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  1. 76 FR 68189 - Healthcare Technology Holdings, Inc.; Analysis of Proposed Agreement Containing Consent Orders To...

    Science.gov (United States)

    2011-11-03

    ... FEDERAL TRADE COMMISSION [File No. 111 0097] Healthcare Technology Holdings, Inc.; Analysis of... Technology Holdings, Inc. (``Healthcare Technology''), subject to final approval, an Agreement Containing... Healthcare Technology's proposed acquisition of SDI Health LLC (``SDI'') from SDI Health Holdings LLC (``SDI...

  2. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  3. Technology demonstration assessment report for X-701B Holding Pond

    International Nuclear Information System (INIS)

    1992-07-01

    This Technology Demonstration Assessment Report (TDAR) was developed to evaluate and recommend the most feasible approach for cleanup of contaminated Minford soils below the X-701B Holding Pond and to summarize closure activities at the Portsmouth Gaseous Diffusion Plant (PORTS)X-701B Holding Pond(X-701B)site. In this TDAR, the recommended alternative and the activities for closure of the X-701B site are discussed. Four treatment technologies chosen for the TD, along with a contingent design, were evaluated to determine which approach would be appropriate for final closure of X-701B. These technologies address removal of soil contamination from the vadose zone and the saturated zone. The four technologies plus the Contingent Design evaluated were: In situ Soil Mixing with Solidification/Stabilization; In situ Soil Mixing with Isothermal Vapor Extraction; In situ Soil Mixing with Thermally Enhanced Vapor Extraction; In situ Soil Mixing with Peroxidation Destruction; and Contingent Closure. These technologies were evaluated according to their performance, reliability, implementability, safety, waste minimization, cost, and implementation time. Based on these criteria, a preferred treatment approach was recommended. The goal of the treatment approach is to apply the most appropriate technology demonstrated at X-231 B in order to reduce Volatile Organic Compounds (VOCs) in the saturated Minford soils directly beneath the X-701B Holding Pond. The closure schedule will include bid and award of two construction contracts, mobilization and demobilization, soil treatment, cap design, and cap construction. The total time required for soil treatment will be established based on actual performance of the soil treatment approach in the field

  4. Holding Pressure and Its Influence on Quality in PIM Technology

    Directory of Open Access Journals (Sweden)

    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.

  5. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  6. Holding the Edge: Maintaining the Defense Technology Base

    Science.gov (United States)

    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

  7. 77 FR 74520 - Encore Clean Energy, Inc., Energy & Engine Technology Corp., Equity Media Holdings Corporation...

    Science.gov (United States)

    2012-12-14

    ... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] Encore Clean Energy, Inc., Energy & Engine Technology Corp., Equity Media Holdings Corporation, eTotalSource, Inc., Extensions, Inc., Firepond, Inc., and GNC Energy Corporation; Order Withdrawing Trading Suspension as to Extensions, Inc. December 12...

  8. 76 FR 70722 - Healthcare Technology Holdings, Inc.; Analysis of Proposed Agreement Containing Consent Orders To...

    Science.gov (United States)

    2011-11-15

    ... FEDERAL TRADE COMMISSION [File No. 111 0097] Healthcare Technology Holdings, Inc.; Analysis of Proposed Agreement Containing Consent Orders To Aid Public Comment Correction In notice document 2011-28497 appearing on pages 68189-68191 in the issue of Thursday, November 3, 2011, make the following corrections: 1...

  9. 77 FR 5865 - China Agro-Technology Holdings Ltd.; Order of Suspension of Trading

    Science.gov (United States)

    2012-02-06

    ... Suspension of Trading February 2, 2012. It appears to the Securities and Exchange Commission that there is a... trading in the securities of China Agro-Technology Holdings Ltd. Therefore, it is ordered, pursuant to Section 12(k) of the Securities Exchange Act of 1934, that trading in the securities of China Agro...

  10. 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.

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

    Science.gov (United States)

    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.

  12. SU-E-J-223: A BOLD Contrast Imaging Sequence to Evaluate Oxygenation Changes Due to Breath Holding for Breast Radiotherapy: A Pilot Study

    Energy Technology Data Exchange (ETDEWEB)

    Adamson, J; Chang, Z; Cai, J; Palta, M; Horton, J; Yin, F; Blitzblau, R [Duke University Medical Center, Durham, NC (United States)

    2015-06-15

    Purpose: To develop a robust MRI sequence to measure BOLD breath hold induced contrast in context of breast radiotherapy. Methods: Two sequences were selected from prior studies as candidates to measure BOLD contrast attributable to breath holding within the breast: (1) T2* based Gradient Echo EPI (TR/TE = 500/41ms, flip angle = 60°), and (2) T2 based Single Shot Fast Spin Echo (SSFSE) (TR/TE = 3000/60ms). We enrolled ten women post-lumpectomy for breast cancer who were undergoing treatment planning for whole breast radiotherapy. Each session utilized a 1.5T GE MRI and 4 channel breast coil with the subject immobilized prone on a custom board. For each sequence, 1–3 planes of the lumpectomy breast were imaged continuously during a background measurement (1min) and intermittent breath holds (20–40s per breath hold, 3–5 holds per sequence). BOLD contrast was quantified as correlation of changes in per-pixel intensity with the breath hold schedule convolved with a hemodynamic response function. Subtle motion was corrected using a deformable registration algorithm. Correlation with breath-holding was considered significant if p<0.001. Results: The percentage of the breast ROI with positive BOLD contrast measured by the two sequences were in agreement with a correlation coefficient of R=0.72 (p=0.02). While both sequences demonstrated areas with strong BOLD response, the response was more systematic throughout the breast for the SSFSE (T2) sequence (% breast with response in the same direction: 51.2%±0.7% for T2* vs. 68.1%±16% for T2). In addition, the T2 sequence was less prone to magnetic susceptibility artifacts, especially in presence of seroma, and provided a more robust image with little distortion or artifacts. Conclusion: A T2 SSFSE sequence shows promise for measuring BOLD contrast in the context of breast radiotherapy utilizing a breath hold technique. Further study in a larger patient cohort is warranted to better refine this novel technique.

  13. SU-E-J-223: A BOLD Contrast Imaging Sequence to Evaluate Oxygenation Changes Due to Breath Holding for Breast Radiotherapy: A Pilot Study

    International Nuclear Information System (INIS)

    Adamson, J; Chang, Z; Cai, J; Palta, M; Horton, J; Yin, F; Blitzblau, R

    2015-01-01

    Purpose: To develop a robust MRI sequence to measure BOLD breath hold induced contrast in context of breast radiotherapy. Methods: Two sequences were selected from prior studies as candidates to measure BOLD contrast attributable to breath holding within the breast: (1) T2* based Gradient Echo EPI (TR/TE = 500/41ms, flip angle = 60°), and (2) T2 based Single Shot Fast Spin Echo (SSFSE) (TR/TE = 3000/60ms). We enrolled ten women post-lumpectomy for breast cancer who were undergoing treatment planning for whole breast radiotherapy. Each session utilized a 1.5T GE MRI and 4 channel breast coil with the subject immobilized prone on a custom board. For each sequence, 1–3 planes of the lumpectomy breast were imaged continuously during a background measurement (1min) and intermittent breath holds (20–40s per breath hold, 3–5 holds per sequence). BOLD contrast was quantified as correlation of changes in per-pixel intensity with the breath hold schedule convolved with a hemodynamic response function. Subtle motion was corrected using a deformable registration algorithm. Correlation with breath-holding was considered significant if p<0.001. Results: The percentage of the breast ROI with positive BOLD contrast measured by the two sequences were in agreement with a correlation coefficient of R=0.72 (p=0.02). While both sequences demonstrated areas with strong BOLD response, the response was more systematic throughout the breast for the SSFSE (T2) sequence (% breast with response in the same direction: 51.2%±0.7% for T2* vs. 68.1%±16% for T2). In addition, the T2 sequence was less prone to magnetic susceptibility artifacts, especially in presence of seroma, and provided a more robust image with little distortion or artifacts. Conclusion: A T2 SSFSE sequence shows promise for measuring BOLD contrast in the context of breast radiotherapy utilizing a breath hold technique. Further study in a larger patient cohort is warranted to better refine this novel technique

  14. [Sequencing technology in gene diagnosis and its application].

    Science.gov (United States)

    Yibin, Guo

    2014-11-01

    The study of gene mutation is one of the hot topics in the field of life science nowadays, and the related detection methods and diagnostic technology have been developed rapidly. Sequencing technology plays an indispensable role in the definite diagnosis and classification of genetic diseases. In this review, we summarize the research progress in sequencing technology, evaluate the advantages and disadvantages of 1(st) ~3(rd) generation of sequencing technology, and describe its application in gene diagnosis. Also we made forecasts and prospects on its development trend.

  15. 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.

  16. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  17. Comparison of next generation sequencing technologies for transcriptome characterization

    Directory of Open Access Journals (Sweden)

    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

  18. Next generation sequencing (NGS)technologies and applications

    Energy Technology Data Exchange (ETDEWEB)

    Vuyisich, Momchilo [Los Alamos National Laboratory

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  19. Diagnosing lung nodules on oncologic MR/PET imaging: Comparison of fast T1-weighted sequences and influence of image acquisition in inspiration and expiration breath-hold

    Energy Technology Data Exchange (ETDEWEB)

    Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios; Brendle, Cornelia; Schmidt, Holger; Pfannenberg, Christina A; LaFougère, Christian; Nikolaou, Konstantin; Schraml, Christina [University Hospital of Tuebingen, Tuebingen (Germany)

    2016-09-15

    First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR/PET patients. In contrast to CT, inspiration versus

  20. Diagnosing Lung Nodules on Oncologic MR/PET Imaging: Comparison of Fast T1-Weighted Sequences and Influence of Image Acquisition in Inspiration and Expiration Breath-Hold

    Energy Technology Data Exchange (ETDEWEB)

    Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Brendle, Cornelia [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Department of Diagnostic and Interventional Neuroradiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Schmidt, Holger; Pfannenberg, Christina A. [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Fougère, Christian la [Department of Nuclear Medicine, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Nikolaou, Konstantin; Schraml, Christina [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany)

    2016-11-01

    First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR/PET patients. In contrast to CT, inspiration versus

  1. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

    International Nuclear Information System (INIS)

    Martin, J.; Villajos, M.; Oses, M. J.; Veintemillas, M.; Rue, M.; Puig, J.; Sentis, M.

    2000-01-01

    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

  8. SEQUENCING BATCH REACTOR: A PROMISING TECHNOLOGY IN WASTEWATER TREATMENT

    Directory of Open Access Journals (Sweden)

    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.

  9. Optimal MR pulse sequences for hepatic hemangiomas : comparison of T2-weighted turbo-spin-echo, T2-weighted breath-hold turbo-spin-echo, and T1-weighted FLASH dynamic imaging

    International Nuclear Information System (INIS)

    Wang, Wen Chao; Choi, Byung Ihn; Han, Joon Koo; Kim, Tae Kyoung; Cho, Soon Gu

    1997-01-01

    To optimize MR imaging pulse sequences in the imaging of hepatic hemangioma and to evaluate on dynamic MR imaging the enhancing characteristics of the lesions. Twenty patients with 35 hemangiomas were studied by using Turbo-spin-echo (TSE) sequence (T2-weighted, T2- and heavily T2-weighted breath-hold) and T1-weighted FLASH imaging acquired before, immediately on, and 1, 3 and 5 minutes after injection of a bolus of Gd-DTPA (0.1mmol/kg). Phased-array multicoil was employed. Images were quantitatively analyzed for lesion-to-liver signal difference to noise ratios (SD/Ns), and lesion-to-liver signal ratios (H/Ls), and qualitatively analyzed for lesion conspicuity. The enhancing characteristics of the hemangiomas were described by measuring the change of signal intensity as a curve in T1-weighted FLASH dynamic imaging. For T2-weighted images, breath-hold T2-weighted TSE had a slightly higher SD/N than other pulse sequences, but there was no statistical difference in three fast pulse sequences (p=0.211). For lesion conspicuity, heavily T2-weighted breath-hold TSE images was superior to T2-weighted breath-hold or non-breath-hold TSE (H/L, 5.75, 3.81, 2.87, respectively, p<0.05). T2-weighted breath-hold TSE imaging was more effective than T2-weighted TSE imaging in removing lesion blurring or lack of sharpness, and there was a 12-fold decrease in acquisition time (20sec versus 245 sec). T1-weighted FLASH dynamic images of normal liver showed peak enhancement at less than 1 minute, and of hemangioma at more than 3 minutes;the degree of enhancement for hemangioma decreased after a 3 minute delay. T2-weighed breath-hold TSE imaging and Gd-DTPA enhanced FLASH dynamic imaging with 5 minutes delay are sufficient for imaging hepatic hemangiomas

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

    Science.gov (United States)

    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...

  11. Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

    Science.gov (United States)

    Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

    2016-01-01

    On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human

  12. 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.

  13. 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).

  14. DNA Polymerases Drive DNA Sequencing-by-Synthesis Technologies: Both Past and Present

    Directory of Open Access Journals (Sweden)

    Cheng-Yao eChen

    2014-06-01

    Full Text Available Next-generation sequencing (NGS technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. E. coli DNA polymerase I proteolytic (Klenow fragment was originally utilized in Sanger's dideoxy chain terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ⱷ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ⱷ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.

  15. Potential use of multispectral imaging technology to identify moisture content and water-holding capacity in cooked pork sausages.

    Science.gov (United States)

    Ma, Fei; Zhang, Bin; Wang, Wu; Li, Peijun; Niu, Xiangli; Chen, Conggui; Zheng, Lei

    2018-03-01

    The traditional detection methods for moisture content (MC) and water-holding capacity (WHC) in cooked pork sausages (CPS) are destructive, time consuming, require skilled personnel and are not suitable for online industry applications. The goal of this work was to explore the potential of multispectral imaging (MSI) in combination with multivariate analysis for the identification of MC and WHC in CPS. Spectra and textures of 156 CPS treated by six salt concentrations (0-2.5%) were analyzed using different calibration models to find the most optimal results of predicting MC and WHC in CPS. By using the fused data of spectra and textures, partial least squares regression models performed well for determining the MC and WHC, with a correlation coefficient (r) of 0.949 and 0.832, respectively. Additionally, their spatial distribution in CPS could be visualized via applying prediction equations to transfer each pixel in the image. Results of satisfactory detection and visualization of the MC and WHC showed that MSI has the potential to serve as a rapid and non-destructive method for use in sausage industry. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  16. A Comprehensive Framework for Information Technology Governance and Localizing it for Automotive Industry of Iran (Case Study: ATLAS Automotive Holding

    Directory of Open Access Journals (Sweden)

    Mohammad Mosakhani

    2017-03-01

    Full Text Available Due to the absence of a comprehensive framework for IT governance, the main objective of the study is to identify all components of IT governance and present them in the form of a comprehensive IT governance framework .The localization of provided framework for the automotive industry is the secondary objective of the study. In this regard, the research questions are: what is the comprehensive framework of IT governance? What are the components and dimensions of a comprehensive framework of IT governance? What is the localized comprehensive framework of IT governance for the Iranian automotive industry? All researches on IT governance were investigated using meta-synthesis qualitative method and were limited to 96 selected articles by performing a meta-synthesis process. Then, the five categories, 19 concepts and 79 codes of IT governance were identified through detailed study of these articles. Then, a comprehensive framework of IT governance was presented. For localizing, a questionnaire designed based on the identified IT governance components, and distributed among the automotive industry experts. Statistical hypothesis testing of collected data led to the rejection of cross/functional job rotation component in the automotive industry. To demonstrate the applicability of the framework, the IT governance status of ATLAS holding company was evaluated based on the comprehensive framework that localized for automotive industry.

  17. The application of the high throughput sequencing technology in the transposable elements.

    Science.gov (United States)

    Liu, Zhen; Xu, Jian-hong

    2015-09-01

    High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

  18. 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.

  19. Treatment of Laboratory Wastewater by Sequence Batch reactor technology

    International Nuclear Information System (INIS)

    Imtiaz, N.; Butt, M.; Khan, R.A.; Saeed, M.T.; Irfan, M.

