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Sample records for time-efficient sequence protocol

  1. A time-efficient acquisition protocol for multipurpose diffusion-weighted microstructural imaging at 7 Tesla.

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    Sepehrband, Farshid; O'Brien, Kieran; Barth, Markus

    2017-12-01

    Several diffusion-weighted MRI techniques have been developed and validated during the past 2 decades. While offering various neuroanatomical inferences, these techniques differ in their proposed optimal acquisition design, preventing clinicians and researchers benefiting from all potential inference methods, particularly when limited time is available. This study reports an optimal design that enables for a time-efficient diffusion-weighted MRI acquisition scheme at 7 Tesla. The primary audience of this article is the typical end user, interested in diffusion-weighted microstructural imaging at 7 Tesla. We tested b-values in the range of 700 to 3000 s/mm 2 with different number of angular diffusion-encoding samples, against a data-driven "gold standard." The suggested design is a protocol with b-values of 1000 and 2500 s/mm 2 , with 25 and 50 samples, uniformly distributed over two shells. We also report a range of protocols in which the results of fitting microstructural models to the diffusion-weighted data had high correlation with the gold standard. We estimated minimum acquisition requirements that enable diffusion tensor imaging, higher angular resolution diffusion-weighted imaging, neurite orientation dispersion, and density imaging and white matter tract integrity across whole brain with isotropic resolution of 1.8 mm in less than 11 min. Magn Reson Med 78:2170-2184, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  2. A Modified Protocol for Bisulfite Genomic Sequencing of Difficult Samples

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    Pappas Jane J

    2009-06-01

    Full Text Available Abstract The bisulfite genomic sequencing protocol is a widely used method for analyzing DNA methylation. It relies on the deamination of unmethylated cytosine residues to uracil; however, its high rates of DNA degradation and incomplete cytosine to uracil conversion often lead to failed experiments, uninformative results, and false positives. Here, we report the addition of a single-step multiple restriction enzyme digestion (MRED designed to differentially digest polymerase chain reaction products amplified from unconverted DNA while leaving those of converted DNA intact. We show that for our model system, RARB2 P2 promoter, use of MRED increased informative sequencings ninefold, and MRED did not alter the clonal representation in one fully methylated cell line, H-596, treated or not with 5-azadeoxycytidine, a methylation inhibitor. We believe that this method may easily be adapted for analyzing other genes and provide guidelines for selecting the most appropriate MRED restriction enzymes.

  3. A Modified Protocol for Bisulfite Genomic Sequencing of Difficult Samples

    Directory of Open Access Journals (Sweden)

    Toulouse André

    2009-01-01

    Full Text Available Abstract The bisulfite genomic sequencing protocol is a widely used method for analyzing DNA methylation. It relies on the deamination of unmethylated cytosine residues to uracil; however, its high rates of DNA degradation and incomplete cytosine to uracil conversion often lead to failed experiments, uninformative results, and false positives. Here, we report the addition of a single-step multiple restriction enzyme digestion (MRED designed to differentially digest polymerase chain reaction products amplified from unconverted DNA while leaving those of converted DNA intact. We show that for our model system, RARB2 P2 promoter, use of MRED increased informative sequencings ninefold, and MRED did not alter the clonal representation in one fully methylated cell line, H-596, treated or not with 5-azadeoxycytidine, a methylation inhibitor. We believe that this method may easily be adapted for analyzing other genes and provide guidelines for selecting the most appropriate MRED restriction enzymes.

  4. Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

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    Aigrain, Louise; Gu, Yong; Quail, Michael A

    2016-06-13

    The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed the democratization of DNA sequencing both in terms of price per sequenced bases and ease to produce DNA libraries. When it comes to preparing DNA sequencing libraries for Illumina, the current market leader, a plethora of kits are available and it can be difficult for the users to determine which kit is the most appropriate and efficient for their applications; the main concerns being not only cost but also minimal bias, yield and time efficiency. We compared 9 commercially available library preparation kits in a systematic manner using the same DNA sample by probing the amount of DNA remaining after each protocol steps using a new droplet digital PCR (ddPCR) assay. This method allows the precise quantification of fragments bearing either adaptors or P5/P7 sequences on both ends just after ligation or PCR enrichment. We also investigated the potential influence of DNA input and DNA fragment size on the final library preparation efficiency. The overall library preparations efficiencies of the libraries show important variations between the different kits with the ones combining several steps into a single one exhibiting some final yields 4 to 7 times higher than the other kits. Detailed ddPCR data also reveal that the adaptor ligation yield itself varies by more than a factor of 10 between kits, certain ligation efficiencies being so low that it could impair the original library complexity and impoverish the sequencing results. When a PCR enrichment step is necessary, lower adaptor-ligated DNA inputs leads to greater amplification yields, hiding the latent disparity between kits. We describe a ddPCR assay that allows us to probe the efficiency of the most critical step in the library preparation, ligation, and to draw conclusion on which kits is more likely to preserve the sample heterogeneity and reduce the need of amplification.

  5. SSh versus TSE sequence protocol in rapid MR examination of pediatric patients with programmable drainage system.

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    Brichtová, Eva; Šenkyřík, J

    2017-05-01

    A low radiation burden is essential during diagnostic procedures in pediatric patients due to their high tissue sensitivity. Using MR examination instead of the routinely used CT reduces the radiation exposure and the risk of adverse stochastic effects. Our retrospective study evaluated the possibility of using ultrafast single-shot (SSh) sequences and turbo spin echo (TSE) sequences in rapid MR brain imaging in pediatric patients with hydrocephalus and a programmable ventriculoperitoneal drainage system. SSh sequences seem to be suitable for examining pediatric patients due to the speed of using this technique, but significant susceptibility artifacts due to the programmable drainage valve degrade the image quality. Therefore, a rapid MR examination protocol based on TSE sequences, less sensitive to artifacts due to ferromagnetic components, has been developed. Of 61 pediatric patients who were examined using MR and the SSh sequence protocol, a group of 15 patients with hydrocephalus and a programmable drainage system also underwent TSE sequence MR imaging. The susceptibility artifact volume in both rapid MR protocols was evaluated using a semiautomatic volumetry system. A statistically significant decrease in the susceptibility artifact volume has been demonstrated in TSE sequence imaging in comparison with SSh sequences. Using TSE sequences reduced the influence of artifacts from the programmable valve, and the image quality in all cases was rated as excellent. In all patients, rapid MR examinations were performed without any need for intravenous sedation or general anesthesia. Our study results strongly suggest the superiority of the TSE sequence MR protocol compared to the SSh sequence protocol in pediatric patients with a programmable ventriculoperitoneal drainage system due to a significant reduction of susceptibility artifact volume. Both rapid sequence MR protocols provide quick and satisfactory brain imaging with no ionizing radiation and a reduced need

  6. Simple protocol for population (Sanger) sequencing for Zika virus genomic regions.

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    Cabral, Gabriela Bastos; Ferreira, João Leandro de Paula; Souza, Renato Pereira de; Cunha, Mariana Sequetin; Luchs, Adriana; Figueiredo, Cristina Adelaide; Brígido, Luís Fernando de Macedo

    2018-01-01

    A number of Zika virus (ZIKV) sequences were obtained using Next-generation sequencing (NGS), a methodology widely applied in genetic diversity studies and virome discovery. However Sanger method is still a robust, affordable, rapid and specific tool to obtain valuable sequences. The aim of this study was to develop a simple and robust Sanger sequencing protocol targeting ZIKV relevant genetic regions, as envelope protein and nonstructural protein 5 (NS5). In addition, phylogenetic analysis of the ZIKV strains obtained using the present protocol and their comparison with previously published NGS sequences were also carried out. Six Vero cells isolates from serum and one urine sample were available to develop the procedure. Primer sets were designed in order to conduct a nested RT-PCR and a Sanger sequencing protocols. Bayesian analysis was used to infer phylogenetic relationships. Seven complete ZIKV envelope protein (1,571 kb) and six partial NS5 (0,798 Kb) were obtained using the protocol, with no amplification of NS5 gene from urine sample. Two NS5 sequences presented ambiguities at positions 495 and 196. Nucleotide analysis of a Sanger sequence and consensus sequence of previously NGS study revealed 100% identity. ZIKV strains described here clustered within the Asian lineage. The present study provided a simple and low-cost Sanger protocol to sequence relevant genes of the ZIKV genome. The identity of Sanger generated sequences with published consensus NGS support the use of Sanger method for ZIKV population studies. The regions evaluated were able to provide robust phylogenetic signals and may be used to conduct molecular epidemiological studies and monitor viral evolution.

  7. The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia.

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    Kumar, Ashwini; Kankainen, Matti; Parsons, Alun; Kallioniemi, Olli; Mattila, Pirkko; Heckman, Caroline A

    2017-08-17

    RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the methodology into the clinic is still hampered by inconsistent results from different RNA-seq protocols and involves further evaluation of its analytical reliability using patient samples. Here, we applied two commonly used RNA-seq library preparation protocols to samples from acute leukemia patients to understand how poly-A-tailed mRNA selection (PA) and ribo-depletion (RD) based RNA-seq library preparation protocols affect gene fusion detection, variant calling, and gene expression profiling. Overall, the protocols produced similar results with consistent outcomes. Nevertheless, the PA protocol was more efficient in quantifying expression of leukemia marker genes and showed better performance in the expression-based classification of leukemia. Independent qRT-PCR experiments verified that the PA protocol better represented total RNA compared to the RD protocol. In contrast, the RD protocol detected a higher number of non-coding RNA features and had better alignment efficiency. The RD protocol also recovered more known fusion-gene events, although variability was seen in fusion gene predictions. The overall findings provide a framework for the use of RNA-seq in a precision medicine setting with limited number of samples and suggest that selection of the library preparation protocol should be based on the objectives of the analysis.

  8. Abbreviated protocol for breast MRI: Are multiple sequences needed for cancer detection?

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    Mango, Victoria L., E-mail: vlm2125@columbia.edu [Columbia University Medical Center, Herbert Irving Pavilion, 161 Fort Washington Avenue, 10th Floor, New York, NY 10032 (United States); Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Morris, Elizabeth A., E-mail: morrise@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); David Dershaw, D., E-mail: dershawd@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Abramson, Andrea, E-mail: abramsoa@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Fry, Charles, E-mail: charles_fry@nymc.edu [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); New York Medical College, 40 Sunshine Cottage Rd, Valhalla, NY 10595 (United States); Moskowitz, Chaya S. [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Hughes, Mary, E-mail: hughesm@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Kaplan, Jennifer, E-mail: kaplanj@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Jochelson, Maxine S., E-mail: jochelsm@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States)

    2015-01-15

    Highlights: • Abbreviated breast MR demonstrates high sensitivity for breast carcinoma detection. • Time to perform/interpret the abbreviated exam is shorter than a standard MRI exam. • An abbreviated breast MRI could reduce costs and make MRI screening more available. - Abstract: Objective: To evaluate the ability of an abbreviated breast magnetic resonance imaging (MRI) protocol, consisting of a precontrast T1 weighted (T1W) image and single early post-contrast T1W image, to detect breast carcinoma. Materials and methods: A HIPAA compliant Institutional Review Board approved review of 100 consecutive breast MRI examinations in patients with biopsy proven unicentric breast carcinoma. 79% were invasive carcinomas and 21% were ductal carcinoma in situ. Four experienced breast radiologists, blinded to carcinoma location, history and prior examinations, assessed the abbreviated protocol evaluating only the first post-contrast T1W image, post-processed subtracted first post-contrast and subtraction maximum intensity projection images. Detection and localization of tumor were compared to the standard full diagnostic examination consisting of 13 pre-contrast, post-contrast and post-processed sequences. Results: All 100 cancers were visualized on initial reading of the abbreviated protocol by at least one reader. The mean sensitivity for each sequence was 96% for the first post-contrast sequence, 96% for the first post-contrast subtraction sequence and 93% for the subtraction MIP sequence. Within each sequence, there was no significant difference between the sensitivities among the 4 readers (p = 0.471, p = 0.656, p = 0.139). Mean interpretation time was 44 s (range 11–167 s). The abbreviated imaging protocol could be performed in approximately 10–15 min, compared to 30–40 min for the standard protocol. Conclusion: An abbreviated breast MRI protocol allows detection of breast carcinoma. One pre and post-contrast T1W sequence may be adequate for detecting

  9. Abbreviated protocol for breast MRI: Are multiple sequences needed for cancer detection?

    International Nuclear Information System (INIS)

    Mango, Victoria L.; Morris, Elizabeth A.; David Dershaw, D.; Abramson, Andrea; Fry, Charles; Moskowitz, Chaya S.; Hughes, Mary; Kaplan, Jennifer; Jochelson, Maxine S.

    2015-01-01

    Highlights: • Abbreviated breast MR demonstrates high sensitivity for breast carcinoma detection. • Time to perform/interpret the abbreviated exam is shorter than a standard MRI exam. • An abbreviated breast MRI could reduce costs and make MRI screening more available. - Abstract: Objective: To evaluate the ability of an abbreviated breast magnetic resonance imaging (MRI) protocol, consisting of a precontrast T1 weighted (T1W) image and single early post-contrast T1W image, to detect breast carcinoma. Materials and methods: A HIPAA compliant Institutional Review Board approved review of 100 consecutive breast MRI examinations in patients with biopsy proven unicentric breast carcinoma. 79% were invasive carcinomas and 21% were ductal carcinoma in situ. Four experienced breast radiologists, blinded to carcinoma location, history and prior examinations, assessed the abbreviated protocol evaluating only the first post-contrast T1W image, post-processed subtracted first post-contrast and subtraction maximum intensity projection images. Detection and localization of tumor were compared to the standard full diagnostic examination consisting of 13 pre-contrast, post-contrast and post-processed sequences. Results: All 100 cancers were visualized on initial reading of the abbreviated protocol by at least one reader. The mean sensitivity for each sequence was 96% for the first post-contrast sequence, 96% for the first post-contrast subtraction sequence and 93% for the subtraction MIP sequence. Within each sequence, there was no significant difference between the sensitivities among the 4 readers (p = 0.471, p = 0.656, p = 0.139). Mean interpretation time was 44 s (range 11–167 s). The abbreviated imaging protocol could be performed in approximately 10–15 min, compared to 30–40 min for the standard protocol. Conclusion: An abbreviated breast MRI protocol allows detection of breast carcinoma. One pre and post-contrast T1W sequence may be adequate for detecting

  10. Using machine learning for sequence-level automated MRI protocol selection in neuroradiology.

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    Brown, Andrew D; Marotta, Thomas R

    2017-10-27

    Incorrect imaging protocol selection can lead to important clinical findings being missed, contributing to both wasted health care resources and patient harm. We present a machine learning method for analyzing the unstructured text of clinical indications and patient demographics from magnetic resonance imaging (MRI) orders to automatically protocol MRI procedures at the sequence level. We compared 3 machine learning models - support vector machine, gradient boosting machine, and random forest - to a baseline model that predicted the most common protocol for all observations in our test set. The gradient boosting machine model significantly outperformed the baseline and demonstrated the best performance of the 3 models in terms of accuracy (95%), precision (86%), recall (80%), and Hamming loss (0.0487). This demonstrates the feasibility of automating sequence selection by applying machine learning to MRI orders. Automated sequence selection has important safety, quality, and financial implications and may facilitate improvements in the quality and safety of medical imaging service delivery. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Seismic Parameters of Mining-Induced Aftershock Sequences for Re-entry Protocol Development

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    Vallejos, Javier A.; Estay, Rodrigo A.

    2018-03-01

    A common characteristic of deep mines in hard rock is induced seismicity. This results from stress changes and rock failure around mining excavations. Following large seismic events, there is an increase in the levels of seismicity, which gradually decay with time. Restricting access to areas of a mine for enough time to allow this decay of seismic events is the main approach in re-entry strategies. The statistical properties of aftershock sequences can be studied with three scaling relations: (1) Gutenberg-Richter frequency magnitude, (2) the modified Omori's law (MOL) for the temporal decay, and (3) Båth's law for the magnitude of the largest aftershock. In this paper, these three scaling relations, in addition to the stochastic Reasenberg-Jones model are applied to study the characteristic parameters of 11 large magnitude mining-induced aftershock sequences in four mines in Ontario, Canada. To provide guidelines for re-entry protocol development, the dependence of the scaling relation parameters on the magnitude of the main event are studied. Some relations between the parameters and the magnitude of the main event are found. Using these relationships and the scaling relations, a space-time-magnitude re-entry protocol is developed. These findings provide a first approximation to concise and well-justified guidelines for re-entry protocol development applicable to the range of mining conditions found in Ontario, Canada.

