for Medicinal Use

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Olena S. Kukolevska

2017-02-01

Full Text Available Abstract Preparation of poly(2-hydroxyethyl methacrylate (PHEMA based nanocomposites using different approaches such as synthesis with water as the porogen, filling of polymer matrix by silica and formation of interpenetrating polymer networks with polyurethane was demonstrated. Incorporation of various biologically active compounds (BAC such as metronidazole, decamethoxin, zinc sulphate, silver nitrate or amino acids glycine and tryptophan into nanocomposites was achieved. BAC were introduced into the polymer matrix either (1 directly, or (2 with a solution of colloidal silica, or (3 through immobilization on silica (sol-densil. Morphology of prepared materials was investigated by laser scanning microscopy and low-vacuum scanning electron microscopy. In vacuum freeze-drying, prior imaging was proposed for improving visualization of the porous structure of composites. The interaction between PHEMA matrix and silica filler was investigated by IR spectroscopy. Adsorption of 2-hydroxyethyl methacrylate and BAC from aqueous solution on the silica surface was also examined. Phase composition and thermal stability of composites were studied by the differential thermogravimetry/differential thermal analysis. Release of BAC into water medium from prepared composites were shown to depend on the synthetic method and differed significantly. Obtained PHEMA-base materials which are characterized by controlled release of BAC have a strong potential for application in manufacturing of different surgical devices like implants, catheters and drainages.

Physics-Based Hazard Assessment for Critical Structures Near Large Earthquake Sources

Science.gov (United States)

Hutchings, L.; Mert, A.; Fahjan, Y.; Novikova, T.; Golara, A.; Miah, M.; Fergany, E.; Foxall, W.

2017-09-01

We argue that for critical structures near large earthquake sources: (1) the ergodic assumption, recent history, and simplified descriptions of the hazard are not appropriate to rely on for earthquake ground motion prediction and can lead to a mis-estimation of the hazard and risk to structures; (2) a physics-based approach can address these issues; (3) a physics-based source model must be provided to generate realistic phasing effects from finite rupture and model near-source ground motion correctly; (4) wave propagations and site response should be site specific; (5) a much wider search of possible sources of ground motion can be achieved computationally with a physics-based approach; (6) unless one utilizes a physics-based approach, the hazard and risk to structures has unknown uncertainties; (7) uncertainties can be reduced with a physics-based approach, but not with an ergodic approach; (8) computational power and computer codes have advanced to the point that risk to structures can be calculated directly from source and site-specific ground motions. Spanning the variability of potential ground motion in a predictive situation is especially difficult for near-source areas, but that is the distance at which the hazard is the greatest. The basis of a "physical-based" approach is ground-motion syntheses derived from physics and an understanding of the earthquake process. This is an overview paper and results from previous studies are used to make the case for these conclusions. Our premise is that 50 years of strong motion records is insufficient to capture all possible ranges of site and propagation path conditions, rupture processes, and spatial geometric relationships between source and site. Predicting future earthquake scenarios is necessary; models that have little or no physical basis but have been tested and adjusted to fit available observations can only "predict" what happened in the past, which should be considered description as opposed to prediction

Brucella detection in blood: comparison of the BacT/Alert standard aerobic bottle, BacT/Alert FAN aerobic bottle and BacT/Alert enhanced FAN aerobic bottle in simulated blood culture.

Science.gov (United States)

Sümerkan, B; Gökahmetoglu, S; Esel, D

2001-07-01

The objective of this study was to compare the performances of the standard aerobic bottle (StAe), FAN aerobic (FANAe) and enhanced FAN aerobic (E-FANAe) (the charcoal component of the FANAe was revised recently to improve the feasibility of Gram smear interpretation) blood culture bottles for BacT/Alert system for the detection of Brucella melitensis in simulated blood culture. Triplicate strains of eight clinical isolates of B. melitensis were studied. Each bottle was inoculated with 5 mL of freshly collected human blood at three different targeted bacterial inocula (10(1), 10(2) and 10(3) CFU/bottle). All bottles were monitored for up to 21 days or until they became positive. The results of time to detection (TTD) on the eight B. melitensis samples were as follows: at 10(1) CFU/bottle, the E-FANAe had a mean TTD significantly shorter than the StAe (48 h vs. 56.2 h, P StAe (41.2 h and 40 h vs. 45.6 h, P StAe, FANAe and E-FANAe were 96, 83 and 58%, respectively. At 10(3) CFU/bottle, the reproducibilities of StAe, FANAe and E-FANAe were 95, 95 and 91%, respectively. Positive results for the presence of bacteria in Gram smears were confirmed in 68% of StAe, 54% of FANAe and 90% of E-FANAe. In case of suspected brucellosis, the combination of one StAe bottle and one E-FANAe bottle seems to provide the highest and fastest recovery of the organism.

Utilizing HPC Network Technologies in High Energy Physics Experiments

CERN Document Server

AUTHOR|(CDS)2088631; The ATLAS collaboration

2017-01-01

Because of their performance characteristics high-performance fabrics like Infiniband or OmniPath are interesting technologies for many local area network applications, including data acquisition systems for high-energy physics experiments like the ATLAS experiment at CERN. This paper analyzes existing APIs for high-performance fabrics and evaluates their suitability for data acquisition systems in terms of performance and domain applicability. The study finds that existing software APIs for high-performance interconnects are focused on applications in high-performance computing with specific workloads and are not compatible with the requirements of data acquisition systems. To evaluate the use of high-performance interconnects in data acquisition systems a custom library, NetIO, is presented and compared against existing technologies. NetIO has a message queue-like interface which matches the ATLAS use case better than traditional HPC APIs like MPI. The architecture of NetIO is based on a interchangeable bac...

Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH.

Science.gov (United States)

Guillaud-Bataille, Marine; Valent, Alexander; Soularue, Pascal; Perot, Christine; Inda, Maria Mar; Receveur, Aline; Smaïli, Sadek; Roest Crollius, Hugues; Bénard, Jean; Bernheim, Alain; Gidrol, Xavier; Danglot, Gisèle

2004-07-29

Comparative genomic hybridization to bacterial artificial chromosome (BAC)-arrays (array-CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci, and the reliable detection of local one-copy-level variations. We report a genome-wide amplification method allowing the same measurement sensitivity, using 1 ng of starting genomic DNA, instead of the classical 1 microg usually necessary. Using a discrete series of DNA fragments, we defined the parameters adapted to the most faithful ligation-mediated PCR amplification and the limits of the technique. The optimized protocol allows a 3000-fold DNA amplification, retaining the quantitative characteristics of the initial genome. Validation of the amplification procedure, using DNA from 10 tumour cell lines hybridized to BAC-arrays of 1500 spots, showed almost perfectly superimposed ratios for the non-amplified and amplified DNAs. Correlation coefficients of 0.96 and 0.99 were observed for regions of low-copy-level variations and all regions, respectively (including in vivo amplified oncogenes). Finally, labelling DNA using two nucleotides bearing the same fluorophore led to a significant increase in reproducibility and to the correct detection of one-copy gain or loss in >90% of the analysed data, even for pseudotriploid tumour genomes.

Design of time interval generator based on hybrid counting method

International Nuclear Information System (INIS)

Yao, Yuan; Wang, Zhaoqi; Lu, Houbing; Chen, Lian; Jin, Ge

2016-01-01

Time Interval Generators (TIGs) are frequently used for the characterizations or timing operations of instruments in particle physics experiments. Though some “off-the-shelf” TIGs can be employed, the necessity of a custom test system or control system makes the TIGs, being implemented in a programmable device desirable. Nowadays, the feasibility of using Field Programmable Gate Arrays (FPGAs) to implement particle physics instrumentation has been validated in the design of Time-to-Digital Converters (TDCs) for precise time measurement. The FPGA-TDC technique is based on the architectures of Tapped Delay Line (TDL), whose delay cells are down to few tens of picosecond. In this case, FPGA-based TIGs with high delay step are preferable allowing the implementation of customized particle physics instrumentations and other utilities on the same FPGA device. A hybrid counting method for designing TIGs with both high resolution and wide range is presented in this paper. The combination of two different counting methods realizing an integratable TIG is described in detail. A specially designed multiplexer for tap selection is emphatically introduced. The special structure of the multiplexer is devised for minimizing the different additional delays caused by the unpredictable routings from different taps to the output. A Kintex-7 FPGA is used for the hybrid counting-based implementation of a TIG, providing a resolution up to 11 ps and an interval range up to 8 s.

Design of time interval generator based on hybrid counting method

Energy Technology Data Exchange (ETDEWEB)

Yao, Yuan [State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Wang, Zhaoqi [State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Lu, Houbing [State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Hefei Electronic Engineering Institute, Hefei 230037 (China); Chen, Lian [State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Jin, Ge, E-mail: goldjin@ustc.edu.cn [State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

2016-10-01

Time Interval Generators (TIGs) are frequently used for the characterizations or timing operations of instruments in particle physics experiments. Though some “off-the-shelf” TIGs can be employed, the necessity of a custom test system or control system makes the TIGs, being implemented in a programmable device desirable. Nowadays, the feasibility of using Field Programmable Gate Arrays (FPGAs) to implement particle physics instrumentation has been validated in the design of Time-to-Digital Converters (TDCs) for precise time measurement. The FPGA-TDC technique is based on the architectures of Tapped Delay Line (TDL), whose delay cells are down to few tens of picosecond. In this case, FPGA-based TIGs with high delay step are preferable allowing the implementation of customized particle physics instrumentations and other utilities on the same FPGA device. A hybrid counting method for designing TIGs with both high resolution and wide range is presented in this paper. The combination of two different counting methods realizing an integratable TIG is described in detail. A specially designed multiplexer for tap selection is emphatically introduced. The special structure of the multiplexer is devised for minimizing the different additional delays caused by the unpredictable routings from different taps to the output. A Kintex-7 FPGA is used for the hybrid counting-based implementation of a TIG, providing a resolution up to 11 ps and an interval range up to 8 s.

Formulation of Biocides Increases Antimicrobial Potency and Mitigates the Enrichment of Nonsusceptible Bacteria in Multispecies Biofilms

Science.gov (United States)

Forbes, Sarah; Cowley, Nicola; Mistry, Hitesh; Amézquita, Alejandro

2017-01-01

ABSTRACT The current investigation aimed to generate data to inform the development of risk assessments of biocide usage. Stabilized domestic drain biofilm microcosms were exposed daily over 6 months to increasing concentrations (0.01% to 1%) of the biocide benzalkonium chloride (BAC) in a simple aqueous solution (BAC-s) or in a complex formulation (BAC-f) representative of a domestic cleaning agent. Biofilms were analyzed by culture, differentiating by bacterial functional group and by BAC or antibiotic susceptibility. Bacterial isolates were identified by 16S rRNA sequencing, and changes in biofilm composition were assessed by high-throughput sequencing. Exposure to BAC-f resulted in significantly larger reductions in levels of viable bacteria than exposure to BAC-s, while bacterial diversity greatly decreased during exposure to both BAC-s and BAC-f, as evidenced by sequencing and viable counts. Increases in the abundance of bacteria exhibiting reduced antibiotic or BAC susceptibility following exposure to BAC at 0.1% were significantly greater for BAC-s than BAC-f. Bacteria with reduced BAC and antibiotic susceptibility were generally suppressed by higher BAC concentrations, and formulation significantly enhanced this effect. Significant decreases in the antimicrobial susceptibility of bacteria isolated from the systems before and after long-term BAC exposure were not detected. In summary, dose-dependent suppression of bacterial viability by BAC was enhanced by formulation. Biocide exposure decreased bacterial diversity and transiently enriched populations of organisms with lower antimicrobial susceptibility, and the effects were subsequently suppressed by exposure to 1% BAC-f, the concentration most closely reflecting deployment in formulated products. IMPORTANCE Assessment of the risks of biocide use has been based mainly on the exposure of axenic cultures of bacteria to biocides in simple aqueous solutions. The current investigation aimed to assess the

Physical Layer Secret-Key Generation Scheme for Transportation Security Sensor Network.

Science.gov (United States)

Yang, Bin; Zhang, Jianfeng

2017-06-28

Wireless Sensor Networks (WSNs) are widely used in different disciplines, including transportation systems, agriculture field environment monitoring, healthcare systems, and industrial monitoring. The security challenge of the wireless communication link between sensor nodes is critical in WSNs. In this paper, we propose a new physical layer secret-key generation scheme for transportation security sensor network. The scheme is based on the cooperation of all the sensor nodes, thus avoiding the key distribution process, which increases the security of the system. Different passive and active attack models are analyzed in this paper. We also prove that when the cooperative node number is large enough, even when the eavesdropper is equipped with multiple antennas, the secret-key is still secure. Numerical results are performed to show the efficiency of the proposed scheme.

Antibacterial Efficiency of Benzalkonium Chloride Base Disinfectant According To European Standard 13727, Chemical Analysis and Validation Studies

OpenAIRE

Yıldırım, Çinel; Çelenk, Veysel

2018-01-01

Antibacterial Efficiency of Benzalkonium Chloride Base Disinfectant According To European Standard 13727, Chemical Analysis and Validation Studies This study was aimed to provide principle of the chemical analyses, antibacterial efficiency test and validation procedures of the most commonly used benzalkonium chloride (BAC) base disinfectant as a biocide. Disinfectant which comprised 20 % BAC concentration was used as a prototype product and active substance was verified with chemical analysis...

Industrial innovation based on fundamental physics

International Nuclear Information System (INIS)

Kogelschatz, Ulrich

2002-01-01

Industrial innovation frequently results from an improved understanding of basic physics. Scientific discoveries quite often lead to engineering inventions that have not been the target of the original investigations. Examples are given from the field of plasma physics and plasma technology. High voltage circuit breakers, ozone generators, high power CO 2 lasers, excimer lamps, and plasma display panels have profited substantially from initially purely scientific investigations. In the meantime they have reached multi-billion dollar market shares

Health Physics Positions Data Base

International Nuclear Information System (INIS)

Kerr, G.D.; Borges, T.; Stafford, R.S.; Lu, P.Y.; Carter, D.

1992-05-01

The Health Physics Positions (HPPOS) Data Base of the Nuclear Regulatory Commission (NRC) is a collection of summaries of NRC staff positions on a wide range of topics in radiation protection (health physics). The bases for the data base are 247 original documents in the form of letters, memoranda, and excerpts from technical reports. The HPPOS Data Base was developed by the NRC Headquarters and Regional Offices to help ensure uniformity in inspections, enforcement, and licensing actions

Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar

Directory of Open Access Journals (Sweden)

Jurman Irena

2010-03-01

Full Text Available Abstract Background Most of the grapevine (Vitis vinifera L. cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. Results We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. Conclusions We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.

The Next Generation Science Standards: A Focus on Physical Science

Science.gov (United States)

Krajcik, Joe

2013-01-01

This article describes ways to adapt U.S. science curriculum to the U.S. National Research Council (NRC) "Framework for K-12 Science Education" and "Next Generation of Science Standards" (NGSS), noting their focus on teaching the physical sciences. The overall goal of the Framework and NGSS is to help all learners develop the…

An evaluation of three processing methods and the effect of reduced culture times for faster direct identification of pathogens from BacT/ALERT blood cultures by MALDI-TOF MS.