    2012-01-01

    These studies were conducted on the characterization and treatment of sewage mixed with waste -water of research and testing laboratory (PCSIR Laboratories Lahore). In this study all the parameters COD, BOD and TSS etc of influent (untreated waste-water) and effluent (treated waste-water) were characterized using the standard methods of examination for water and waste-water. All the results of the analyzed waste-water parameters were above the National Environmental Quality Standards (NEQS) set at National level. Treatment of waste-water was carried out by conventional sequencing batch reactor technique (SBR) using aeration and settling technique in the same treatment reactor at laboratory scale. The results of COD after treatment were reduced from (90-95 %), BOD (95-97 %) and TSS (96-99 %) and the reclaimed effluent quality was suitable for gardening purposes. (author)

  20. 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

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

    Science.gov (United States)

    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.

  2. 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...

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. Free-breathing dynamic liver examination using a radial 3D T1-weighted gradient echo sequence with moderate undersampling for patients with limited breath-holding capacity

    Energy Technology Data Exchange (ETDEWEB)

    Kaltenbach, Benjamin, E-mail: benjamin.kaltenbach@kgu.de [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany); Roman, Andrei; Polkowski, Christoph; Gruber-Rouh, Tatjana [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany); Bauer, Ralf W. [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany); Divison of Radiology and Nuclear Medicine, Kantonsspital, St. Gallen (Switzerland); Hammerstingl, Renate; Vogl, Thomas J.; Zangos, Stephan [Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt am Main (Germany)

    2017-01-15

    Highlights: • Respiratory artifacts are a frequent problem in abdominal MR imaging. • Non-diagnostic examinations could be reduced using free-breathing us-radial-VIBE for dynamic liver examination in challenging patients. • Streak artifacts are characteristic for an undersampled radial acquisition but do not affect diagnostic validity. - Abstract: Purpose: To compare free-breathing radial VIBE with moderate undersampling (us-radial-VIBE) with a standard breathhold T1-weighted volumetric interpolated sequence (3D GRE VIBE) in patients unable to suspend respiration during dynamic liver examination. Material and methods: 23 consecutive patients underwent dynamic liver MR examination using the free-breathing us-radial-VIBE sequence as part of their oncologic follow-up. All patients were eligible for the free-breathing protocol due to severe respiratory artifacts at the planning or precontrast sequences. The us-radial-VIBE acquisitions were compared to the patientś last staging liver MRI including a standard breathhold 3D GRE VIBE. For an objective image evaluation, signal intensity (SI), image noise (IN), signal-to-noise ratio (SNR) and contrast-enhancement ratio (CER) were compared. Representative image quality parameters, including typical artifacts were independently, retrospectively and blindly scored by four readers. Results: Us-radial-VIBE had significant lower SNR (p < 0.0001) and higher IN (p < 0.0001), whereas SI did not differ (p = 0.62). Temporal resolution assessed with CER in the arterial phase showed higher values for us-radial-VIBE (p = 0.028). Subjective image quality parameters received generally slightly higher scores for 3D GRE VIBE. In a smaller subgroup comprising patients with severe respiratory artifacts also at reference breathhold 3D GRE VIBE examination, us-radial-VIBE showed significantly higher image quality scores. Furthermore, there were generally more severe respiratory artifacts in 3D GRE VIBE, whereas streaking was characteristic

  6. 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…

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.)

  12. 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.

  13. 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.

  14. [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.

  15. 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.

  16. 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.

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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 ...

  10. 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.

  11. 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)

  12. 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

  13. 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

  14. 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

  15. 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.

  16. "Like Holding an Umbrella Before It Rains": Acceptability of Future Rectal Microbicides Among Men Who Have Sex With Men in India-A Modified Technology Acceptance Model.

    Science.gov (United States)

    Chakrapani, Venkatesan; Newman, Peter A; Shunmugam, Murali; Mengle, Shruta; Nelson, Ruban; Rubincam, Clara; Kumar, Pushpesh

    2017-07-01

    Topical rectal microbicides (RMs) are a new prevention technology in development that aims to reduce the risk of HIV acquisition from anal sex. We examined RM acceptability among men who have sex with men (MSM) in India. We conducted a qualitative exploratory study guided by a modified Technology Acceptance Model, with 10 focus groups ( n = 61) of MSM and 10 key informant interviews. Data were explored using framework analysis. RM acceptability was influenced by technological contexts: perceived usefulness of RMs, perceived ease of use of RM and applicator, and habits around condom and lubricant use; individual and interpersonal contexts: perceived relevance and preferences for product formulation and dosing frequency; and MSM community/social contexts: perceived social approval, RM-related stigma, social support. Implementation of RMs for MSM in India may be supported by multi-level interventions that engage community-based organizations in destigmatizing and distributing RMs, ideally gel-based products that enable on-demand use before sex.

  17. Detecting novel genetic mutations in Chinese Usher syndrome families using next-generation sequencing technology.

    Science.gov (United States)

    Qu, Ling-Hui; Jin, Xin; Xu, Hai-Wei; Li, Shi-Ying; Yin, Zheng-Qin

    2015-02-01

    Usher syndrome (USH) is the most common cause of combined blindness and deafness inherited in an autosomal recessive mode. Molecular diagnosis is of great significance in revealing the molecular pathogenesis and aiding the clinical diagnosis of this disease. However, molecular diagnosis remains a challenge due to high phenotypic and genetic heterogeneity in USH. This study explored an approach for detecting disease-causing genetic mutations in candidate genes in five index cases from unrelated USH families based on targeted next-generation sequencing (NGS) technology. Through systematic data analysis using an established bioinformatics pipeline and segregation analysis, 10 pathogenic mutations in the USH disease genes were identified in the five USH families. Six of these mutations were novel: c.4398G > A and EX38-49del in MYO7A, c.988_989delAT in USH1C, c.15104_15105delCA and c.6875_6876insG in USH2A. All novel variations segregated with the disease phenotypes in their respective families and were absent from ethnically matched control individuals. This study expanded the mutation spectrum of USH and revealed the genotype-phenotype relationships of the novel USH mutations in Chinese patients. Moreover, this study proved that targeted NGS is an accurate and effective method for detecting genetic mutations related to USH. The identification of pathogenic mutations is of great significance for elucidating the underlying pathophysiology of USH.

  18. Integration of microbiological, epidemiological and next generation sequencing technologies data for the managing of nosocomial infections

    Directory of Open Access Journals (Sweden)

    Matteo Brilli

    2018-02-01

    Full Text Available At its core, the work of clinical microbiologists consists in the retrieving of a few bytes of information (species identification; metabolic capacities; staining and antigenic properties; antibiotic resistance profiles, etc. from pathogenic agents. The development of next generation sequencing technologies (NGS, and the possibility to determine the entire genome for bacterial pathogens, fungi and protozoans will likely introduce a breakthrough in the amount of information generated by clinical microbiology laboratories: from bytes to Megabytes of information, for a single isolate. In parallel, the development of novel informatics tools, designed for the management and analysis of the so-called Big Data, offers the possibility to search for patterns in databases collecting genomic and microbiological information on the pathogens, as well as epidemiological data and information on the clinical parameters of the patients. Nosocomial infections and antibiotic resistance will likely represent major challenges for clinical microbiologists, in the next decades. In this paper, we describe how bacterial genomics based on NGS, integrated with novel informatic tools, could contribute to the control of hospital infections and multi-drug resistant pathogens.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. 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

  2. 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.

  3. 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

  4. Technology trajectories and the selection of optimal R and D project sequences

    NARCIS (Netherlands)

    van Bommel, Ties; Mahieu, R.J.; Nijssen, E.J.

    2014-01-01

    Given a set of R&D projects drawing on the same underlying technology, a technology trajectory refers to the order in which projects are executed. Due to their technological interdependence, the successful execution of one project can increase a firm's technological capability, and help to

  5. 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

  6. 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.

  7. 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...

  8. Molecular-Sized DNA or RNA Sequencing Machine | NCI Technology Transfer Center | TTC

    Science.gov (United States)

    The National Cancer Institute's Gene Regulation and Chromosome Biology Laboratory is seeking statements of capability or interest from parties interested in collaborative research to co-develop a molecular-sized DNA or RNA sequencing machine.

  9. 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.

  10. 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

  11. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Directory of Open Access Journals (Sweden)

    Chengwei Luo

    Full Text Available Next-generation sequencing (NGS is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage correlated highly between the two platforms (R(2>0.9. Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  12. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Science.gov (United States)

    Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T

    2012-01-01

    Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R(2)>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  13. 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.

  14. The use of a phased-array surface coil and breath-holding in MRI of the liver. Comparison of conventional SE, fat-suppressed GRE, and TSE sequences

    International Nuclear Information System (INIS)

    Helmberger, T.; Holzknecht, N.; Lackerbauer, C.A.; Mueller-Lisse, U.; Schnarkowski, P.; Gauger, J.; Reiser, M.

    1995-01-01

    To determine the efficacy of fast MRI techniques using a taylored imaging design (breathhold and array-surface coil), conventional T1-, T2-weighted spin-echo (SE) sequences and breathhold gradient-echo (GRE) T1- and breathhold fast SE T2-weighted images were compared. 20 patients with proven focal liver lesions were studied on a 1.5 Tesla system. Conventional SE T1- und T2-weighted imaging, as well as GRE T1- and fast SE T2-weighted imaging was performed. Fast imaging was done during breathhold using an array-surface coil. For all sequences signal-to-noise ratios (S/N) and liver-to-lesion-contrast ratios (L/L) were measured and statistically compared. Regarding image quality parameters, S/N and L/L, there was no significant difference between the conventional and fast imaging techniques. However, GRE imaging was superior (84.8%) to conventional imaging for breathing and pulsation artifacts, while fast SE T2 imaging was equal regarding breathing artifacts, but superior (51.5%) regarding pulsation artifacts. The number of detected hepatic lesions was identical in all sequences. The fast MRI techniques demonstrated a superiority to conventional imaging regarding image quality and presence of artifacts. (orig.) [de

  15. 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.

  16. 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.

  17. 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.

  18. Left ventricular function assessment using a fast 3D gradient echo pulse sequence: comparison to standard multi-breath hold 2D steady state free precession imaging and accounting for papillary muscles and trabeculations.

    Science.gov (United States)

    Sievers, Burkhard; Schrader, Sebastian; Rehwald, Wolfgang; Hunold, Peter; Barkhausen, Joerg; Erbel, Raimund

    2011-06-01

    Papillary muscles and trabeculae for ventricular function analysis are known to significantly contribute to accurate volume and mass measurements. Fast imaging techniques such as three-dimensional steady-state free precession (3D SSFP) are increasingly being used to speed up imaging time, but sacrifice spatial resolution. It is unknown whether 3D SSFP, despite its reduced spatial resolution, allows for exact delineation of papillary muscles and trabeculations. We therefore compared 3D SSFP ventricular function measurements to those measured from standard multi-breath hold two-dimensional steady-state free precession cine images (standard 2D SSFP). 14 healthy subjects and 14 patients with impaired left ventricularfunction underwent 1.5 Tesla cine imaging. A stack of short axis images covering the left ventricle was acquired with 2D SSFP and 3D SSFP. Left ventricular volumes, ejection fraction, and mass were determined. Analysis was performed by substracting papillary muscles and trabeculae from left ventricular volumes. In addition, reproducibility was assessed. EDV, ESV, EF, and mass were not significantly different between 2D SSFP and 3D SSFP (mean difference healthy subjects: -0.06 +/- 3.2 ml, 0.54 +/- 2.2 ml, -0.45 +/- 1.8%, and 1.13 +/- 0.8 g, respectively; patients: 1.36 +/- 2.8 ml, -0.15 3.5 ml, 0.86 +/- 2.5%, and 0.91 +/- 0.9 g, respectively; P > or = 0.095). Intra- and interobserver variability was not different for 2D SSFP (P > or = 0.64 and P > or = 0.397) and 3D SSFP (P > or = 0.53 and P > or = 0.47). Differences in volumes, EF, and mass measurements between 3D SSFP and standard 2D SSFP are very small, and not statistically significant. 3D SSFP may be used for accurate ventricular function assessment when papillary muscles and trabeculations are to be taken into account.

  19. The Application of Next Generation Sequencing Technology on Noninvasive Prenatal Test

    DEFF Research Database (Denmark)

    Jiang, Hui

    There are nearly 7000 rare diseases that have been reported in the world. Although most of them occur with a frequency of less than one in 2000, in total about 6% of the population suffers from rare diseases. These rare diseases are often caused by changes in genes, which is currently lack of eff...... diseases and monogenetic diseases in a noninvasively manner. The new approach has great potential to be wildly used in the worldwide with the decreasing in sequencing costs, and therefore play an incredible role to prevent rare diseases....

  20. 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....

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Characterization of microflora in Latin-style cheeses by next-generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Lusk Tina S

    2012-11-01

    Full Text Available Abstract Background Cheese contamination can occur at numerous stages in the manufacturing process including the use of improperly pasteurized or raw milk. Of concern is the potential contamination by Listeria monocytogenes and other pathogenic bacteria that find the high moisture levels and moderate pH of popular Latin-style cheeses like queso fresco a hospitable environment. In the investigation of a foodborne outbreak, samples typically undergo enrichment in broth for 24 hours followed by selective agar plating to isolate bacterial colonies for confirmatory testing. The broth enrichment step may also enable background microflora to proliferate, which can confound subsequent analysis if not inhibited by effective broth or agar additives. We used 16S rRNA gene sequencing to provide a preliminary survey of bacterial species associated with three brands of Latin-style cheeses after 24-hour broth enrichment. Results Brand A showed a greater diversity than the other two cheese brands (Brands B and C at nearly every taxonomic level except phylum. Brand B showed the least diversity and was dominated by a single bacterial taxon, Exiguobacterium, not previously reported in cheese. This genus was also found in Brand C, although Lactococcus was prominent, an expected finding since this bacteria belongs to the group of lactic acid bacteria (LAB commonly found in fermented foods. Conclusions The contrasting diversity observed in Latin-style cheese was surprising, demonstrating that despite similarity of cheese type, raw materials and cheese making conditions appear to play a critical role in the microflora composition of the final product. The high bacterial diversity associated with Brand A suggests it may have been prepared with raw materials of high bacterial diversity or influenced by the ecology of the processing environment. Additionally, the presence of Exiguobacterium in high proportions (96% in Brand B and, to a lesser extent, Brand C (46%, may

  6. A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology.

    Science.gov (United States)

    Lucarelli, Marco; Porcaro, Luigi; Biffignandi, Alice; Costantino, Lucy; Giannone, Valentina; Alberti, Luisella; Bruno, Sabina Maria; Corbetta, Carlo; Torresani, Erminio; Colombo, Carla; Seia, Manuela

    2017-09-01

    Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we developed, validated, and tested a laboratory assay for an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population. Overall, 1426 dried blood spots from neonatal screening, 402 genomic DNA samples from various origins, and 1138 genomic DNA samples from patients with CF were analyzed. The assay showed excellent analytical and diagnostic operative characteristics. We identified and experimentally validated 159 (of 188) CFTR mutations. The assay achieved detection rates of 95.0% and 95.6% in two large-scale case series of CF patients from central and northern Italy, respectively. These detection rates are among the highest reported so far with a genetic test for CF based on a mutation panel. This assay appears to be well suited for diagnostics, neonatal and carrier screening, and assisted reproduction, and it represents a considerable advantage in CF genetic counseling. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  7. 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....

  8. 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...

  9. Investigating the mechanisms of glyphosate resistance in goosegrass (Eleusine indica (L.) Gaertn.) by RNA sequencing technology.

    Science.gov (United States)

    Chen, Jingchao; Huang, Hongjuan; Wei, Shouhui; Huang, Zhaofeng; Wang, Xu; Zhang, Chaoxian

    2017-01-01

    Glyphosate is an important non-selective herbicide that is in common use worldwide. However, evolved glyphosate-resistant (GR) weeds significantly affect crop yields. Unfortunately, the mechanisms underlying resistance in GR weeds, such as goosegrass (Eleusine indica (L.) Gaertn.), an annual weed found worldwide, have not been fully elucidated. In this study, transcriptome analysis was conducted to further assess the potential mechanisms of glyphosate resistance in goosegrass. The RNA sequencing libraries generated 24 597 462 clean reads. De novo assembly analysis produced 48 852 UniGenes with an average length of 847 bp. All UniGenes were annotated using seven databases. Sixteen candidate differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time PCR (qRT-PCR). Among these UniGenes, the EPSPS and PFK genes were constitutively up-regulated in resistant (R) individuals and showed a higher copy number than that in susceptible (S) individuals. The expressions of four UniGenes relevant to photosynthesis were inhibited by glyphosate in S individuals, and this toxic response was confirmed by gas exchange analysis. Two UniGenes annotated as glutathione transferase (GST) were constitutively up-regulated in R individuals, and were induced by glyphosate both in R and S. In addition, the GST activities in R individuals were higher than in S. Our research confirmed that two UniGenes (PFK, EPSPS) were strongly associated with target resistance, and two GST-annotated UniGenes may play a role in metabolic glyphosate resistance in goosegrass. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  10. 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.