  12. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

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    Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

    2016-01-01

    The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

  13. Gene length and detection bias in single cell RNA sequencing protocols [version 1; referees: 2 approved

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    Belinda Phipson

    2017-04-01

    Full Text Available Background: Single cell RNA sequencing (scRNA-seq has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, many technical challenges need to be overcome during data generation. Due to minute amounts of starting material, samples undergo extensive amplification, increasing technical variability. A solution for mitigating amplification biases is to include unique molecular identifiers (UMIs, which tag individual molecules. Transcript abundances are then estimated from the number of unique UMIs aligning to a specific gene, with PCR duplicates resulting in copies of the UMI not included in expression estimates. Methods: Here we investigate the effect of gene length bias in scRNA-Seq across a variety of datasets that differ in terms of capture technology, library preparation, cell types and species. Results: We find that scRNA-seq datasets that have been sequenced using a full-length transcript protocol exhibit gene length bias akin to bulk RNA-seq data. Specifically, shorter genes tend to have lower counts and a higher rate of dropout. In contrast, protocols that include UMIs do not exhibit gene length bias, with a mostly uniform rate of dropout across genes of varying length. Across four different scRNA-Seq datasets profiling mouse embryonic stem cells (mESCs, we found the subset of genes that are only detected in the UMI datasets tended to be shorter, while the subset of genes detected only in the full-length datasets tended to be longer. Conclusions: We find that the choice of scRNA-seq protocol influences the detection rate of genes, and that full-length datasets exhibit gene-length bias. In addition, despite clear differences between UMI and full-length transcript data, we illustrate that full-length and UMI data can be combined to reveal the underlying biology

  14. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.

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    Marine, Rachel; Polson, Shawn W; Ravel, Jacques; Hatfull, Graham; Russell, Daniel; Sullivan, Matthew; Syed, Fraz; Dumas, Michael; Wommack, K Eric

    2011-11-01

    Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions. De novo genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.

  15. Time-Efficient Cloning Attacks Identification in Large-Scale RFID Systems

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    Ju-min Zhao

    2017-01-01

    Full Text Available Radio Frequency Identification (RFID is an emerging technology for electronic labeling of objects for the purpose of automatically identifying, categorizing, locating, and tracking the objects. But in their current form RFID systems are susceptible to cloning attacks that seriously threaten RFID applications but are hard to prevent. Existing protocols aimed at detecting whether there are cloning attacks in single-reader RFID systems. In this paper, we investigate the cloning attacks identification in the multireader scenario and first propose a time-efficient protocol, called the time-efficient Cloning Attacks Identification Protocol (CAIP to identify all cloned tags in multireaders RFID systems. We evaluate the performance of CAIP through extensive simulations. The results show that CAIP can identify all the cloned tags in large-scale RFID systems fairly fast with required accuracy.

  16. Protocols for 16S rDNA Array Analyses of Microbial Communities by Sequence-Specific Labeling of DNA Probes

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    Knut Rudi

    2003-01-01

    Full Text Available Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and regions with relatively high variability. The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes. Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.

  17. MR arthrography of the shoulder: Optimizing pulse sequence protocols for the evaluation of cartilage and labrum

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    Guermazi, Ali, E-mail: Ali.Guermazi@aspetar.com [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Jomaah, Nabil [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Hayashi, Daichi [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Department of Radiology, Bridgeport Hospital, Yale University School of Medicine, 267 Grant Street, Bridgeport, CT 06610 (United States); Jarraya, Mohamed [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Silva, Jose Roberto [Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Niu, Jingbo [Clinical Epidemiology Research and Training Unit, Boston University School of Medicine, 650 Albany Street, Suite 200, Boston, MA 02118 (United States); Almusa, Emad; Landreau, Philippe [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); and others

    2014-08-15

    Objectives: To compare axial T1weighted fat-saturated (T1w fs) and T1w non-fs sequences, and coronal T1w-fs and T2w-fs sequences, for evaluation of cartilage and labrum using CT arthrography (CTA) as the reference. Methods: Patients had MR arthrography (MRA) and CTA of the shoulder on the same day. Cartilage was assessed for superficial and full thickness focal and diffuse damage. Labral lesions were graded for Bankart variants and SLAP lesions. CTA images were read for the same features. The diagnostic performance of MRA including area under the curve (AUC) was evaluated against CTA. Results: When comparing axial sequences, the diagnostic performance for cartilage lesion detection on T1w non-fs was 61.9% (sensitivity) 93.6% (specificity) and 89.5% (accuracy) with AUC 0.782, while that for T1w fs was 61.9%, 94.0%, 89.8% and 0.783. For labral assessment, it was 89.1%, 93.0%, 91.4% and 0.919 for T1w non-fs, and 89.9%, 94.0%, 92.6% and 0.922 for T1w fs. Comparing coronal sequences, diagnostic performance for cartilage was 42.5%, 97.5%, 89.8% and 0.702 for T1w fs, and 38.4%, 98.7%, 90.2%, and 0.686 for T2w fs. For the labrum it was 85.1%, 87.5%, 86.2%, and 0.868 for T1w fs, and 75.7%, 97.5%, 80.8% and 0.816 for T2w fs. Conclusions: Axial T1w fs and T1w non-fs sequences are comparable in their ability to diagnose cartilage and labral lesions. Coronal T1w fs sequence offers slightly higher sensitivity but slightly lower specificity than T2w fs sequence for diagnosis of cartilage and labral lesions.

  18. MR arthrography of the shoulder: Optimizing pulse sequence protocols for the evaluation of cartilage and labrum

    International Nuclear Information System (INIS)

    Guermazi, Ali; Jomaah, Nabil; Hayashi, Daichi; Jarraya, Mohamed; Silva, Jose Roberto; Niu, Jingbo; Almusa, Emad; Landreau, Philippe

    2014-01-01

    Objectives: To compare axial T1weighted fat-saturated (T1w fs) and T1w non-fs sequences, and coronal T1w-fs and T2w-fs sequences, for evaluation of cartilage and labrum using CT arthrography (CTA) as the reference. Methods: Patients had MR arthrography (MRA) and CTA of the shoulder on the same day. Cartilage was assessed for superficial and full thickness focal and diffuse damage. Labral lesions were graded for Bankart variants and SLAP lesions. CTA images were read for the same features. The diagnostic performance of MRA including area under the curve (AUC) was evaluated against CTA. Results: When comparing axial sequences, the diagnostic performance for cartilage lesion detection on T1w non-fs was 61.9% (sensitivity) 93.6% (specificity) and 89.5% (accuracy) with AUC 0.782, while that for T1w fs was 61.9%, 94.0%, 89.8% and 0.783. For labral assessment, it was 89.1%, 93.0%, 91.4% and 0.919 for T1w non-fs, and 89.9%, 94.0%, 92.6% and 0.922 for T1w fs. Comparing coronal sequences, diagnostic performance for cartilage was 42.5%, 97.5%, 89.8% and 0.702 for T1w fs, and 38.4%, 98.7%, 90.2%, and 0.686 for T2w fs. For the labrum it was 85.1%, 87.5%, 86.2%, and 0.868 for T1w fs, and 75.7%, 97.5%, 80.8% and 0.816 for T2w fs. Conclusions: Axial T1w fs and T1w non-fs sequences are comparable in their ability to diagnose cartilage and labral lesions. Coronal T1w fs sequence offers slightly higher sensitivity but slightly lower specificity than T2w fs sequence for diagnosis of cartilage and labral lesions

  19. Optimizing the MRI protocol of the sacroiliac joints in Spondyloarthritis: which para-axial sequence should be used?

    Energy Technology Data Exchange (ETDEWEB)

    Giraudo, Chiara; Weber, Michael; Platzgummer, Hannes; Kainberger, Franz; Schueller-Weidekamm, Claudia [Medical University of Vienna, Vienna General Hospital, Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging und Image-guided Therapy, Vienna (Austria); Magnaldi, Silvia [Fondazione Poliambulanza Istituto Ospedaliero, Dipartimento di Radiologia e Diagnostica per Immagini, Brescia (Italy); Puchner, Antonia [Medical University of Vienna, Vienna General Hospital, Division of Rheumatology, Department of Internal Medicine III, Vienna (Austria)

    2016-01-15

    To assess the diagnostic value of para-axial T2w-TSE (paT2) and fat-suppressed proton density (paPD-FS) MRI sequences for the evaluation of the sacroiliac joint (SIJ) of patients with axial Spondylarthritis (SpA). One hundred and six patients with clinical findings suggestive of SpA underwent an MR protocol of the SIJ with additional paPD-FS (41 patients) and paT2 (105 patients). Acute (bone marrow oedema [BME], enthesitis, capsulitis, synovitis) and chronic findings (erosions, ankylosis) were assessed by paPD-FS and compared with the gold standard post-contrast sequences, whereas chronic features (because of the lack of fat suppression) were evaluated on paT2 and compared with pcT1. paPD-FS demonstrated high sensitivity (98.9 %) and specificity (99.1 %) for BME; sensitivity and specificity for synovitis and enthesitis were 100 %; 85.7 % and 100 %, respectively, for capsulitis. paPD-FS and paT2 showed 100 % sensitivity and specificity for ankylosis; for erosions, paT2 demonstrated 85.3 % sensitivity and 100 % specificity, whereas paPD-FS, respectively, 98 % and 100 %. PaT2 and paPD-FS provided precious information enabling an accurate interpretation of the heterogeneous findings of SpA. paPD-FS showed good results in detecting acute and chronic lesions and its inclusion in a routine MR examination of the SIJ could increase the diagnostic performance of a pre-contrast protocol. (orig.)

  20. A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.

    Science.gov (United States)

    Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C; Quake, Stephen R; Burkholder, William F

    2013-01-01

    Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

  1. Efficient RNA extraction protocol for the wood mangrove species Laguncularia racemosa suited for next-generation RNA sequencing

    International Nuclear Information System (INIS)

    Wilwerth, M. W.; Rossetto, P.

    2016-01-01

    Mangrove flora and habitat have immeasurable importance in marine and coastal ecology as well as in the economy. Despite their importance, they are constantly threatened by oil spill accidents and environmental contamination; therefore, it is crucial to understand the changes in gene expression to better predict toxicity in these plants. Among the species of Atlantic coast mangrove (Americas and Africa), Laguncularia racemosa, or white mangrove, is a conspicuous species. The wide distribution of L. racemosa in areas where marine oil exploration is rapidly increasing make it a candidate mangrove species model to uncover the impact of oil spills at the molecular level with the use of massive transcriptome sequencing. However, for this purpose, the RNA extraction protocol should ensure low levels of contaminants and structure integrity. In this study, eight RNA extraction methods were tested and analysed using downstream applications. The InviTrap Spin Plant RNA Mini Kit performed best with regard to purity and integrity. Moreover, the obtained RNA was submitted to cDNA synthesis and RT-PCR, successfully generating amplification products of the expected size. These Results show the applicability of the RNA obtained here for downstream methodologies, such as the construction of cDNA libraries for the Illumina Hi-seq platform. (author)

  2. Improving the time efficiency of the Fourier synthesis method for slice selection in magnetic resonance imaging.

    Science.gov (United States)

    Tahayori, B; Khaneja, N; Johnston, L A; Farrell, P M; Mareels, I M Y

    2016-01-01

    The design of slice selective pulses for magnetic resonance imaging can be cast as an optimal control problem. The Fourier synthesis method is an existing approach to solve these optimal control problems. In this method the gradient field as well as the excitation field are switched rapidly and their amplitudes are calculated based on a Fourier series expansion. Here, we provide a novel insight into the Fourier synthesis method via representing the Bloch equation in spherical coordinates. Based on the spherical Bloch equation, we propose an alternative sequence of pulses that can be used for slice selection which is more time efficient compared to the original method. Simulation results demonstrate that while the performance of both methods is approximately the same, the required time for the proposed sequence of pulses is half of the original sequence of pulses. Furthermore, the slice selectivity of both sequences of pulses changes with radio frequency field inhomogeneities in a similar way. We also introduce a measure, referred to as gradient complexity, to compare the performance of both sequences of pulses. This measure indicates that for a desired level of uniformity in the excited slice, the gradient complexity for the proposed sequence of pulses is less than the original sequence. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  3. Message and time efficient multi-broadcast schemes

    Directory of Open Access Journals (Sweden)

    Liron Levin

    2013-10-01

    Full Text Available We consider message and time efficient broadcasting and multi-broadcasting in wireless ad-hoc networks, where a subset of nodes, each with a unique rumor, wish to broadcast their rumors to all destinations while minimizing the total number of transmissions and total time until all rumors arrive to their destination. Under centralized settings, we introduce a novel approximation algorithm that provides almost optimal results with respect to the number of transmissions and total time, separately. Later on, we show how to efficiently implement this algorithm under distributed settings, where the nodes have only local information about their surroundings. In addition, we show multiple approximation techniques based on the network collision detection capabilities and explain how to calibrate the algorithms' parameters to produce optimal results for time and messages.

  4. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    OpenAIRE

    Farkhondeh Saba; Moslem Papizadeh; Javad Khansha; Mahshid Sedghi; Mehrnoosh Rasooli; Mohammad Ali Amoozegar; Mohammad Reza Soudi; Seyed Abolhassan Shahzadeh Fazeli

    2016-01-01

    Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR). Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Me...

  5. High resolution MR eye protocol optimization: Comparison between 3D-CISS, 3D-PSIF and 3D-VIBE sequences.

    Science.gov (United States)

    Tsiapa, Irene; Tsilimbaris, Miltiadis K; Papadaki, Efrosini; Bouziotis, Penelope; Pallikaris, Ioannis G; Karantanas, Apostolos H; Maris, Thomas G

    2015-11-01

    The purpose of this study was to compare selected MRI pulse sequences and to evaluate their utility for depicting specific anatomic regions in the eye. A High-Resolution (HR) 0.08 × 0.08 × 0.60 mm(3) MRI protocol was developed on a 1.5-T clinical system and applied in the left eye of an albino rabbit, utilizing a small field of view surface coil. The comprehensive MRI protocol consisted of two 3D (T2/T1)w sequences (3D-PSIF and 3D-CISS), and one 3D T1w sequence (3D-VIBE). The T1w 3D-VIBE sequence was acquired, before and after intravenous injection of 0.2 mmol/kgr gadolinium-DTPA. Signal-to-Noise Ratios (SNR) and Contrast-to-Noise Ratios (CNR) amongst specific eye anatomical areas were calculated for each sequence. The presence of artifacts was rated subjectively utilizing a 5 point scale. 3D-PSIF and 3D-CISS provide better delineation and visualization of the eye as compared with 3D-VIBE sequences. 3D-CISS images present the highest SNR and revealed better discrimination of the ocular surrounding tissues; its basic drawback though is related to ghost artifacts appearing in the anterior chamber and resulting in the lowest image quality. In post-contrast imaging, the T1w 3D-VIBE sequence provided the best overall image quality. Moreover, 3D (T2/T1)w sequences can provide good anatomic depiction of the eye segments. Agreement between the two independent readers was good. Optimization of a comprehensive MR eye imaging protocol is achieved. A higher SNR, a better spatial resolution and a reduction of the total scan time were obtained, thus making clinical MRI systems more reliable in eye imaging. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  6. Plant DNA detection from grasshopper guts: A step-by-step protocol, from tissue preparation to obtaining plant DNA sequences.

    Science.gov (United States)

    Avanesyan, Alina

    2014-02-01

    A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. • The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA) gene and was tested in several feeding experiments. Plant DNA was obtained at seven time points post-ingestion from whole guts and separate gut sections, and was detectable up to 12 h post-ingestion in nymphs and 22 h post-ingestion in adult grasshoppers. • The proposed protocol is an effective, relatively quick, and low-cost method of detecting plant DNA from the grasshopper gut and its different sections. This has important applications, from exploring plant "movement" during food consumption, to detecting plant-insect interactions.

  7. A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia.

    Science.gov (United States)

    Dan, Tong; Liu, Wenjun; Sun, Zhihong; Lv, Qiang; Xu, Haiyan; Song, Yuqin; Zhang, Heping

    2014-06-09

    Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China. Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates. Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics.

  8. A simple protocol for the extraction and sequence analysis of DNA from study skin of museum collections

    Directory of Open Access Journals (Sweden)

    Nadia de Moraes-Barros

    2007-01-01

    Full Text Available Museum collections have been widely used as sources of biological samples for molecular biology studies and there are several methodologies and techniques to obtain and analyze DNA from tissues archived in museums, but most of these protocols have been developed for a specific tissue or are commercial kits. We present a simple protocol for extracting and amplifying DNA segments from sloth museum specimens. With this simple protocol we analyzed DNA fragments from 64% of 64 skin samples from three-toed sloths (Bradypus variegatus and Bradypus tridactylus archived in three different museums: 43 samples from the University of São Paulo Museum of Zoology (Museu de Zoologia da Universidade de São Paulo, MUZUSP São Paulo, São Paulo, Brazil; 18 samples from the Emílio Goeldi Museum (Museu Paraense Emílio Goeldi, MPEG, Belém, Pará, Brazil; and 3 samples from the Museum of Vertebrate Zoology (MVZ University of California, Berkeley, USA. The specimens sampled ranged in age from 18 to 108 years old. Our methodology allowed the recovery of up to 700 bp of mitochondrial DNA and 400 bp of nuclear genes. Thereafter, it is useful for genetic diversity studies of three-toed sloths and could be applied to other animals.

