Comparison of next generation sequencing technologies for transcriptome characterization

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Soltis Douglas E

2009-08-01

Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants.

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Sucher, Nikolaus J; Hennell, James R; Carles, Maria C

2012-01-01

DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

Directory of Open Access Journals (Sweden)

Jiang Du

2009-07-01

Full Text Available The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen, with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs. SV reconstruction is considered the most challenging step in human genome re-sequencing. (It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome. To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of

Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Nutrition and Agriculture.

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Next-generation sequencing technologies are able to produce high-throughput short sequence reads in a cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. Here I survey their major applications ranging...

Breath-hold MR imaging of focal liver lesions: comparison of fast and ultrafast techniques

International Nuclear Information System (INIS)

Gaa, J.; Fischer, H.

1996-01-01

The performance of breath-hold MR imaging using two T2-weighted hybrid sequences (TSE, TGSE), two T2-weighted single-shot sequences (HASTE, EPI-SE), and one T1-weighted gradient-echo sequence (FLASH) was compared with a standard conventional T2-weighted SE sequence in 20 patients with focal liver lesions. Liver signal-to-noise ratio was highest for the FLASH sequence (54.3±8.3) and the HASTE (41.1±12.5) sequence, whereas the highest spleen-liver contrast-to-noise ratio was obtained by the TSE sequence (38.9±20.7). Lesion-liver CNR was highest with the TSE sequence (63.9±21.4). With both TSE and HASTE significantly (p<0.01) more lesions were detected as compared with SE and EPI-SE sequences. Our results indicate that breath-hold TSE and HASTE sequences will eventually replace conventional T2-weighted SE techniques due to their insensitivity to motion artifacts, superior lesions detectability and inherently short acquisition times. (orig.)

Holding Pressure and Its Influence on Quality in PIM Technology

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Pavel Petera

2012-01-01

Full Text Available The PIM (powder injection molding process consists of several steps in which faults can occur. The quality of the part that is produced usually cannot be seen until the end of the process. It is therefore necessary to find a way to discover the fault earlier in the process. The cause of defects is very often “phase separation” (inhomogeneity in powder distribution, which can also be influenced by the holding pressure. This paper evaluates the powder distribution with a new method based on density measurement. Measurements were made using various holding pressure values.

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

Science.gov (United States)

Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

2012-01-01

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

Application of genotyping by sequencing technology to a variety of crop breeding programs.

Science.gov (United States)

Kim, Changsoo; Guo, Hui; Kong, Wenqian; Chandnani, Rahul; Shuang, Lan-Shuan; Paterson, Andrew H

2016-01-01

Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The Citadel cannot hold: technologies go outside the hospital, patients and doctors too.

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Stoeckle, J D

1995-01-01

Use of the acute hospital has markedly decreased over the past four decades for various reasons: the decentralization of diagnostic treatment technologies to out-of-hospital sites; the clinical substitutions of quick diagnostic testing of the ambulatory patient for the longer diagnostic testing of the hospitalized patient; the diminished use of hospital bed rest and the expanded use of exercise for treatment; the corporate organization of hospital work that emphasizes efficiency; and the group practice organization of generalists and specialists that avoids hospital use for the diagnosis of complex disorders in ambulatory patients. A smaller domain for hospital bed care and renewed attention to chronic disease and prevention in the community diminish the hold of the acute hospital on care. The evolution of more collaborative, decentralized arrangements promises to be a positive development for community care.

DSAP: deep-sequencing small RNA analysis pipeline.

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Huang, Po-Jung; Liu, Yi-Chung; Lee, Chi-Ching; Lin, Wei-Chen; Gan, Richie Ruei-Chi; Lyu, Ping-Chiang; Tang, Petrus

2010-07-01

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log(2)-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

Linearization of weak hand holds in Russian Sign Language

NARCIS (Netherlands)

Kimmelman, V.

2017-01-01

Russian Sign Language (RSL) makes use of constructions involving manual simultaneity, in particular, weak hand holds, where one hand is being held in the location and configuration of a sign, while the other simultaneously produces one sign or a sequence of several signs. In this paper, I argue that

T2-weighted MR imaging of liver lesions: a prospective evaluation comparing turbo spin-echo, breath-hold turbo spin-echo and half-Fourier turbo spin-echo (HASTE) sequences; Estudio de lesiones hepaticas con imagenes de resonancia magnetica potenciadas en T2: evaluacion prospectiva comparando secuencias turbo eco del espin, turbo eco del espin con respiracion sostenida y half-Fourier turbo eco del espin (HASTE)

Energy Technology Data Exchange (ETDEWEB)

Martin, J.; Villajos, M.; Oses, M. J.; Veintemillas, M.; Rue, M.; Puig, J.; Sentis, M. [Fundacion Parc Tauli. Sabadell (Spain)

2000-07-01

To compare turbo spin-echo (TSE), breath-hold TSE and half-Fourier acquisition single-shot turbo spin-echo (HASTE) sequences quantitatively and qualitatively in T2-weighted images of liver lesions. The authors evaluated prospectively 89 liver lesions in 73 patients using a 1.0-T magnetic resonance system to compare TSE, breath-hold TSE and HASTE sequences. The quantitative parameters were: lesion-to-liver contrast and lesion-to-liver contrast-to-noise ratio. The qualitative analysis was performed by two observers in consensus who examined four parameters: respiratory artifacts, lesion edge definition, intrahepatic vessel definition and image quality. Repeated measures analysis of variance was utilized to compare the quantitative variables and Friedman's nonparametric test for the qualitative parameters. In quantitative terms, the lesion-to-liver contrast was similar in TSE and breath-hold TSE sequences (2.45{+-}1.44 versus 2.60{+-}1.66), both of which were significantly better than the HASTE sequence (1.12{+-}0.72; p<0.001). The lesion-to-liver contrast-to-noise ratio was significantly higher in the TSE sequence (62.60{+-}46.40 versus 40.22{+-}25.35 versus 50.90{+-}32.10 for TSE, breath-hold TSE and HASTE sequences, respectively; p<0.001). In the qualitative comparisons, the HASTE sequence was significantly better than the TSE and breath-hold TSE sequences (p<0.001) in terms of artifacts and definition of lesion edge and intrahepatic vessels. Image quality was also significantly greater in the HASTE sequence (p<0.001). In quantitative terms, the TSE sequence is better than the breath-hold TSE and HASTE sequences, but there are no movement artifacts in the HASTE sequence, which is also significantly superior to TSE and breath-hold TSE sequences in qualitative terms and, thus, can be employed for T2-weighted images in liver studies. (Author) 17 refs.

Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing.

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Schwessinger, Benjamin; Rathjen, John P

2017-01-01

Wheat rust fungi are complex organisms with a complete life cycle that involves two different host plants and five different spore types. During the asexual infection cycle on wheat, rusts produce massive amounts of dikaryotic urediniospores. These spores are dikaryotic (two nuclei) with each nucleus containing one haploid genome. This dikaryotic state is likely to contribute to their evolutionary success, making them some of the major wheat pathogens globally. Despite this, most published wheat rust genomes are highly fragmented and contain very little haplotype-specific sequence information. Current long-read sequencing technologies hold great promise to provide more contiguous and haplotype-phased genome assemblies. Long reads are able to span repetitive regions and phase structural differences between the haplomes. This increased genome resolution enables the identification of complex loci and the study of genome evolution beyond simple nucleotide polymorphisms. Long-read technologies require pure high molecular weight DNA as an input for sequencing. Here, we describe a DNA extraction protocol for rust spores that yields pure double-stranded DNA molecules with molecular weight of >50 kilo-base pairs (kbp). The isolated DNA is of sufficient purity for PacBio long-read sequencing, but may require additional purification for other sequencing technologies such as Nanopore and 10× Genomics.

The history and advances of reversible terminators used in new generations of sequencing technology.

Science.gov (United States)

Chen, Fei; Dong, Mengxing; Ge, Meng; Zhu, Lingxiang; Ren, Lufeng; Liu, Guocheng; Mu, Rong

2013-02-01

DNA sequencing using reversible terminators, as one sequencing by synthesis strategy, has garnered a great deal of interest due to its popular application in the second-generation high-throughput DNA sequencing technology. In this review, we provided its history of development, classification, and working mechanism of this technology. We also outlined the screening strategies for DNA polymerases to accommodate the reversible terminators as substrates during polymerization; particularly, we introduced the "REAP" method developed by us. At the end of this review, we discussed current limitations of this approach and provided potential solutions to extend its application. Copyright © 2013. Production and hosting by Elsevier Ltd.

Multi-center transferability of a breath-hold T2 technique for myocardial iron assessment

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Chan Godfrey CF

2008-02-01

Full Text Available Abstract Background Cardiac iron overload is the leading cause of death in thalassemia major and is usually assessed using myocardial T2* measurements. Recently a cardiovascular magnetic resonance (CMR breath-hold T2 sequence has been developed as a possible alternative. This cardiac T2 technique has good interstudy reproducibility, but its transferability to different centres has not yet been investigated. Methods and Results The breath-hold black blood spin echo T2 sequence was installed and validated on 1.5T Siemens MR scanners at 4 different centres across the world. Using this sequence, 5–10 thalassemia patients from each centre were scanned twice locally within a week for local interstudy reproducibility (n = 34 and all were rescanned within one month at the standardization centre in London (intersite reproducibility. The local interstudy reproducibility (coefficient of variance and mean difference were 4.4% and -0.06 ms. The intersite reproducibility and mean difference between scanners were 5.2% and -0.07 ms. Conclusion The breath-hold myocardial T2 technique is transferable between Siemens scanners with good intersite and local interstudy reproducibility. This technique may have value in the diagnosis and management of patients with iron overload conditions such as thalassemia.

INNOVATION DEVELOPMENT MANAGEMENT IN VERTICALLY INTEGRATED HOLDING COMPANY

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Natalya T. Uspenskaja

2015-01-01

Full Text Available The trend towards production consolidation and integration processes taking place both in the Russian and global economies leads to development of business associations, with a holding company being the most common form inRussiaand around the globe. The evidence in favor of the formation of holding companies is that they can benefit from the scale (bulk purchasing, centralized stuff training; in the global capital and exports markets they can be more effective than smaller businesses and, if non-profitable, a loss-making structure is easier to liquidate than the entire company; holding companies and associations can be an effective defender from political interference. As the importance of the well-functioning and harmonized procedure for the companies’ integration will increase (especially in the context of Russian business, where specific features of many areas of the production system imply the use of holding oligopolies as the most effective form of market structures, there is a need in their more profound study and, in particular, in the analysis of the most important technologies of the general integration procedure. The article outlines the relevance of innovative development management of vertically integrated holding systems, lists principles of innovative activity management and considers the features of innovation management of a vertically integrated holding company. The objective of the research is to study theoretical and practical aspects of innovative development management in vertically integrated holding systems. The object of research is management structures in innovative holding companies. While working on the article, the following methods of economic research were used: abstract and logical method, empirical method, method of expert evaluations, as well as methods of structural and functional and statistical analysis. 

Technology development for gene discovery and full-length sequencing

Energy Technology Data Exchange (ETDEWEB)

Marcelo Bento Soares

2004-07-19

In previous years, with support from the U.S. Department of Energy, we developed methods for construction of normalized and subtracted cDNA libraries, and constructed hundreds of high-quality libraries for production of Expressed Sequence Tags (ESTs). Our clones were made widely available to the scientific community through the IMAGE Consortium, and millions of ESTs were produced from our libraries either by collaborators or by our own sequencing laboratory at the University of Iowa. During this grant period, we focused on (1) the development of a method for preferential cloning of tissue-specific and/or rare transcripts, (2) its utilization to expedite EST-based gene discovery for the NIH Mouse Brain Molecular Anatomy Project, (3) further development and optimization of a method for construction of full-length-enriched cDNA libraries, and (4) modification of a plasmid vector to maximize efficiency of full-length cDNA sequencing by the transposon-mediated approach. It is noteworthy that the technology developed for preferential cloning of rare mRNAs enabled identification of over 2,000 mouse transcripts differentially expressed in the hippocampus. In addition, the method that we optimized for construction of full-length-enriched cDNA libraries was successfully utilized for the production of approximately fifty libraries from the developing mouse nervous system, from which over 2,500 full-ORF-containing cDNAs have been identified and accurately sequenced in their entirety either by our group or by the NIH-Mammalian Gene Collection Program Sequencing Team.

Blazar Sequence in Fermi Era Liang Chen

Indian Academy of Sciences (India)

Abstract. In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power- high-synchrotron-peaked and ...

Comparing microarrays and next-generation sequencing technologies for microbial ecology research.

Science.gov (United States)

Roh, Seong Woon; Abell, Guy C J; Kim, Kyoung-Ho; Nam, Young-Do; Bae, Jin-Woo

2010-06-01

Recent advances in molecular biology have resulted in the application of DNA microarrays and next-generation sequencing (NGS) technologies to the field of microbial ecology. This review aims to examine the strengths and weaknesses of each of the methodologies, including depth and ease of analysis, throughput and cost-effectiveness. It also intends to highlight the optimal application of each of the individual technologies toward the study of a particular environment and identify potential synergies between the two main technologies, whereby both sample number and coverage can be maximized. We suggest that the efficient use of microarray and NGS technologies will allow researchers to advance the field of microbial ecology, and importantly, improve our understanding of the role of microorganisms in their various environments.

Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology.

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William E Stutz

Full Text Available Genes of the vertebrate major histocompatibility complex (MHC are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems:1 a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2 a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci--Stepwise Threshold Clustering (STC--that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.

Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology.

Science.gov (United States)

Tanase, Koji; Nishitani, Chikako; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Ohmiya, Akemi; Onozaki, Takashi

2012-07-02

Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. We constructed a normalized cDNA library and a 3'-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

Transcriptome analysis of carnation (Dianthus caryophyllus L. based on next-generation sequencing technology

Directory of Open Access Journals (Sweden)

Tanase Koji

2012-07-01

Full Text Available Abstract Background Carnation (Dianthus caryophyllus L., in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. Results We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380 of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. Conclusions We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

Science.gov (United States)

Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

2018-04-02

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious

FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies.

Science.gov (United States)

Wilson, Carolyn A; Simonyan, Vahan

2014-01-01

Applications of next-generation sequencing (NGS) technologies require availability and access to an information technology (IT) infrastructure and bioinformatics tools for large amounts of data storage and analyses. The U.S. Food and Drug Administration (FDA) anticipates that the use of NGS data to support regulatory submissions will continue to increase as the scientific and clinical communities become more familiar with the technologies and identify more ways to apply these advanced methods to support development and evaluation of new biomedical products. FDA laboratories are conducting research on different NGS platforms and developing the IT infrastructure and bioinformatics tools needed to enable regulatory evaluation of the technologies and the data sponsors will submit. A High-performance Integrated Virtual Environment, or HIVE, has been launched, and development and refinement continues as a collaborative effort between the FDA and George Washington University to provide the tools to support these needs. The use of a highly parallelized environment facilitated by use of distributed cloud storage and computation has resulted in a platform that is both rapid and responsive to changing scientific needs. The FDA plans to further develop in-house capacity in this area, while also supporting engagement by the external community, by sponsoring an open, public workshop to discuss NGS technologies and data formats standardization, and to promote the adoption of interoperability protocols in September 2014. Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and

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

Directory of Open Access Journals (Sweden)

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

Electric Holding Company Areas

Data.gov (United States)

Department of Homeland Security — Holding companies are electric power utilities that have a holding company structure. This vector polygon layer represents the area served by electric power holding...

Magnetic Resonance Imaging in Breath-Hold Divers with Cerebral Decompression Sickness

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Ryu Matsuo

2014-01-01

Full Text Available The mechanism of cerebral decompression sickness (DCS is still unclear. We report 2 cases of breath-hold divers with cerebral DCS in whom magnetic resonance imaging (MRI demonstrated distinctive characteristics. One case presented right hemiparesthesia, diplopia, and gait disturbance after breath-hold diving into the sea at a depth of 20 m. Brain MRI with fluid-attenuated inversion recovery (FLAIR sequence revealed multiple hyperintense lesions in the right frontal lobe, bilateral thalamus, pons, and right cerebellar hemisphere. The second case presented visual and gait disturbance after repetitive breath-hold diving into the sea. FLAIR imaging showed hyperintense areas in the bilateral occipito-parietal lobes. In both cases, diffusion-weighted imaging and apparent diffusion coefficient mapping revealed hyperintense areas in the lesions identified by FLAIR. Moreover, follow-up MRI showed attenuation of the FLAIR signal abnormalities. These findings are suggestive of transient hyperpermeability in the microvasculature as a possible cause of cerebral DCS.

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

KAUST Repository

Cahill, Matt J.

2010-07-12

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

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

Directory of Open Access Journals (Sweden)

Matt J Cahill

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

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

KAUST Repository

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

2010-01-01

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

SPIO-enhanced MR imaging for HCC detection in cirrhotic patient : comparison of various techniques for optimal sequence selection

International Nuclear Information System (INIS)

Kim, In Hwan; Lee, Jeong Min; Kwak, Hyo Sung; Kim, Chong Soo; Yu, Hee Chul; Kim, Tae Kon; Lee Soo Tiek

2000-01-01

To compare the efficacy of breathhold and non-breathhold sequences in the detection of hepatocellular carcinoma (HCC) in cirrhotic patients using superparamagnetic iron oxide (SPIO)-enhanced MR imaging, and to determine the optimal sequence combination. By means of unenhanced and iron-oxide-enhanced MRI, 29 patients with 49 nodular HCCs were evaluated for the presence of HCC nodules. Twenty-one were male and eight were female, and their ages ranged from 38 to 71 (mean, 56) years. Eight different MR sequences were used, including four non-breath-hold sequences and four breath-hold, and images were obtained before and after the administration of SPIO particles. Non-breath-hold sequences included T2-, proton density-weighted SE, and TSE imaging, while breath-hold sequences comprised T1-weighted fast low-angle shot (T1w FLASH), half-Fourier acquisition single shot turbo spine echo (HASTE), T2-weighted fast imaging with steady-state free precession (T2 * wFISP) and T2-weighted breath-hold TSE (T2wBHTSE). Image analysis involved both quantitative and qualitative analysis. The quantitative parameters calculated were signal-to noise (S/N) ratios for livers and tumors, contrast to noise (C/N) ratios for tumors seen on precontrast and postcontrast images, and percentage of signal intensity loss (PSIL) after SPIO injection. Images were analysed qualitatively in terms of image artifacts and lesion conspicuity, and prior to calculating sensitivity, the number of lesions detected using various pulse sequences were counted. SPIO had a marked effect on liver S/N ratio but a minimal effect on tumor S/N ratio. PSIL was best in T2 * wFISP images, while T2wSE images showed the second-best results (p less than 0.05). Tumor-to-liver C/N values were also highest with T2 * wFISP, while T2wTSE and HASTE images were next. Qualitative study showed that non-breath hold images and FISP were better than breath hold images in terms of lesion conspicuity. The latter, however, were much better

Controllable deterioration rate for time-dependent demand and time-varying holding cost

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Mishra Vinod Kumar

2014-01-01

Full Text Available In this paper, we develop an inventory model for non-instantaneous deteriorating items under the consideration of the facts: deterioration rate can be controlled by using the preservation technology (PT during deteriorating period, and holding cost and demand rate both are linear function of time, which was treated as constant in most of the deteriorating inventory models. So in this paper, we developed a deterministic inventory model for non-instantaneous deteriorating items in which both demand rate and holding cost are a linear function of time, deterioration rate is constant, backlogging rate is variable and depend on the length of the next replenishment, shortages are allowed and partially backlogged. The model is solved analytically by minimizing the total cost of the inventory system. The model can be applied to optimizing the total inventory cost of non-instantaneous deteriorating items inventory for the business enterprises, where the preservation technology is used to control the deterioration rate, and demand & holding cost both are a linear function of time.

The first FDA marketing authorizations of next-generation sequencing technology and tests: challenges, solutions and impact for future assays.

Science.gov (United States)

Bijwaard, Karen; Dickey, Jennifer S; Kelm, Kellie; Težak, Živana

2015-01-01

The rapid emergence and clinical translation of novel high-throughput sequencing technologies created a need to clarify the regulatory pathway for the evaluation and authorization of these unique technologies. Recently, the US FDA authorized for marketing four next generation sequencing (NGS)-based diagnostic devices which consisted of two heritable disease-specific assays, library preparation reagents and a NGS platform that are intended for human germline targeted sequencing from whole blood. These first authorizations can serve as a case study in how different types of NGS-based technology are reviewed by the FDA. In this manuscript we describe challenges associated with the evaluation of these novel technologies and provide an overview of what was reviewed. Besides making validated NGS-based devices available for in vitro diagnostic use, these first authorizations create a regulatory path for similar future instruments and assays.

Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain.

Science.gov (United States)

Yang, Xiang; Noyes, Noelle R; Doster, Enrique; Martin, Jennifer N; Linke, Lyndsey M; Magnuson, Roberta J; Yang, Hua; Geornaras, Ifigenia; Woerner, Dale R; Jones, Kenneth L; Ruiz, Jaime; Boucher, Christina; Morley, Paul S; Belk, Keith E

2016-04-01

Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni,C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica,E. coli, and C. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes. Copyright © 2016 Yang et al.

Comparison of 3D two-point Dixon and standard 2D dual-echo breath-hold sequences for detection and quantification of fat content in renal angiomyolipoma

International Nuclear Information System (INIS)

Rosenkrantz, Andrew B.; Raj, Sean; Babb, James S.; Chandarana, Hersh

2012-01-01

Purpose: To assess the utility of a 3D two-point Dixon sequence with water–fat decomposition for quantification of fat content of renal angiomyolipoma (AML). Methods: 84 patients underwent renal MRI including 2D in-and-opposed-phase (IP and OP) sequence and 3D two-point Dixon sequence that generates four image sets [IP, OP, water-only (WO), and fat-only (FO)] within one breath-hold. Two radiologists reviewed 2D and 3D images during separate sessions to identify fat-containing renal masses measuring at least 1 cm. For identified lesions subsequently confirmed to represent AML, ROIs were placed at matching locations on 2D and 3D images and used to calculate 2D and 3D SI index [(SI IP − SI OP )/SI IP ] and 3D fat fraction (FF) [SI FO /(SI FO + SI WO )]. 2D and 3D SI index were compared with 3D FF using Pearson correlation coefficients. Results: 41 AMLs were identified in 6 patients. While all were identified using the 3D sequence, 39 were identified using the 2D sequence, with the remaining 2 AMLs retrospectively visible on 2D images but measuring under 1 cm. Among 32 AMLs with a 3D FF of over 50%, both 2D and 3D SI index showed a statistically significant inverse correlation with 3D FF (2D SI index : r = −0.63, p = 0.0010; 3D SI index : r = −0.97, p index , is not limited by ambiguity of water or fat dominance. This may assist clinical management of AML given evidence that fat content predicts embolization response.

31 CFR 800.217 - Hold.

Science.gov (United States)

2010-07-01

... and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF INVESTMENT... FOREIGN PERSONS Definitions § 800.217 Hold. The terms hold(s) and holding mean legal or beneficial ownership, whether direct or indirect, whether through fiduciaries, agents, or other means. ...

Holding the Edge: Maintaining the Defense Technology Base

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1989-04-01

psychological , with the shedding of isolationist technology that is close or equal to that of the United attitudes and inhibitions. Reaction by European States...are directed toward aleveling could work against what should be a good common set of enabling technologies, with applica- leeida carld work aanst

Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences

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Alessandra Traini

2013-01-01

Full Text Available Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences.

Science.gov (United States)

Traini, Alessandra; Iorizzo, Massimo; Mann, Harpartap; Bradeen, James M; Carputo, Domenico; Frusciante, Luigi; Chiusano, Maria Luisa

2013-01-01

Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

[Application of next-generation semiconductor sequencing technologies in genetic diagnosis of inherited cardiomyopathies].

Science.gov (United States)

Zhao, Yue; Zhang, Hong; Xia, Xue-shan

2015-07-01

Inherited cardiomyopathy is the most common hereditary cardiac disease. It also causes a significant proportion of sudden cardiac deaths in young adults and athletes. So far, approximately one hundred genes have been reported to be involved in cardiomyopathies through different mechanisms. Therefore, the identification of the genetic basis and disease mechanisms of cardiomyopathies are important for establishing a clinical diagnosis and genetic testing. Next-generation semiconductor sequencing (NGSS) technology platform is a high-throughput sequencer capable of analyzing clinically derived genomes with high productivity, sensitivity and specificity. It was launched in 2010 by Life Technologies of USA, and it is based on a high density semiconductor chip, which was covered with tens of thousands of wells. NGSS has been successfully used in candidate gene mutation screening to identify hereditary disease. In this review, we summarize these genetic variations, challenge and application of NGSS in inherited cardiomyopathy, and its value in disease diagnosis, prevention and treatment.

Comparative study of fast T 2-weighted images using respiratory triggered, breath-hold, fat suppression and phased array multi coil for liver evaluation by magnetic resonance imaging

International Nuclear Information System (INIS)

Abbehusen, Cristiane L.; D'Ippolito, Giuseppe; Palacio, Glaucia A.S.; Szejnfeld, Jacob

2003-01-01

The objective of this study was to compare both qualitatively and quantitatively six T 2-weighted turbo spin-echo sequences varying the respiratory compensation technique, associating or not fat tissue suppression and using different types of coils. We performed a prospective study of 71 consecutive patients that were submitted to MRI of the liver using a 1.5 T magnet. The six following pulse sequences were used: fat-suppressed respiratory triggered with conventional body coil; breath-hold fat-suppressed with conventional body coil; non-suppressed respiratory triggered with conventional body coil; breath-hold non fat-suppressed with conventional body coil; fat-suppressed respiratory triggered with phased-array multi coil; breath-hold fat-suppressed with phased-array multi coil. Images were analyzed quantitatively by measuring the signal-to-noise ratios and qualitatively by evaluating the sharpness of hepatic contours, visibility of intrahepatic vessels and other segmental landmarks, and the presence of artifacts. Results: the qualitative analysis showed that the mean values obtained with the six sequences were 7.8, 4.6, 7.9, 5.2, 6.7 and 4.6 respectively. The respiratory-triggered sequences were better than the breath-hold sequences in both qualitative and quantitative analysis (p < 0.001). No significant differences in the values of signal-to-noise ratios and in overall image quality were found between the sequences with and without fat suppression (p . 0.05). The sequences using the body coil were similar in terms of image quality (p . 0.05) and better regarding signal-to-noise ratios than those obtained with the phased=array multi coil (p ,0.001). Our qualitative and quantitative results suggest that the best MRI sequences for the valuation of the liver are the sequences with respiratory triggering using a conventional body coil, with or without fat suppression. (author)

Usability of Particle Film Technology and Water Holding Materials to Improve Drought Tolerance in Gossypium hirsutum L. Plants

Science.gov (United States)

Roy, K.; Zwieniecki, M.

2017-12-01

Cotton (Gossypium hirsutum L.) is relatively drought resistant and thus is planted widely in many semi-arid and arid parts of the world, many of which are usually deprived of modern water management technologies. Since the productivity of cotton plants depends on water availability, we carried out the present research aiming at testing two different low cost and arid-environment friendly water efficient techniques: application of particle film technology on leaves to reduce the transpiration rate (kaolin dust), and use of organic material to improve the soil water holding capacity (cotton wool). In details, kaolin (3% and 5%; weight:volume) mixed in water was sprayed on the upper surface of the leaves of young plants, and small amounts of cotton wool (0.1%, 0.3% and 0.5%; weight:weight) were mixed into the soils. The study showed that kaolin spray was useful as a transpiration reducing agent only if plants have adequate water in the soil (well irrigated) but not under water stress conditions. In addition, mixing a small amount of cotton wool into the soil can significantly increase the amount of water available to the plants, and extend the benefit of kaolin application on plants.

On statistical acceleration convergence of double sequences

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Bipan Hazarika

2017-04-01

Full Text Available In this article the notion of statistical acceleration convergence of double sequences in Pringsheim's sense has been introduced. We prove the decompostion theorems for  statistical acceleration convergence of double sequences and some theorems related to that concept have been established using the four dimensional matrix transformations. We provided some examples, where the results of acceleration convergence fails to hold for the statistical cases.

Accurate step-hold tracking of smoothly varying periodic and aperiodic probability.

Science.gov (United States)

Ricci, Matthew; Gallistel, Randy

2017-07-01

Subjects observing many samples from a Bernoulli distribution are able to perceive an estimate of the generating parameter. A question of fundamental importance is how the current percept-what we think the probability now is-depends on the sequence of observed samples. Answers to this question are strongly constrained by the manner in which the current percept changes in response to changes in the hidden parameter. Subjects do not update their percept trial-by-trial when the hidden probability undergoes unpredictable and unsignaled step changes; instead, they update it only intermittently in a step-hold pattern. It could be that the step-hold pattern is not essential to the perception of probability and is only an artifact of step changes in the hidden parameter. However, we now report that the step-hold pattern obtains even when the parameter varies slowly and smoothly. It obtains even when the smooth variation is periodic (sinusoidal) and perceived as such. We elaborate on a previously published theory that accounts for: (i) the quantitative properties of the step-hold update pattern; (ii) subjects' quick and accurate reporting of changes; (iii) subjects' second thoughts about previously reported changes; (iv) subjects' detection of higher-order structure in patterns of change. We also call attention to the challenges these results pose for trial-by-trial updating theories.

SEQUENCING BATCH REACTOR: A PROMISING TECHNOLOGY IN WASTEWATER TREATMENT

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A. H. Mahvi

2008-04-01

Full Text Available Discharge of domestic and industrial wastewater to surface or groundwater is very dangerous to the environment. Therefore treatment of any kind of wastewater to produce effluent with good quality is necessary. In this regard choosing an effective treatment system is important. Sequencing batch reactor is a modification of activated sludge process which has been successfully used to treat municipal and industrial wastewater. The process could be applied for nutrients removal, high biochemical oxygen demand containing industrial wastewater, wastewater containing toxic materials such as cyanide, copper, chromium, lead and nickel, food industries effluents, landfill leachates and tannery wastewater. Of the process advantages are single-tank configuration, small foot print, easily expandable, simple operation and low capital costs. Many researches have been conducted on this treatment technology. The authors had been conducted some investigations on a modification of sequencing batch reactor. Their studies resulted in very high percentage removal of biochemical oxygen demand, chemical oxygen demand, total kjeldahl nitrogen, total nitrogen, total phosphorus and total suspended solids respectively. This paper reviews some of the published works in addition to experiences of the authors.

78 FR 23162 - Supervision and Regulation Assessments for Bank Holding Companies and Savings and Loan Holding...

Science.gov (United States)

2013-04-18

... bank holding company's Consolidated Financial Statements for Bank Holding Companies (FR Y-9C) forms; \\3... Balance Sheet of the BHC's Consolidated Financial Statements for Bank Holding Companies (FR Y-9C) (OMB No... holding companies with $50 billion or more in total consolidated assets, and nonbank financial companies...

Students' Guided Reinvention of Definition of Limit of a Sequence with Interactive Technology

Science.gov (United States)

Flores, Alfinio; Park, Jungeun

2016-01-01

In a course emphasizing interactive technology, 19 students, including 18 mathematics education majors, mostly in their first year, reinvented the definition of limit of a sequence while working in small cooperative groups. The class spent four sessions of 75 minutes each on a cyclical process of guided reinvention of the definition of limit of a…

An on-line BCI for control of hand grasp sequence and holding using adaptive probabilistic neural network.

Science.gov (United States)

Hazrati, Mehrnaz Kh; Erfanian, Abbas

2008-01-01

This paper presents a new EEG-based Brain-Computer Interface (BCI) for on-line controlling the sequence of hand grasping and holding in a virtual reality environment. The goal of this research is to develop an interaction technique that will allow the BCI to be effective in real-world scenarios for hand grasp control. Moreover, for consistency of man-machine interface, it is desirable the intended movement to be what the subject imagines. For this purpose, we developed an on-line BCI which was based on the classification of EEG associated with imagination of the movement of hand grasping and resting state. A classifier based on probabilistic neural network (PNN) was introduced for classifying the EEG. The PNN is a feedforward neural network that realizes the Bayes decision discriminant function by estimating probability density function using mixtures of Gaussian kernels. Two types of classification schemes were considered here for on-line hand control: adaptive and static. In contrast to static classification, the adaptive classifier was continuously updated on-line during recording. The experimental evaluation on six subjects on different days demonstrated that by using the static scheme, a classification accuracy as high as the rate obtained by the adaptive scheme can be achieved. At the best case, an average classification accuracy of 93.0% and 85.8% was obtained using adaptive and static scheme, respectively. The results obtained from more than 1500 trials on six subjects showed that interactive virtual reality environment can be used as an effective tool for subject training in BCI.

The advantages of SMRT sequencing

OpenAIRE

Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

2013-01-01

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

12 CFR 584.2-2 - Permissible bank holding company activities of savings and loan holding companies.

Science.gov (United States)

2010-01-01

... savings and loan holding companies. 584.2-2 Section 584.2-2 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY SAVINGS AND LOAN HOLDING COMPANIES § 584.2-2 Permissible bank holding company activities of savings and loan holding companies. (a) General. For purposes of § 584.2(b)(6)(i) of this part...

Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation

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Wang Yong

2011-10-01

Full Text Available Abstract Background With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched. Results In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in Escherichia coli and Saccharomyces cerevisiae respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology. Conclusions By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.

A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

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Yu Cao

2017-09-01

Full Text Available The development of next generation sequencing (NGS techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents or a food manufacturing facility econiche (e.g., floor drain. To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.

A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

Science.gov (United States)

Cao, Yu; Fanning, Séamus; Proos, Sinéad; Jordan, Kieran; Srikumar, Shabarinath

2017-01-01

The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods. PMID:29033905

Single breath hold 3D cardiac cine MRI using kat-ARC: preliminary results at 1.5T.

Science.gov (United States)

Jeong, Daniel; Schiebler, Mark L; Lai, Peng; Wang, Kang; Vigen, Karl K; François, Christopher J

2015-04-01

Validation of a new single breath-hold, three-dimensional, cine balanced steady-state free precession (3D cine bSSFP) cardiac magnetic resonance (CMR) sequence for left ventricular function. CMR examinations were performed on fifteen patients and three healthy volunteers on a clinical 1.5T scanner using a two-dimensional (2D) cine balanced SSFP CMR sequence (2D cine bSSFP) followed by an investigational 3D cine bSSFP pulse sequence acquired within a single breath hold. Left ventricular end diastolic volume (LVEDV), end systolic volume (LVESV), ejection fraction (LVEF), and myocardial mass were independently segmented on a workstation by two experienced radiologists. Blood pool to myocardial contrast was evaluated in consensus using a Likert scale. Bland-Altman analysis was used to compare these quantitative and nominal measurements for the two sequences. The average acquisition time was significantly shorter for the 3D cine bSSFP than for 2D cine bSSFP (0.36 ± 0.03 vs. 8.5 ± 2.3 min) p = 0.0002. Bland-Altman analyses [bias and (limits of agreement)] of the data derived from these two methods revealed that the LVEF 0.9% (-4.7, 6.4), LVEDV 4.9 ml (-23.0, 32.8), LVESV -0.2 ml (-22.4, 21.9), and myocardial mass -0.4 g (-23.8, 23.0) were not significantly different. There was excellent intraclass correlation for intra-observer variability (0.981, 0.989, 0.997, 0.985) and inter-observer variability (0.903, 0.954, 0.970, 0.842) for LVEF, LVEDV, LVESV, and myocardial mass respectively. 3D cine bSSFP allows for accurate single breath-hold volumetric cine CMR which enables substantial improvements in scanner time efficiency without sacrificing diagnostic accuracy.

Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation.

Directory of Open Access Journals (Sweden)

Si-Yang Liu

Full Text Available Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing data and the methylome comparisons with other fungi confirm that the DNA methylation level of this fungus is negligible. Further investigation into the DNA methyltransferase of Aspergillus uncovers its close relationship with RID-like enzymes as well as its divergence with the methyltransferase of species with validated DNA methylation. The lack of repeat contents of the A. flavus' genome and the high RIP-index of the small amount of remanent repeat potentially support our speculation that DNA methylation may be absent in A. flavus or that it may possess de novo DNA methylation which occurs very transiently during the obscure sexual stage of this fungal species. This work contributes to our understanding on the DNA methylation status of A. flavus, as well as reinforces our views on the DNA methylation in fungal species. In addition, our strategy of applying bisulfite sequencing to DNA methylation detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species.

12 CFR 225.82 - How does a bank holding company elect to become a financial holding company?

Science.gov (United States)

2010-01-01

... holding company to become a financial holding company shall not be effective if, during the period...) Effective date of election—(1) In general. An election filed by a bank holding company under paragraph (a... financial holding company is effective prior to the 31st day after the date that a complete declaration was...

SPECIALIZATION AND SUSTAINABLE DEVELOPMENT OF AGRICULTURAL HOLDINGS

Directory of Open Access Journals (Sweden)

Zofia Kołoszko-Chomentowska

2016-03-01

Full Text Available In the present article, an attempt was made to assess the sustainability of agricultural holdings with diff erent directions of production. Agricultural holdings in the Podlaskie voivodeship registered in the FADN system in 2011–2012 were investigated. Assessment accounted for agroecological indicators (share of permanent grasslands, share of cereals in crops, soil coverage with vegetation, stock density and economic indicators (profi tableness of land and labor. Analysis was conducted according to a classifi cation into agricultural holding types: fi eldcrops, dairy cattle, and granivores. Fieldcrop and granivore holdings achieved more favourable environmental sustainability indicators. Holdings specializing in dairy cattle breeding posed a threat to the natural environment, mainly due to their excessive stock density. Economic sustainability assessment showed that granivore holdings were assessed most favorably. In these holdings, holding income per full-time worker was 37% greater than in fi eldcrop holdings and 57% greater than in dairy cattle holdings.

Inflation, operating cycle, and cash holdings

Directory of Open Access Journals (Sweden)

Yanchao Wang

2014-12-01

Full Text Available A corporate cash-holding strategy is a trade-off between the costs and benefits of holding cash. At the macrolevel, firms are inclined to adjust and optimize their cash-holding strategies in response to changes in purchasing power due to inflation. At the microlevel, the operating cycle, which indicates the speed and turnover of corporate cash flow, also influences the corporate cash-holding strategy. Firms flexibly adjust their cash-holding strategies in response to changes in the internal and external environment, which is referred to as the cash adjustment strategy. We examine these predicted relationships using a sample of listed firms in China’s stock market over the 1998–2009 period. Consistent with our predictions, the empirical results indicate a significant negative association between cash holdings and the CPI, but the relationship is reversed when the CPI reaches a certain level. There is also a U-shaped relationship between operating cycle and cash holdings, and this relationship is similarly influenced by changes in the inflation level. In examining the macroeconomic environment and microlevel firm-specific characteristics simultaneously, our findings supplement the literature on firms’ cash-holding strategies and provide theoretical and practical implications.

Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging

Energy Technology Data Exchange (ETDEWEB)

Nolte-Ernsting, C.C.A.; Tacke, J.; Adam, G.B.; Haage, P.; Guenther, R.W. [Univ. of Technology, Aachen (Germany). Dept. of Diagnostic Radiology; Jung, P.; Jakse, G. [Univ. of Technology, Aachen (Germany). Dept. of Urology

2001-01-01

The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p < 0.0001). Susceptibility effects were more pronounced on GRE EPI MR urograms and calculi measured 0.8-21.7% greater in diameter compared with conventional GRE sequences. Increased spatial resolution degraded the image quality only in GRE-EPI urograms. (orig.)

Ultrasonic methods for locating hold-up

International Nuclear Information System (INIS)

Sinha, D.N.; Olinger, C.T.

1995-01-01

Hold-up remains one of the major contributing factors to unaccounted for materials and can be a costly problem in decontamination and decommissioning activities. Ultrasonic techniques are being developed to noninvasively monitor hold-up in process equipment where the inner surface of such equipment may be in contact with the hold-up material. These techniques may be useful in improving hold-up measurements as well as optimizing decontamination techniques

Search Technologies | NCI Technology Transfer Center | TTC

Science.gov (United States)

Our team of technology transfer specialists has specialized training in invention reporting, patenting, patent strategy, executing technology transfer agreements and marketing. TTC is comprised of professionals with diverse legal, scientific, and business/marketing expertise. Most of our staff hold doctorate-level technical and/or legal training.

Available Technologies | NCI Technology Transfer Center | TTC

Science.gov (United States)

Our team of technology transfer specialists has specialized training in invention reporting, patenting, patent strategy, executing technology transfer agreements and marketing. TTC is comprised of professionals with diverse legal, scientific, and business/marketing expertise. Most of our staff hold doctorate-level technical and/or legal training.

Holding fast.

Science.gov (United States)

Gourville, John T

2005-06-01

CEO Peter Walsh faces a classic innovator's dilemma. His company, Crescordia, produces high-quality metal plates, pins, and screws that orthopedic surgeons use to repair broken bones. In fact, because the company has for decades refused to compromise on quality, there are orthopedic surgeons who use nothing but Crescordia hardware. And now these customers have begun to clamor for the next generation technology: resorbable hardware. Resorbables offer clear advantages over the traditional hardware. Like dissolving sutures, resorbable plates and screws are made of biodegradable polymers. They hold up long enough to support a healing bone, then gradually and harmlessly disintegrate in the patient's body. Surgeons are especially looking forward to using resorbables on children, so kids won't have to undergo a second operation to remove the old hardware after their bones heal, a common procedure in pediatrics. The new products, however, are not yet reliable; they fail about 8% of the time, sometimes disintegrating before the bone completely heals and sometimes not ever fully disintegrating. That's why Crescordia, mindful of its hard-earned reputation, has delayed launching a line using the new technology. But time is running out. A few competitors have begun to sell resorbables despite their imperfections, and these companies are picking up market share. Should Crescordia join the fray and risk tarnishing its brand? Or should the company sit tight until it can offer a perfect product? Commenting on this fictional case study are Robert A. Lutz, vice chairman of product development at General Motors; Clayton M. Christensen, the Robert and Jane Cizik Professor of Business Administration at Harvard Business School; Jason Wittes, a senior equity analyst covering medical supplies and devices at Leerink Swann; and Nick Galakatos, a general partner of MPM Capital.

In vivo proton MRS of normal pancreas metabolites during breath-holding and free-breathing

International Nuclear Information System (INIS)

Su, T.-H.; Jin, E.-H.; Shen, H.; Zhang, Y.; He, W.

2012-01-01

Aim: To characterize normal pancreas metabolites using in vivo proton magnetic resonance spectroscopy ( 1 H MRS) at 3 T under conditions of breath-holding and free-breathing. Materials and methods: The pancreases of 32 healthy volunteers were examined using 1 H MRS during breath-holding and free-breathing acquisitions in a single-voxel point-resolved selective spectroscopy sequence (PRESS) technique using a 3 T MRI system. Resonances were compared between paired spectra of the two breathing modes. Furthermore, correlations between lipid (Lip) content and age, body-mass index (BMI), as well as choline (Cho) peak visibility of the normal pancreas were analysed during breath-holding. Results: Twenty-nine pairs of spectra were successfully obtained showing three major resonances, Lip, Cho, cholesterol and the unsaturated parts of the olefinic region of fatty acids (Chol + Unsat). Breath-hold spectra were generally better, with higher signal-to-noise ratios (SNR; Z=–2.646, p = 0.008) and Cho peak visible status (Z=–2.449, p = 0.014). Correlations were significant between spectra acquired by the two breathing modes, especially for Lip height, Lip area, and the area of other peaks at 1.9–4.1 ppm. However, the Lip resonance was significantly different between the spectra of the two breathing modes (p 1 H MRS of the normal pancreas at 3 T is technically feasible and can characterize several metabolites. 1 H MRS during breath-holding acquisition is superior to that during free-breathing acquisition.

Tube holding system

International Nuclear Information System (INIS)

Cunningham, R.C.

1978-01-01

A tube holding rig is described for the lateral support of tubes arranged in tight parcels in a heat exchanger. This tube holding rig includes not less than two tube supporting assemblies, with a space between them, located crosswise with respect to the tubes, each supporting assembly comprising a first set of parallel components in contact with the tubes, whilst a second set of components is also in contact with the tubes. These two sets of parts together define apertures through which the tubes pass [fr

Sequence assembly

DEFF Research Database (Denmark)

Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

2009-01-01

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

The Impact of Sustainable Development Technology on a Small Economy-The Case of Energy-Saving Technology.

Science.gov (United States)

Chen, Xiding; Huang, Qinghua; Huang, Weilun; Li, Xue

2018-02-08

We investigated the impact of a sustainable development technology on the macroeconomic variables in a small economy utilizing a case study with a stochastically improving energy saving technology and a stochastically increasing energy price. The results show the technological displacement effects of energy saving technology are stronger, but there are more ambiguous instantaneous returns to physical capital. However, the energy saving technology's displacement effects might not affect the conditions under which the Harberger-Laursen-Metzler (HLM) effect holds. The effects of rising energy prices on bonds are stronger, and there are more ambiguous instantaneous returns, but the conditions under which the HLM effect holds are different.

Regulation of Cross-holdings between European Companies

DEFF Research Database (Denmark)

Sørensen, Karsten Engsig

2003-01-01

Cross-holdings can be a barrier to takeovers, and they may have other disadvantages. This article analyses how cross-holdings may be regulated to avoid these negative effects.......Cross-holdings can be a barrier to takeovers, and they may have other disadvantages. This article analyses how cross-holdings may be regulated to avoid these negative effects....

Analysis of artefacts and detail resolution of lung MRI with breath-hold T1-weighted gradient-echo and T2-weighted fast spin-echo sequences with respiratory triggering

International Nuclear Information System (INIS)

Biederer, J.; Reuter, M.; Both, M.; Grimm, J.; Heller, M.; Muhle, C.; Graessner, J.

2002-01-01

The aim of this study was to evaluate feasibility and limitations of two MR sequences for imaging of the lung using a semi-quantitative rating scale. Ten healthy volunteers were assessed with a breath-hold T1-weighted gradient-recalled-echo (TR/TE=129/2.2 ms, matrix 173 x 256) and a T2-weighted turbo spin-echo (TSE) sequence with respiratory triggering (TR/TE=3000-5000/120 ms, matrix 270 x 512) in axial 6-mm slices. The T1-weighted GRE protocol included a pre-saturation pulse over the mediastinal structures. Artefacts and resolution of vessel/airway structures in each lung segment were evaluated by two observers (10 volunteers, 180 segments). Cardiac and vessel pulsation artefacts predominated on T1-weighted GRE, respiration artefacts on T2-weighted TSE (lingula and middle lobe). Pre-saturation of the mediastinum reduced pulsation artefacts on T1-weighted GRE. T1-weighted GRE images were improved by bright flow signal of vessels, whereas image quality of T2-weighted TSE was reduced by black-blood effects in central parts of the lung. Delineation of lung periphery and the mediastinum was superior with T2-weighted TSE. Segmental/sub-segmental vessels (up to fourth/fifth order) and bronchi (up to third order) were identified. All 180 lung segments were imaged in diagnostic quality with at least one of the two sequences (T1-weighted GRE not diagnostic in 9 of 180, T2-weighted TSE in 4 of 180). Both sequences were found to be complementary: superior identification of gross lung anatomy with T1-weighted GRE and higher detail resolution in the periphery and the mediastinum with T2-weighted TSE. (orig.)

Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

DEFF Research Database (Denmark)

Mak, Sarah Siu Tze Mak; Gopalakrishnan, Shyam Sunder; Carøe, Christian

2017-01-01

on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples. Results: The data generated was largely comparable between sequencing platforms...... difference was also observed in the mitochondrial DNA percentages recovered (p = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA. Conclusions......: Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested...

Collective behaviors of book holding durations

Science.gov (United States)

Li, Ren-De; Guo, Qiang; Han, Jing-Ti; Liu, Jian-Guo

2016-10-01

Duration can directly reflect the collective reading behaviors of library user book holding. In this paper, by introducing the burstiness and memory coefficients, we empirically investigate the collective book holding behavior of three university libraries. The statistical results show that there are similar properties among the students with different backgrounds, presenting the burstiness = - 0.2 and memory = 0.5 for three datasets, which indicates that memory and random effects coexist in student book holding durations. In addition, we analyze the behavior patterns without duplicate durations by merging a series of books borrowed and returned at the same time. The results show the average burstiness B increases to -0.16 and memory M drops to 0.16 for three datasets, which indicates that both duplicate behavior and student's preference affect the memory effect. Furthermore, we present a model which assumes student's next book holding duration follows the previous one with probability p, and with probability 1 - p, the student would hold the book independently. The experimental results show that the presented model can reproduce the burstiness and memory effect of student book holding durations when p = 0.5 for empirical datasets and p = 0.2 for de-duplicate datasets, which indicate that the student's preferential holding behavior occurs with the probability p. This work helps in deeply understanding the regularity of duration-based human behaviors.

Breath-Hold Diving.

Science.gov (United States)

Fitz-Clarke, John R

2018-03-25

Breath-hold diving is practiced by recreational divers, seafood divers, military divers, and competitive athletes. It involves highly integrated physiology and extreme responses. This article reviews human breath-hold diving physiology beginning with an historical overview followed by a summary of foundational research and a survey of some contemporary issues. Immersion and cardiovascular adjustments promote a blood shift into the heart and chest vasculature. Autonomic responses include diving bradycardia, peripheral vasoconstriction, and splenic contraction, which help conserve oxygen. Competitive divers use a technique of lung hyperinflation that raises initial volume and airway pressure to facilitate longer apnea times and greater depths. Gas compression at depth leads to sequential alveolar collapse. Airway pressure decreases with depth and becomes negative relative to ambient due to limited chest compliance at low lung volumes, raising the risk of pulmonary injury called "squeeze," characterized by postdive coughing, wheezing, and hemoptysis. Hypoxia and hypercapnia influence the terminal breakpoint beyond which voluntary apnea cannot be sustained. Ascent blackout due to hypoxia is a danger during long breath-holds, and has become common amongst high-level competitors who can suppress their urge to breathe. Decompression sickness due to nitrogen accumulation causing bubble formation can occur after multiple repetitive dives, or after single deep dives during depth record attempts. Humans experience responses similar to those seen in diving mammals, but to a lesser degree. The deepest sled-assisted breath-hold dive was to 214 m. Factors that might determine ultimate human depth capabilities are discussed. © 2018 American Physiological Society. Compr Physiol 8:585-630, 2018. Copyright © 2018 American Physiological Society. All rights reserved.

EVALUATION OF THE IMPACT OF INNOVATIVE PROJECTS ON THE COMPETITIVENESS OF AGRICULTURAL HOLDINGS IN SLOVAK REPUBLIC

Directory of Open Access Journals (Sweden)

Ľubica RUMANOVSKÁ

2013-01-01

Full Text Available The scientific paper evaluates the impact of innovative projects on the competitiveness of agricultural holdings in SR. Evaluation of the impact of innovative projects on competitiveness of agricultural holdings was realized on the selected holdings in Nitra and Trnava region. For the evaluation was used RCR coefficient. With the use of RCR coefficient could be confirmed the scientific hypothesis - The innovative projects realized through Program for rural development SR 2007-2013 have positive impact on competitiveness of agricultural holdings. The possibilities for EU financial support for innovative projects in SR represent important source for introduction of new innovative technologies into production process and in future they can significantly contribute to the growth of competitiveness of agricultural subjects. Therefore, to increase competitiveness of agricultural holdings it is important to focus on modernization of machinery and buildings, use of natural sources for energy production, but also to increase the education and the flow of information between rural inhabitants, mainly farmers. In competitive area of EU agricultural sector it is necessary that agricultural holdings will innovate, not only to create independent flow of innovative products and knowledge, but also to increase its value on internal market. Agricultural holdings –receivers of financial support – have expressed the opinion that financial support realized through PRD SR 2007-2013 had definitely allowed them to implement new processes and products.

Mure skal holde zombierne ude

DEFF Research Database (Denmark)

Stockmarr, Leila

2013-01-01

Vi bygger som besatte mure og barrierer for at holde flygtninge ude og tæmme de negative konsekvenser af den neoliberale globalisering.......Vi bygger som besatte mure og barrierer for at holde flygtninge ude og tæmme de negative konsekvenser af den neoliberale globalisering....

Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

Science.gov (United States)

Gimode, Davis; Odeny, Damaris A; de Villiers, Etienne P; Wanyonyi, Solomon; Dida, Mathews M; Mneney, Emmarold E; Muchugi, Alice; Machuka, Jesse; de Villiers, Santie M

2016-01-01

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional

Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

Directory of Open Access Journals (Sweden)

Davis Gimode

Full Text Available Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS technologies to develop both Simple Sequence Repeat (SSR and Single Nucleotide Polymorphism (SNP markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included

Usefulness of breath-hold cardiac cine MR imaging with a middle field MRI system

Energy Technology Data Exchange (ETDEWEB)

Matsumura, Kentaro; Sato, Kiyoto; Aono, Masaki; Inoshita, Kenji; Utsumi, Naoko [Kagawa Inoshita Hospital, Ohnohara (Japan)

1999-07-01

To assess the accuracy of contrast-enhanced, single breath-hold cine MR imaging in calculating left ventricular volume and ejection fraction, we compared MR measurements with those obtained by using cine ventriculography in 60 patients. Fast cine MR images were acquired with a middle field MR system (0.5 T). A breath-hold single slice multi-phase fast gradient-echo (Fast Card) sequence was used to obtain fast cine MR images with the following parameters; TR of 16 ms, TE of 3 ms, flip angle of 30 degree, matrix elements of 256 x 128, view per segment of 6, field of view of 350 x 260 mm and one excitation. Left ventricular end-diastolic volume and ejection fraction obtained with contrast-enhanced Fast Card correlated well with those obtained with cine ventriculography (end-diastolic volume, y=1.00x+14.0, r=0.904, p<0.001; ejection fraction, y=0.961x+2.8, r=0.936, p<0.001). Our results show that contrast enhanced breath-hold cardiac cine MR imaging on horizontal long-axis view using a middle field MR system is an accurate method for evaluating left ventricular volume and ejection fraction. (author)

The Impact of Sustainable Development Technology on a Small Economy—The Case of Energy-Saving Technology

Directory of Open Access Journals (Sweden)

Xiding Chen

2018-02-01

Full Text Available We investigated the impact of a sustainable development technology on the macroeconomic variables in a small economy utilizing a case study with a stochastically improving energy saving technology and a stochastically increasing energy price. The results show the technological displacement effects of energy saving technology are stronger, but there are more ambiguous instantaneous returns to physical capital. However, the energy saving technology’s displacement effects might not affect the conditions under which the Harberger-Laursen-Metzler (HLM effect holds. The effects of rising energy prices on bonds are stronger, and there are more ambiguous instantaneous returns, but the conditions under which the HLM effect holds are different.

The Impact of Sustainable Development Technology on a Small Economy—The Case of Energy-Saving Technology

Science.gov (United States)

Huang, Qinghua; Huang, Weilun; Li, Xue

2018-01-01

We investigated the impact of a sustainable development technology on the macroeconomic variables in a small economy utilizing a case study with a stochastically improving energy saving technology and a stochastically increasing energy price. The results show the technological displacement effects of energy saving technology are stronger, but there are more ambiguous instantaneous returns to physical capital. However, the energy saving technology’s displacement effects might not affect the conditions under which the Harberger-Laursen-Metzler (HLM) effect holds. The effects of rising energy prices on bonds are stronger, and there are more ambiguous instantaneous returns, but the conditions under which the HLM effect holds are different. PMID:29419788

Quantum-Sequencing: Fast electronic single DNA molecule sequencing

Science.gov (United States)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

The Impact of “Omic” and Imaging Technologies on Assessing the Host Immune Response to Biodefence Agents

Directory of Open Access Journals (Sweden)

Julia A. Tree

2014-01-01

Full Text Available Understanding the interactions between host and pathogen is important for the development and assessment of medical countermeasures to infectious agents, including potential biodefence pathogens such as Bacillus anthracis, Ebola virus, and Francisella tularensis. This review focuses on technological advances which allow this interaction to be studied in much greater detail. Namely, the use of “omic” technologies (next generation sequencing, DNA, and protein microarrays for dissecting the underlying host response to infection at the molecular level; optical imaging techniques (flow cytometry and fluorescence microscopy for assessing cellular responses to infection; and biophotonic imaging for visualising the infectious disease process. All of these technologies hold great promise for important breakthroughs in the rational development of vaccines and therapeutics for biodefence agents.

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

Directory of Open Access Journals (Sweden)

Marta Brozynska

Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

Digital technology and human development: A charter for nature conservation

NARCIS (Netherlands)

Maffey, G.; Homans, H.; Banks, K.; Arts, K.A.J.

2015-01-01

The application of digital technology in conservation holds much potential for advancing the understanding of, and facilitating interaction with, the natural world. In other sectors, digital technology has long been used to engage communities and share information. Human development—which holds

Allowance Holdings and Transfers Data Inventory

Data.gov (United States)

U.S. Environmental Protection Agency — The Allowance Holdings and Transfers Data Inventory contains measured data on holdings and transactions of allowances under the NOx Budget Trading Program (NBP), a...

Special Issue: Next Generation DNA Sequencing

Directory of Open Access Journals (Sweden)

Paul Richardson

2010-10-01

Full Text Available Next Generation Sequencing (NGS refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance. The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche, Illumina (formerly Solexa Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies and the Heliscope (Helicos Corporation. The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...

12 CFR 1252.1 - Enterprise portfolio holding criteria.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 7 2010-01-01 2010-01-01 false Enterprise portfolio holding criteria. 1252.1 Section 1252.1 Banks and Banking FEDERAL HOUSING FINANCE AGENCY ENTERPRISES PORTFOLIO HOLDINGS § 1252.1 Enterprise portfolio holding criteria. The Enterprises are required to comply with the portfolio holdings...

12 CFR 225.124 - Foreign bank holding companies.

Science.gov (United States)

2010-01-01

... SYSTEM BANK HOLDING COMPANIES AND CHANGE IN BANK CONTROL (REGULATION Y) Regulations Financial Holding Companies Interpretations § 225.124 Foreign bank holding companies. (a) Effective December 1, 1971, the... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Foreign bank holding companies. 225.124 Section...

Excess cash holdings and shareholder value

OpenAIRE

Lee, Edward; Powell, Ronan

2011-01-01

We examine the determinants of corporate cash holdings in Australia and the impact on shareholder wealth of holding excess cash. Our results show that a trade-off model best explains the level of a firm’s cash holdings in Australia. We find that 'transitory' excess cash firms earn significantly higher risk-adjusted returns compared to 'persistent' excess cash firms, suggesting that the market penalises firms that hoard cash. The marginal value of cash also declines with larger cash balances, ...

Applications of Genomic Sequencing in Pediatric CNS Tumors.

Science.gov (United States)

Bavle, Abhishek A; Lin, Frank Y; Parsons, D Williams

2016-05-01

Recent advances in genome-scale sequencing methods have resulted in a significant increase in our understanding of the biology of human cancers. When applied to pediatric central nervous system (CNS) tumors, these remarkable technological breakthroughs have facilitated the molecular characterization of multiple tumor types, provided new insights into the genetic basis of these cancers, and prompted innovative strategies that are changing the management paradigm in pediatric neuro-oncology. Genomic tests have begun to affect medical decision making in a number of ways, from delineating histopathologically similar tumor types into distinct molecular subgroups that correlate with clinical characteristics, to guiding the addition of novel therapeutic agents for patients with high-risk or poor-prognosis tumors, or alternatively, reducing treatment intensity for those with a favorable prognosis. Genomic sequencing has also had a significant impact on translational research strategies in pediatric CNS tumors, resulting in wide-ranging applications that have the potential to direct the rational preclinical screening of novel therapeutic agents, shed light on tumor heterogeneity and evolution, and highlight differences (or similarities) between pediatric and adult CNS tumors. Finally, in addition to allowing the identification of somatic (tumor-specific) mutations, the analysis of patient-matched constitutional (germline) DNA has facilitated the detection of pathogenic germline alterations in cancer genes in patients with CNS tumors, with critical implications for genetic counseling and tumor surveillance strategies for children with familial predisposition syndromes. As our understanding of the molecular landscape of pediatric CNS tumors continues to advance, innovative applications of genomic sequencing hold significant promise for further improving the care of children with these cancers.

12 CFR 575.14 - Subsidiary holding companies.

Science.gov (United States)

2010-01-01

... follows: Federal MHC Subsidiary Holding Company Charter Section 1. Corporate title. The full corporate... subsidiary holding company available for distribution, in cash or in kind. Each share of common stock shall... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Subsidiary holding companies. 575.14 Section...

Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

Directory of Open Access Journals (Sweden)

Materne Michael

2011-05-01

Full Text Available Abstract Background Lentil (Lens culinaris Medik. is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs. De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

Characterizing ncRNAs in human pathogenic protists using high-throughput sequencing technology

Directory of Open Access Journals (Sweden)

Lesley Joan Collins

2011-12-01

Full Text Available ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, snoRNAs and long ncRNAs on a genomic scale making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.

Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology

Science.gov (United States)

Collins, Lesley Joan

2011-01-01

ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases. PMID:22303390

Advancement and application of bubble detector technology

International Nuclear Information System (INIS)

Buckner, M.A.; Casson, W.H.; Sims, C.S.

1991-01-01

A new technology is vying for position in the dosimetry community. This relatively young technology is building upon the foundation of the bubble chamber, conceptualized by Glaser in 1952. Although the attitudes surrounding this technology are somewhat mixed, applications of this technology hold great promise for the future of neutron dosimetry. The Dosimetry Applications Research facility of Oak Ridge National Laboratory is looking into some innovative applications of this technology. The authors are investigating options for overcoming its limiting features in hopes of achieving an unprecedented level of proficiency in neutron detection. Among these are the developing and testing of a Combination Area Neutron Spectrometer, CANS, assessing the plausibility of extremity applications, the assembly of an alternative reader for research, investigation of temperature-related effects and how to correct for them and considerations on the coming of age of neutron dosimetry via real time detection of bubble formation in Bubble Technology Industries Inc. detectors. The authors attempt to answer the questions: (1) What areas hold the greatest promise for application of this emerging technology?; (2) What obstacles must be overcome before full-blown application becomes a reality?; and (3) What might the future hold?

Sports-related lung injury during breath-hold diving

Directory of Open Access Journals (Sweden)

Tanja Mijacika

2016-12-01

Full Text Available The number of people practising recreational breath-hold diving is constantly growing, thereby increasing the need for knowledge of the acute and chronic effects such a sport could have on the health of participants. Breath-hold diving is potentially dangerous, mainly because of associated extreme environmental factors such as increased hydrostatic pressure, hypoxia, hypercapnia, hypothermia and strenuous exercise. In this article we focus on the effects of breath-hold diving on pulmonary function. Respiratory symptoms have been reported in almost 25% of breath-hold divers after repetitive diving sessions. Acutely, repetitive breath-hold diving may result in increased transpulmonary capillary pressure, leading to noncardiogenic oedema and/or alveolar haemorrhage. Furthermore, during a breath-hold dive, the chest and lungs are compressed by the increasing pressure of water. Rapid changes in lung air volume during descent or ascent can result in a lung injury known as pulmonary barotrauma. Factors that may influence individual susceptibility to breath-hold diving-induced lung injury range from underlying pulmonary or cardiac dysfunction to genetic predisposition. According to the available data, breath-holding does not result in chronic lung injury. However, studies of large populations of breath-hold divers are necessary to firmly exclude long-term lung damage.

Selecting Security Technology Providers

Science.gov (United States)

Schneider, Tod

2009-01-01

The world of security technology holds great promise, but it is fraught with opportunities for expensive missteps and misapplications. The quality of the security technology consultants and system integrators one uses will have a direct bearing on how well his school masters this complex subject. Security technology consultants help determine…

49 CFR 178.338-9 - Holding time.

Science.gov (United States)

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Holding time. 178.338-9 Section 178.338-9... Specifications for Containers for Motor Vehicle Transportation § 178.338-9 Holding time. (a) “Holding time” is the time, as determined by testing, that will elapse from loading until the pressure of the contents...

DNA Sequencing by Capillary Electrophoresis

Science.gov (United States)

Karger, Barry L.; Guttman, Andras

2009-01-01

Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

Science.gov (United States)

Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

2018-01-01

Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.

Holdings of the Federal German Government in 1988

International Nuclear Information System (INIS)

1989-01-01

The report provides an overview of the direct and more important indirect holdings of the Federal German Government and its special assets ERP, Compensation Fund, Federal Mail and Federal Railway. Part A provides a total survey of the number of government holdings. For the direct holdings of the Federal Government and its special assets the shares in nominal capital and registered foundation capital, number of employees and dividend on profits are presented. In Parts B to M, the narrative parts, the most important holdings are reported on more in detail (sphere of activities, economic development, composition of the corporate bodies). The listing order does not reflect any order of importance. The following part N contains alphabetic indexes. Indexes I and II list all the direct holdings of the Federal Government and its special assets irrespective of the nominal capital volume and share of holdings. In index III, are listed only companies with corporate activites and a nominal capital of at least 100.000 German Marks of which the Federal Government and/or its special assets hold directly or indirectly at least 25 percent. Holdings of these undertakings of which the Federal Government does not have majority ownership, and which are not dependent on it under the regulations governing shareholdings either, are not considered. (orig.) [de

Breath-Holding Spells

Science.gov (United States)

... reviewed: October 2016 More on this topic for: Parents Is It Normal for Children to Hold Their Breath? Taming Tempers Disciplining Your Child Disciplining Your Toddler Temper Tantrums Separation Anxiety View more About Us Contact Us Partners ...

Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

KAUST Repository

Wong, Ka-Chun; Peng, Chengbin; Li, Yue

2015-01-01

With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene's function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website: http://www.cs.toronto.edu/∼wkc/FullSignalRanker/ © 2015 IEEE.

Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

KAUST Repository

Wong, Ka-Chun

2015-04-20

With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene\\'s function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins\\' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website: http://www.cs.toronto.edu/∼wkc/FullSignalRanker/ © 2015 IEEE.

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

Science.gov (United States)

Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

2012-01-01

Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast

Oxford Nanopore MinION Sequencing and Genome Assembly

Directory of Open Access Journals (Sweden)

Hengyun Lu

2016-10-01

Full Text Available The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS technology. The third-generation sequencing (TGS technology, led by Pacific Biosciences (PacBio, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT. MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

76 FR 20459 - Savings and Loan Holding Company Application

Science.gov (United States)

2011-04-12

... DEPARTMENT OF THE TREASURY Office of Thrift Supervision Savings and Loan Holding Company... concerning the following information collection. Title of Proposal: Savings and Loan Holding Company... officer of a savings and loan holding company, or any individual who owns, controls, or holds with power...

High-throughput sequence alignment using Graphics Processing Units

Directory of Open Access Journals (Sweden)

Trapnell Cole

2007-12-01

Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

Interactive thresholded volumetry of abdominal fat using breath-hold T1-weighted magnetic resonance imaging

International Nuclear Information System (INIS)

Wittsack, H.J.; Cohnen, M.; Jung, G.; Moedder, U.; Poll, L.; Kapitza, C.; Heinemann, L.

2006-01-01

Purpose: development of a feasible and reliable method for determining abdominal fat using breath-hold T1-weighted magnetic resonance imaging. Materials and methods: the high image contrast of T1-weighted gradient echo MR sequences makes it possible to differentiate between abdominal fat and non-fat tissue. To obtain a high signal-to-noise ratio, the measurements are usually performed using phased array surface coils. Inhomogeneity of the coil sensitivity leads to inhomogeneity of the image intensities. Therefore, to examine the volume of abdominal fat, an automatic algorithm for intensity correction must be implemented. The analysis of the image histogram results in a threshold to separate fat from other tissue. Automatic segmentation using this threshold results directly in the fat volumes. The separation of intraabdominal and subcutaneous fat is performed by interactive selection in a last step. Results: the described correction of inhomogeneity allows for the segmentation of the images using a global threshold. The use of semiautomatic interactive volumetry makes the analysis more subjective. The variance of volumetry between observers was 4.6%. The mean time for image analysis of a T1-weighted investigation lasted less than 6 minutes. Conclusion: the described method facilitates reliable determination of abdominal fat within a reasonable period of time. Using breath-hold MR sequences, the time of examination is less than 5 minutes per patient. (orig.)

Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

Directory of Open Access Journals (Sweden)

Giorgio Palù

2011-11-01

Full Text Available Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS, provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.

Blue breath holding is benign.

OpenAIRE

Stephenson, J B

1991-01-01

In their recent publication in this journal, Southall et al described typical cyanotic breath holding spells, both in otherwise healthy children and in those with brainstem lesions and other malformations. Their suggestions regarding possible autonomic disturbances may require further study, but they have adduced no scientific evidence to contradict the accepted view that in the intact child blue breath holding spells are benign. Those families in which an infant suffers an 'apparently life t...

Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection.

Science.gov (United States)

Zopf, Agnes; Raim, Roman; Danzer, Martin; Niklas, Norbert; Spilka, Rita; Pröll, Johannes; Gabriel, Christian; Nechansky, Andreas; Roucka, Markus

2015-03-01

The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.

The Determinants and Implications of Corporate Cash Holdings

OpenAIRE

Tim Opler; Lee Pinkowitz; Rene Stulz; Rohan Williamson

1997-01-01

We examine the determinants and implications of holdings of cash and marketable" securities by publicly traded U.S. firms in the 1971-1994 period. Firms with strong growth" opportunities and riskier cash flows hold relatively high ratios of cash to total assets. Firms" that have the greatest access to the capital markets (e.g. large firms and those with credit" ratings) tend to hold lower ratios of cash to total assets. These results are consistent with the" view that firms hold liquid assets...