  11. [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.

  12. 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.

  13. 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.

  14. 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

  15. In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip® technology

    Directory of Open Access Journals (Sweden)

    Ye Shui Q

    2005-05-01

    Full Text Available Abstract Background Genomic approaches in large animal models (canine, ovine etc are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis. Results Gene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A. Due to interspecies genetic differences, only 14 ± 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 ± 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip®. Conclusion The experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology.

  16. 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.

  17. 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

  18. Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies.

    Science.gov (United States)

    Goddard, Katrina A B; Whitlock, Evelyn P; Berg, Jonathan S; Williams, Marc S; Webber, Elizabeth M; Webster, Jennifer A; Lin, Jennifer S; Schrader, Kasmintan A; Campos-Outcalt, Doug; Offit, Kenneth; Feigelson, Heather Spencer; Hollombe, Celine

    2013-09-01

    The aim of this study was to develop, operationalize, and pilot test a transparent, reproducible, and evidence-informed method to determine when to report incidental findings from next-generation sequencing technologies. Using evidence-based principles, we proposed a three-stage process. Stage I "rules out" incidental findings below a minimal threshold of evidence and is evaluated using inter-rater agreement and comparison with an expert-based approach. Stage II documents criteria for clinical actionability using a standardized approach to allow experts to consistently consider and recommend whether results should be routinely reported (stage III). We used expert opinion to determine the face validity of stages II and III using three case studies. We evaluated the time and effort for stages I and II. For stage I, we assessed 99 conditions and found high inter-rater agreement (89%), and strong agreement with a separate expert-based method. Case studies for familial adenomatous polyposis, hereditary hemochromatosis, and α1-antitrypsin deficiency were all recommended for routine reporting as incidental findings. The method requires definition of clinically actionable incidental findings and provide documentation and pilot testing of a feasible method that is scalable to the whole genome.

  19. 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.

  20. 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.

  1. 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. ...

  2. 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.

  3. 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.

  4. 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...

  5. 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

  6. INNOVATION DEVELOPMENT MANAGEMENT IN VERTICALLY INTEGRATED HOLDING COMPANY

    Directory of Open Access Journals (Sweden)

    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. 

  7. 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...

  8. 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

  9. Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry.

    Science.gov (United States)

    Babrak, Lmar; McGarvey, Jeffery A; Stanker, Larry H; Hnasko, Robert

    2017-10-01

    Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibodies (rAb). This determination can be achieved by sequence analysis of immunoglobulin (Ig) transcripts obtained from a monoclonal antibody (MAb) producing hybridoma and subsequent expression of a rAb. However the polyploidy nature of a hybridoma cell often results in the added expression of aberrant immunoglobulin-like transcripts or even production of anomalous antibodies which can confound production of rAb. An incorrect VR sequence will result in a non-functional rAb and de novo assembly of Ig primary structure without a sequence map is challenging. To address these problems, we have developed a methodology which combines: 1) selective PCR amplification of VR from both the heavy and light chain IgG from hybridoma, 2) molecular cloning and DNA sequence analysis and 3) tandem mass spectrometry (MS/MS) on enzyme digests obtained from the purified IgG. Peptide analysis proceeds by evaluating coverage of the predicted primary protein sequence provided by the initial DNA maps for the VR. This methodology serves to both identify and verify the primary structure of the MAb VR for production as rAb. Published by Elsevier Ltd.

  10. A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology.

    Science.gov (United States)

    Kravatsky, Yuri; Chechetkin, Vladimir; Fedoseeva, Daria; Gorbacheva, Maria; Kravatskaya, Galina; Kretova, Olga; Tchurikov, Nickolai

    2017-11-23

    The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs), requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s). Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s). The suggested bioinformatic pipeline combines the available programs and the ad hoc scripts based on an original algorithm of the search for the conserved targets in the deep sequencing data. We also present the statistical criteria for the threshold of reliable mutation detection and for the assessment of variations between corresponding data sets. These criteria are robust against the possible sequencing errors in the reads. As an example, the bioinformatic pipeline is applied to the study of the conservation of RNA interference (RNAi) targets in human immunodeficiency virus 1 (HIV-1) subtype A. The developed pipeline is freely available to download at the website http://virmut.eimb.ru/. Brief comments and comparisons between VirMut and other pipelines are also presented.

  11. A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Yuri Kravatsky

    2017-11-01

    Full Text Available The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs, requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s. Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s. The suggested bioinformatic pipeline combines the available programs and the ad hoc scripts based on an original algorithm of the search for the conserved targets in the deep sequencing data. We also present the statistical criteria for the threshold of reliable mutation detection and for the assessment of variations between corresponding data sets. These criteria are robust against the possible sequencing errors in the reads. As an example, the bioinformatic pipeline is applied to the study of the conservation of RNA interference (RNAi targets in human immunodeficiency virus 1 (HIV-1 subtype A. The developed pipeline is freely available to download at the website http://virmut.eimb.ru/. Brief comments and comparisons between VirMut and other pipelines are also presented.

  12. High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology

    DEFF Research Database (Denmark)

    Nag, Sidsel; Dalgaard, Marlene Danner; Kofoed, Poul-Erik

    2017-01-01

    Genetic polymorphisms in P. falciparum can be used to indicate the parasite's susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom...... designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well...

  13. 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...

  14. 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.

  15. ALICE Holds Up to Challenge

    CERN Multimedia

    2006-01-01

    ALICE's main austenitic stainless steel support structure (the Space Frame) has recently gone through many tests that proved quite challenging: insuring the structure is sound and lowering it horizontally into the ALICE cavern. This structure is constructed to hold the large volume detectors, such as the Time Projection Chamber, Transition Radiation Detector and Time of Flight inside the ALICE solenoid magnet. After the final assembly at CERN, two large mobile cranes were needed for the job of lifting and turning the 14 tonne frame onto its side. Once shifted, it was placed in Building SX2, one of the surface assembly areas designated for ALICE. The structure, which is 8 m in diameter and 7 m long, underwent many tests in its new position. Geometric control tests were performed by measuring each of the 18 cells and placing wooden or metal samples constructed to the same dimensions as the real thing inside the structure. The most important check was the movement of the real Time Projection Chamber from its s...

  16. Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry

    Science.gov (United States)

    Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibo...

  17. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.

    Science.gov (United States)

    Chandrasekharappa, Settara C; Lach, Francis P; Kimble, Danielle C; Kamat, Aparna; Teer, Jamie K; Donovan, Frank X; Flynn, Elizabeth; Sen, Shurjo K; Thongthip, Supawat; Sanborn, Erica; Smogorzewska, Agata; Auerbach, Arleen D; Ostrander, Elaine A

    2013-05-30

    Current methods for detecting mutations in Fanconi anemia (FA)-suspected patients are inefficient and often miss mutations. We have applied recent advances in DNA sequencing and genomic capture to the diagnosis of FA. Specifically, we used custom molecular inversion probes or TruSeq-enrichment oligos to capture and sequence FA and related genes, including introns, from 27 samples from the International Fanconi Anemia Registry at The Rockefeller University. DNA sequencing was complemented with custom array comparative genomic hybridization (aCGH) and RNA sequencing (RNA-seq) analysis. aCGH identified deletions/duplications in 4 different FA genes. RNA-seq analysis revealed lack of allele specific expression associated with a deletion and splicing defects caused by missense, synonymous, and deep-in-intron variants. The combination of TruSeq-targeted capture, aCGH, and RNA-seq enabled us to identify the complementation group and biallelic germline mutations in all 27 families: FANCA (7), FANCB (3), FANCC (3), FANCD1 (1), FANCD2 (3), FANCF (2), FANCG (2), FANCI (1), FANCJ (2), and FANCL (3). FANCC mutations are often the cause of FA in patients of Ashkenazi Jewish (AJ) ancestry, and we identified 2 novel FANCC mutations in 2 patients of AJ ancestry. We describe here a strategy for efficient molecular diagnosis of FA.

  18. Learning with Technology: Video Modeling with Concrete-Representational-Abstract Sequencing for Students with Autism Spectrum Disorder

    Science.gov (United States)

    Yakubova, Gulnoza; Hughes, Elizabeth M.; Shinaberry, Megan

    2016-01-01

    The purpose of this study was to determine the effectiveness of a video modeling intervention with concrete-representational-abstract instructional sequence in teaching mathematics concepts to students with autism spectrum disorder (ASD). A multiple baseline across skills design of single-case experimental methodology was used to determine the…

  19. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

    Directory of Open Access Journals (Sweden)

    Chao Shiaoman

    2011-01-01

    Full Text Available Abstract Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM analysis. Of these, 52 (54% were polymorphic between parents of the Ogle1040 × TAM O-301 (OT mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide

  20. DSAP: deep-sequencing small RNA analysis pipeline.

    Science.gov (United States)

    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.

  1. 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

  2. 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

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

    OpenAIRE

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

    2012-01-01

    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, ...

  4. 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, ...

  5. Learning with Technology: Video Modeling with Concrete-Representational-Abstract Sequencing for Students with Autism Spectrum Disorder.

    Science.gov (United States)

    Yakubova, Gulnoza; Hughes, Elizabeth M; Shinaberry, Megan

    2016-07-01

    The purpose of this study was to determine the effectiveness of a video modeling intervention with concrete-representational-abstract instructional sequence in teaching mathematics concepts to students with autism spectrum disorder (ASD). A multiple baseline across skills design of single-case experimental methodology was used to determine the effectiveness of the intervention on the acquisition and maintenance of addition, subtraction, and number comparison skills for four elementary school students with ASD. Findings supported the effectiveness of the intervention in improving skill acquisition and maintenance at a 3-week follow-up. Implications for practice and future research are discussed.

  6. First study on gene expression of cement proteins and potential adhesion-related genes of a membranous-based barnacle as revealed from Next-Generation Sequencing technology

    KAUST Repository

    Lin, Hsiu Chin; Wong, Yue Him; Tsang, Ling Ming; Chu, Ka Hou; Qian, Pei Yuan; Chan, Benny K K

    2013-01-01

    This is the first study applying Next-Generation Sequencing (NGS) technology to survey the kinds, expression location, and pattern of adhesion-related genes in a membranous-based barnacle. A total of 77,528,326 and 59,244,468 raw sequence reads of total RNA were generated from the prosoma and the basis of Tetraclita japonica formosana, respectively. In addition, 55,441 and 67,774 genes were further assembled and analyzed. The combined sequence data from both body parts generates a total of 79,833 genes of which 47.7% were shared. Homologues of barnacle cement proteins - CP-19K, -52K, and -100K - were found and all were dominantly expressed at the basis where the cement gland complex is located. This is the main area where transcripts of cement proteins and other potential adhesion-related genes were detected. The absence of another common barnacle cement protein, CP-20K, in the adult transcriptome suggested a possible life-stage restricted gene function and/or a different mechanism in adhesion between membranous-based and calcareous-based barnacles. © 2013 © 2013 Taylor & Francis.

  7. First study on gene expression of cement proteins and potential adhesion-related genes of a membranous-based barnacle as revealed from Next-Generation Sequencing technology

    KAUST Repository

    Lin, Hsiu Chin

    2013-12-12

    This is the first study applying Next-Generation Sequencing (NGS) technology to survey the kinds, expression location, and pattern of adhesion-related genes in a membranous-based barnacle. A total of 77,528,326 and 59,244,468 raw sequence reads of total RNA were generated from the prosoma and the basis of Tetraclita japonica formosana, respectively. In addition, 55,441 and 67,774 genes were further assembled and analyzed. The combined sequence data from both body parts generates a total of 79,833 genes of which 47.7% were shared. Homologues of barnacle cement proteins - CP-19K, -52K, and -100K - were found and all were dominantly expressed at the basis where the cement gland complex is located. This is the main area where transcripts of cement proteins and other potential adhesion-related genes were detected. The absence of another common barnacle cement protein, CP-20K, in the adult transcriptome suggested a possible life-stage restricted gene function and/or a different mechanism in adhesion between membranous-based and calcareous-based barnacles. © 2013 © 2013 Taylor & Francis.

  8. The usefulness of DNA sequencing after extraction by Whatman FTA filter matrix technology and phenotypic tests for differentiation of Candida albicans and Candida dubliniensis.

    Science.gov (United States)

    Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Muslumanoglu, Hamza

    2014-02-01

    Since C. dubliniensis is similar to C. albicans phenotypically, it can be misidentified as C. albicans. We aimed to investigate the prevalence of C. dubliniensis among isolates previously identified as C. albicans in our stocks and to compare the phenotypic methods and DNA sequencing of D1/D2 region on the ribosomal large subunit (rLSU) gene. A total of 850 isolates included in this study. Phenotypic identification was performed based on germ tube formation, chlamydospore production, colony colors on chromogenic agar, inability of growth at 45 °C and growth on hypertonic Sabouraud dextrose agar. Eighty isolates compatible with C. dubliniensis by at least one phenotypic test were included in the sequence analysis. Nested PCR amplification of D1/D2 region of the rLSU gene was performed after the fungal DNA extraction by Whatman FTA filter paper technology. The sequencing analysis of PCR products carried out by an automated capillary gel electrophoresis device. The rate of C. dubliniensis was 2.35 % (n = 20) among isolates previously described as C. albicans. Consequently, none of the phenotypic tests provided satisfactory performance alone in our study, and molecular methods required special equipment and high cost. Thus, at least two phenotypic methods can be used for identification of C. dubliniensis, and molecular methods can be used for confirmation.

  9. 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.

  10. Identification and Characterization of Epstein-Barr Virus Genomes in Lung Carcinoma Biopsy Samples by Next-Generation Sequencing Technology.

    Science.gov (United States)

    Wang, Shanshan; Xiong, Hongchao; Yan, Shi; Wu, Nan; Lu, Zheming

    2016-05-18

    Epstein-Barr virus (EBV) has been detected in the tumor cells of several cancers, including some cases of lung carcinoma (LC). However, the genomic characteristics and diversity of EBV strains associated with LC are poorly understood. In this study, we sequenced the EBV genomes isolated from four primary LC tumor biopsy samples, designated LC1 to LC4. Comparative analysis demonstrated that LC strains were more closely related to GD1 strain. Compared to GD1 reference genome, a total of 520 variations in all, including 498 substitutions, 12 insertions, and 10 deletions were found. Latent genes were found to harbor the most numbers of nonsynonymous mutations. Phylogenetic analysis showed that all LC strains were closely related to Asian EBV strains, whereas different from African/American strains. LC2 genome was distinct from the other three LC genomes, suggesting at least two parental lineages of EBV among the LC genomes may exist. All LC strains could be classified as China 1 and V-val subtype according to the amino acid sequence of LMP1 and EBNA1, respectively. In conclusion, our results showed the genomic diversity among EBV genomes isolated from LC, which might facilitate to uncover the previously unknown variations of pathogenic significance.

  11. Existing and emerging detection technologies for DNA (Deoxyribonucleic Acid) finger printing, sequencing, bio- and analytical chips: a multidisciplinary development unifying molecular biology, chemical and electronics engineering.

    Science.gov (United States)

    Kumar Khanna, Vinod

    2007-01-01

    The current status and research trends of detection techniques for DNA-based analysis such as DNA finger printing, sequencing, biochips and allied fields are examined. An overview of main detectors is presented vis-à-vis these DNA operations. The biochip method is explained, the role of micro- and nanoelectronic technologies in biochip realization is highlighted, various optical and electrical detection principles employed in biochips are indicated, and the operational mechanisms of these detection devices are described. Although a diversity of biochips for diagnostic and therapeutic applications has been demonstrated in research laboratories worldwide, only some of these chips have entered the clinical market, and more chips are awaiting commercialization. The necessity of tagging is eliminated in refractive-index change based devices, but the basic flaw of indirect nature of most detection methodologies can only be overcome by generic and/or reagentless DNA sensors such as the conductance-based approach and the DNA-single electron transistor (DNA-SET) structure. Devices of the electrical detection-based category are expected to pave the pathway for the next-generation DNA chips. The review provides a comprehensive coverage of the detection technologies for DNA finger printing, sequencing and related techniques, encompassing a variety of methods from the primitive art to the state-of-the-art scenario as well as promising methods for the future.