  9. Plant DNA Detection from Grasshopper Guts: A Step-by-Step Protocol, from Tissue Preparation to Obtaining Plant DNA Sequences

    Directory of Open Access Journals (Sweden)

    Alina Avanesyan

    2014-02-01

    Full Text Available Premise of the study: A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. Methods and Results: The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA gene and was tested in several feeding experiments. Plant DNA was obtained at seven time points post-ingestion from whole guts and separate gut sections, and was detectable up to 12 h post-ingestion in nymphs and 22 h post-ingestion in adult grasshoppers. Conclusions: The proposed protocol is an effective, relatively quick, and low-cost method of detecting plant DNA from the grasshopper gut and its different sections. This has important applications, from exploring plant “movement” during food consumption, to detecting plant–insect interactions.

  10. Comprehensive small animal imaging strategies on a clinical 3 T dedicated head MR-scanner; adapted methods and sequence protocols in CNS pathologies.

    Directory of Open Access Journals (Sweden)

    Deepu R Pillai

    Full Text Available BACKGROUND: Small animal models of human diseases are an indispensable aspect of pre-clinical research. Being dynamic, most pathologies demand extensive longitudinal monitoring to understand disease mechanisms, drug efficacy and side effects. These considerations often demand the concomitant development of monitoring systems with sufficient temporal and spatial resolution. METHODOLOGY AND RESULTS: This study attempts to configure and optimize a clinical 3 Tesla magnetic resonance scanner to facilitate imaging of small animal central nervous system pathologies. The hardware of the scanner was complemented by a custom-built, 4-channel phased array coil system. Extensive modification of standard sequence protocols was carried out based on tissue relaxometric calculations. Proton density differences between the gray and white matter of the rodent spinal cord along with transverse relaxation due to magnetic susceptibility differences at the cortex and striatum of both rats and mice demonstrated statistically significant differences. The employed parallel imaging reconstruction algorithms had distinct properties dependent on the sequence type and in the presence of the contrast agent. The attempt to morphologically phenotype a normal healthy rat brain in multiple planes delineated a number of anatomical regions, and all the clinically relevant sequels following acute cerebral ischemia could be adequately characterized. Changes in blood-brain-barrier permeability following ischemia-reperfusion were also apparent at a later time. Typical characteristics of intra-cerebral haemorrhage at acute and chronic stages were also visualized up to one month. Two models of rodent spinal cord injury were adequately characterized and closely mimicked the results of histological studies. In the employed rodent animal handling system a mouse model of glioblastoma was also studied with unequivocal results. CONCLUSIONS: The implemented customizations including extensive

  11. A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat

    Directory of Open Access Journals (Sweden)

    Nap Jan-Peter

    2007-04-01

    Full Text Available Abstract Background The Affymetrix GeneChip technology uses multiple probes per gene to measure its expression level. Individual probe signals can vary widely, which hampers proper interpretation. This variation can be caused by probes that do not properly match their target gene or that match multiple genes. To determine the accuracy of Affymetrix arrays, we developed an extensive verification protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome databases. Results Applying this protocol to Affymetrix Mouse Genome arrays (the earlier U74Av2 and the newer 430 2.0 array, the number of sequence-verified probes with perfect matches was no less than 85% and 95%, respectively; and for 74% and 85% of the probe sets all probes were sequence verified. The latter percentages increased to 80% and 94% after discarding one or two unverifiable probes per probe set, and even further to 84% and 97% when, in addition, allowing for one or two mismatches between probe and target gene. Similar results were obtained for other mouse arrays, as well as for human and rat arrays. Based on these data, refined chip definition files for all arrays are provided online. Researchers can choose the version appropriate for their study to (reanalyze expression data. Conclusion The accuracy of Affymetrix probe sequences is higher than previously reported, particularly on newer arrays. Yet, refined probe set definitions have clear effects on the detection of differentially expressed genes. We demonstrate that the interpretation of the results of Affymetrix arrays is improved when the new chip definition files are used.

  12. Performance evaluation of a mitogenome capture and Illumina sequencing protocol using non-probative, case-type skeletal samples: Implications for the use of a positive control in a next-generation sequencing procedure.

    Science.gov (United States)

    Marshall, Charla; Sturk-Andreaggi, Kimberly; Daniels-Higginbotham, Jennifer; Oliver, Robert Sean; Barritt-Ross, Suzanne; McMahon, Timothy P

    2017-11-01

    Next-generation ancient DNA technologies have the potential to assist in the analysis of degraded DNA extracted from forensic specimens. Mitochondrial genome (mitogenome) sequencing, specifically, may be of benefit to samples that fail to yield forensically relevant genetic information using conventional PCR-based techniques. This report summarizes the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory's (AFMES-AFDIL) performance evaluation of a Next-Generation Sequencing protocol for degraded and chemically treated past accounting samples. The procedure involves hybridization capture for targeted enrichment of mitochondrial DNA, massively parallel sequencing using Illumina chemistry, and an automated bioinformatic pipeline for forensic mtDNA profile generation. A total of 22 non-probative samples and associated controls were processed in the present study, spanning a range of DNA quantity and quality. Data were generated from over 100 DNA libraries by ten DNA analysts over the course of five months. The results show that the mitogenome sequencing procedure is reliable and robust, sensitive to low template (one ng control DNA) as well as degraded DNA, and specific to the analysis of the human mitogenome. Haplotypes were overall concordant between NGS replicates and with previously generated Sanger control region data. Due to the inherent risk for contamination when working with low-template, degraded DNA, a contamination assessment was performed. The consumables were shown to be void of human DNA contaminants and suitable for forensic use. Reagent blanks and negative controls were analyzed to determine the background signal of the procedure. This background signal was then used to set analytical and reporting thresholds, which were designated at 4.0X (limit of detection) and 10.0X (limit of quantiation) average coverage across the mitogenome, respectively. Nearly all human samples exceeded the reporting threshold, although coverage

  13. On using multiple routing metrics with destination sequenced distance vector protocol for MultiHop wireless ad hoc networks

    Science.gov (United States)

    Mehic, M.; Fazio, P.; Voznak, M.; Partila, P.; Komosny, D.; Tovarek, J.; Chmelikova, Z.

    2016-05-01

    A mobile ad hoc network is a collection of mobile nodes which communicate without a fixed backbone or centralized infrastructure. Due to the frequent mobility of nodes, routes connecting two distant nodes may change. Therefore, it is not possible to establish a priori fixed paths for message delivery through the network. Because of its importance, routing is the most studied problem in mobile ad hoc networks. In addition, if the Quality of Service (QoS) is demanded, one must guarantee the QoS not only over a single hop but over an entire wireless multi-hop path which may not be a trivial task. In turns, this requires the propagation of QoS information within the network. The key to the support of QoS reporting is QoS routing, which provides path QoS information at each source. To support QoS for real-time traffic one needs to know not only minimum delay on the path to the destination but also the bandwidth available on it. Therefore, throughput, end-to-end delay, and routing overhead are traditional performance metrics used to evaluate the performance of routing protocol. To obtain additional information about the link, most of quality-link metrics are based on calculation of the lost probabilities of links by broadcasting probe packets. In this paper, we address the problem of including multiple routing metrics in existing routing packets that are broadcasted through the network. We evaluate the efficiency of such approach with modified version of DSDV routing protocols in ns-3 simulator.

  14. A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

    Science.gov (United States)

    Moser, Lindsey A.; Ramirez-Carvajal, Lisbeth; Puri, Vinita; Pauszek, Steven J.; Matthews, Krystal; Dilley, Kari A.; Mullan, Clancy; McGraw, Jennifer; Khayat, Michael; Beeri, Karen; Yee, Anthony; Dugan, Vivien; Heise, Mark T.; Frieman, Matthew B.; Rodriguez, Luis L.; Bernard, Kristen A.; Wentworth, David E.

    2016-01-01

    processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories. PMID:27822536

  15. Obtaining representative community profiles of anaerobic digesters through optimisation of 16S rRNA amplicon sequencing protocols

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; McIlroy, Simon Jon; Karst, Søren Michael

    RNA gene amplicon sequencing is rapid, cheap, high throughput, and has high taxonomic resolution. However, biases are introduced in multiple steps of this approach, including non-representative DNA extraction and uneven taxonomic coverage of selected PCR primers, potentially giving a skewed view...... parameters involving harsher lysis conditions than recommended for the commercial kit, and appeared to be similar for both the mesophilic and thermophilic reactor biomass samples. The community profiling was found to be greatly influenced by the selected PCR primers, and showed that in silico designed...

  16. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    Directory of Open Access Journals (Sweden)

    Farkhondeh Saba

    2017-01-01

    Full Text Available Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR. Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Methods:  According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications. Results:   This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.Conclusion:   Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.

  17. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    Directory of Open Access Journals (Sweden)

    Farkhondeh Saba

    2016-09-01

    Full Text Available Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR. Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Methods:  According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications. Results:   This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.Conclusion:   Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.

  18. An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing.

    Science.gov (United States)

    Amini, Parisa; Ettlin, Julia; Opitz, Lennart; Clementi, Elena; Malbon, Alexandra; Markkanen, Enni

    2017-08-23

    Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA-protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection (LCM) to isolate specific subpopulations of cells, recovery of sufficient RNA for analysis with reverse-transcription quantitative PCR (RT-qPCR) or next-generation sequencing (NGS) becomes very cumbersome and difficult. We excised matched cancer-associated stroma (CAS) and normal stroma from clinical specimen of FFPE canine mammary tumours using LCM, and compared the commonly used protease-based RNA isolation procedure with an adapted novel technique that additionally incorporates a focused ultrasonication step. We successfully adapted a protocol that uses focused ultrasonication to isolate RNA from small amounts of deparaffinised, stained, clinical LCM samples. Using this approach, we found that total RNA yields could be increased by 8- to 12-fold compared to a commonly used protease-based extraction technique. Surprisingly, RNA extracted using this new approach was qualitatively at least equal if not superior compared to the old approach, as Cq values in RT-qPCR were on average 2.3-fold lower using the new method. Finally, we demonstrate that RNA extracted using the new method performs comparably in NGS as well. We present a successful isolation protocol for extraction of RNA from difficult and limiting FFPE tissue samples that enables successful analysis of small sections of clinically relevant specimen. The possibility to study gene expression signatures in specific small sections of archival FFPE tissue, which often entail large amounts of highly relevant clinical follow-up data, unlocks a new dimension of hitherto difficult-to-analyse samples which now

  19. Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements-identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland.

    Science.gov (United States)

    Stadler, Tanja; Meinel, Dominik; Aguilar-Bultet, Lisandra; Huisman, Jana S; Schindler, Ruth; Egli, Adrian; Seth-Smith, Helena M B; Eichenberger, Lucas; Brodmann, Peter; Hübner, Philipp; Bagutti, Claudia; Tschudin-Sutter, Sarah

    2018-02-17

    Extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producing Escherichia coli was increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control. This protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment. This study has been approved by the local ethics committee (Ethikkommission Nordwest

  20. Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland

    Science.gov (United States)

    Stadler, Tanja; Meinel, Dominik; Aguilar-Bultet, Lisandra; Huisman, Jana S; Schindler, Ruth; Egli, Adrian; Seth-Smith, Helena M B; Eichenberger, Lucas; Brodmann, Peter; Hübner, Philipp; Bagutti, Claudia; Tschudin-Sutter, Sarah

    2018-01-01

    Introduction Extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producing Escherichia coli was increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control. Methods and analysis This protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment. Ethics and dissemination This study has been approved by the

  1. Plant DNA detection from grasshopper guts: A step-by-step protocol, from tissue preparation to obtaining plant DNA sequences 1

    OpenAIRE

    Avanesyan, Alina

    2014-01-01

    Premise of the study: A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. Methods and Results: The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA) gene and was te...

  2. Time Efficiency Of Point-Of-Sale Payment Methods: Preliminary Results

    OpenAIRE

    Micha ł Polasik,; Jakub Górka; Gracjan Wilczewski; Janusz Kunkowski; Karolina Przenajkowska

    2010-01-01

    This article presents a wide range of differ ent payment methods used at Point-Of-Sales from traditional cash and standard cards to contactless cards, RFID stickers and mobile payments (NFC and remote). All payment instruments are compared under the criterion of time efficiency that means the duration of a payment tr ansaction. The measurement of payment transactions was undertaken with the help of a novel research technique based on a digital chronography of vid...

  3. Accuracy, reproducibility, and time efficiency of dental measurements using different technologies.

    Science.gov (United States)

    Grünheid, Thorsten; Patel, Nishant; De Felippe, Nanci L; Wey, Andrew; Gaillard, Philippe R; Larson, Brent E

    2014-02-01

    Historically, orthodontists have taken dental measurements on plaster models. Technological advances now allow orthodontists to take these measurements on digital models. In this study, we aimed to assess the accuracy, reproducibility, and time efficiency of dental measurements taken on 3 types of digital models. emodels (GeoDigm, Falcon Heights, Minn), SureSmile models (OraMetrix, Richardson, Tex), and AnatoModels (Anatomage, San Jose, Calif) were made for 30 patients. Mesiodistal tooth-width measurements taken on these digital models were timed and compared with those on the corresponding plaster models, which were used as the gold standard. Accuracy and reproducibility were assessed using the Bland-Altman method. Differences in time efficiency were tested for statistical significance with 1-way analysis of variance. Measurements on SureSmile models were the most accurate, followed by those on emodels and AnatoModels. Measurements taken on SureSmile models were also the most reproducible. Measurements taken on SureSmile models and emodels were significantly faster than those taken on AnatoModels and plaster models. Tooth-width measurements on digital models can be as accurate as, and might be more reproducible and significantly faster than, those taken on plaster models. Of the models studied, the SureSmile models provided the best combination of accuracy, reproducibility, and time efficiency of measurement. Copyright © 2014 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

  4. Plant DNA detection from grasshopper guts: A step-by-step protocol, from tissue preparation to obtaining plant DNA sequences1

    Science.gov (United States)

    Avanesyan, Alina

    2014-01-01

    • Premise of the study: A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. • Methods and Results: The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA) gene and was tested in several feeding experiments. Plant DNA was obtained at seven time points post-ingestion from whole guts and separate gut sections, and was detectable up to 12 h post-ingestion in nymphs and 22 h post-ingestion in adult grasshoppers. • Conclusions: The proposed protocol is an effective, relatively quick, and low-cost method of detecting plant DNA from the grasshopper gut and its different sections. This has important applications, from exploring plant “movement” during food consumption, to detecting plant–insect interactions. PMID:25202604

  5. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

    Directory of Open Access Journals (Sweden)

    Olivier Loudig

    2017-03-01

    Full Text Available Formalin-fixed paraffin-embedded (FFPE specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases and women who did not develop invasive breast cancer within the same time interval (control. Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.

  6. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens.

    Science.gov (United States)

    Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J; Rohan, Thomas; Ben-Dov, Iddo Z

    2017-03-14

    Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.

  7. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

    Science.gov (United States)

    Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J.; Rohan, Thomas; Ben-Dov, Iddo Z.

    2017-01-01

    Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens. PMID:28335433

  8. Educating pediatric residents about breastfeeding: evaluation of 3 time-efficient teaching strategies.

    Science.gov (United States)

    Tender, Jennifer A F; Cuzzi, Sandra; Kind, Terry; Simmens, Samuel J; Blatt, Benjamin; Greenberg, Larrie

    2014-11-01

    Previously reported breastfeeding curricula for residents have combined different teaching methods, have focused on knowledge and attitudes, and have been time-intensive. This study aimed to evaluate 3 time-efficient breastfeeding curricula for effectiveness in regard to pediatric residents' knowledge, confidence, and skills in managing a simulated breastfeeding scenario. First-year pediatric residents during their 4-week community hospital newborn nursery rotation were consecutively assigned to 1 of 3 groups. Group 1 shadowed an International Board Certified Lactation Consultant (IBCLC) for 1 hour; group 2 watched a 25-minute case-based breastfeeding DVD; and group 3 observed a 3-hour prenatal parent breastfeeding class (CLS). Residents were assessed by (1) a pretest and posttest evaluating their breastfeeding knowledge and confidence, and (2) a clinical skills scenario managing a breastfeeding standardized patient (SP). Thirty-nine pediatric residents participated in the study (11 in IBCLC, 16 DVD, 12 CLS) over a 1-year period. All groups significantly improved their knowledge scores and confidence in managing breastfeeding problems, with the IBCLC group showing more improvement in knowledge than the other groups (P = .02) and a higher rating of their teaching method (P = .01). All groups performed well on the SP clinical skills scenario, with no significant difference between groups. All 3 teaching methods were time-efficient and produced important gains in knowledge and confidence, with residents in the IBCLC group demonstrating greatest improvement in knowledge and a higher rating of their teaching method. Our study provides support for 3 methods of teaching residents breastfeeding management and demonstrates that IBCLCs are well-received as interprofessional educators. © The Author(s) 2014.