12 CFR 583.20 - Savings and loan holding company.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Savings and loan holding company. 583.20... REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.20 Savings and loan holding company. The term savings and loan holding company means any company that directly or indirectly controls a savings...

Applications of nanotechnology, next generation sequencing and microarrays in biomedical research.

Science.gov (United States)

Elingaramil, Sauli; Li, Xiaolong; He, Nongyue

2013-07-01

Next-generation sequencing technologies, microarrays and advances in bio nanotechnology have had an enormous impact on research within a short time frame. This impact appears certain to increase further as many biomedical institutions are now acquiring these prevailing new technologies. Beyond conventional sampling of genome content, wide-ranging applications are rapidly evolving for next-generation sequencing, microarrays and nanotechnology. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted re sequencing and discovery of transcription factor binding sites, noncoding RNA expression profiling and molecular diagnostics. This paper thus discusses current applications of nanotechnology, next-generation sequencing technologies and microarrays in biomedical research and highlights the transforming potential these technologies offer.

77 FR 58203 - AER Energy Resources, Inc.; Alto Group Holdings, Inc.; Bizrocket.Com Inc.; Fox Petroleum, Inc...

Science.gov (United States)

2012-09-19

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] AER Energy Resources, Inc.; Alto Group Holdings, Inc.; Bizrocket.Com Inc.; Fox Petroleum, Inc.; Geopulse Explorations Inc.; Global Technologies... accuracy of press releases concerning the company's revenues. 4. Fox Petroleum, Inc. is a Nevada...

Creditor rights, country governance, and corporate cash holdings

NARCIS (Netherlands)

Seifert, Bruce; Gonenc, Halit

2016-01-01

This study examines the impact of creditor rights and country governance on cash holdings using a sample of firms from 47 countries. We hypothesize that cash holdings are smaller when both creditor rights and country governance are high. In these circumstances firms will not need to hold as much

A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

Directory of Open Access Journals (Sweden)

Wenyu Zhang

Full Text Available The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers.

12 CFR 583.12 - Multiple savings and loan holding company.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Multiple savings and loan holding company. 583... DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.12 Multiple savings and loan holding company. The term multiple savings and loan holding company means any savings and loan holding...

12 CFR 583.11 - Diversified savings and loan holding company.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Diversified savings and loan holding company... DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.11 Diversified savings and loan holding company. The term diversified savings and loan holding company means any savings and loan holding...

12 CFR 225.81 - What is a financial holding company?

Science.gov (United States)

2010-01-01

... RESERVE SYSTEM BANK HOLDING COMPANIES AND CHANGE IN BANK CONTROL (REGULATION Y) Regulations Financial Holding Companies § 225.81 What is a financial holding company? (a) Definition. A financial holding... 12 Banks and Banking 3 2010-01-01 2010-01-01 false What is a financial holding company? 225.81...

Assessment of voluntary deep inspiration breath-hold with CINE imaging for breast radiotherapy.

Science.gov (United States)

Estoesta, Reuben Patrick; Attwood, Lani; Naehrig, Diana; Claridge-Mackonis, Elizabeth; Odgers, David; Martin, Darren; Pham, Melissa; Toohey, Joanne; Carroll, Susan

2017-10-01

Deep Inspiration Breath-Hold (DIBH) techniques for breast cancer radiation therapy (RT) have reduced cardiac dose compared to Free Breathing (FB). Recently, a voluntary deep inspiration breath-hold (vDIBH) technique was established using in-room lasers and skin tattoos to monitor breath-hold. An in-house quality assessment of positional reproducibility during RT delivery with vDIBH in patients with left-sided breast cancer was evaluated. The electronic portal imaging device (EPID) was used in cinematographic (CINE) mode to capture a sequence of images during beam delivery. Weekly CINE images were retrospectively assessed for 20 left-sided breast cancer patients receiving RT in vDIBH, and compared with CINE images of 20 patients treated in FB. The intra-beam motion was assessed and the distance from the beam central axis (CA) to the internal chest wall (ICW) was measured on each CINE image. These were then compared to the planned distance on digitally reconstructed radiograph (DRR). The maximum intra-beam motion for any one patient measurement was 0.30 cm for vDIBH and 0.20 cm for FB. The mean difference between the distance from the CA to ICW on DRR and the equivalent distance on CINE imaging (as treated) was 0.28 cm (SD 0.17) for vDIBH patients and 0.25 cm (SD 0.14) for FB patients (P = 0.458). The measured values were comparable for patients undergoing RT in vDIBH, and for those in FB. This quality assessment showed that using in-room lasers and skin tattoos to independently monitor breath-hold in vDIBH as detected by 'on-treatment' CINE imaging is safe and effective. © 2017 The Royal Australian and New Zealand College of Radiologists.

Automatic start-up system of nuclear reactor based on sequence control technology

International Nuclear Information System (INIS)

Zhang Yao; Zhang Dafa; Peng Huaqing

2009-01-01

A conceptive design of an automatic start-up system based on the sequence control for the nuclear reactors is given in this paper, so as to solve the problems during the start-up process, such as the long operation time, low automatic control level and high accident rate. The start-up process and its requirements are analyzed in detail at first. Then,the principle, the architecture, the key technologies of the automatic start-up system of nuclear reactors are designed and discussed. With the designed system, the automatic start-up of the nuclear reactor can be realized,the work load of the operator can be reduced,and the safety and efficiency of the nuclear power plant during its start-up can be improved. (authors)

Single-cell sequencing in stem cell biology.

Science.gov (United States)

Wen, Lu; Tang, Fuchou

2016-04-15

Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequencing technologies serve as powerful tools to dissect cellular heterogeneity comprehensively and to identify distinct phenotypic cell types, even within a 'homogeneous' stem cell population. These technologies, including single-cell genome, epigenome, and transcriptome sequencing technologies, have been developing rapidly in recent years. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. In this review, we discuss the recent progress as well as future perspectives in the methodologies and applications of single-cell omic sequencing technologies.

Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology.

Science.gov (United States)

Sasaki, Katsutomo; Mitsuda, Nobutaka; Nashima, Kenji; Kishimoto, Kyutaro; Katayose, Yuichi; Kanamori, Hiroyuki; Ohmiya, Akemi

2017-09-04

Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. To obtain useful information about molecular bases for floral traits of chrysanthemums, we read expressed sequence tags (ESTs) of chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3'-UTR, and 5'-UTR cDNAs derived from various tissues of chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in chrysanthemums. We confirmed that our chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of chrysanthemums including the myriad cultivars at the molecular level.

Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology

Directory of Open Access Journals (Sweden)

Bercelin Maniangou

2017-05-01

Full Text Available The impact of natural killer (NK cell alloreactivity on hematopoietic stem cell transplantation (HSCT outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR/KIR ligand genetic combinations studied, and KIR+ NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR+ NK cells. We, therefore, speculate that polymorphisms may alter donor KIR+ NK cell phenotype/function thus modulating post-HSCT KIR+ NK cell alloreactivity. To investigate KIR allele polymorphisms of all KIR genes, we developed a next-generation sequencing (NGS technology on a MiSeq platform. To ensure the reliability and specificity of our method, genomic DNA from well-characterized cell lines were used; high-resolution KIR typing results obtained were then compared to those previously reported. Two different bioinformatic pipelines were used allowing the attribution of sequencing reads to specific KIR genes and the assignment of KIR alleles for each KIR gene. Our results demonstrated successful long-range KIR gene amplifications of all reference samples using intergenic KIR primers. The alignment of reads to the human genome reference (hg19 using BiRD pipeline or visualization of data using Profiler software demonstrated that all KIR genes were completely sequenced with a sufficient read depth (mean 317× for all loci and a high percentage of mapping (mean 93% for all loci. Comparison of high-resolution KIR typing obtained to those published data using exome capture resulted in a reported concordance rate of 95% for centromeric and telomeric KIR genes. Overall, our results suggest that NGS can be used to investigate the broad KIR allelic polymorphism. Hence, these data improve our knowledge, not only on KIR+ NK cell alloreactivity in

Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

Directory of Open Access Journals (Sweden)

Joern Toedling

Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

Technologies for the people: a future in the making

Energy Technology Data Exchange (ETDEWEB)

Sharma, D.C.

2004-09-01

India's post-independence policy of using science and technology for national development, and investment in research and development infrastructure resulted in success in space, atomic energy, missile development and supercomputing. Use of space technology has impacted directly or indirectly the vast majority of India's billion plus population. Developments in a number of emerging technologies in recent years hold the promise of impacting the future of ordinary Indians in significant ways, if a proper policy and enabling environment are provided. New telecom technologies - a digital rural exchange and a wireless access system - are beginning to touch the lives of common people. Development of a low-cost hand held computing device, use of hybrid telemedicine systems to extend modem healthcare to the unreached, and other innovative uses of IT at the grassroots also hold promise for the future. Biotechnology too has the potential to deliver cost-effective vaccines and drugs, but the future of GM crops is uncertain due to growing opposition. Some of these emerging technologies hold promise for future, provided a positive policy and enabling environment. (author)

CRISPR-Cas9 technology: applications in genome engineering, development of sequence-specific antimicrobials, and future prospects.

Science.gov (United States)

de la Fuente-Núñez, César; Lu, Timothy K

2017-02-20

The development of CRISPR-Cas9 technology has revolutionized our ability to edit DNA and to modulate expression levels of genes of interest, thus providing powerful tools to accelerate the precise engineering of a wide range of organisms. In addition, the CRISPR-Cas system can be harnessed to design "precision" antimicrobials that target bacterial pathogens in a DNA sequence-specific manner. This capability will enable killing of drug-resistant microbes by selectively targeting genes involved in antibiotic resistance, biofilm formation and virulence. Here, we review the origins and mechanistic basis of CRISPR-Cas systems, discuss how this technology can be leveraged to provide a range of applications in both eukaryotic and prokaryotic systems, and finish by outlining limitations and future prospects.

Phase-Type Models of Channel-Holding Times in Cellular Communication Systems

DEFF Research Database (Denmark)

Christensen, Thomas Kaare; Nielsen, Bo Friis; Iversen, Villy Bæk

2004-01-01

In this paper, we derive the distribution of the channel-holding time when both cell-residence and call-holding times are phase-type distributed. Furthermore, the distribution of the number of handovers, the conditional channel-holding time distributions, and the channel-holding time when cell re...... residence times are correlated are derived. All distributions are of phase type, making them very general and flexible. The channel-holding times are of importance in performance evaluation and simulation of cellular mobile communication systems.......In this paper, we derive the distribution of the channel-holding time when both cell-residence and call-holding times are phase-type distributed. Furthermore, the distribution of the number of handovers, the conditional channel-holding time distributions, and the channel-holding time when cell...

Biosensors for DNA sequence detection

Science.gov (United States)

Vercoutere, Wenonah; Akeson, Mark

2002-01-01

DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

Governance mechanisms, investment opportunity set and SMEs cash holdings

OpenAIRE

Belghitar, Yacine; Khan, James

2013-01-01

This study analyses the effect of firm characteristics and governance mechanisms on cash holdings for a sample of UK SMEs. The results show that UK SMEs with greater cash flow volatility and institutional investors hold more cash; whereas levered and dividend paying SMEs with non-executive ownership hold less cash. We also find that ownership structure is significant only in explaining the cash holdings for firms with high growth investment opportunities, and leverage is only significant in e...

Application of Next-generation Sequencing in Clinical Molecular Diagnostics

Directory of Open Access Journals (Sweden)

Morteza Seifi

2017-05-01

Full Text Available ABSTRACT Next-generation sequencing (NGS is the catch all terms that used to explain several different modern sequencing technologies which let us to sequence nucleic acids much more rapidly and cheaply than the formerly used Sanger sequencing, and as such have revolutionized the study of molecular biology and genomics with excellent resolution and accuracy. Over the past years, many academic companies and institutions have continued technological advances to expand NGS applications from research to the clinic. In this review, the performance and technical features of current NGS platforms were described. Furthermore, advances in the applying of NGS technologies towards the progress of clinical molecular diagnostics were emphasized. General advantages and disadvantages of each sequencing system are summarized and compared to guide the selection of NGS platforms for specific research aims.

Graphene nanodevices for DNA sequencing

NARCIS (Netherlands)

Heerema, S.J.; Dekker, C.

2016-01-01

Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

Gelada vocal sequences follow Menzerath’s linguistic law

Science.gov (United States)

Gustison, Morgan L.; Semple, Stuart; Ferrer-i-Cancho, Ramon; Bergman, Thore J.

2016-01-01

Identifying universal principles underpinning diverse natural systems is a key goal of the life sciences. A powerful approach in addressing this goal has been to test whether patterns consistent with linguistic laws are found in nonhuman animals. Menzerath’s law is a linguistic law that states that, the larger the construct, the smaller the size of its constituents. Here, to our knowledge, we present the first evidence that Menzerath’s law holds in the vocal communication of a nonhuman species. We show that, in vocal sequences of wild male geladas (Theropithecus gelada), construct size (sequence size in number of calls) is negatively correlated with constituent size (duration of calls). Call duration does not vary significantly with position in the sequence, but call sequence composition does change with sequence size and most call types are abbreviated in larger sequences. We also find that intercall intervals follow the same relationship with sequence size as do calls. Finally, we provide formal mathematical support for the idea that Menzerath’s law reflects compression—the principle of minimizing the expected length of a code. Our findings suggest that a common principle underpins human and gelada vocal communication, highlighting the value of exploring the applicability of linguistic laws in vocal systems outside the realm of language. PMID:27091968

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

Science.gov (United States)

Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

2014-02-01

Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

75 FR 18482 - Environmental Technologies Trade Advisory Committee (ETTAC)

Science.gov (United States)

2010-04-12

... DEPARTMENT OF COMMERCE Environmental Technologies Trade Advisory Committee (ETTAC) AGENCY... Environmental Technologies Trade Advisory Committee (ETTAC) will hold its quarterly meeting to discuss environmental technologies trade liberalization, industry competitiveness issues, and general Committee...

76 FR 35085 - Savings and Loan Holding Company Application

Science.gov (United States)

2011-06-15

... DEPARTMENT OF THE TREASURY Office of Thrift Supervision Savings and Loan Holding Company... Proposal: Savings Loan Holding Company Application. OMB Number: 1550-0015. Form Numbers: H-(e). Description... that no company, or any director or officer of a savings and loan holding company, or any individual...

76 FR 25732 - Order of Suspension of Trading; In the Matter of Advanced Refractive Technologies, Inc., Bluebook...

Science.gov (United States)

2011-05-05

... of Advanced Refractive Technologies, Inc., Bluebook International Holding Co. (The), CBCom, Inc., Gener8xion Entertainment, Inc., Group Long Distance Inc., HiEnergy Technologies, Inc., and Holter Technologies Holding, A.G. (n/k/a International Consortium Corp.) It appears to the Securities and Exchange...

75 FR 52716 - Environmental Technologies Trade Advisory Committee (ETTAC)

Science.gov (United States)

2010-08-27

... DEPARTMENT OF COMMERCE Environmental Technologies Trade Advisory Committee (ETTAC) AGENCY... Environmental Technologies Trade Advisory Committee (ETTAC) will hold its quarterly meeting to discuss environmental technologies industry competitiveness issues, the National Export Initiative, and general...

Sequencing, lot sizing and scheduling in job shops: the common cycle approach

NARCIS (Netherlands)

Ouenniche, J.; Boctor, F.F.

1998-01-01

This paper deals with the multi-product, finite horizon, static demand, sequencing, lot sizing and scheduling problem in a job shop environment where the objective is to minimize the sum of setup and inventory holding costs while satisfying the demand with no backlogging. To solve this problem, we

A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

Science.gov (United States)

Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

2012-10-01

One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

Directory of Open Access Journals (Sweden)

Alves-Ferreira Marcelo

2008-09-01

Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

75 FR 1590 - Environmental Technologies Trade Advisory Committee (ETTAC)

Science.gov (United States)

2010-01-12

... DEPARTMENT OF COMMERCE Environmental Technologies Trade Advisory Committee (ETTAC) AGENCY... Environmental Technologies Trade Advisory Committee (ETTAC) will hold its first plenary meeting of 2010 to discuss environmental technologies trade liberalization, industry competitiveness issues, and general...

Examining Preservice Elementary Teachers' Technology Self-Efficacy: Impact of Mobile Technology-Based Physics Curriculum

Science.gov (United States)

Menon, Deepika; Chandrasekhar, Meera; Kosztin, Dorina; Steinhoff, Douglas

2017-01-01

While iPads and other mobile devices are gaining popularity in educational settings, challenges associated with teachers' use of technology continue to hold true. Preparing preservice teachers within teacher preparation programs to gain experience learning and teaching science using mobile technologies is critical for them to develop positive…

"Hold Harmless" Option for Staff Babysitting and Employee References

Science.gov (United States)

Bruno, Holly Elissa

2010-01-01

Help for educators and administrators may be on the way in the form of "hold harmless" documents that allow for flexibility in enforcing program policies. Having a "No Babysitting policy," and "Hold Harmless" documentation will not stop one's program from being sued. However, with the "No Babysitting policy" and "Hold Harmless" documentation…

Improving livestock for agriculture - technological progress from random transgenesis to precision genome editing heralds a new era.

Science.gov (United States)

Laible, Götz; Wei, Jingwei; Wagner, Stefan

2015-01-01

Humans have a long history in shaping the genetic makeup of livestock to optimize production and meet growing human demands for food and other animal products. Until recently, this has only been possible through traditional breeding and selection, which is a painstakingly slow process of accumulating incremental gains over a long period. The development of transgenic livestock technology offers a more direct approach with the possibility for making genetic improvements with greater impact and within a single generation. However, initially the technology was hampered by technical difficulties and limitations, which have now largely been overcome by progressive improvements over the past 30 years. Particularly, the advent of genome editing in combination with homologous recombination has added a new level of efficiency and precision that holds much promise for the genetic improvement of livestock using the increasing knowledge of the phenotypic impact of genetic sequence variants. So far not a single line of transgenic livestock has gained approval for commercialization. The step change to genome-edited livestock with precise sequence changes may accelerate the path to market, provided applications of this new technology for agriculture can deliver, in addition to economic incentives for producers, also compelling benefits for animals, consumers, and the environment. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accelerators in Science and Technology

CERN Document Server

Kailas, S

2002-01-01

Accelerators built for basic research in frontier areas of science have become important and inevitable tools in many areas of science and technology. Accelerators are examples of science driven high technology development. Accelerators are used for a wide ranging applications, besides basic research. Accelerator based multidisciplinary research holds great promise

The Parent Control in the Mechanical Engineering Management-Holding

Science.gov (United States)

Šnircová, Jana; Hodulíková, Petra; Joehnk, Peter

2012-12-01

The group of entities under the control of parent, so called holding, is arisen as the result and the most often used form of the business concentration nowadays. The paper is focused to find special tasks of parent company for to preserve effective unified economic control in the management-holding. The unified economic control the holding exists in the conditions of the main conflict of interest - holding is not a legal but economic unit and the connected companies into it have a legal autonomy with the economic dependence. The unified economic control limits the financial independence of every individual company of the holding. The attention in the paper is concentrated to the management concept of the parent control, i.e. the parent company supervises the control of intragroup flows and all of subsidiaries production activities.

PENGARUH KUALITAS AKRUAL DAN LEVERAGE TERHADAP CASH HOLDING PERUSAHAAN

Directory of Open Access Journals (Sweden)

Anggita Langgeng Wijaya

2010-12-01

Full Text Available This research tests the effect of accrual quality and leverage on corporate cash holding for a sample of manufacturing company listed in Indonesian Stock Exchange over the period 2006-2007. This research also tests the role of asymmetric information as a mediating variable on the relation between accrual quality and cash holding. Population of this research is 197 manufacturing companies at the Indonesian Stock Exchange. This research uses the purposive sampling method. Hypothesis test of this research em­ploys multiple regression analysis and path analysis. The results show that: accrual quality does not affect asymmetric information; asymmetric information positively affects corporate cash holdings; asymmetric information is not a mediating variable on the relation between accrual quality and cash holding; leverage negatively affects corporate cash holding.

Genome Sequence Databases (Overview): Sequencing and Assembly

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla L.

2009-01-01

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

Korean Investment in EU through Holding Companies: A Case Study

Directory of Open Access Journals (Sweden)

Seong-Bong Lee

1998-09-01

Full Text Available When transnational enterprises set subsidiary companies in certain area, their major aim is to invest indirectly through the holding companies which hold invested share. Especially, because of the geographical neighborhood and economic integration, investing by holding companies is common in Europe. In Europe, taking full advantage of holding company is out of the following two reasons. Firstly, the efficiency and flexibility of the manage strategy of a group could be elevated by making full use of the holding company. Secondly, the transnational enterprises have the possibility of flexible management at the tax strategy level. Recently, the Korean companies are making the best use of holding companies when they are Marching into the EU. In the year 1996, group K purchased 8 enterprises of a certain industry section of B, a German company, setting holding companies in Germany. The analysis result of the case shows that the manage efficiency could be risen and the taxation could be reduced by way of making use of holding companies. As to the Korean investment efficiency of overseas indirect investment in EU, this thesis brought forward a blueprint about integrating the local companies.

Rock Equity Holdings, LLC

Science.gov (United States)

The EPA is providing notice of an Administrative Penalty Assessment in the form of an Expedited Storm Water Settlement Agreement against Rock Equity Holdings, LLC, for alleged violations at The Cove at Kettlestone/98th Street Reconstruction located at 3015

NextGen Flight Deck Surface Trajectory-Based Operations (STBO): Contingency Holds

Science.gov (United States)

Bakowski, Deborah Lee; Hooey, Becky Lee; Foyle, David C.; Wolter, Cynthia A.; Cheng, Lara W. S.

2013-01-01

The purpose of this pilot-in-the-loop taxi simulation was to investigate a NextGen Surface Trajectory-Based Operations (STBO) concept called "contingency holds." The contingency-hold concept parses a taxi route into segments, allowing an air traffic control (ATC) surface traffic management (STM) system to hold an aircraft when necessary for safety. Under nominal conditions, if the intersection or active runway crossing is clear, the hold is removed, allowing the aircraft to continue taxiing without slowing, thus improving taxi efficiency, while minimizing the excessive brake use, fuel burn, and emissions associated with stop-and-go taxi. However, when a potential traffic conflict exists, the hold remains in place as a fail-safe mechanism. In this departure operations simulation, the taxi clearance included a required time of arrival (RTA) to a specified intersection. The flight deck was equipped with speed-guidance avionics to aid the pilot in safely meeting the RTA. On two trials, the contingency hold was not released, and pilots were required to stop. On two trials the contingency hold was released 15 sec prior to the RTA, and on two trials the contingency hold was released 30 sec prior to the RTA. When the hold remained in place, all pilots complied with the hold. Results also showed that when the hold was released at 15-sec or 30-sec prior to the RTA, the 30-sec release allowed pilots to maintain nominal taxi speed, thus supporting continuous traffic flow; whereas, the 15-sec release did not. The contingency-hold concept, with at least a 30-sec release, allows pilots to improve taxiing efficiency by reducing braking, slowing, and stopping, but still maintains safety in that no pilots "busted" the clearance holds. Overall, the evidence suggests that the contingency-hold concept is a viable concept for optimizing efficiency while maintaining safety.

A short-breath-hold technique for lung pO2 mapping with 3He MRI.

Science.gov (United States)

Miller, G Wilson; Mugler, John P; Altes, Talissa A; Cai, Jing; Mata, Jaime F; de Lange, Eduard E; Tobias, William A; Cates, Gordon D; Brookeman, James R

2010-01-01

A pulse-sequence strategy was developed for generating regional maps of alveolar oxygen partial pressure (pO2) in a single 6-sec breath hold, for use in human subjects with impaired lung function. Like previously described methods, pO2 values are obtained by measuring the oxygen-induced T1 relaxation of inhaled hyperpolarized 3He. Unlike other methods, only two 3He images are acquired: one with reverse-centric and the other with centric phase-encoding order. This phase-encoding arrangement minimizes the effects of regional flip-angle variations, so that an accurate map of instantaneous pO2 can be calculated from two images acquired a few seconds apart. By combining this phase-encoding strategy with variable flip angles, the vast majority of the hyperpolarized magnetization goes directly into the T1 measurement, minimizing noise in the resulting pO2 map. The short-breath-hold pulse sequence was tested in phantoms containing known O2 concentrations. The mean difference between measured and prepared pO2 values was 1 mm Hg. The method was also tested in four healthy volunteers and three lung-transplant patients. Maps of healthy subjects were largely uniform, whereas focal regions of abnormal pO2 were observed in diseased subjects. Mean pO2 values varied with inhaled O2 concentration. Mean pO2 was consistent with normal steady-state values in subjects who inhaled 3He diluted only with room air. Copyright (c) 2009 Wiley-Liss, Inc.

The water holding capacity of bark in Danish angiosperm trees

DEFF Research Database (Denmark)

Larsen, Hanne Marie Ellegård; Rasmussen, Hanne Nina; Nord-Larsen, Thomas

The water holding capacity of bark in seven Danish angiosperm trees was examined. The aim of the study was (1) to examine height trends and (2) bark thickness trends in relation to the water holding capacity and (3) to determine interspecific differences. The wet-weight and dry-weight of a total...... number of 427 bark samples were measured. The water holding capacity was calculated as the difference between wet-weight and dry-weight per wet-weight. The water holding capacity increased with elevation in most tree species and contrary to the expectation, thinner bark generally had a higher water...... holding capacity. Differences in the water holding capacity of bark may influence the occurrence and distribution of a wide range of bark-living organisms including the distribution of corticolous lichens....

SU-E-J-62: Breath Hold for Left-Sided Breast Cancer: Visually Monitored Deep Inspiration Breath Hold Amplitude Evaluated Using Real-Time Position Management

Energy Technology Data Exchange (ETDEWEB)

Conroy, L; Quirk, S; Smith, WL [The University of Calgary, Calgary, AB (Canada); Tom Baker Cancer Centre, Calgary, AB (Canada); Yeung, R; Phan, T [The University of Calgary, Calgary, AB (Canada); Hudson, A [Tom Baker Cancer Centre, Calgary, AB (Canada)

2015-06-15

Purpose: We used Real-Time Position Management (RPM) to evaluate breath hold amplitude and variability when gating with a visually monitored deep inspiration breath hold technique (VM-DIBH) with retrospective cine image chest wall position verification. Methods: Ten patients with left-sided breast cancer were treated using VM-DIBH. Respiratory motion was passively collected once weekly using RPM with the marker block positioned at the xiphoid process. Cine images on the tangent medial field were acquired on fractions with RPM monitoring for retrospective verification of chest wall position during breath hold. The amplitude and duration of all breath holds on which treatment beams were delivered were extracted from the RPM traces. Breath hold position coverage was evaluated for symmetric RPM gating windows from ± 1 to 5 mm centered on the average breath hold amplitude of the first measured fraction as a baseline. Results: The average (range) breath hold amplitude and duration was 18 mm (3–36 mm) and 19 s (7–34 s). The average (range) of amplitude standard deviation per patient over all breath holds was 2.7 mm (1.2–5.7 mm). With the largest allowable RPM gating window (± 5 mm), 4 of 10 VM-DIBH patients would have had ≥ 10% of their breath hold positions excluded by RPM. Cine verification of the chest wall position during the medial tangent field showed that the chest wall was greater than 5 mm from the baseline in only 1 out of 4 excluded patients. Cine images verify the chest wall/breast position only, whether this variation is acceptable in terms of heart sparing is a subject of future investigation. Conclusion: VM-DIBH allows for greater breath hold amplitude variability than using a 5 mm gating window with RPM, while maintaining chest wall positioning accuracy within 5 mm for the majority of patients.

Descriptors of Modular Formation of Accounting and Analytical Cluster in Innovation Development of Agricultural Holdings

Directory of Open Access Journals (Sweden)

Zhanna Degaltseva

2015-11-01

Full Text Available In the context of the division of accounting into financial accounting, taxation accounting, management accounting and statistical accounting a problem of improving their relationship arises. The accounting and analytical cluster plays the role of the correlating factor of the relationship between the subdivisions of the agricultural holding property. To improve its work a modular principle of its building based on information technology was introduced. Practical implementation of modular accounting and analytical cluster revealed its shortcomings. They were as follows: each type of account and each production unit used its own natural and cost parameters. The number and nature of these parameters were different. To eliminate the shortcomings in the information security of managers and specialists of the agricultural holding, we attempt to develop a methodology for establishing a rational number of descriptors (binding parameters for each module. The proposed descriptors are designed on the basis of validity of the methodological approach to their calculations and legal support. The proposed method allowed to limit the asymmetric information in all kinds of records, to improve its quality and to bring a synergistic effect from the scale and structure of the use of the agricultural holdings property complex.

Cash Holdings and Mutual Fund Performance

OpenAIRE

Mikhail Simutin

2014-01-01

Cash holdings of equity mutual funds impose a drag on fund performance but also allow managers to make quick investments in attractive stocks and satisfy outflows without costly fire sales. This article shows that actively managed equity funds with high abnormal cash—that is, with cash holdings in excess of the level predicted by fund attributes—outperform their low abnormal cash peers by over 2% per year. Managers carrying high abnormal cash compensate for the low return on cash by making su...

Is Whole-Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients With Solid Tumors.

Science.gov (United States)

McCullough, Laurence B; Slashinski, Melody J; McGuire, Amy L; Street, Richard L; Eng, Christine M; Gibbs, Richard A; Parsons, D William; Plon, Sharon E

2016-03-01

It has been anticipated that physician and parents will be ill prepared or unprepared for the clinical introduction of genome sequencing, making it ethically disruptive. As a part of the Baylor Advancing Sequencing in Childhood Cancer Care study, we conducted semistructured interviews with 16 pediatric oncologists and 40 parents of pediatric patients with cancer prior to the return of sequencing results. We elicited expectations and attitudes concerning the impact of sequencing on clinical decision making, clinical utility, and treatment expectations from both groups. Using accepted methods of qualitative research to analyze interview transcripts, we completed a thematic analysis to provide inductive insights into their views of sequencing. Our major findings reveal that neither pediatric oncologists nor parents anticipate sequencing to be an ethically disruptive technology, because they expect to be prepared to integrate sequencing results into their existing approaches to learning and using new clinical information for care. Pediatric oncologists do not expect sequencing results to be more complex than other diagnostic information and plan simply to incorporate these data into their evidence-based approach to clinical practice, although they were concerned about impact on parents. For parents, there is an urgency to protect their child's health and in this context they expect genomic information to better prepare them to participate in decisions about their child's care. Our data do not support the concern that introducing genome sequencing into childhood cancer care will be ethically disruptive, that is, leave physicians or parents ill prepared or unprepared to make responsible decisions about patient care. © 2015 Wiley Periodicals, Inc.

Is Whole Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients with Solid Tumors

Science.gov (United States)

McCullough, Laurence B.; Slashinski, Melody J.; McGuire, Amy L.; Street, Richard L.; Eng, Christine M.; Gibbs, Richard A.; Parsons, D. Williams; Plon, Sharon E.

2016-01-01

Background Some anticipate that physician and parents will be ill-prepared or unprepared for the clinical introduction of genome sequencing, making it ethically disruptive. Procedure As part of the Baylor Advancing Sequencing in Childhood Cancer Care (BASIC3) study, we conducted semi-structured interviews with 16 pediatric oncologists and 40 parents of pediatric patients with cancer prior to the return of sequencing results. We elicited expectations and attitudes concerning the impact of sequencing on clinical decision-making, clinical utility, and treatment expectations from both groups. Using accepted methods of qualitative research to analyze interview transcripts, we completed a thematic analysis to provide inductive insights into their views of sequencing. Results Our major findings reveal that neither pediatric oncologists nor parents anticipate sequencing to be an ethically disruptive technology, because they expect to be prepared to integrate sequencing results into their existing approaches to learning and using new clinical information for care. Pediatric oncologists do not expect sequencing results to be more complex than other diagnostic information and plan simply to incorporate these data into their evidence-based approach to clinical practice although they were concerned about impact on parents. For parents, there is an urgency to protect their chil's health and in this context they expect genomic information to better prepare them to participate in decisions about their chil's care. Conclusion Our data do not support concern that introducing genome sequencing into childhood cancer care will be ethically disruptive, i.e., leave physicians or parents ill-prepared or unprepared to make responsible decisions about patient care. PMID:26505993

Geoseq: a tool for dissecting deep-sequencing datasets

Directory of Open Access Journals (Sweden)

Homann Robert

2010-10-01

Full Text Available Abstract Background Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO, Sequence Read Archive (SRA hosted by the NCBI, or the DNA Data Bank of Japan (ddbj. Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Results Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment. Conclusions Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a identify differential isoform expression in mRNA-seq datasets, b identify miRNAs (microRNAs in libraries, and identify mature and star sequences in miRNAS and c to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.

12 CFR Appendix E to Part 360 - Hold File Structure

Science.gov (United States)

2010-01-01

... ReasonReason for the hold. Possible values are: Character (2). • LN = Loan Collateral Hold • LG = Court... structure of the data file to provide information to the FDIC for each legal or collateral hold placed on a...

Genomic sequencing in clinical trials

OpenAIRE

Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

2011-01-01

Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

Multiple job holding, local labor markets, and the business cycle

Directory of Open Access Journals (Sweden)

Barry T. Hirsch

2016-04-01

Full Text Available Abstract About 5 % of US workers hold multiple jobs, which can exacerbate or mitigate employment changes over the business cycle. Theory is ambiguous and prior literature is not fully conclusive. We examine the relationship between multiple job holding and local unemployment rates using a large Current Population Survey data set of workers in urban labor markets during 1998–2013. Labor markets with high unemployment have moderately lower rates of multiple job holding. Yet no relationship between multiple job holding and unemployment is found within markets over time, with near-zero estimates being precisely estimated. Multiple job holding is largely acyclic. JEL Classification: J21

Automated Inventory Control System for Nigeria Power Holding

African Journals Online (AJOL)

PROF. O. E. OSUAGWU

2013-09-01

Sep 1, 2013 ... Power Holding Company of Nigeria (PHCN) currently holds in excess of millions in spare parts inventory ... equipment/utilities at all times in view of stochastic item ... line contingency and small conductor sizing lines which are ...

Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

DEFF Research Database (Denmark)

Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

2013-01-01

to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

Cash Holdings Policy: a Dynamic Analysis of Brazilian Companies

Directory of Open Access Journals (Sweden)

Fadwa Muhieddine Dahrouge

2013-09-01

Full Text Available This paper investigates how corporate cash holdings were adjusted over time for Brazilian companies during the crisis of 2008-2009. We adopt a dynamic model of corporate cash holdings to evaluate the main determinants for the speed of adjustment of cash holdings at the optimum level. We find evidence that: a the adjustment costs of Brazilian companies are high implying a delay in reaching the optimum level of cash; b the low speed adjustment to the optimum level is due to the limited availability of credit and the high cost of bank debt; c during crisis, the changes in working capital are positively related to the level of cash holdings providing evidence that companies prefer finance to growth with liquidity; d companies have looked for long-term financing to secure liquidity rather than investing on fixed assets, implying a negative relationship between investment and cash holding.