  12. 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 ...

  13. Can OPEC hold it together?

    International Nuclear Information System (INIS)

    Lauerman, V.

    2002-01-01

    This presentation described the status of OPEC and whether it can continue to operate under the current economic situation. OPEC is the most successful commodity cartel in history, but the author cautions that it is only a matter of time before it self destructs. OPEC has not served the interest of Saudi Arabia in the past and it will not be able to serve its interest in the future without strong incremental demand for OPEC oil. The author stated that OPEC is threatened by Islamic fundamentalists and by financial difficulty due to a decline in export revenues. Other threats for OPEC are environmental, strategic and technological. The author concluded that Saudi Arabia is likely to choose to abandon OPEC, because the cartel will continue to be at the mercy of world oil demand and non-OPEC supply. 19 figs

  14. 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.

  15. 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.

  16. 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.

  17. Development and characterization of 26 novel microsatellite loci for the trochid gastropod Gibbula divaricata (Linnaeus, 1758, using Illumina MiSeq next generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Violeta López-Márquez

    2016-03-01

    Full Text Available In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snail Gibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genus Gibbula, as G. rarilineata and G. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found.

  18. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

    Science.gov (United States)

    Borsu, Laetitia; Intrieri, Julie; Thampi, Linta; Yu, Helena; Riely, Gregory; Nafa, Khedoudja; Chandramohan, Raghu; Ladanyi, Marc; Arcila, Maria E

    2016-11-01

    Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  19. 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.)

  20. 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

  1. 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...

  2. 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...

  3. De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNA-Seq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana.

    Science.gov (United States)

    Castellanos-Martínez, Sheila; Arteta, David; Catarino, Susana; Gestal, Camino

    2014-01-01

    Octopus vulgaris is a highly valuable species of great commercial interest and excellent candidate for aquaculture diversification; however, the octopus' well-being is impaired by pathogens, of which the gastrointestinal coccidian parasite Aggregata octopiana is one of the most important. The knowledge of the molecular mechanisms of the immune response in cephalopods, especially in octopus is scarce. The transcriptome of the hemocytes of O. vulgaris was de novo sequenced using the high-throughput paired-end Illumina technology to identify genes involved in immune defense and to understand the molecular basis of octopus tolerance/resistance to coccidiosis. A bi-directional mRNA library was constructed from hemocytes of two groups of octopus according to the infection by A. octopiana, sick octopus, suffering coccidiosis, and healthy octopus, and reads were de novo assembled together. The differential expression of transcripts was analysed using the general assembly as a reference for mapping the reads from each condition. After sequencing, a total of 75,571,280 high quality reads were obtained from the sick octopus group and 74,731,646 from the healthy group. The general transcriptome of the O. vulgaris hemocytes was assembled in 254,506 contigs. A total of 48,225 contigs were successfully identified, and 538 transcripts exhibited differential expression between groups of infection. The general transcriptome revealed genes involved in pathways like NF-kB, TLR and Complement. Differential expression of TLR-2, PGRP, C1q and PRDX genes due to infection was validated using RT-qPCR. In sick octopuses, only TLR-2 was up-regulated in hemocytes, but all of them were up-regulated in caecum and gills. The transcriptome reported here de novo establishes the first molecular clues to understand how the octopus immune system works and interacts with a highly pathogenic coccidian. The data provided here will contribute to identification of biomarkers for octopus resistance against

  4. 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...

  5. 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...

  6. 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

  7. 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.…

  8. 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 ...

  9. 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.

  10. 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.

  11. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  13. 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.

  14. Technology.

    Science.gov (United States)

    Online-Offline, 1998

    1998-01-01

    Focuses on technology, on advances in such areas as aeronautics, electronics, physics, the space sciences, as well as computers and the attendant progress in medicine, robotics, and artificial intelligence. Describes educational resources for elementary and middle school students, including Web sites, CD-ROMs and software, videotapes, books,…

  15. 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...

  16. 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...

  17. 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...

  18. 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....

  19. 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...

  20. 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.

  1. Saskatchewan Energy Holdings Ltd. consolidated financial statements

    Energy Technology Data Exchange (ETDEWEB)

    1991-01-01

    The consolidated financial statements of Saskatchewan Energy Holdings Ltd. (formerly Saskatchewan Energy Corporation) as of December 31, 1990, and the consolidated statements of earnings and retained earnings and changes in cash position for the year are presented. Data include an inventory of supplies, natural gas in storage, property, plant and equipment. Financial statements are also presented for the year ending December 31, 1989, with comparative figures for the seven months ending December 31, 1988.

  2. Saskatchewan Energy Holdings Ltd. consolidated financial statements

    International Nuclear Information System (INIS)

    1991-01-01

    The consolidated financial statements of Saskatchewan Energy Holdings Ltd. (formerly Saskatchewan Energy Corporation) as of December 31, 1990, and the consolidated statements of earnings and retained earnings and changes in cash position for the year are presented. Data include an inventory of supplies, natural gas in storage, property, plant and equipment. Financial statements are also presented for the year ending December 31, 1989, with comparative figures for the seven months ending December 31, 1988

  3. 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...

  4. 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...

  5. Technology

    Directory of Open Access Journals (Sweden)

    Xu Jing

    2016-01-01

    Full Text Available The traditional answer card reading method using OMR (Optical Mark Reader, most commonly, OMR special card special use, less versatile, high cost, aiming at the existing problems proposed a method based on pattern recognition of the answer card identification method. Using the method based on Line Segment Detector to detect the tilt of the image, the existence of tilt image rotation correction, and eventually achieve positioning and detection of answers to the answer sheet .Pattern recognition technology for automatic reading, high accuracy, detect faster

  6. 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.

  7. A mathematical model of aerosol holding chambers

    DEFF Research Database (Denmark)

    Zak, M; Madsen, J; Berg, E

    1999-01-01

    A mathematical model of aerosol delivery from holding chambers (spacers) was developed incorporating tidal volume (VT), chamber volume (Vch), apparatus dead space (VD), effect of valve insufficiency and other leaks, loss of aerosol by immediate impact on the chamber wall, and fallout of aerosol...... in the chamber with time. Four different spacers were connected via filters to a mechanical lung model, and aerosol delivery during "breathing" was determined from drug recovery from the filters. The formula correctly predicted the delivery of budesonide aerosol from the AeroChamber (Trudell Medical, London...

  8. 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

  9. Hold-down device for nuclear reactor

    International Nuclear Information System (INIS)

    Leclercq, J.; Bonnamour, M.

    1984-01-01

    The present device can be used in nuclear reactors and more particularly in pressurized water reactors consisting of coupled fuel assemblies, certain of which are equipped with non-displaceable elements carried by an unsertable member. The device comprises the unsertable member provided with at least two sets of springs which transmit the load of an upper structure common to the fuel assemblies ajacent that which supports the unsertable member. The device is used to hold-down fuel assemblies which are subjected to the forces of circulating coolant [fr

  10. 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

  11. MIM Holdings Limited 1984 annual report

    Energy Technology Data Exchange (ETDEWEB)

    1984-01-01

    M.I.M. Holdings Limited is a major mining and mineral processing company formed in 1970. The group traces its origins to 1924 following the discovery of silver lead zinc started in 1931 and parallel production of silver lead zinc ore at Mount Isa the previous year. Today the MIM group is a diversified mineral, coal and metal producing and marketing organisation. Details of the company's principal activities over the last year, and accounts and management information for the last year are presented.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

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

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

    Science.gov (United States)

    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.

  15. 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.

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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

  1. 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...

  2. "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…

  3. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

  5. Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

    Directory of Open Access Journals (Sweden)

    Rodrigo Pessôa

    Full Text Available BACKGROUND: Here, we report on the partial and full-length genomic (FLG variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs, 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP and 7 adult T-cell leukemia/lymphoma (ATLL patients, using an Illumina paired-end protocol. METHODS: Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. RESULTS: A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14 and FLG (n = 76 data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5% individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA and that 4 individuals (4.5% were infected with the Japanese sub-subtypes (aB. A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. CONCLUSIONS: This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data

  6. Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

    Science.gov (United States)

    Pessôa, Rodrigo; Watanabe, Jaqueline Tomoko; Nukui, Youko; Pereira, Juliana; Casseb, Jorge; Kasseb, Jorge; de Oliveira, Augusto César Penalva; Segurado, Aluisio Cotrim; Sanabani, Sabri Saeed

    2014-01-01

    Here, we report on the partial and full-length genomic (FLG) variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs), 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and 7 adult T-cell leukemia/lymphoma (ATLL) patients, using an Illumina paired-end protocol. Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14) and FLG (n = 76) data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5%) individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA) and that 4 individuals (4.5%) were infected with the Japanese sub-subtypes (aB). A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data will add to our current understanding of the

  7. 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

  8. Simultaneous discrimination of species and strains in Lactobacillus rhamnosus using species-specific PCR combined with multiplex mini-sequencing technology.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Lina; Chu, Wen-Shen

    2015-12-01

    This study described the use of species-specific PCR in combination with SNaPshot mini-sequencing to achieve species identification and strain differentiation in Lactobacillus rhamnosus. To develop species-specific PCR and strain subtyping primers, the dnaJ gene was used as a target, and its corresponding sequences were analyzed both in Lb. rhamnosus and in a subset of its phylogenetically closest species. The results indicated that the species-specific primer pair was indeed specific for Lb. rhamnosus, and the mini-sequencing assay was able to unambiguously distinguish Lb. rhamnosus strains into different haplotypes. In conclusion, we have successfully developed a rapid, accurate and cost-effective assay for inter- and intraspecies discrimination of Lb. rhamnosus, which can be applied to achieve efficient quality control of probiotic products. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. 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...

  10. 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.

  11. 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

  12. On statistical acceleration convergence of double sequences

    Directory of Open Access Journals (Sweden)

    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.

  13. 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…

  14. Holding the Competitive Edge Through Outsourcing

    DEFF Research Database (Denmark)

    Svensson, Carsten; Christensen, Henrik Bjørn

    2002-01-01

    Outsourcing - once considered a defensive tool for cost reduction - has proven to be an effective acquisition tool enabling aggressive technology development, A multi case study in 7 Danish machinery equipment manufacture illustrate a number of similar issues/challengers in their development e...

  15. 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....

  16. 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.

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. 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...

  2. 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.

  3. 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.

  4. 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

  5. Recent Ground Hold and Rapid Depressurization Testing of Multilayer Systems

    Science.gov (United States)

    Johnson, Wesley L.

    2014-01-01

    In the development of flight insulation systems for large cryogenic orbital storage (spray on foam and multilayer insulation), testing need include all environments that are experienced during flight. While large efforts have been expended on studying, bounding, and modeling the orbital performance of the insulation systems, little effort has been expended on the ground hold and ascent phases of a mission. Historical cryogenic in-space systems that have flown have been able to ignore these phases of flight due to the insulation system being within a vacuum jacket. In the development phase of the Nuclear Mars Vehicle and the Shuttle Nuclear Vehicle, several insulation systems were evaluated for the full mission cycle. Since that time there had been minimal work on these phases of flight until the Constellation program began investigating cryogenic service modules and long duration upper stages. With the inception of the Cryogenic Propellant Storage and Transfer Technology Demonstration Mission, a specific need was seen for the data and as such, several tests were added to the Cryogenic Boil-off Reduction System liquid hydrogen test matrix to provide more data on a insulation system. Testing was attempted with both gaseous nitrogen (GN2) and gaseous helium (GHe) backfills. The initial tests with nitrogen backfill were not successfully completed due to nitrogen liquefaction and solidification preventing the rapid pumpdown of the vacuum chamber. Subsequent helium backfill tests were successful and showed minimal degradation. The results are compared to the historical data.

  6. Development of severe accident evaluation technology (level 2 PSA) for sodium-cooled fast reactors. (5) Identification of dominant factors in ex-vessel accident sequences

    International Nuclear Information System (INIS)

    Ohno, Shuji; Seino, Hiroshi; Miyahara, Shinya

    2009-01-01

    The evaluation of accident progression outside of a reactor vessel (ex-vessel) and subsequent transfer behavior of radioactive materials is of great importance from the viewpoint of Level 2 PSA. Hence typical ex-vessel accident sequences in the JAEA Sodium-cooled Fast Reactor are qualitatively discussed in this paper and dominant behaviors or factors in the sequences are investigated through parametric calculations using the CONTAIN/LMR code. Scenarios to be focused on are, 1) sodium vapor leakage from the reactor vessel and 2) sodium-concrete reaction, which are both to be considered in the accident category of LOHRS (loss of heat removal system) and might be followed by an early containment failure due to the thermal effect of sodium combustion and hydrogen burning respectively. The calculated results clarify that the sodium vapor leak rate and the scale of sodium-concrete reaction are the important factors to dominate the ex-vessel accident progression. In addition to the understandings of the dominant factors, the analyzed results also provide the specific information such as pressure loading value to the containment and the timing of pressurization, which is indispensable as technical base in Level 2 PSA for developing event trees and for quantifying the accident consequences. (author)

  7. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology.

    Science.gov (United States)

    Yi, Liuxi; Gao, Fengyun; Siqin, Bateer; Zhou, Yu; Li, Qiang; Zhao, Xiaoqing; Jia, Xiaoyun; Zhang, Hui

    2017-01-01

    Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.

  8. 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...

  9. 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...

  10. 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

  11. 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...

  12. 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.

  13. 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 ...

  14. 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...

  15. 基于二次参数化技术的风电机组序列化建模%Wind turbine sequence modeling based on secondary parametric technology

    Institute of Scientific and Technical Information of China (English)

    高青风; 孙振兴; 滕伟; 柳亦兵

    2012-01-01

    针对常规建模方法在庞大复杂风电机组应用上的不足,在建立单台风电机组全参数化模型的基础上,以风电机组序列整体为研究对象,根据同序列不同功率机组之间各零部件设计参数变化规律,研究应用二次参数化技术和参数序列化方法实现了高效的风电机组模型建立与管理;并结合三维模型参数驱动技术,研发了风电机组序列建模系统,可有效减少建模和造型工作量、降低设计失误率、提高设计效率,验证了该建模方法的正确性与合理性.%According to the disadvantages of conventional modeling methods for large and complex wind turbines, a highly efficient modeling method is proposed in this paper. Based on a fully parametric model of a single wind turbine, it took the whole sequence of wind turbines as the research object, and realized the fast modeling via secondary parametric technology according to the change law of design parameters of different wind turbines in the same sequence. A sequence modeling system for wind turbines was also developed by combining with parameter-driven modeling technology. The system can effectively reduce the workload and design error rate, improve design efficiency, and prove the correctness and rationality of the modeling method.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. Next-generation sequencing technology a new tool for killer cell immunoglobulin-like receptor allele typing in hematopoietic stem cell transplantation.

    Science.gov (United States)

    Maniangou, B; Retière, C; Gagne, K

    2018-02-01

    Killer cell Immunoglobulin-like Receptor (KIR) genes are a family of genes located together within the leukocyte receptor cluster on human chromosome 19q13.4. To date, 17 KIR genes have been identified including nine inhibitory genes (2DL1/L2/L3/L4/L5A/L5B, 3DL1/L2/L3), six activating genes (2DS1/S2/S3/S4/S5, 3DS1) and two pseudogenes (2DP1, 3DP1) classified into group A (KIR A) and group B (KIR B) haplotypes. The number and the nature of KIR genes vary between the individuals. In addition, these KIR genes are known to be polymorphic at allelic level (907 alleles described in July 2017). KIR genes encode for receptors which are predominantly expressed by Natural Killer (NK) cells. KIR receptors recognize HLA class I molecules and are able to kill residual recipient leukemia cells, and thus reduce the likelihood of relapse. KIR alleles of Hematopoietic Stem Cell (HSC) donor would require to be known (Alicata et al. Eur J Immunol 2016) because the KIR allele polymorphism may affect both the KIR + NK cell phenotype and function (Gagne et al. Eur J Immunol 2013; Bari R, et al. Sci Rep 2016) as well as HSCT outcome (Boudreau et al. JCO 2017). The introduction of the Next Generation Sequencing (NGS) has overcome current conventional DNA sequencing method limitations, known to be time consuming. Recently, a novel NGS KIR allele typing approach of all KIR genes was developed by our team in Nantes from 30 reference DNAs (Maniangou et al. Front in Immunol 2017). This NGS KIR allele typing approach is simple, fast, reliable, specific and showed a concordance rate of 95% for centromeric and telomeric KIR genes in comparison with high-resolution KIR typing obtained to those published data using exome capture (Norman PJ et al. Am J Hum Genet 2016). This NGS KIR allele typing approach may also be used in reproduction and to better study KIR + NK cell implication in the control of viral infections. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  2. Inhibition of expression in Escherichia coli of a virulence regulator MglB of Francisella tularensis using external guide sequence technology.