Science.gov (United States)

Loonen, A J M; Jansz, A R; Stalpers, J; Wolffs, P F G; van den Brule, A J C

2012-07-01

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is a fast and reliable method for the identification of bacteria from agar media. Direct identification from positive blood cultures should decrease the time to obtaining the result. In this study, three different processing methods for the rapid direct identification of bacteria from positive blood culture bottles were compared. In total, 101 positive aerobe BacT/ALERT bottles were included in this study. Aliquots from all bottles were used for three bacterial processing methods, i.e. the commercially available Bruker's MALDI Sepsityper kit, the commercially available Molzym's MolYsis Basic5 kit and a centrifugation/washing method. In addition, the best method was used to evaluate the possibility of MALDI application after a reduced incubation time of 7 h of Staphylococcus aureus- and Escherichia coli-spiked (1,000, 100 and 10 colony-forming units [CFU]) aerobe BacT/ALERT blood cultures. Sixty-six (65%), 51 (50.5%) and 79 (78%) bottles were identified correctly at the species level when the centrifugation/washing method, MolYsis Basic 5 and Sepsityper were used, respectively. Incorrect identification was obtained in 35 (35%), 50 (49.5%) and 22 (22%) bottles, respectively. Gram-positive cocci were correctly identified in 33/52 (64%) of the cases. However, Gram-negative rods showed a correct identification in 45/47 (96%) of all bottles when the Sepsityper kit was used. Seven hours of pre-incubation of S. aureus- and E. coli-spiked aerobe BacT/ALERT blood cultures never resulted in reliable identification with MALDI-TOF MS. Sepsityper is superior for the direct identification of microorganisms from aerobe BacT/ALERT bottles. Gram-negative pathogens show better results compared to Gram-positive bacteria. Reduced incubation followed by MALDI-TOF MS did not result in faster reliable identification.

Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae.

Science.gov (United States)

Zuriaga, Elena; Molina, Laura; Badenes, María Luisa; Romero, Carlos

2012-06-01

S-locus products (S-RNase and F-box proteins) are essential for the gametophytic self-incompatibility (GSI) specific recognition in Prunus. However, accumulated genetic evidence suggests that other S-locus unlinked factors are also required for GSI. For instance, GSI breakdown was associated with a pollen-part mutation unlinked to the S-locus in the apricot (Prunus armeniaca L.) cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported. A segregation distortion loci mapping strategy, based on a selectively genotyped population, was used to map the M-locus. In addition, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping oligonucleotides probes, and BAC-end sequences (BES) were blasted against Rosaceae genomes to perform micro-synteny analysis. The M-locus was mapped to the distal part of chr.3 flanked by two SSR markers within an interval of 1.8 cM corresponding to ~364 Kb in the peach (Prunus persica L. Batsch) genome. In the integrated genetic-physical map of this region, BES were mapped against the peach scaffold_3 and BACs were anchored to the apricot map. Micro-syntenic blocks were detected in apple (Malus × domestica Borkh.) LG17/9 and strawberry (Fragaria vesca L.) FG6 chromosomes. The M-locus fine-scale mapping provides a solid basis for self-compatibility marker-assisted selection and for positional cloning of the underlying gene, a necessary goal to elucidate the pollen rejection mechanism in Prunus. In a wider context, the syntenic regions identified in peach, apple and strawberry might be useful to interpret GSI evolution in Rosaceae.

Rhipicephalus (Boophilus) microplus strain Deutsch, 5 BAC clone sequencing, including two encoding Cytochrome P450s and one encoding CzEst9 carboxylesterase

Science.gov (United States)

The cattle tick, Rhipicephalus (Boophilus) microplus, has a genome over 2.4 times the size of the human genome, and with over 70% of repetitive DNA, this genome would prove very costly to sequence at today's prices and difficult to assemble and analyze. BAC clones give insight into the genome struct...

Efficient generation of long-distance conditional alleles using recombineering and a dual selection strategy in replicate plates

Directory of Open Access Journals (Sweden)

Liang Hong-Erh

2009-07-01

Full Text Available Abstract Background Conditional knockout mice are a useful tool to study the function of gene products in a tissue-specific or inducible manner. Classical approaches to generate targeting vectors for conditional alleles are often limited by the availability of suitable restriction sites. Furthermore, plasmid-based targeting vectors can only cover a few kB of DNA which precludes the generation of targeting vectors where the two loxP sites are placed far apart. These limitations have been overcome in the recent past by using homologous recombination of bacterial artificial chromosomes (BACs in Escherichia coli to produce large targeting vector containing two different loxP-flanked selection cassettes so that a single targeting event is sufficient to introduce loxP-sites a great distances into the mouse genome. However, the final targeted allele should be free of selection cassettes and screening for correct removal of selection cassettes can be a laborious task. Therefore, we developed a new strategy to rapidly identify ES cells containing the desired allele. Results Using BAC recombineering we generated a single targeting vector which contained two different selection cassettes that were flanked by loxP-loxP sites or by FRT-FRT/loxP sites so that they could be deleted sequentially by Cre- and FLPe-recombinases, respectively. Transfected ES cells were first selected in the presence of both antibiotics in vitro before correctly targeted clones were identified by Southern blot. After transfection of a Cre recombinase expression plasmid ES cell clones were selected on replicate plates to identify those clones which maintained the FRT-FRT/loxP flanked cassette and lost the loxP-loxP flanked cassette. Using this strategy facilitated the identification of ES cell clones containing the desired allele before blastocyst injection. Conclusion The strategy of ES cell cultures in replicate plates proved to be very efficient in identifying ES cells that had

Promoting physical activity through video games based on self-behavioral models

Directory of Open Access Journals (Sweden)

M. Abreu

2014-06-01

Full Text Available Physical activity is an essential component of a healthy lifestyle, promoting health and preventing various chronic diseases. Despite this evidence, it is known that the younger generations invest much time in sedentary activities such as television viewing, videogames or reading, which potentially can lead to an increase in the prevalence of sedentary behaviors in adulthood. These behaviors have been identified as factors of disturbance in the balance between intake and energy expenditure, contributing to the increasing number of overweight and obese people and, further downstream, the prevalence of cardiovascular diseases and cancer (among others. The emergence of the Exergames (videogames that involve physical activity, either light, moderate or intense and games whose narrative alters pathogenic beliefs, contrary to the potential risk effect of gaming, by combining the playful context of videogames with physical activity (mild to intense. This study discusses some salutogenic principles of a new generation of videogames where virtual and real come together, ipromoting salutogenic behavioral patterns, namely through greater energy expenditure. The ideas are based on theoretical and empirical contributions from health psychology, in addition to the potential of computer technology applicable to traditional videogames and Exergames.

Les Houches guidebook to Monte Carlo generators for hadron collider physics

International Nuclear Information System (INIS)

Dobbs, Matt A.; Frixione, Stefano; Laenen, Eric; Tollefson, Kirsten

2004-01-01

Recently the collider physics community has seen significant advances in the formalisms and implementations of event generators. This review is a primer of the methods commonly used for the simulation of high energy physics events at particle colliders. We provide brief descriptions, references, and links to the specific computer codes which implement the methods. The aim is to provide an overview of the available tools, allowing the reader to ascertain which tool is best for a particular application, but also making clear the limitations of each tool

Les Houches guidebook to Monte Carlo generators for hadron collider physics

CERN Document Server

Dobbs, M.A.; Laenen, Eric; Tollefson, K.; Baer, H.; Boos, E.; Cox, B.; Engel, R.; Giele, W.; Huston, J.; Ilyin, S.; Kersevan, B.; Krauss, F.; Kurihara, Y.; Lonnblad, L.; Maltoni, F.; Mangano, M.; Odaka, S.; Richardson, P.; Ryd, A.; Sjostrand, T.; Skands, Peter Z.; Was, Z.; Webber, B.R.; Zeppenfeld, D.

2005-01-01

Recently the collider physics community has seen significant advances in the formalisms and implementations of event generators. This review is a primer of the methods commonly used for the simulation of high energy physics events at particle colliders. We provide brief descriptions, references, and links to the specific computer codes which implement the methods. The aim is to provide an overview of the available tools, allowing the reader to ascertain which tool is best for a particular application, but also making clear the limitations of each tool.

Towards the generation of random bits at terahertz rates based on a chaotic semiconductor laser

International Nuclear Information System (INIS)

Kanter, Ido; Aviad, Yaara; Reidler, Igor; Cohen, Elad; Rosenbluh, Michael

2010-01-01

Random bit generators (RBGs) are important in many aspects of statistical physics and crucial in Monte-Carlo simulations, stochastic modeling and quantum cryptography. The quality of a RBG is measured by the unpredictability of the bit string it produces and the speed at which the truly random bits can be generated. Deterministic algorithms generate pseudo-random numbers at high data rates as they are only limited by electronic hardware speed, but their unpredictability is limited by the very nature of their deterministic origin. It is widely accepted that the core of any true RBG must be an intrinsically non-deterministic physical process, e.g. measuring thermal noise from a resistor. Owing to low signal levels, such systems are highly susceptible to bias, introduced by amplification, and to small nonrandom external perturbations resulting in a limited generation rate, typically less than 100M bit/s. We present a physical random bit generator, based on a chaotic semiconductor laser, having delayed optical feedback, which operates reliably at rates up to 300Gbit/s. The method uses a high derivative of the digitized chaotic laser intensity and generates the random sequence by retaining a number of the least significant bits of the high derivative value. The method is insensitive to laser operational parameters and eliminates the necessity for all external constraints such as incommensurate sampling rates and laser external cavity round trip time. The randomness of long bit strings is verified by standard statistical tests.

Towards the generation of random bits at terahertz rates based on a chaotic semiconductor laser

Science.gov (United States)

Kanter, Ido; Aviad, Yaara; Reidler, Igor; Cohen, Elad; Rosenbluh, Michael

2010-06-01

Random bit generators (RBGs) are important in many aspects of statistical physics and crucial in Monte-Carlo simulations, stochastic modeling and quantum cryptography. The quality of a RBG is measured by the unpredictability of the bit string it produces and the speed at which the truly random bits can be generated. Deterministic algorithms generate pseudo-random numbers at high data rates as they are only limited by electronic hardware speed, but their unpredictability is limited by the very nature of their deterministic origin. It is widely accepted that the core of any true RBG must be an intrinsically non-deterministic physical process, e.g. measuring thermal noise from a resistor. Owing to low signal levels, such systems are highly susceptible to bias, introduced by amplification, and to small nonrandom external perturbations resulting in a limited generation rate, typically less than 100M bit/s. We present a physical random bit generator, based on a chaotic semiconductor laser, having delayed optical feedback, which operates reliably at rates up to 300Gbit/s. The method uses a high derivative of the digitized chaotic laser intensity and generates the random sequence by retaining a number of the least significant bits of the high derivative value. The method is insensitive to laser operational parameters and eliminates the necessity for all external constraints such as incommensurate sampling rates and laser external cavity round trip time. The randomness of long bit strings is verified by standard statistical tests.

Restoring San Xavier del Bac, "Our Church": Tohono O'odham Work to Restore the 200-Year-Old Church Built by Their Ancestors.

Science.gov (United States)

Fontana, Bernard L.

1995-01-01

The Tohono O'odham built Mission San Xavier del Bac for Franciscan missionaries in the late 1700s and have protected and cared for it through changing circumstances ever since. As part of a massive restoration project, outstanding experts have been restoring the church's painted and sculpted interior and training local Tohono O'odham to be…

Entropy Generation and Human Aging: Lifespan Entropy and Effect of Physical Activity Level

Science.gov (United States)

Silva, Carlos; Annamalai, Kalyan

2008-06-01

The first and second laws of thermodynamics were applied to biochemical reactions typical of human metabolism. An open-system model was used for a human body. Energy conservation, availability and entropy balances were performed to obtain the entropy generated for the main food components. Quantitative results for entropy generation were obtained as a function of age using the databases from the U.S. Food and Nutrition Board (FNB) and Centers for Disease Control and Prevention (CDC), which provide energy requirements and food intake composition as a function of age, weight and stature. Numerical integration was performed through human lifespan for different levels of physical activity. Results were presented and analyzed. Entropy generated over the lifespan of average individuals (natural death) was found to be 11,404 kJ/ºK per kg of body mass with a rate of generation three times higher on infants than on the elderly. The entropy generated predicts a life span of 73.78 and 81.61 years for the average U.S. male and female individuals respectively, which are values that closely match the average lifespan from statistics (74.63 and 80.36 years). From the analysis of the effect of different activity levels, it is shown that entropy generated increases with physical activity, suggesting that exercise should be kept to a “healthy minimum” if entropy generation is to be minimized.

Tailored motivational message generation: A model and practical framework for real-time physical activity coaching.

Science.gov (United States)

Op den Akker, Harm; Cabrita, Miriam; Op den Akker, Rieks; Jones, Valerie M; Hermens, Hermie J

2015-06-01

This paper presents a comprehensive and practical framework for automatic generation of real-time tailored messages in behavior change applications. Basic aspects of motivational messages are time, intention, content and presentation. Tailoring of messages to the individual user may involve all aspects of communication. A linear modular system is presented for generating such messages. It is explained how properties of user and context are taken into account in each of the modules of the system and how they affect the linguistic presentation of the generated messages. The model of motivational messages presented is based on an analysis of existing literature as well as the analysis of a corpus of motivational messages used in previous studies. The model extends existing 'ontology-based' approaches to message generation for real-time coaching systems found in the literature. Practical examples are given on how simple tailoring rules can be implemented throughout the various stages of the framework. Such examples can guide further research by clarifying what it means to use e.g. user targeting to tailor a message. As primary example we look at the issue of promoting daily physical activity. Future work is pointed out in applying the present model and framework, defining efficient ways of evaluating individual tailoring components, and improving effectiveness through the creation of accurate and complete user- and context models. Copyright © 2015 Elsevier Inc. All rights reserved.

Physics Based Modeling of Compressible Turbulance

Science.gov (United States)

2016-11-07

AFRL-AFOSR-VA-TR-2016-0345 PHYSICS -BASED MODELING OF COMPRESSIBLE TURBULENCE PARVIZ MOIN LELAND STANFORD JUNIOR UNIV CA Final Report 09/13/2016...on the AFOSR project (FA9550-11-1-0111) entitled: Physics based modeling of compressible turbulence. The period of performance was, June 15, 2011...by ANSI Std. Z39.18 Page 1 of 2FORM SF 298 11/10/2016https://livelink.ebs.afrl.af.mil/livelink/llisapi.dll PHYSICS -BASED MODELING OF COMPRESSIBLE

Digital lock-in amplifier based on soundcard interface for physics laboratory

Science.gov (United States)

Sinlapanuntakul, J.; Kijamnajsuk, P.; Jetjamnong, C.; Chotikaprakhan, S.

2017-09-01

The purpose of this paper is to develop a digital lock-in amplifier based on soundcard interface for undergraduate physics laboratory. Both series and parallel RLC circuit laboratory are tested because of its well-known, easy to understand and simple confirm. The sinusoidal signal at the frequency of 10 Hz - 15 kHz is generated to the circuits. The amplitude and phase of the voltage drop across the resistor, R are measured in 10 step decade. The signals from soundcard interface and lock-in amplifier are compared. The results give a good correlation. It indicates that the design digital lock-in amplifier is promising for undergraduate physic laboratory.