Technology Specialisation 1, 2 & 3 Compendium

DEFF Research Database (Denmark)

Tambo, Torben; Koch, Christian; Hansen, Hans Henrik

2010-01-01

and progressive move forward inspired by the spirit of engineering. This compendium gives broad information on many aspects of the Technology Specialisation project courses relating to aim, method, mentor company roles, individual versus group performance, scientific motivation and many other issues. The content......Within the Master of Science in Technology-based Business Development study program, Technology Specialisations are the recurring technological stronghold. The Technology Specialisations should hold the students focus on the technological platform of this program and ideally constitute a continuous...

Does imminent threat capture and hold attention?

Science.gov (United States)

Koster, Ernst H W; Crombez, Geert; Van Damme, Stefaan; Verschuere, Bruno; De Houwer, Jan

2004-09-01

According to models of attention and emotion, threat captures and holds attention. In behavioral tasks, robust evidence has been found for attentional holding but not for attentional capture by threat. An important explanation for the absence of attentional capture effects is that the visual stimuli used posed no genuine threat. The present study investigated whether visual cues that signal an aversive white noise can elicit attentional capture and holding effects. Cues presented in an attentional task were simultaneously provided with a threat value through an aversive conditioning procedure. Response latencies showed that threatening cues captured and held attention. These results support recent views on attention to threat, proposing that imminent threat captures attention in everyone. (c) 2004 APA, all rights reserved

26 CFR 1.552-1 - Definition of foreign personal holding company.

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 7 2010-04-01 2010-04-01 true Definition of foreign personal holding company. 1...) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Foreign Personal Holding Companies § 1.552-1 Definition of foreign personal holding company. (a) A foreign personal holding company is any foreign...

Corporate Governance, Cash Holdings, and Firm Value: Evidence from Japan

OpenAIRE

Qi Luo; Toyohiko Hachiya

2005-01-01

This paper presents evidence on cash holdings for Japanese firms listed on the Tokyo Stock Exchange, focusing on the impact of corporate governance factors in cash holdings and the implication of cash holdings to firm value. We find that insider ownership and bank relations of firms play a significant role in determining cash holdings. Our results indicate that foreign stockholders select profitable firms to invest, and these firms have higher levels of cash. We document evidence that cash ho...

Massively parallel sequencing of forensic STRs

DEFF Research Database (Denmark)

Parson, Walther; Ballard, David; Budowle, Bruce

2016-01-01

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

Applying Next Generation Sequencing to Skeletal Development and Disease

OpenAIRE

Bowen, Margot Elizabeth

2013-01-01

Next Generation Sequencing (NGS) technologies have dramatically increased the throughput and lowered the cost of DNA sequencing. In this thesis, I apply these technologies to unresolved questions in skeletal development and disease. Firstly, I use targeted re-sequencing of genomic DNA to identify the genetic cause of the cartilage tumor syndrome, metachondromatosis (MC). I show that the majority of MC patients carry heterozygous loss-of-function mutations in the PTPN11 gene, which encodes a p...

Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

OpenAIRE

Yang, Xiang; Noyes, Noelle R.; Doster, Enrique; Martin, Jennifer N.; Linke, Lyndsey M.; Magnuson, Roberta J.; Yang, Hua; Geornaras, Ifigenia; Woerner, Dale R.; Jones, Kenneth L.; Ruiz, Jaime; Boucher, Christina; Morley, Paul S.; Belk, Keith E.

2016-01-01

Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bact...

Adaptive Basis Selection for Exponential Family Smoothing Splines with Application in Joint Modeling of Multiple Sequencing Samples

OpenAIRE

Ma, Ping; Zhang, Nan; Huang, Jianhua Z.; Zhong, Wenxuan

2017-01-01

Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments in parallel. After the resulting sequences (short reads) are mapped to the genome, one gets a sequence of short read counts along the genome. Effective extraction of signals in these short read counts is the key to the success of sequencing technologies. No...

Cembrit Holding A/S: At the crossroads

DEFF Research Database (Denmark)

Turcan, Romeo V.

2017-01-01

This is a Teaching Note (product number: 8B17M008) for the "Cembrit Holding A/S: At the crossroads" case (product number - 9B17M008) published by Ivey Publishing.......This is a Teaching Note (product number: 8B17M008) for the "Cembrit Holding A/S: At the crossroads" case (product number - 9B17M008) published by Ivey Publishing....

Patent holdings of US biotherapeutic companies in major markets.

Science.gov (United States)

Sebastian, Teena E; Yerram, Chandra Bindu; Saberwal, Gayatri

2009-05-01

In previous studies we examined the (United States, US) patent holdings of 109 largely North American biotech companies developing therapeutics that, in particular, have an interest in discovery stage science. There appears little correlation between the number of patents and the number of products of individual companies. Here we quantified and compared the 103 US-headquartered companies' patent holdings in Australia, Canada, Europe, Japan and the US. The companies demonstrate variable and surprising patterns of patent holdings across these countries or regions. For most companies, patent holdings are not in proportion to the importance of the country as a biotech or pharma market. These results have implications for the patenting strategies of small biotech companies involved in drug discovery.

Transmission Grating and Optics Technology Development for the Arcus Explorer Mission

Science.gov (United States)

Heilmann, Ralf; Arcus Team

2018-01-01

Arcus is a high-resolution x-ray spectroscopy MIDEX mission selected for a Phase A concept study. It is designed to explore structure formation through measurements of hot baryon distributions, feedback from black holes, and the formation and evolution of stars, disks, and exoplanet atmospheres. The design provides unprecedented sensitivity in the 1.2-5 nm wavelength band with effective area above 450 sqcm and spectral resolution R > 2500. The Arcus technology is based on 12 m-focal length silicon pore optics (SPO) developed for the European Athena mission, and critical-angle transmission (CAT) x-ray diffraction gratings and x-ray CCDs developed at MIT. The modular design consists of four parallel channels, each channel holding an optics petal, followed by a grating petal. CAT gratings are lightweight, alignment insensitive, high-efficiency x-ray transmission gratings that blaze into high diffraction orders, leading to high spectral resolution. Each optics petal represents an azimuthal sub-aperture of a full Wolter optic. The sub-aperturing effect increases spectral resolving power further. Two CCD readout strips receive photons from each channel, including higher-energy photons in 0th order. Each optics petal holds 34 SPO modules. Each grating petal holds 34 grating windows, and each window holds 4-6 grating facets. A grating facet consists of a silicon grating membrane, bonded to a flexure frame that interfaces with the grating window. We report on a sequence of tests with increasing complexity that systematically increase the Technology Readiness Level (TRL) for the combination of CAT gratings and SPOs towards TLR 6. CAT gratings have been evaluated in x rays for diffraction efficiency (> 30% at 2.5 nm) and for resolving power (R> 10,000). A CAT grating/SPO combination was measured at R ~ 3100 at blaze angles smaller than design values, exceeding Arcus requirements. Efficiency and resolving power were not impacted by vibration and thermal testing of gratings. A

Differentiation between focal malignant marrow-replacing lesions and benign red marrow deposition of the spine with T2*-corrected fat-signal fraction map using a three -echo volume interpolated breath-hold gradient echo dixon sequence

International Nuclear Information System (INIS)

Kim, Yong Pyo; Kim, Sung Jun; Chung, Tae Sub; Yoo, Yeon Hwa; Yoon, Choon Sik; Kanneengiesser, Stephan; Paek, Moon Young; Song, Ho Taek; Lee, Young Han; Suh, Jin Suck

2014-01-01

To assess the feasibility of T2 * -corrected fat-signal fraction (FF) map by using the three-echo volume interpolated breath-hold gradient echo (VIBE) Dixon sequence to differentiate between malignant marrow-replacing lesions and benign red marrow deposition of vertebrae. We assessed 32 lesions from 32 patients who underwent magnetic resonance imaging after being referred for assessment of a known or possible vertebral marrow abnormality. The lesions were divided into 21 malignant marrow-replacing lesions and 11 benign red marrow depositions. Three sequences for the parameter measurements were obtained by using a 1.5-T MR imaging scanner as follows: three-echo VIBE Dixon sequence for FF; conventional T1-weighted imaging for the lesion-disc ratio (LDR); pre- and post-gadolinium enhanced fat-suppressed T1-weighted images for the contrast-enhancement ratio (CER). A region of interest was drawn for each lesion for parameter measurements. The areas under the curve (AUC) of the parameters and their sensitivities and specificities at the most ideal cutoff values from receiver operating characteristic curve analysis were obtained. AUC, sensitivity, and specificity were respectively compared between FF and CER. The AUCs of FF, LDR, and CER were 0.96, 0.80, and 0.72, respectively. In the comparison of diagnostic performance between the FF and CER, the FF showed a significantly larger AUC as compared to the CER (p = 0.030), although the difference of sensitivity (p = 0.157) and specificity (p = 0.157) were not significant. Fat-signal fraction measurement using T2 * -corrected three-echo VIBE Dixon sequence is feasible and has a more accurate diagnostic performance, than the CER, in distinguishing benign red marrow deposition from malignant bone marrow-replacing lesions.

Divide and conquer: enriching environmental sequencing data.

Directory of Open Access Journals (Sweden)

Anne Bergeron

2007-09-01

Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

76 FR 54717 - Supervised Securities Holding Companies Registration

Science.gov (United States)

2011-09-02

... other financial statements submitted to the securities holding company's current consolidated supervisor... Y-9ES), The Supplement to the Consolidated Financial Statements for Bank Holding Companies (FR Y-9CS... Companies (FR Y-6), The Report of Foreign Banking Organizations (FR Y-7), The Consolidated Financial...

7 CFR 981.52 - Holding requirement and delivery.

Science.gov (United States)

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Holding requirement and delivery. 981.52 Section 981.52 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING... delivery. Each handler shall, at all times, hold in his possession or under his control, in proper storage...

Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

DEFF Research Database (Denmark)

Alquezar-Planas, David E; Fordyce, Sarah Louise

2012-01-01

Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

Sequencing of BAC pools by different next generation sequencing platforms and strategies

Directory of Open Access Journals (Sweden)

Scholz Uwe

2011-10-01

Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

Examination of self-navigating MR-sequences for perfusion imaging of the kidneys; Untersuchung von selbstnavigierenden MR-Sequenzen fuer die Perfusionsbildgebung der Nieren

Energy Technology Data Exchange (ETDEWEB)

Lietzmann, Florian; Zoellner, Frank G.; Schad, Lothar R. [Heidelberg Univ. Medizinische Fakultaet Mannheim (Germany). Computerunterstuetzte Klinische Medizin; Michaely, Henrik J. [Heidelberg Univ. Medizinische Fakultaet Mannheim (Germany). Inst. fuer Klinische Radiologie und Nuklearmedizin

2010-07-01

Due to the worldwide increasing number of cases of chronic kidney diseases renal imaging - as a non-invasive technique in magnetic resonance imaging - has become a very important tool for an early diagnosis of probable insufficiencies and malfunction. Especially, dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) provides a technique to derive physiological parameters like renal blood flow or glomerular filtration rate. Similar to the entire field of abdominal imaging, the major problems are motion artifacts that primarily arise from the patient's respiration. The self-navigating BLADE-sequence with a post processing motion correction is an approach that does not require breath holding and is therefore also easily applicable to patients who are not able to undergo multiple breath hold examinations. In this work, a T1-weighted BLADE-sequence was optimized to demonstrate the feasibility of this technique to perfusion imaging. The number of phase-encoding lines of one BLADE has a direct impact on the reduction of motion artifacts. In comparison to standard DCE-MRI sequences, the developed BLADE-sequence with optimized number of phase encoding lines could significantly reduce motion artifacts. A quantitative analysis revealed that up to a 50% displacement of the kidneys could be corrected. Therefore, it was demonstrated that dynamic motion corrected measurements without the need of a breath hold-technique are feasible. (orig.)

PBL og de sammensatte hold på kandidatuddannelser

DEFF Research Database (Denmark)

Engen, Mie; Fallov, Mia Arp; Jensen, Rune Hagel Skaarup

Denne rapport omhandler pædagogiske udfordringer og muligheder i Aalborgs Problembaserede Læringstilgang (PBL), når den omsættes til pædagogisk og didaktisk handling på kandidatuddannelser med sammensatte hold. Sammensatte hold betyder i denne sammenhæng kandidatuddannelser, hvor de optagne stude...

34 CFR 200.73 - Applicable hold-harmless provisions.

Science.gov (United States)

2010-07-01

... meet the eligibility requirements for a basic grant, targeted grant, or education finance incentive... Improving Basic Programs Operated by Local Educational Agencies Allocations to Leas § 200.73 Applicable hold... provided in § 200.100(d), an SEA must apply the hold-harmless requirement separately for basic grants...

Voluntary Breath-hold Technique for Reducing Heart Dose in Left Breast Radiotherapy

Science.gov (United States)

Bartlett, Frederick R.; Colgan, Ruth M.; Donovan, Ellen M.; Carr, Karen; Landeg, Steven; Clements, Nicola; McNair, Helen A.; Locke, Imogen; Evans, Philip M.; Haviland, Joanne S.; Yarnold, John R.; Kirby, Anna M.

2014-01-01

Breath-holding techniques reduce the amount of radiation received by cardiac structures during tangential-field left breast radiotherapy. With these techniques, patients hold their breath while radiotherapy is delivered, pushing the heart down and away from the radiotherapy field. Despite clear dosimetric benefits, these techniques are not yet in widespread use. One reason for this is that commercially available solutions require specialist equipment, necessitating not only significant capital investment, but often also incurring ongoing costs such as a need for daily disposable mouthpieces. The voluntary breath-hold technique described here does not require any additional specialist equipment. All breath-holding techniques require a surrogate to monitor breath-hold consistency and whether breath-hold is maintained. Voluntary breath-hold uses the distance moved by the anterior and lateral reference marks (tattoos) away from the treatment room lasers in breath-hold to monitor consistency at CT-planning and treatment setup. Light fields are then used to monitor breath-hold consistency prior to and during radiotherapy delivery. PMID:25046661

Effect of holding office on the behavior of politicians.

Science.gov (United States)

Enemark, Daniel; Gibson, Clark C; McCubbins, Mathew D; Seim, Brigitte

2016-11-29

Reciprocity is central to our understanding of politics. Most political exchanges-whether they involve legislative vote trading, interbranch bargaining, constituent service, or even the corrupt exchange of public resources for private wealth-require reciprocity. But how does reciprocity arise? Do government officials learn reciprocity while holding office, or do recruitment and selection practices favor those who already adhere to a norm of reciprocity? We recruit Zambian politicians who narrowly won or lost a previous election to play behavioral games that provide a measure of reciprocity. This combination of regression discontinuity and experimental designs allows us to estimate the effect of holding office on behavior. We find that holding office increases adherence to the norm of reciprocity. This study identifies causal effects of holding office on politicians' behavior.

Next-Generation Sequencing: From Understanding Biology to Personalized Medicine

Directory of Open Access Journals (Sweden)

Benjamin Meder

2013-03-01

Full Text Available Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.

Ethical aspects of technogenic catastrophes sequences on the example of the Chernobyl accident

International Nuclear Information System (INIS)

Mel'nov, S.B.; Sarana, Yu.V.

2009-01-01

It is examined such ethical aspects of technogenic catastrophes sequences on the example of Chernobyl disaster, as violation of individual right to get information about the environment condition, getting the liquidator status, maintenance of all ethical norms while holding of biomedical research on disaster victims, and forming of social-ecological stress. (authors)

Development of hold down plate of INGLE fuel assembly

International Nuclear Information System (INIS)

Kim, Hyeong Koo; Kim, Kyu Tae

1996-07-01

Hold down plate for the INGLE fuel which has been designed for high performance in the standpoints of thermal margin and structural integrity compared to current fuel for YGN 3/4 and UCN 3/4 has been developed and its structural integrity has been verified based on the eh stress analysis. The design feature of the developed hold down plate has not only perfect compatibility with the reactor internals of Korea standard reactor, but also brand-new locking mechanism between upper tie plate and guide tubes. This locking mechanism introduced to the INGLE fuel provides very simple and reliable reconstitutability. In this report, finite element stress analysis with the aid of the ANSYS code as a solver and the MSC/PATRAN code as a pre and post processor were performed to verify structural integrity of the hold down plate considering various load cases which seem to be applied to the hold down plate during its lifetime. Based on the analysis results, the developed hold down plate for INGLE fuel sustains structural integrity under considered load conditions. 3 tabs., 16 figs., 9 refs. (Author)

Hardware Accelerated Sequence Alignment with Traceback

Directory of Open Access Journals (Sweden)

Scott Lloyd

2009-01-01

in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

A New Rootedness? Education in the Technological Age

Science.gov (United States)

Glendinning, Simon

2018-01-01

This paper explores the challenges facing educators in a time when modern technology, and especially modern social technology, has an increasingly powerful hold on our lives. The educational challenge does not primarily concern questions concerning the use of technology in the classroom, or as part of the learning environment, but a changeover in…

Partnering Events | NCI Technology Transfer Center | TTC

Science.gov (United States)

Our team of technology transfer specialists has specialized training in invention reporting, patenting, patent strategy, executing technology transfer agreements and marketing. TTC is comprised of professionals with diverse legal, scientific, and business/marketing expertise. Most of our staff hold doctorate-level technical and/or legal training.

Inaugural Genomics Automation Congress and the coming deluge of sequencing data.

Science.gov (United States)

Creighton, Chad J

2010-10-01

Presentations at Select Biosciences's first 'Genomics Automation Congress' (Boston, MA, USA) in 2010 focused on next-generation sequencing and the platforms and methodology around them. The meeting provided an overview of sequencing technologies, both new and emerging. Speakers shared their recent work on applying sequencing to profile cells for various levels of biomolecular complexity, including DNA sequences, DNA copy, DNA methylation, mRNA and microRNA. With sequencing time and costs continuing to drop dramatically, a virtual explosion of very large sequencing datasets is at hand, which will probably present challenges and opportunities for high-level data analysis and interpretation, as well as for information technology infrastructure.

Intangible Capital and Corporate Cash Holdings: Theory and Evidence

OpenAIRE

Dalida Kadyrzhanova; Antonio Falato; Jae Sim

2012-01-01

The rise in intangible capital is a fundamental driver of the secular trend in US corporate cash holdings over the last decades. We construct a new measure of intangible capital and show that intangible capital is the most important firm-level determinant of corporate cash holdings. Our measure accounts for almost as much of the secular increase in cash since the 1980s as all other standard determinants together. We then develop a new model of corporate cash holdings that introduces intangibl...

26 CFR 301.6501(f)-1 - Personal holding company tax.

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 18 2010-04-01 2010-04-01 false Personal holding company tax. 301.6501(f)-1... Collection § 301.6501(f)-1 Personal holding company tax. If a corporation which is a personal holding company... time during the last half of such taxable year, more than 50 percent in value of the outstanding...

Effect of holding office on the behavior of politicians

Science.gov (United States)

Enemark, Daniel; Gibson, Clark C.; McCubbins, Mathew D.; Seim, Brigitte

2016-01-01

Reciprocity is central to our understanding of politics. Most political exchanges—whether they involve legislative vote trading, interbranch bargaining, constituent service, or even the corrupt exchange of public resources for private wealth—require reciprocity. But how does reciprocity arise? Do government officials learn reciprocity while holding office, or do recruitment and selection practices favor those who already adhere to a norm of reciprocity? We recruit Zambian politicians who narrowly won or lost a previous election to play behavioral games that provide a measure of reciprocity. This combination of regression discontinuity and experimental designs allows us to estimate the effect of holding office on behavior. We find that holding office increases adherence to the norm of reciprocity. This study identifies causal effects of holding office on politicians’ behavior. PMID:27856736

The Holding Company as an Instrument of Companies’ Tax-Financial Policy Formation

Directory of Open Access Journals (Sweden)

Dominik Gajewski

2013-03-01

Full Text Available The aim of this article is to present the holding institution as an economic and taxation solution. This article describes the holding company, indicates its advantages and disadvantages, and compares it to similar solutions. The main goal of holding companies is to change tax policies. As a result of these institutions, companies can change their tax status and economic situation. The holding institution influences the economic development of its constituent companies. The functioning of a holding company also has great importance for economic development. Establishing holdings is a worldwide trend that may be realised through various models.

Specifics of financial management of holdings when managing cash-flow

Directory of Open Access Journals (Sweden)

David Ficbauer

2010-01-01

Full Text Available Concentration and cooperation belong to the main attributes of the modern business life. Business competition makes the start of a new business more difficult. Just the moment of concentration and cooperation can make the break to the new business easier. This can be achieved by including new businesses into holding companies. Basically there are two ways how to do a business. These depend on whether company carries out many lines of business or on the amount of asset. The first way is to cover everything with one enterprise and thus to create one accounting unit. The second way is based on a foundation of a holding structure with subsidiaries and the holder on the top. In fact holding is a specific way how to cover business by many subsidiaries.The goal of this article is to describe specifics of a financial management of holdings when managing cash-flow. The focus is on reasons of holding structure and usage of both theoretical and other models of managing cash such as Baumol model, Miller-Orr model and Beránek model. As transfers within the holding organization belong to the main advantageous of holding, the way how to transfer finance from one subsidiary to other or from subsidiary to holder or reversely is handled here.

Academic performance in a pharmacotherapeutics course sequence taught synchronously on two campuses using distance education technology.

Science.gov (United States)

Steinberg, Michael; Morin, Anna K

2011-10-10

To compare the academic performance of campus-based students in a pharmacotherapeutics course with that of students at a distant campus taught via synchronous teleconferencing. Examination scores and final course grades for campus-based and distant students completing the case-based pharmacotherapeutics course sequence over a 5-year period were collected and analyzed. The mean examination scores and final course grades were not significantly different between students on the 2 campuses. The use of synchronous distance education technology to teach students does not affect students' academic performance when used in an active-learning, case-based pharmacotherapeutics course.

Small forest holdings could be combined for hunting leases

Science.gov (United States)

John J. Stransky; Lowell K. Halls

1969-01-01

Most forest land acreage in the South is in small holdings. Much-needed hunting land, and income for rural landowners, could be provided by combining small forest holdings into large units and teasing the hunting rights.

A hybrid breath hold and continued respiration-triggered technique for time-resolved 3D MRI perfusion studies in lung cancer

International Nuclear Information System (INIS)

Hintze, C.; Stemmer, A.; Bock, M.

2010-01-01

Assessment of lung cancer perfusion is impaired by respiratory motion. Imaging times for contrast agent wash-out studies often exceed breath hold capabilities, and respiration triggering reduces temporal resolution. Temporally resolved volume acquisition of entire tumors is required to assess heterogeneity. Therefore, we developed and evaluated an MR measurement technique that exceeds a single breath hold, and provides a variable temporal resolution during acquisition while suspending breath-dependent motion. 20 patients with suspected lung cancer were subjected to perfusion studies using a spoiled 3D gradient echo sequence after bolus injection of 0.07 mmol/kg body weight of Gd-DTPA. 10 acquisitions in expiratory breath hold were followed by 50 navigator-triggered acquisitions under free breathing. Post-processing allowed for co-registration of the 3D data sets. An ROI-based visualization of the signal-time curves was performed. In all cases motion-suspended, time-resolved volume data sets (40 x 33 x 10 cm 3 , voxel size: 2.1 x 2.1 x 5.0 mm 3 ) were generated with a variable, initially high temporal resolution (2.25 sec) that was synchronized with the breath pattern and covered up to 8(1)/(2) min. In 7 / 20 cases a remaining offset could be reduced by rigid co-registration. The tumors showed fast wash-in, followed by rapid signal decay (8 / 20) or a plateau. The feasibility of a perfusion study with hybrid breath hold and navigator-triggered time-resolved 3D MRI which combines high initial temporal resolution during breath hold with a long wash-out period under free breathing was demonstrated. (orig.)

Quantifying population genetic differentiation from next-generation sequencing data

DEFF Research Database (Denmark)

Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

2013-01-01

method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based...... on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled......Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data...

Why do firms hold so much cash? A tax-based explanation

OpenAIRE

C. Fritz Foley; Jay C. Hartzell; Sheridan Titman; Garry Twite

2006-01-01

U.S. corporations hold significant amounts of cash on their balance sheets, and these cash holdings have been justified in the existing empirical literature by transaction costs and precautionary motives. An additional explanation, considered in this study, is that U.S. multinational firms hold cash in their foreign subsidiaries because of the tax costs associated with repatriating foreign income. Consistent with this hypothesis, firms that face higher repatriation tax burdens hold higher lev...

The contribution of next generation sequencing to epilepsy genetics

DEFF Research Database (Denmark)

Møller, Rikke S.; Dahl, Hans A.; Helbig, Ingo

2015-01-01

During the last decade, next generation sequencing technologies such as targeted gene panels, whole exome sequencing and whole genome sequencing have led to an explosion of gene identifications in monogenic epilepsies including both familial epilepsies and severe epilepsies, often referred to as ...

Comparative study of fast T 2-weighted images using respiratory triggered, breath-hold, fat suppression and phased array multi coil for liver evaluation by magnetic resonance imaging; Estudo comparativo das sequencias rapidas ponderadas em T2, utilizando-se sincronizacao respiratoria, apneia, supressao de gordura, bobina de corpo e bobina de sinergia para a avaliacao do figado pela ressonancia magnetica

Energy Technology Data Exchange (ETDEWEB)

Abbehusen, Cristiane L.; D' Ippolito, Giuseppe; Palacio, Glaucia A.S.; Szejnfeld, Jacob [Universidade Federal de Sao Paulo (UNIFESP), SP (Brazil). Escola Paulista de Medicina (EPM). Dept. de Diagnostico por Imagem]. E-mail: cabbehusen@hotmail.com

2003-10-01

The objective of this study was to compare both qualitatively and quantitatively six T 2-weighted turbo spin-echo sequences varying the respiratory compensation technique, associating or not fat tissue suppression and using different types of coils. We performed a prospective study of 71 consecutive patients that were submitted to MRI of the liver using a 1.5 T magnet. The six following pulse sequences were used: fat-suppressed respiratory triggered with conventional body coil; breath-hold fat-suppressed with conventional body coil; non-suppressed respiratory triggered with conventional body coil; breath-hold non fat-suppressed with conventional body coil; fat-suppressed respiratory triggered with phased-array multi coil; breath-hold fat-suppressed with phased-array multi coil. Images were analyzed quantitatively by measuring the signal-to-noise ratios and qualitatively by evaluating the sharpness of hepatic contours, visibility of intrahepatic vessels and other segmental landmarks, and the presence of artifacts. Results: the qualitative analysis showed that the mean values obtained with the six sequences were 7.8, 4.6, 7.9, 5.2, 6.7 and 4.6 respectively. The respiratory-triggered sequences were better than the breath-hold sequences in both qualitative and quantitative analysis (p < 0.001). No significant differences in the values of signal-to-noise ratios and in overall image quality were found between the sequences with and without fat suppression (p . 0.05). The sequences using the body coil were similar in terms of image quality (p . 0.05) and better regarding signal-to-noise ratios than those obtained with the phased=array multi coil (p ,0.001). Our qualitative and quantitative results suggest that the best MRI sequences for the valuation of the liver are the sequences with respiratory triggering using a conventional body coil, with or without fat suppression. (author)

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

Science.gov (United States)

Ramos, Antonio M.; Crooijmans, Richard P. M. A.; Affara, Nabeel A.; Amaral, Andreia J.; Archibald, Alan L.; Beever, Jonathan E.; Bendixen, Christian; Churcher, Carol; Clark, Richard; Dehais, Patrick; Hansen, Mark S.; Hedegaard, Jakob; Hu, Zhi-Liang; Kerstens, Hindrik H.; Law, Andy S.; Megens, Hendrik-Jan; Milan, Denis; Nonneman, Danny J.; Rohrer, Gary A.; Rothschild, Max F.; Smith, Tim P. L.; Schnabel, Robert D.; Van Tassell, Curt P.; Taylor, Jeremy F.; Wiedmann, Ralph T.; Schook, Lawrence B.; Groenen, Martien A. M.

2009-01-01

Background The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs. PMID:19654876

Impact of breath holding on cardiovascular respiratory and cerebrovascular health.

Science.gov (United States)

Dujic, Zeljko; Breskovic, Toni

2012-06-01

Human underwater breath-hold diving is a fascinating example of applied environmental physiology. In combination with swimming, it is one of the most popular forms of summer outdoor physical activities. It is performed by a variety of individuals ranging from elite breath-hold divers, underwater hockey and rugby players, synchronized and sprint swimmers, spear fishermen, sponge harvesters and up to recreational swimmers. Very few data currently exist concerning the influence of regular breath holding on possible health risks such as cerebrovascular, cardiovascular and respiratory diseases. A literature search of the PubMed electronic search engine using keywords 'breath-hold diving' and 'apnoea diving' was performed. This review focuses on recent advances in knowledge regarding possibly harmful physiological changes and/or potential health risks associated with breath-hold diving. Available evidence indicates that deep breath-hold dives can be very dangerous and can cause serious acute health problems such a collapse of the lungs, barotrauma at descent and ascent, pulmonary oedema and alveolar haemorrhage, cardiac arrest, blackouts, nitrogen narcosis, decompression sickness and death. Moreover, even shallow apnoea dives, which are far more frequent, can present a significant health risk. The state of affairs is disturbing as athletes, as well as recreational individuals, practice voluntary apnoea on a regular basis. Long-term health risks of frequent maximal breath holds are at present unknown, but should be addressed in future research. Clearly, further studies are needed to better understand the mechanisms related to the possible development or worsening of different clinical disorders in recreational or competitive breath holding and to determine the potential changes in training/competition regimens in order to prevent these adverse events.

Leverage, Asymmetric Information, Firm Value, and Cash Holdings in Indonesia

Directory of Open Access Journals (Sweden)

Aldea Mita Cheryta

2018-02-01

Full Text Available This research aimed to analyze the effect of leverage and asymmetry information on the firm value through cash holding as mediation variable. The populations of this research were all the firms which listed on the Indonesia Stock Exchange since 2012 – 2015. A sample of this research was saturated sample and census, consisted 56 firms related the population criteria.  This research used secondary data from the firm financial report through path analysis method. This research showed that leverage had a negative effect on the cash holdings, asymmetry information had a negative effect on the firm value through cash holding, and cash holding had a negative effect on the firm value.  With leverage and effect on cash, holding cannot affect the firm value, due to investor risk-averse, investor risk seeker, and neutral investor has their own point of view in assessing the company. Cash holdings can lead to asymmetric information that can lead to agency conflict that can affect a company's performance, so that indirectly, with the existence of asymmetry information had an effect on the declining the firm value. 

Application of high-throughput DNA sequencing in phytopathology.

Science.gov (United States)

Studholme, David J; Glover, Rachel H; Boonham, Neil

2011-01-01

The new sequencing technologies are already making a big impact in academic research on medically important microbes and may soon revolutionize diagnostics, epidemiology, and infection control. Plant pathology also stands to gain from exploiting these opportunities. This manuscript reviews some applications of these high-throughput sequencing methods that are relevant to phytopathology, with emphasis on the associated computational and bioinformatics challenges and their solutions. Second-generation sequencing technologies have recently been exploited in genomics of both prokaryotic and eukaryotic plant pathogens. They are also proving to be useful in diagnostics, especially with respect to viruses. Copyright © 2011 by Annual Reviews. All rights reserved.

A Hold-down Margin Assessment using Statistical Method for the PWR Fuel Assembly

International Nuclear Information System (INIS)

Jeon, S. Y.; Park, N. K.; Lee, K. S.; Kim, H. K.

2007-01-01

The hold-down springs provide an acceptable hold down force against hydraulic uplift force absorbing the length change of the fuel assembly relative to the space between the upper and lower core plates in PWR. These length changes are mainly due to the thermal expansion, irradiation growth and creep down of the fuel assemblies. There are two kinds of hold-down springs depending on the different design concept of the reactor internals of the PWR in Korea, one is a leaf-type hold down spring for Westinghouse type plants and the other is a coil-type hold-down spring for OPR1000 (Optimized Power Reactor 1000). There are four sets of hold-down springs in each fuel assembly for leaf type hold-down spring and each set of the hold-down springs consists of multiple tapered leaves to form a cantilever leaf spring set. The length, width and thickness of the spring leaves are selected to provide the desired spring constant, deflection range, and hold down force. There are four coil springs in each fuel assembly for coil-type hold-down spring. In this study, the hold-down forces and margins were calculated for the leaf-type and coil-type hold-down springs considering geometrical data of the fuel assembly and its components, length changes of the fuel assembly due to thermal expansion, irradiation growth, creep, and irradiation relaxation. The hold-down spring forces were calculated deterministically and statistically to investigate the benefit of the statistical calculation method in view of hold-down margin. The Monte-Carlo simulation method was used for the statistical hold down force calculation

Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

Directory of Open Access Journals (Sweden)

Thierry-Mieg Danielle

2009-06-01

Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

Liquid holding recovery and photoreactivation of the ultraviolet-inactivated vibrios

International Nuclear Information System (INIS)

Banerjee, S.K.; Chatterjee, S.N.

1981-01-01

The kinetics of liquid holding recovery and photoreactivation of the ultra-violet-inactivated vibrios have been investigated. Photoreactivation was highest (about 80%) for Vibrio cholerae (classical) strains but the liquid holding recovery was highest (about 29%) for Vibrio parahemolyticus ones. Significance of the differences between any two of the four vibrio biotypes in respect of their liquid holding recovery and also photoreactivation was analysed statistically. (auth.)

The Future of Learning Technology: Some Tentative Predictions

Science.gov (United States)

Rushby, Nick

2013-01-01

This paper is a snapshot of an evolving vision of what the future may hold for learning technology. It offers three personal visions of the future and raises many questions that need to be explored if learning technology is to realise its full potential.

First Complete Genomic Sequence of a Rabies Virus from the Republic of Tajikistan Obtained Directly from a Flinders Technology Associates Card

OpenAIRE

Goharriz, H.; Marston, D. A.; Sharifzoda, F.; Ellis, R. J.; Horton, D. L.; Khakimov, T.; Whatmore, A.; Khamroev, K.; Makhmadshoev, A. N.; Bazarov, M.; Fooks, A. R.; Banyard, A. C.

2017-01-01

ABSTRACT A brain homogenate derived from a rabid dog in the district of Tojikobod, Republic of Tajikistan, was applied to a Flinders Technology Associates (FTA) card. A full-genome sequence of rabies virus (RABV) was generated from the FTA card directly without extraction, demonstrating the utility of these cards for readily obtaining genetic data.