    Directory of Open Access Journals (Sweden)

    Gaoping Xiao

    Full Text Available External guide sequences (EGSs have successfully been used to inhibit expression of target genes at the post-transcriptional level in both prokaryotes and eukaryotes. We previously reported that EGS accessible and cleavable sites in the target RNAs can rapidly be identified by screening random EGS (rEGS libraries. Here the method of screening rEGS libraries and a partial RNase T1 digestion assay were used to identify sites accessible to EGSs in the mRNA of a global virulence regulator MglB from Francisella tularensis, a Gram-negative pathogenic bacterium. Specific EGSs were subsequently designed and their activities in terms of the cleavage of mglB mRNA by RNase P were tested in vitro and in vivo. EGS73, EGS148, and EGS155 in both stem and M1 EGS constructs induced mglB mRNA cleavage in vitro. Expression of stem EGS73 and EGS155 in Escherichia coli resulted in significant reduction of the mglB mRNA level coded for the F. tularensis mglB gene inserted in those cells.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. Water holding capacity of meat from rabbits (Belgian Giant breed

    Directory of Open Access Journals (Sweden)

    Gabriela Tărnăuceanu Frunză

    2016-03-01

    Full Text Available Abstract. Meat science has always been most interested in practical applications and macroscopic effects of internal/external factors in relation to water holding capacity (WHC. Research has been motivated by technological and sensory aspects, both finally linked to economic benefits. The objective of this study was to assess the effects of gender and different muscle groups from rabbits on WHC of their meat. Determining WHC was carried out by compression of the meat over filter paper between two plates. The biological material was collected from 56 Belgian Giant breed rabbits (25 males and 31 females. Aged 11-12 months, the rabbits had an average body weight of 11.5 kg. Measurements were performed on the muscles Longissimus dorsi (LD, Psoas major (PM and Semimembranosus (SM 24 hours after slaughter. The percentage of WHC was calculated as ratio (per cent of weight of released water to intact meat. WHC for females, in LD, had an average value of 8%, in PM it had an average value of 9.31%, and in SM it had an average value of 12.91%. For males, WHC in LD was 7.6%, in PM 8.23% and in SM 11.43%. The average value for WHC was higher for females than for males. Regarding the statistical significance of differences by gender, distinct significant differences for SM and very significant differences for PM were recorded. For PM, a higher average value of WHC is probably due to the smaller diameter of muscle fibres and also to water higher percentage of them.

  5. 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)

  6. 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...

  7. 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...

  8. 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...

  9. 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.

  10. 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

  11. Rock Equity Holdings, LLC - Clean Water Act Public Notice

    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

  12. 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.

  13. 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.

  14. 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.

  15. 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....

  16. 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...

  17. 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

  18. 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-...

  19. High Density Linkage Map Construction and Mapping of Yield Trait QTLs in Maize (Zea mays) Using the Genotyping-by-Sequencing (GBS) Technology

    Science.gov (United States)

    Su, Chengfu; Wang, Wei; Gong, Shunliang; Zuo, Jinghui; Li, Shujiang; Xu, Shizhong

    2017-01-01

    Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and

  20. 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. 

  1. 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.

  2. 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.)

  3. 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)

  4. 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...

  5. 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...

  6. 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...

  7. 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 ...

  8. 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...

  9. 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...

  10. 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...

  11. 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)

  12. 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.

  13. 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.

  14. 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.

  15. 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.)

  16. 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.

  17. A Ship Cargo Hold Inspection Approach Using Laser Vision Systems

    OpenAIRE

    SHEN Yang; ZHAO Ning; LIU Haiwei; MI Chao

    2013-01-01

    Our paper represents a vision system based on the laser measurement system (LMS) for bulk ship inspection. The LMS scanner with 2-axis servo system is installed on the ship loader to build the shape of the ship. Then, a group of real-time image processing algorithms are implemented to compute the shape of the cargo hold, the inclination angle of the ship and the relative position between the ship loader and the cargo hold. Based on those computed inspection data of the ship, the ship loader c...

  18. 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.

  19. The Effect of Holding a Research Chair on Scientists’ Impact

    Energy Technology Data Exchange (ETDEWEB)

    Mirnezami, S.R.; Beaudry, C.

    2016-07-01

    This paper examines the effect of holding Canada Research Chair (CRC) on a scientist’s number of citations as a measure of research impact, based on an econometric analysis with combined data on Quebec scientists’ funding and journal publication. Using Generalized Least Square (GLS) method for regression analysis, the results show that holding either tier-1 or tier- 2 of CRC significantly and positively results in conducting research with higher impact. This finding, however, does not necessarily imply that the others are the lesser scientists. (Author)

  20. 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.

  1. 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.

  2. 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. [...

  3. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  4. 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...

  5. Astronaut Dale Gardner holds up for sale sign after EVA

    Science.gov (United States)

    1984-01-01

    Astronaut Dale A. Gardner, having just completed the major portion of his second extravehicular activity (EVA) period in three days, holds up a 'for sale' sign. Astronaut Joseph P. ALlen IV, who also participated in the two EVA's, is reflected in Gardner's helmet visor. A portion of each of two recovered satellites is in the lower right corner, with Westar nearer Discovery's aft.

  6. 31 CFR 346.5 - Limitation on holdings.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false Limitation on holdings. 346.5 Section 346.5 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) FISCAL SERVICE... deducted in any one year be in equal amounts. While it is permissible for an eligible married couple to...

  7. Physiological alterations in UV-irradiated cells: liquid holding recovery

    International Nuclear Information System (INIS)

    Aragao, B.R.

    1980-01-01

    The biochemical and physiological alterations that occur in ultraviolet irradiated cells, during liquid holding have been studied. Incubation in buffer acts not to interfer directly with the mechanic repairs but by promoting metabolic alterations that would block some irreversible and lethal physiological responses. (L.M.J.) [pt

  8. 26 CFR 1.543-1 - Personal holding company income.

    Science.gov (United States)

    2010-04-01

    ..., franchises, and other like property. It does not, however, include rents. For rules relating to rents see... from futures transactions in commodities. Gross income and personal holding company income include the amount by which the gains exceed the losses from futures transactions in any commodity on or subject to...

  9. Water holding capacity and enzymatic modification of pressed potato fibres

    NARCIS (Netherlands)

    Ramasamy, U.

    2014-01-01

    Cell wall polysaccharides (CWPs) contribute to the water holding capacity (WHC) of fibre rich feeds, such as pressed potato fibres (PPF). However, the role of CWPs on the WHC of PPF was unidentified so far.

    PPF was characterized to be abundant in arabinogalactan (AG) linked

  10. Implementing the South African water policy: holding the vision ...

    African Journals Online (AJOL)

    Implementing the South African water policy: holding the vision while exploring an uncharted mountain. HM MacKay, KH Rogers, DJ Roux. Abstract. This paper discusses the long-term implementation of the South African National Water Policy of 1997, and addresses some of the difficult issues of the management and ...

  11. Carbon Dioxide Changes in Hyperventilation and Breath-hold Diving

    African Journals Online (AJOL)

    1974-01-05

    Jan 5, 1974 ... South Africa. S. Afr. Med. l., 48, 18 (1974). Under conditions of normal atmospheric pressure, breath- holding results in important changes in the mechanism whereby the CO, is transported ... haemoglobin in the face of falling CO, output to the ... Hong,' in a field study of Korean diving women, noted that they ...

  12. Swiveling Lathe Jaw Concept for Holding Irregular Pieces

    Science.gov (United States)

    David, J.

    1966-01-01

    Clamp holds irregularly shaped pieces in lathe chuck without damage and eliminates excessive time in selecting optimum mounting. Interchangeable jaws ride in standard jaw slots but swivel so that the jaw face bears evenly against the workpiece regardless of contour. The jaws can be used on both engine and turret lathes.

  13. Sample-hold and analog multiplexer for multidetector systems

    Energy Technology Data Exchange (ETDEWEB)

    Goswami, G C; Ghoshdostidar, M R; Ghosh, B; Chaudhuri, N [North Bengal Univ., Darjeeling (India). Dept. of Physics

    1982-08-15

    A new sample-hold circuit with an analog multiplexer system is described. Designed for multichannel acquistion of data from an air shower array, the system is being used for accurate measurements of pulse heights from 16 channels by the use of a single ADC.

  14. OFFSHORIZATION AS MAIN PROBLEM OF HOLDING GROUPS TAXATION

    Directory of Open Access Journals (Sweden)

    Y. Petlenko

    2016-01-01

    Full Text Available At this article, we have analyzed and systematized the conditions of holdings' activity to reduce the taxation level in countries and on the territory of special, so-called offshore, jurisdiction. In addition, we have made a suggestionhow to regulatean offshore capital flows inorder to prevent from tax frauds.

  15. 17 CFR 450.4 - Custodial holdings of government securities.

    Science.gov (United States)

    2010-04-01

    ... securities as of the close of business upon the instruction of such broker or dealer, it shall send a... depository institution's control or direction that are not in its physical possession, where the securities... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Custodial holdings of...

  16. Holding device for gas-cooled reactor fuel elements

    International Nuclear Information System (INIS)

    Hensolt, T.

    1980-01-01

    The sheathed fuel elements of the GCFR are inserted with their pedestal in a grid plate arranged below the reactor core and are clamped there. The clamping force as well as the force required for hydraulic holding-down against the flow pressure of the coolant are applied through the differential pressure between inlet and outlet of the coolant. (DG) [de

  17. farm size holding in northern nigeria: a remote sensing assessment ...

    African Journals Online (AJOL)

    currys

    2014-04-02

    Apr 2, 2014 ... FARM HOLDINGS IN NORTHERN NIGERIA AND IMPLICATION FOR. FOOD SECURITY: A ... about 80.0% of the export earnings in Sub-Saharan Africa. It is the source of .... They rear herds of goats, cattle, donkeys and ...

  18. Voluntary breath holding affects spontaneous brain activity measured by magnetoencephalography

    NARCIS (Netherlands)

    Schellart, N. A.; Reits, D.

    1999-01-01

    Spontaneous brain activity was measured by multichannel magnetoencephalography (MEG) during voluntary breath holds. Significant changes in the activity are limited to the alpha rhythm: 0.25 Hz frequency increase and narrowing of the peak. The area of alpha activity shifts slightly toward (fronto-)

  19. 31 CFR 223.16 - List of certificate holding companies.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false List of certificate holding companies. 223.16 Section 223.16 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) FISCAL SERVICE, DEPARTMENT OF THE TREASURY FINANCIAL MANAGEMENT SERVICE SURETY COMPANIES DOING BUSINESS...

  20. 77 FR 32881 - Supervised Securities Holding Company Registration

    Science.gov (United States)

    2012-06-04

    ...), The Report of Foreign Banking Organizations (FR Y-7), The Consolidated Financial Statements for Bank... Y-9ES), The Supplement to the Consolidated Financial Statements for Bank Holding Companies (FR Y-9CS... comprehensive consolidated supervision by a foreign regulator, a nonbank financial company supervised by the...

  1. The myth of the early aviation patent hold-up

    DEFF Research Database (Denmark)

    Katznelson, Ron D; Howells, John

    2015-01-01

    The prevailing historical accounts of the formation of the U.S. aircraft “patent pool” in 1917 assume the U.S. Government necessarily intervened to alleviate a patent hold-up among private aircraft manufacturers. We show these accounts to be inconsistent with the historical facts. We show that de...

  2. 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...

  3. 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.

  4. 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...

  5. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  7. 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.

  8. 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.

  9. 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...

  10. 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...

  11. 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...

  12. Emulsifying salt increase stability of cheese emulsions during holding

    DEFF Research Database (Denmark)

    Hougaard, Anni Bygvrå; Sijbrandij, Anna G.; Varming, Camilla

    2015-01-01

    In cheese powder production, cheese is mixed and melted with water and emulsifying salt to form an emulsion (cheese feed) which is required to remain stable at 60°C for 1h and during further processing until spray drying. Addition of emulsifying salts ensures this, but recent demands for reduction...... of sodium and phosphate in foods makes production of cheese powder without or with minimal amounts of emulsifying salts desirable. The present work uses a centrifugation method to characterize stability of model cheese feeds. Stability of cheese feed with emulsifying salt increased with holding time at 60°C......, especially when no stirring was applied. No change in stability during holding was observed in cheese feeds without emulsifying salt. This effect is suggested to be due to continued exerted functionality of the emulsifying salt, possibly through reorganizations of the mineral balance....

  13. 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.

  14. 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.

  15. 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...

  16. Corporate cash holdings: Determinants and implications from Vietnamese market

    OpenAIRE

    Cap, Kim Hoang

    2014-01-01

    2014 dissertation for MSc in International Accounting and Finance. Selected by academic staff as a good example of a masters level dissertation. This paper investigates the determination of corporate cash holdings in Vietnam. The sample includes Vietnamese publicly-traded firms for the period 2010-2013. Determinants include financial indicators as firm-specific characteristics and state ownership as an institutional factor for the purpose of exploring the existence of agency costs for this em...

  17. How Seniors Change Their Asset Holdings During Retirement

    OpenAIRE

    Karen Smith; Mauricio Soto; Rudolph G. Penner

    2009-01-01

    We use the 1998-2006 waves of the Health and Retirement Study (HRS) to investigate how households change their asset holdings at older ages. We find a notable increase in the net worth of older households between 1998 and 2006, with most of the growth due to housing. Our results indicate that, through 2006, older households did not spend all of their capital gains. This asset accumulation provides older households with a financial cushion for the turbulence experienced after 2007. The wealth ...

  18. 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

  19. 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

  20. 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.

  1. 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.)

  2. 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

  3. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  4. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  5. Developing drug formularies for the "National Medical Holding" JSC.

    Science.gov (United States)

    Akhmadyar, N S; Khairulin, B E; Amangeldy-Kyzy, S; Ospanov, M A

    2015-01-01

    One of the main problems of drug provision of multidisciplinary hospitals is the necessity to improve the efficiency of budget spending. Despite the efforts undertaken in Kazakhstan for improving the mechanism of drug distribution (creation of the Kazakhstan National Formulary, Unified National Health System, the handbook of medicines (drugs) costs in the electronic register of inpatients (ERI), having a single distributor), the number of unresolved issues still remain."National Medical Holding" JSC (NMH) was established in 2008 and unites 6 innovational healthcare facilities with up to 1431 beds (700 children and 731 adults), located in the medical cluster - which are "National Research Center for Maternal and Child Health" JSC (NRCMC), "Republic Children's Rehabilitation Center" JSC (RCRC), "Republican Diagnostic Center" JSC (RDC), "National Centre for Neurosurgery" JSC (NCN), "National Research Center for Oncology and Transplantation" JSC (NRCOT) and "National Research Cardiac Surgery Center" JSC (NRCSC). The main purpose of NMH is to create an internationally competitive "Hospital of the Future", which will provide the citizens of Kazakhstan and others with a wide range of medical services based on advanced medical technology, modern hospital management, international quality and safety standards. These services include emergency care, outpatient diagnostic services, obstetrics and gynecology, neonatal care, internal medicine, neurosurgery, cardiac surgery, transplantation, cancer care for children and adults, as well as rehabilitation treatment. To create a program of development of a drug formulary of NMH and its subsidiaries. In order to create drug formularies of NMH, analytical, software and statistical methods were used.AII subsidiary organizations of NMH (5 out of 6) except for the NRCOT have been accredited by Joint Commission International (JCI) standards, which ensure the safety of patients and clinical staff, by improving the technological

  6. 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

  7. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  8. 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

  9. 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...

  10. 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.

  11. 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.

  12. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  13. 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.

  14. 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...