  9. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

    Science.gov (United States)

    Townsley, Brad T.; Covington, Michael F.; Ichihashi, Yasunori; Zumstein, Kristina; Sinha, Neelima R.

    2015-01-01

    Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries. PMID:26052336

  10. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

    Directory of Open Access Journals (Sweden)

    Brad Thomas Townsley

    2015-05-01

    Full Text Available Next Generation Sequencing (NGS is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE libraries and can easily extend to full transcript coverage shotgun (SHO type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

  11. Bioremediation protocols

    National Research Council Canada - National Science Library

    Sheehan, David

    1997-01-01

    ..., .. . . . . .. ,. . . .. . . . . . . . .. . . . . .. . . .. . .. 3 2 Granular Nina Sludge Christiansen, Consortia lndra for Bioremediation, M. Mathrani, and Birgitte K. Ahring . 23 PART II PROTOCOLS...

  12. Time efficient way to calculate oxygen transfer areas and power input in cylindrical disposable shaken bioreactors.

    Science.gov (United States)

    Klöckner, Wolf; Lattermann, Clemens; Pursche, Franz; Büchs, Jochen; Werner, Sören; Eibl, Dieter

    2014-01-01

    Disposable orbitally shaken bioreactors are a promising alternative to stirred or wave agitated systems for mammalian and plant cell cultivation, because they provide a homogeneous and well-defined liquid distribution together with a simple and cost-efficient design. Cultivation conditions in the surface-aerated bioreactors are mainly affected by the size of the volumetric oxygen transfer area (a) and the volumetric power input (P∕VL ) that both result from the liquid distribution during shaking. Since Computational Fluid Dynamics (CFD)-commonly applied to simulate the liquid distribution in such bioreactors-needs high computing power, this technique is poorly suited to investigate the influence of many different operating conditions in various scales. Thus, the aim of this paper is to introduce a new mathematical model for calculating the values of a and P∕VL for liquids with water-like viscosities. The model equations were derived from the balance of centrifugal and gravitational forces exerted during shaking. A good agreement was found among calculated values for a and P∕VL , CFD simulation values and empirical results. The newly proposed model enables a time efficient way to calculate the oxygen transfer areas and power input for various shaking frequencies, filling volumes and shaking and reactor diameters. All these parameters can be calculated fast and with little computing power. © 2014 American Institute of Chemical Engineers.

  13. In Search of a Time Efficient Approach to Crack and Delamination Growth Predictions in Composites

    Science.gov (United States)

    Krueger, Ronald; Carvalho, Nelson

    2016-01-01

    Analysis benchmarking was used to assess the accuracy and time efficiency of algorithms suitable for automated delamination growth analysis. First, the Floating Node Method (FNM) was introduced and its combination with a simple exponential growth law (Paris Law) and Virtual Crack Closure technique (VCCT) was discussed. Implementation of the method into a user element (UEL) in Abaqus/Standard(Registered TradeMark) was also presented. For the assessment of growth prediction capabilities, an existing benchmark case based on the Double Cantilever Beam (DCB) specimen was briefly summarized. Additionally, the development of new benchmark cases based on the Mixed-Mode Bending (MMB) specimen to assess the growth prediction capabilities under mixed-mode I/II conditions was discussed in detail. A comparison was presented, in which the benchmark cases were used to assess the existing low-cycle fatigue analysis tool in Abaqus/Standard(Registered TradeMark) in comparison to the FNM-VCCT fatigue growth analysis implementation. The low-cycle fatigue analysis tool in Abaqus/Standard(Registered TradeMark) was able to yield results that were in good agreement with the DCB benchmark example. Results for the MMB benchmark cases, however, only captured the trend correctly. The user element (FNM-VCCT) always yielded results that were in excellent agreement with all benchmark cases, at a fraction of the analysis time. The ability to assess the implementation of two methods in one finite element code illustrated the value of establishing benchmark solutions.

  14. Adhesion of resin materials to S2-glass unidirectional and E-glass multidirectional fiber reinforced composites: effect of polymerization sequence protocols.

    Science.gov (United States)

    Polacek, Petr; Pavelka, Vladimir; Ozcan, Mutlu

    2013-12-01

    To evaluate the effect of different polymerization sequences employed during application of bis-GMAbased particulate filler composites (PFC) or a flowable resin (FR) on fiber-reinforced composite (FRC). Unidirectional, pre-impregnated S2-glass fibers (Dentapreg) and multidirectional preimpregnated E-glass fibers (Dentapreg) (length: 40 mm; thickness: 0.5 mm) were obtained (N = 144, n = 12 per group) and embedded in translucent silicone material with the adhesion surface exposed. The resulting specimens were randomly divided into 12 groups for the following application sequences: a) FRC+PFC (photopolymerized in one step), b) FRC+FR (photopolymerized in one step), c) FRC+PFC (photopolymerized individually), d) FRC+FR (photopolymerized individually), e) FRC (photopolymerized)+intermediate adhesive resin and PFC (photopolymerized in one step), f) FRC (photopolymerized)+intermediate adhesive resin and FR (photopolymerized in one step). The sequences of unidirectional (groups a to f) were repeated for multidirectional (groups g to l) FRCs. PFCs were debonded from the FRC surfaces using the shear bond test in a universal testing machine (1 mm/min). On additional specimens from each FRC type, thermogravimetric analysis (TGA) was performed to characterize the fiber weight content (Wf) (N = 6, n = 3 per group). After debonding, all specimens were analyzed using SEM to categorize the failure modes. The data were statistically analyzed using 3-way ANOVA and Tukey's tests (α = 0.05). Significant effects of the FRC type (S2 or E-glass) (p resin type (PFC or FR) (p TGA revealed 55 ± 3 wt% fiber content for multidirectional and 60 ± 3 wt% for unidirectional FRCs tested. Multidirectional pre-impregnated E-glass fibers cannot be recommended in combination with the PFC and FR materials tested in this study. Application of an intermediate adhesive resin layer increases the adhesion of both PFC and FR to unidirectional FRC. FRC and FR can be polymerized in one step, but FRC and PFC

  15. Cryptographic Protocols:

    DEFF Research Database (Denmark)

    Geisler, Martin Joakim Bittel

    with a variant of the classic BGW protocol. The protocol is secure against a semi-honest adversary. In Chapter 4 we describe a new protocol for VIFF that is secure against malicious adversaries. The protocol guarantees termination if the adversary allows a preprocessing phase to terminate, in which...... systems hosted by an untrusted provider. It guarantees atomic read and write operations on the shared data when the service is correct and preserves fork-linearizability when the service is faulty. A prototype has been implemented on top of the Subversion revision control system; benchmarks show...

  16. Next-generation sequencing diagnostics of bacteremia in sepsis (Next GeneSiS-Trial): Study protocol of a prospective, observational, noninterventional, multicenter, clinical trial.

    Science.gov (United States)

    Brenner, Thorsten; Decker, Sebastian O; Grumaz, Silke; Stevens, Philip; Bruckner, Thomas; Schmoch, Thomas; Pletz, Mathias W; Bracht, Hendrik; Hofer, Stefan; Marx, Gernot; Weigand, Markus A; Sohn, Kai

    2018-02-01

    Sepsis remains a major challenge, even in modern intensive care medicine. The identification of the causative pathogen is crucial for an early optimization of the antimicrobial treatment regime. In this context, culture-based diagnostic procedures (e.g., blood cultures) represent the standard of care, although they are associated with relevant limitations. Accordingly, culture-independent molecular diagnostic procedures might be of help for the identification of the causative pathogen in infected patients. The concept of an unbiased sequence analysis of circulating cell-free DNA (cfDNA) from plasma samples of septic patients by next-generation sequencing (NGS) has recently been identified to be a promising diagnostic platform for critically ill patients suffering from bloodstream infections. Although this new approach might be more sensitive and specific than culture-based state-of-the-art technologies, additional clinical trials are needed to exactly define the performance as well as clinical value of a NGS-based approach. Next GeneSiS is a prospective, observational, noninterventional, multicenter study to assess the diagnostic performance of a NGS-based approach for the detection of relevant infecting organisms in patients with suspected or proven sepsis [according to recent sepsis definitions (sepsis-3)] by the use of the quantitative sepsis indicating quantifier (SIQ) score in comparison to standard (culture-based) microbiological diagnostics. The clinical value of this NGS-based approach will be estimated by a panel of independent clinical specialists, retrospectively identifying potential changes in patients' management based on NGS results. Further subgroup analyses will focus on the clinical value especially for patients suffering from a failure of empiric treatment within the first 3 days after onset [as assessed by death of the patient or lack of improvement of the patient's clinical condition (in terms of an inadequate decrease of SOFA-score) or

  17. Diagnostic Hearing Assessment in Schools: Validity and Time Efficiency of Automated Audiometry.

    Science.gov (United States)

    Mahomed-Asmail, Faheema; Swanepoel, De Wet; Eikelboom, Robert H

    2016-01-01

    Poor follow-up compliance from school-based hearing screening typically undermines the efficacy of school-based hearing screening programs. Onsite diagnostic audiometry with automation may reduce false positives and ensure directed referrals. To investigate the validity and time efficiency of automated diagnostic air- and bone-conduction audiometry for children in a natural school environment following hearing screening. A within-subject repeated measures design was employed to compare air- and bone-conduction pure-tone thresholds (0.5-4 kHz), measured by manual and automated pure-tone audiometry. Sixty-two children, 25 males and 37 females, with an average age of 8 yr (standard deviation [SD] = 0.92; range = 6-10 yr) were recruited for this study. The participants included 30 children who failed on a hearing screening and 32 children who passed a hearing screening. Threshold comparisons were made for air- and bone-conduction thresholds across ears tested with manual and automated audiometry. To avoid a floor effect thresholds of 15 dB HL were excluded in analyses. The Wilcoxon signed ranked test was used to compare threshold correspondence for manual and automated thresholds and the paired samples t-test was used to compare test time. Statistical significance was set as p ≤ 0.05. 85.7% of air-conduction thresholds and 44.6% of bone-conduction thresholds corresponded within the normal range (15 dB HL) for manual and automated audiometry. Both manual and automated audiometry air- and bone-conduction thresholds exceeded 15 dB HL in 9.9% and 34.0% of thresholds, respectively. For these thresholds, average absolute differences for air- and bone-conduction thresholds were 6.3 (SD = 8.3) and 2.2 dB (SD = 3.6) and they corresponded within 10 dB across frequencies in 87.7% and 100.0%, respectively. There was no significant difference between manual and automated air- and bone-conduction across frequencies for these thresholds. Using onsite automated diagnostic audiometry

  18. Evaluation of MRI sequences for quantitative T1 brain mapping

    Science.gov (United States)

    Tsialios, P.; Thrippleton, M.; Glatz, A.; Pernet, C.

    2017-11-01

    T1 mapping constitutes a quantitative MRI technique finding significant application in brain imaging. It allows evaluation of contrast uptake, blood perfusion, volume, providing a more specific biomarker of disease progression compared to conventional T1-weighted images. While there are many techniques for T1-mapping there is a wide range of reported T1-values in tissues, raising the issue of protocols reproducibility and standardization. The gold standard for obtaining T1-maps is based on acquiring IR-SE sequence. Widely used alternative sequences are IR-SE-EPI, VFA (DESPOT), DESPOT-HIFI and MP2RAGE that speed up scanning and fitting procedures. A custom MRI phantom was used to assess the reproducibility and accuracy of the different methods. All scans were performed using a 3T Siemens Prisma scanner. The acquired data processed using two different codes. The main difference was observed for VFA (DESPOT) which grossly overestimated T1 relaxation time by 214 ms [126 270] compared to the IR-SE sequence. MP2RAGE and DESPOT-HIFI sequences gave slightly shorter time than IR-SE (~20 to 30ms) and can be considered as alternative and time-efficient methods for acquiring accurate T1 maps of the human brain, while IR-SE-EPI gave identical result, at a cost of a lower image quality.

  19. Variable Circular Collimator in Robotic Radiosurgery : A Time-Efficient Alternative to a Mini-Multileaf Collimator?

    NARCIS (Netherlands)

    Van de Water, S.; Hoogeman, M.S.; Breedveld, S.; Nuyttens, J.J.M.E.; Schaart, D.R.; Heijmen, B.J.M.

    2011-01-01

    urpose Compared with many small circular beams used in CyberKnife treatments, beam’s eye view-shaped fields are generally more time-efficient for dose delivery. However, beam’s eye view-shaping devices, such as a mini-multileaf collimator (mMLC), are not presently available for CyberKnife, although

  20. Balancing creativity and time efficiency in multi-team R&D projects: The alignment of formal and informal networks

    DEFF Research Database (Denmark)

    Kratzer, Jan; Gemuenden, Hans Georg; Lettl, Christopher

    2008-01-01

    and their effect on the challenge to balance project creativity and time efficiency. In order to analyse this issue data in two multi-team R&D projects in space industry are collected. There are two intriguing findings that are partly contradicting the state-of-the art knowledge. First, formally ascribed design...

  1. Geneva protocols

    International Nuclear Information System (INIS)

    Kimminich, O.

    1990-01-01

    The First Protocol Additional to the Geneva Conventions of 1949 and relating to the Protection of Victims of International Armed Conflicts contains provisions prohibiting indiscriminate attacks. Nuclear warfare as such is not mentioned in the Protocol. It has been asserted that the Protocol does not apply to nuclear weapons for several reasons. However, close analysis shows that the rules governing the application of means and methods of warfare cannot exempt the nuclear weapons. If nuclear weapons are applied in a manner not consistent with article 51 of Protocol I, their use is forbidden by this article even in situations in which general international law might grant an exception from the ban on nuclear weapons, as in the case of reprisal. (orig./HSCH) [de

  2. Development and Demonstration of Measurement-Time Efficient Methods for Impedance Spectroscopy of Electrode and Sensor Arrays

    OpenAIRE

    Cooper, Kevin R.; Smith, Matthew; Johnson, Derek

    2008-01-01

    The development of impedance-based array devices is hindered by a lack of robust platforms and methods upon which to evaluate and interrogate sensors. One aspect to be addressed is the development of measurement-time efficient techniques for broadband impedance spectroscopy of large electrode arrays. The objective of this work was to substantially increase the low frequency impedance measurement throughput capability of a large channel count array analyzer by developing true parallel measurem...

  3. Immunochemical protocols

    National Research Council Canada - National Science Library

    Pound, John D

    1998-01-01

    ... easy and important refinements often are not published. This much anticipated 2nd edition of Immunochemzcal Protocols therefore aims to provide a user-friendly up-to-date handbook of reliable techniques selected to suit the needs of molecular biologists. It covers the full breadth of the relevant established immunochemical methods, from protein blotting and immunoa...

  4. DNA Sequencing in Undergraduate Laboratory Courses.

    Science.gov (United States)

    Hamilton, Robert G.

    1997-01-01

    Discusses strategies to duplicate current research protocols using biochemical methods of analysis. Describes the use of the Silver Sequence kit that provides a technically simple and relatively inexpensive DNA sequencing exercise. (JRH)

  5. High-intensity interval training (HIT) for effective and time-efficient pre-surgical exercise interventions.

    Science.gov (United States)

    Weston, Matthew; Weston, Kathryn L; Prentis, James M; Snowden, Chris P

    2016-01-01

    The advancement of perioperative medicine is leading to greater diversity in development of pre-surgical interventions, implemented to reduce patient surgical risk and enhance post-surgical recovery. Of these interventions, the prescription of pre-operative exercise training is gathering momentum as a realistic means for enhancing patient surgical outcome. Indeed, the general benefits of exercise training have the potential to pre-operatively optimise several pre-surgical risks factors, including cardiorespiratory function, frailty and cognitive function. Any exercise programme incorporated into the pre-operative pathway of care needs to be effective and time efficient in that any fitness gains are achievable in the limited period between the decision for surgery and operation (e.g. 4 weeks). Fortunately, there is a large volume of research describing effective and time-efficient exercise training programmes within the discipline of sports science. Accordingly, the objective of our commentary is to synthesise contemporary exercise training research, both from non-clinical and clinical populations, with the overarching aim of informing the development of effective and time-efficient pre-surgical exercise training programmes. The development of such exercise training programmes requires the careful consideration of several key principles, namely frequency, intensity, time, type and progression of exercise. Therefore, in light of more recent evidence demonstrating the effectiveness and time efficiency of high-intensity interval training-which involves brief bouts of intense exercise interspersed with longer recovery periods-the principles of exercise training programme design will be discussed mainly in the context of such high-intensity interval training programmes. Other issues pertinent to the development, implementation and evaluation of pre-operative exercise training programmes, such as individual exercise prescription, training session monitoring and potential

  6. Beyond protocols

    DEFF Research Database (Denmark)

    Vanderhoeven, Sonia; Branquart, Etienne; Casaer, Jim

    2017-01-01

    Risk assessment tools for listing invasive alien species need to incorporate all available evidence and expertise. Beyond the wealth of protocols developed to date, we argue that the current way of performing risk analysis has several shortcomings. In particular, lack of data on ecological impacts...... process can be applied to better capture opinions of different experts, thereby maximizing the evidential basis. Elaborating on manageability of invasive species is further needed to fully answer all risk analysis requirements. Tackling the issue of invasive species urges better handling of the acquired...