Breath-hold gadolinium-enhanced MRA : clinical application

International Nuclear Information System (INIS)

Kang, Sung Gwon; Kang, Ji Hee; Kim, Won Hong; Lim, Myung Kwan; Cho, Young Kook; Cho, Soon Gu; Suh, Chang Hae

1998-01-01

The purpose of this study is to compare breath-hold gadolinium enhanced MR angiography (MRA) with digital subtraction angiography. Ten patients underwent angiography and breath-hold gadolinium enhanced MRA; the latter performed at 1.5T with 3D FSPGR after a bolus injection of gadopentetate dimeglumine (0.4m mol/kg). Seven of ten pathologic conditions (70%) evaluated by both techniques had a similar appearance. The conditions examined were as follows: the artery feeding renal cell carcinoma(n=2); renal artery stenosis (n=2); pulmonary AVM(n=2); abdominal aortic aneurysm (n=1); atheromatous plaque in the lower abdominal aorta (n=1); an enlarged bronchial artery (n=1); and an aberrant renal artery (n=1). For evaluating an anatomic relationship, a reconstructed 3D image obtained by MRA is more advantageous. Breath hold contrast enhanced MRA is a potentially useful noninvasive screening method for detecting vascular abnormality of the aorta and its branches. (author). 13 refs., 1 tab., 4 figs

Breath-hold gadolinium-enhanced MRA : clinical application

Energy Technology Data Exchange (ETDEWEB)

Kang, Sung Gwon; Kang, Ji Hee; Kim, Won Hong; Lim, Myung Kwan; Cho, Young Kook; Cho, Soon Gu; Suh, Chang Hae [Inha University Hospital, Inchon (Korea, Republic of)

1998-05-01

The purpose of this study is to compare breath-hold gadolinium enhanced MR angiography (MRA) with digital subtraction angiography. Ten patients underwent angiography and breath-hold gadolinium enhanced MRA; the latter performed at 1.5T with 3D FSPGR after a bolus injection of gadopentetate dimeglumine (0.4m mol/kg). Seven of ten pathologic conditions (70%) evaluated by both techniques had a similar appearance. The conditions examined were as follows: the artery feeding renal cell carcinoma(n=2); renal artery stenosis (n=2); pulmonary AVM(n=2); abdominal aortic aneurysm (n=1); atheromatous plaque in the lower abdominal aorta (n=1); an enlarged bronchial artery (n=1); and an aberrant renal artery (n=1). For evaluating an anatomic relationship, a reconstructed 3D image obtained by MRA is more advantageous. Breath hold contrast enhanced MRA is a potentially useful noninvasive screening method for detecting vascular abnormality of the aorta and its branches. (author). 13 refs., 1 tab., 4 figs.

Corporate Cash Holdings and Shareholder Risk : Investigating the relationship between corporate cash holdings and the risk of stocks listed on the Stockholm Stock Exchange

OpenAIRE

Olausson, Jonas; Löfgren, Christoffer

2013-01-01

Corporate cash holdings is a topic constantly under review, companies hoarding cash are criticized by shareholders who rather have companies using their cash for new investments or dividend payouts. Recent academic research has discovered that levels of cash holding are high in times when risk is deemed to be high and found that levels of corporate cash holdings are substantially higher than they used to, making more coverage and a better understanding of the phenomenon crucial. This thesis i...

Quantitative phenotyping via deep barcode sequencing.

Science.gov (United States)

Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

2009-10-01

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

From Genome Sequence to Taxonomy - A Skeptic’s View

DEFF Research Database (Denmark)

Özen, Asli Ismihan; Vesth, Tammi Camilla; Ussery, David

2012-01-01

The relative ease of sequencing bacterial genomes has resulted in thousands of sequenced bacterial genomes available in the public databases. This same technology now allows for using the entire genome sequence as an identifier for an organism. There are many methods available which attempt to us...

First Complete Genomic Sequence of a Rabies Virus from the Republic of Tajikistan Obtained Directly from a Flinders Technology Associates Card.

Science.gov (United States)

Goharriz, H; Marston, D A; Sharifzoda, F; Ellis, R J; Horton, D L; Khakimov, T; Whatmore, A; Khamroev, K; Makhmadshoev, A N; Bazarov, M; Fooks, A R; Banyard, A C

2017-07-06

A brain homogenate derived from a rabid dog in the district of Tojikobod, Republic of Tajikistan, was applied to a Flinders Technology Associates (FTA) card. A full-genome sequence of rabies virus (RABV) was generated from the FTA card directly without extraction, demonstrating the utility of these cards for readily obtaining genetic data. © Crown copyright 2017.

Open source tools to exploit DNA sequence data from livestock species

Science.gov (United States)

Next-Generation Sequencing (NGS) is a recent technological development that allows researchers to rapidly determine the DNA sequence of an individual. The decrease in cost of NGS has brought the technology into the realm of practical applications in livestock genomics, where it can be used to genera...

The Holding Power of Anchors

Indian Academy of Sciences (India)

The efficiency of an anchor may be expressed as the ratio (holding force + weight of anchor). In dry sand .... the market at the beginning of the coming season in three sizes, namely 20, 35 and. 60 lb. These are ... Taylor frozen-flow hypothesis.

75 FR 21050 - V-GPO, Inc., Valesc Holdings, Inc., Venture Stores, Inc., Vertigo Theme Parks, Inc. (f/k/a Snap2...

Science.gov (United States)

2010-04-22

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] V-GPO, Inc., Valesc Holdings, Inc., Venture Stores, Inc., Vertigo Theme Parks, Inc. (f/k/a Snap2 Corp.), Videolan Technologies, Inc., VisionGateway... Commission that there is a lack of current and accurate information concerning the securities of Vertigo...

3D hybrid profile order technique in a single breath-hold 3D T2-weighted fast spin-echo sequence: Usefulness in diagnosis of small liver lesions.

Science.gov (United States)

Hirata, Kenichiro; Nakaura, Takeshi; Okuaki, Tomoyuki; Tsuda, Noriko; Taguchi, Narumi; Oda, Seitaro; Utsunomiya, Daisuke; Yamashita, Yasuyuki

2018-01-01

We compared the efficacy of three-dimensional (3D) isotropic T2-weighted fast spin-echo imaging using a 3D hybrid profile order technique with a single-breath-hold (3D-Hybrid BH) with a two-dimensional (2D) T2-weighted fast spin-echo conventional respiratory-gated (2D-Conventional RG) technique for visualising small liver lesions. This study was approved by our institutional review board. The requirement to obtain written informed consent was waived. Fifty patients with small (≤15mm) hepatocellular carcinomas (HCC) (n=26), or benign cysts (n=24), had undergone hepatic MRI including both 2D-Conventional RG and 3D-Hybrid BH. We calculated the signal-to-noise ratio (SNR) and tumour-to-liver contrast (TLC). The diagnostic performance of the two protocols was analysed. The image acquisition time was 89% shorter with the 3D-Hybrid BH than with 2D-Conventional RG. There was no significant difference in the SNR between the two protocols. The area under the curve (AUC) of the TLC was significantly higher on 3D-Hybrid BH than on 2D-Conventional RG. The 3D-Hybrid BH sequence significantly improved diagnostic performance for small liver lesions with a shorter image acquisition time without sacrificing accuracy. Copyright © 2017. Published by Elsevier B.V.

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

KAUST Repository

Sepúlveda, Nuno

2013-02-26

Background: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model.Results: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates.Conclusions: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data. 2013 Seplveda et al.; licensee BioMed Central Ltd.

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

Science.gov (United States)

Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G

2013-02-26

The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data.

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

KAUST Repository

Sepú lveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G

2013-01-01

Background: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model.Results: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates.Conclusions: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data. 2013 Seplveda et al.; licensee BioMed Central Ltd.

DESIGN OF INFORMATION MANAGEMENT SYSTEM OF VERTICALLY INTEGRATED AGRICULTURAL HOLDINGS

Directory of Open Access Journals (Sweden)

Александр Витальевич ШМАТКО

2015-05-01

Full Text Available The paper deals with an approach to the design and development of information systems for the management and optimization of the organizational structure of vertically integrated agricultural holdings. A review of the problems of building and improving the organizational structure of vertically integrated agricultural holding is made. A method of constructing a discrete model management structure agricultural holding, which minimizes the costs associated with attracting applicants to work, is proposed.

FRESCO: Referential compression of highly similar sequences.

Science.gov (United States)

Wandelt, Sebastian; Leser, Ulf

2013-01-01

In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

Energy Technology Data Exchange (ETDEWEB)

Schmutz, Jeremy

2013-03-01

Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on New approaches and technologies to sequence de novo plant reference genomes at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Genomic prediction in families of perennial ryegrass based on genotyping-by-sequencing

DEFF Research Database (Denmark)

Ashraf, Bilal

In this thesis we investigate the potential for genomic prediction in perennial ryegrass using genotyping-by-sequencing (GBS) data. Association method based on family-based breeding systems was developed, genomic heritabilities, genomic prediction accurancies and effects of some key factors wer...... explored. Results show that low sequencing depth caused underestimation of allele substitution effects in GWAS and overestimation of genomic heritability in prediction studies. Other factors susch as SNP marker density, population structure and size of training population influenced accuracy of genomic...... prediction. Overall, GBS allows for genomic prediction in breeding families of perennial ryegrass and holds good potential to expedite genetic gain and encourage the application of genomic prediction...

78 FR 31590 - Sears Holdings Management Corporation, A Division Of Sears Holdings Corporation, Hoffman Estates...

Science.gov (United States)

2013-05-24

... (``My position at Sears had nothing to do with Analytics or space Management. I worked in Marketing... firm clarified that one petitioner supplied print marketing management services, another petitioner... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-81,253] Sears Holdings Management...

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

OpenAIRE

Bräutigam, Andrea; Gowik, Udo

2010-01-01

Next generation sequencing (NGS) technologies have opened fascinating opportunities for the analysis of plants with and without a sequenced genome on a genomic scale. During the last few years, NGS methods have become widely available and cost effective. They can be applied to a wide variety of biological questions, from the sequencing of complete eukaryotic genomes and transcriptomes, to the genome-scale analysis of DNA-protein interactions. In this review, we focus on the use of NGS for pla...

Genome sequence of Stachybotrys chartarum Strain 51-11

Science.gov (United States)

Stachybotrys chartarum strain 51-11 genome was sequenced by shotgun sequencing utilizing Illumina Hiseq 2000 and PacBio long read technology. Since Stachybotrys chartarum has been implicated in health impacts within water-damaged buildings, any information extracted from the geno...

On Education and Training Appropriate Information Technology for ...

African Journals Online (AJOL)

While information technology (IT) potentially holds promise in the technological advancement of developing countries, it is a revolution whose diffusion needs to be assessed. With the advent of IT in developing societies, education and training should play a significant role in IT policy dissemination and initiatives. Education ...

effectiveness of technological options for minimising production risks

African Journals Online (AJOL)

ACSS

preferred technologies in reducing production risk related to climate variability in Eastern Uganda. Data for this study were ..... Set of technological options employed by farmers to reduce climate-induced production risk. Dummy = 1 if farmer. 0.71. 0.46 ..... cation exchange capacity for holding nutrients against leaching loss.

Clinical applications of sequencing take center stage

OpenAIRE

Glusman, Gustavo

2013-01-01

A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013. This year's Advances in Genome Biology and Technology (AGBT) meeting reflected the current state of 'next generation' sequencing (NGS) technologies: significantly reduced competition and innovation, and a strong focus on standardization and application. Announcements of technological breakthroughs - a hallmark of previous AGBT meetings - were markedly absent, but existin...

Implementace analýzy FMEA v rámci logistické technologie Just-in-Sequence

OpenAIRE

FRANĚK, Václav

2013-01-01

The main objective of this master thesis is to design implementation of FMEA analysis in logistics technology Just-in-Sequence at company Robert Bosch in České Budějovice. The operational objective is to define process and product produced by technology Just-in-Sequence. Analyze newly developed technology Just-in-Sequence and compare its advantages over the original method.

Rhipicephalus microplus dataset of nonredundant raw sequence reads from 454 GS FLX sequencing of Cot-selected (Cot = 660) genomic DNA

Science.gov (United States)

A reassociation kinetics-based approach was used to reduce the complexity of genomic DNA from the Deutsch laboratory strain of the cattle tick, Rhipicephalus microplus, to facilitate genome sequencing. Selected genomic DNA (Cot value = 660) was sequenced using 454 GS FLX technology, resulting in 356...

Working memory for sequences of temporal durations reveals a volatile single-item store

Directory of Open Access Journals (Sweden)

Sanjay G Manohar

2016-10-01

Full Text Available When a sequence is held in working memory, different items are retained with differing fidelity. Here we ask whether a sequence of brief time intervals that must be remembered show recency effects, similar to those observed in verbal and visuospatial working memory. It has been suggested that prioritising some items over others can be accounted for by a focus of attention, maintaining some items in a privileged state. We therefore also investigated whether such benefits are vulnerable to disruption by attention or expectation. Participants listened to sequences of one to five tones, of varying durations (200ms to 2s. Subsequently, the length of one of the tones in the sequence had to be reproduced by holding a key. The discrepancy between the reproduced and actual durations quantified the fidelity of memory for auditory durations. Recall precision decreased with the number of items that had to be remembered, and was better for the first and last items of sequences, in line with set-size and serial position effects seen in other modalities. To test whether attentional filtering demands might impair performance, an irrelevant variation in pitch was introduced in some blocks of trials. In those blocks, memory precision was worse for sequences that consisted of only one item, i.e. the smallest memory set size. Thus, when irrelevant information was present, the benefit of having only one item in memory is attenuated. Finally we examined whether expectation could interfere with memory. On half the trials, the number of items in the upcoming sequence was cued. When the number of items was known in advance, performance was paradoxically worse when the sequence consisted of only one item. Thus the benefit of having only one item to remember is stronger when it is unexpectedly the only item. Our results suggest that similar mechanisms are used to hold auditory time durations in working memory, as for visual or verbal stimuli. Further, solitary items were

Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

Science.gov (United States)

Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

2017-07-01

DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

The Capability to Hold Property

NARCIS (Netherlands)

Claassen, Rutger

2015-01-01

This paper discusses the question of whether a capability theory of justice (such as that of Martha Nussbaum) should accept a basic “capability to hold property.” Answering this question is vital for bridging the gap between abstract capability theories of justice and their institutional

C-14/I-29 Preservation and Hold Time Survey

Energy Technology Data Exchange (ETDEWEB)

Kitchen, S. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2015-04-08

Preservation and hold time of radionuclides must account for both nuclear half-lives and nonnuclear loss mechanisms, but variations in the latter are often neglected. Metals-based defaults are inappropriate for long-lived non-metals C-14 and I-129, which are vulnerable to chemical and biological volatilization. Non-acidification is already widely practiced for them. Recommended addition measures from radiological and chemical literature include glass containers where possible, water filtration where possible, headspace minimization, light shielding, cold (4°C) storage and unfiltered water hold time of 28 days. Soil hold time may need to be shortened when water-logged, excessively sandy, or still adjusting to significant new contamination.

Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

Directory of Open Access Journals (Sweden)

Chengxi Ye

2016-06-01

Full Text Available Motivation. The third generation sequencing (3GS technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15–40%, significantly higher than those of the prevalent next generation sequencing (NGS technologies (less than 1%. Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc.

Googling DNA sequences on the World Wide Web.

Science.gov (United States)

Hajibabaei, Mehrdad; Singer, Gregory A C

2009-11-10

New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google. We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results. Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web.

Estimating animal movement contacts between holdings of different production types.

Science.gov (United States)

Lindström, Tom; Sisson, Scott A; Lewerin, Susanna Stenberg; Wennergren, Uno

2010-06-01

Animal movement poses a great risk for disease transmission between holdings. Heterogeneous contact patterns are known to influence the dynamics of disease transmission and should be included in modeling. Using pig movement data from Sweden as an example, we present a method for quantification of between holding contact probabilities based on different production types. The data contained seven production types: Sow pool center, Sow pool satellite, Farrow-to-finish, Nucleus herd, Piglet producer, Multiplying herd and Fattening herd. The method also estimates how much different production types will determine the contact pattern of holdings that have more than one type. The method is based on Bayesian analysis and uses data from central databases of animal movement. Holdings with different production types are estimated to vary in the frequency of contacts as well as in what type of holding they have contact with, and the direction of the contacts. Movements from Multiplying herds to Sow pool centers, Nucleus herds to other Nucleus herds, Sow pool centers to Sow pool satellites, Sow pool satellites to Sow pool centers and Nucleus herds to Multiplying herds were estimated to be most common relative to the abundance of the production types. We show with a simulation study that these contact patterns may also be expected to result in substantial differences in disease transmission via animal movements, depending on the index holding. Simulating transmission for a 1 year period showed that the median number of infected holdings was 1 (i.e. only the index holding infected) if the infection started at a Fattening herd and 2161 if the infection started on a Nucleus herd. We conclude that it is valuable to include production types in models of disease transmission and the method presented in this paper may be used for such models when appropriate data is available. We also argue that keeping records of production types is of great value since it may be helpful in risk

Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa

Directory of Open Access Journals (Sweden)

Pazos-Navarro María

2011-12-01

Full Text Available Abstract Background Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species. Results 432,306 mRNA molecules were sampled from a leaf transcriptome of a single B. bituminosa plant using Roche 454 pyrosequencing, resulting in an average read length of 345 bp (149.1 Mbp in total. Sequences were assembled into 3,838 isotigs/contigs representing putatively unique gene transcripts. Gene ontology descriptors were identified for 3,419 sequences. Raw sequence reads containing simple sequence repeat (SSR motifs were identified, and 240 primer pairs flanking these motifs were designed. Of 87 primer pairs developed this way, 75 (86.2% successfully amplified primarily single fragments by PCR. Fragment analysis using 20 primer pairs in 79 accessions of B. bituminosa detected 130 alleles at 21 SSR loci. Genetic diversity analyses confirmed that variation at these SSR loci accurately reflected known taxonomic relationships in original collections of B. bituminosa and provided additional evidence that a division of the botanical variety bituminosa into two according to geographical origin (Mediterranean region and Canary Islands may be appropriate. Evidence of cross-pollination was also found between botanical varieties within a B. bituminosa breeding programme. Conclusions B. bituminosa can no longer be considered a genomic orphan species, having now a large (albeit incomplete repertoire of expressed gene sequences that can serve as a resource for future genetic studies. This

Understanding invasion history and predicting invasive niches using genetic sequencing technology in Australia: case studies from Cucurbitaceae and Boraginaceae.

Science.gov (United States)

Shaik, Razia S; Zhu, Xiaocheng; Clements, David R; Weston, Leslie A

2016-01-01

Part of the challenge in dealing with invasive plant species is that they seldom represent a uniform, static entity. Often, an accurate understanding of the history of plant introduction and knowledge of the real levels of genetic diversity present in species and populations of importance is lacking. Currently, the role of genetic diversity in promoting the successful establishment of invasive plants is not well defined. Genetic profiling of invasive plants should enhance our understanding of the dynamics of colonization in the invaded range. Recent advances in DNA sequencing technology have greatly facilitated the rapid and complete assessment of plant population genetics. Here, we apply our current understanding of the genetics and ecophysiology of plant invasions to recent work on Australian plant invaders from the Cucurbitaceae and Boraginaceae. The Cucurbitaceae study showed that both prickly paddy melon ( Cucumis myriocarpus ) and camel melon ( Citrullus lanatus ) were represented by only a single genotype in Australia, implying that each was probably introduced as a single introduction event. In contrast, a third invasive melon, Citrullus colocynthis , possessed a moderate level of genetic diversity in Australia and was potentially introduced to the continent at least twice. The Boraginaceae study demonstrated the value of comparing two similar congeneric species; one, Echium plantagineum , is highly invasive and genetically diverse, whereas the other, Echium vulgare , exhibits less genetic diversity and occupies a more limited ecological niche. Sequence analysis provided precise identification of invasive plant species, as well as information on genetic diversity and phylogeographic history. Improved sequencing technologies will continue to allow greater resolution of genetic relationships among invasive plant populations, thereby potentially improving our ability to predict the impact of these relationships upon future spread and better manage invaders

An inventory model of instantaneous deteriorating items with controllable deterioration rate for time dependent demand and holding cost

Directory of Open Access Journals (Sweden)

Vinod Kumar Mishra

2013-06-01

Full Text Available Purpose: The purpose of this paper to develop an inventory model for instantaneous deteriorating items with the consideration of the facts that the deterioration rate can be controlled by using the preservation technology (PT and the holding cost & demand rate both are linear function of time which was treated as constant in most of the deteriorating inventory model. Design/methodology/approach: Developed the mathematical equation of deterministic deteriorating inventory model in which demand rate and holding cost both is linear function of time, deterioration rate is constant, backlogging rate is variable and depend on the length of the next replenishment, shortages are allowed and partially backlogged and obtain an analytical solution which optimizes the total cost of the proposed inventory model. Findings: The model can be applied for optimizing the total inventory cost of deteriorating items inventory for such business enterprises where they use the preservation technology to control the deterioration rate under other assumptions of the model. Originality/value: The inventory system for deteriorating items has been an object of study for a long time, but little is known about the effect of investing in reducing the rate of product deterioration and their significant impact in the business. The proposed model is effective as well as efficient for the business organization that uses the preservation technology to reduce the deterioration rate of the instantaneous deteriorating items of the inventory.

From Conventional to Next Generation Sequencing of Epstein-Barr Virus Genomes.

Science.gov (United States)

Kwok, Hin; Chiang, Alan Kwok Shing

2016-02-24

Genomic sequences of Epstein-Barr virus (EBV) have been of interest because the virus is associated with cancers, such as nasopharyngeal carcinoma, and conditions such as infectious mononucleosis. The progress of whole-genome EBV sequencing has been limited by the inefficiency and cost of the first-generation sequencing technology. With the advancement of next-generation sequencing (NGS) and target enrichment strategies, increasing number of EBV genomes has been published. These genomes were sequenced using different approaches, either with or without EBV DNA enrichment. This review provides an overview of the EBV genomes published to date, and a description of the sequencing technology and bioinformatic analyses employed in generating these sequences. We further explored ways through which the quality of sequencing data can be improved, such as using DNA oligos for capture hybridization, and longer insert size and read length in the sequencing runs. These advances will enable large-scale genomic sequencing of EBV which will facilitate a better understanding of the genetic variations of EBV in different geographic regions and discovery of potentially pathogenic variants in specific diseases.

From Conventional to Next Generation Sequencing of Epstein-Barr Virus Genomes

Directory of Open Access Journals (Sweden)

Hin Kwok

2016-02-01

Full Text Available Genomic sequences of Epstein–Barr virus (EBV have been of interest because the virus is associated with cancers, such as nasopharyngeal carcinoma, and conditions such as infectious mononucleosis. The progress of whole-genome EBV sequencing has been limited by the inefficiency and cost of the first-generation sequencing technology. With the advancement of next-generation sequencing (NGS and target enrichment strategies, increasing number of EBV genomes has been published. These genomes were sequenced using different approaches, either with or without EBV DNA enrichment. This review provides an overview of the EBV genomes published to date, and a description of the sequencing technology and bioinformatic analyses employed in generating these sequences. We further explored ways through which the quality of sequencing data can be improved, such as using DNA oligos for capture hybridization, and longer insert size and read length in the sequencing runs. These advances will enable large-scale genomic sequencing of EBV which will facilitate a better understanding of the genetic variations of EBV in different geographic regions and discovery of potentially pathogenic variants in specific diseases.

The carbon holdings of northern Ecuador's mangrove forests

OpenAIRE

Hamilton, Stuart E.; Lovette, John; Borbor, Mercy; Millones, Marco

2016-01-01

Within a GIS environment, we combine field measures of mangrove diameter, mangrove species distribution, and mangrove density with remotely sensed measures of mangrove location and mangrove canopy cover to estimate the mangrove carbon holdings of northern Ecuador. We find that the four northern estuaries of Ecuador contain approximately 7,742,999 t (plus or minus 15.47 percent) of standing carbon. Of particular high carbon holdings are the Rhizophora mangle dominated mangrove stands found in-...

Convergence and Spanish technological specialization: the role of multinational companies

International Nuclear Information System (INIS)

Urraca Ruiz, A.

2007-01-01

Using patent data from EPO from 1978 to 2003, this paper aims to identify the role of MNE in the determination of technological specialization trends and convergence in Spain and the extend to which the technological activity of these companies helps to define the technical distribution of competence in the country.The main findings are: (i) Spain reduces its technological distances to world along the whole period; (ii) Spanish convergence process does not seem to be accompanied by greater specialization, but greater diversification of its technological competence; (iii) Spain is specialized in a few technical fields characterized by being less dynamic and pervasive; (iv) MNE do not seem to hold strong competence in those technical fields where Spain holds technological strengths but do help to convergence process thought diversification of competence process, which is a consequence of the performance of MNE in host catching up countries, more focused on duplication of their home countries.(Author)

The climate technology initiative

International Nuclear Information System (INIS)

Smith, Adam

2000-01-01

The CTI (Climate Technology Initiative) aims to promote those technologies which cause the minimum of harm to the environment: reducing emissions of greenhouse gases and supporting those countries most vulnerable to climate change are priorities. A strong case for cogeneration is made and it is pointed out that both the European Union and the USA aim to double their cogeneration capacity by 2010. The CTI holds training courses and seminars all over the world where the barriers to the expansion of climate-friendly technology are discussed. The article also mentions the CTI Co-operation Technology Implementation Plan, research and development, its website and search engine, its presence at all UNFCCC events and its awards programme

The climate technology initiative

Energy Technology Data Exchange (ETDEWEB)

Smith, Adam [International Energy Agency, Climate Technology Initiative, Paris (France)

2000-12-01

The CTI (Climate Technology Initiative) aims to promote those technologies which cause the minimum of harm to the environment: reducing emissions of greenhouse gases and supporting those countries most vulnerable to climate change are priorities. A strong case for cogeneration is made and it is pointed out that both the European Union and the USA aim to double their cogeneration capacity by 2010. The CTI holds training courses and seminars all over the world where the barriers to the expansion of climate-friendly technology are discussed. The article also mentions the CTI Co-operation Technology Implementation Plan, research and development, its website and search engine, its presence at all UNFCCC events and its awards programme.

Primary EFL Teachers' Technology Use in China: Patterns and Perceptions

Science.gov (United States)

Li, Guofang; Ni, Xiaopeng

2011-01-01

Drawing on survey data, this paper examines the patterns and perceptions of technology use by primary EFL teachers in China. Findings suggest that although Chinese EFL teachers hold positive attitudes toward the value of technology for teaching and learning, they use technology mainly for teacher-centered purposes, such as teaching preparation and…

Complete Genome Sequence of Ikoma Lyssavirus

OpenAIRE

Marston, Denise A.; Ellis, Richard J.; Horton, Daniel L.; Kuzmin, Ivan V.; Wise, Emma L.; McElhinney, Lorraine M.; Banyard, Ashley C.; Ngeleja, Chanasa; Keyyu, Julius; Cleaveland, Sarah; Lembo, Tiziana; Rupprecht, Charles E.; Fooks, Anthony R.

2012-01-01

Lyssaviruses (family Rhabdoviridae) constitute one of the most important groups of viral zoonoses globally. All lyssaviruses cause the disease rabies, an acute progressive encephalitis for which, once symptoms occur, there is no effective cure. Currently available vaccines are highly protective against the predominantly circulating lyssavirus species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence for a novel lyssavirus, Ikoma lyssavirus (IKOV), isol...

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

NARCIS (Netherlands)

Buschmann, Tilo; Bystrykh, Leonid V.

2013-01-01

Background: High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called

The Design of Bulk Carrier Cargo Holds State Integrated Monitoring System

Directory of Open Access Journals (Sweden)

Gao Ru-jiang

2016-01-01

Full Text Available Most ship cargo hold Internal uses artificial watch or is unattended. Therefore, it is impossible to know the appropriate information of the cargo holds Internal timely and accurately. Cargo damage and ship accidents occurred frequently. Automation remote processing and monitoring alarm system for the bulk carrier is an important part of the marine automation. The system plays a significant role to guarantee the navigation safety for bulk carriers. The paper introduced the important parts of the integrated monitoring system, structural design, hardware configuration, various modules communication transmission and various data processing software design were included. Based on embedded development, the real time information including the cargo hold internal humidity temperature, oxygen concentration, smoke gas concentration, cold water well level and other data were collected, as well the hatch closed state was detected and the cargo hold internal real time video information was collected. Then the real-time communication between the control display and acquisition modules were assured. By adjusting the corresponding buttons on the bridge according to the monitoring information, so that the cargo hold always in a safe environment, so as to avoid cargo hold accidents.

An integrated semiconductor device enabling non-optical genome sequencing.

Science.gov (United States)

Rothberg, Jonathan M; Hinz, Wolfgang; Rearick, Todd M; Schultz, Jonathan; Mileski, William; Davey, Mel; Leamon, John H; Johnson, Kim; Milgrew, Mark J; Edwards, Matthew; Hoon, Jeremy; Simons, Jan F; Marran, David; Myers, Jason W; Davidson, John F; Branting, Annika; Nobile, John R; Puc, Bernard P; Light, David; Clark, Travis A; Huber, Martin; Branciforte, Jeffrey T; Stoner, Isaac B; Cawley, Simon E; Lyons, Michael; Fu, Yutao; Homer, Nils; Sedova, Marina; Miao, Xin; Reed, Brian; Sabina, Jeffrey; Feierstein, Erika; Schorn, Michelle; Alanjary, Mohammad; Dimalanta, Eileen; Dressman, Devin; Kasinskas, Rachel; Sokolsky, Tanya; Fidanza, Jacqueline A; Namsaraev, Eugeni; McKernan, Kevin J; Williams, Alan; Roth, G Thomas; Bustillo, James

2011-07-20

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.

The performance and risk of Hartalega Holdings Berhad

OpenAIRE

Wong, Kah Wai

2017-01-01

The purpose of the study is to investigate the overall performance of Hartalega Holdings Berhad and specific risk factors and macroeconomic factors are influence on profitability performance. The data obtained from annual report of Hartalega Holdings Berhad during the years 2011 to 2015. The measurement of financial ratios and regression analysis used to see the overall performance and risk of the company. The study found that performance of the company is unfavourable due to the decreasing m...

Next-Generation Sequencing for Infectious Disease Diagnosis and Management: A Report of the Association for Molecular Pathology.

Science.gov (United States)

Lefterova, Martina I; Suarez, Carlos J; Banaei, Niaz; Pinsky, Benjamin A

2015-11-01

Next-generation sequencing (NGS) technologies are increasingly being used for diagnosis and monitoring of infectious diseases. Herein, we review the application of NGS in clinical microbiology, focusing on genotypic resistance testing, direct detection of unknown disease-associated pathogens in clinical specimens, investigation of microbial population diversity in the human host, and strain typing. We have organized the review into three main sections: i) applications in clinical virology, ii) applications in clinical bacteriology, mycobacteriology, and mycology, and iii) validation, quality control, and maintenance of proficiency. Although NGS holds enormous promise for clinical infectious disease testing, many challenges remain, including automation, standardizing technical protocols and bioinformatics pipelines, improving reference databases, establishing proficiency testing and quality control measures, and reducing cost and turnaround time, all of which would be necessary for widespread adoption of NGS in clinical microbiology laboratories. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

FY 1993 Report on the technical results. Research and development of extreme handling technologies at atomic/molecular levels (Development of technologies for forming highly functional stock materials for power generation environments); 1993 nendo genshi bunshi kyokugen sosa gijutsu no kenkyu kaihatsu seika hokokusho. Hatsuden kankyoyo kokino sozai keisei gijutsu kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1994-03-01

This research and development project is aimed at development of the technologies for observing/handling solid surfaces and organic molecules at the atomic level by the mechanical probe; forming the fine structures of optional atomic sequences using fine electron beams and surface chemical characteristics; simulation by the first principle calculation to theoretically predict the atom/molecule surface reactions in a process; and producing new materials substitutes for semiconductors, in order to develop the atom/molecule observing and handling technologies as the common basic technologies for the various industrial areas, e.g., new materials, electronics, biotechnology and chemical. The research/survey activities are directed to (1) development of the technologies for observing the atoms and molecules on solid surfaces, (2) development of technologies for observing/handling intra-spatial atom groups, (3) development of the theoretical technologies for the atomic/molecular processes, and (4) auxiliary activities. The item (2) is intended to obtain the basic knowledge of the principles and devices for handling atom groups in a free space by spatial electromagnetic field handling or the like, and principles of state observation methods, including their possibilities. The item (4) holds the information-exchange meetings. (NEDO)

Expert cognition in the production sequence of Acheulian cleavers at Gesher Benot Ya'aqov, Israel: A lithic and cognitive analysis.

Science.gov (United States)

Herzlinger, Gadi; Wynn, Thomas; Goren-Inbar, Naama

2017-01-01

Stone cleavers are one of the most distinctive components of the Acheulian toolkit. These tools were produced as part of a long and complex reduction sequence and they provide indications for planning and remarkable knapping skill. These aspects hold implications regarding the cognitive complexity and abilities of their makers and users. In this study we have analyzed a cleaver assemblage originating from the Acheulian site of Gesher Benot Ya'aqov, Israel, to provide a reconstruction of the chaîne opératoire which structured their production. This reduction sequence was taken as the basis for a cognitive analysis which allowed us to draw conclusion regarding numerous behavioral and cognitive aspects of the GBY hominins. The results indicate that the cleavers production incorporated a highly specific sequence of decisions and actions which resulted in three distinct modes of cleavers modification. Furthermore, the decision to produce a cleaver must have been taken very early in the sequence, thus differentiating its production from that of handaxes. The substantial predetermination and the specific reduction sequence provide evidence that the Gesher Benot Ya'aqov hominins had a number of cognitive categories such as a general 'tool concept' and a more specific 'cleaver concept', setting them apart from earlier tool-producing hominins and extant tool-using non-human primates. Furthermore, it appears that the Gesher Benot Ya'aqov lithic technology was governed by expert cognition, which is the kind of thinking typical of modern human experts in their various domains. Thus, the results provide direct indications that important components of modern cognition have been well established in the minds of the Gesher Benot Ya'aqov hominins.

Next Generation DNA Sequencing and the Future of Genomic Medicine

OpenAIRE

Anderson, Matthew W.; Schrijver, Iris

2010-01-01

In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpreta...

Determinants of corporate cash holdings: Evidence from Portuguese publicly traded firms

Directory of Open Access Journals (Sweden)

Fernandes, Filipa

2017-05-01

Full Text Available This paper investigates the determinants of cash holdings of publicly traded Portuguese firms. We find that such firms hold less cash than similar companies operating in countries where both shareholders and creditors’ rights are more tightly protected by the law. In addition, our regression results suggest that leverage, other liquid assets, and firm growth are negatively correlated with our sample firms’ cash holdings whereas long-term debt and financial distress are positively correlated. Our findings cannot be reconciled with just one of the existent theories (trade-off, pecking order and free cashflow theory, and emphasize the importance of a country’s legal, institutional, and economic environment for explaining firms’ cash holdings decisions.