  15. Cognitive-motor interference while grasping, lifting and holding objects.

    Directory of Open Access Journals (Sweden)

    Erwan Guillery

    Full Text Available In daily life, object manipulation is usually performed concurrently to the execution of cognitive tasks. The aim of the present study was to determine which aspects of precision grip require cognitive resources using a motor-cognitive dual-task paradigm. Eighteen healthy participants took part in the experiment, which comprised two conditions. In the first condition, participants performed a motor task without any concomitant cognitive task. They were instructed to grip, lift and hold an apparatus incorporating strain gauges allowing a continuous measurement of the force perpendicular to each contact surface (grip force, GF as well as the total tangential force applied on the object (load force, LF. In the second condition, participants performed the same motor task while concurrently performing a cognitive task consisting in a complex visual search combined with counting. In the dual-task condition, we found a significant increase in the duration of the preload phase (time between initial contact of the fingers with the apparatus and onset of the load force, as well as a significant increase of the grip force during the holding phase, indicating that the cognitive task interfered with the initial force scaling performed during the preload phase and the fine-tuning of grip force during the hold phase. These findings indicate that these aspects of precision grip require cognitive resources. In contrast, other aspects of the precision grip, such as the temporal coupling between grip and load forces, were not affected by the cognitive task, suggesting that they reflect more automatic processes. Taken together, our results suggest that assessing the dynamic and temporal parameters of precision grip in the context of a concurrent cognitive task may constitute a more ecological and better-suited tool to characterize motor dysfunction in patients.

  16. 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 ...

  17. 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...

  18. Public Utility Holding Company Act of 1935: 1935--1992

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-15

    This report provides an economic and legislative history and analysis of the Public Utilities Holding Company Act (PUHCA) of 1935. This Act was substantially amended for the first time in 1992 by passage of the Energy Policy Act (EPACT). The report also includes a discussion of the issues which led to the amendment of PUHCA and projections of the impact of these changes on the electric industry. The report should be of use to Federal and State regulators, trade associations, electric utilities, independent power producers, as well as decision-makers in Congress and the Administration.

  19. Cash Holdings and Leverage of German Listed Firms

    DEFF Research Database (Denmark)

    Rapp, Marc Steffen; Killi, Andreas Maximilian

    2016-01-01

    We examine cash holdings and leverage levels of German listed (non-financial and non-utility) firms. We document a secular increase in cash ratios over the last twenty years (1992–2011), reducing the net debt book leverage ratio for the average sample firm close to zero. Using prediction models...... firms are associated with measures of uncertainty faced by firms. Our results suggest that German firms have increased (reduced) their cash (net debt leverage) levels over time in order to adopt more precautionary financial policies....

  20. Inefficient Job Destructions and Training with Hold-up

    DEFF Research Database (Denmark)

    Chéron, Arnaud; Rouland, Benedicte

    2011-01-01

    This paper develops an equilibrium search model with endogenous job destructions and where firms decide at the time of job entry how much to invest in match-specific human capital. We first show that job destruction and training investment decisions are strongly complementary. It is possible...... that there are no firings at equilibrium. Further, training investments are confronted to a hold-up problem making the decentralized equilibrium always inefficient. We show therefore that both training subsidies and firing taxes must be implemented to bring back efficiency....

  1. 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.

  2. 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.

  3. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  4. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  5. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  6. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  7. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  8. Decompression sickness in breath-hold divers: a review.

    Science.gov (United States)

    Lemaitre, Frederic; Fahlman, Andreas; Gardette, Bernard; Kohshi, Kiyotaka

    2009-12-01

    Although it has been generally assumed that the risk of decompression sickness is virtually zero during a single breath-hold dive in humans, repeated dives may result in a cumulative increase in the tissue and blood nitrogen tension. Many species of marine mammals perform extensive foraging bouts with deep and long dives interspersed by a short surface interval, and some human divers regularly perform repeated dives to 30-40 m or a single dive to more than 200 m, all of which may result in nitrogen concentrations that elicit symptoms of decompression sickness. Neurological problems have been reported in humans after single or repeated dives and recent necropsy reports in stranded marine mammals were suggestive of decompression sickness-like symptoms. Modelling attempts have suggested that marine mammals may live permanently with elevated nitrogen concentrations and may be at risk when altering their dive behaviour. In humans, non-pathogenic bubbles have been recorded and symptoms of decompression sickness have been reported after repeated dives to modest depths. The mechanisms implicated in these accidents indicate that repeated breath-hold dives with short surface intervals are factors that predispose to decompression sickness. During deep diving, the effect of pulmonary shunts and/or lung collapse may play a major role in reducing the incidence of decompression sickness in humans and marine mammals.

  9. Hold-up monitoring system for plutonium process tanks

    International Nuclear Information System (INIS)

    Zhu Rongbao; Jin Huimin; Tan Yajun

    1994-01-01

    The development of hold-up monitoring system for plutonium process tanks and a calculation method for α activities deposited in containers and inner walls of pipe are described. The hardware of monitoring system consists of a portable HPGe detector, a φ50 mm x 60 mm NaI(Tl) detector, γ-ray tungsten collimators, ORTEC92X Spectrum Master and an AST-286 computer. The software of system includes Maestro Tm for Window3 and a PHOUP1 hold-up application software for user. The Monte-Carlo simulation calculation supported by MCNP software is performed for the probability calculation of all the unscattering γ-rays reaching to the detection positions from the source terms deposited in the complicated tanks. A measurement mean value for different positions is used to minimize the effect of heterogeneous distribution of source term. The sensitivity is better than 3.7 x 10 6 Bq/kg (steel) for a plutonium simulation source on a 3-8 mm thick steel plate surrounded by 0.8 x 10 -10 C/kg·s γ field from long-life fission products

  10. Clinical Efficacy of Piracetam on Breath Holding Spells in Children

    Directory of Open Access Journals (Sweden)

    F. Ashrafzadeh

    2004-07-01

    Full Text Available Breath holding spells (BHS is a type of syncope in children , most commonly encontered in the early years of life. Although these athacks don't damage the brain , if these are frequent or prolonged cause , parents frighten , so physician should intervent. In this study we evaluated clinical efficacy of piracetam on B.H.S of children in Mashhad Ghaem Hospital during 2001-2002.In this double blind placebo control study , piracetam or placebo on a randomized basis was administered to children with 40 mg/kg/day in 2 divided doses for 2 months. From the 41 children that were enrolled , 21 cases received piracetam and 20 cases received placebo. Parents denoted the numbers of spells two months before and two months after taking drug. Control of breath holding spells were observed in 90.5% of patients in the group taking piracetam as compared with 40% in the group taking placebo (P = 0.002. Of the all patients 10 cases had iron deficiency anemia so they had taken elemental Fe too. The side effects were the same in these two groups. The results of this study indicated that piracetam was efficient for the treatment of children with B.H.S without greater incidence adverse effects than placebo.

  11. Noise distribution of a peak track and hold circuit

    International Nuclear Information System (INIS)

    Seller, Paul; Hardie, Alec L.; Morrissey, Quentin

    2012-01-01

    Noise in linear electronic circuits is well characterised in terms of power spectral density in the frequency domain and the Normal probability density function in the time domain. For instance a charge preamplifier followed by a simple time independent pulse shaping circuit produces an output with a predictable, easily calculated Normal density function. By the Ergodic Principle this is true if the signal is sampled randomly in time or the experiment is run many times and measured at a fixed time after the circuit is released from reset. Apart from well defined cases, the time of the sample after release of reset does not affect the density function. If this signal is then passed through a peak track-and-hold circuit the situation is very different. The probability density function of the sampled signal is no longer Normal and the function changes with the time of the sample after release of reset. This density function can be classified by the Gumbel probability density function which characterises the Extreme Value Distribution of a defined number of Normally distributed values. The number of peaks in the signal is an important factor in the analysis. This issue is analysed theoretically and compared with a time domain noise simulation programme. This is then related to a real electronic circuit used for low-noise X-ray measurements and shows how the low-energy resolution of this system is significantly degraded when using a peak track-and-hold.

  12. A Haptic Guided Robotic System for Endoscope Positioning and Holding.

    Science.gov (United States)

    Cabuk, Burak; Ceylan, Savas; Anik, Ihsan; Tugasaygi, Mehtap; Kizir, Selcuk

    2015-01-01

    To determine the feasibility, advantages, and disadvantages of using a robot for holding and maneuvering the endoscope in transnasal transsphenoidal surgery. The system used in this study was a Stewart Platform based robotic system that was developed by Kocaeli University Department of Mechatronics Engineering for positioning and holding of endoscope. After the first use on an artificial head model, the system was used on six fresh postmortem bodies that were provided by the Morgue Specialization Department of the Forensic Medicine Institute (Istanbul, Turkey). The setup required for robotic system was easy, the time for registration procedure and setup of the robot takes 15 minutes. The resistance was felt on haptic arm in case of contact or friction with adjacent tissues. The adaptation process was shorter with the mouse to manipulate the endoscope. The endoscopic transsphenoidal approach was achieved with the robotic system. The endoscope was guided to the sphenoid ostium with the help of the robotic arm. This robotic system can be used in endoscopic transsphenoidal surgery as an endoscope positioner and holder. The robot is able to change the position easily with the help of an assistant and prevents tremor, and provides a better field of vision for work.

  13. 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...

  14. 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.

  15. 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

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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.

  2. 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.

  3. 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...

  4. Water addition, evaporation and water holding capacity of poultry litter.

    Science.gov (United States)

    Dunlop, Mark W; Blackall, Patrick J; Stuetz, Richard M

    2015-12-15

    Litter moisture content has been related to ammonia, dust and odour emissions as well as bird health and welfare. Improved understanding of the water holding properties of poultry litter as well as water additions to litter and evaporation from litter will contribute to improved litter moisture management during the meat chicken grow-out. The purpose of this paper is to demonstrate how management and environmental conditions over the course of a grow-out affect the volume of water A) applied to litter, B) able to be stored in litter, and C) evaporated from litter on a daily basis. The same unit of measurement has been used to enable direct comparison-litres of water per square metre of poultry shed floor area, L/m(2), assuming a litter depth of 5cm. An equation was developed to estimate the amount of water added to litter from bird excretion and drinking spillage, which are sources of regular water application to the litter. Using this equation showed that water applied to litter from these sources changes over the course of a grow-out, and can be as much as 3.2L/m(2)/day. Over a 56day grow-out, the total quantity of water added to the litter was estimated to be 104L/m(2). Litter porosity, water holding capacity and water evaporation rates from litter were measured experimentally. Litter porosity decreased and water holding capacity increased over the course of a grow-out due to manure addition. Water evaporation rates at 25°C and 50% relative humidity ranged from 0.5 to 10L/m(2)/day. Evaporation rates increased with litter moisture content and air speed. Maintaining dry litter at the peak of a grow-out is likely to be challenging because evaporation rates from dry litter may be insufficient to remove the quantity of water added to the litter on a daily basis. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

  5. 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.

  6. 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.

  7. 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...

  8. 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...

  9. 78 FR 36189 - Formations of, Acquisitions by, and Mergers of Savings and Loan Holding Companies

    Science.gov (United States)

    2013-06-17

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Savings and Loan Holding... CFR part 239), and all other applicable statutes and regulations to become a savings and loan holding... savings association and nonbanking companies owned by the savings and loan holding company, including the...

  10. 76 FR 16477 - General Reporting and Recordkeeping by Savings Associations and Savings and Loan Holding Companies

    Science.gov (United States)

    2011-03-23

    ... Savings Associations and Savings and Loan Holding Companies AGENCY: Office of Thrift Supervision (OTS...), 12 CFR 562.4 (audit of savings association, savings and loan holding company, or affiliate), 12 CFR... the savings association), 12 CFR 584.1(f) (books and records of each savings and loan holding company...

  11. 76 FR 31680 - General Reporting and Recordkeeping by Savings Associations and Savings and Loan Holding Companies

    Science.gov (United States)

    2011-06-01

    ... Savings Associations and Savings and Loan Holding Companies AGENCY: Office of Thrift Supervision (OTS... Savings and Loan Holding Companies. OMB Number: 1550-0011. Form Number: N/A. Description: This information...), 12 CFR 562.4 (audit of savings association, savings and loan holding company, or affiliate), 12 CFR...

  12. 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...

  13. 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...

  14. 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

  15. 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...

  16. 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...

  17. 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.

  18. DOES UNCOVERED INTEREST RATE PARITY HOLD IN TURKEY?

    Directory of Open Access Journals (Sweden)

    Ozcan Karahan

    2012-01-01

    Full Text Available Most of the earlier empirical studies focusing on developed countries failed to give evidence in favor of the Uncovered Interest Rate Parity (UIP. After intensive financial liberalization processes and mostly preferred free exchange rate regimes, a new area of research starts to involve the investigation whether UIP holds for developing economies differently. Accordingly, we tested the UIP for Turkey’s monthly interest rate and exchange rate data between 2002 and 2011. We run conventional regressions in the form of Ordinary Least Squares (OLS and used a simple Generalized Autoregressive Conditional Heteroskedasticity (GARCH analysis. The empirical results of both methods do not support the validity of UIP for Turkey. Thus, together with most of the earlier empirical studies focusing on developed countries and detecting the invalidity of UIP, we can argue that the experience of Turkey and developed economies are not different.

  19. An internal superconducting ''holding-coil'' for frozen spin targets

    International Nuclear Information System (INIS)

    Dutz, H.; Gehring, R.; Goertz, S.; Kraemer, D.; Meyer, W.; Reicherz, G.; Thomas, A.

    1995-01-01

    A new concept of a small superconducting holding magnet, placed inside a polarizing refrigerator, has been developed for frozen spin targets. The superconducting wire has been wound on the inner cooling shield of the vertical dilution refrigerator of the Bonn frozen spin target. The maximum field of the magnet is 0.35 T. The total thickness of the superconducting coil consisting of the wire and the copper carrier is of the order of 500 μm. Based on this concept, a frozen spin target is under construction for the measurement of the Gerasimov-Drell-Hearn sum rule with polarized real photons at the Mainz microtron MAMI and the Bonn electron stretcher accelerator ELSA. ((orig.))

  20. An internal superconducting ``holding-coil`` for frozen spin targets

    Energy Technology Data Exchange (ETDEWEB)

    Dutz, H. [Bonn Univ. (Germany). Physikalisches Inst.; Gehring, R. [Bonn Univ. (Germany). Physikalisches Inst.; Goertz, S. [Bonn Univ. (Germany). Physikalisches Inst.; Kraemer, D. [Bonn Univ. (Germany). Physikalisches Inst.; Meyer, W. [Bonn Univ. (Germany). Physikalisches Inst.; Reicherz, G. [Bonn Univ. (Germany). Physikalisches Inst.; Thomas, A. [Bonn Univ. (Germany). Physikalisches Inst.

    1995-03-01

    A new concept of a small superconducting holding magnet, placed inside a polarizing refrigerator, has been developed for frozen spin targets. The superconducting wire has been wound on the inner cooling shield of the vertical dilution refrigerator of the Bonn frozen spin target. The maximum field of the magnet is 0.35 T. The total thickness of the superconducting coil consisting of the wire and the copper carrier is of the order of 500 {mu}m. Based on this concept, a frozen spin target is under construction for the measurement of the Gerasimov-Drell-Hearn sum rule with polarized real photons at the Mainz microtron MAMI and the Bonn electron stretcher accelerator ELSA. ((orig.))

  1. Role of cerebral blood flow in extreme breath holding.

    Science.gov (United States)

    Bain, Anthony R; Ainslie, Philip N; Hoiland, Ryan L; Willie, Chris K; MacLeod, David B; Madden, Dennis; Maslov, Petra Zubin; Drviš, Ivan; Dujić, Željko

    2016-01-01

    The role of cerebral blood flow (CBF) on a maximal breath-hold (BH) in ultra-elite divers was examined. Divers (n = 7) performed one control BH, and one BH following oral administration of the non-selective cyclooxygenase inhibitor indomethacin (1.2 mg/kg). Arterial blood gases and CBF were measured prior to (baseline), and at BH termination. Compared to control, indomethacin reduced baseline CBF and cerebral delivery of oxygen (CDO 2 ) by about 26% (p tension was higher following oral administration of indomethacin compared to control (4.05 ± 0.45 vs. 3.44 ± 0.32 kPa). The absolute increase in CBF from baseline to the termination of apnea was lower with indomethacin (p = 0.01). These findings indicate that the impact of CBF on maximal BH time is likely attributable to its influence on cerebral H + washout, and therefore central chemoreceptive drive to breathe, rather than to CDO 2 .