Algebras Generated by Geometric Scalar Forms and their Applications in Physics and Social Sciences

International Nuclear Information System (INIS)

Keller, Jaime

2008-01-01

The present paper analyzes the consequences of defining that the geometric scalar form is not necessarily quadratic, but in general K-atic, that is obtained from the K th power of the linear form, requiring {e i ;i = 1,...,N;(e i ) K = 1} and d-vector Σ i x i e i . We consider the algebras which are thus generated, for positive integer K, a generalization of the geometric algebras we know under the names of Clifford or Grassmann algebras. We then obtain a set of geometric K-algebras. We also consider the generalization of special functions of geometry which corresponds to the K-order scalar forms (as trigonometric functions and other related geometric functions which are based on the use of quadratic forms). We present an overview of the use of quadratic forms in physics as in our general theory, we have called START. And, in order to give an introduction to the use of the more general K-algebras and to the possible application to sciences other than physics, the application to social sciences is considered.For the applications to physics we show that quadratic spaces are a fundamental clue to understand the structure of theoretical physics (see, for example, Keller in ICNAAM 2005 and 2006).

NATURAL MUTATION IN THE GENE OF RESPONSE REGULATOR BgrR RESULTING IN REPRESSION OF Bac PROTEIN SYNTHESIS, A PATHOGENICITY FACTOR OF STREPTOCOCCUS AGALACTIAE

Directory of Open Access Journals (Sweden)

A. S. Rozhdestvenskaya

2013-01-01

Full Text Available Abstract. Streptococcus agalactiae can cause variety of diseases of newborns and adults. For successful colonization of different human tissues and organs as well as for suppression of the host immune system S. agalactiae expresses numerous virulence factors. For coordinated expression of the virulence genes S. agalactiae employs regulatory molecules including regulatory proteins of two-component systems. Results of the present study demonstrated that in S. agalactiae strain A49V the natural mutation in the brgR gene encoding for BgrR regulatory protein, which is component of regulatory system BgrRS, resulted in the repression of Bac protein synthesis, a virulence factor of S. agalactiae. A single nucleotide deletion in the bgrR gene has caused a shift of the reading frame and the changes in the primary, secondary and tertiary structures of the BgrR protein. The loss of functional activity of BgrR protein in A49V strain and repression of Bac protein synthesis have increased virulence of the strain in experimental animal streptococcal infection.

Toward Inverse Control of Physics-Based Sound Synthesis

Science.gov (United States)

Pfalz, A.; Berdahl, E.

2017-05-01

Long Short-Term Memory networks (LSTMs) can be trained to realize inverse control of physics-based sound synthesizers. Physics-based sound synthesizers simulate the laws of physics to produce output sound according to input gesture signals. When a user's gestures are measured in real time, she or he can use them to control physics-based sound synthesizers, thereby creating simulated virtual instruments. An intriguing question is how to program a computer to learn to play such physics-based models. This work demonstrates that LSTMs can be trained to accomplish this inverse control task with four physics-based sound synthesizers.

Next Generation Driver for Attosecond and Laser-plasma Physics.

Science.gov (United States)

Rivas, D E; Borot, A; Cardenas, D E; Marcus, G; Gu, X; Herrmann, D; Xu, J; Tan, J; Kormin, D; Ma, G; Dallari, W; Tsakiris, G D; Földes, I B; Chou, S-W; Weidman, M; Bergues, B; Wittmann, T; Schröder, H; Tzallas, P; Charalambidis, D; Razskazovskaya, O; Pervak, V; Krausz, F; Veisz, L

2017-07-12

The observation and manipulation of electron dynamics in matter call for attosecond light pulses, routinely available from high-order harmonic generation driven by few-femtosecond lasers. However, the energy limitation of these lasers supports only weak sources and correspondingly linear attosecond studies. Here we report on an optical parametric synthesizer designed for nonlinear attosecond optics and relativistic laser-plasma physics. This synthesizer uniquely combines ultra-relativistic focused intensities of about 10 20  W/cm 2 with a pulse duration of sub-two carrier-wave cycles. The coherent combination of two sequentially amplified and complementary spectral ranges yields sub-5-fs pulses with multi-TW peak power. The application of this source allows the generation of a broad spectral continuum at 100-eV photon energy in gases as well as high-order harmonics in relativistic plasmas. Unprecedented spatio-temporal confinement of light now permits the investigation of electric-field-driven electron phenomena in the relativistic regime and ultimately the rise of next-generation intense isolated attosecond sources.

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

Czech Academy of Sciences Publication Activity Database

Bartoš, Jan; Paux, E.; Kofler, R.; Havránková, Miroslava; Kopecký, David; Suchánková, Pavla; Šafář, Jan; Šimková, Hana; Town, C.D.; Lelley, T.; Feuillet, C.; Doležel, Jaroslav

2008-01-01

Roč. 8, č. 95 (2008), s. 1-12 ISSN 1471-2229 R&D Projects: GA ČR GP521/06/P412; GA ČR GD521/05/H013; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC libraries * flow-sorted chromosomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.030, year: 2008

Entropy Generation and Human Aging: Lifespan Entropy and Effect of Physical Activity Level

Directory of Open Access Journals (Sweden)

Kalyan Annamalai

2008-06-01

Full Text Available The first and second laws of thermodynamics were applied to biochemical reactions typical of human metabolism. An open-system model was used for a human body. Energy conservation, availability and entropy balances were performed to obtain the entropy generated for the main food components. Quantitative results for entropy generation were obtained as a function of age using the databases from the U.S. Food and Nutrition Board (FNB and Centers for Disease Control and Prevention (CDC, which provide energy requirements and food intake composition as a function of age, weight and stature. Numerical integration was performed through human lifespan for different levels of physical activity. Results were presented and analyzed. Entropy generated over the lifespan of average individuals (natural death was found to be 11,404 kJ/ºK per kg of body mass with a rate of generation three times higher on infants than on the elderly. The entropy generated predicts a life span of 73.78 and 81.61 years for the average U.S. male and female individuals respectively, which are values that closely match the average lifespan from statistics (74.63 and 80.36 years. From the analysis of the effect of different activity levels, it is shown that entropy generated increases with physical activity, suggesting that exercise should be kept to a “healthy minimum” if entropy generation is to be minimized.

Validity of physical activity and cardiorespiratory fitness in the Danish cohort 'Diet, Cancer and Health - Next Generations'

DEFF Research Database (Denmark)

Lerche, Lene; Olsen, Anja; Petersen, Kristina Elin Nielsen

2017-01-01

). When validating the questionnaire-derived measures of PA, leisure time physical activity was not correlated with VO2 max. Positive correlations were found for sports overall, but these were only significant for men: total hours per week of sports (r=0.26), MET-hours per week of sports (r=0......Valid assessments of physical activity (PA) and cardiorespiratory fitness (CRF) is essential in epidemiological studies to define dose-response relationship for e.g. formulating thorough recommendations of an appropriate pattern of PA to maintain good health. The aim of this study was to validate...... the Danish step test, the physical activity questionnaire Active-Q and self-rated fitness against directly measured maximal oxygen uptake (VO2 max). A population based subsample (n=125) was included from the 'Diet, Cancer and Health - Next Generations' (DCH-NG) cohort which is under establishment. Validity...

Semantic attributes based texture generation

Science.gov (United States)

Chi, Huifang; Gan, Yanhai; Qi, Lin; Dong, Junyu; Madessa, Amanuel Hirpa

2018-04-01

Semantic attributes are commonly used for texture description. They can be used to describe the information of a texture, such as patterns, textons, distributions, brightness, and so on. Generally speaking, semantic attributes are more concrete descriptors than perceptual features. Therefore, it is practical to generate texture images from semantic attributes. In this paper, we propose to generate high-quality texture images from semantic attributes. Over the last two decades, several works have been done on texture synthesis and generation. Most of them focusing on example-based texture synthesis and procedural texture generation. Semantic attributes based texture generation still deserves more devotion. Gan et al. proposed a useful joint model for perception driven texture generation. However, perceptual features are nonobjective spatial statistics used by humans to distinguish different textures in pre-attentive situations. To give more describing information about texture appearance, semantic attributes which are more in line with human description habits are desired. In this paper, we use sigmoid cross entropy loss in an auxiliary model to provide enough information for a generator. Consequently, the discriminator is released from the relatively intractable mission of figuring out the joint distribution of condition vectors and samples. To demonstrate the validity of our method, we compare our method to Gan et al.'s method on generating textures by designing experiments on PTD and DTD. All experimental results show that our model can generate textures from semantic attributes.

Analysis of pre-service physics teacher skills designing simple physics experiments based technology

Science.gov (United States)

Susilawati; Huda, C.; Kurniawan, W.; Masturi; Khoiri, N.

2018-03-01

Pre-service physics teacher skill in designing simple experiment set is very important in adding understanding of student concept and practicing scientific skill in laboratory. This study describes the skills of physics students in designing simple experiments based technologicall. The experimental design stages include simple tool design and sensor modification. The research method used is descriptive method with the number of research samples 25 students and 5 variations of simple physics experimental design. Based on the results of interviews and observations obtained the results of pre-service physics teacher skill analysis in designing simple experimental physics charged technology is good. Based on observation result, pre-service physics teacher skill in designing simple experiment is good while modification and sensor application are still not good. This suggests that pre-service physics teacher still need a lot of practice and do experiments in designing physics experiments using sensor modifications. Based on the interview result, it is found that students have high enough motivation to perform laboratory activities actively and students have high curiosity to be skilled at making simple practicum tool for physics experiment.

Compare the influence of several methods dehydrate of cajuput (Melaleuca cajuputi) honey from Bac Lieu - Vietnam

Science.gov (United States)

Nam, Nguyen Xuan; Phuc, Nguyen Chi; Oanh, Huynh Ngoc; Hien, Phan Phuoc

2017-09-01

The aim of this research was exhaustive to valuate the effects of 5 methods used to dehydrate of cajuput honey from Bac Lieu - Vietnam include thermal, microwave, ultrasonic wave, silicagel, vacuum processing on water content of honey. Beside that, comparing the effects on honey quality with the industrial-scale processing. The main honey quality paramenters (reducing sugar (RS), hydroxymethylfurfural (HMF), diastase number (DN), water and colour) of cajuput honey were analyzed. RS content were analyzed by DNS method, HMF under AOAC 980.23, diastase activity based on AOAC 958.09, water content according to AOAC 969.38B and colour parameters (L*, a*, b*) were established in the CIE system. The physico-chemical characteristics of fresh honey was as follows: water content 23.18%, RS 717.42 mg/g, HMF 4.24 mg/kg, DN 4.85 mg/kg, colour parameters L*a*b* 39.51-10.51-31.81. The results of the analysis showed that excepts ultrasonic wave processing (22.93%), the other methods allowed to dehydrate of cajuput honey (thermal - 18.73%, microwave - 16.87%, silicagel - 17.86%, vacuum - 17.35% and industrial-scale processing - 16.85%).

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

Science.gov (United States)

Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

2011-04-01

Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

Physics and Novel Schemes of Laser Radiation Pressure Acceleration for Quasi-monoenergetic Proton Generation

Energy Technology Data Exchange (ETDEWEB)

Liu, Chuan S. [Univ. of Maryland, College Park, MD (United States). Dept. of Physics; Shao, Xi [Univ. of Maryland, College Park, MD (United States)

2016-06-14

The main objective of our work is to provide theoretical basis and modeling support for the design and experimental setup of compact laser proton accelerator to produce high quality proton beams tunable with energy from 50 to 250 MeV using short pulse sub-petawatt laser. We performed theoretical and computational studies of energy scaling and Raleigh--Taylor instability development in laser radiation pressure acceleration (RPA) and developed novel RPA-based schemes to remedy/suppress instabilities for high-quality quasimonoenergetic proton beam generation as we proposed. During the project period, we published nine peer-reviewed journal papers and made twenty conference presentations including six invited talks on our work. The project supported one graduate student who received his PhD degree in physics in 2013 and supported two post-doctoral associates. We also mentored three high school students and one undergraduate student of physics major by inspiring their interests and having them involved in the project.

Impact of Physical Abuse on Internalizing Behavior Across Generations.

Science.gov (United States)

Esteves, Kyle; Gray, Sarah A O; Theall, Katherine P; Drury, Stacy S

2017-10-01

This study investigated the multigenerational impact of mothers' own exposure to physical maltreatment on internalizing symptoms in her child after accounting for her parenting practices, depression, and the child's own exposure to stressful life events. Children ( n = 101, ages 5-16), predominantly African American, were recruited into this cross sectional study using ethnographic mapping and targeted sampling for high-risk neighborhoods. Mothers reported retrospectively on their own exposure to physical maltreatment in childhood, their parenting practices, as well as current depressive symptoms. Maternal report of her child's exposure to stressful life events and child behavior was also collected. Maternal childhood exposure to physical maltreatment was significantly associated with her child's internalizing symptoms ( p = .004); this effect remained after accounting for child sex, maternal depressive symptoms, harsh parenting practices, and the child's own exposure to stressful life events. Formal tests of mediation through these pathways were non-significant. Findings suggest mothers' experience of childhood maltreatment contributes uniquely to children's internalizing symptoms, potentially through previously uncharacterized pathways. Examination of additional behavioral, psychosocial and biological pathways may help better describe the multi-generational effects of child maltreatment.

Co-oxidation of carcinogenic polycyclic aromatic hydrocarbons with some biologically active compounds (BAC)

Energy Technology Data Exchange (ETDEWEB)

Gubergrits, M.Y.

1978-09-01

Oxidation of benzo(a)pyrene (BP) initiated by UV or gamma irradiation was promoted by benz(a)anthracene and 7,12-dimethylbenz(a)anthracene (DMBA) and inhibited by pyrene, dibenz(a,c)anthracene, and asymmetric benz(a)antharacene. The effects of these BAC commonly occurring together with BP in industrial wastes, increased with their concentrations. Phenol and 3-methylcholanthrene strongly promoted BP oxidation when present at low concentrations and inhibited it at high concentrations. Consistent promoting effect was also observed in BP co-oxidation with adipic acid, ..cap alpha..-naphthoflavon, and vitamin E, whereas succinic, azelaic, ferulic, gallic, and chlorogenic acids, rutin, and vitamin C acted as inhibitors. Most saturated dicarboxylic acids studied did not affect BP oxidation at 1:1 acid-BP molar ratio. The kinetics of 7,12-DMBA photooxidation inhibition by some metabolic intermediates, e.g., DMBA endo-peroxide, were also studied.

Welcome to America, welcome to college: Comparing the effects of immigrant generation and college generation on physical science and engineering career

Science.gov (United States)

Lung, Florin; Potvin, Geoff; Sonnert, Gerhard; Sadler, Philip M.

2013-01-01

Students enter college with social, cultural, and economic resources (well described Bourdieu's concepts of habitus and capital) that significantly impact their goals, actions, and successes. Two important determinants of the amount and type of resources available to students are their immigrant generation and college generation status. Drawing on a national sample of 6860 freshmen enrolled in college English, we compare and contrast the effects of immigrant generation with those of college generation status on physical science and engineering career intentions to explore some of the challenges faced by the first in the family to become an American and/or go to college.

Development of canine herpesvirus based antifertility vaccines for foxes using bacterial artificial chromosomes.

Science.gov (United States)

Strive, Tanja; Hardy, Christopher M; French, Nigel; Wright, John D; Nagaraja, Nitin; Reubel, Gerhard H

2006-02-13

Using bacterial artificial chromosome (BAC) technology, a canine herpesvirus (CHV)-based recombinant vaccine vector was produced for the development of an antifertility vaccine for foxes. Infectious viruses were recovered following transfection of canid cells with a BAC plasmid carrying the complete CHV genome. In vitro growth characteristics of BAC-derived viruses were similar to that of wildtype (wt)-CHV. Two recombinant antigens, fox zona pellucida protein subunit 3 (fZPC) and enhanced green fluorescent protein (EGFP) as control antigen, were inserted into thymidine kinase (TK) locus of the CHV genome and shown to be efficiently expressed in vitro. Inoculation of foxes with transgenic CHVs induced CHV specific antibodies, but was innocuous and failed to elicit transgene-specific antibody responses. Infectious virus or viral DNA was not detected in mucosal secretions or tissues of vaccinated foxes. The CHV-BAC system proved to be a quick and reliable method to manipulate the CHV genome. It will help to readily apply changes in the vector design in order to improve virus replication in vivo.