Image sequence analysis

CERN Document Server

1981-01-01

The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

FUNCTIONING OF AGRICULTURAL HOLDINGS IN UKRAINE: STRONG AND WEAK SIDES

Directory of Open Access Journals (Sweden)

Postgraduate, assistant Sergii Ivanovich TODORIUK

2014-06-01

Full Text Available One of the organizational forms of the agricultural management which is gaining popularity in the world is agricultural holdings. The essence of agricultural holdings is considered in the article. Also the peculiarities of their functioning in Ukraine and determination of the strengths and weaknesses of their activities is defined, as well as perspectives of their further functioning. Agrarian holding, as a relatively new organizational legal form of managing in Ukraine has its advantages and disadvantages. As the experience shows the advantages of agrarian holdings over the subjects of management are revealed mainly in the economic sphere. While their disadvantages over the subjects of management are revealed in social and ecological spheres. This is a negative moment considering the implementation in Ukraine of the concept of the sustainable development, which means the combination of these main components (economic component, environmental component, social component.

Robotics in rehabilitation: technology as destiny.

Science.gov (United States)

Stein, Joel

2012-11-01

Robotic aids for rehabilitation hold considerable promise but have not yet achieved widespread clinical adoption. Barriers to adoption include the limited data on efficacy, the single-purpose design of existing robots, financial considerations, and clinician lack of familiarity with this technology. Although the path forward to clinical adoption may be slow and have several false starts, the labor-saving aspect of robotic technology will ultimately ensure its adoption.

Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

Science.gov (United States)

Chatterjee, Aniruddha; Rodger, Euan J.; Stockwell, Peter A.; Weeks, Robert J.; Morison, Ian M.

2012-01-01

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background. PMID:23193365

A computational genomics pipeline for prokaryotic sequencing projects.

Science.gov (United States)

Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King

2010-08-01

New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

Control of cooperative manipulators in holding deformable objects

Science.gov (United States)

Alkathiri, A. A.; Azlan, N. Z.

2017-11-01

This paper presents the implementation of a control system to control cooperative manipulators to hold deformable objects. The aim is to hold the deformable object without having information on the shape and stiffness of the deformable object beforehand. The prototype of a pair of manipulators has been designed and built to test the controller. A force sensor and a rotary encoder are used to give feedback to the controller, which controls the DC motor actuators accordingly. A position proportional-integral-derivative (PID) controller technique has been applied for one of the manipulators and a PID force control technique is applied to the other. Simulations and experimental tests have been conducted on models and the controller has been implemented on the real plant. Both simulation and test results prove that the implemented control technique has successfully provided the desired position and force to hold the deformable object with maximum experimental errors of 0.34mm and 50mN respectively.

The effect of three holding tank chemicals on anaerobic wastewater treatment

OpenAIRE

Howard, Samuel Clarence

1988-01-01

Sewage-holding tanks aboard recreational boats store human wastes, thereby preventing the direct discharge of wastewater to the aquatic environment. Water-conserving toilets and limited holding tank volumes produce a highly concentrated waste that must be periodically dumped to a wastewater treatment system. Prior to disposal, many boat operators add commercial preparations to control odors produced in their chemical toilets and holding tanks. The objective of this study was to determine t...

Bacterial identification and subtyping using DNA microarray and DNA sequencing.

Science.gov (United States)

Al-Khaldi, Sufian F; Mossoba, Magdi M; Allard, Marc M; Lienau, E Kurt; Brown, Eric D

2012-01-01

The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

Technology transfer

International Nuclear Information System (INIS)

Anon.

1977-01-01

Illustrated by the example of the FRG's nuclear energy exports, it is shown that the nuclear technology transfer leads to new dimensions of intergovernmental relations, which hold within themselves on account of multiple state-to-state, scientific, industrial and - last but not least - personal contacts the chance of far-reaching friendships between countries and people. If the chance is taken, this can also be seen as an important contribution towards maintaining the peace. (orig.) [de

12 CFR 584.4 - Certain acquisitions by savings and loan holding companies.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Certain acquisitions by savings and loan... TREASURY SAVINGS AND LOAN HOLDING COMPANIES § 584.4 Certain acquisitions by savings and loan holding companies. (a) Acquisitions by a savings and loan holding company of more than five percent of a non...

SOIL VAPOR EXTRACTION TECHNOLOGY: REFERENCE HANDBOOK

Science.gov (United States)

Soil vapor extraction (SVE) systems are being used in Increasing numbers because of the many advantages these systems hold over other soil treatment technologies. SVE systems appear to be simple in design and operation, yet the fundamentals governing subsurface vapor transport ar...

Why not stop transfer of technology

Energy Technology Data Exchange (ETDEWEB)

Baumer, J M

1979-01-01

One of the crucial themes in the dialogue between rich and poor nations is the nature and volume of the transfer of technology from the industrialized to the developing world. In contrast to the demand of overcoming the technology gap, Prof. Baumer argues that the postulate should rather be formulated as reduction of technological dependence. Industrialized countries say without technology, there is no growth; they say modern technology is the right technology. They are indeed against a cutting of costs and basically against simplifying the getting hold of their technology. Of prime importance is the development of technology at the site of the problems themselves. Problems can be solved in technically quite different ways - from simple to very complicated - and drawer-technology is only in the rarest cases the best solution. (MCW)

Snake Genome Sequencing: Results and Future Prospects.

Science.gov (United States)

Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

2016-12-01

Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Snake Genome Sequencing: Results and Future Prospects

Directory of Open Access Journals (Sweden)

Harald M. I. Kerkkamp

2016-12-01

Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.

Science.gov (United States)

Gowrisankar, Sivakumar; Lerner-Ellis, Jordan P; Cox, Stephanie; White, Emily T; Manion, Megan; LeVan, Kevin; Liu, Jonathan; Farwell, Lisa M; Iartchouk, Oleg; Rehm, Heidi L; Funke, Birgit H

2010-11-01

Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.

Technological sequence of creating components of the training system of the future officers to the management of physical training

Directory of Open Access Journals (Sweden)

Olkhovy O.M.

2012-09-01

Full Text Available The goal is to determine constructive ways of sequence of constructing components of the training system of the future officers to carry out official questions of managing the physical training in the process of the further military career. The structural logic circuit of the interconnections stages of optimum cycle management and technological sequence of constructing the components of the training system of the future officers to the management of physical training, which provides: definition of requirements to the typical problems of professional activities on the issues of the leadership, organization and conducting of physical training, the creation of the phased system model cadets training, training of the curriculum discipline ″Physical education, special physical training and sport″; model creation and definition of criteria of the integral evaluation of the readiness of the future officers to the management of physical training was determined through the analysis more than thirty documentary and scientific literature.

Holding a candle to innovation in concentrating solar power technologies: A study drawing on patent data

International Nuclear Information System (INIS)

Braun, Frauke G.; Hooper, Elizabeth; Wand, Robert; Zloczysti, Petra

2011-01-01

Improved understanding of the innovative pathways of renewable energy technologies is vital if we are to make the transition to a low carbon economy. This study presents new evidence on innovation and industry dynamics in concentrating solar power (CSP) technologies. Though CSP is undergoing a renaissance, existing innovation studies have explored innovative activity in solar technologies in general, ignoring the major differences between solar photovoltaic and CSP technologies. This study, based on patent data, examines the level and dynamics of innovative activity in CSP between 1978 and 2004. Our unique contribution, based on engineering expertise and detailed datawork, is a classification system mapping CSP technologies to the International Patent Classification (IPC) system. The innovation performance of CSP is found to be surprisingly weak compared to the patent boom in other green technologies. Performance was strong around 1980 before falling dramatically, and has only recently begun to show signs of recovery. Innovation and R and D are concentrated in high-tech countries; the US, Germany and Japan, which do not necessarily have high domestic CSP potential. Large CSP potential is, therefore, not a sufficient condition for innovation. Innovators must possess economic and scientific capabilities. - Research highlights: → We develop a new classification system which allows us to map innovation in CSP technologies to the International Patent Classification System. → Evidence of innovation patterns in concentrating solar power technologies is presented. → Innovation performance in CSP is surprisingly weak compared to patenting in other green technologies, despite its strong potential as a low carbon power generation technology.

Technologies for Collaborative Business Process Management

NARCIS (Netherlands)

Sadiq, Shazia; Reichert, M.U.; Schulz, Karsten

Business process management (BPM) has become an extensive area of research with several specialized aspects. BPM is viewed from highly diverse angles ranging from a management strategy to a software system. It is widely acknowledged that process enforcement technologies hold the potential to provide

High voltage holding in the negative ion sources with cesium deposition

Energy Technology Data Exchange (ETDEWEB)

Belchenko, Yu.; Abdrashitov, G.; Ivanov, A.; Sanin, A.; Sotnikov, O., E-mail: O.Z.Sotnikov@inp.nsk.su [Budker Institute of Nuclear Physics, Siberian Branch of Russian Academy of Sciences, Novosibirsk (Russian Federation)

2016-02-15

High voltage holding of the large surface-plasma negative ion source with cesium deposition was studied. It was found that heating of ion-optical system electrodes to temperature >100 °C facilitates the source conditioning by high voltage pulses in vacuum and by beam shots. The procedure of electrode conditioning and the data on high-voltage holding in the negative ion source with small cesium seed are described. The mechanism of high voltage holding improvement by depletion of cesium coverage is discussed.

JVM: Java Visual Mapping tool for next generation sequencing read.

Science.gov (United States)

Yang, Ye; Liu, Juan

2015-01-01

We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.

Exploring the Mechanisms of Gastrointestinal Cancer Development Using Deep Sequencing Analysis

International Nuclear Information System (INIS)

Matsumoto, Tomonori; Shimizu, Takahiro; Takai, Atsushi; Marusawa, Hiroyuki

2015-01-01

Next-generation sequencing (NGS) technologies have revolutionized cancer genomics due to their high throughput sequencing capacity. Reports of the gene mutation profiles of various cancers by many researchers, including international cancer genome research consortia, have increased over recent years. In addition to detecting somatic mutations in tumor cells, NGS technologies enable us to approach the subject of carcinogenic mechanisms from new perspectives. Deep sequencing, a method of optimizing the high throughput capacity of NGS technologies, allows for the detection of genetic aberrations in small subsets of premalignant and/or tumor cells in noncancerous chronically inflamed tissues. Genome-wide NGS data also make it possible to clarify the mutational signatures of each cancer tissue by identifying the precise pattern of nucleotide alterations in the cancer genome, providing new information regarding the mechanisms of tumorigenesis. In this review, we highlight these new methods taking advantage of NGS technologies, and discuss our current understanding of carcinogenic mechanisms elucidated from such approaches

Exploring the Mechanisms of Gastrointestinal Cancer Development Using Deep Sequencing Analysis

Energy Technology Data Exchange (ETDEWEB)

Matsumoto, Tomonori; Shimizu, Takahiro; Takai, Atsushi; Marusawa, Hiroyuki, E-mail: maru@kuhp.kyoto-u.ac.jp [Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507 (Japan)

2015-06-15

Next-generation sequencing (NGS) technologies have revolutionized cancer genomics due to their high throughput sequencing capacity. Reports of the gene mutation profiles of various cancers by many researchers, including international cancer genome research consortia, have increased over recent years. In addition to detecting somatic mutations in tumor cells, NGS technologies enable us to approach the subject of carcinogenic mechanisms from new perspectives. Deep sequencing, a method of optimizing the high throughput capacity of NGS technologies, allows for the detection of genetic aberrations in small subsets of premalignant and/or tumor cells in noncancerous chronically inflamed tissues. Genome-wide NGS data also make it possible to clarify the mutational signatures of each cancer tissue by identifying the precise pattern of nucleotide alterations in the cancer genome, providing new information regarding the mechanisms of tumorigenesis. In this review, we highlight these new methods taking advantage of NGS technologies, and discuss our current understanding of carcinogenic mechanisms elucidated from such approaches.

12 CFR 584.2a - Exempt savings and loan holding companies and grandfathered activities.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Exempt savings and loan holding companies and... THE TREASURY SAVINGS AND LOAN HOLDING COMPANIES § 584.2a Exempt savings and loan holding companies and grandfathered activities. (a) Exempt savings and loan holding companies. (1) The following savings and loan...

Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

Directory of Open Access Journals (Sweden)

Martin Mascher

Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

Human genome project: revolutionizing biology through leveraging technology

Science.gov (United States)

Dahl, Carol A.; Strausberg, Robert L.

1996-04-01

The Human Genome Project (HGP) is an international project to develop genetic, physical, and sequence-based maps of the human genome. Since the inception of the HGP it has been clear that substantially improved technology would be required to meet the scientific goals, particularly in order to acquire the complete sequence of the human genome, and that these technologies coupled with the information forthcoming from the project would have a dramatic effect on the way biomedical research is performed in the future. In this paper, we discuss the state-of-the-art for genomic DNA sequencing, technological challenges that remain, and the potential technological paths that could yield substantially improved genomic sequencing technology. The impact of the technology developed from the HGP is broad-reaching and a discussion of other research and medical applications that are leveraging HGP-derived DNA analysis technologies is included. The multidisciplinary approach to the development of new technologies that has been successful for the HGP provides a paradigm for facilitating new genomic approaches toward understanding the biological role of functional elements and systems within the cell, including those encoded within genomic DNA and their molecular products.

Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics

Directory of Open Access Journals (Sweden)

Rama R Gullapalli

2012-01-01

Full Text Available The Human Genome Project (HGP provided the initial draft of mankind′s DNA sequence in 2001. The HGP was produced by 23 collaborating laboratories using Sanger sequencing of mapped regions as well as shotgun sequencing techniques in a process that occupied 13 years at a cost of ~$3 billion. Today, Next Generation Sequencing (NGS techniques represent the next phase in the evolution of DNA sequencing technology at dramatically reduced cost compared to traditional Sanger sequencing. A single laboratory today can sequence the entire human genome in a few days for a few thousand dollars in reagents and staff time. Routine whole exome or even whole genome sequencing of clinical patients is well within the realm of affordability for many academic institutions across the country. This paper reviews current sequencing technology methods and upcoming advancements in sequencing technology as well as challenges associated with data generation, data manipulation and data storage. Implementation of routine NGS data in cancer genomics is discussed along with potential pitfalls in the interpretation of the NGS data. The overarching importance of bioinformatics in the clinical implementation of NGS is emphasized. [7] We also review the issue of physician education which also is an important consideration for the successful implementation of NGS in the clinical workplace. NGS technologies represent a golden opportunity for the next generation of pathologists to be at the leading edge of the personalized medicine approaches coming our way. Often under-emphasized issues of data access and control as well as potential ethical implications of whole genome NGS sequencing are also discussed. Despite some challenges, it′s hard not to be optimistic about the future of personalized genome sequencing and its potential impact on patient care and the advancement of knowledge of human biology and disease in the near future.

In vitro holding and PLD-repair. Pt. 2

International Nuclear Information System (INIS)

Stevenson, A.F.G.; Palackal, T.; Lange, C.S.

1989-01-01

The repair of potentially lethal damage (PLDR) in mammalian cells is expected to be better in quiescent cultures since PLD is supposedly fixed during cycle progression. Plateau phase cultures, therefore, serve as models because of assumed mitotic quiescence. Four established cell lines (V79, CHO, L5178Y and HELA) and one euploid cell strain IMR-90 have been analysed by flow cytometry and electron microscopy to address questions on quiescence in the plateau phase and the effect of holding (induction of quiescence by nutrient privation). In contrast to commonly held views, our results indicate that the quiescent fraction in cultures from transformed cells is exceedingly low (1% or less). Plateau phase cultures of transformed cells are constantly turning over. Euploid cells like the IMR-90 show true quiescence in the plateau phase. Holding causes typical cytopathological changes. These changes have been ultrastructurely characterised. Resistant sub-populations of cells can be selected out under holding-conditions. Such selected cells show completely different radiobiological characteristics, which raise questions on the interpretation of data on PLDR. (orig.)

Probe-holding apparatus for holding a probe for checking steam generator tubes particularly in a nuclear reactor installation

International Nuclear Information System (INIS)

Adamowski, A.; Gagny; Gallet, G.; Lhermitte, J.; Monne, M.; Vautherot, G.

1984-01-01

Probe-holding apparatus for holding a probe for checking steam generator tubes particularly in a nuclear reactor installation. The apparatus comprises a telescopic arm supported via a ball and socket joint from a support mounted in or near an access aperture in a chamber at one end of the steam generator. A probe guide is carried by a carriage pivotally mounted at the other end of the telescopic arm. The carriage includes an endless belt having a series of spaced projections which engage into the ends of the tubes, the projections being spaced by a distance equal to the tube pitch or a multiple thereof. The belt is driven by a stepping motor in order to move the carriage and place the probe guide opposite different ones of the tubes

Genetic sequences derived from suppression subtractive ...

African Journals Online (AJOL)

STORAGESEVER

2008-06-17

Jun 17, 2008 ... their possible roles in Xanthomonas albilineans ... Technology, P. O. Box 1334, Durban 4000, Republic of South Africa. Accepted 4 ... Clones selected were sequenced (using a Perkin Elmer ABI PRISM Dye terminator cycle.

Quality Assurance Challenges for Motion-Adaptive Radiation Therapy: Gating, Breath Holding, and Four-Dimensional Computed Tomography

International Nuclear Information System (INIS)

Jiang, Steve B.; Wolfgang, John; Mageras, Gig S.

2008-01-01

Compared with conventional three-dimensional (3D) conformal radiation therapy and intensity-modulated radiation therapy treatments, quality assurance (QA) for motion-adaptive radiation therapy involves various challenges because of the added temporal dimension. Here we discuss those challenges for three specific techniques related to motion-adaptive therapy: namely respiratory gating, breath holding, and four-dimensional computed tomography. Similar to the introduction of any other new technologies in clinical practice, typical QA measures should be taken for these techniques also, including initial testing of equipment and clinical procedures, as well as frequent QA examinations during the early stage of implementation. Here, rather than covering every QA aspect in depth, we focus on some major QA challenges. The biggest QA challenge for gating and breath holding is how to ensure treatment accuracy when internal target position is predicted using external surrogates. Recommended QA measures for each component of treatment, including simulation, planning, patient positioning, and treatment delivery and verification, are discussed. For four-dimensional computed tomography, some major QA challenges have also been discussed

Reflections on the Development of a Machine Vision Technology for the Forest Products

Science.gov (United States)

Richard W. Conners; D.Earl Kline; Philip A. Araman; Robert L. Brisbon

1992-01-01

The authors have approximately 25 years experience in developing machine vision technology for the forest products industry. Based on this experience this paper will attempt to realistically predict what the future holds for this technology. In particular, this paper will attempt to describe some of the benefits this technology will offer, describe how the technology...

Identification of Meconopsis species by a DNA barcode sequence ...

African Journals Online (AJOL)

Deoxyribonucleic acid (DNA) barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Species identification is necessary for the authentication of traditional plant based medicines. Although a consensus has not been agreed regarding which DNA sequences can be used as ...

Ancestral Sequence Reconstruction with Maximum Parsimony.

Science.gov (United States)

Herbst, Lina; Fischer, Mareike

2017-12-01

One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

Science.gov (United States)

Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

2016-07-01

The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

problems in spinning in kolfe house-hold utencil factory abstract ...

African Journals Online (AJOL)

Kolfe House-Hold Utensil Factory in Addis Ababa, is producing different types of utensils for house-hold use from commercial aluminium. Deep drawing or/and spinning are the methods used for shaping this metal to desired shape and size, though some small parts are cast too. One of their products is kettle, which is.

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.

Science.gov (United States)

Schlaberg, Robert; Chiu, Charles Y; Miller, Steve; Procop, Gary W; Weinstock, George

2017-06-01

- Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. - To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. - Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. - Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

Directory of Open Access Journals (Sweden)

Quail Michael A

2012-07-01

Full Text Available Abstract Background Next generation sequencing (NGS technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. Results Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform. Conclusions All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.

Empowerment Amongst Teachers Holding Leadership Positions

Science.gov (United States)

Avidov-Ungar, Orit; Friedman, Izhak; Olshtain, Elite

2014-01-01

This study used semi-structured in-depth interviews to explore empowerment patterns among teachers who hold leadership positions in school. Our qualitative analysis presents a hierarchical ladder with three types of empowerment amongst these teachers, ranging from limited empowerment through rewarding empowerment to change-enhancing empowerment.…

12 CFR 1732.7 - Record hold.

Science.gov (United States)

2010-01-01

... Banking OFFICE OF FEDERAL HOUSING ENTERPRISE OVERSIGHT, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT SAFETY AND SOUNDNESS RECORD RETENTION Record Retention Program § 1732.7 Record hold. (a) Definition. For... Enterprise or OFHEO that the Enterprise is to retain records relating to a particular issue in connection...

Noninvasive prenatal paternity testing (NIPAT) through maternal plasma DNA sequencing

DEFF Research Database (Denmark)

Jiang, Haojun; Xie, Yifan; Li, Xuchao

2016-01-01

developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels......Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we...... paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future....

Sequencing intractable DNA to close microbial genomes.

Directory of Open Access Journals (Sweden)

Richard A Hurt

Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

Sequencing Intractable DNA to Close Microbial Genomes

Energy Technology Data Exchange (ETDEWEB)

Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

2012-01-01

Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

Scalable Kernel Methods and Algorithms for General Sequence Analysis

Science.gov (United States)

Kuksa, Pavel

2011-01-01

Analysis of large-scale sequential data has become an important task in machine learning and pattern recognition, inspired in part by numerous scientific and technological applications such as the document and text classification or the analysis of biological sequences. However, current computational methods for sequence comparison still lack…

A Real-Time Holding Decision Rule Accounting for Passenger Travel Cost

NARCIS (Netherlands)

Laskaris,; Cats, O.; Jenelius, E; Viti, F

2016-01-01

Holding has been extensively investigated as a strategy to mitigate the inherently stochastic nature of public transport operations. Holding focuses on either regulating vehicle headways using a rule-based approach or minimizing passenger travel cost by employing optimization models. This paper

Monte Carlo study of holding forces for tank cars on grades

Science.gov (United States)

2013-04-15

This paper describes a numerical procedure to examine the holding forces needed to secure a cut of railroad tank cars staged on a grade during loading and unloading operations. Holding forces are created by applying emergency brake systems and blocki...

Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform

Directory of Open Access Journals (Sweden)

De Keulenaer Sarah

2012-05-01

Full Text Available Abstract Background Hereditary hearing loss (HL can originate from mutations in one of many genes involved in the complex process of hearing. Identification of the genetic defects in patients is currently labor intensive and expensive. While screening with Sanger sequencing for GJB2 mutations is common, this is not the case for the other known deafness genes (> 60. Next generation sequencing technology (NGS has the potential to be much more cost efficient. Published methods mainly use hybridization based target enrichment procedures that are time saving and efficient, but lead to loss in sensitivity. In this study we used a semi-automated PCR amplification and NGS in order to combine high sensitivity, speed and cost efficiency. Results In this proof of concept study, we screened 15 autosomal recessive deafness genes in 5 patients with congenital genetic deafness. 646 specific primer pairs for all exons and most of the UTR of the 15 selected genes were designed using primerXL. Using patient specific identifiers, all amplicons were pooled and analyzed using the Roche 454 NGS technology. Three of these patients are members of families in which a region of interest has previously been characterized by linkage studies. In these, we were able to identify two new mutations in CDH23 and OTOF. For another patient, the etiology of deafness was unclear, and no causal mutation was found. In a fifth patient, included as a positive control, we could confirm a known mutation in TMC1. Conclusions We have developed an assay that holds great promise as a tool for screening patients with familial autosomal recessive nonsyndromal hearing loss (ARNSHL. For the first time, an efficient, reliable and cost effective genetic test, based on PCR enrichment, for newborns with undiagnosed deafness is available.

How Important Is a Reproducible Breath Hold for Deep Inspiration Breath Hold Breast Radiation Therapy?

International Nuclear Information System (INIS)

Wiant, David; Wentworth, Stacy; Liu, Han; Sintay, Benjamin

2015-01-01

Purpose: Deep inspiration breath hold (DIBH) for left-sided breast cancer has been shown to reduce heart dose. Surface imaging helps to ensure accurate breast positioning, but it does not guarantee a reproducible breath hold (BH) at DIBH treatments. We examine the effects of variable BH positions for DIBH treatments. Methods and Materials: Twenty-five patients who underwent free breathing (FB) and DIBH scans were reviewed. Four plans were created for each patient: FB, DIBH, FB-DIBH (the DIBH plans were copied to the FB images and recalculated, and image registration was based on breast tissue), and P-DIBH (a partial BH with the heart shifted midway between the FB and DIBH positions). The FB-DIBH plans give a “worst-case” scenario for surface imaging DIBH, where the breast is aligned by surface imaging but the patient is not holding their breath. Kolmogorov-Smirnov tests were used to compare the dose metrics. Results: The DIBH plans gave lower heart dose and comparable breast coverage versus FB in all cases. The FB-DIBH plans showed no significant difference versus FB plans for breast coverage, mean heart dose, or maximum heart dose (P≥.10). The mean heart dose differed between FB-DIBH and FB by <2 Gy for all cases, and the maximum heart dose differed by <2 Gy for 21 cases. The P-DIBH plans showed significantly lower mean heart dose than FB (P<.01). The mean heart doses for the P-DIBH plans were < FB for 22 cases, the maximum dose was < FB for 18 cases. Conclusions: A DIBH plan delivered to a FB patient setup with surface imaging will yield dosimetry similar to that of a plan created and delivered FB. A DIBH plan delivered with even a partial BH can give reduced heart dose compared with FB techniques.

How Important Is a Reproducible Breath Hold for Deep Inspiration Breath Hold Breast Radiation Therapy?

Energy Technology Data Exchange (ETDEWEB)

Wiant, David, E-mail: David.wiant@conehealth.com; Wentworth, Stacy; Liu, Han; Sintay, Benjamin

2015-11-15

Purpose: Deep inspiration breath hold (DIBH) for left-sided breast cancer has been shown to reduce heart dose. Surface imaging helps to ensure accurate breast positioning, but it does not guarantee a reproducible breath hold (BH) at DIBH treatments. We examine the effects of variable BH positions for DIBH treatments. Methods and Materials: Twenty-five patients who underwent free breathing (FB) and DIBH scans were reviewed. Four plans were created for each patient: FB, DIBH, FB-DIBH (the DIBH plans were copied to the FB images and recalculated, and image registration was based on breast tissue), and P-DIBH (a partial BH with the heart shifted midway between the FB and DIBH positions). The FB-DIBH plans give a “worst-case” scenario for surface imaging DIBH, where the breast is aligned by surface imaging but the patient is not holding their breath. Kolmogorov-Smirnov tests were used to compare the dose metrics. Results: The DIBH plans gave lower heart dose and comparable breast coverage versus FB in all cases. The FB-DIBH plans showed no significant difference versus FB plans for breast coverage, mean heart dose, or maximum heart dose (P≥.10). The mean heart dose differed between FB-DIBH and FB by <2 Gy for all cases, and the maximum heart dose differed by <2 Gy for 21 cases. The P-DIBH plans showed significantly lower mean heart dose than FB (P<.01). The mean heart doses for the P-DIBH plans were

Molten core material holding device in a nuclear reactor

International Nuclear Information System (INIS)

Nakamura, Hisashi; Tanaka, Nobuo; Takahashi, Katsuro.

1985-01-01

Purpose: To improve the function of cooling to hold molten core materials in a molten core material holding device. Constitution: Plenum structures are formed into a pan-like configuration, in which liners made of metal having high melting point and relatively high heat conductivity such as tantalum, tungsten, rhenium or alloys thereof are integrally appended to hold and directly cool the molten reactor core materials. Further, a plurality of heat pipes, passing through the plenum structures, facing the cooling portion thereof to the coolants at the outer side and immersing the heating portion into the molten core materials fallen to deposit in the inner liners are disposed radially. Furthermore, heat pipes embodded in the plenum structure are disposed in the same manner below the liners. Thus, the plenum structures and the molten reactor core materials can be cooled at a high efficiency. (Seki, T.)

IMPROVEMENT OF ROAD-HOLDING ABILITY FOR “BELARUS” TRACTORS

Directory of Open Access Journals (Sweden)

V. P. Boikov

2016-01-01

Full Text Available Introduction of new efficient braking systems for energy-packed tractors is of great importance for agricultural production. Foreign tractor manufacturing companies are implementing brake systems and in addition to their main function they fulfil function for holding of the given driving direction. The paper considers achievements in the field of electronic systems for tractor road-holding ability. A diagram on proportion of high-power tractors in total export volume of tractors and machinery manufactured in Belarus in the period of 2007–2010 has been drawn in the paper. The paper also proposes a comparative diagram on tractor speeds of international manufacturers which can serve as indicators of speed and road-holding ability of tractors with special electronic systems and without them. The paper contains an analysis of various braking mechanisms of planetary gears and detailed description of their design. A scheme of a laboratory facility for investigation of planetary gear usage as a breaking mechanism while changing conditions of jamming has been presented in the paper. The paper provides description on graph dependencies of current strength and voltage on as a function of the braking torque which is applied to a planetary gear. Nowadays energy-packed “Belarus”-tractors of Class 5 do not have a separate braking for each of four wheels. Therefore, it is proposed to use planetary gearbox of the rear-axle drive being available in every wheel as the basis of a service brake with the purpose to implement the described design. Using such scheme it is possible to execute an introduction of electronic systems for road-holding ability. A generalized scheme of an electronic system for tractor road-holding ability which can ensure separate breaking of all tractor wheels has been drawn out on the basis of the existing automotive electronic systems.

Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification

Science.gov (United States)

Wu, Lucia R.; Chen, Sherry X.; Wu, Yalei; Patel, Abhijit A.; Zhang, David Yu

2018-01-01

Rare DNA-sequence variants hold important clinical and biological information, but existing detection techniques are expensive, complex, allele-specific, or don’t allow for significant multiplexing. Here, we report a temperature-robust polymerase-chain-reaction method, which we term blocker displacement amplification (BDA), that selectively amplifies all sequence variants, including single-nucleotide variants (SNVs), within a roughly 20-nucleotide window by 1,000-fold over wild-type sequences. This allows for easy detection and quantitation of hundreds of potential variants originally at ≤0.1% in allele frequency. BDA is compatible with inexpensive thermocycler instrumentation and employs a rationally designed competitive hybridization reaction to achieve comparable enrichment performance across annealing temperatures ranging from 56 °C to 64 °C. To show the sequence generality of BDA, we demonstrate enrichment of 156 SNVs and the reliable detection of single-digit copies. We also show that the BDA detection of rare driver mutations in cell-free DNA samples extracted from the blood plasma of lung-cancer patients is highly consistent with deep sequencing using molecular lineage tags, with a receiver operator characteristic accuracy of 95%. PMID:29805844

Factors Affecting Corporate Cash Holding of Non-Financial Firms in Pakistan

Directory of Open Access Journals (Sweden)

Atif Kafayat

2014-06-01

Full Text Available The previous researches explore the question of why firms hold cash. But there are few researches done in developing countries like Pakistan. The need for cash is characterized by its policies of firms regarding capital structure, working capital requirements, cash flow management, dividend payments, and asset management. In this paper, the impact of these factors is normally analyzed under the framework of Tradeoff theory, Pecking Order Theory and Free Cash Flow Theory. This paper focuses on determining the level of corporate cash holdings of non-financial Pakistani firms, and cash holding requirement among different industries. The data is set for period of 2008- 2012 by using the data of 40companies and 6 industries. The findings of the study support the theories. Which show that firm size, net working capital, leverage, Capital Expenditure and Dividend significantly affect the cash holdings of non-financial firms in Pakistan.

Towards Developing an Industry-Validated Food Technology Curriculum in Afghanistan

Science.gov (United States)

Ebner, Paul; McNamara, Kevin; Deering, Amanda; Oliver, Haley; Rahimi, Mirwais; Faisal, Hamid

2017-01-01

Afghanistan remains an agrarian country with most analyses holding food production and processing as key to recovery. To date, however, there are no public or private higher education departments focused on food technology. To bridge this gap, Herat University initiated a new academic department conferring BS degrees in food technology. Models for…

How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

Directory of Open Access Journals (Sweden)

Alevtina Ruban

2017-10-01

Full Text Available Accessory, supernumerary, or—most simply—B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS, their structure comprises fragments of standard (A chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.

Circumstellar Material on and off the Main Sequence

Science.gov (United States)

Steele, Amy; Debes, John H.; Deming, Drake

2017-06-01

There is evidence of circumstellar material around main sequence, giant, and white dwarf stars that originates from the small-body population of planetary systems. These bodies tell us something about the chemistry and evolution of protoplanetary disks and the planetary systems they form. What happens to this material as its host star evolves off the main sequence, and how does that inform our understanding of the typical chemistry of rocky bodies in planetary systems? In this talk, I will discuss the composition(s) of circumstellar material on and off the main sequence to begin to answer the question, “Is Earth normal?” In particular, I look at three types of debris disks to understand the typical chemistry of planetary systems—young debris disks, debris disks around giant stars, and dust around white dwarfs. I will review the current understanding on how to infer dust composition for each class of disk, and present new work on constraining dust composition from infrared excesses around main sequence and giant stars. Finally, dusty and polluted white dwarfs hold a unique key to our understanding of the composition of rocky bodies around other stars. In particular, I will discuss WD1145+017, which has a transiting, disintegrating planetesimal. I will review what we know about this system through high speed photometry and spectroscopy and present new work on understanding the complex interplay of physics that creates white dwarf pollution from the disintegration of rocky bodies.

The Determinants of Corporate Cash Holdings- An Empirical study from UK Firms

OpenAIRE

GUO, YI

2013-01-01

Cash holding is most important financial decision in the company management strategy. In this dissertation, the determinants of corporate cash holdings in UK non-financial publicly traded firms over the period from 2003 to 2012 are investigated. Our study finds that growth opportunities and cash flow and cash flow variability are positively associated with the level of corporate cash holdings, while firm size, leverage, net working capital, bank debt and dividend payment have negative impact ...

Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

Science.gov (United States)

Galián, José A; Rosato, Marcela; Rosselló, Josep A

2014-03-01

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.

12 CFR 575.10 - Acquisition and disposition of savings associations, savings and loan holding companies, and...

Science.gov (United States)

2010-01-01

... associations, savings and loan holding companies, and other corporations by mutual holding companies. 575.10... COMPANIES § 575.10 Acquisition and disposition of savings associations, savings and loan holding companies... savings and loan holding company in the stock form that is not a subsidiary holding company, provided the...

Internationalization and Corporate Cash Holdings: Evidence from Brazil and Mexico

Directory of Open Access Journals (Sweden)

Newton Arata

2015-05-01

Full Text Available This research expands on previous studies of cash holdings and their determinants by studying the relationship between the degree of internationalization and the level of corporate cash holdings. We used a sample of nonfinancial, publicly traded companies from Brazil and Mexico for the period from 2006 to 2010. Our results suggest that the degree of internationalization is a determinant of cash, and that cash holding increases quadratically as the degree of company internationalization grows. Such behavior was different from the North American company studies in Chiang and Wang (2011. Similar to previous studies, both Trade-off and Pecking Order predictions are relevant control variables in our model. Finally, companies held less cash on their balance sheets during the precrisis period.

Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi?

Science.gov (United States)

Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Erturan, Zayre; Ener, Beyza; Akdagli, Sevtap Arikan; Muslumanoglu, Hamza; Cetinkaya, Zafer

2015-10-01

Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis. © 2015 Blackwell Verlag GmbH.