  7. MHC protocols

    National Research Council Canada - National Science Library

    Powis, Stephen H; Vaughan, Robert W

    2003-01-01

    ... because it contains genes encoding components of the complement pathway. The entire human MHC has recently been sequenced (1) and each subregion is now known to contain many other genes, a number of which have immunological functions. The study of polymorphism within the MHC is well established, because the region contains the highly polymorphic HLA genes. HLA polym...

  8. Time-Efficiency Analysis Comparing Digital and Conventional Workflows for Implant Crowns: A Prospective Clinical Crossover Trial.

    Science.gov (United States)

    Joda, Tim; Brägger, Urs

    2015-01-01

    To compare time-efficiency in the production of implant crowns using a digital workflow versus the conventional pathway. This prospective clinical study used a crossover design that included 20 study participants receiving single-tooth replacements in posterior sites. Each patient received a customized titanium abutment plus a computer-aided design/computer-assisted manufacture (CAD/CAM) zirconia suprastructure (for those in the test group, using digital workflow) and a standardized titanium abutment plus a porcelain-fused-to-metal crown (for those in the control group, using a conventional pathway). The start of the implant prosthetic treatment was established as the baseline. Time-efficiency analysis was defined as the primary outcome, and was measured for every single clinical and laboratory work step in minutes. Statistical analysis was calculated with the Wilcoxon rank sum test. All crowns could be provided within two clinical appointments, independent of the manufacturing process. The mean total production time, as the sum of clinical plus laboratory work steps, was significantly different. The mean ± standard deviation (SD) time was 185.4 ± 17.9 minutes for the digital workflow process and 223.0 ± 26.2 minutes for the conventional pathway (P = .0001). Therefore, digital processing for overall treatment was 16% faster. Detailed analysis for the clinical treatment revealed a significantly reduced mean ± SD chair time of 27.3 ± 3.4 minutes for the test group compared with 33.2 ± 4.9 minutes for the control group (P = .0001). Similar results were found for the mean laboratory work time, with a significant decrease of 158.1 ± 17.2 minutes for the test group vs 189.8 ± 25.3 minutes for the control group (P = .0001). Only a few studies have investigated efficiency parameters of digital workflows compared with conventional pathways in implant dental medicine. This investigation shows that the digital workflow seems to be more time-efficient than the

  9. Neuro MR: protocols.

    Science.gov (United States)

    Mikulis, David J; Roberts, Timothy P L

    2007-10-01

    Clinical MRI depends on a symbiosis between MR physics and clinical requirements. The imaging solutions are based on a balance between the "palette" of available image contrasts derived from nuclear spin physics and tissue biophysics, and clinical determinants such as the anticipated pathology and efficient use of imaging time. Imaging is therefore optimized to maximize diagnostic sensitivity and specificity through the development of protocols organized along the lines of major disease categories. In the other part of this two-part review, the primary determinants of image contrast, including T1, T2, and T2*, were highlighted. The development of pulse sequences designed to optimize each of these image contrasts was discussed and the impact of technological innovation (parallel imaging and high-field systems) on the manner in which these sequences could be modified to improve clinical efficacy was further emphasized. The scope of that discussion was broadened to include the application of: 1) water diffusion imaging used primarily for detection of pathologies that restrict the free movement of water in the tissues and for defining fiber tracts in the brain; 2) the intravenous administration of exogenous contrast agents (gadolinium-diethylene triamine pentaacetic acid [GdDTPA]) for assessment of blood-brain-barrier (BBB) defects and brain blood flow; and 3) MR spectroscopy (MRS) for assessment of brain metabolites. The goal of this part is to discuss how these acquisitions are combined into specific protocols that can effectively detect and characterize, or in keeping with our artistic analogy, "paint" each of the major diseases affecting the central nervous system (CNS). This work concludes with a discussion of image artifacts and pitfalls in image interpretation, which, in spite our best efforts to minimize or eliminate them, continue to occur. Much of the ensuing discussion is based on our own institutional experience. Protocols, therefore, do not necessarily

  10. Reflexions about imaging technique and examination protocol 2. MR-examination protocol

    International Nuclear Information System (INIS)

    Wichmann, Werner

    2004-01-01

    Adequate imaging protocol is crucial for any imaging technique. As MR is a time consuming examination, the physician serves the patient best, when he/she makes the best choice of sequences, which answer the question of the clinician and provide a definite diagnosis. Although any patient requires an individual protocol, some general rules should be known

  11. Illumina Sequencing of Bisulfite-Converted DNA Libraries.

    Science.gov (United States)

    Lizardi, Paul M; Yan, Qin; Wajapeyee, Narendra

    2017-11-01

    Here we describe a standard MethylC-seq protocol using single-read sequencing on an Illumina Genome Analyzer II platform. The protocol involves ligation of methylated sequencing adaptors to sonicated genomic DNA, gel purification, sodium bisulfite conversion, polymerase chain reaction (PCR) amplification, and sequencing. © 2017 Cold Spring Harbor Laboratory Press.

  12. Scheduling of House Development Projects with CPM and PERT Method for Time Efficiency (Case Study: House Type 36)

    Science.gov (United States)

    Kholil, Muhammad; Nurul Alfa, Bonitasari; Hariadi, Madjumsyah

    2018-04-01

    Network planning is one of the management techniques used to plan and control the implementation of a project, which shows the relationship between activities. The objective of this research is to arrange network planning on house construction project on CV. XYZ and to know the role of network planning in increasing the efficiency of time so that can be obtained the optimal project completion period. This research uses descriptive method, where the data collected by direct observation to the company, interview, and literature study. The result of this research is optimal time planning in project work. Based on the results of the research, it can be concluded that the use of the both methods in scheduling of house construction project gives very significant effect on the completion time of the project. The company’s CPM (Critical Path Method) method can complete the project with 131 days, PERT (Program Evaluation Review and Technique) Method takes 136 days. Based on PERT calculation obtained Z = -0.66 or 0,2546 (from normal distribution table), and also obtained the value of probability or probability is 74,54%. This means that the possibility of house construction project activities can be completed on time is high enough. While without using both methods the project completion time takes 173 days. So using the CPM method, the company can save time up to 42 days and has time efficiency by using network planning.

  13. Time-Efficiency of Sorting Chironomidae Surface-Floating Pupal Exuviae Samples from Urban Trout Streams in Northeast Minnesota, USA

    Directory of Open Access Journals (Sweden)

    Alyssa M Anderson

    2012-10-01

    Full Text Available Collections of Chironomidae surface-floating pupal exuviae (SFPE provide an effective means of assessing water quality in streams. Although not widely used in the United States, the technique is not new and has been shown to be more cost-efficient than traditional dip-net sampling techniques in organically enriched stream in an urban landscape. The intent of this research was to document the efficiency of sorting SFPE samples relative to dip-net samples in trout streams with catchments varying in amount of urbanization and differences in impervious surface. Samples of both SFPE and dip-nets were collected from 17 sample sites located on 12 trout streams in Duluth, MN, USA. We quantified time needed to sort subsamples of 100 macroinvertebrates from dip-net samples, and less than or greater than 100 chironomid exuviae from SFPE samples. For larger samples of SFPE, the time required to subsample up to 300 exuviae was also recorded. The average time to sort subsamples of 100 specimens was 22.5 minutes for SFPE samples, compared to 32.7 minutes for 100 macroinvertebrates in dip-net samples. Average time to sort up to 300 exuviae was 37.7 minutes. These results indicate that sorting SFPE samples is more time-efficient than traditional dip-net techniques in trout streams with varying catchment characteristics.doi: 10.5324/fn.v31i0.1380.Published online: 17 October 2012.

  14. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  15. Prior-knowledge-independent equalization to improve battery uniformity with energy efficiency and time efficiency for lithium-ion battery

    International Nuclear Information System (INIS)

    Zhang, Shumei; Qiang, Jiaxi; Yang, Lin; Zhao, Xiaowei

    2016-01-01

    To improve battery uniformity as well as energy efficiency and time efficiency, a SOC (state of charge)-based equalization by AGA (adaptive genetic algorithm) is proposed on basis of two-stage DC/DC converters. The simulation results indicate that compared with FLC (fuzzy logic controller) equalization, the standard deviation of final SOC is improved by 78.7% while energy efficiency is improved by 6.01% and equalization time is decreased by 20% for AGA equalization of extreme dispersion. Additionally, AGA improves the battery uniformity by 30.77% with shortening equalization time by 16.29% and saving energy loss by 1.51% compared with FLC for equalization of regular dispersion. For further validation, the equalization optimization is verified by experiment based on the data-driven parameter identification method which is used to enhance the real-time capability of AGA. For AGA equalization of extreme dispersion, the standard deviation of final SOC is just 0.41% while equalization time prolongs only 14 min and energy efficiency is decreased by 0.81% compared with simulation results. Moreover, not only the standard deviation of final SOC is just 0.28% but also the energy efficiency is decreased by 0.69% and equalization time prolongs by 10.4 min compared with the simulation results for equalization of regular dispersion. - Highlights: • Issues of over equalization, time consumption and energy loss are addressed. • A SOC-based equalization is proposed based on adaptive genetic algorithm. • The equalization aims to improve battery uniformity, efficiency of energy and time. • Data-driven parameter identification is used to enhance the real-time capability.

  16. Protocol Implementation Generator

    DEFF Research Database (Denmark)

    Carvalho Quaresma, Jose Nuno; Probst, Christian W.

    2010-01-01

    necessary tools. In this paper, we present the Protocol Implementation Generator (PiG), a framework that can be used to add protocol generation to protocol negotiation, or to easily share and implement new protocols throughout a network. PiG enables the sharing, verification, and translation...... of communication protocols. With it, partners can suggest a new protocol by sending its specification. After formally verifying the specification, each partner generates an implementation, which can then be used for establishing communication. We also present a practical realisation of the Protocol Implementation...... Generator framework based on the LySatool and a translator from the LySa language into C or Java....

  17. "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.

  18. Network Memory Protocol

    National Research Council Canada - National Science Library

    Wilcox, D

    1997-01-01

    This report presents initial research into the design of a new computer system local area network transport layer protocol, designated the network memory protocol, which provides clients with direct...

  19. 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 transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  20. Demarcation of Security in Authentication Protocols

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    2011-01-01

    Security analysis of communication protocols is a slippery business; many “secure” protocols later turn out to be insecure. Among many, two complains are more frequent: inadequate definition of security and unstated assumptions in the security model. In our experience, one principal cause...... for such state of affairs is an apparent overlap of security and correctness, which may lead to many sloppy security definitions and security models. Although there is no inherent need to separate security and correctness requirements, practically, such separation is significant. It makes security analysis...... easier, and enables us to define security goals with a fine granularity. We present one such separation, by introducing the notion of binding sequence as a security primitive. A binding sequence, roughly speaking, is the only required security property of an authentication protocol. All other...

  1. Security Property Validation of the Sensor Network Encryption Protocol (SNEP

    Directory of Open Access Journals (Sweden)

    Salekul Islam

    2015-07-01

    Full Text Available Since wireless sensor networks (WSNs have been designed to be deployed in an unsecured, public environment, secured communication is really vital for their wide-spread use. Among all of the communication protocols developed for WSN, the Security Protocols for Sensor Networks (SPINS is exceptional, as it has been designed with security as a goal. SPINS is composed of two building blocks: Secure Network Encryption Protocol (SNEP and the “micro” version of the Timed Efficient Streaming Loss-tolerant Authentication (TESLA, named μTESLA. From the inception of SPINS, a number of efforts have been made to validate its security properties. In this paper, we have validated the security properties of SNEP by using an automated security protocol validation tool, named AVISPA. Using the protocol specification language, HLPSL, we model two combined scenarios—node to node key agreement and counter exchange protocols—followed by data transmission. Next, we validate the security properties of these combined protocols, using different AVISPA back-ends. AVISPA reports the models we have developed free from attacks. However, by analyzing the key distribution sub-protocol, we find one threat of a potential DoS attack that we have demonstrated by modeling in AVISPA. Finally, we propose a modification, and AVISPA reports this modified version free from the potential DoS attack.

  2. Application Framework with Abstractions for Protocol and Agent Role

    DEFF Research Database (Denmark)

    Kristensen, Bent Bruun

    2016-01-01

    In multi-agent systems, agents interact by sending and receiving messages and the actual sequences of message form interaction structures between agents. Protocols and agents organized internally by agent roles support these interaction structures. Description and use of protocols based on agent ...... roles are supported by a simple and expressive application framework....

  3. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  4. Network Authentication Protocol Studies

    Science.gov (United States)

    2009-04-01

    This is called the “Decision Diffie-Hellman Problem” ( DDH ) [68]. For the protocols discussed in this paper, the cryptographic strength of the generated...group key is solely dependent upon the strength of the underlying two-party protocols. That said, we will not address the DDH problem further in this

  5. Recombinant gene expression protocols

    National Research Council Canada - National Science Library

    Tuan, Rocky S

    1997-01-01

    .... A fundamental requirement for successful recombinant gene expression is the design of the cloning vector and the choice of the host organism for expression. Recombinant Gene Expression Protocols grows out of the need for a laboratory manual that provides the reader the background and rationale, as well as the practical protocols for the preparation of...

  6. Linear Logical Voting Protocols

    DEFF Research Database (Denmark)

    DeYoung, Henry; Schürmann, Carsten

    2012-01-01

    . In response, we promote linear logic as a high-level language for both specifying and implementing voting protocols. Our linear logical specifications of the single-winner first-past-the-post (SW- FPTP) and single transferable vote (STV) protocols demonstrate that this approach leads to concise...

  7. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...... as possible. Evaluations show that the proposed protocol provides considerable gains over the standard tree splitting protocol applying SIC. The improvement comes at the expense of an increased feedback and receiver complexity....

  8. Heart-Rate Variability During Deep Sleep in World-Class Alpine Skiers: A Time-Efficient Alternative to Morning Supine Measurements.

    Science.gov (United States)

    Herzig, David; Testorelli, Moreno; Olstad, Daniela Schäfer; Erlacher, Daniel; Achermann, Peter; Eser, Prisca; Wilhelm, Matthias

    2017-05-01

    It is increasingly popular to use heart-rate variability (HRV) to tailor training for athletes. A time-efficient method is HRV assessment during deep sleep. To validate the selection of deep-sleep segments identified by RR intervals with simultaneous electroencephalography (EEG) recordings and to compare HRV parameters of these segments with those of standard morning supine measurements. In 11 world-class alpine skiers, RR intervals were monitored during 10 nights, and simultaneous EEGs were recorded during 2-4 nights. Deep sleep was determined from the HRV signal and verified by delta power from the EEG recordings. Four further segments were chosen for HRV determination, namely, a 4-h segment from midnight to 4 AM and three 5-min segments: 1 just before awakening, 1 after waking in supine position, and 1 in standing after orthostatic challenge. Training load was recorded every day. A total of 80 night and 68 morning measurements of 9 athletes were analyzed. Good correspondence between the phases selected by RR intervals vs those selected by EEG was found. Concerning root-mean-squared difference of successive RR intervals (RMSSD), a marker for parasympathetic activity, the best relationship with the morning supine measurement was found in deep sleep. HRV is a simple tool for approximating deep-sleep phases, and HRV measurement during deep sleep could provide a time-efficient alternative to HRV in supine position.

  9. Magnetic resonance imaging protocols for paediatric neuroradiology

    International Nuclear Information System (INIS)

    Saunders, Dawn E.; Thompson, Clare; Gunny, Roxanne; Jones, Rod; Cox, Tim; Chong, Wui Khean

    2007-01-01

    Increasingly, radiologists are encouraged to have protocols for all imaging studies and to include imaging guidelines in care pathways set up by the referring clinicians. This is particularly advantageous in MRI where magnet time is limited and a radiologist's review of each patient's images often results in additional sequences and longer scanning times without the advantage of improvement in diagnostic ability. The difficulties of imaging small children and the challenges presented to the radiologist as the brain develops are discussed. We present our protocols for imaging the brain and spine of children based on 20 years experience of paediatric neurological MRI. The protocols are adapted to suit children under the age of 2 years, small body parts and paediatric clinical scenarios. (orig.)

  10. Comparison of a new whole-body continuous-table-movement protocol versus a standard whole-body MR protocol for the assessment of multiple myeloma.