Generation of Unbiased Ionospheric Corrections in Brazilian Region for GNSS positioning based on SSR concept

Science.gov (United States)

Monico, J. F. G.; De Oliveira, P. S., Jr.; Morel, L.; Fund, F.; Durand, S.; Durand, F.

2017-12-01

Mitigation of ionospheric effects on GNSS (Global Navigation Satellite System) signals is very challenging, especially for GNSS positioning applications based on SSR (State Space Representation) concept, which requires the knowledge of spatial correlated errors with considerable accuracy level (centimeter). The presence of satellite and receiver hardware biases on GNSS measurements difficult the proper estimation of ionospheric corrections, reducing their physical meaning. This problematic can lead to ionospheric corrections biased of several meters and often presenting negative values, which is physically not possible. In this contribution, we discuss a strategy to obtain SSR ionospheric corrections based on GNSS measurements from CORS (Continuous Operation Reference Stations) Networks with minimal presence of hardware biases and consequently physical meaning. Preliminary results are presented on generation and application of such corrections for simulated users located in Brazilian region under high level of ionospheric activity.

A Method for the Realization of an Interruption Generator Based on Voltage Source Converters

Directory of Open Access Journals (Sweden)

Junhui Li

2017-10-01

Full Text Available In this paper we described the structure and working principle of an interruption generator based on voltage source converters (VSCs. The main circuit parameters of the VSCs are determined according to the target of power transfer capability, harmonic suppression, and dynamic response capability. A state feedback linearization method in nonlinear differential geometry theory was used for dq axis current decoupling, based on the mathematical model used in the dq coordinate system of VSCs. The direct current control strategy was adopted to achieve the independent regulation of active power and reactive power. The proportional integral (PI link was used to optimize the dynamic performance of the controller, and PI parameters were adjusted. Disturbance voltage waves were generated by the regular sampling method. PSCAD/EMTDC simulation results and physical prototype experiments showed that the device could generate various disturbance voltage waveforms steadily, and had good dynamic and steady-state performance.

Analyses of karyotypes and comparative physical locations of the ...

African Journals Online (AJOL)

The frequencies of signal detection of the marker, RG556 and the BAC clone, 44B4, were 8.0 and 41.3% in O. sativa, while 9.0 and 42.3% in O. officinalis, respectively. Based on a comparative RFLP map of a wild rice, O. officinalis and O. sativa, comparative analyses of karyotypes of O. officinalis were demonstrated firstly ...

Candidate gene database and transcript map for peach, a model species for fruit trees.

Science.gov (United States)

Horn, Renate; Lecouls, Anne-Claire; Callahan, Ann; Dandekar, Abhaya; Garay, Lilibeth; McCord, Per; Howad, Werner; Chan, Helen; Verde, Ignazio; Main, Doreen; Jung, Sook; Georgi, Laura; Forrest, Sam; Mook, Jennifer; Zhebentyayeva, Tatyana; Yu, Yeisoo; Kim, Hye Ran; Jesudurai, Christopher; Sosinski, Bryon; Arús, Pere; Baird, Vance; Parfitt, Dan; Reighard, Gregory; Scorza, Ralph; Tomkins, Jeffrey; Wing, Rod; Abbott, Albert Glenn

2005-05-01

Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single "best hit" match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).].

Physics data bases and their use

International Nuclear Information System (INIS)

Gault, F.D.

1981-01-01

The physics data base is examined as a passive archive, an active marketing device for new data, and as a resource centre producing informal commentary through the work of its compilers. The relative importance to its function of wide availability through networks, ease of retrieval of the desired data, and packages for manipulating and displaying the information retrieved is considered. Throughout examples are drawn from various compilations including the elementary particle data bases maintained by the Particle Data Group in the UK at the Rutherford and Appleton Laboratory. The future of the physics data base in supporting but not supplanting the publication of papers on experimental physics is discussed. (orig.)

Physical trust-based persistent authentication

DEFF Research Database (Denmark)

Fujita, Masahiro; Jensen, Christian D.; Arimura, Shiori

2015-01-01

propose a new type of persistent authentication, called Persistent Authentication Based On physical Trust (PABOT). PABOT uses a context of “physical trust relationship” that is built by visual contact between users, and thus can offer a persistent authentication mechanism with better usability and higher...

Inquiry based learning in physical education

DEFF Research Database (Denmark)

Østergaard, Lars Domino

2014-01-01

The present project is a case study founded on the decreasing motivation and engagement in physical education. The project suggests inquiry based learning (IBL) as an educational methodology. This may help to turn the trend as IBL has shown to engage and motivate students at different educational...... levels and within different subjects. In this pilot research project performed at a physical education teacher education program, qualitative methods were chosen to investigate students’ motivation and engagement within an IBL-unit in physical education and to accentuate challenges, advantages...... and disadvantages within the IBL-methodology in relation to students’ motivation. Instructed in guided inquiry, 32 students of physical education in a teacher training college worked with inquiry based learning in physical education over a four week period. During the IBL-unit, qualitative data such as the students...

A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

Directory of Open Access Journals (Sweden)

Giattina Emily

2011-09-01

Full Text Available Abstract Background Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. Results A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF of Bacterial Artificial Chromosome (BAC clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. Conclusions A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes. All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account

A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

Science.gov (United States)

2011-01-01

Background Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. Results A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. Conclusions A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes. All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123

BAC and RNA sequencing reveal the brown planthopper resistance gene BPH15 in a recombination cold spot that mediates a unique defense mechanism.

Science.gov (United States)

Lv, Wentang; Du, Ba; Shangguan, Xinxin; Zhao, Yan; Pan, Yufang; Zhu, Lili; He, Yuqing; He, Guangcun

2014-08-11

Brown planthopper (BPH, Nilaparvata lugens Stål), is the most destructive phloem-feeding insect pest of rice (Oryza sativa). The BPH-resistance gene BPH15 has been proved to be effective in controlling the pest and widely applied in rice breeding programs. Nevertheless, molecular mechanism of the resistance remain unclear. In this study, we narrowed down the position of BPH15 on chromosome 4 and investigated the transcriptome of BPH15 rice after BPH attacked. We analyzed 13,000 BC2F2 plants of cross between susceptible rice TN1 and the recombinant inbred line RI93 that carrying the BPH15 gene from original resistant donor B5. BPH15 was mapped to a 0.0269 cM region on chromosome 4, which is 210-kb in the reference genome of Nipponbare. Sequencing bacterial artificial chromosome (BAC) clones that span the BPH15 region revealed that the physical size of BPH15 region in resistant rice B5 is 580-kb, much bigger than the corresponding region in the reference genome of Nipponbare. There were 87 predicted genes in the BPH15 region in resistant rice. The expression profiles of predicted genes were analyzed. Four jacalin-related lectin proteins genes and one LRR protein gene were found constitutively expressed in resistant parent and considered the candidate genes of BPH15. The transcriptomes of resistant BPH15 introgression line and the susceptible recipient line were analyzed using high-throughput RNA sequencing. In total, 2,914 differentially expressed genes (DEGs) were identified. BPH-responsive transcript profiles were distinct between resistant and susceptible plants and between the early stage (6 h after infestation, HAI) and late stage (48 HAI). The key defense mechanism was related to jasmonate signaling, ethylene signaling, receptor kinase, MAPK cascades, Ca(2+) signaling, PR genes, transcription factors, and protein posttranslational modifications. Our work combined BAC and RNA sequencing to identify candidate genes of BPH15 and revealed the resistance mechanism

LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

Directory of Open Access Journals (Sweden)

Feuillet Catherine

2010-11-01

Full Text Available Abstract Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC software, which often results in short contig lengths (of 3-5 clones before merging as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs. Results To address these problems, we propose a novel approach that: (i reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly

Enabling full-field physics-based optical proximity correction via dynamic model generation

Science.gov (United States)

Lam, Michael; Clifford, Chris; Raghunathan, Ananthan; Fenger, Germain; Adam, Kostas

2017-07-01

As extreme ultraviolet lithography becomes closer to reality for high volume production, its peculiar modeling challenges related to both inter and intrafield effects have necessitated building an optical proximity correction (OPC) infrastructure that operates with field position dependency. Previous state-of-the-art approaches to modeling field dependency used piecewise constant models where static input models are assigned to specific x/y-positions within the field. OPC and simulation could assign the proper static model based on simulation-level placement. However, in the realm of 7 and 5 nm feature sizes, small discontinuities in OPC from piecewise constant model changes can cause unacceptable levels of edge placement errors. The introduction of dynamic model generation (DMG) can be shown to effectively avoid these dislocations by providing unique mask and optical models per simulation region, allowing a near continuum of models through the field. DMG allows unique models for electromagnetic field, apodization, aberrations, etc. to vary through the entire field and provides a capability to precisely and accurately model systematic field signatures.

Combination of statistical and physically based methods to assess shallow slide susceptibility at the basin scale

Science.gov (United States)

Oliveira, Sérgio C.; Zêzere, José L.; Lajas, Sara; Melo, Raquel

2017-07-01

Approaches used to assess shallow slide susceptibility at the basin scale are conceptually different depending on the use of statistical or physically based methods. The former are based on the assumption that the same causes are more likely to produce the same effects, whereas the latter are based on the comparison between forces which tend to promote movement along the slope and the counteracting forces that are resistant to motion. Within this general framework, this work tests two hypotheses: (i) although conceptually and methodologically distinct, the statistical and deterministic methods generate similar shallow slide susceptibility results regarding the model's predictive capacity and spatial agreement; and (ii) the combination of shallow slide susceptibility maps obtained with statistical and physically based methods, for the same study area, generate a more reliable susceptibility model for shallow slide occurrence. These hypotheses were tested at a small test site (13.9 km2) located north of Lisbon (Portugal), using a statistical method (the information value method, IV) and a physically based method (the infinite slope method, IS). The landslide susceptibility maps produced with the statistical and deterministic methods were combined into a new landslide susceptibility map. The latter was based on a set of integration rules defined by the cross tabulation of the susceptibility classes of both maps and analysis of the corresponding contingency tables. The results demonstrate a higher predictive capacity of the new shallow slide susceptibility map, which combines the independent results obtained with statistical and physically based models. Moreover, the combination of the two models allowed the identification of areas where the results of the information value and the infinite slope methods are contradictory. Thus, these areas were classified as uncertain and deserve additional investigation at a more detailed scale.

Physics of steam generators and visit of Saint-Marcel plant

International Nuclear Information System (INIS)

Gillet, N.; Gloaguen, C.; Holcblat, A.; Borsoi, L.; Adobes, A.; David, F.; Greiner, E.; Pascal-Ribot, S.; Gauchet, J.P.; Mercier, L.; Leomy, F.

2004-01-01

This document gathers the transparencies presented at the 6. technical session of the French nuclear energy society (SFEN) in June 2004. The main topic was the physics of steam generators: 1 - description (G. Paudroux, J.Y. Guena, M. Petit); 2 - thermo-hydraulics (A. Holcblat, F. David, S. Pascal-Ribot); 3 - mechanics (N. Gillet, L. Borsoi, A. Adobes); 4 - monitoring and maintenance means (J.P. Gauchet, L. Mercier, F. Leomy); 5 - replacement (C. Gloaguen, E. Greiner). (J.S.)

Automated mass spectrum generation for new physics

CERN Document Server

Alloul, Adam; De Causmaecker, Karen; Fuks, Benjamin; Rausch de Traubenberg, Michel

2013-01-01

We describe an extension of the FeynRules package dedicated to the automatic generation of the mass spectrum associated with any Lagrangian-based quantum field theory. After introducing a simplified way to implement particle mixings, we present a new class of FeynRules functions allowing both for the analytical computation of all the model mass matrices and for the generation of a C++ package, dubbed ASperGe. This program can then be further employed for a numerical evaluation of the rotation matrices necessary to diagonalize the field basis. We illustrate these features in the context of the Two-Higgs-Doublet Model, the Minimal Left-Right Symmetric Standard Model and the Minimal Supersymmetric Standard Model.

Implementation of a RANLUX Based Pseudo-Random Number Generator in FPGA Using VHDL and Impulse C

OpenAIRE

Agnieszka Dąbrowska-Boruch; Grzegorz Gancarczyk; Kazimierz Wiatr

2014-01-01

Monte Carlo simulations are widely used e.g. in the field of physics and molecular modelling. The main role played in these is by the high performance random number generators, such as RANLUX or MERSSENE TWISTER. In this paper the authors introduce the world's first implementation of the RANLUX algorithm on an FPGA platform for high performance computing purposes. A significant speed-up of one generator instance over 60 times, compared with a graphic card based solution, can be noticed. Compa...

Physics-based Space Weather Forecasting in the Project for Solar-Terrestrial Environment Prediction (PSTEP) in Japan

Science.gov (United States)

Kusano, K.

2016-12-01

Project for Solar-Terrestrial Environment Prediction (PSTEP) is a Japanese nation-wide research collaboration, which was recently launched. PSTEP aims to develop a synergistic interaction between predictive and scientific studies of the solar-terrestrial environment and to establish the basis for next-generation space weather forecasting using the state-of-the-art observation systems and the physics-based models. For this project, we coordinate the four research groups, which develop (1) the integration of space weather forecast system, (2) the physics-based solar storm prediction, (3) the predictive models of magnetosphere and ionosphere dynamics, and (4) the model of solar cycle activity and its impact on climate, respectively. In this project, we will build the coordinated physics-based model to answer the fundamental questions concerning the onset of solar eruptions and the mechanism for radiation belt dynamics in the Earth's magnetosphere. In this paper, we will show the strategy of PSTEP, and discuss about the role and prospect of the physics-based space weather forecasting system being developed by PSTEP.

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

OpenAIRE

Zuccolo, Andrea; Bowers, John E; Estill, James C; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, Jos? Luis; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; Duarte, Jill; Tang, Haibao; Ayyampalayam, Saravanaraj; Rounsley, Steve; Kudrna, Dave

2011-01-01

Background Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome....

QCAPUF: QCA-based physically unclonable function as a hardware security primitive

Science.gov (United States)

Abutaleb, M. M.

2018-04-01

Physically unclonable functions (PUFs) are increasingly used as innovative security primitives to provide the hardware authentication and identification as well as the secret key generation based on unique and random variations in identically fabricated devices. Security and low power have appeared to become two crucial necessities to modern designs. As an emerging nanoelectronic technology, a quantum-dot cellular automata (QCA) can achieve ultra-low power consumption as well as an extremely small area for implementing digital designs. However, there are various classes of permanent defects that can happen during the manufacture of QCA devices. The recent extensive research has been focused on how to eliminate errors in QCA structures resulting from fabrication variances. By a completely different vision, to turn this disadvantage into an advantage, this paper presents a novel QCA-based PUF (QCAPUF) architecture to exploit the unique physical characteristics of fabricated QCA cells in order to produce different hardware fingerprint instances. This architecture is composed of proposed logic and interconnect blocks that have critical vulnerabilities and perform unexpected logical operations. The behaviour of QCAPUF is thoroughly analysed through physical relations and simulations. Results confirm that the proposed QCAPUF has state of the art PUF characteristics in the QCA technology. This paper will serve as a basis for further research into QCA-based hardware security primitives and applications.