  2. Governance of Open Source Software Foundations: Who Holds the Power?

    Directory of Open Access Journals (Sweden)

    Ludovico Prattico

    2012-12-01

    Full Text Available The research reported in this article attempts to discover who holds the power in open source software foundations through the analysis of governance documents. Artificial neural network analysis is used to analyse the content of the bylaws of six open source foundations (Apache, Eclipse, GNOME, Plone, Python, and SPI for the purpose of identifying power structures. Results of the research suggest that: i the actions of an open source software foundation are centered around one of three groups: Members, Chairman/President/Executive Director, and Board of Directors; ii in only one of the six foundations is the Board of Directors responsible for both the community and the product; and iii artificial neural network analysis of the content of bylaws provides unbiased insights of the power structure of open source software foundations. These results may prove useful to those who contribute to open source foundations and use their products and services.

  3. 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.

  4. 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.

  5. Business and production performance of different types of agricultural holdings

    Directory of Open Access Journals (Sweden)

    Katarina Rosić

    2016-12-01

    Full Text Available Farm Accountancy Data Network (FADN was established in the EU in 1965 and now it is obligated for all member states of the EU. The system is based on an annual collection of production, economic and financial data from a representative sample of comercial farms, classified into groups according to the criteria of economic farm size, type of agricultural production and regional affiliation. Research made by FADN system represent the European Commission instrument for evaluating the income of agricultural producers and determining the impact of the Common Agricultural Policy of the EU on their business. In this paper the comparison is made between production and economic indicators of different types of agricultural holdings (field crops; horticulture crops; permanent crops, orchards and olive yards; dairy farms; grazing livestock; pig and poultry farms and mixed farms. On the basis of Standard Results for the year 2014 it is possible to conclude that in Croatia field crops and grazing livestock farms lead by their utilized agricultural area. Pig and poultry farming have the most livestock units, while the most working hours is spent in the cultivation of vegetables and flowers. The highest values of labor productivity have holdings that are engaged in the production of vegetables and flowers, while the lowest labor productivity have grazing livestock farms. Cost-effectiveness of all types of farms exceeding a value of 1. The highest value of the gross income is achieved at pig and poultry farms, while the smallest has a mixed type of farms. The average farm direct payments account for a high 44% in the net income, and the largest share of direct payments in the net income has field crop type of farms.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. A digital divide: Kiswahili holds the key | Kamau | Journal of ...

    African Journals Online (AJOL)

    Journal of Language, Technology & Entrepreneurship in Africa. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 1, No 1 (2007) >. Log in or Register to get access to full text downloads.

  12. 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.

  13. 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.

  14. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. MEMS-based clamp with a passive hold function for precision position retaining of micro manipulators

    International Nuclear Information System (INIS)

    Brouwer, D M; Van Dijk, J; Soemers, H M J R; De Jong, B R; De Boer, M J; Jansen, H V; Krijnen, G J M

    2009-01-01

    In this paper the design, modeling and fabrication of a precision MEMS-based clamp with a relatively large clamping force are presented. The purpose of the clamp is to mechanically fix a six-degree-of-freedom (DOF) MEMS-based sample manipulator (Brouwer et al J. Int. Soc. Precis. Eng. Nanotechnol. submitted) once the sample has been positioned in all DOFs. The clamping force is generated by a rotational electrostatic comb-drive actuator and can be latched passively by a parallel plate type electrostatically driven locking device. The clamp design is based on the principles of exact constraint design, resulting in a high actuation compliance (flexibility) combined with a high suspension stiffness. Therefore, a relatively large blocking force of 1.4 mN in relation to the used area of 1.8 mm 2 is obtained. The fabrication is based on silicon bulk micromachining technology and combines a high-aspect-ratio deep reactive ion etching (DRIE), conformal deposition of low-pressure chemical vapor deposition (LPCVD) silicon nitride and an anisotropic potassium hydroxide (KOH) backside etching technology. Special attention is given to void reduction of Si x N y trench isolation and reduction of heating phenomena during front-side release etching. Guidelines are given for the applied process. Measurements showed that the clamp was able to fix, hold and release a test actuator. The dynamic behavior was in good agreement with the modal analysis

  20. Effects of Calcination Holding Time on Properties of Wide Band Gap Willemite Semiconductor Nanoparticles by the Polymer Thermal Treatment Method

    Directory of Open Access Journals (Sweden)

    Ibrahim Mustapha Alibe

    2018-04-01

    Full Text Available Willemite is a wide band gap semiconductor used in modern day technology for optoelectronics application. In this study, a new simple technique with less energy consumption is proposed. Willemite nanoparticles (NPs were produced via a water–based solution consisting of a metallic precursor, polyvinylpyrrolidone (PVP, and underwent a calcination process at 900 °C for several holding times between 1–4 h. The FT–IR and Raman spectra indicated the presence of metal oxide bands as well as the effective removal of PVP. The degree of the crystallization and formation of the NPs were determined by XRD. The mean crystallite size of the NPs was between 18.23–27.40 nm. The morphology, particle shape and size distribution were viewed with HR-TEM and FESEM analysis. The willemite NPs aggregate from the smaller to larger particles with an increase in calcination holding time from 1–4 h with the sizes ranging between 19.74–29.71 nm. The energy values obtained from the experimental band gap decreased with increasing the holding time over the range of 5.39 eV at 1 h to at 5.27 at 4 h. These values match well with band gap obtained from the Mott and Davis model for direct transition. The findings in this study are very promising and can justify the use of these novel materials as a potential candidate for green luminescent optoelectronic applications.

  1. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  2. Seal Formation Mechanism Beneath Animal Waste Holding Ponds

    Science.gov (United States)

    Cihan, A.; Tyner, J. S.; Wright, W. C.

    2005-12-01

    Infiltration of animal waste from holding ponds can cause contamination of groundwater. Typically, the initial flux from a pond decreases rapidly as a seal of animal waste particulates is deposited at the base of the pond. The purpose of this study was to investigate the mechanism of the seal formation. Twenty-four soil columns (10-cm diameter by 43-cm long) were hand-packed with sand, silty loam or clay soils. A 2.3 m column of dairy or swine waste was applied to the top of the each column. The leakage rate from each column was measured with respect to time to analyze the effect of seal formation on different soil textures and animal waste types. We tested our hypothesis that seal growth and the subsequent decrease of leachate production adheres to a filter cake growth model. Said model predicts that the cumulative leakage rate is proportional to the square root of time and to the square root of the height of the waste.

  3. Antigen Loss Variants: Catching Hold of Escaping Foes.

    Science.gov (United States)

    Vyas, Maulik; Müller, Rolf; Pogge von Strandmann, Elke

    2017-01-01

    Since mid-1990s, the field of cancer immunotherapy has seen steady growth and selected immunotherapies are now a routine and preferred therapeutic option of certain malignancies. Both active and passive cancer immunotherapies exploit the fact that tumor cells express specific antigens on the cell surface, thereby mounting an immune response specifically against malignant cells. It is well established that cancer cells typically lose surface antigens following natural or therapy-induced selective pressure and these antigen-loss variants are often the population that causes therapy-resistant relapse. CD19 and CD20 antigen loss in acute lymphocytic leukemia and chronic lymphocytic leukemia, respectively, and lineage switching in leukemia associated with mixed lineage leukemia (MLL) gene rearrangements are well-documented evidences in this regard. Although increasing number of novel immunotherapies are being developed, majority of these do not address the control of antigen loss variants. Here, we review the occurrence of antigen loss variants in leukemia and discuss the therapeutic strategies to tackle the same. We also present an approach of dual-targeting immunoligand effectively retargeting NK cells against antigen loss variants in MLL-associated leukemia. Novel immunotherapies simultaneously targeting more than one tumor antigen certainly hold promise to completely eradicate tumor and prevent therapy-resistant relapses.

  4. Role of cerebral blood flow in extreme breath holding

    Directory of Open Access Journals (Sweden)

    Bain Anthony R.

    2016-01-01

    Full Text Available The role of cerebral blood flow (CBF on a maximal breath-hold (BH in ultra-elite divers was examined. Divers (n = 7 performed one control BH, and one BH following oral administration of the non-selective cyclooxygenase inhibitor indomethacin (1.2 mg/kg. Arterial blood gases and CBF were measured prior to (baseline, and at BH termination. Compared to control, indomethacin reduced baseline CBF and cerebral delivery of oxygen (CDO2 by about 26% (p < 0.01. Indomethacin reduced maximal BH time from 339 ± 51 to 319 ± 57 seconds (p = 0.04. In both conditions, the CDO2 remained unchanged from baseline to the termination of apnea. At BH termination, arterial oxygen tension was higher following oral administration of indomethacin compared to control (4.05 ± 0.45 vs. 3.44 ± 0.32 kPa. The absolute increase in CBF from baseline to the termination of apnea was lower with indomethacin (p = 0.01. These findings indicate that the impact of CBF on maximal BH time is likely attributable to its influence on cerebral H+ washout, and therefore central chemoreceptive drive to breathe, rather than to CDO2.

  5. Dead space variability of face masks for valved holding chambers.

    Science.gov (United States)

    Amirav, Israel; Newhouse, Michael T

    2008-03-01

    Valved holding chambers with masks are commonly used to deliver inhaled medications to young children with asthma. Optimal mask properties such as their dead space volume have received little attention. The smaller the mask the more likely it is that a greater proportion of the dose in the VHC will be inhaled with each breath, thus speeding VHC emptying and improving overall aerosol delivery efficiency and dose. Masks may have different DSV and thus different performance. To compare both physical dead space and functional dead space of different face masks under various applied pressures. The DSV of three commonly used face masks of VHCs was measured by water displacement both under various pressures (to simulate real-life application, dynamic DSV) and under no pressure (static DSV). There was a great variability of both static and dynamic dead space among various face mask for VHCs, which is probably related to their flexibility. Different masks have different DSV characteristics. This variability should be taken into account when comparing the clinical efficacy of various VHCs.

  6. Three-dimensional imaging of hold baggage for airport security

    Directory of Open Access Journals (Sweden)

    S. Kolokytha

    2014-06-01

    Full Text Available This study describes a cost-effective check-in baggage screening system, based on "on-belt tomosynthesis" (ObT and close-range photogrammetry, that is designed to address the limitations of the most common system used, conventional projection radiography. The latter's limitations can lead to loss of information and an increase in baggage handling time, as baggage is manually searched or screened with more advanced systems. This project proposes a system that overcomes such limitations creating a cost-effective automated pseudo-3D imaging system, by combining x-ray and optical imaging to form digital tomograms. Tomographic reconstruction requires a knowledge of the change in geometry between multiple x-ray views of a common object. This is uniquely achieved using a close range photogrammetric system based on a small network of web-cameras. This paper presents the recent developments of the ObT system and describes recent findings of the photogrammetric system implementation. Based on these positive results, future work on the advancement of the ObT system as a cost-effective pseudo-3D imaging of hold baggage for airport security is proposed.

  7. Studies of radiation blistering effects on voltage holding

    International Nuclear Information System (INIS)

    Miley, G.H.

    1975-01-01

    The surfaces of niobium and tungsten wires were blistered by 300-keV helium-ion irradiation and then tested for voltage holding. A cylindrical projection-tube technique was employed so that regions of strong electron emission could be observed and later examined with a scanning electron microscope (SEM). Blistering was found to cause significant increases in pre-breakdown currents. However, these currents tend to saturate over a region corresponding to around 200-400 kV/cm surface field such that the ultimate voltage breakdown limit is not seriously reduced. Emission image observations and SEM photographs suggest that, in many cases, parts of the blistered surface are gradually erected by the strong surface fields, but this may not occur until after several arc breakdowns. SEM photographs also indicate that vapor from the anode may play an important part in the breakdown mechanism. Implications of these results to the design of devices important to fusion development, such as direct collectors and ion sources, are briefly discussed. The importance of future in situ irradiation-voltage experiments is also stressed. (U.S.)

  8. Holding fast: the experience of collaboration in a competitive environment.

    Science.gov (United States)

    Fear, Heather; Barnett, Pauline

    2003-03-01

    Collaboration is one of the cornerstones of health promotion, with the literature indicating a range of circumstances under which it can either succeed or be undermined. In New Zealand in the 1990s, a market structure for health made collaboration of all kinds exceptionally difficult. This paper traces the efforts of a group of nutrition agencies (Agencies for Nutrition Action) to defy the popular wisdom and persist with collaborative efforts. The agencies were unsuccessful in their attempts to develop joint campaigns, but were very successful in advocacy and intersectoral action that did not threaten the position of individual agencies in the competitive environment. It is possible that the collaboration could have been more effective if agencies had been willing to surrender some autonomy and commit themselves to supporting a more independent new organization. However, this would have compromised not only their individual integrity but also their commitment to a relationship of equals. In 'holding fast' to a belief in health promotion, the ANA resisted being coopted by a now discredited market system, and emerged with its integrity and that of its participating agencies intact. ANA is now well positioned to work within an emerging policy environment that is more supportive of health promotion.

  9. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  10. U.S. Solar Holdings Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, Jake [U.S. Solar Holdings, Boise, ID (United States); Stekli, Joe [U.S. Solar Holdings, Boise, ID (United States); Rueckert, Tommy [U.S. Solar Holdings, Boise, ID (United States); Irwin, Levi [U.S. Solar Holdings, Boise, ID (United States); Mehos, Mark [U.S. Solar Holdings, Boise, ID (United States); Ho, Cliff [U.S. Solar Holdings, Boise, ID (United States)

    2012-03-06

    This report summarizes the work of the US Solar Thermal Storage LLC (“USSTS”) team on SandShifter subproject for Phase 2 of U.S. Department of Energy’s FOA #DE-FC36-08GO18155.005. This subproject develops a new-to-the-world, disruptive technology which leverages an abundant, inexpensive, and benign material, Sand, for application in Thermal Energy Storage (TES) in association with power generation from Concentrating Solar Thermal (CST) systems. Sand, as a standalone TES media, has a 10 to 25X cost per unit of storage capacity cost advantage over the prevailing technology, molten salt. The work summarized herein suggests that SandShifter, which has a non-linear cost curve favoring higher hours of storage, could likely achieve economics of $15 per kWh-th or less for several hours of storage in high temperature steam- or salt-as-HTF configurations with further technology development.

  11. Genome sequencing for obstetricians & gynaecologists | Kent ...

    African Journals Online (AJOL)

    The medical profession has been waiting for a decade to be invigorated by the sequencing of the human genome, arguably the greatest scientific project ever. The technology has been spectacular but the results of the project have yielded more unexpected results than definitive answers – many about the very nature of our ...

  12. 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.

  13. 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.

  14. 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.

  15. Aplikace logistických technologií Just-in-Time a Just-in-Sequence ve společnosti Robert Bosch spol. s r.o.

    OpenAIRE

    ŠTEFKOVÁ, Iveta

    2009-01-01

    This work is mostly oriented to define theory and application of principle Just in Time ( JIT ), Just in Sequence (JIS ) and related methods in Robert Bosch Ltd.Part goals are define theoretical basis of JIT and JIS from knowledge of Czech and foreign literature and detailed analysis of particular methods. Each method is well evaluated with all its pros and cons. Further observations engaged method of Kanban, Heijunka, MRPI, MRPII, which are close related to JIT and JIS. This work precisely d...

  16. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  17. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  18. Rain Forests: Do They Hold Up the Sky?

    Science.gov (United States)

    Shaw, Donna Gail; Dybdahl, Claudia S.

    1992-01-01

    This paper uses the topic of rain forests to demonstrate how a meaningful and relevant Science, Technology, and Society program can be designed for intermediate-level students. Students create and immerse themselves in a tropical rain forest, explore the forest ecosystem and peoples, and consider solutions to the problem of deforestation. (JDD)

  19. INTRODUCTION Curing is holding fruits at temperatures and ...

    African Journals Online (AJOL)

    and most postharvest fungi are wound pathogens ... Department of Biology, the Federal University of Technology, PMB 704, Akure. NIGERIA ... and 9% weight loss before storage in normal atmosphere at 28 C and 85% relative humidity. ... The causal organisms were Penicillium digitatum, Phytophthora sp. and ... laboratory.

  20. 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...