    Science.gov (United States)

    Weckbach, S; Michaely, H J; Stemmer, A; Schoenberg, S O; Dinter, D J

    2010-12-01

    To evaluate a whole body (WB) continuous-table-movement (CTM) MR protocol for the assessment of multiple myeloma (MM) in comparison to a step-by-step WB protocol. Eighteen patients with MM were examined at 1.5T using a WB CTM protocol (axial T2-w fs BLADE, T1-w GRE sequence) and a step-by-step WB protocol including coronal/sagittal T1-w SE and STIR sequences as reference. Protocol time was assessed. Image quality, artefacts, liver/spleen assessability, and the ability to depict bone marrow lesions less than or greater than 1 cm as well as diffuse infiltration and soft tissue lesions were rated. Potential changes in the Durie and Salmon Plus stage and the detectability of complications were assessed. Mean protocol time was 6:38 min (CTM) compared to 24:32 min (standard). Image quality was comparable. Artefacts were more prominent using the CTM protocol (P = 0.0039). Organ assessability was better using the CTM protocol (P < 0.001). Depiction of bone marrow and soft tissue lesions was identical without a staging shift. Vertebral fractures were not detected using the CTM protocol. The new protocol allows a higher patient throughput and facilitates the depiction of extramedullary lesions. However, as long as vertebral fractures are not detectable, the protocol cannot be safely used for clinical routine without the acquisition of an additional sagittal sequence.

  11. Comparison of a new whole-body continuous-table-movement protocol versus a standard whole-body MR protocol for the assessment of multiple myeloma

    International Nuclear Information System (INIS)

    Weckbach, S.; Michaely, H.J.; Schoenberg, S.O.; Dinter, D.J.; Stemmer, A.

    2010-01-01

    To evaluate a whole body (WB) continuous-table-movement (CTM) MR protocol for the assessment of multiple myeloma (MM) in comparison to a step-by-step WB protocol. Eighteen patients with MM were examined at 1.5T using a WB CTM protocol (axial T2-w fs BLADE, T1-w GRE sequence) and a step-by-step WB protocol including coronal/sagittal T1-w SE and STIR sequences as reference. Protocol time was assessed. Image quality, artefacts, liver/spleen assessability, and the ability to depict bone marrow lesions less than or greater than 1 cm as well as diffuse infiltration and soft tissue lesions were rated. Potential changes in the Durie and Salmon Plus stage and the detectability of complications were assessed. Mean protocol time was 6:38 min (CTM) compared to 24:32 min (standard). Image quality was comparable. Artefacts were more prominent using the CTM protocol (P = 0.0039). Organ assessability was better using the CTM protocol (P < 0.001). Depiction of bone marrow and soft tissue lesions was identical without a staging shift. Vertebral fractures were not detected using the CTM protocol. The new protocol allows a higher patient throughput and facilitates the depiction of extramedullary lesions. However, as long as vertebral fractures are not detectable, the protocol cannot be safely used for clinical routine without the acquisition of an additional sagittal sequence. (orig.)

  12. Image analysis for DNA sequencing

    International Nuclear Information System (INIS)

    Palaniappan, K.; Huang, T.S.

    1991-01-01

    This paper reports that there is a great deal of interest in automating the process of DNA (deoxyribonucleic acid) sequencing to support the analysis of genomic DNA such as the Human and Mouse Genome projects. In one class of gel-based sequencing protocols autoradiograph images are generated in the final step and usually require manual interpretation to reconstruct the DNA sequence represented by the image. The need to handle a large volume of sequence information necessitates automation of the manual autoradiograph reading step through image analysis in order to reduce the length of time required to obtain sequence data and reduce transcription errors. Various adaptive image enhancement, segmentation and alignment methods were applied to autoradiograph images. The methods are adaptive to the local characteristics of the image such as noise, background signal, or presence of edges. Once the two-dimensional data is converted to a set of aligned one-dimensional profiles waveform analysis is used to determine the location of each band which represents one nucleotide in the sequence. Different classification strategies including a rule-based approach are investigated to map the profile signals, augmented with the original two-dimensional image data as necessary, to textual DNA sequence information

  13. Zebrafish embryology and cartilage staining protocols for high school students.

    Science.gov (United States)

    Emran, Farida; Brooks, Jacqueline M; Zimmerman, Steven R; Johnson, Susan L; Lue, Robert A

    2009-06-01

    The Life Sciences-Howard Hughes Medical Institute Outreach Program at Harvard University supports high school science education by offering an on-campus program for students and their teachers to participate in investigative, hands-on laboratory sessions. The outreach program has recently designed and launched a successful zebrafish embryology protocol that we present here. The main objectives of this protocol are to introduce students to zebrafish as a model research organism and to provide students with direct experience with current techniques used in embryological research. The content of the lab is designed to generate discussions on embryology, genetics, fertilization, natural selection, and animal adaptation. The protocol produces reliable results in a time-efficient manner using a minimum of reagents. The protocol presented here consists of three sections: observations of live zebrafish larvae at different developmental stages, cartilage staining of zebrafish larvae, and a mutant hunt involving identification of two zebrafish mutants (nacre and chokh). Here, we describe the protocol, show the results obtained for each section, and suggest possible alternatives for different lab settings.

  14. ATM and Internet protocol

    CERN Document Server

    Bentall, M; Turton, B

    1998-01-01

    Asynchronous Transfer Mode (ATM) is a protocol that allows data, sound and video being transferred between independent networks via ISDN links to be supplied to, and interpreted by, the various system protocols.ATM and Internet Protocol explains the working of the ATM and B-ISDN network for readers with a basic understanding of telecommunications. It provides a handy reference to everyone working with ATM who may not require the full standards in detail, but need a comprehensive guide to ATM. A substantial section is devoted to the problems of running IP over ATM and there is some discussion o

  15. Playing With Population Protocols

    Directory of Open Access Journals (Sweden)

    Xavier Koegler

    2009-06-01

    Full Text Available Population protocols have been introduced as a model of sensor networks consisting of very limited mobile agents with no control over their own movement: A collection of anonymous agents, modeled by finite automata, interact in pairs according to some rules. Predicates on the initial configurations that can be computed by such protocols have been characterized under several hypotheses. We discuss here whether and when the rules of interactions between agents can be seen as a game from game theory. We do so by discussing several basic protocols.

  16. Mobile Internet Protocol Analysis

    National Research Council Canada - National Science Library

    Brachfeld, Lawrence

    1999-01-01

    ...) and User Datagram Protocol (UDP). Mobile IP allows mobile computers to send and receive packets addressed with their home network IP address, regardless of the IP address of their current point of attachment on the Internet...

  17. USA-USSR protocol

    CERN Multimedia

    1970-01-01

    On 30 November the USA Atomic Energy Commission and the USSR State Committee for the Utilization of Atomic Energy signed, in Washington, a protocol 'on carrying out of joint projects in the field of high energy physics at the accelerators of the National Accelerator Laboratory (Batavia) and the Institute for High Energy Physics (Serpukhov)'. The protocol will be in force for five years and can be extended by mutual agreement.

  18. Principles of Protocol Design

    DEFF Research Database (Denmark)

    Sharp, Robin

    This is a new and updated edition of a book first published in 1994. The book introduces the reader to the principles used in the construction of a large range of modern data communication protocols, as used in distributed computer systems of all kinds. The approach taken is rather a formal one......, primarily based on descriptions of the protocols in the notation of CSP (Communicating Sequential Processes)....

  19. Moebius sequence

    DEFF Research Database (Denmark)

    Pedersen, Line Kjeldgaard; Maimburg, Rikke Damkjær; Hertz, Jens Michael

    2017-01-01

    and photographical evaluation. Five patients maintained the diagnosis of MS according to the diagnostic criteria. RESULTS: All five patients had bilateral facial and abducens paralysis confirmed by ophthalmological examination. Three of five had normal brain MR imaging. Two had missing facial nerves and one had......BACKGROUND: Moebius Sequence (MS) is a rare disorder defined by bilateral congenital paralysis of the abducens and facial nerves in combination with various odontological, craniofacial, ophthalmological and orthopaedic conditions. The aetiology is still unknown; but both genetic (de novo mutations...

  20. Generating Exome Enriched Sequencing Libraries from Formalin-Fixed, Paraffin-Embedded Tissue DNA for Next Generation Sequencing

    Science.gov (United States)

    Marosy, Beth A.; Craig, Brian D.; Hetrick, Kurt N.; Witmer, P. Dane; Ling, Hua; Griffith, Sean M.; Myers, Ben; Ostrander, Elaine A.; Stanford, Janet L.; Brody, Lawrence C.; Doheny, Kimberly F.

    2016-01-01

    This unit describes a protocol for generating exome enriched sequencing libraries using DNA extracted from Formalin Fixed Paraffin Embedded (FFPE) samples. Utilizing commercially available kits, we present a low input FFPE workflow starting with 50ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution targeted selection for exons, followed by sequencing using the Illumina next generation short read sequencing platform. PMID:28075488

  1. In silico toxicology protocols.

    Science.gov (United States)

    Myatt, Glenn J; Ahlberg, Ernst; Akahori, Yumi; Allen, David; Amberg, Alexander; Anger, Lennart T; Aptula, Aynur; Auerbach, Scott; Beilke, Lisa; Bellion, Phillip; Benigni, Romualdo; Bercu, Joel; Booth, Ewan D; Bower, Dave; Brigo, Alessandro; Burden, Natalie; Cammerer, Zoryana; Cronin, Mark T D; Cross, Kevin P; Custer, Laura; Dettwiler, Magdalena; Dobo, Krista; Ford, Kevin A; Fortin, Marie C; Gad-McDonald, Samantha E; Gellatly, Nichola; Gervais, Véronique; Glover, Kyle P; Glowienke, Susanne; Van Gompel, Jacky; Gutsell, Steve; Hardy, Barry; Harvey, James S; Hillegass, Jedd; Honma, Masamitsu; Hsieh, Jui-Hua; Hsu, Chia-Wen; Hughes, Kathy; Johnson, Candice; Jolly, Robert; Jones, David; Kemper, Ray; Kenyon, Michelle O; Kim, Marlene T; Kruhlak, Naomi L; Kulkarni, Sunil A; Kümmerer, Klaus; Leavitt, Penny; Majer, Bernhard; Masten, Scott; Miller, Scott; Moser, Janet; Mumtaz, Moiz; Muster, Wolfgang; Neilson, Louise; Oprea, Tudor I; Patlewicz, Grace; Paulino, Alexandre; Lo Piparo, Elena; Powley, Mark; Quigley, Donald P; Reddy, M Vijayaraj; Richarz, Andrea-Nicole; Ruiz, Patricia; Schilter, Benoit; Serafimova, Rositsa; Simpson, Wendy; Stavitskaya, Lidiya; Stidl, Reinhard; Suarez-Rodriguez, Diana; Szabo, David T; Teasdale, Andrew; Trejo-Martin, Alejandra; Valentin, Jean-Pierre; Vuorinen, Anna; Wall, Brian A; Watts, Pete; White, Angela T; Wichard, Joerg; Witt, Kristine L; Woolley, Adam; Woolley, David; Zwickl, Craig; Hasselgren, Catrin

    2018-04-17

    The present publication surveys several applications of in silico (i.e., computational) toxicology approaches across different industries and institutions. It highlights the need to develop standardized protocols when conducting toxicity-related predictions. This contribution articulates the information needed for protocols to support in silico predictions for major toxicological endpoints of concern (e.g., genetic toxicity, carcinogenicity, acute toxicity, reproductive toxicity, developmental toxicity) across several industries and regulatory bodies. Such novel in silico toxicology (IST) protocols, when fully developed and implemented, will ensure in silico toxicological assessments are performed and evaluated in a consistent, reproducible, and well-documented manner across industries and regulatory bodies to support wider uptake and acceptance of the approaches. The development of IST protocols is an initiative developed through a collaboration among an international consortium to reflect the state-of-the-art in in silico toxicology for hazard identification and characterization. A general outline for describing the development of such protocols is included and it is based on in silico predictions and/or available experimental data for a defined series of relevant toxicological effects or mechanisms. The publication presents a novel approach for determining the reliability of in silico predictions alongside experimental data. In addition, we discuss how to determine the level of confidence in the assessment based on the relevance and reliability of the information. Copyright © 2018. Published by Elsevier Inc.

  2. Protocols for quantum binary voting

    Science.gov (United States)

    Thapliyal, Kishore; Sharma, Rishi Dutt; Pathak, Anirban

    Two new protocols for quantum binary voting are proposed. One of the proposed protocols is designed using a standard scheme for controlled deterministic secure quantum communication (CDSQC), and the other one is designed using the idea of quantum cryptographic switch, which uses a technique known as permutation of particles. A few possible alternative approaches to accomplish the same task (quantum binary voting) have also been discussed. Security of the proposed protocols is analyzed. Further, the efficiencies of the proposed protocols are computed, and are compared with that of the existing protocols. The comparison has established that the proposed protocols are more efficient than the existing protocols.

  3. Business protocol in integrated Europe

    OpenAIRE

    Pavelová, Nina

    2009-01-01

    The first chapter devotes to definitions of basic terms such as protocol or business protocol, to differences between protocol and etiquette, and between social etiquette and business etiquette. The second chapter focuses on the factors influencing the European business protocol. The third chapter is devoted to the etiquette of business protocol in the European countries. It touches the topics such as punctuality and planning of business appointment, greeting, business cards, dress and appear...

  4. DNA repair protocols

    DEFF Research Database (Denmark)

    Bjergbæk, Lotte

    In its 3rd edition, this Methods in Molecular Biology(TM) book covers the eukaryotic response to genomic insult including advanced protocols and standard techniques in the field of DNA repair. Offers expert guidance for DNA repair, recombination, and replication. Current knowledge of the mechanisms...... that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including...... recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly...

  5. A novel approach to multiple sequence alignment using hadoop data grids.

    Science.gov (United States)

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

  6. CRAFT (complete reduction to amplitude frequency table)--robust and time-efficient Bayesian approach for quantitative mixture analysis by NMR.

    Science.gov (United States)

    Krishnamurthy, Krish

    2013-12-01

    The intrinsic quantitative nature of NMR is increasingly exploited in areas ranging from complex mixture analysis (as in metabolomics and reaction monitoring) to quality assurance/control. Complex NMR spectra are more common than not, and therefore, extraction of quantitative information generally involves significant prior knowledge and/or operator interaction to characterize resonances of interest. Moreover, in most NMR-based metabolomic experiments, the signals from metabolites are normally present as a mixture of overlapping resonances, making quantification difficult. Time-domain Bayesian approaches have been reported to be better than conventional frequency-domain analysis at identifying subtle changes in signal amplitude. We discuss an approach that exploits Bayesian analysis to achieve a complete reduction to amplitude frequency table (CRAFT) in an automated and time-efficient fashion - thus converting the time-domain FID to a frequency-amplitude table. CRAFT uses a two-step approach to FID analysis. First, the FID is digitally filtered and downsampled to several sub FIDs, and secondly, these sub FIDs are then modeled as sums of decaying sinusoids using the Bayesian approach. CRAFT tables can be used for further data mining of quantitative information using fingerprint chemical shifts of compounds of interest and/or statistical analysis of modulation of chemical quantity in a biological study (metabolomics) or process study (reaction monitoring) or quality assurance/control. The basic principles behind this approach as well as results to evaluate the effectiveness of this approach in mixture analysis are presented. Copyright © 2013 John Wiley & Sons, Ltd.

  7. Principles of Protocol Design

    DEFF Research Database (Denmark)

    Sharp, Robin

    This is a new and updated edition of a book first published in 1994. The book introduces the reader to the principles used in the construction of a large range of modern data communication protocols, as used in distributed computer systems of all kinds. The approach taken is rather a formal one...

  8. Frameworks for Protocol Implementation

    NARCIS (Netherlands)

    de Barros Barbosa, Ciro; de barros Barbosa, C.; Ferreira Pires, Luis; Pires, L.F.; van Sinderen, Marten J.

    1998-01-01

    This paper reports on the development of a catalogue of frameworks for protocol implementation. Frameworks are software structures developed for a specific application domain, which can be re-used in the implementation of various different concrete systems in this domain. By using frameworks we aim

  9. Critical Response Protocol

    Science.gov (United States)

    Ellingson, Charlene; Roehrig, Gillian; Bakkum, Kris; Dubinsky, Janet M.

    2016-01-01

    This article introduces the Critical Response Protocol (CRP), an arts-based technique that engages students in equitable critical discourse and aligns with the "Next Generation Science Standards" vision for providing students opportunities for language learning while advancing science learning (NGSS Lead States 2013). CRP helps teachers…

  10. Updating protocols prodigy.

    Science.gov (United States)

    Ambrose, Kate

    2005-04-01

    If you are updating protocols, why not try the Prodigy website, at www.prodigy.nhs.uk ? It is a source of clinical knowledge on a range oftopics that is based on best evidence and organised to support clinical decision making.