A physical action potential generator: design, implementation and evaluation.

Science.gov (United States)

Latorre, Malcolm A; Chan, Adrian D C; Wårdell, Karin

2015-01-01

The objective was to develop a physical action potential generator (Paxon) with the ability to generate a stable, repeatable, programmable, and physiological-like action potential. The Paxon has an equivalent of 40 nodes of Ranvier that were mimicked using resin embedded gold wires (Ø = 20 μm). These nodes were software controlled and the action potentials were initiated by a start trigger. Clinically used Ag-AgCl electrodes were coupled to the Paxon for functional testing. The Paxon's action potential parameters were tunable using a second order mathematical equation to generate physiologically relevant output, which was accomplished by varying the number of nodes involved (1-40 in incremental steps of 1) and the node drive potential (0-2.8 V in 0.7 mV steps), while keeping a fixed inter-nodal timing and test electrode configuration. A system noise floor of 0.07 ± 0.01 μV was calculated over 50 runs. A differential test electrode recorded a peak positive amplitude of 1.5 ± 0.05 mV (gain of 40x) at time 196.4 ± 0.06 ms, including a post trigger delay. The Paxon's programmable action potential like signal has the possibility to be used as a validation test platform for medical surface electrodes and their attached systems.

Profiling physical activity motivation based on self-determination theory: a cluster analysis approach.

Science.gov (United States)

Friederichs, Stijn Ah; Bolman, Catherine; Oenema, Anke; Lechner, Lilian

2015-01-01

In order to promote physical activity uptake and maintenance in individuals who do not comply with physical activity guidelines, it is important to increase our understanding of physical activity motivation among this group. The present study aimed to examine motivational profiles in a large sample of adults who do not comply with physical activity guidelines. The sample for this study consisted of 2473 individuals (31.4% male; age 44.6 ± 12.9). In order to generate motivational profiles based on motivational regulation, a cluster analysis was conducted. One-way analyses of variance were then used to compare the clusters in terms of demographics, physical activity level, motivation to be active and subjective experience while being active. Three motivational clusters were derived based on motivational regulation scores: a low motivation cluster, a controlled motivation cluster and an autonomous motivation cluster. These clusters differed significantly from each other with respect to physical activity behavior, motivation to be active and subjective experience while being active. Overall, the autonomous motivation cluster displayed more favorable characteristics compared to the other two clusters. The results of this study provide additional support for the importance of autonomous motivation in the context of physical activity behavior. The three derived clusters may be relevant in the context of physical activity interventions as individuals within the different clusters might benefit most from different intervention approaches. In addition, this study shows that cluster analysis is a useful method for differentiating between motivational profiles in large groups of individuals who do not comply with physical activity guidelines.

Physical phenomena in a low-temperature non-equilibrium plasma and in MHD generators with non-equilibrium conductivity

International Nuclear Information System (INIS)

Velikhov, E.P.; Golubev, V.S.; Dykhne, A.M.

1976-01-01

The paper assesses the position in 1975 of theoretical and experimental work on the physics of a magnetohydrodynamic generator with non-equilibrium plasma conductivity. This research started at the beginning of the 1960s; as work on the properties of thermally non-equilibrium plasma in magnetic fields and also in MHD generator ducts progressed, a number of phenomena were discovered and investigated that had either been unknown in plasma physics or had remained uninvestigated until that time: ionization instability and ionization turbulence of plasma in a magnetic field, acoustic instability of a plasma with anisotropic conductivity, the non-equilibrium ionization wave and the energy balance of a non-equilibrium plasma. At the same time, it was discovered what physical requirements an MHD generator with non-equilibrium conductivity must satisfy to achieve high efficiency in converting the thermal or kinetic energy of the gas flow into electric energy. The experiments on MHD power generation with thermally non-equilibrium plasma carried out up to 1975 indicated that it should be possible to achieve conversion efficiencies of up to 20-30%. (author)

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

Science.gov (United States)

Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.

2010-01-01

Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis, especially for rare types of gliomas. Moreover, the biological basis for the marked intratumoral heterogeneity in gliomas is most readily addressed in FFPE material. Therefore, for gliomas, the ability to use DNA from FFPE tissue is essential for both clinical and research applications. In this study, we have constructed a custom bacterial artificial chromosome (BAC) array and show excellent sensitivity and specificity for detecting CNAs in a panel of paired frozen and FFPE glioma samples. Our study demonstrates a high concordance rate between CNAs detected in FFPE compared to frozen DNA. We have also developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. This labeling technique was applied to a panel of biphasic anaplastic oligoastrocytomas (AOA) to identify genetic changes unique to each component. Together, results from these studies suggest that BAC and oligonucleotide aCGH are sensitive tools for detecting CNAs in FFPE DNA, and can enable genome-wide analysis of rare, small and/or histologically heterogeneous gliomas. PMID:21080181

Physical Therapists' Perceptions of School-Based Practices.

Science.gov (United States)

Holt, Sheryl L; Kuperstein, Janice; Effgen, Susan K

2015-01-01

Surveys have reported that most school-based physical therapists perceive ideal practices are not commonly implemented in their settings. Our aim was to obtain a more in-depth understanding of these perceptions through open-ended inquiry. Qualitative data were derived from voluntary open-ended responses provided upon completion of a survey regarding school-based physical therapy practice. Of the survey's 561 participants, 250 provided open-ended commentaries that were analyzed using interpretive phenomenology. Six qualitative themes emerged from the open-ended responses, including: In quest: Meeting students' school-based needs via physical therapy; Seeking relatedness: Finding working teams in the school system; Building understanding: Developing a voice/identity in the school context; Stretched beyond limits: Managing workloads; Networking: Coordinating services outside school to meet student needs; Defying definition: What does working in an educational model mean? School-based physical therapists seek to meet educationally relevant physical therapy needs of students, ages 3 to 21 years. Successes appear woven of a multitude of factors such as therapist expertise, team dynamics, and district supports.

Meet the Next Generation's Physics Teachers at Physics on Stage

CERN Document Server

2000-01-01

Physics on Stage is an international festival held at CERN where physics teachers from 22 countries will gather to invent new ways of making physics more interesting to students. From 6 to 11 November CERN will be flooded by 450 high school physics teachers from 22 European countries! So don't be surprised if you can't find a place to sit down in the cafeteria! People from Austria, Belgium, Bulgaria, The Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Luxembourg, the Netherlands, Norway, Poland, Portugal, The Slovak Republic, Spain, Sweden, Switzerland and the United Kingdom will come here to show, discuss, and invent new ways of teaching physics and making the subject more interesting for school children and the general public. Indeed the lack of interest in Physics is a worrying concern ­ for example in Germany the number of first year physics students has dropped more than 30 percent in the last ten years! In the UK the number of physics graduates training to be ...

Conceptual study on deep-underground energy generation base

International Nuclear Information System (INIS)

Hayano, M.; Okawa, T.

1992-01-01

Mitsubishi Atomic Power Industries, Inc. (MAPI) and Taisei Corporation have started a conceptual study on a deep-underground energy generation base for future cities in the 21st century around the metropolitan area, which will be increasingly important from viewpoints of the autonomy and sharing of the energy supply to the future cities. The energy generation base consists of a gas cooled reactor with naturally safety features as the energy source, an electric generation base using the Alkali Metal Thermo-electric Converter (AMTEC), a hydrogen production plant with the Solid Polymer Electrolyte (SPE), a hydrogen storage plant with the Metal Hydride (MH), and a desalination plant. This paper describes a concept of the energy generation base and the structure in the deep-underground, in soft soil, then the basic system of each plant, and finally discusses the feasibility of the deep-underground energy generation base. (author)

Non-Darcy flow of water-based carbon nanotubes with nonlinear radiation and heat generation/absorption

Directory of Open Access Journals (Sweden)

T. Hayat

2018-03-01

Full Text Available Here modeling and computations are presented to introduce the novel concept of Darcy-Forchheimer three-dimensional flow of water-based carbon nanotubes with nonlinear thermal radiation and heat generation/absorption. Bidirectional stretching surface induces the flow. Darcy’s law is commonly replace by Forchheimer relation. Xue model is implemented for nonliquid transport mechanism. Nonlinear formulation based upon conservation laws of mass, momentum and energy is first modeled and then solved by optimal homotopy analysis technique. Optimal estimations of auxiliary variables are obtained. Importance of influential variables on the velocity and thermal fields is interpreted graphically. Moreover velocity and temperature gradients are discussed and analyzed. Physical interpretation of influential variables is examined. Keywords: Porous medium, Heat generation/absorption, SWCNTs and MWCNTs, Nonlinear radiation

Benchmark problem suite for reactor physics study of LWR next generation fuels

International Nuclear Information System (INIS)

Yamamoto, Akio; Ikehara, Tadashi; Ito, Takuya; Saji, Etsuro

2002-01-01

This paper proposes a benchmark problem suite for studying the physics of next-generation fuels of light water reactors. The target discharge burnup of the next-generation fuel was set to 70 GWd/t considering the increasing trend in discharge burnup of light water reactor fuels. The UO 2 and MOX fuels are included in the benchmark specifications. The benchmark problem consists of three different geometries: fuel pin cell, PWR fuel assembly and BWR fuel assembly. In the pin cell problem, detailed nuclear characteristics such as burnup dependence of nuclide-wise reactivity were included in the required calculation results to facilitate the study of reactor physics. In the assembly benchmark problems, important parameters for in-core fuel management such as local peaking factors and reactivity coefficients were included in the required results. The benchmark problems provide comprehensive test problems for next-generation light water reactor fuels with extended high burnup. Furthermore, since the pin cell, the PWR assembly and the BWR assembly problems are independent, analyses of the entire benchmark suite is not necessary: e.g., the set of pin cell and PWR fuel assembly problems will be suitable for those in charge of PWR in-core fuel management, and the set of pin cell and BWR fuel assembly problems for those in charge of BWR in-core fuel management. (author)

A Methodology for Physical Interconnection Decisions of Next Generation Transport Networks

DEFF Research Database (Denmark)

Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Madsen, Ole Brun

2011-01-01

of possibilities when designing the physical network interconnection. This paper develops and presents a methodology in order to deal with aspects related to the interconnection problem of optical transport networks. This methodology is presented as independent puzzle pieces, covering diverse topics going from......The physical interconnection for optical transport networks has critical relevance in the overall network performance and deployment costs. As telecommunication services and technologies evolve, the provisioning of higher capacity and reliability levels is becoming essential for the proper...... development of Next Generation Networks. Currently, there is a lack of specific procedures that describe the basic guidelines to design such networks better than "best possible performance for the lowest investment". Therefore, the research from different points of view will allow a broader space...

Reconstructing Macroeconomics Based on Statistical Physics

Science.gov (United States)

Aoki, Masanao; Yoshikawa, Hiroshi

We believe that time has come to integrate the new approach based on statistical physics or econophysics into macroeconomics. Toward this goal, there must be more dialogues between physicists and economists. In this paper, we argue that there is no reason why the methods of statistical physics so successful in many fields of natural sciences cannot be usefully applied to macroeconomics that is meant to analyze the macroeconomy comprising a large number of economic agents. It is, in fact, weird to regard the macroeconomy as a homothetic enlargement of the representative micro agent. We trust the bright future of the new approach to macroeconomies based on statistical physics.

A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map.

Science.gov (United States)

Solignac, Michel; Mougel, Florence; Vautrin, Dominique; Monnerot, Monique; Cornuet, Jean-Marie

2007-01-01

The honey bee is a key model for social behavior and this feature led to the selection of the species for genome sequencing. A genetic map is a necessary companion to the sequence. In addition, because there was originally no physical map for the honey bee genome project, a meiotic map was the only resource for organizing the sequence assembly on the chromosomes. We present the genetic (meiotic) map here and describe the main features that emerged from comparison with the sequence-based physical map. The genetic map of the honey bee is saturated and the chromosomes are oriented from the centromeric to the telomeric regions. The map is based on 2,008 markers and is about 40 Morgans (M) long, resulting in a marker density of one every 2.05 centiMorgans (cM). For the 186 megabases (Mb) of the genome mapped and assembled, this corresponds to a very high average recombination rate of 22.04 cM/Mb. Honey bee meiosis shows a relatively homogeneous recombination rate along and across chromosomes, as well as within and between individuals. Interference is higher than inferred from the Kosambi function of distance. In addition, numerous recombination hotspots are dispersed over the genome. The very large genetic length of the honey bee genome, its small physical size and an almost complete genome sequence with a relatively low number of genes suggest a very promising future for association mapping in the honey bee, particularly as the existence of haploid males allows easy bulk segregant analysis.

Generation of initial geometries for the simulation of the physical system in the DualPHYsics code

International Nuclear Information System (INIS)

Segura Q, E.

2013-01-01

In the diverse research areas of the Instituto Nacional de Investigaciones Nucleares (ININ) are different activities related to science and technology, one of great interest is the study and treatment of the collection and storage of radioactive waste. Therefore at ININ the draft on the simulation of the pollutants diffusion in the soil through a porous medium (third stage) has this problem inherent aspects, hence a need for such a situation is to generate the initial geometry of the physical system For the realization of the simulation method is implemented smoothed particle hydrodynamics (SPH). This method runs in DualSPHysics code, which has great versatility and ability to simulate phenomena of any physical system where hydrodynamic aspects combine. In order to simulate a physical system DualSPHysics code, you need to preset the initial geometry of the system of interest, then this is included in the input file of the code. The simulation sets the initial geometry through regular geometric bodies positioned at different points in space. This was done through a programming language (Fortran, C + +, Java, etc..). This methodology will provide the basis to simulate more complex geometries future positions and form. (Author)

Research-based active-learning instruction in physics

Science.gov (United States)

Meltzer, David E.; Thornton, Ronald K.

2013-04-01

The development of research-based active-learning instructional methods in physics has significantly altered the landscape of U.S. physics education during the past 20 years. Based on a recent review [D.E. Meltzer and R.K. Thornton, Am. J. Phys. 80, 478 (2012)], we define these methods as those (1) explicitly based on research in the learning and teaching of physics, (2) that incorporate classroom and/or laboratory activities that require students to express their thinking through speaking, writing, or other actions that go beyond listening and the copying of notes, or execution of prescribed procedures, and (3) that have been tested repeatedly in actual classroom settings and have yielded objective evidence of improved student learning. We describe some key features common to methods in current use. These features focus on (a) recognizing and addressing students' physics ideas, and (b) guiding students to solve problems in realistic physical settings, in novel and diverse contexts, and to justify or explain the reasoning they have used.

Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

Science.gov (United States)

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

2014-01-01

Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger. PMID:24608928

Physics Instruction Utilizing Culture-Based Pedagogy

Directory of Open Access Journals (Sweden)

Nerrie E. Malaluan

2015-11-01

Full Text Available This research assessed topics in physics where culture-based pedagogy may be utilized and the applicability of Batangueño culture to these topics. It also determined the visual presentations which canbe prepared by teachers to incorporate Batangueñoculture in physics instruction. The end purpose of the study was to develop a teaching guide using culture-based pedagogy to reinforce the student’s learning, and help them achieve high academic performance. Descriptive method was adopted with questionnaire as tool in gathering data. Interviews and focus group discussions were also conducted. Thirty physics teachers in public secondary schools of the Division of Batangas City served as respondents. Purposive sampling was applied in determining the respondents. Frequency, percentage, ranking and weighted mean were statistical tools applied. Findings revealed that the culture-based pedagogy that could be utilized in teaching physics was on topics: Constant and Uniformly Acceleration; Work, Power and Energy; Laws of Motion; Projectile Motion; Heat and Light. Batangueño culture was found applicable in teaching physics. The visual presentations which could be used were pictures, powerpoint and video clips. Moreover, the proposed teaching guide utilizing culture-based pedagogy may be used by teachersto heighten students’ interest and motivation and to attain active participation and high achievement. It may be a reference of employing Batangueño culture in teaching the topics. It was recommended that the output be presented to the school heads and supervisors for their comments and suggestions for enrichment of content and application of culture-based pedagogy not only in science but in other learning areas.