Reliable quantification of BOLD fMRI cerebrovascular reactivity despite poor breath-hold performance.

Science.gov (United States)

Bright, Molly G; Murphy, Kevin

2013-12-01

Cerebrovascular reactivity (CVR) can be mapped using BOLD fMRI to provide a clinical insight into vascular health that can be used to diagnose cerebrovascular disease. Breath-holds are a readily accessible method for producing the required arterial CO2 increases but their implementation into clinical studies is limited by concerns that patients will demonstrate highly variable performance of breath-hold challenges. This study assesses the repeatability of CVR measurements despite poor task performance, to determine if and how robust results could be achieved with breath-holds in patients. Twelve healthy volunteers were scanned at 3 T. Six functional scans were acquired, each consisting of 6 breath-hold challenges (10, 15, or 20 s duration) interleaved with periods of paced breathing. These scans simulated the varying breath-hold consistency and ability levels that may occur in patient data. Uniform ramps, time-scaled ramps, and end-tidal CO2 data were used as regressors in a general linear model in order to measure CVR at the grey matter, regional, and voxelwise level. The intraclass correlation coefficient (ICC) quantified the repeatability of the CVR measurement for each breath-hold regressor type and scale of interest across the variable task performances. The ramp regressors did not fully account for variability in breath-hold performance and did not achieve acceptable repeatability (ICC0.4). Further analysis of intra-subject CVR variability across the brain (ICCspatial and voxelwise correlation) supported the use of end-tidal CO2 data to extract robust whole-brain CVR maps, despite variability in breath-hold performance. We conclude that the incorporation of end-tidal CO2 monitoring into scanning enables robust, repeatable measurement of CVR that makes breath-hold challenges suitable for routine clinical practice. © 2013.

An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

Directory of Open Access Journals (Sweden)

Herring Christopher D

2007-08-01

Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

Directory of Open Access Journals (Sweden)

Xu Xiangming

2010-12-01

Full Text Available Abstract Background Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. Results The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. Conclusions We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.

Anatomic and Pathologic Variability During Radiotherapy for a Hybrid Active Breath-Hold Gating Technique

International Nuclear Information System (INIS)

Glide-Hurst, Carri K.; Gopan, Ellen; Hugo, Geoffrey D.

2010-01-01

Purpose: To evaluate intra- and interfraction variability of tumor and lung volume and position using a hybrid active breath-hold gating technique. Methods and Materials: A total of 159 repeat normal inspiration active breath-hold CTs were acquired weekly during radiotherapy for 9 lung cancer patients (12-21 scans per patient). A physician delineated the gross tumor volume (GTV), lungs, and spinal cord on the first breath-hold CT, and contours were propagated semiautomatically. Intra- and interfraction variability of tumor and lung position and volume were evaluated. Tumor centroid and border variability were quantified. Results: On average, intrafraction variability of lung and GTV centroid position was 0.1). Increases in free-breathing tidal volume were associated with increases in breath-hold ipsilateral lung volume (p < 0.05). Conclusions: The breath-hold technique was reproducible within 2 mm during each fraction. Interfraction variability of GTV position and shape was substantial because of tumor volume and breath-hold lung volume change during therapy. These results support the feasibility of a hybrid breath-hold gating technique and suggest that online image guidance would be beneficial.

26 CFR 53.4943-5 - Present holdings acquired by trust or a will.

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 17 2010-04-01 2010-04-01 false Present holdings acquired by trust or a will... Business Holdings § 53.4943-5 Present holdings acquired by trust or a will. (a) Interests to which section... terms of a will executed on or before May 26, 1969. (3) Certain revocable trusts. If an interest in a...

Breath-hold duration in man and the diving response induced by face immersion.

Science.gov (United States)

Sterba, J A; Lundgren, C E

1988-09-01

The objective of this study in 5 selected volunteer subjects was to see whether the circulatory diving response which is elicited by breath holding and by cold water on the face would affect the duration of maximal-effort breath holds. Compared to control measurements (breath holding during resting, breathing with 35 degrees C water on the face) breath holding with the face cooled by 20 degrees C water caused a 12% reduction of heart rate, 6% reduction of cardiac output, 33% reduction in [corrected] forearm blood flow, and 9% rise in mean arterial blood pressure, but there was no difference in breath-hold duration (control and experimental both 94 s). There were also no differences in time of appearance of the first involuntary respiratory efforts during breath holding, in alveolar gas exchange, or in breaking-point alveolar O2 and CO2 tensions. When the diving response was magnified by a brief bout of exercise so that there was a 19% [corrected] reduction in heart rate, 23% reduction in cardiac output, and 48% reduction in forearm blood flow, breath-hold duration was still unaffected by face cooling. Compared to intermittent immersions, continuous exposure of the face to cold water abolished the diving response, probably by a cold adaptation of facial thermal receptors. These results with cooling of the face only are consistent with our earlier finding that there was a negative correlation between the duration of a maximal-effort breath hold and the diving response during whole-body submersion in cold water.

Heterogeneity among methicillin-resistant Staphylococcus aureus from Italian pig finishing holdings

DEFF Research Database (Denmark)

Battisti, A.; Franco, A.; Merialdi, G.

2010-01-01

A survey for methicillin-resistant Staphylococcus aureus (MRSA) in finishing pig holdings was carried out in Italy in 2008. MRSA isolates were characterised by spa-. SCCmec- and antimicrobial susceptibility typing. A prevalence of 38% (45/118, 95% CI 29.4-46.9%) positive holdings was observed...

The Release 6 reference sequence of the Drosophila melanogaster genome.

Science.gov (United States)

Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H; Park, Soo; Mendez, Ivonne; Galle, Samuel E; Booth, Benjamin W; Pfeiffer, Barret D; George, Reed A; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V; Andreyeva, Evgeniya N; Boldyreva, Lidiya V; Marra, Marco; Carvalho, A Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F; Rubin, Gerald M; Karpen, Gary H; Celniker, Susan E

2015-03-01

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads. © 2015 Hoskins et al.; Published by Cold Spring Harbor Laboratory Press.

Enhanced Dynamic Algorithm of Genome Sequence Alignments

OpenAIRE

Arabi E. keshk

2014-01-01

The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between se...

Do elite breath-hold divers suffer from mild short-term memory impairments?

Science.gov (United States)

Billaut, François; Gueit, Patrice; Faure, Sylvane; Costalat, Guillaume; Lemaître, Frédéric

2018-03-01

Repeated apneas are associated with severe hypoxemia that may ultimately lead to loss of consciousness in some breath-hold divers. Despite increasing number of practitioners, the relationship between apnea-induced hypoxia and neurocognitive functions is still poorly understood in the sport of free diving. To shed light onto this phenomenon, we examined the impact of long-term breath-hold diving training on attentional processing, short-term memory, and long-term mnesic and executive functions. Thirty-six men matched for age, height, and weight were separated into the following 3 groups: (i) 12 elite breath-hold divers (EBHD), mean static apnea best time 371 s, 105 months mean apnea experience; (ii) 12 novice breath-hold divers, mean best time 243 s, 8.75 months mean apnea experience; and (iii) 12 physical education students with no breath-hold diving experience; all of these participants performed varied written and computerized neuropsychological tasks. Compared with the 2 other groups, the EBHD group was slower to complete the interference card during a Stroop test (F [1,33] = 4.70, p short-term memory impairments.

Pengaruh krisis keuangan global dan karakteristik perusahaan terhadap cash holding perusahaan di Indonesia

Directory of Open Access Journals (Sweden)

Bambang Sutrisno

2016-12-01

Full Text Available The aim of this study is to examine the effect of the global financial crisis and firm characteristics on corporate cash holdings in Indonesia. A total of 101 manufacturing firms listed in the Indonesia Stock Exchange from 2005 to 2014 are examined. This study employs panel regression with fixed effect model. The results show that Indonesia firms hold more cash during the global financial crisis than in the normal times. Investment opportunities set and divident payment have positive effect on cash holding, meanwhile firm size, capital expenditure, liquid assets substitutes, and leverage have negative effect on cash holding. 

Can we still beat "buy-and-hold" for individual stocks?

Science.gov (United States)

Hui, Eddie C. M.; Kevin Chan, Ka Kwan

2014-09-01

Many investors seek for a trading strategy to beat the "buy-and-hold" strategy. In light of this, Hui and Yam (2014) and Hui et al. (2014) derived a trading strategy from the Shiryaev-Zhou index, and found that the resulting strategy outperformed the "buy-and-hold" strategy for western and Asian securitized real estate indices respectively. However, whether the trading strategy works on individual stocks or not is still unknown. This is the first study to test whether the trading strategy can beat the "buy-and-hold" strategy on individual stocks. We construct two trading strategies and compare the resulting profits with the profits arising from the "buy-and-hold" strategy on Hang Seng Index (HSI), Hang Seng Property (HSP) Index and 12 constituent stocks of HSI during the period December 29, 1995-December 31, 2013. The second strategy (Strategy 2) is a new strategy which incorporates short-selling, and has the effect of multiplying the profit. The results show that our trading strategies are less effective on individual stocks than on stock indices, and are more effective on property stocks than on non-property stocks. Moreover, our strategies outperform "buy-and-hold" by a larger extent on stocks of which the Shiryaev-Zhou indices fluctuate less frequently. Furthermore, by tracking the resulting profits of the three strategies at different times along the whole period of observation, our strategies work better during "bad times" than during "good times". This reflects that our trading strategies are especially useful in protecting investors from substantial loss during market downturns.

The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

International Nuclear Information System (INIS)

Chen, Chung H.

2004-01-01

The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

Genomic sequencing: assessing the health care system, policy, and big-data implications.

Science.gov (United States)

Phillips, Kathryn A; Trosman, Julia R; Kelley, Robin K; Pletcher, Mark J; Douglas, Michael P; Weldon, Christine B

2014-07-01

New genomic sequencing technologies enable the high-speed analysis of multiple genes simultaneously, including all of those in a person's genome. Sequencing is a prominent example of a "big data" technology because of the massive amount of information it produces and its complexity, diversity, and timeliness. Our objective in this article is to provide a policy primer on sequencing and illustrate how it can affect health care system and policy issues. Toward this end, we developed an easily applied classification of sequencing based on inputs, methods, and outputs. We used it to examine the implications of sequencing for three health care system and policy issues: making care more patient-centered, developing coverage and reimbursement policies, and assessing economic value. We conclude that sequencing has great promise but that policy challenges include how to optimize patient engagement as well as privacy, develop coverage policies that distinguish research from clinical uses and account for bioinformatics costs, and determine the economic value of sequencing through complex economic models that take into account multiple findings and downstream costs. Project HOPE—The People-to-People Health Foundation, Inc.

Generation of control sequences for a pilot-disassembly system

Science.gov (United States)

Seliger, Guenther; Kim, Hyung-Ju; Keil, Thomas

2002-02-01

Closing the product and material cycles has emerged as a paradigm for industry in the 21st century. Disassembly plays a key role in a life cycle economy since it enables the recovery of resources. A partly automated disassembly system should adapt to a large variety of products and different degrees of devaluation. Also the amounts of products to be disassembled can vary strongly. To cope with these demands an approach to generate on-line disassembly control sequences will be presented. In order to react on these demands the technological feasibility is considered within a procedure for the generation of disassembly control sequences. Procedures are designed to find available and technologically feasible disassembly processes. The control system is formed by modularised and parameterised control units in the cell level within the entire control architecture. In the first development stage product and process analyses at the sample product washing machine were executed. Furthermore a generalized disassembly process was defined. Afterwards these processes were structured in primary and secondary functions. In the second stage the disassembly control at the technological level was investigated. Factors were the availability of the disassembly tools and the technological feasibility of the disassembly processes within the disassembly system. Technical alternative disassembly processes are determined as a result of availability of the tools and technological feasibility of processes. The fourth phase was the concept for the generation of the disassembly control sequences. The approach will be proved in a prototypical disassembly system.

Genetic mapping using the Diversity Arrays Technology (DArT) : application and validation using the whole-genome sequences of Arabidopsis thaliana and the fungal wheat pathogen Mycosphaerella graminicola

NARCIS (Netherlands)

Wittenberg, A.H.J.

2007-01-01

Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds- to thousands of restriction site based polymorphisms between genotypes and does not require DNA sequence

The diploid genome sequence of an Asian individual

DEFF Research Database (Denmark)

Wang, Jun; Wang, Wei; Li, Ruiqiang

2008-01-01

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we...... used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP...... identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J...

29 CFR 452.40 - Prior office holding.

Science.gov (United States)

2010-07-01

... DISCLOSURE ACT OF 1959 Candidacy for Office; Reasonable Qualifications § 452.40 Prior office holding. A.... 26 26 Wirtz v. Hotel, Motel and Club Employees Union, Local 6, 391 U.S. 492 at 504. The Court stated...

Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

Science.gov (United States)

Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Mu-Chiou; Wang, Li-Tin; Huang, Lina; Lee, Fwu-Ling

2012-10-01

To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.

Kidney motion during free breathing and breath hold for MR-guided radiotherapy

International Nuclear Information System (INIS)

Stam, Mette K; Van Vulpen, Marco; Intven, Martijn; Crijns, Sjoerd P M; Lagendijk, Jan J W; Raaymakers, Bas W; Barendrecht, Maurits M; Zonnenberg, Bernard A

2013-01-01

Current treatments for renal cell carcinoma have a high complication rate due to the invasiveness of the treatment. With the MRI-linac it may be possible to treat renal tumours non-invasively with high-precision radiotherapy. This is expected to reduce complications. To deliver a static dose distribution, radiation gating will be used. In this study the reproducibility and efficiency of free breathing gating and a breath hold treatment of the kidney was investigated. For 15 patients with a renal lesion the kidney motion during 2 min of free breathing and 10 consecutive expiration breath holds was studied with 2D cine MRI. The variability in kidney expiration position and treatment efficiency for gating windows of 1 to 20 mm was measured for both breathing patterns. Additionally the time trend in free breathing and the variation in expiration breath hold kidney position with baseline shift correction was determined. In 80% of the patients the variation in expiration position during free breathing is smaller than 2 mm. No clinically relevant time trends were detected. The variation in expiration breath hold is for all patients larger than the free breathing expiration variation. Gating on free breathing is, for gating windows of 1 to 5 mm more efficient than breath hold without baseline correction. When applying a baseline correction to the breath hold it increases the treatment efficiency. The kidney position is more reproducible in expiration free breathing than non-guided expiration breath hold. For small gating windows it is also more time efficient. Since free breathing also seems more comfortable for the patients it is the preferred breathing pattern for MRI-Linac treatments of the kidney. (paper)

Evaluation of pancreatic cancer by multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging at 3.0 T

International Nuclear Information System (INIS)

Yao, Xiuzhong; Zeng, Mengsu; Wang, He; Sun, Fei; Rao, Shengxiang; Ji, Yuan

2012-01-01

Objective: To investigate the microcirculation in pancreatic cancer by pharmacokinetic analysis of multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging at 3.0 T. Materials and methods: Multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging was performed in 40 healthy volunteers and 40 patients with pancreatic cancer proven by histopathology using an axial three-dimensions fat-saturated T1-weighted spoiled-gradient echo sequence at 3.0 T. A two compartment model with T1 correction was used to quantify the transfer constant, the rate constant of backflux from the extravascular extracellular space to the plasma and the extravascular extracellular space fractional volume in pancreatic cancer, obstructive pancreatitis distal to the malignant tumor, adjacent pancreatic tissue proximal to the tumor and normal pancreas. All parameters were statistically analyzed. Results: Statistical differences were noticed in both the transfer constant (p = 0.000075) and the rate constant of backflux (p = 0.006) among different tissues. Both the transfer constant and the rate constant of backflux in pancreatic cancer were statistically lower than those in normal pancreas and adjacent pancreatic tissue (p < 0.05). Both the transfer constant and the rate constant of backflux in obstructive pancreatitis were statistically lower than those in normal pancreas and adjacent pancreatic tissue (p < 0.05). The extravascular extracellular space fractional volume in pancreatic cancer was statistically lager than that in normal pancreas (p = 0.002). Conclusion: Multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging offers a useful technique to evaluate the microenvironment in pancreatic cancer at 3.0 T. Compared to normal pancreas, pancreatic cancer has lower transfer constant, rate constant of backflux and larger extravascular extracellular space fractional volume.

Evaluation of pancreatic cancer by multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging at 3.0 T

Energy Technology Data Exchange (ETDEWEB)

Yao, Xiuzhong, E-mail: yao.xiuzhong@zs-hospital.sh.cn [Department of Radiology, Zhongshan Hospital of Fudan University and Department of Medical Image, Shanghai Medical College of Fudan University, No. 138, Fenglin Road, Xuhui District, Shanghai 200032 (China); Zeng, Mengsu, E-mail: zengmengsu@gmail.com [Department of Radiology, Zhongshan Hospital of Fudan University and Department of Medical Image, Shanghai Medical College of Fudan University, No. 138, Fenglin Road, Xuhui District, Shanghai 200032 (China); Wang, He, E-mail: herry258@hotmail.com [Global Applied Science Laboratory of GE Healthcare, No. 1, Huatuo Road, Zhangjiang Hi-tech Park, Pudong District, Shanghai 201203 (China); Sun, Fei, E-mail: fei.sun@med.ge.com [Global Applied Science Laboratory of GE Healthcare, No. 1, Huatuo Road, Zhangjiang Hi-tech Park, Pudong District, Shanghai 201203 (China); Rao, Shengxiang, E-mail: rao.shengxiang@zs-hospital.sh.cn [Department of Radiology, Zhongshan Hospital of Fudan University and Department of Medical Image, Shanghai Medical College of Fudan University, No. 138, Fenglin Road, Xuhui District, Shanghai 200032 (China); Ji, Yuan, E-mail: Ji.yuan@zs-hospital.sh.cn [Department of Pathology, Zhongshan Hospital of Fudan University, No. 138, Fenglin Road, Xuhui District, Shanghai 200032 (China)

2012-08-15

Objective: To investigate the microcirculation in pancreatic cancer by pharmacokinetic analysis of multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging at 3.0 T. Materials and methods: Multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging was performed in 40 healthy volunteers and 40 patients with pancreatic cancer proven by histopathology using an axial three-dimensions fat-saturated T1-weighted spoiled-gradient echo sequence at 3.0 T. A two compartment model with T1 correction was used to quantify the transfer constant, the rate constant of backflux from the extravascular extracellular space to the plasma and the extravascular extracellular space fractional volume in pancreatic cancer, obstructive pancreatitis distal to the malignant tumor, adjacent pancreatic tissue proximal to the tumor and normal pancreas. All parameters were statistically analyzed. Results: Statistical differences were noticed in both the transfer constant (p = 0.000075) and the rate constant of backflux (p = 0.006) among different tissues. Both the transfer constant and the rate constant of backflux in pancreatic cancer were statistically lower than those in normal pancreas and adjacent pancreatic tissue (p < 0.05). Both the transfer constant and the rate constant of backflux in obstructive pancreatitis were statistically lower than those in normal pancreas and adjacent pancreatic tissue (p < 0.05). The extravascular extracellular space fractional volume in pancreatic cancer was statistically lager than that in normal pancreas (p = 0.002). Conclusion: Multiple breath-hold dynamic contrast-enhanced magnetic resonance imaging offers a useful technique to evaluate the microenvironment in pancreatic cancer at 3.0 T. Compared to normal pancreas, pancreatic cancer has lower transfer constant, rate constant of backflux and larger extravascular extracellular space fractional volume.

Enhanced throughput for infrared automated DNA sequencing

Science.gov (United States)

Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

1995-04-01

Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

Sequence Matching Analysis for Curriculum Development

Directory of Open Access Journals (Sweden)

Liem Yenny Bendatu

2015-06-01

Full Text Available Many organizations apply information technologies to support their business processes. Using the information technologies, the actual events are recorded and utilized to conform with predefined model. Conformance checking is an approach to measure the fitness and appropriateness between process model and actual events. However, when there are multiple events with the same timestamp, the traditional approach unfit to result such measures. This study attempts to develop a sequence matching analysis. Considering conformance checking as the basis of this approach, this proposed approach utilizes the current control flow technique in process mining domain. A case study in the field of educational process has been conducted. This study also proposes a curriculum analysis framework to test the proposed approach. By considering the learning sequence of students, it results some measurements for curriculum development. Finally, the result of the proposed approach has been verified by relevant instructors for further development.

Applications and challenges of next-generation sequencing in Brassica species.

Science.gov (United States)

Wei, Lijuan; Xiao, Meili; Hayward, Alice; Fu, Donghui

2013-12-01

Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Science.gov (United States)

Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

2016-09-01

Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

Intelligent computer aided training systems in the real world: Making the technology accessible to the educational mainstream

Science.gov (United States)

Kovarik, Madeline

1993-01-01

Intelligent computer aided training systems hold great promise for the application of this technology to mainstream education and training. Yet, this technology, which holds such a vast potential impact for the future of education and training, has had little impact beyond the enclaves of government research labs. This is largely due to the inaccessibility of the technology to those individuals in whose hands it can have the greatest impact, teachers and educators. Simply throwing technology at an educator and expecting them to use it as an effective tool is not the answer. This paper provides a background into the use of technology as a training tool. MindLink, developed by HyperTech Systems, provides trainers with a powerful rule-based tool that can be integrated directly into a Windows application. By embedding expert systems technology it becomes more accessible and easier to master.

SeqCompress: an algorithm for biological sequence compression.

Science.gov (United States)

Sardaraz, Muhammad; Tahir, Muhammad; Ikram, Ataul Aziz; Bajwa, Hassan

2014-10-01

The growth of Next Generation Sequencing technologies presents significant research challenges, specifically to design bioinformatics tools that handle massive amount of data efficiently. Biological sequence data storage cost has become a noticeable proportion of total cost in the generation and analysis. Particularly increase in DNA sequencing rate is significantly outstripping the rate of increase in disk storage capacity, which may go beyond the limit of storage capacity. It is essential to develop algorithms that handle large data sets via better memory management. This article presents a DNA sequence compression algorithm SeqCompress that copes with the space complexity of biological sequences. The algorithm is based on lossless data compression and uses statistical model as well as arithmetic coding to compress DNA sequences. The proposed algorithm is compared with recent specialized compression tools for biological sequences. Experimental results show that proposed algorithm has better compression gain as compared to other existing algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

DEFF Research Database (Denmark)

Willenbrock, Hanni; Salomon, Jesper; Søkilde, Rolf

2009-01-01

Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two...... technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate...... better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification....

CASH HOLDING, GOOD CORPORATE GOVERNANCE AND FIRM VALUE

Directory of Open Access Journals (Sweden)

Prana Wahyu Nisasmara

2016-12-01

Full Text Available This research aims to understand the influence of profitability, capital structure, cash holding, and GCG (Good Corporate Governance on firm value.  The samples of this study were the property sector and real estate companies listed on Indonesia Stock Exchange (IDX in the period of 2008-2013. The data used from the annual report company. The methods of data analysis were multiple regression models and analyzed using IBM SPSS software. The results of this study are profitability has no influence on firm value, capital structure has positive influence on firm value, cash holding has no influence on firm value and GCG a has a positive influence on firm value.

Package Holds Five Monolithic Microwave Integrated Circuits

Science.gov (United States)

Mysoor, Narayan R.; Decker, D. Richard; Olson, Hilding M.

1996-01-01

Packages protect and hold monolithic microwave integrated circuit (MMIC) chips while providing dc and radio-frequency (RF) electrical connections for chips undergoing development. Required to be compact, lightweight, and rugged. Designed to minimize undesired resonances, reflections, losses, and impedance mismatches.

12 CFR 1500.3 - What are the holding periods permitted for merchant banking investments?

Science.gov (United States)

2010-01-01

... includes a depository institution controlled by the financial holding company and any subsidiary of such a depository institution. (4) Approval required to hold interests held in excess of time limit. A financial... financial holding company; (iii) Market conditions; (iv) The nature of the portfolio company's business; (v...

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.

Science.gov (United States)

DeMaere, Matthew Z; Darling, Aaron E

2018-02-01

Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences. The simulator models the basic spatial structure in genomes that is commonly observed in Hi-C and 3C datasets, including the distance-decay relationship in proximity ligation, differences in the frequency of interaction within and across chromosomes, and the structure imposed by cells. A means to model the 3D structure of randomly generated topologically associating domains is provided. The simulator considers several sources of error common to 3C and Hi-C library preparation and sequencing methods, including spurious proximity ligation events and sequencing error. We have introduced the first comprehensive simulator for 3C and Hi-C sequencing protocols. We expect the simulator to have use in testing of Hi-C data analysis algorithms, as well as more general value for experimental design, where questions such as the required depth of sequencing, enzyme choice, and other decisions can be made in advance in order to ensure adequate statistical power with respect to experimental hypothesis testing.

Identifying structural variants using linked-read sequencing data.

Science.gov (United States)

Elyanow, Rebecca; Wu, Hsin-Ta; Raphael, Benjamin J

2017-11-03

Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (~5-10) DNA molecules ~50Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in a individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification - including two recent methods that also analyze linked-reads - on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes. Software is available at compbio.cs.brown.edu/software. braphael@princeton.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Step voltage with periodic hold-up etching: A novel porous silicon formation

International Nuclear Information System (INIS)

Naddaf, M.; Awad, F.; Soukeih, M.

2007-01-01

A novel etching method for preparing light-emitting porous silicon (PS) is developed. A gradient steps (staircase) voltage is applied and hold-up for different periods of time between p-type silicon wafers and a graphite electrode in HF based solutions periodically. The single applied staircase voltage (0-30 V) is ramped in equal steps of 0.5 V for 6 s, and hold at 30 V for 30 s at a current of 6 mA. The current during hold-up time (0 V) was less than 10 μA. The room temperature photoluminescence (PL) behavior of the PS samples as a function of etching parameters has been investigated. The intensity of PL peak is initially increased and blue shifted on increasing etching time, but decreased after prolonged time. These are correlated with the study of changes in surface morphology using atomic force microscope (AFM), porosity and electrical conductance measurements. The time of holding-up the applied voltage during the formation process is found to highly affect the PS properties. On increasing the holding-up time, the intensity of PL peak is increased and blue shifted. The contribution of holding-up the applied steps during the formation process of PS is seen to be more or less similar to the post chemical etching process. It is demonstrated that this method can yield a porous silicon layer with stronger photoluminescence intensity and blue shifted than the porous silicon layer prepared by DC etching

Step voltage with periodic hold-up etching: A novel porous silicon formation

Energy Technology Data Exchange (ETDEWEB)

Naddaf, M. [Department of Physics, Atomic Energy Commission of Syria (AECS), Damascus P.O. Box 6091 (Syrian Arab Republic)]. E-mail: scientific@aec.org.sy; Awad, F. [Department of Physics, Atomic Energy Commission of Syria (AECS), Damascus P.O. Box 6091 (Syrian Arab Republic); Soukeih, M. [Department of Physics, Atomic Energy Commission of Syria (AECS), Damascus P.O. Box 6091 (Syrian Arab Republic)

2007-05-16

A novel etching method for preparing light-emitting porous silicon (PS) is developed. A gradient steps (staircase) voltage is applied and hold-up for different periods of time between p-type silicon wafers and a graphite electrode in HF based solutions periodically. The single applied staircase voltage (0-30 V) is ramped in equal steps of 0.5 V for 6 s, and hold at 30 V for 30 s at a current of 6 mA. The current during hold-up time (0 V) was less than 10 {mu}A. The room temperature photoluminescence (PL) behavior of the PS samples as a function of etching parameters has been investigated. The intensity of PL peak is initially increased and blue shifted on increasing etching time, but decreased after prolonged time. These are correlated with the study of changes in surface morphology using atomic force microscope (AFM), porosity and electrical conductance measurements. The time of holding-up the applied voltage during the formation process is found to highly affect the PS properties. On increasing the holding-up time, the intensity of PL peak is increased and blue shifted. The contribution of holding-up the applied steps during the formation process of PS is seen to be more or less similar to the post chemical etching process. It is demonstrated that this method can yield a porous silicon layer with stronger photoluminescence intensity and blue shifted than the porous silicon layer prepared by DC etching.

12 CFR 225.172 - What are the holding periods permitted for merchant banking investments?

Science.gov (United States)

2010-01-01

... institution controlled by the financial holding company and any subsidiary of such a depository institution... company to the company and the risks that disposing of the investment may pose to the financial holding... history of involvement by the financial holding company in the management and operations of the company...

New Technology, Changing Pedagogies? Exploring the Concept of Remote Teaching Placement Supervision

Science.gov (United States)

Chilton, Helen; McCracken, Wendy

2017-01-01

Mobile technologies continue to have a growing influence on contemporary society, are becoming more commonplace within tertiary educational settings and hold the potential to impact on the learning process. This project evaluation considers the perspectives of participants who trialled the use of new technology to enable remote supervision and…

Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.

Science.gov (United States)

Humble, Emily; Thorne, Michael A S; Forcada, Jaume; Hoffman, Joseph I

2016-08-26

Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be

78 FR 26032 - Change in Bank Control Notices; Acquisitions of Shares of a Bank or Bank Holding Company

Science.gov (United States)

2013-05-03

..., North Carolina; Frank B. Holding, Sr., Smithfield, North Carolina; Ella Ann Holding, Smithfield, North..., individually and together with Olivia Britton Holding, Raleigh, North Carolina; Frank B. Holding, Sr... Brown Holding, Jr., Raleigh, North Carolina; Frank B. Holding, Sr., Smithfield, North Carolina; Ella Ann...

Can multi-slice or navigator-gated R2* MRI replace single-slice breath-hold acquisition for hepatic iron quantification?

International Nuclear Information System (INIS)

Loeffler, Ralf B.; McCarville, M.B.; Song, Ruitian; Hillenbrand, Claudia M.; Wagstaff, Anne W.; Smeltzer, Matthew P.; Krafft, Axel J.; Hankins, Jane S.

2017-01-01

Liver R2* values calculated from multi-gradient echo (mGRE) magnetic resonance images (MRI) are strongly correlated with hepatic iron concentration (HIC) as shown in several independently derived biopsy calibration studies. These calibrations were established for axial single-slice breath-hold imaging at the location of the portal vein. Scanning in multi-slice mode makes the exam more efficient, since whole-liver coverage can be achieved with two breath-holds and the optimal slice can be selected afterward. Navigator echoes remove the need for breath-holds and allow use in sedated patients. To evaluate if the existing biopsy calibrations can be applied to multi-slice and navigator-controlled mGRE imaging in children with hepatic iron overload, by testing if there is a bias-free correlation between single-slice R2* and multi-slice or multi-slice navigator controlled R2*. This study included MRI data from 71 patients with transfusional iron overload, who received an MRI exam to estimate HIC using gradient echo sequences. Patient scans contained 2 or 3 of the following imaging methods used for analysis: single-slice images (n = 71), multi-slice images (n = 69) and navigator-controlled images (n = 17). Small and large blood corrected region of interests were selected on axial images of the liver to obtain R2* values for all data sets. Bland-Altman and linear regression analysis were used to compare R2* values from single-slice images to those of multi-slice images and navigator-controlled images. Bland-Altman analysis showed that all imaging method comparisons were strongly associated with each other and had high correlation coefficients (0.98 ≤ r ≤ 1.00) with P-values ≤0.0001. Linear regression yielded slopes that were close to 1. We found that navigator-gated or breath-held multi-slice R2* MRI for HIC determination measures R2* values comparable to the biopsy-validated single-slice, single breath-hold scan. We conclude that these three R2* methods can be

Can multi-slice or navigator-gated R2* MRI replace single-slice breath-hold acquisition for hepatic iron quantification?

Energy Technology Data Exchange (ETDEWEB)

Loeffler, Ralf B.; McCarville, M.B.; Song, Ruitian; Hillenbrand, Claudia M. [St. Jude Children' s Research Hospital, Diagnostic Imaging, Memphis, TN (United States); Wagstaff, Anne W. [St. Jude Children' s Research Hospital, Diagnostic Imaging, Memphis, TN (United States); Rhodes College, Memphis, TN (United States); University of Alabama at Birmingham School of Medicine, Birmingham, AL (United States); Smeltzer, Matthew P. [St. Jude Children' s Research Hospital, Department of Biostatistics, Memphis, TN (United States); University of Memphis, Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, Memphis, TN (United States); Krafft, Axel J. [St. Jude Children' s Research Hospital, Diagnostic Imaging, Memphis, TN (United States); University Hospital Center Freiburg, Department of Radiology, Freiburg (Germany); Hankins, Jane S. [St. Jude Children' s Research Hospital, Department of Hematology, Memphis, TN (United States)

2017-01-15

Liver R2* values calculated from multi-gradient echo (mGRE) magnetic resonance images (MRI) are strongly correlated with hepatic iron concentration (HIC) as shown in several independently derived biopsy calibration studies. These calibrations were established for axial single-slice breath-hold imaging at the location of the portal vein. Scanning in multi-slice mode makes the exam more efficient, since whole-liver coverage can be achieved with two breath-holds and the optimal slice can be selected afterward. Navigator echoes remove the need for breath-holds and allow use in sedated patients. To evaluate if the existing biopsy calibrations can be applied to multi-slice and navigator-controlled mGRE imaging in children with hepatic iron overload, by testing if there is a bias-free correlation between single-slice R2* and multi-slice or multi-slice navigator controlled R2*. This study included MRI data from 71 patients with transfusional iron overload, who received an MRI exam to estimate HIC using gradient echo sequences. Patient scans contained 2 or 3 of the following imaging methods used for analysis: single-slice images (n = 71), multi-slice images (n = 69) and navigator-controlled images (n = 17). Small and large blood corrected region of interests were selected on axial images of the liver to obtain R2* values for all data sets. Bland-Altman and linear regression analysis were used to compare R2* values from single-slice images to those of multi-slice images and navigator-controlled images. Bland-Altman analysis showed that all imaging method comparisons were strongly associated with each other and had high correlation coefficients (0.98 ≤ r ≤ 1.00) with P-values ≤0.0001. Linear regression yielded slopes that were close to 1. We found that navigator-gated or breath-held multi-slice R2* MRI for HIC determination measures R2* values comparable to the biopsy-validated single-slice, single breath-hold scan. We conclude that these three R2* methods can be

The Economics of an Admissions Holding Unit.