  1. Self-face Captures, Holds, and Biases Attention.

    Science.gov (United States)

    Wójcik, Michał J; Nowicka, Maria M; Kotlewska, Ilona; Nowicka, Anna

    2017-01-01

    The implicit self-recognition process may take place already in the pre-attentive stages of perception. After a silent stimulus has captured attention, it is passed on to the attentive stage where it can affect decision making and responding. Numerous studies show that the presence of self-referential information affects almost every cognitive level. These effects may share a common and fundamental basis in an attentional mechanism, conceptualized as attentional bias: the exaggerated deployment of attentional resources to a salient stimulus. A gold standard in attentional bias research is the dot-probe paradigm. In this task, a prominent stimulus (cue) and a neutral stimulus are presented in different spatial locations, followed by the presentation of a target. In the current study we aimed at investigating whether the self-face captures, holds and biases attention when presented as a task-irrelevant stimulus. In two dot-probe experiments coupled with the event-related potential (ERP) technique we analyzed the following relevant ERPs components: N2pc and SPCN which reflect attentional shifts and the maintenance of attention, respectively. An inter-stimulus interval separating face-cues and probes (800 ms) was introduced only in the first experiment. In line with our predictions, in Experiment 1 the self-face elicited the N2pc and the SPCN component. In Experiment 2 in addition to N2pc, an attentional bias was observed. Our results indicate that unintentional self-face processing disables the top-down control setting to filter out distractors, thus leading to the engagement of attentional resources and visual short-term memory.

  2. Characterization plan for the waste holding basin (3513 impoundment)

    International Nuclear Information System (INIS)

    Stansfield, R.G.; Francis, C.W.

    1986-09-01

    US Department of Energy (DOE) facilities are required to comply fully with all federal and state regulations. In response to this requirement, the Oak Ridge National Laboratory (ORNL) has established the remedial action program, to provide comprehensive management of areas where past research, development, and waste management activities have been conducted and have resulted in residual contamination of facilities or the environment. One of the objectives of this program is to define the extent of contamination at these sites. The intent is to document the known environmental characteristics of the sites and identify the additional actions, such as sampling, analytical measurements, and modeling, necessary to confirm contamination and the possible migration of contaminants from the sites. One of these sites is the waste holding basin (3513 impoundment). The 3513 impoundment is an unlined waste settling basin constructed in 1944 for collection of ORNL wastewater before its discharge into White Oak Creek. Operation of the facility ceased in 1976 when a new process waste treatment plant came into operation. Considerable site-specific environmental information has been developed over the years relative to the type and quantities of radionuclides and hazardous substances contained in the pond water and sediment. The concentrations and patterns of distribution for many of the radionuclides in the aquatic biota as well as for the terrestrial plants growing on the berm of the impoundment have been determined by DOE ecological studies. Recently, some data were collected that evaluate the extent of contaminant movement to the groundwater. Results from these studies are summarized in this report. Also included in this report is an outline of additional tasks needed to obtain the necessary information to model the transport and dose pathways of hazardous substances from the site

  3. Self-face Captures, Holds, and Biases Attention

    Directory of Open Access Journals (Sweden)

    Michał J. Wójcik

    2018-01-01

    Full Text Available The implicit self-recognition process may take place already in the pre-attentive stages of perception. After a silent stimulus has captured attention, it is passed on to the attentive stage where it can affect decision making and responding. Numerous studies show that the presence of self-referential information affects almost every cognitive level. These effects may share a common and fundamental basis in an attentional mechanism, conceptualized as attentional bias: the exaggerated deployment of attentional resources to a salient stimulus. A gold standard in attentional bias research is the dot-probe paradigm. In this task, a prominent stimulus (cue and a neutral stimulus are presented in different spatial locations, followed by the presentation of a target. In the current study we aimed at investigating whether the self-face captures, holds and biases attention when presented as a task-irrelevant stimulus. In two dot-probe experiments coupled with the event-related potential (ERP technique we analyzed the following relevant ERPs components: N2pc and SPCN which reflect attentional shifts and the maintenance of attention, respectively. An inter-stimulus interval separating face-cues and probes (800 ms was introduced only in the first experiment. In line with our predictions, in Experiment 1 the self-face elicited the N2pc and the SPCN component. In Experiment 2 in addition to N2pc, an attentional bias was observed. Our results indicate that unintentional self-face processing disables the top-down control setting to filter out distractors, thus leading to the engagement of attentional resources and visual short-term memory.

  4. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  5. 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.

  6. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  7. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  8. 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.

  9. 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...

  10. 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...

  11. 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 ...

  12. Trend Definition or Holding Strategy: What Determines the Profitability of Candlestick Technical Trading Strategies?

    OpenAIRE

    Tsung-Hsun Lu; Yi-Chi Chen; Yu-Chin Hsu

    2014-01-01

    We ask what determines the profitability of candlestick patterns. Is it the definition of trend and/or the holding strategy that one uses in candlestick charting analysis? To answer this, we conduct a systematic investigation by considering three definitions of trend and four holding strategies. Based on the DJIA components data, we find that eight three-day reversal patterns with a Caginalp-Laurent holding strategy are profitable after we account for data-snooping bias. We also find that our...

  13. 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.)

  14. Apparatus and method for generating a magnetic field by rotation of a charge holding object

    Science.gov (United States)

    Gerald, II, Rex E.; Vukovic, Lela [Westchester, IL; Rathke, Jerome W [Homer Glenn, IL

    2009-10-13

    A device and a method for the production of a magnetic field using a Charge Holding Object that is mechanically rotated. In a preferred embodiment, a Charge Holding Object surrounding a sample rotates and subjects the sample to one or more magnetic fields. The one or more magnetic fields are used by NMR Electronics connected to an NMR Conductor positioned within the Charge Holding Object to perform NMR analysis of the sample.

  15. 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...

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  3. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  4. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  5. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  6. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  7. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  8. Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

    NARCIS (Netherlands)

    Mobegi, Fredrick M; Cremers, Amelieke J H; de Jonge, Marien I; Bentley, Stephen D; van Hijum, Sacha A F T; Zomer, Aldert|info:eu-repo/dai/nl/304642754

    2017-01-01

    Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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 ...

  14. 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…

  15. 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...

  16. 14 CFR 11.51 - May I request that FAA hold a public meeting on a rulemaking action?

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false May I request that FAA hold a public... Meetings and Other Proceedings § 11.51 May I request that FAA hold a public meeting on a rulemaking action? Yes, you may request that we hold a public meeting. FAA holds a public meeting when we need more than...

  17. Who will hold capacity in an era of uncertainty and unbundling

    International Nuclear Information System (INIS)

    Wirick, J.P.Jr.

    2002-01-01

    This presentation addressed the role that local distribution companies (LDC) will play in the natural gas industry with reference to the impacts of unbundling and how state regulators should react to LDCs exceeding allowable capacity reserve margins. The paper discussed how enforced behaviour has emerged within the traditional natural gas industry. The author states that the industry went into its first chaotic state when open access transportation came into force. It went into the second chaotic state when it was again destabilized by the forces of energy convergence, residential unbundling, ownership transfer, market pricing and technological innovation. The author described the synergistic effects of energy convergence with market pricing, along with the effects of residential energy unbundling and whether it should cover the natural gas commodity or just the capacity. The chaotic states have taught the industry valuable lessons in terms of pricing, service to customers and implications for both the industry and regulators. The author states that LDC unbundling should change who holds capacity, claiming that it has to, particularly if customers choose a different supplier. Unbundling means that the LDC allows residential customers to buy from someone other than the LDC. He also states that there is a need for pipelines to charge market-based rates. tabs., figs

  18. 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

  19. 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...

  20. Protecting chips against hold time violations due to variability

    CERN Document Server

    Neuberger, Gustavo; Reis, Ricardo

    2013-01-01

    With the development of Very-Deep Sub-Micron technologies, process variability is becoming increasingly important and is a very important issue in the design of complex circuits. Process variability is the statistical variation of process parameters, meaning that these parameters do not have always the same value, but become a random variable, with a given mean value and standard deviation. This effect can lead to several issues in digital circuit design.The logical consequence of this parameter variation is that circuit characteristics, as delay and power, also become random variables. Becaus

  1. Complete genome sequence of Ikoma lyssavirus.

    Science.gov (United States)

    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

    2012-09-01

    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), isolated from an African civet in Tanzania displaying clinical signs of rabies. Genetically, this virus is the most divergent within the genus Lyssavirus. Characterization of the genome will help to improve our understanding of lyssavirus diversity and enable investigation into vaccine-induced immunity and protection.

  2. Quality of Milk for Cheese Production on Registered Agricultural Holdings in Vojvodina

    Directory of Open Access Journals (Sweden)

    Popović Vranješ Anka

    2017-12-01

    Full Text Available Currently, milk producers in Vojvodina on registered agricultural holdings (RAHs have great experience and knowledge in managing their farms, including primary production, processing and sales. However, for a smaller number of manufacturers, there is still room for organizational and technological improvement of production. Nowadays, goat breeding is a very important part of sustainable production, rural development, and represents a very important part of rural development and employment of people. The course of goat breeding in our country is milk-meat, where milk is usually a priority. For the successful production of cheese, the quality of raw milk plays a critical role. It affects the quality of cheese in terms of a chemical composition, microbiological quality, the presence of chemical residues and organoleptic properties. Cheese is mostly made from cow, goat and sheep milk. The valuable components of milk are proteins and fats. These can also be defined as parameters of utilization, since they indicate how much cheese can be obtained from milk. On average, cow milk contains 3.64% fat, 3.22% protein, and 8.52% non-fat dry matter (NFDM. Higher differences in milk fat content (minimum 3.25%, maximum 4.36% were found in milk from RAHs. Recently, the production of milk with higher fat content has become important, since in Serbian milk there is not enough milk fat, so some processors are obliged to import it in the form of butter and cream. In addition to the chemical composition, the microbiological quality of milk is important to maintain successful cheese production. Regarding our findings, the standard plate count (SPC and the somatic cell count (SCC in samples from most RAHs did not exceed the values specified in Regulation (EC 853/2004. Moreover, goat and sheep milk was in agreement with the technological quality of milk for cheese production, in terms of chemical composition.

  3. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  4. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  5. 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.

  6. 26 CFR 1.951-3 - Coordination of subpart F with foreign personal holding company provisions.

    Science.gov (United States)

    2010-04-01

    ... personal holding company and not a controlled foreign corporation and the earnings and profits of such... earnings and profits of $10,000, derives $10,000 of income which is both foreign personal holding company... the earnings and profits of P Corporation for 1966) in earnings invested in United States property...

  7. 75 FR 37804 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2010-06-30

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The...: 1. Woori Finance Holdings Co., Ltd, Seoul, Korea; to acquire at least 51 percent of the voting shares of Hanmi Financial Corp., Los Angeles, California, and thereby indirectly acquire Hanmi Bank, Los...

  8. 75 FR 13763 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2010-03-23

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The..., California 94105-1579: 1. North Asia Investment Corporation, Seoul, Korea; to become a bank holding company by acquiring 100 percent of the voting shares of Pacific City Financial Corporation, and Pacific City...

  9. 77 FR 48983 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2012-08-15

    ..., Vice President) 33 Liberty Street, New York, New York 10045-0001: 1. Hana Financial Group Inc., Seoul, Korea; to become a bank holding company by acquiring 71.37 percent of the voting shares of BNB Financial... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The...

  10. 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.

  11. 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...

  12. 77 FR 3774 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2012-01-25

    ..., Dupont, Indiana. River Valley Financial Bank, Madison, Indiana, the existing thrift subsidiary of... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company...

  13. 76 FR 67190 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2011-10-31

    ... Bank, Dover, Ohio, a thrift, upon its conversion to a national bank. B. Federal Reserve Bank of Atlanta... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company...

  14. 75 FR 11888 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2010-03-12

    ... acquiring 87.31 percent of the voting shares of People's Bank of Seneca, Seneca, Missouri. B. Federal... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company...

  15. 12 CFR 225.143 - Policy statement on nonvoting equity investments by bank holding companies.

    Science.gov (United States)

    2010-01-01

    ... CONTROL (REGULATION Y) Regulations Financial Holding Companies Interpretations § 225.143 Policy statement on nonvoting equity investments by bank holding companies. (a) Introduction. (1) In recent months, a... company has the power, directly or indirectly, to exercise a controlling influence over the management or...

  16. 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...

  17. 12 CFR 225.21 - Prohibited nonbanking activities and acquisitions; exempt bank holding companies.

    Science.gov (United States)

    2010-01-01

    ... CONTROL (REGULATION Y) Regulations Nonbanking Activities and Acquisitions by Bank Holding Companies § 225... company or a subsidiary may not engage in, or acquire or control, directly or indirectly, voting... Internal Revenue Code (26 U.S.C. 501(c)). (3) Companies granted hardship exemption. Any bank holding...

  18. 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.

    2015-01-01

    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…

  19. 29 CFR 452.32 - Persons who may be candidates and hold office; secret ballot elections.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 2 2010-07-01 2010-07-01 false Persons who may be candidates and hold office; secret... Qualifications § 452.32 Persons who may be candidates and hold office; secret ballot elections. Section 401(e) provides that in any election of officers required by the Act which is held by secret ballot, every member...

  20. 76 FR 60494 - Formations of, Acquisitions by, and Mergers of Savings and Loan Holding Companies; Correction

    Science.gov (United States)

    2011-09-29

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Savings and Loan Holding Companies; Correction This notice corrects a notice (FR Doc. 2011-24388) published on page 58812 of the... with Polonia Bancorp, Inc., Baltimore, Maryland, which proposes to become a savings and loan holding...

  1. 78 FR 17206 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2013-03-20

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  2. 78 FR 41063 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2013-07-09

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... acquisition of a nonbanking company, the review also includes whether the acquisition of the nonbanking...

  3. 75 FR 30405 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2010-06-01

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  4. 78 FR 37222 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2013-06-20

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  5. 78 FR 7430 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2013-02-01

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  6. 77 FR 38816 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2012-06-29

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  7. 77 FR 64993 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2012-10-24

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  8. 77 FR 69454 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2012-11-19

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... acquisition of a nonbanking company, the review also includes whether the acquisition of the nonbanking...

  9. 77 FR 48156 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2012-08-13

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  10. 77 FR 42312 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2012-07-18

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... acquisition of a nonbanking company, the review also includes whether the acquisition of the nonbanking...

  11. 75 FR 26961 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2010-05-13

    ... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company... involves the acquisition of a nonbanking company, the review also includes whether the acquisition of the...

  12. 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

  13. 78 FR 48637 - Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption...

    Science.gov (United States)

    2013-08-09

    ... Produce for Human Consumption; Extension of Comment Periods AGENCY: Food and Drug Administration, HHS... for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption,'' that appeared in... ``Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption'' with a 120...

  14. 78 FR 11611 - Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption...

    Science.gov (United States)

    2013-02-19

    ... Produce for Human Consumption; Extension of Comment Period for Information Collection Provisions AGENCY..., Harvesting, Packing, and Holding of Produce for Human Consumption'' that appeared in the Federal Register of... ``Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption.'' FOR FURTHER...

  15. Effects of Holding Methods and Time on the Vitamin Contents of Five ...

    African Journals Online (AJOL)

    The five leafy vegetables are fair sources of thiamin, riboflavin and niacin. There were losses in the vitamins as holding time increased, regardless of the holding method employed. The rate of loss of vitamins was highest in Lot I (the unwrapped leaves that were kept in a shade both day and night). The rate of loss of vitamins ...

  16. 75 FR 35030 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2010-06-21

    ... outstanding shares of Paragon Commercial Corporation, and its subsidiary, Paragon Commercial Bank, both of... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company...

  17. 75 FR 13129 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2010-03-18

    ... acquiring 100 percent of Circle Bank upon conversion of the bank from an industrial bank to a commercial... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company...

  18. 78 FR 57154 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2013-09-17

    ..., Maryland, to a state chartered commercial bank. B. Federal Reserve Bank of Dallas (E. Ann Worthy, Vice... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company...

  19. 76 FR 63923 - Formations of, Acquisitions by, and Mergers of Bank Holding Companies

    Science.gov (United States)

    2011-10-14

    ... Security Bank of Washington, Mountlake Terrace, Washington, from a state savings bank to a commercial bank... FEDERAL RESERVE SYSTEM Formations of, Acquisitions by, and Mergers of Bank Holding Companies The companies listed in this notice have applied to the Board for approval, pursuant to the Bank Holding Company...

  20. Do social factors influence investment behavior and performance? Evidence from mutual fund holdings

    NARCIS (Netherlands)

    Borgers, Arian; Derwall, J.M.M.; Koedijk, Kees; ter Horst, Jenke

    2015-01-01

    We study the economic significance of social dimensions in investment decisions by analyzing the holdings of U.S. equity mutual funds over the period 2004-2012. Using these holdings, we measure funds' exposures to socially sensitive stocks in order to answer two questions. What explains