BEAT: A Web-Based Boolean Expression Fault-Based Test Case Generation Tool

Science.gov (United States)

Chen, T. Y.; Grant, D. D.; Lau, M. F.; Ng, S. P.; Vasa, V. R.

2006-01-01

BEAT is a Web-based system that generates fault-based test cases from Boolean expressions. It is based on the integration of our several fault-based test case selection strategies. The generated test cases are considered to be fault-based, because they are aiming at the detection of particular faults. For example, when the Boolean expression is in…

Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation.

Science.gov (United States)

Crucello, Aline; Sforça, Danilo Augusto; Horta, Maria Augusta Crivelente; dos Santos, Clelton Aparecido; Viana, Américo José Carvalho; Beloti, Lilian Luzia; de Toledo, Marcelo Augusto Szymanski; Vincentz, Michel; Kuroshu, Reginaldo Massanobu; de Souza, Anete Pereira

2015-01-01

Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

Permanent magnet based dipole magnets for next generation light sources

Directory of Open Access Journals (Sweden)

Takahiro Watanabe

2017-07-01

Full Text Available We have developed permanent magnet based dipole magnets for the next generation light sources. Permanent magnets are advantageous over electromagnets in that they consume less power, are physically more compact, and there is a less risk of power supply failure. However, experience with electromagnets and permanent magnets in the field of accelerators shows that there are still challenges to replacing main magnets of accelerators for light sources with permanent magnets. These include the adjustability of the magnetic field, the temperature dependence of permanent magnets, and the issue of demagnetization. In this paper, we present a design for magnets for future light sources, supported by experimental and numerical results.

Data base of reactor physics experimental results in Kyoto University critical assembly experimental facilities

International Nuclear Information System (INIS)

Ichihara, Chihiro; Fujine, Shigenori; Hayashi, Masatoshi

1986-01-01

The Kyoto University critical assembly experimental facilities belong to the Kyoto University Research Reactor Institute, and are the versatile critical assembly constructed for experimentally studying reactor physics and reactor engineering. The facilities are those for common utilization by universities in whole Japan. During more than ten years since the initial criticality in 1974, various experiments on reactor physics and reactor engineering have been carried out using many experimental facilities such as two solidmoderated cores, a light water-moderated core and a neutron generator. The kinds of the experiment carried out were diverse, and to find out the required data from them is very troublesome, accordingly it has become necessary to make a data base which can be processed by a computer with the data accumulated during the past more than ten years. The outline of the data base, the data base CAEX using personal computers, the data base supported by a large computer and so on are reported. (Kako, I.)

Hardware random number generator base on monostable multivibrators dedicated for distributed measurement and control systems

Science.gov (United States)

Czernik, Pawel

2013-10-01

The hardware random number generator based on the 74121 monostable multivibrators for applications in cryptographically secure distributed measurement and control systems with asymmetric resources was presented. This device was implemented on the basis of the physical electronic vibration generator in which the circuit is composed of two "loop" 74121 monostable multivibrators, D flip-flop and external clock signal source. The clock signal, witch control D flip-flop was generated by a computer on one of the parallel port pins. There was presented programmed the author's acquisition process of random data from the measuring system to a computer. The presented system was designed, builded and thoroughly tested in the term of cryptographic security in our laboratory, what there is the most important part of this publication. Real cryptographic security was tested based on the author's software and the software environment called RDieHarder. The obtained results was here presented and analyzed in detail with particular reference to the specificity of distributed measurement and control systems with asymmetric resources.

Control-Oriented First Principles-Based Model of a Diesel Generator

DEFF Research Database (Denmark)

Knudsen, Jesper Viese; Bendtsen, Jan Dimon; Andersen, Palle

2016-01-01

This paper presents the development of a control-oriented tenth-order nonlinear model of a diesel driven generator set, using first principles modeling. The model provides physical system insight, while keeping the complexity at a level where it can be a tool for future design of improved automatic...... generation control (AGC), by including important nonlinearities of the machine. The nonlinearities are, as would be expected for a generator, primarily of bilinear nature. Validation of the model is done with measurements on a 60 kVA/48 kW diesel driven generator set in island operation during steps...

Evidence-based intervention in physical activity

DEFF Research Database (Denmark)

Heath, Gregory W; Parra, Diana C; Sarmiento, Olga L

2012-01-01

Promotion of physical activity is a priority for health agencies. We searched for reviews of physical activity interventions, published between 2000 and 2011, and identified effective, promising, or emerging interventions from around the world. The informational approaches of community......-wide and mass media campaigns, and short physical activity messages targeting key community sites are recommended. Behavioural and social approaches are effective, introducing social support for physical activity within communities and worksites, and school-based strategies that encompass physical education......, classroom activities, after-school sports, and active transport. Recommended environmental and policy approaches include creation and improvement of access to places for physical activity with informational outreach activities, community-scale and street-scale urban design and land use, active transport...

Next Generation Sequencing of Classical Swine Fever Virus and Border Disease virus cloned in Bacterial Artificial Chromosomes

DEFF Research Database (Denmark)

Fahnøe, Ulrik; Höper, Dirk; Beer, martin

2012-01-01

artificial chromosomes (BACs). From these BACs, RNA copies of the viral genomes can be transcribed in vitro and upon transfection of these RNAs into mammalian cells, autonomous replication of the viral genome occurs and infectious progeny can be rescued. However, we have observed that virus progeny can...

Physical activity level of three generation families. Genetic and environmental factors

Directory of Open Access Journals (Sweden)

Raquel Nichele de Chaves

2010-09-01

Full Text Available This study aims (1 to investigate the presence of familial aggregation in physical activity (PA levels and sedentary behavior (SB among members of three generations families and (2 to estimate the magnitude of additive genetic influences on PA and SB phenotypes. The sample consisted of 100 extended families covering three generations (n=1034, from the Lisbon area, Portugal. Phenotypes were assessed via the short version of the self-administered International Physical Activity Questionnaire (IPAQ-SF. Measured phenotypes: total physical activity (TPA; vigorous (VPA; moderate (MPA; walking; time spent in sitting time (ST, watching television (WT and PA levels classification. Body mass index (BMI was calculated. Exploratory family analysis in all phenotypes was conducted in PEDSTATS software. The genetic component (h2 and shared environmental effect were estimated using maximum likelihood implemented in the SOLAR software package. All graphs were done in HLM software. Sex, age, sex*age, age2, sex*age2 and BMI were used as covariates. Significant level was set at 0,05. Genetic component estimates (h2 were as follows: TPA h2=0,28±0,06 (p<0.0001; VPA h2=0,35±0,06 (p<0.0001; MPA h2=0,29±0,06 (p<0.0001; walking h2=0,40±0,06 (p<0.0001; ST h2=0,29±0,06 (p<0.0001; WT h2=0,15±0,06 (p<0.003 and determination of the level physical activity h2=0,35±0,14 (p<0.007. Shared environmental effect was not significant. These results showed a low-to-moderate genetic contribution, between 15% to 40% of the total variability, in the PA and SB phenotypes. The genetic factors have low to moderate influence in this sample. Non-shared environmental factors appear to have the major contribution in these phenotypes.

Laminated chemical and physical micro-jet actuators based on conductive media

Science.gov (United States)

Gadiraju, Priya D.

2008-04-01

placing it between two closely spaced electrodes. The first concept is demonstrated for the application of projectile maneuvering where energetic solid propellant is used in generating a high velocity gaseous jet and the second concept is demonstrated for transdermal drug delivery application where a rapid physical jet of a non-energetic propellant is generated. In the case of chemical-based microactuators, the feasibility of using conductive solid propellant based actuators for maneuvering a 25 mm bluff body projectile spinning at 600 Hz is presented. Several conductive solid propellants are developed and characterized for their electrical conductivity and required ignition energy. Finally, the propellant integrated microactuators are characterized for performance in terms of impulse delivered, thrust generated and duration of the jet. These experimental results are then compared to predicted results from simulations. In the case of physical based microactuators, the feasibility of using released physical jets from the microactuator array for transdermal drug delivery application is presented. Several bio-compatible and FDA-approved liquids are used as propellants and are characterized in terms of thrusts delivered and duration of the released jets. These thermo-mechanical jets are then used to expose skin locally so as to create micro conduits in the stratum corneum layer of skin. Both thermal effects and thermo-mechanical effects of the jet on exposed skin are studied. For both cases, histology of exposed skin is presented and its permeability to drug analog molecules is studied.

Rule-based Test Generation with Mind Maps

Directory of Open Access Journals (Sweden)

Dimitry Polivaev

2012-02-01

Full Text Available This paper introduces basic concepts of rule based test generation with mind maps, and reports experiences learned from industrial application of this technique in the domain of smart card testing by Giesecke & Devrient GmbH over the last years. It describes the formalization of test selection criteria used by our test generator, our test generation architecture and test generation framework.

Isolation of BAC Clones Containing Conserved Genes from Libraries of Three Distantly Related Moths: A Useful Resource for Comparative Genomics of Lepidoptera

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Yuji Yasukochi

2011-01-01

Full Text Available Lepidoptera, butterflies and moths, is the second largest animal order and includes numerous agricultural pests. To facilitate comparative genomics in Lepidoptera, we isolated BAC clones containing conserved and putative single-copy genes from libraries of three pests, Heliothis virescens, Ostrinia nubilalis, and Plutella xylostella, harboring the haploid chromosome number, =31, which are not closely related with each other or with the silkworm, Bombyx mori, (=28, the sequenced model lepidopteran. A total of 108–184 clones representing 101–182 conserved genes were isolated for each species. For 79 genes, clones were isolated from more than two species, which will be useful as common markers for analysis using fluorescence in situ hybridization (FISH, as well as for comparison of genome sequence among multiple species. The PCR-based clone isolation method presented here is applicable to species which lack a sequenced genome but have a significant collection of cDNA or EST sequences.

Pulsed corona generation using a diode-based pulsed power generator

Science.gov (United States)

Pemen, A. J. M.; Grekhov, I. V.; van Heesch, E. J. M.; Yan, K.; Nair, S. A.; Korotkov, S. V.

2003-10-01

Pulsed plasma techniques serve a wide range of unconventional processes, such as gas and water processing, hydrogen production, and nanotechnology. Extending research on promising applications, such as pulsed corona processing, depends to a great extent on the availability of reliable, efficient and repetitive high-voltage pulsed power technology. Heavy-duty opening switches are the most critical components in high-voltage pulsed power systems with inductive energy storage. At the Ioffe Institute, an unconventional switching mechanism has been found, based on the fast recovery process in a diode. This article discusses the application of such a "drift-step-recovery-diode" for pulsed corona plasma generation. The principle of the diode-based nanosecond high-voltage generator will be discussed. The generator will be coupled to a corona reactor via a transmission-line transformer. The advantages of this concept, such as easy voltage transformation, load matching, switch protection and easy coupling with a dc bias voltage, will be discussed. The developed circuit is tested at both a resistive load and various corona reactors. Methods to optimize the energy transfer to a corona reactor have been evaluated. The impedance matching between the pulse generator and corona reactor can be significantly improved by using a dc bias voltage. At good matching, the corona energy increases and less energy reflects back to the generator. Matching can also be slightly improved by increasing the temperature in the corona reactor. More effective is to reduce the reactor pressure.

Using Physical Context-Based Authentication against External Attacks: Models and Protocols

Directory of Open Access Journals (Sweden)

Wilson S. Melo

2018-01-01

Full Text Available Modern systems are increasingly dependent on the integration of physical processes and information technologies. This trend is remarkable in applications involving sensor networks, cyberphysical systems, and Internet of Things. Despite its complexity, such integration results in physical context information that can be used to improve security, especially authentication. In this paper, we show that entities sharing the same physical context can use it for establishing a secure communication channel and protecting each other against external attacks. We present such approach proposing a theoretical model for generating unique bitstreams. Two different protocols are suggested. Each one is evaluated using probabilistic analysis and simulation. In the end, we implement the authentication mechanism in a case study using networks radio signal as physical event generator. The results demonstrate the performance of each of the protocols and their suitability for applications in real world.

Conserved synteny of genes between chromosome 15 of Bombyx mori and a chromosome of Manduca sexta shown by five-color BAC-FISH

Czech Academy of Sciences Publication Activity Database

Sahara, K.; Yoshido, A.; Marec, František; Vrbová, Iva; Zhang, H. B.; Wu, Ch. C.; Goldsmith, M. R.; Yasukochi, Y.

2007-01-01

Roč. 50, č. 11 (2007), s. 1061-1065 ISSN 0831-2796 R&D Projects: GA ČR GA206/06/1860 Grant - others:Japan Society for the Promotion of Science(JP) 18380037; US National Science Foundation(US) IBN0208388 Institutional research plan: CEZ:AV0Z50070508 Source of funding: O - operačné programy ; O - operačné programy Keywords : BAC-FISH * Bombyx mori * chromosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.785, year: 2007

Updates to the Generation of Physics Data Inputs for MAMMOTH Simulations of the Transient Reactor Test Facility - FY2016

Energy Technology Data Exchange (ETDEWEB)

Ortensi, Javier [Idaho National Lab. (INL), Idaho Falls, ID (United States); Baker, Benjamin Allen [Idaho National Lab. (INL), Idaho Falls, ID (United States); Schunert, Sebastian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wang, Yaqi [Idaho National Lab. (INL), Idaho Falls, ID (United States); Gleicher, Frederick Nathan [Idaho National Lab. (INL), Idaho Falls, ID (United States); DeHart, Mark David [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2016-06-01

The INL is currently evolving the modeling and simulation (M&S) capability that will enable improved core operation as well as design and analysis of TREAT experiments. This M&S capability primarily uses MAMMOTH, a reactor physics application being developed under Multi-physics Object Oriented Simulation Environment (MOOSE) framework. MAMMOTH allows the coupling of a number of other MOOSE-based applications. This second year of work has been devoted to the generation of a deterministic reference solution for the full core, the preparation of anisotropic diffusion coefficients, the testing of the SPH equivalence method, and the improvement of the control rod modeling. In addition, this report includes the progress made in the modeling of the M8 core configuration and experiment vehicle since January of this year.

Enriching Triangle Mesh Animations with Physically Based Simulation.

Science.gov (United States)

Li, Yijing; Xu, Hongyi; Barbic, Jernej

2017-10-01

We present a system to combine arbitrary triangle mesh animations with physically based Finite Element Method (FEM) simulation, enabling control over the combination both in space and time. The input is a triangle mesh animation obtained using any method, such as keyframed animation, character rigging, 3D scanning, or geometric shape modeling. The input may be non-physical, crude or even incomplete. The user provides weights, specified using a minimal user interface, for how much physically based simulation should be allowed to modify the animation in any region of the model, and in time. Our system then computes a physically-based animation that is constrained to the input animation to the amount prescribed by these weights. This permits smoothly turning physics on and off over space and time, making it possible for the output to strictly follow the input, to evolve purely based on physically based simulation, and anything in between. Achieving such results requires a careful combination of several system components. We propose and analyze these components, including proper automatic creation of simulation meshes (even for non-manifold and self-colliding undeformed triangle meshes), converting triangle mesh animations into animations of the simulation mesh, and resolving collisions and self-collisions while following the input.