Science.gov (United States)

Schreyer, Kraftin E; Martin, Richard

2017-06-01

With increasing attention to the actual cost of delivering care, return-on-investment calculations take on new significance. Boarded patients in the emergency department (ED) are harmful to clinical care and have significant financial opportunity costs. We hypothesize that investment in an admissions holding unit for admitted ED patients not only captures opportunity cost but also significantly lowers direct cost of care. This was a three-phase study at a busy urban teaching center with significant walkout rate. We first determined the true cost of maintaining a staffed ED bed for one patient-hour and compared it to alternative settings. The opportunity cost for patients leaving without being seen was then conservatively estimated. Lastly, a convenience sample of admitted patients boarding in the ED was observed continuously from one hour after decision-to-admit until physical departure from the ED to capture a record of every interaction with a nurse or physician. Personnel costs per patient bed-hour were $58.20 for the ED, $24.80 for an inpatient floor, $19.20 for the inpatient observation unit, and $10.40 for an admissions holding area. An eight-bed holding unit operating at practical capacity would free 57.4 hours of bed space in the ED and allow treatment of 20 additional patients. This could yield increased revenues of $27,796 per day and capture opportunity cost of $6.09 million over 219 days, in return for extra staffing costs of $218,650. Analysis of resources used for boarded patients was determined by continuous observation of a convenience sample of ED-boarded patients, which found near-zero interactions with both nursing and physicians during the boarding interval. Resource expense per ED bed-hour is more than twice that in non-critical care inpatient units. Despite the high cost of available resources, boarded non-critical patients receive virtually no nursing or physician attention. An admissions holding unit is remarkably effective in avoiding the

The Economics of an Admissions Holding Unit

Directory of Open Access Journals (Sweden)

Kraftin E. Schreyer

2017-05-01

Full Text Available Introduction: With increasing attention to the actual cost of delivering care, return-on-investment calculations take on new significance. Boarded patients in the emergency department (ED are harmful to clinical care and have significant financial opportunity costs. We hypothesize that investment in an admissions holding unit for admitted ED patients not only captures opportunity cost but also significantly lowers direct cost of care. Methods: This was a three-phase study at a busy urban teaching center with significant walkout rate. We first determined the true cost of maintaining a staffed ED bed for one patient-hour and compared it to alternative settings. The opportunity cost for patients leaving without being seen was then conservatively estimated. Lastly, a convenience sample of admitted patients boarding in the ED was observed continuously from one hour after decision-to-admit until physical departure from the ED to capture a record of every interaction with a nurse or physician. Results: Personnel costs per patient bed-hour were $58.20 for the ED, $24.80 for an inpatient floor, $19.20 for the inpatient observation unit, and $10.40 for an admissions holding area. An eight-bed holding unit operating at practical capacity would free 57.4 hours of bed space in the ED and allow treatment of 20 additional patients. This could yield increased revenues of $27,796 per day and capture opportunity cost of $6.09 million over 219 days, in return for extra staffing costs of $218,650. Analysis of resources used for boarded patients was determined by continuous observation of a convenience sample of ED-boarded patients, which found near-zero interactions with both nursing and physicians during the boarding interval. Conclusion: Resource expense per ED bed-hour is more than twice that in non-critical care inpatient units. Despite the high cost of available resources, boarded non-critical patients receive virtually no nursing or physician attention. An

Making Women Count: Gender-Typing, Technology and Path Dependencies in Dutch Statistical Data Processing

NARCIS (Netherlands)

van den Ende, Jan; van Oost, Elizabeth C.J.

2001-01-01

This article is a longitudinal analysis of the relation between gendered labour divisions and new data processing technologies at the Dutch Central Bureau of Statistics (CBS). Following social-constructivist and evolutionary economic approaches, the authors hold that the relation between technology

The ins and outs of breath holding: simple demonstrations of complex respiratory physiology.

Science.gov (United States)

Skow, Rachel J; Day, Trevor A; Fuller, Jonathan E; Bruce, Christina D; Steinback, Craig D

2015-09-01

The physiology of breath holding is complex, and voluntary breath-hold duration is affected by many factors, including practice, psychology, respiratory chemoreflexes, and lung stretch. In this activity, we outline a number of simple laboratory activities or classroom demonstrations that illustrate the complexity of the integrative physiology behind breath-hold duration. These activities require minimal equipment and are easily adapted to small-group demonstrations or a larger-group inquiry format where students can design a protocol and collect and analyze data from their classmates. Specifically, breath-hold duration is measured during a number of maneuvers, including after end expiration, end inspiration, voluntary prior hyperventilation, and inspired hyperoxia. Further activities illustrate the potential contribution of chemoreflexes through rebreathing and repeated rebreathing after a maximum breath hold. The outcome measures resulting from each intervention are easily visualized and plotted and can comprise a comprehensive data set to illustrate and discuss complex and integrated cardiorespiratory physiology. Copyright © 2015 The American Physiological Society.

Contrast-enhanced Magnetic Resonance Imaging of Pelvic Bone Metastases at 3.0 T: Comparison Between 3-dimensional T1-weighted CAIPIRINHA-VIBE Sequence and 2-dimensional T1-weighted Turbo Spin-Echo Sequence.

Science.gov (United States)

Yoon, Min A; Hong, Suk-Joo; Lee, Kyu-Chong; Lee, Chang Hee

2018-06-12

This study aimed to compare 3-dimensional T1-weighted gradient-echo sequence (CAIPIRINHA-volumetric interpolated breath-hold examination [VIBE]) with 2-dimensional T1-weighted turbo spin-echo sequence for contrast-enhanced magnetic resonance imaging (MRI) of pelvic bone metastases at 3.0 T. Thirty-one contrast-enhanced MRIs of pelvic bone metastases were included. Two contrast-enhanced sequences were evaluated for the following parameters: overall image quality, sharpness of pelvic bone, iliac vessel clarity, artifact severity, and conspicuity and edge sharpness of the smallest metastases. Quantitative analysis was performed by calculating signal-to-noise ratio and contrast-to-noise ratio of the smallest metastases. Significant differences between the 2 sequences were assessed. CAIPIRINHA-VIBE had higher scores for overall image quality, pelvic bone sharpness, iliac vessel clarity, and edge sharpness of the metastatic lesions, and had less artifacts (all P 0.05). Our results suggest that CAIPIRINHA-VIBE may be superior to turbo spin-echo for contrast-enhanced MRI of pelvic bone metastases at 3.0 T.

21 CFR 111.465 - What requirements apply to holding reserve samples of dietary supplements?

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 2 2010-04-01 2010-04-01 false What requirements apply to holding reserve samples... Distributing § 111.465 What requirements apply to holding reserve samples of dietary supplements? (a) You must hold reserve samples of dietary supplements in a manner that protects against contamination and...

Organizational suggestion system in the era of holding by developing an innovative model : the case of bonyade ta avon holding in Iran(an applied model

Directory of Open Access Journals (Sweden)

Meysam Ghasemi

2010-01-01

Full Text Available One of the popular ways of taking advantage of personnel creativity is through suggestionsystems. Our main question is how to implement suggestion system in holding with conglomeratestructure. The paper presents an innovative model that were named ITFSK Model with accordanceof Bonayade Taavone (a holding that has many companies and institutions with conglomeratestructure. ITFSK is a model that explains how participation management and suggestion system isimplemented effectively in huge Enterprises (holding and this approach brings continuousimprovement (kaizen and it impacts the productivity of these enterprises.The paper is based on field research and the research in Bonyade Tavan that has 22 companies and2 institutions that activity fields of the subholdings is very varied.Our model consists of five main parts such as ideas bank, think-tank, feedback, sharing ofknowledge and kaizen that was named ITFSK.Implementation of “Suggestion system” rules has immediate and significant effects on theproductivity of activities in the jobs, thus influencing the performance of processes in the analyzedorganization. Suggestion system can result in kaizen and innovation in environment oforganization.The model was used to implement and evaluate a suggestion system of holding with conglomeratedstructure. The application of the model to evaluate the suggestion system provided some goodinsights and highlighted some areas of improvement.

Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products

Science.gov (United States)

Gomez-Escribano, Juan Pablo; Alt, Silke; Bibb, Mervyn J.

2016-01-01

Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a substantial increase in the quality of the data, having moved from obtaining a draft genome sequence comprised of several hundred short contigs, sometimes of doubtful reliability, to the possibility of obtaining an almost complete and accurate chromosome sequence in a single contig, allowing a detailed study of gene clusters and the design of strategies for refactoring and full gene cluster synthesis. The impact that these technologies are having in the discovery and study of natural products from actinobacteria, including those from the marine environment, is only starting to be realised. In this review we provide a historical perspective of the field, analyse the strengths and limitations of the most relevant technologies, and share the insights acquired during our genome mining projects. PMID:27089350

Report on achievements of research and development of an automatic sewing system in fiscal 1986. Cloth handling technology; 1986 nendo jido hosei system no kenkyu kaihatsu seika hokokusho. Kiji handling gijutsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1987-03-01

The Automatic Sewing System Technology Research Association was commissioned from the Agency of Industrial Science and Technology on the 'development of an automatic sewing system'. The association has performed the research and development by dividing the subject into such component technologies as a total system and sewing preparation and processing technology, a sewing and assembling technology, a cloth handling technology, and a system management and control technology. This paper reports the achievement of the research on the cloth handling technology. This technology may be divided into such component technologies as (1) the cloth holding technology, (2) the high-functional positioning technology, and (3) the soft cloth moving technology. For the technology (1), development was made on the principle models, such as the vertical holding and parallel holding type modules and the cloth operating type module, as well as on the principle model for an auxiliary equipment for holding cloth edges. For the technology (2), development was made on the handler, controller, and coordinated operation control and teaching system. Discussions were given on optimal device configuration, functions required in the devices, and evaluation methods, as the high-functional positioning technology for the sewing process and pressing process. Prototype devices were designed and fabricated. For the technology (3), prototype models of the improved version were fabricated for the stock module and confluence model, their functions and performances were confirmed, and problems and points requiring improvement were extracted for prototype fabrication. (NEDO)

Report on achievements of research and development of an automatic sewing system in fiscal 1986. Cloth handling technology; 1986 nendo jido hosei system no kenkyu kaihatsu seika hokokusho. Kiji handling gijutsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1987-03-01

The Automatic Sewing System Technology Research Association was commissioned from the Agency of Industrial Science and Technology on the 'development of an automatic sewing system'. The association has performed the research and development by dividing the subject into such component technologies as a total system and sewing preparation and processing technology, a sewing and assembling technology, a cloth handling technology, and a system management and control technology. This paper reports the achievement of the research on the cloth handling technology. This technology may be divided into such component technologies as (1) the cloth holding technology, (2) the high-functional positioning technology, and (3) the soft cloth moving technology. For the technology (1), development was made on the principle models, such as the vertical holding and parallel holding type modules and the cloth operating type module, as well as on the principle model for an auxiliary equipment for holding cloth edges. For the technology (2), development was made on the handler, controller, and coordinated operation control and teaching system. Discussions were given on optimal device configuration, functions required in the devices, and evaluation methods, as the high-functional positioning technology for the sewing process and pressing process. Prototype devices were designed and fabricated. For the technology (3), prototype models of the improved version were fabricated for the stock module and confluence model, their functions and performances were confirmed, and problems and points requiring improvement were extracted for prototype fabrication. (NEDO)

On the optimal trimming of high-throughput mRNA sequence data

Directory of Open Access Journals (Sweden)

Matthew D MacManes

2014-01-01

Full Text Available The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score < 2 or < 5, is optimal for most studies across a wide variety of metrics.

Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO.

Science.gov (United States)

Fraiture, Marie-Alice; Saltykova, Assia; Hoffman, Stefan; Winand, Raf; Deforce, Dieter; Vanneste, Kevin; De Keersmaecker, Sigrid C J; Roosens, Nancy H C

2018-05-21

In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region. This DNA walking is performed on transgenic elements, commonly found in GMO, that were earlier detected by real-time PCR (qPCR) screening. Previously, we have demonstrated the ability of this approach to detect unauthorized GMO via the identification of unique transgene flanking regions and the unnatural associations of elements from the transgenic cassette. In the present study, we investigate the feasibility to integrate the described workflow with the MinION Next-Generation-Sequencing (NGS). The MinION sequencing platform can provide long read-lengths and deal with heterogenic DNA libraries, allowing for rapid and efficient delivery of sequences of interest. In addition, the ability of this NGS platform to characterize unauthorized and unknown GMO without any a priori knowledge has been assessed.

Genetic diagnosis of Duchenne and Becker muscular dystrophy using next-generation sequencing technology: comprehensive mutational search in a single platform.

Science.gov (United States)

Lim, Byung Chan; Lee, Seungbok; Shin, Jong-Yeon; Kim, Jong-Il; Hwang, Hee; Kim, Ki Joong; Hwang, Yong Seung; Seo, Jeong-Sun; Chae, Jong Hee

2011-11-01

Duchenne muscular dystrophy or Becker muscular dystrophy might be a suitable candidate disease for application of next-generation sequencing in the genetic diagnosis because the complex mutational spectrum and the large size of the dystrophin gene require two or more analytical methods and have a high cost. The authors tested whether large deletions/duplications or small mutations, such as point mutations or short insertions/deletions of the dystrophin gene, could be predicted accurately in a single platform using next-generation sequencing technology. A custom solution-based target enrichment kit was designed to capture whole genomic regions of the dystrophin gene and other muscular-dystrophy-related genes. A multiplexing strategy, wherein four differently bar-coded samples were captured and sequenced together in a single lane of the Illumina Genome Analyser, was applied. The study subjects were 25 16 with deficient dystrophin expression without a large deletion/duplication and 9 with a known large deletion/duplication. Nearly 100% of the exonic region of the dystrophin gene was covered by at least eight reads with a mean read depth of 107. Pathogenic small mutations were identified in 15 of the 16 patients without a large deletion/duplication. Using these 16 patients as the standard, the authors' method accurately predicted the deleted or duplicated exons in the 9 patients with known mutations. Inclusion of non-coding regions and paired-end sequence analysis enabled accurate identification by increasing the read depth and providing information about the breakpoint junction. The current method has an advantage for the genetic diagnosis of Duchenne muscular dystrophy and Becker muscular dystrophy wherein a comprehensive mutational search may be feasible using a single platform.

A conceptual holding model for veterinary applications

Directory of Open Access Journals (Sweden)

Nicola Ferrè

2014-05-01

Full Text Available Spatial references are required when geographical information systems (GIS are used for the collection, storage and management of data. In the veterinary domain, the spatial component of a holding (of animals is usually defined by coordinates, and no other relevant information needs to be interpreted or used for manipulation of the data in the GIS environment provided. Users trying to integrate or reuse spatial data organised in such a way, frequently face the problem of data incompatibility and inconsistency. The root of the problem lies in differences with respect to syntax as well as variations in the semantic, spatial and temporal representations of the geographic features. To overcome these problems and to facilitate the inter-operability of different GIS, spatial data must be defined according to a “schema” that includes the definition, acquisition, analysis, access, presentation and transfer of such data between different users and systems. We propose an application “schema” of holdings for GIS applications in the veterinary domain according to the European directive framework (directive 2007/2/EC - INSPIRE. The conceptual model put forward has been developed at two specific levels to produce the essential and the abstract model, respectively. The former establishes the conceptual linkage of the system design to the real world, while the latter describes how the system or software works. The result is an application “schema” that formalises and unifies the information-theoretic foundations of how to spatially represent a holding in order to ensure straightforward information-sharing within the veterinary community.

Model-based quality assessment and base-calling for second-generation sequencing data.

Science.gov (United States)

Bravo, Héctor Corrada; Irizarry, Rafael A

2010-09-01

Second-generation sequencing (sec-gen) technology can sequence millions of short fragments of DNA in parallel, making it capable of assembling complex genomes for a small fraction of the price and time of previous technologies. In fact, a recently formed international consortium, the 1000 Genomes Project, plans to fully sequence the genomes of approximately 1200 people. The prospect of comparative analysis at the sequence level of a large number of samples across multiple populations may be achieved within the next five years. These data present unprecedented challenges in statistical analysis. For instance, analysis operates on millions of short nucleotide sequences, or reads-strings of A,C,G, or T's, between 30 and 100 characters long-which are the result of complex processing of noisy continuous fluorescence intensity measurements known as base-calling. The complexity of the base-calling discretization process results in reads of widely varying quality within and across sequence samples. This variation in processing quality results in infrequent but systematic errors that we have found to mislead downstream analysis of the discretized sequence read data. For instance, a central goal of the 1000 Genomes Project is to quantify across-sample variation at the single nucleotide level. At this resolution, small error rates in sequencing prove significant, especially for rare variants. Sec-gen sequencing is a relatively new technology for which potential biases and sources of obscuring variation are not yet fully understood. Therefore, modeling and quantifying the uncertainty inherent in the generation of sequence reads is of utmost importance. In this article, we present a simple model to capture uncertainty arising in the base-calling procedure of the Illumina/Solexa GA platform. Model parameters have a straightforward interpretation in terms of the chemistry of base-calling allowing for informative and easily interpretable metrics that capture the variability in

[Research on soil bacteria under the impact of sealed CO2 leakage by high-throughput sequencing technology].

Science.gov (United States)

Tian, Di; Ma, Xin; Li, Yu-E; Zha, Liang-Song; Wu, Yang; Zou, Xiao-Xia; Liu, Shuang

2013-10-01

Carbon dioxide Capture and Storage has provided a new option for mitigating global anthropogenic CO2 emission with its unique advantages. However, there is a risk of the sealed CO2 leakage, bringing a serious threat to the ecology system. It is widely known that soil microorganisms are closely related to soil health, while the study on the impact of sequestered CO2 leakage on soil microorganisms is quite deficient. In this study, the leakage scenarios of sealed CO2 were constructed and the 16S rRNA genes of soil bacteria were sequenced by Illumina high-throughput sequencing technology on Miseq platform, and related biological analysis was conducted to explore the changes of soil bacterial abundance, diversity and structure. There were 486,645 reads for 43,017 OTUs of 15 soil samples and the results of biological analysis showed that there were differences in the abundance, diversity and community structure of soil bacterial community under different CO, leakage scenarios while the abundance and diversity of the bacterial community declined with the amplification of CO2 leakage quantity and leakage time, and some bacteria species became the dominant bacteria species in the bacteria community, therefore the increase of Acidobacteria species would be a biological indicator for the impact of sealed CO2 leakage on soil ecology system.

The International Nucleotide Sequence Database Collaboration.

Science.gov (United States)

Cochrane, Guy; Karsch-Mizrachi, Ilene; Nakamura, Yasukazu

2011-01-01

Under the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy. In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.

Are Economists More Likely to Hold Stocks?

DEFF Research Database (Denmark)

Christiansen, Charlotte; Joensen, Eyðfrið Juanna Schrøter; Rangvid, Jesper

A unique data set enables us to test the hypothesis that due to informational advantages economists are more likely to hold stocks than otherwise identical investors. Weconfirm that economists have a significantly higher probability of participating in the stockmarket than investors with any other...

Investasi: Komparasi Strategi Buy and Hold dengan Pendekatan Teknikal

Directory of Open Access Journals (Sweden)

Natica Ardani

2012-01-01

Full Text Available This research aims to analyse effectivity of technical analysis moving average compare to buy and hold strategy on index LQ-45 (as emerging market and S&P500 (as developed market. Using descriptive approach, this research analysed by metastock program with moving average exponential crossovers method. This research data samples use LQ45 and S&P500 from year 2001-2011. The findings of this research indicate that technical analysis more effective when economic situation on crisis (bearish. Whereas buy and hold strategy more effective on good economic condition (bullish. The results consistent for LQ-45 and S&P500.

KSC Education Technology Research and Development Plan

Science.gov (United States)

Odell, Michael R. L.

2003-01-01

Educational technology is facilitating new approaches to teaching and learning science, technology, engineering, and mathematics (STEM) education. Cognitive research is beginning to inform educators about how students learn providing a basis for design of more effective learning environments incorporating technology. At the same time, access to computers, the Internet and other technology tools are becoming common features in K-20 classrooms. Encouraged by these developments, STEM educators are transforming traditional STEM education into active learning environments that hold the promise of enhancing learning. This document illustrates the use of technology in STEM education today, identifies possible areas of development, links this development to the NASA Strategic Plan, and makes recommendations for the Kennedy Space Center (KSC) Education Office for consideration in the research, development, and design of new educational technologies and applications.

In-process hold-up as a measure of safeguards significance

International Nuclear Information System (INIS)

Hamlin, A.G.

1983-01-01

This paper examines the use of the in-process hold-up itself, as a measure of safeguards significance. It is argued that for any process plant it is possible to define design limits for in-process hold-up, outside which the plant will not operate, or will operate in a detectably abnormal manner. It follows, therefore, that if the in-process hold-up can be derived at frequent intervals by input/output analysis from the start of the campaign, the only diversion that can be made from it during that campaign is limited to the quantity necessary to move the apparent in-process hold-up from its normal operating condition to the upper limiting condition. It also follows that detection of this diversion is as positive for protracted diversion as for abrupt diversion. If that part of the in-process inventory that is only measurable by input/output analysis has an upper operating limit that differs from its normal operating limit by less than a significant safeguards quantity of the material in question, the IAEA's criteria for both quantity and timeliness can be met by a combination of input/output analysis to determine in-process hold-up during the campaign, together with a material balance over the campaign. The paper examines the possibility of applying this measure to process plants in general, discusses means of minimizing the in-process inventory that must be determined by input/output analysis, and the performance required of the input and output analysis. It concludes that with current precision of measurement and with one input and one output batch per day, each measured, the method would be satisfactory for a campaign lasting nearly a year and involving 6 tonnes of plutonium. The paper examines the considerable advantages in verification that would arise from limiting safeguards analyses to the two points of input and output. (author)

Conference Proceedings: Petro-tech 1998 - petroleum information technology : making IT work for Canada's petroleum industry

International Nuclear Information System (INIS)

1998-01-01

The value of information technology in the petroleum industry was explored at this conference. A total of 18 papers were presented in five sessions. The dominant themes of the five sessions were: (1) information technology, delivering value or simply a utility, (2) information technology, corporate drive or passenger, (3) managing and measuring information technology investments, (4) what does the future hold for information technology, and (5) web technology. tabs., figs

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Science.gov (United States)

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Directory of Open Access Journals (Sweden)

Nathan D. Olson

2015-03-01

Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

Sequence analysis and over-expression of ribosomal protein S28 ...

African Journals Online (AJOL)

RPS28 is a component of the 40S small ribosomal subunit encoded by RPS28 gene, which is specific to eukaryotes. The cDNA and the genomic sequence of RPS28 were cloned successfully from the Giant Panda using RT-PCR technology and Touchdown-PCR, respectively. Both sequences were analyzed preliminarily ...

A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology.

Science.gov (United States)

Wang, Jing; Yang, Xue; Chen, Haofeng; Wang, Xuewei; Wang, Xiangyu; Fang, Yi; Jia, Zhenyu; Gao, Jidong

2017-07-11

RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples. By combining Reverse Transcription-Multiple Ligation-dependent Amplification method and next generation sequencing technology, RT-MLPSeq overcomes the limit of probe length in multiplex ligation-dependent probe amplification assay and thus could detect expression levels of transcripts without quantitative limitations. We proved that different RT-MLPSeq probes targeting on the same transcripts have highly consistent results and the starting RNA/cDNA input could be as little as 1 ng. RT-MLPSeq also presented consistent relative RNA levels of selected 13 genes with reverse transcription quantitative PCR. Finally, we demonstrated the application of the new RT-MLPSeq method by measuring the mRNA expression levels of 21 genes which can be used for accurate calculation of the breast cancer recurrence score - an index that has been widely used for managing breast cancer patients.

Time discretization of the point kinetic equations using matrix exponential method and First-Order Hold

International Nuclear Information System (INIS)

Park, Yujin; Kazantzis, Nikolaos; Parlos, Alexander G.; Chong, Kil To

2013-01-01

Highlights: • Numerical solution for stiff differential equations using matrix exponential method. • The approximation is based on First Order Hold assumption. • Various input examples applied to the point kinetics equations. • The method shows superior useful and effective activity. - Abstract: A system of nonlinear differential equations is derived to model the dynamics of neutron density and the delayed neutron precursors within a point kinetics equation modeling framework for a nuclear reactor. The point kinetic equations are mathematically characterized as stiff, occasionally nonlinear, ordinary differential equations, posing significant challenges when numerical solutions are sought and traditionally resulting in the need for smaller time step intervals within various computational schemes. In light of the above realization, the present paper proposes a new discretization method inspired by system-theoretic notions and technically based on a combination of the matrix exponential method (MEM) and the First-Order Hold (FOH) assumption. Under the proposed time discretization structure, the sampled-data representation of the nonlinear point kinetic system of equations is derived. The performance of the proposed time discretization procedure is evaluated using several case studies with sinusoidal reactivity profiles and multiple input examples (reactivity and neutron source function). It is shown, that by applying the proposed method under a First-Order Hold for the neutron density and the precursor concentrations at each time step interval, the stiffness problem associated with the point kinetic equations can be adequately addressed and resolved. Finally, as evidenced by the aforementioned detailed simulation studies, the proposed method retains its validity and accuracy for a wide range of reactor operating conditions, including large sampling periods dictated by physical and/or technical limitations associated with the current state of sensor and

Applicability of the 3D-VIBE sequence to whole brain imaging

International Nuclear Information System (INIS)

Makabe, Takeshi; Nakamura, Manami; Moriyama, Ryo

2009-01-01

The volumetric interpolated breath-hold examination (VIBE) method has been developed imaging also holds its breath in an abdomen, and to do three-dimensional T1WI in possible time in gradient echo sequence, and applied to dynamic study mainly and planning for time reduction using an interpolation and partial fourier. We considered the condition for imaging to do whole brain as high resolution image using VIBE. Even if base matrix was maintained when an interpolation and partial fourier were used too much excessively by Phantom experiment, the resolution of multiplanar reconstruction (MPR) image fell. There was a limit of the interpolation therefore to maintain the resolution as voxel. Signal-to-noise ratio (SNR) fell by flip angle (FA) increase by the applicability to the head, and peak existed in about 15 deg in contrast-to-noise ratio (CNR) of white matter and gray matter. Therefore by it's clinical and optimizing the imaging condition of VIBE, whole brain, it was imaging possible in about 3 minutes as high resolution image. (author)

ENERGY STAR Certified Commercial Hot Food Holding Cabinet

Data.gov (United States)

U.S. Environmental Protection Agency — Certified models meet all ENERGY STAR requirements as listed in the Version 2.0 ENERGY STAR Program Requirements for Commercial Hot Food Holding Cabinets that are...

Impact of cash conversion cycle on cash holding – A study on FMCG sector

Directory of Open Access Journals (Sweden)

Somnath Das

2017-11-01

Full Text Available In today’s environment, cash conversion cycle is randomly used as a measure of liquidity of the organizations. Cash conversion cycle is considered as the length of time between raw-materials and collection of cash from debtors. It can be used as a benchmarking competitors or comparing companies. On the other hand, Cash holding is one of the most important financial decisions that a manager has to make in any organization. Some organizations hold more cash and some organizations hold less cash. In this study, we perform a survey to make a relationship between Cash Conversion Cycle and Cash Holding.

Stock Liquidity and Corporate Cash Holdings: Feedback and the Cash as Ammunition Hypothesis

OpenAIRE

Nyborg, Kjell G; Wang, Zexi

2013-01-01

The paper contributes to the literature on corporate cash holdings by showing that there is a financial markets channel that affects corporations’ cash holdings. Leaning on the literature on stock price feedback to firm fundamentals, we advance the hypothesis that firms with more liquid stocks hold more cash, ceteris paribus, as ammunition to defend against negative cascades or stimulate positive ones. This contrasts with an alternative view that firms with more liquid stocks are less financi...

Do More Economists Hold Stocks?

DEFF Research Database (Denmark)

Christiansen, Charlotte; Joensen, Juanna Schröter; Rangvid, Jesper

A unique data set enables us to test the hypothesis that more economists than otherwise identical investors hold stocks due to informational advantages. We confirm that economists have a significantly higher probability of participating in the stock market than investors with any other education......, even when controlling for several background characteristics. We make use of a large register-based panel data set containing detailed information on the educational attainments and various financial and socioeconomic variables. We model the stock market participation decision by the probit model...

Diverse Presentation of Breath Holding Spells: Two Case Reports with Literature Review

Directory of Open Access Journals (Sweden)

Geetanjali Rathore

2013-01-01

Full Text Available Breath holding spells are a common and dramatic form of syncope and anoxic seizure in infancy. They are usually triggered by an emotional stimuli or minor trauma. Based on the color change, they are classified into 3 types, cyanotic, pallid, and mixed. Pallid breath holding spells result from exaggerated, vagally-mediated cardiac inhibition, whereas the more common, cyanotic breathholding spells are of more complex pathogenesis which is not completely understood. A detailed and accurate history is the mainstay of diagnosis. An EKG should be strongly considered to rule out long QT syndrome. Spontaneous resolution of breath-holding spells is usually seen, without any adverse developmental and intellectual sequelae. Rare cases of status epilepticus, prolonged asystole, and sudden death have been reported. Reassurance and education is the mainstay of therapy. Occasionally, pharmacologic intervention with iron, piracetam; atropine may be of benefit. Here we present 2 cases, one of each, pallid and cyanotic breath holding spells.

Management of High-Throughput DNA Sequencing Projects: Alpheus.

Science.gov (United States)

Miller, Neil A; Kingsmore, Stephen F; Farmer, Andrew; Langley, Raymond J; Mudge, Joann; Crow, John A; Gonzalez, Alvaro J; Schilkey, Faye D; Kim, Ryan J; van Velkinburgh, Jennifer; May, Gregory D; Black, C Forrest; Myers, M Kathy; Utsey, John P; Frost, Nicholas S; Sugarbaker, David J; Bueno, Raphael; Gullans, Stephen R; Baxter, Susan M; Day, Steve W; Retzel, Ernest F

2008-12-26

High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multi-gigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem's SOLiD (sequencing-by-ligation). Alpheus enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. Alpheus is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls based on consistency, expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. Alpheus also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.

Human genetics and genomics a decade after the release of the draft sequence of the human genome

Science.gov (United States)

2011-01-01

Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade. PMID:22155605

Field-based species identification in eukaryotes using real-time nanopore sequencing.

OpenAIRE

Papadopulos, Alexander; Devey, Dion; Helmstetter, Andrew; Parker, Joe

2017-01-01

Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, the generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potenti...

De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

Science.gov (United States)

Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

2016-01-01

Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

Venezuela and Chavez: What the Future Holds...

Science.gov (United States)

2010-04-01

government made public 26 presidential decrees that had been enacted. These acts: ...covered such areas as tourism , railways, social security, and...great prosperity or a harbinger of doom to the region, and for this reason the United States must prepare for the many paths that the future holds

Biosketch Ashok Venkitaraman holds the Ursula Zoellner ...

Indian Academy of Sciences (India)

ashok

Ashok Venkitaraman holds the Ursula Zoellner Professorship of Cancer Research at the University of Cambridge, and is the Director of the Medical Research Council. (MRC) Cancer Cell Unit there. He learnt and practiced medicine at the Christian. Medical College, Vellore, before completing his Ph.D. at University College ...

Information technology investments must deliver value

International Nuclear Information System (INIS)

Schulz, Y.

1998-01-01

The value of information technology (IT) management for the petroleum industry was discussed. There are currently two points of view regarding the subject. Adherents of one view hold that the strategic uses of information technology are relevant to the oil and gas industry, while those opposed find no demonstrated connection between information technology investments and business results. This paper addresses the impact of the information paradox, but maintains that information technology is not only valuable but essential to the oil and gas industry. This paper maintains that whenever it is perceived as being of limited use and too expensive, it is usually because it is not well managed. Value management can and should lead to superior outcomes. Neither exploration, nor drilling nor production, nor marketing could exist without information technology as the value is imperative. To further make the case, the nature of information technology value management and the strategies required to achieve value from information technology are reviewed. figs

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.

Automated daily breath hold stability measurements by real-time imaging in radiotherapy of breast cancer

NARCIS (Netherlands)

De Boer, Hans C J; Van Den Bongard, Desirée J G; van Asselen, B

2016-01-01

Background and purpose Breath hold is increasingly used for cardiac sparing in left-sided breast cancer irradiation. We have developed a fast automated method to verify breath hold stability in each treatment fraction. Material and methods We evaluated 504 patients treated with breath hold. Moderate

Pengaruh Holding Time Terhadap Kekeruhan Pada Sampel Air Sungai Babura Dengan Metode Turbidimetri

OpenAIRE

Ashari, Dian

2010-01-01

Turbidity define the water optic determined based on amount of lihgts absorbed by materials in water. Turbidity caused by organic and inorganic materials which suspended and solved (such as mud and smooth sand), also organic and inorganic materials which in form of plankton and other microorganism. In this case, I study about holding time influence to turbidity, on trial this show very influencing a period of holding time to turbidity. Where a period of holding time at maximum turbidity sampl...

26 CFR 53.4943-7 - Special rules for readjustments involving grandfathered holdings.

Science.gov (United States)

2010-04-01

... in Z will represent 50% of the fair market value of the outstanding Z stock. (ii) Under the... 26 Internal Revenue 17 2010-04-01 2010-04-01 false Special rules for readjustments involving... Excess Business Holdings § 53.4943-7 Special rules for readjustments involving grandfathered holdings. (a...

41 CFR 109-1.5202 - Establishment of a personal property holdings baseline.

Science.gov (United States)

2010-07-01

... personal property holdings baseline. 109-1.5202 Section 109-1.5202 Public Contracts and Property Management...-1.5202 Establishment of a personal property holdings baseline. (a) If the contractor is a new... baseline or may perform a complete physical inventory of all personal property. This physical inventory is...

Shedding light on the Early Pleistocene of TD6 (Gran Dolina, Atapuerca, Spain): The technological sequence and occupational inferences.

Science.gov (United States)

Mosquera, Marina; Ollé, Andreu; Rodríguez-Álvarez, Xose Pedro; Carbonell, Eudald

2018-01-01

This paper aims to update the information available on the lithic assemblage from the entire sequence of TD6 now that the most recent excavations have been completed, and to explore possible changes in both occupational patterns and technological strategies evidenced in the unit. This is the first study to analyse the entire TD6 sequence, including subunits TD6.3 and TD6.1, which have never been studied, along with the better-known TD6.2 Homo antecessor-bearing subunit. We also present an analysis of several lithic refits found in TD6, as well as certain technical features that may help characterise the hominin occupations. The archaeo-palaeontological record from TD6 consists of 9,452 faunal remains, 443 coprolites, 1,046 lithic pieces, 170 hominin remains and 91 Celtis seeds. The characteristics of this record seem to indicate two main stages of occupation. In the oldest subunit, TD6.3, the lithic assemblage points to the light and limited hominin occupation of the cave, which does, however, grow over the course of the level. In contrast, the lithic assemblages from TD6.2 and TD6.1 are rich and varied, which may reflect Gran Dolina cave's establishment as a landmark in the region. Despite the occupational differences between the lowermost subunit and the rest of the deposit, technologically the TD6 lithic assemblage is extremely homogeneous throughout. In addition, the composition and spatial distribution of the 12 groups of lithic refits found in unit TD6, as well as the in situ nature of the assemblage demonstrate the high degree of preservation at the site. This may help clarify the nature of the Early Pleistocene hominin occupations of TD6, and raise reasonable doubt about the latest interpretations that support the ex situ character of the assemblage as a whole.

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS Data in Plants

Directory of Open Access Journals (Sweden)

Sima Taheri

2018-02-01

Full Text Available Microsatellites, or simple sequence repeats (SSRs, are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq and related tools for mining and development of microsatellites in plants.