  11. Model Additional Protocol

    International Nuclear Information System (INIS)

    Rockwood, Laura

    2001-01-01

    Since the end of the cold war a series of events has changed the circumstances and requirements of the safeguards system. The discovery of a clandestine nuclear weapons program in Iraq, the continuing difficulty in verifying the initial report of Democratic People's Republic of Korea upon entry into force of their safeguards agreement, and the decision of the South African Government to give up its nuclear weapons program and join the Treaty on the Non-Proliferation of Nuclear Weapons have all played a role in an ambitious effort by IAEA Member States and the Secretariat to strengthen the safeguards system. A major milestone in this effort was reached in May 1997 when the IAEA Board of Governors approved a Model Protocol Additional to Safeguards Agreements. The Model Additional Protocol was negotiated over a period of less than a year by an open-ended committee of the Board involving some 70 Member States and two regional inspectorates. The IAEA is now in the process of negotiating additional protocols, State by State, and implementing them. These additional protocols will provide the IAEA with rights of access to information about all activities related to the use of nuclear material in States with comprehensive safeguards agreements and greatly expanded physical access for IAEA inspectors to confirm or verify this information. In conjunction with this, the IAEA is working on the integration of these measures with those provided for in comprehensive safeguards agreements, with a view to maximizing the effectiveness and efficiency, within available resources, the implementation of safeguards. Details concerning the Model Additional Protocol are given. (author)

  12. Deciphering the RNA landscape by RNAome sequencing.

    Science.gov (United States)

    Derks, Kasper W J; Misovic, Branislav; van den Hout, Mirjam C G N; Kockx, Christel E M; Gomez, Cesar Payan; Brouwer, Rutger W W; Vrieling, Harry; Hoeijmakers, Jan H J; van IJcken, Wilfred F J; Pothof, Joris

    2015-01-01

    Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods.

  13. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  14. Sequence Alignment and Homology Search with BLAST and ClustalW.

    Science.gov (United States)

    Hung, Jui-Hung; Weng, Zhiping

    2016-11-01

    This protocol illustrates the steps of searching a sequence database with BLAST, which in essence performs pairwise alignment between the query sequence and each target sequence in the database. Steps for performing multiple sequence alignments with ClustalW are then described. Argonaute 2 (Ago2) is an essential component for small interfering RNA (siRNA)-directed RNA interference (RNAi) in fruit flies. This protocol uses Ago2 to demonstrate how to search for all Ago2 paralogs in the fly proteome using BLAST and to obtain a multiple sequence alignment of these sequences with ClustalW. © 2016 Cold Spring Harbor Laboratory Press.

  15. Symmetric cryptographic protocols

    CERN Document Server

    Ramkumar, Mahalingam

    2014-01-01

    This book focuses on protocols and constructions that make good use of symmetric pseudo random functions (PRF) like block ciphers and hash functions - the building blocks for symmetric cryptography. Readers will benefit from detailed discussion of several strategies for utilizing symmetric PRFs. Coverage includes various key distribution strategies for unicast, broadcast and multicast security, and strategies for constructing efficient digests of dynamic databases using binary hash trees.   •        Provides detailed coverage of symmetric key protocols •        Describes various applications of symmetric building blocks •        Includes strategies for constructing compact and efficient digests of dynamic databases

  16. Phototherapy Modalities and Protocols

    Directory of Open Access Journals (Sweden)

    Ayten Ferahbaş

    2010-12-01

    Full Text Available Over the past few years, the development of irradiation devices with new emission spectra has led to an expanded role for phototherapy in the treatment of skin diseases. This development is best illustrated by the increasing frequency with which 311 nm UVB phototherapy is used for the treatment of psoriasis and vitiligo, especially. Another example is UVA1 340-400 nm. UVA1 was first used to treat patients with atopic dermatitis, but it has been found to be efficacious in several other skin diseases. This is overview of the protocols for phototherapy with UV in the treatment of skin diseases as currently used according to recent literature review. There are, of course, other protocols in use that are effective.

  17. Diplomacy and Diplomatic Protocol

    Directory of Open Access Journals (Sweden)

    Lect. Ph.D Oana Iucu

    2008-12-01

    Full Text Available The present study aims to observe relationships and determining factors between diplomacyand diplomatic protocol as outlined by historical and contextual analyses. The approach is very dynamic,provided that concepts are able to show their richness, antiquity and polyvalence at the level of connotations,semantics, grammatical and social syntax. The fact that this information is up to date determines anattitude of appreciation and a state of positive contamination.

  18. Dysphonia risk screening protocol

    Science.gov (United States)

    Nemr, Katia; Simões-Zenari, Marcia; da Trindade Duarte, João Marcos; Lobrigate, Karen Elena; Bagatini, Flavia Alves

    2016-01-01

    OBJECTIVE: To propose and test the applicability of a dysphonia risk screening protocol with score calculation in individuals with and without dysphonia. METHOD: This descriptive cross-sectional study included 365 individuals (41 children, 142 adult women, 91 adult men and 91 seniors) divided into a dysphonic group and a non-dysphonic group. The protocol consisted of 18 questions and a score was calculated using a 10-cm visual analog scale. The measured value on the visual analog scale was added to the overall score, along with other partial scores. Speech samples allowed for analysis/assessment of the overall degree of vocal deviation and initial definition of the respective groups and after six months, the separation of the groups was confirmed using an acoustic analysis. RESULTS: The mean total scores were different between the groups in all samples. Values ranged between 37.0 and 57.85 in the dysphonic group and between 12.95 and 19.28 in the non-dysphonic group, with overall means of 46.09 and 15.55, respectively. High sensitivity and specificity were demonstrated when discriminating between the groups with the following cut-off points: 22.50 (children), 29.25 (adult women), 22.75 (adult men), and 27.10 (seniors). CONCLUSION: The protocol demonstrated high sensitivity and specificity in differentiating groups of individuals with and without dysphonia in different sample groups and is thus an effective instrument for use in voice clinics. PMID:27074171

  19. Dysphonia risk screening protocol

    Directory of Open Access Journals (Sweden)

    Katia Nemr

    2016-03-01

    Full Text Available OBJECTIVE: To propose and test the applicability of a dysphonia risk screening protocol with score calculation in individuals with and without dysphonia. METHOD: This descriptive cross-sectional study included 365 individuals (41 children, 142 adult women, 91 adult men and 91 seniors divided into a dysphonic group and a non-dysphonic group. The protocol consisted of 18 questions and a score was calculated using a 10-cm visual analog scale. The measured value on the visual analog scale was added to the overall score, along with other partial scores. Speech samples allowed for analysis/assessment of the overall degree of vocal deviation and initial definition of the respective groups and after six months, the separation of the groups was confirmed using an acoustic analysis. RESULTS: The mean total scores were different between the groups in all samples. Values ranged between 37.0 and 57.85 in the dysphonic group and between 12.95 and 19.28 in the non-dysphonic group, with overall means of 46.09 and 15.55, respectively. High sensitivity and specificity were demonstrated when discriminating between the groups with the following cut-off points: 22.50 (children, 29.25 (adult women, 22.75 (adult men, and 27.10 (seniors. CONCLUSION: The protocol demonstrated high sensitivity and specificity in differentiating groups of individuals with and without dysphonia in different sample groups and is thus an effective instrument for use in voice clinics.

  20. Automatic Validation of Protocol Narration

    DEFF Research Database (Denmark)

    Bodei, Chiara; Buchholtz, Mikael; Degano, Pierpablo

    2003-01-01

    We perform a systematic expansion of protocol narrations into terms of a process algebra in order to make precise some of the detailed checks that need to be made in a protocol. We then apply static analysis technology to develop an automatic validation procedure for protocols. Finally, we...

  1. Design and Analysis of Transport Protocols for Reliable High-Speed Communications

    NARCIS (Netherlands)

    Oláh, A.

    1997-01-01

    The design and analysis of transport protocols for reliable communications constitutes the topic of this dissertation. These transport protocols guarantee the sequenced and complete delivery of user data over networks which may lose, duplicate and reorder packets. Reliable transport services are

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

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure tha...

  3. New Communication Network Protocol for a Data Acquisition System

    Science.gov (United States)

    Uchida, T.; Fujii, H.; Nagasaka, Y.; Tanaka, M.

    2006-02-01

    An event builder based on communication networks has been used in high-energy physics experiments, and various networks have been adopted, for example, IEEE 802.3 (Ethernet), asynchronous transfer mode (ATM), and so on. In particular, Ethernet is widely used because its infrastructure is very cost effective. Many systems adopt standard protocols that are designed for a general network. However, in the case of an event builder, the communication pattern between stations is different from that in a general network. The unique communication pattern causes congestion, and thus makes it difficulty to quantitatively design the network. To solve this problem, we have developed a simple network protocol for a data acquisition (DAQ) system. The protocol is designed to keep the sequence of senders so that no congestion occurs. We implemented the protocol on a small hardware component [a field programmable gate array (FPGA)] and measured the performance, so that it will be ready for a generic DAQ system

  4. Use of limited MR protocol (coronal STIR) in the evaluation of patients with hip pain

    International Nuclear Information System (INIS)

    Khoury, N.J.; Birjawi, G.A.; Hourani, M.H.; Chaaya, M.

    2003-01-01

    To assess the role of a limited MR protocol (coronal STIR) as the initial part of the MR examination in patients with hip pain. Eighty-five patients presenting with hip pain, and normal radiographs of the pelvis, and who underwent our full MR protocol for hips were included retrospectively in the study. The full protocol consists of coronal T1-weighted and short tau inversion-recovery (STIR), and axial T2-weighted sequences. Ninety-three MR examinations were performed. Two radiologists interpreted the STIR (limited) examinations and the full studies separately, masked to each other's findings and to the final diagnosis. Comparison between the two protocols was then undertaken. For both readers, all normal MR examinations on the coronal STIR limited protocol were normal on the full protocol, with an interobserver reliability of 0.96. The STIR protocol was able to detect the presence or absence of an abnormality in 100% of cases (sensitivity). The STIR-only protocol provided a specific diagnosis in only 65% of cases (specificity). A normal coronal STIR study of the hips in patients with hip pain and normal radiographs precludes the need for further pelvic MR sequences. Any abnormality detected on this limited protocol should be further assessed by additional MR sequences. (orig.)

  5. 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.

  6. Compositional mining of multiple object API protocols through state abstraction.

    Science.gov (United States)

    Dai, Ziying; Mao, Xiaoguang; Lei, Yan; Qi, Yuhua; Wang, Rui; Gu, Bin

    2013-01-01

    API protocols specify correct sequences of method invocations. Despite their usefulness, API protocols are often unavailable in practice because writing them is cumbersome and error prone. Multiple object API protocols are more expressive than single object API protocols. However, the huge number of objects of typical object-oriented programs poses a major challenge to the automatic mining of multiple object API protocols: besides maintaining scalability, it is important to capture various object interactions. Current approaches utilize various heuristics to focus on small sets of methods. In this paper, we present a general, scalable, multiple object API protocols mining approach that can capture all object interactions. Our approach uses abstract field values to label object states during the mining process. We first mine single object typestates as finite state automata whose transitions are annotated with states of interacting objects before and after the execution of the corresponding method and then construct multiple object API protocols by composing these annotated single object typestates. We implement our approach for Java and evaluate it through a series of experiments.

  7. Compositional Mining of Multiple Object API Protocols through State Abstraction

    Directory of Open Access Journals (Sweden)

    Ziying Dai

    2013-01-01

    Full Text Available API protocols specify correct sequences of method invocations. Despite their usefulness, API protocols are often unavailable in practice because writing them is cumbersome and error prone. Multiple object API protocols are more expressive than single object API protocols. However, the huge number of objects of typical object-oriented programs poses a major challenge to the automatic mining of multiple object API protocols: besides maintaining scalability, it is important to capture various object interactions. Current approaches utilize various heuristics to focus on small sets of methods. In this paper, we present a general, scalable, multiple object API protocols mining approach that can capture all object interactions. Our approach uses abstract field values to label object states during the mining process. We first mine single object typestates as finite state automata whose transitions are annotated with states of interacting objects before and after the execution of the corresponding method and then construct multiple object API protocols by composing these annotated single object typestates. We implement our approach for Java and evaluate it through a series of experiments.

  8. The sequence of sequencers: The history of sequencing DNA

    Science.gov (United States)

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  9. FRENCH PROTOCOL CARDS

    CERN Multimedia

    Division du Personnel

    1999-01-01

    Senior officials, holders of FRENCH PROTOCOL cards (blue cards) due to expire on 31.12.1999, are requested to return these cards and those of family members, for extension to:Bureau des cartes, bâtiment 33.1-025Should the 3 spaces for authentication on the back of the card be full, please enclose 2 passport photographs for a new card.In the case of children aged 14 and over, an attestation of dependency and a school certificate should be returned with the card.Personnel DivisionTel. 79494/74683

  10. FRENCH PROTOCOL CARDS

    CERN Multimedia

    Division des Ressources Humaines; Human Resources Division; Tel. 74683-79494

    2000-01-01

    Senior officials, holders of FRENCH PROTOCOL cards (blue cards) due to expire on 31.12.2000, are requested to return these cards and those of family members, for extension to: Bureau des cartes, Bât 33.1-009/1-015 Should the three spaces for authentication on the back of the card be full, please enclose two passport photographs for a new card. In the case of children aged 14 and over, an attestation of dependency and a school certificate should be returned with the card.

  11. 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...

  12. Two-label peak-height encoded DNA sequencing by capillary gel electrophoresis: three examples.

    OpenAIRE

    Chen, D; Harke, H R; Dovichi, N J

    1992-01-01

    We report a modification to the peak-height encoded DNA sequencing technique of Tabor and Richardson. As in the original protocol, the sequencing reaction uses modified T7 polymerase with manganese rather than magnesium to produce very uniform incorporation of each dideoxynucleoside. To improve sequencing accuracy, two fluorescently labeled primers are employed in separate sequencing reactions. As an example, one sequencing reaction uses a FAM-labeled primer with dideoxyadenosine triphosphate...

  13. Security and SCADA protocols

    International Nuclear Information System (INIS)

    Igure, V. M.; Williams, R. D.

    2006-01-01

    Supervisory control and data acquisition (SCADA) networks have replaced discrete wiring for many industrial processes, and the efficiency of the network alternative suggests a trend toward more SCADA networks in the future. This paper broadly considers SCADA to include distributed control systems (DCS) and digital control systems. These networks offer many advantages, but they also introduce potential vulnerabilities that can be exploited by adversaries. Inter-connectivity exposes SCADA networks to many of the same threats that face the public internet and many of the established defenses therefore show promise if adapted to the SCADA differences. This paper provides an overview of security issues in SCADA networks and ongoing efforts to improve the security of these networks. Initially, a few samples from the range of threats to SCADA network security are offered. Next, attention is focused on security assessment of SCADA communication protocols. Three challenges must be addressed to strengthen SCADA networks. Access control mechanisms need to be introduced or strengthened, improvements are needed inside of the network to enhance security and network monitoring, and SCADA security management improvements and policies are needed. This paper discusses each of these challenges. This paper uses the Profibus protocol as an example to illustrate some of the vulnerabilities that arise within SCADA networks. The example Profibus security assessment establishes a network model and an attacker model before proceeding to a list of example attacks. (authors)

  14. Datafit. A new work flow oriented approach for time efficient data preparation, validation and flagging of time series data from environmental monitoring

    International Nuclear Information System (INIS)

    Ries, Ludwig

    2013-01-01

    Standardized quality assurance according to UN/WMO Global Atmosphere Watch (GAW) data quality objectives is essential for a homogeneous high level of data quality in GAW world data centers. However data processing and data preparation often times is done individually and in a non-standardized way. As an additional problem interactive data validation can be a very time consuming step on a GAW measurement station. In front of this background a new approach for a software solution with a set of time efficient and standardized methods is proposed which also can be used as a tool for future standardization of data quality assurance on GAW measurement stations. In general in order to prepare measurement data a set of methods is required. In the framework of this program the methods are ranked in two groups: first - simpler methods for managing structural changes and corrections in the time series data and second - higher developed methods for assuring a correct time structure, graphical control and flagging non representative data and for the calculation of differently or higher aggregated mean values and statistical values. By fulfilling the auxiliary condition that data treatment at first has to be finished with application of methods of group one the user is practically free in finding and selecting its way for a solution. Once the user has found an ordered set of methods and parameters which is a sufficient solution for the preparation of the actual data, the solution can be stored as a set of parameters for the individual project. This enables the user for repeating the solution at another time to another set of time series data which are produced with the same data format from the same instrument. This structure is characteristic and useful for continuous environmental monitoring which produces a high amount of time series data with a constant data format. By saving all intermediate results in a hierarchical way with a fixed naming convention, in a later time the

  15. 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.

  16. The Evolution of Web Protocols

    OpenAIRE

    Kelly, B

    1999-01-01

    This paper outlines the evolution of World Wide Web protocols. The paper reviews the original protocols developed for the web, in addressing, transport and data formats. A review of developments of the protocols is given, including developments of web data formats (HTML 4.0, cascading stylesheets and XML), transport (HTTP/1.1 and HTTP/NG) and addressing (URLs). The paper describes how the web initially lacked a metadata architecture and outlines the emergence of a metadata architecture for th...