Evaluation of frame aggregation schemes for the p-persistent based next generation WLANS

Science.gov (United States)

Ahmad, Ashar; Anna, Kiran; Bassiouni, Mostafa A.

2010-04-01

The next Generation IEEE 802.11n is designed to improve the throughput of the existing standard 802.11. It aims to achieve this by increasing the data rate from 54 Mbps to 600 Mbps with the help of physical layer enhancements. Therefore, the Medium Access Layer (MAC) requires improvements to fully utilize the capabilities of the enhanced 802.11n physical layer. In this paper, we present the performance evaluation results of two frame aggregation schemes viz., MAC Protocol Data Unit Aggregation (A-MPDU) and MAC Service Data Unit Aggregation (A-MSDU) and study their performance impact when the two schemes are incorporated in a p-persistent based 802.11n. The simulation results have shown that the two schemes achieve consistent performance improvement over the standard non-aggregation scheme.

A Phox2b BAC Transgenic Rat Line Useful for Understanding Respiratory Rhythm Generator Neural Circuitry.

Directory of Open Access Journals (Sweden)

Keiko Ikeda

Full Text Available The key role of the respiratory neural center is respiratory rhythm generation to maintain homeostasis through the control of arterial blood pCO2/pH and pO2 levels. The neuronal network responsible for respiratory rhythm generation in neonatal rat resides in the ventral side of the medulla and is composed of two groups; the parafacial respiratory group (pFRG and the pre-Bötzinger complex group (preBötC. The pFRG partially overlaps in the retrotrapezoid nucleus (RTN, which was originally identified in adult cats and rats. Part of the pre-inspiratory (Pre-I neurons in the RTN/pFRG serves as central chemoreceptor neurons and the CO2 sensitive Pre-I neurons express homeobox gene Phox2b. Phox2b encodes a transcription factor and is essential for the development of the sensory-motor visceral circuits. Mutations in human PHOX2B cause congenital hypoventilation syndrome, which is characterized by blunted ventilatory response to hypercapnia. Here we describe the generation of a novel transgenic (Tg rat harboring fluorescently labeled Pre-I neurons in the RTN/pFRG. In addition, the Tg rat showed fluorescent signals in autonomic enteric neurons and carotid bodies. Because the Tg rat expresses inducible Cre recombinase in PHOX2B-positive cells during development, it is a potentially powerful tool for dissecting the entire picture of the respiratory neural network during development and for identifying the CO2/O2 sensor molecules in the adult central and peripheral nervous systems.

Developing the learning physical science curriculum: Adapting a small enrollment, laboratory and discussion based physical science course for large enrollments

Science.gov (United States)

Goldberg, Fred; Price, Edward; Robinson, Stephen; Boyd-Harlow, Danielle; McKean, Michael

2012-06-01

We report on the adaptation of the small enrollment, lab and discussion based physical science course, Physical Science and Everyday Thinking (PSET), for a large-enrollment, lecture-style setting. Like PSET, the new Learning Physical Science (LEPS) curriculum was designed around specific principles based on research on learning to meet the needs of nonscience students, especially prospective and practicing elementary and middle school teachers. We describe the structure of the two curricula and the adaptation process, including a detailed comparison of similar activities from the two curricula and a case study of a LEPS classroom implementation. In LEPS, short instructor-guided lessons replace lengthier small group activities, and movies, rather than hands-on investigations, provide the evidence used to support and test ideas. LEPS promotes student peer interaction as an important part of sense making via “clicker” questions, rather than small group and whole class discussions typical of PSET. Examples of student dialog indicate that this format is capable of generating substantive student discussion and successfully enacting the design principles. Field-test data show similar student content learning gains with the two curricula. Nevertheless, because of classroom constraints, some important practices of science that were an integral part of PSET were not included in LEPS.

Developing the learning physical science curriculum: Adapting a small enrollment, laboratory and discussion based physical science course for large enrollments

Directory of Open Access Journals (Sweden)

Fred Goldberg1

2012-05-01

Full Text Available We report on the adaptation of the small enrollment, lab and discussion based physical science course, Physical Science and Everyday Thinking (PSET, for a large-enrollment, lecture-style setting. Like PSET, the new Learning Physical Science (LEPS curriculum was designed around specific principles based on research on learning to meet the needs of nonscience students, especially prospective and practicing elementary and middle school teachers. We describe the structure of the two curricula and the adaptation process, including a detailed comparison of similar activities from the two curricula and a case study of a LEPS classroom implementation. In LEPS, short instructor-guided lessons replace lengthier small group activities, and movies, rather than hands-on investigations, provide the evidence used to support and test ideas. LEPS promotes student peer interaction as an important part of sense making via “clicker” questions, rather than small group and whole class discussions typical of PSET. Examples of student dialog indicate that this format is capable of generating substantive student discussion and successfully enacting the design principles. Field-test data show similar student content learning gains with the two curricula. Nevertheless, because of classroom constraints, some important practices of science that were an integral part of PSET were not included in LEPS.

A Novel Distributed Economic Model Predictive Control Approach for Building Air-Conditioning Systems in Microgrids

Directory of Open Access Journals (Sweden)

Xinan Zhang

2018-04-01

Full Text Available With the penetration of grid-connected renewable energy generation, microgrids are facing stability and power quality problems caused by renewable intermittency. To alleviate such problems, demand side management (DSM of responsive loads, such as building air-conditioning system (BACS, has been proposed and studied. In recent years, numerous control approaches have been published for proper management of single BACS. The majority of these approaches focus on either the control of BACS for attenuating power fluctuations in the grid or the operating cost minimization on behalf of the residents. These two control objectives are paramount for BACS control in microgrids and can be conflicting. As such, they should be considered together in control design. As individual buildings may have different owners/residents, it is natural to control different BACSs in an autonomous and self-interested manner to minimize the operational costs for the owners/residents. Unfortunately, such “selfish” operation can result in abrupt and large power fluctuations at the point of common coupling (PCC of the microgrid due to lack of coordination. Consequently, the original objective of mitigating power fluctuations generated by renewable intermittency cannot be achieved. To minimize the operating costs of individual BACSs and simultaneously ensure desirable overall power flow at PCC, this paper proposes a novel distributed control framework based on the dissipativity theory. The proposed method achieves the objective of renewable intermittency mitigation through proper coordination of distributed BACS controllers and is scalable and computationally efficient. Simulation studies are carried out to illustrate the efficacy of the proposed control framework.

The Development of Enterprise Systems based on Cyber- Physical Systems Principles

Directory of Open Access Journals (Sweden)

Ioan Ştefan Sacală

2014-12-01

Full Text Available Research in the area of Cyber-Physical Systems (CPS and Internet of Things (IoT become, in the last 3 years a priority for both research entities and companies. Implementing Enterprise Systems based on the two paradigms is focused on merging real and virtual objects and thus deals with an increased degree of complexity. The aim of the present paper is to discuss an Enterprise Architecture and a Framework based on the integration of CPS and IoT technologies within Enterprise Systems. An important aspect is related to process mining implemented in two focus areas: the ability to generate business processes from data acquired from sensors and the ability to integrate sensor acquired data with existing business processes.

Stability improvement of induction generator-based wind turbine systems

DEFF Research Database (Denmark)

Chen, Zhe; Hu, Y.; Blaabjerg, Frede

2007-01-01

The stability improvement of induction-generator-based wind turbine systems under power system fault conditions has been studied. Two types of generators are considered, namely rotor short-circuited induction generators and dynamic slip-controlled wound rotor induction generators. The factors...... affecting the stability are analysed. The characteristics of the induction-generator-based wind turbines are described, and possible methods of improving stability of the wind generators are discussed. The system modelling is presented, and then the discussed methods of improving stability are investigated...

Functional characterization of a prokaryotic Kir channel.

Science.gov (United States)

Enkvetchakul, Decha; Bhattacharyya, Jaya; Jeliazkova, Iana; Groesbeck, Darcy K; Cukras, Catherine A; Nichols, Colin G

2004-11-05

The Kir gene family encodes inward rectifying K+ (Kir) channels that are widespread and critical regulators of excitability in eukaryotic cells. A related gene family (KirBac) has recently been identified in prokaryotes. While a crystal structure of one member, Kir-Bac1.1, has been solved, there has been no functional characterization of any KirBac gene products. Here we present functional characterization of KirBac1.1 reconstituted in liposomes. Utilizing a 86Rb+ uptake assay, we demonstrate that KirBac1.1 generates a K+ -selective permeation path that is inhibited by extraliposomal Ba2+ and Ca2+ ions. In contrast to KcsA (an acid-activated bacterial potassium channel), KirBac1.1 is inhibited by extraliposomal acid (pKa approximately 6). This characterization of KirBac1.1 activity now paves the way for further correlation of structure and function in this model Kir channel.

Generation of structural topologies using efficient technique based on sorted compliances

Science.gov (United States)

Mazur, Monika; Tajs-Zielińska, Katarzyna; Bochenek, Bogdan

2018-01-01

Topology optimization, although well recognized is still widely developed. It has gained recently more attention since large computational ability become available for designers. This process is stimulated simultaneously by variety of emerging, innovative optimization methods. It is observed that traditional gradient-based mathematical programming algorithms, in many cases, are replaced by novel and e cient heuristic methods inspired by biological, chemical or physical phenomena. These methods become useful tools for structural optimization because of their versatility and easy numerical implementation. In this paper engineering implementation of a novel heuristic algorithm for minimum compliance topology optimization is discussed. The performance of the topology generator is based on implementation of a special function utilizing information of compliance distribution within the design space. With a view to cope with engineering problems the algorithm has been combined with structural analysis system Ansys.

A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS)

Czech Academy of Sciences Publication Activity Database

Šimková, Hana; Šafář, Jan; Suchánková, Pavla; Kovářová, Pavlína; Bartoš, Jan; Kubaláková, Marie; Janda, Jaroslav; Čihalíková, Jarmila; Mago, R.; Lelley, T.; Doležel, Jaroslav

2008-01-01

Roč. 9, č. 237 (2008), s. 101-109 ISSN 1471-2164 R&D Projects: GA ČR GA521/04/0607; GA ČR GP521/05/P257; GA ČR GD521/05/H013; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : flow cytometry * flow-sorted chromosomes * BAC library Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.926, year: 2008

Four generations and Higgs physics

Energy Technology Data Exchange (ETDEWEB)

Kribs, Graham D. [Department of Physics and Institute of Theoretical Science, University of Oregon, Eugene (United States); Plehn, Tilman [SUPA, School of Physics, University of Edinburgh (United Kingdom); Spannowsky, Michael [Institut fuer Theoretische Physik, Universitaet Karlsruhe (Germany); Tait, Tim M.P. [HEP Division, Argonne National Laboratory (United States)

2008-07-01

A fourth generation has been considered and forgotten or discarded several times, wrongly leaving the impression that it is either ruled out or disfavored by experimental data. We revisit a fourth generation of chiral matter in the light of present electroweak precision data and deduce effects on Higgs phenomenology. We find a chiral fourth generation to be a viable model which can yield interesting signatures at the LHC, e.g. production rates are enhanced, weak-boson-fusion channels are suppressed, angular distributions are modified and Higgs pairs can be observed.

Using Case Studies in Calculus-based Physics

Science.gov (United States)

Katz, Debora M.

2006-12-01

Do your students believe that the physics only works in your classroom or laboratory? Or do they see that physics underlies their everyday experience? Case studies in physics help students connect physics principles to their everyday experience. For decades, case studies have been used to teach law, medicine and biology, but they are rarely used in physics. I am working on a calculus-based physics textbook for scientists and engineers. Case studies are woven into each chapter. Stop by and get a case study to test out in your classroom. I would love to get your feedback.

Inquiry-based problem solving in introductory physics

Science.gov (United States)

Koleci, Carolann

What makes problem solving in physics difficult? How do students solve physics problems, and how does this compare to an expert physicist's strategy? Over the past twenty years, physics education research has revealed several differences between novice and expert problem solving. The work of Chi, Feltovich, and Glaser demonstrates that novices tend to categorize problems based on surface features, while experts categorize according to theory, principles, or concepts1. If there are differences between how problems are categorized, then are there differences between how physics problems are solved? Learning more about the problem solving process, including how students like to learn and what is most effective, requires both qualitative and quantitative analysis. In an effort to learn how novices and experts solve introductory electricity problems, a series of in-depth interviews were conducted, transcribed, and analyzed, using both qualitative and quantitative methods. One-way ANOVA tests were performed in order to learn if there are any significant problem solving differences between: (a) novices and experts, (b) genders, (c) students who like to answer questions in class and those who don't, (d) students who like to ask questions in class and those who don't, (e) students employing an interrogative approach to problem solving and those who don't, and (f) those who like physics and those who dislike it. The results of both the qualitative and quantitative methods reveal that inquiry-based problem solving is prevalent among novices and experts, and frequently leads to the correct physics. These findings serve as impetus for the third dimension of this work: the development of Choose Your Own Adventure Physics(c) (CYOAP), an innovative teaching tool in physics which encourages inquiry-based problem solving. 1Chi, M., P. Feltovich, R. Glaser, "Categorization and Representation of Physics Problems by Experts and Novices", Cognitive Science, 5, 121--152 (1981).

Hydrogen-based power generation from bioethanol steam reforming

Energy Technology Data Exchange (ETDEWEB)

Tasnadi-Asztalos, Zs., E-mail: tazsolt@chem.ubbcluj.ro; Cormos, C. C., E-mail: cormos@chem.ubbcluj.ro; Agachi, P. S. [Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, 11 Arany Janos, Postal code: 400028, Cluj-Napoca (Romania)

2015-12-23

This paper is evaluating two power generation concepts based on hydrogen produced from bioethanol steam reforming at industrial scale without and with carbon capture. The power generation from bioethanol conversion is based on two important steps: hydrogen production from bioethanol catalytic steam reforming and electricity generation using a hydrogen-fuelled gas turbine. As carbon capture method to be assessed in hydrogen-based power generation from bioethanol steam reforming, the gas-liquid absorption using methyl-di-ethanol-amine (MDEA) was used. Bioethanol is a renewable energy carrier mainly produced from biomass fermentation. Steam reforming of bioethanol (SRE) provides a promising method for hydrogen and power production from renewable resources. SRE is performed at high temperatures (e.g. 800-900°C) to reduce the reforming by-products (e.g. ethane, ethene). The power generation from hydrogen was done with M701G2 gas turbine (334 MW net power output). Hydrogen was obtained through catalytic steam reforming of bioethanol without and with carbon capture. For the evaluated plant concepts the following key performance indicators were assessed: fuel consumption, gross and net power outputs, net electrical efficiency, ancillary consumptions, carbon capture rate, specific CO{sub 2} emission etc. As the results show, the power generation based on bioethanol conversion has high energy efficiency and low carbon footprint.

Hydrogen-based power generation from bioethanol steam reforming

International Nuclear Information System (INIS)

Tasnadi-Asztalos, Zs.; Cormos, C. C.; Agachi, P. S.

2015-01-01

This paper is evaluating two power generation concepts based on hydrogen produced from bioethanol steam reforming at industrial scale without and with carbon capture. The power generation from bioethanol conversion is based on two important steps: hydrogen production from bioethanol catalytic steam reforming and electricity generation using a hydrogen-fuelled gas turbine. As carbon capture method to be assessed in hydrogen-based power generation from bioethanol steam reforming, the gas-liquid absorption using methyl-di-ethanol-amine (MDEA) was used. Bioethanol is a renewable energy carrier mainly produced from biomass fermentation. Steam reforming of bioethanol (SRE) provides a promising method for hydrogen and power production from renewable resources. SRE is performed at high temperatures (e.g. 800-900°C) to reduce the reforming by-products (e.g. ethane, ethene). The power generation from hydrogen was done with M701G2 gas turbine (334 MW net power output). Hydrogen was obtained through catalytic steam reforming of bioethanol without and with carbon capture. For the evaluated plant concepts the following key performance indicators were assessed: fuel consumption, gross and net power outputs, net electrical efficiency, ancillary consumptions, carbon capture rate, specific CO 2 emission etc. As the results show, the power generation based on bioethanol conversion has high energy efficiency and low carbon footprint

Hydrogen-based power generation from bioethanol steam reforming

Science.gov (United States)

Tasnadi-Asztalos, Zs.; Cormos, C. C.; Agachi, P. S.

2015-12-01

This paper is evaluating two power generation concepts based on hydrogen produced from bioethanol steam reforming at industrial scale without and with carbon capture. The power generation from bioethanol conversion is based on two important steps: hydrogen production from bioethanol catalytic steam reforming and electricity generation using a hydrogen-fuelled gas turbine. As carbon capture method to be assessed in hydrogen-based power generation from bioethanol steam reforming, the gas-liquid absorption using methyl-di-ethanol-amine (MDEA) was used. Bioethanol is a renewable energy carrier mainly produced from biomass fermentation. Steam reforming of bioethanol (SRE) provides a promising method for hydrogen and power production from renewable resources. SRE is performed at high temperatures (e.g. 800-900°C) to reduce the reforming by-products (e.g. ethane, ethene). The power generation from hydrogen was done with M701G2 gas turbine (334 MW net power output). Hydrogen was obtained through catalytic steam reforming of bioethanol without and with carbon capture. For the evaluated plant concepts the following key performance indicators were assessed: fuel consumption, gross and net power outputs, net electrical efficiency, ancillary consumptions, carbon capture rate, specific CO2 emission etc. As the results show, the power generation based on bioethanol conversion has high energy efficiency and low carbon footprint.

Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

Directory of Open Access Journals (Sweden)

Changqing Liu

2014-03-01

Full Text Available Bacterial artificial chromosome (BAC libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12, consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger.

Estimating evaporative vapor generation from automobiles based on parking activities

International Nuclear Information System (INIS)

Dong, Xinyi; Tschantz, Michael; Fu, Joshua S.

2015-01-01

A new approach is proposed to quantify the evaporative vapor generation based on real parking activity data. As compared to the existing methods, two improvements are applied in this new approach to reduce the uncertainties: First, evaporative vapor generation from diurnal parking events is usually calculated based on estimated average parking duration for the whole fleet, while in this study, vapor generation rate is calculated based on parking activities distribution. Second, rather than using the daily temperature gradient, this study uses hourly temperature observations to derive the hourly incremental vapor generation rates. The parking distribution and hourly incremental vapor generation rates are then adopted with Wade–Reddy's equation to estimate the weighted average evaporative generation. We find that hourly incremental rates can better describe the temporal variations of vapor generation, and the weighted vapor generation rate is 5–8% less than calculation without considering parking activity. - Highlights: • We applied real parking distribution data to estimate evaporative vapor generation. • We applied real hourly temperature data to estimate hourly incremental vapor generation rate. • Evaporative emission for Florence is estimated based on parking distribution and hourly rate. - A new approach is proposed to quantify the weighted evaporative vapor generation based on parking distribution with an hourly incremental vapor generation rate

Modeling Long-term Creep Performance for Welded Nickel-base Superalloy Structures for Power Generation Systems

Energy Technology Data Exchange (ETDEWEB)

Shen, Chen [GE Global Research, NIskayuna, NY (United States); Gupta, Vipul [GE Global Research, NIskayuna, NY (United States); Huang, Shenyan [GE Global Research, NIskayuna, NY (United States); Soare, Monica [GE Global Research, NIskayuna, NY (United States); Zhao, Pengyang [GE Global Research, NIskayuna, NY (United States); Wang, Yunzhi [GE Global Research, NIskayuna, NY (United States)

2017-02-28

The goal of this project is to model long-term creep performance for nickel-base superalloy weldments in high temperature power generation systems. The project uses physics-based modeling methodologies and algorithms for predicting alloy properties in heterogeneous material structures. The modeling methodology will be demonstrated on a gas turbine combustor liner weldment of Haynes 282 precipitate-strengthened nickel-base superalloy. The major developments are: (1) microstructure-property relationships under creep conditions and microstructure characterization (2) modeling inhomogeneous microstructure in superalloy weld (3) modeling mesoscale plastic deformation in superalloy weld and (4) a constitutive creep model that accounts for weld and base metal microstructure and their long term evolution. The developed modeling technology is aimed to provide a more efficient and accurate assessment of a material’s long-term performance compared with current testing and extrapolation methods. This modeling technology will also accelerate development and qualification of new materials in advanced power generation systems. This document is a final technical report for the project, covering efforts conducted from October 2014 to December 2016.

DNA-based random number generation in security circuitry.

Science.gov (United States)

Gearheart, Christy M; Arazi, Benjamin; Rouchka, Eric C

2010-06-01

DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. This research focuses on further developing DNA-based methodologies to mimic digital data manipulation. While exhibiting fundamental principles, this work was done in conjunction with the vision that DNA-based circuitry, when the technology matures, will form the basis for a tamper-proof security module, revolutionizing the meaning and concept of tamper-proofing and possibly preventing it altogether based on accurate scientific observations. A paramount part of such a solution would be self-generation of random numbers. A novel prototype schema employs solid phase synthesis of oligonucleotides for random construction of DNA sequences; temporary storage and retrieval is achieved through plasmid vectors. A discussion of how to evaluate sequence randomness is included, as well as how these techniques are applied to a simulation of the random number generation circuitry. Simulation results show generated sequences successfully pass three selected NIST random number generation tests specified for security applications.

Structural Acoustic Physics Based Modeling of Curved Composite Shells

Science.gov (United States)

2017-09-19

NUWC-NPT Technical Report 12,236 19 September 2017 Structural Acoustic Physics -Based Modeling of Curved Composite Shells Rachel E. Hesse...SUBTITLE Structural Acoustic Physics -Based Modeling of Curved Composite Shells 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...study was to use physics -based modeling (PBM) to investigate wave propagations through curved shells that are subjected to acoustic excitation. An

Genome Improvement at JGI-HAGSC

Energy Technology Data Exchange (ETDEWEB)

Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

2012-03-03

Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

Income and Physical Activity among Adults: Evidence from Self-Reported and Pedometer-Based Physical Activity Measurements.

Science.gov (United States)

Kari, Jaana T; Pehkonen, Jaakko; Hirvensalo, Mirja; Yang, Xiaolin; Hutri-Kähönen, Nina; Raitakari, Olli T; Tammelin, Tuija H

2015-01-01

This study examined the relationship between income and physical activity by using three measures to illustrate daily physical activity: the self-reported physical activity index for leisure-time physical activity, pedometer-based total steps for overall daily physical activity, and pedometer-based aerobic steps that reflect continuous steps for more than 10 min at a time. The study population consisted of 753 adults from Finland (mean age 41.7 years; 64% women) who participated in 2011 in the follow-up of the ongoing Young Finns study. Ordinary least squares models were used to evaluate the associations between income and physical activity. The consistency of the results was explored by using register-based income information from Statistics Finland, employing the instrumental variable approach, and dividing the pedometer-based physical activity according to weekdays and weekend days. The results indicated that higher income was associated with higher self-reported physical activity for both genders. The results were robust to the inclusion of the control variables and the use of register-based income information. However, the pedometer-based results were gender-specific and depended on the measurement day (weekday vs. weekend day). In more detail, the association was positive for women and negative or non-existing for men. According to the measurement day, among women, income was positively associated with aerobic steps despite the measurement day and with totals steps measured on the weekend. Among men, income was negatively associated with aerobic steps measured on weekdays. The results indicate that there is an association between income and physical activity, but the association is gender-specific and depends on the measurement type of physical activity.

An integrable low-cost hardware random number generator

Science.gov (United States)

Ranasinghe, Damith C.; Lim, Daihyun; Devadas, Srinivas; Jamali, Behnam; Zhu, Zheng; Cole, Peter H.

2005-02-01

A hardware random number generator is different from a pseudo-random number generator; a pseudo-random number generator approximates the assumed behavior of a real hardware random number generator. Simple pseudo random number generators suffices for most applications, however for demanding situations such as the generation of cryptographic keys, requires an efficient and a cost effective source of random numbers. Arbiter-based Physical Unclonable Functions (PUFs) proposed for physical authentication of ICs exploits statistical delay variation of wires and transistors across integrated circuits, as a result of process variations, to build a secret key unique to each IC. Experimental results and theoretical studies show that a sufficient amount of variation exits across IC"s. This variation enables each IC to be identified securely. It is possible to exploit the unreliability of these PUF responses to build a physical random number generator. There exists measurement noise, which comes from the instability of an arbiter when it is in a racing condition. There exist challenges whose responses are unpredictable. Without environmental variations, the responses of these challenges are random in repeated measurements. Compared to other physical random number generators, the PUF-based random number generators can be a compact and a low-power solution since the generator need only be turned on when required. A 64-stage PUF circuit costs less than 1000 gates and the circuit can be implemented using a standard IC manufacturing processes. In this paper we have presented a fast and an efficient random number generator, and analysed the quality of random numbers produced using an array of tests used by the National Institute of Standards and Technology to evaluate the randomness of random number generators designed for cryptographic applications.

Code-Hopping Based Transmission Scheme for Wireless Physical-Layer Security

Directory of Open Access Journals (Sweden)

Liuguo Yin

2018-01-01

Full Text Available Due to the broadcast and time-varying natures of wireless channels, traditional communication systems that provide data encryption at the application layer suffer many challenges such as error diffusion. In this paper, we propose a code-hopping based secrecy transmission scheme that uses dynamic nonsystematic low-density parity-check (LDPC codes and automatic repeat-request (ARQ mechanism to jointly encode and encrypt source messages at the physical layer. In this scheme, secret keys at the transmitter and the legitimate receiver are generated dynamically upon the source messages that have been transmitted successfully. During the transmission, each source message is jointly encoded and encrypted by a parity-check matrix, which is dynamically selected from a set of LDPC matrices based on the shared dynamic secret key. As for the eavesdropper (Eve, the uncorrectable decoding errors prevent her from generating the same secret key as the legitimate parties. Thus she cannot select the correct LDPC matrix to recover the source message. We demonstrate that our scheme can be compatible with traditional cryptosystems and enhance the security without sacrificing the error-correction performance. Numerical results show that the bit error rate (BER of Eve approaches 0.5 as the number of transmitted source messages increases and the security gap of the system is small.

Developing iPad-Based Physics Simulations That Can Help People Learn Newtonian Physics Concepts

Science.gov (United States)

Lee, Young-Jin

2015-01-01

The aims of this study are: (1) to develop iPad-based computer simulations called iSimPhysics that can help people learn Newtonian physics concepts; and (2) to assess its educational benefits and pedagogical usefulness. To facilitate learning, iSimPhysics visualizes abstract physics concepts, and allows for conducting a series of computer…

Object-Oriented Modeling of an Energy Harvesting System Based on Thermoelectric Generators

Science.gov (United States)

Nesarajah, Marco; Frey, Georg

This paper deals with the modeling of an energy harvesting system based on thermoelectric generators (TEG), and the validation of the model by means of a test bench. TEGs are capable to improve the overall energy efficiency of energy systems, e.g. combustion engines or heating systems, by using the remaining waste heat to generate electrical power. Previously, a component-oriented model of the TEG itself was developed in Modelica® language. With this model any TEG can be described and simulated given the material properties and the physical dimension. Now, this model was extended by the surrounding components to a complete model of a thermoelectric energy harvesting system. In addition to the TEG, the model contains the cooling system, the heat source, and the power electronics. To validate the simulation model, a test bench was built and installed on an oil-fired household heating system. The paper reports results of the measurements and discusses the validity of the developed simulation models. Furthermore, the efficiency of the proposed energy harvesting system is derived and possible improvements based on design variations tested in the simulation model are proposed.

Automatic Tamil lyric generation based on ontological interpretation ...

Indian Academy of Sciences (India)

This system proposes an -gram based approach to automatic Tamil lyric generation, by the ontological semantic interpretation of the input scene. The approach is based on identifying the semantics conveyed in the scenario, thereby making the system understand the situation and generate lyrics accordingly. The heart of ...

Extending synchrotron-based atomic physics experiments into the hard X-ray region

International Nuclear Information System (INIS)

LeBrun, T.

1996-01-01

The high-brightness, hard x-ray beams available from third-generation synchrotron sources are opening new opportunities to study the deepest inner shells of atoms, an area where little work has been done and phenomena not observed in less tightly bound inner-shells are manifested. In addition scattering processes which are weak at lower energies become important, providing another tool to investigate atomic structure as well as an opportunity to study photon/atom interactions beyond photoabsorption. In this contribution the authors discuss some of the issues related to extending synchrotron-based atomic physics experiments into the hard x-ray region from the physical and the experimental point of view. They close with a discussion of a technique, resonant Raman scattering, that may prove invaluable in determining the spectra of the very highly-excited states resulting from the excitation of deep inner shells

The Physical Basis of Lg Generation by Explosion Sources

Energy Technology Data Exchange (ETDEWEB)

J. L. Stevens; G. E. Baker; H. Xu; T. J. Bennett; N. Rimer; S. D. Day

2004-12-20

The goal of this project has been to develop a quantitative predictive capability for explosion-generated Lg phases with a sound and unambiguous physical basis. The research program consisted of a theoretical investigation of explosion-generated Lg combined with an observational study. The specific question addressed by this research program is how the Lg phase is generated by underground nuclear explosions. This question is fundamental to how Lg phases are interpreted for use in explosion yield estimation and earthquake/explosion discrimination. To constrain modeling, we have extensively reviewed the existing literature and complemented that work with an examination of several explosion data sets, most notably: (1) Degelen Mountain explosions recorded between 7 and 57 km, with corresponding recordings at Borovoye, at approximately 650 km; (2) recordings from Russian deep seismic sounding experiments; (3) NTS explosion sources including the NPE and nuclear tests covering a range of source depths and media properties. A simple point explosion in an infinite medium generates no shear waves, so the Lg phase is generated entirely by non-spherical components of the source and conversions through reflections and scattering. We find that the most important contributors to the Lg phase are: (1) P to S conversion at the free surface and other near source interfaces, (2) S waves generated directly by a realistically distributed explosion source including nonlinear effects due to the free surface and gravity, and (3) Rg scattering to Lg. Additional effects that contribute significantly to Lg are scattering of converted S phases that traps more of the converted P-to-S in the crust, and randomization of the components of Lg. The pS phase from a spherically symmetric explosion source in media with P-wave velocity less than upper mantle S-wave velocity is trapped in the crust and can explain the observed radial and vertical Lg. The free surface pS converted phase from the same