  17. A protected password change protocol

    OpenAIRE

    Wang, Ren-Chiun; Yang, Chou-Chen; Mo, Kun-Ru

    2005-01-01

    Some protected password change protocols were proposed. However, the previous protocols were easily vulnerable to several attacks such as denial of service, password guessing, stolen-verifier and impersonation atacks etc. Recently, Chang et al. proposed a simple authenticated key agreement and protected password change protocol for enhancing the security and efficiency. In this paper, authors shall show that password guessing, denial of service and known-key attacks can work in their password...

  18. Static Validation of Security Protocols

    DEFF Research Database (Denmark)

    Bodei, Chiara; Buchholtz, Mikael; Degano, P.

    2005-01-01

    We methodically expand protocol narrations into terms of a process algebra in order to specify some of the checks that need to be made in a protocol. We then apply static analysis technology to develop an automatic validation procedure for protocols. Finally, we demonstrate that these techniques ...... suffice to identify several authentication flaws in symmetric and asymmetric key protocols such as Needham-Schroeder symmetric key, Otway-Rees, Yahalom, Andrew secure RPC, Needham-Schroeder asymmetric key, and Beller-Chang-Yacobi MSR...

  19. Host Identity Protocol Proxy

    Science.gov (United States)

    Salmela, Patrik; Melén, Jan

    The Host Identity Protocol (HIP) is one of the more recent designs that challenge the current Internet architecture. The main features of HIP are security and the identifier-locator split, which solves the problem of overloading the IP address with two separate tasks. This paper studies the possibility of providing HIP services to legacy hosts via a HIP proxy. Making a host HIP enabled requires that the IP-stack of the host is updated to support HIP. From a network administrator's perspective this can be a large obstacle. However, by providing HIP from a centralized point, a HIP proxy, the transition to begin using HIP can be made smoother. This and other arguments for a HIP proxy will be presented in this paper along with an analysis of a prototype HIP proxy and its performance.

  20. Unconditionally Secure Protocols

    DEFF Research Database (Denmark)

    Meldgaard, Sigurd Torkel

    This thesis contains research on the theory of secure multi-party computation (MPC). Especially information theoretically (as opposed to computationally) secure protocols. It contains results from two main lines of work. One line on Information Theoretically Secure Oblivious RAMS, and how....... We construct an oblivious RAM that hides the client's access pattern with information theoretic security with an amortized $\\log^3 N$ query overhead. And how to employ a second server that is guaranteed not to conspire with the first to improve the overhead to $\\log^2 N$, while also avoiding...... they are used to speed up secure computation. An Oblivious RAM is a construction for a client with a small $O(1)$ internal memory to store $N$ pieces of data on a server while revealing nothing more than the size of the memory $N$, and the number of accesses. This specifically includes hiding the access pattern...

  1. Protocols for Scholarly Communication

    CERN Document Server

    Pepe, Alberto; Pepe, Alberto; Yeomans, Joanne

    2007-01-01

    CERN, the European Organization for Nuclear Research, has operated an institutional preprint repository for more than 10 years. The repository contains over 850,000 records of which more than 450,000 are full-text OA preprints, mostly in the field of particle physics, and it is integrated with the library's holdings of books, conference proceedings, journals and other grey literature. In order to encourage effective propagation and open access to scholarly material, CERN is implementing a range of innovative library services into its document repository: automatic keywording, reference extraction, collaborative management tools and bibliometric tools. Some of these services, such as user reviewing and automatic metadata extraction, could make up an interesting testbed for future publishing solutions and certainly provide an exciting environment for e-science possibilities. The future protocol for scientific communication should naturally guide authors towards OA publication and CERN wants to help reach a full...

  2. BS Seeker: precise mapping for bisulfite sequencing

    Directory of Open Access Journals (Sweden)

    Pellegrini Matteo

    2010-04-01

    Full Text Available Abstract Background Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated reads, where the unmethylated Cs are converted to Ts. We have developed BS Seeker, an approach that converts the genome to a three-letter alphabet and uses Bowtie to align bisulfite-treated reads to a reference genome. It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings. Results We tested our aligner on synthetic data, a bisulfite-converted Arabidopsis library, and human libraries generated from two different experimental protocols. We evaluated the performance of our approach and compared it to other bisulfite aligners. The results demonstrate that among the aligners tested, BS Seeker is more versatile and faster. When mapping to the human genome, BS Seeker generates alignments significantly faster than RMAP and BSMAP. Furthermore, BS Seeker is the only alignment tool that can explicitly account for tags which are generated by certain library construction protocols. Conclusions BS Seeker provides fast and accurate mapping of bisulfite-converted reads. It can work with BS reads generated from the two different experimental protocols, and is able to efficiently map reads to large mammalian genomes. The Python program is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html.

  3. Massively parallel signature sequencing.

    Science.gov (United States)

    Zhou, Daixing; Rao, Mahendra S; Walker, Roger; Khrebtukova, Irina; Haudenschild, Christian D; Miura, Takumi; Decola, Shannon; Vermaas, Eric; Moon, Keith; Vasicek, Thomas J

    2006-01-01

    Massively parallel signature sequencing is an ultra-high throughput sequencing technology. It can simultaneously sequence millions of sequence tags, and, therefore, is ideal for whole genome analysis. When applied to expression profiling, it reveals almost every transcript in the sample and provides its accurate expression level. This chapter describes the technology and its application in establishing stem cell transcriptome databases.

  4. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    IAS Admin

    as a sum of two primes (for even numbers) and three primes (for odd numbers). We call this the Goldbach sequence g(n), which may be converted into a binary sequence b(n) by mapping each even number to 0 and each odd number to 1. The resulting binary sequences may be used as pseudorandom sequences in ...

  5. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.

    Science.gov (United States)

    Vrancken, Bram; Trovão, Nídia Sequeira; Baele, Guy; van Wijngaerden, Eric; Vandamme, Anne-Mieke; van Laethem, Kristel; Lemey, Philippe

    2016-01-07

    Genetic analyses play a central role in infectious disease research. Massively parallelized "mechanical cloning" and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure--from nucleic acid extraction to sequencing--should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping.

  6. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  7. Resource Usage Protocols for Iterators

    NARCIS (Netherlands)

    Huisman, Marieke; Haack, C.; Müller, P.; Hurlin, C.

    We discuss usage protocols for iterator objects that prevent concurrent modifications of the underlying collection while iterators are in progress. We formalize these protocols in Java-like object interfaces, enriched with separation logic contracts. We present examples of iterator clients and

  8. Gene probes: principles and protocols

    National Research Council Canada - National Science Library

    Aquino de Muro, Marilena; Rapley, Ralph

    2002-01-01

    ... of labeled DNA has allowed genes to be mapped to single chromosomes and in many cases to a single chromosome band, promoting significant advance in human genome mapping. Gene Probes: Principles and Protocols presents the principles for gene probe design, labeling, detection, target format, and hybridization conditions together with detailed protocols, accom...

  9. Developing frameworks for protocol implementation

    NARCIS (Netherlands)

    de Barros Barbosa, C.; de barros Barbosa, C.; Ferreira Pires, Luis

    1999-01-01

    This paper presents a method to develop frameworks for protocol implementation. Frameworks are software structures developed for a specific application domain, which can be reused in the implementation of various different concrete systems in this domain. The use of frameworks support a protocol

  10. 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.

  11. Dynamic contrast-enhanced MRI in orbital lymphoproliferative disorders: Effects of region of interest selection methods on time efficiency, measurement reproducibility, and diagnostic ability.

    Science.gov (United States)

    Qian, Wen; Xu, Xiao-Quan; Hu, Hao; Su, Guo-Yi; Wu, Jiang-Fen; Shi, Hai-Bin; Wu, Fei-Yun

    2017-09-18

    Previous studies indicated that dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) could serve as a useful biomarker for differentiating malignant from benign orbital lymphoproliferative disorders (OLPDs). To investigate the influence of different region of interest (ROI) selection methods on the measurements of DCE-MRI parameters, and their diagnostic ability in discriminating malignant from benign OLPDs. Retrospective study. In all, 46 patients with OLPDs (22 benign and 24 malignant). 3.T DCE-MRI using a 2D turbo fast low angle shot sequence postcontrast. DCE-MRI data were analyzed using three different ROI selection methods, including whole-tumor ROI (ROI WT ), single-slice ROI (ROI SS ) and hot-spot ROI (ROI HS ). Quantitative parameters (K trans , K ep , V e ) were calculated based on a modified Tofts model. Analysis of variance test, intraclass correlation coefficient (ICC), Bland-Altman plots, independent t-test, and receiver operating characteristic curve analyses were used for statistical analyses. The time required for outlining ROI WT was significantly longer than ROI SS and ROI HS (P measurements of DCE-MRI-derived parameters based on ROI HS demonstrated lowest ICC, followed by ROI SS and ROI WT . Malignant OLPDs showed significantly higher K ep than benign mimics (P methods could have an influence on the measurements of DCE-MRI parameters. Taking measurement time, reproducibility, and diagnostic ability into account, we suggest single-slice ROI to be used for differentiating malignant from benign OLPDs in clinical practice. 3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2017. © 2017 International Society for Magnetic Resonance in Medicine.

  12. Protocols.io: Virtual Communities for Protocol Development and Discussion.

    Science.gov (United States)

    Teytelman, Leonid; Stoliartchouk, Alexei; Kindler, Lori; Hurwitz, Bonnie L

    2016-08-01

    The detailed know-how to implement research protocols frequently remains restricted to the research group that developed the method or technology. This knowledge often exists at a level that is too detailed for inclusion in the methods section of scientific articles. Consequently, methods are not easily reproduced, leading to a loss of time and effort by other researchers. The challenge is to develop a method-centered collaborative platform to connect with fellow researchers and discover state-of-the-art knowledge. Protocols.io is an open-access platform for detailing, sharing, and discussing molecular and computational protocols that can be useful before, during, and after publication of research results.

  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. Implementation of Next-Generation Sequencing (NGS) for HLA Genotyping

    DEFF Research Database (Denmark)

    Christiansen, Mette

    2015-01-01

    Introduction It has become increasingly difficult to attain high resolution HLA typing without ambiguities when employing SBT and PCR-SSP. NGS is well-suited for HLA typing as it delivers highly accurate and unambiguous results. We validated a NGS protocol developed for use with the Illumina Mi......Seq. Methods and Materials Without any prior NGS experience, we implemented a protocol consisting of LR-PCR of 5 loci (HLA-A, B, C, DRB1, and DQB1), library prep with two different indexing strategies: a) locus-specific indexing and b) sample-specific indexing. Sequencing was paired-end 250 bp sequencing......, and sequence analysis was performed with Twin HLA (Omixon). Results Two sequencing runs of the Omixon Holotype X4 kit yielded an average output of 5.3 Gb per run. Analysis was limited to 20K reads for all the indexes resulting in an average consensus coverage of 332 for locus specific indexing and 59...

  15. Inaudible functional MRI using a truly mute gradient echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Marcar, V.L. [University of Zurich, Department of Psychology, Neuropsychology, Treichlerstrasse 10, 8032 Zurich (Switzerland); Girard, F. [GE Medical Systems SA, 283, rue de la Miniere B.P. 34, 78533 Buc Cedex (France); Rinkel, Y.; Schneider, J.F.; Martin, E. [University Children' s Hospital, Neuroradiology and Magnetic Resonance, Department of Diagnostic Imaging, Steinwiesstrasse 75, 8032 Zurich (Switzerland)

    2002-11-01

    We performed functional MRI experiments using a mute version of a gradient echo sequence on adult volunteers using either a simple visual stimulus (flicker goggles: 4 subjects) or an auditory stimulus (music: 4 subjects). Because the mute sequence delivers fewer images per unit time than a fast echo planar imaging (EPI) sequence, we explored our data using a parametric ANOVA test and a non-parametric Wilcoxon-Mann-Whitney test in addition to performing a cross-correlation analysis. All three methods were in close agreement regarding the location of the BOLD contrast signal change. We demonstrated that, using appropriate statistical analysis, functional MRI using an MR sequence that is acoustically inaudible to the subject is feasible. Furthermore compared with the ''silent'' event-related procedures involving an EPI protocol, our mGE protocol compares favourably with respect to experiment time and the BOLD signal. (orig.)

  16. Protein Sequencing with Tandem Mass Spectrometry

    Science.gov (United States)

    Ziady, Assem G.; Kinter, Michael

    The recent introduction of electrospray ionization techniques that are suitable for peptides and whole proteins has allowed for the design of mass spectrometric protocols that provide accurate sequence information for proteins. The advantages gained by these approaches over traditional Edman Degradation sequencing include faster analysis and femtomole, sometimes attomole, sensitivity. The ability to efficiently identify proteins has allowed investigators to conduct studies on their differential expression or modification in response to various treatments or disease states. In this chapter, we discuss the use of electrospray tandem mass spectrometry, a technique whereby protein-derived peptides are subjected to fragmentation in the gas phase, revealing sequence information for the protein. This powerful technique has been instrumental for the study of proteins and markers associated with various disorders, including heart disease, cancer, and cystic fibrosis. We use the study of protein expression in cystic fibrosis as an example.

  17. Protocol converter for serial communication between digital rectifier controllers and a power plant SCADA system

    Directory of Open Access Journals (Sweden)

    Vukić Vladimir Đ.

    2016-01-01

    Full Text Available The paper describes the protocol converter INT-485-MBRTU, developed for serial communication between the thyristor rectifier (based on the proprietary protocol "INT-CPD-05", according to standard RS-485 and the SCADA system (based on protocol "Modbus RTU", of the same standard in the thermal power plant "Nikola Tesla B1". Elementary data on industrial communication protocols and communication gateways were provided. The basic technical characteristics of the "Omron" programmable logic controller CJ series were described, as well as the developed device INT-485-MBRTU. Protocol converters with two versions of communication software were tested, differing only in one control word, intended for a forced successive change of communication sequences, in opposite to automatic sequence relieve. The device iNT-485-MBRTU, with the program for forced successive change of communication sequences, demonstrated the reliability of data transfer of 100 %, in a sample of approximately 480 messages. For nearly the same sample, the same protocol converter, with a version of the program without any type of message identifiers, transferred less than 60 % of the foreseen data. During multiple sixty-hour tests, the reliability of data transfer of at least 99.9979% was recorded, in 100% of the analysed cases, and for a sample of nearly 96,000 pairs of the send and receive messages. We analysed the results and estimated the additional possibilities for application of the INT-485-MBRTU protocol converter.

  18. 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...

  19. 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.

  20. 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....

  1. SIP protocol model for OMNET++

    Directory of Open Access Journals (Sweden)

    Jan Kucerak

    2016-01-01

    Full Text Available The article describes our new SIP protocol implementation for the OMNeT++ simulation framework. OMNeT++ simulation framework provides an extensive support of IP related protocols, nevertheless a working SIP protocol implementation is missing. Real measurements were also done using a SIPp traffic generator and the results are compared to those obtained by our new SIP model. Since this work is a part of bigger project concerned strictly on measuring "first response times" over networks with a faulty transmission links, the actually collected statistics are focused only this way.

  2. Chest magnetic resonance imaging: a protocol suggestion

    Directory of Open Access Journals (Sweden)

    Bruno Hochhegger

    2015-12-01

    Full Text Available Abstract In the recent years, with the development of ultrafast sequences, magnetic resonance imaging (MRI has been established as a valuable diagnostic modality in body imaging. Because of improvements in speed and image quality, MRI is now ready for routine clinical use also in the study of pulmonary diseases. The main advantage of MRI of the lungs is its unique combination of morphological and functional assessment in a single imaging session. In this article, the authors review most technical aspects and suggest a protocol for performing chest MRI. The authors also describe the three major clinical indications for MRI of the lungs: staging of lung tumors; evaluation of pulmonary vascular diseases; and investigation of pulmonary abnormalities in patients who should not be exposed to radiation.

  3. Chest magnetic resonance imaging: a protocol suggestion*

    Science.gov (United States)

    Hochhegger, Bruno; de Souza, Vinícius Valério Silveira; Marchiori, Edson; Irion, Klaus Loureiro; Souza Jr., Arthur Soares; Elias Junior, Jorge; Rodrigues, Rosana Souza; Barreto, Miriam Menna; Escuissato, Dante Luiz; Mançano, Alexandre Dias; Araujo Neto, César Augusto; Guimarães, Marcos Duarte; Nin, Carlos Schuler; Santos, Marcel Koenigkam; Silva, Jorge Luiz Pereira e

    2015-01-01

    In the recent years, with the development of ultrafast sequences, magnetic resonance imaging (MRI) has been established as a valuable diagnostic modality in body imaging. Because of improvements in speed and image quality, MRI is now ready for routine clinical use also in the study of pulmonary diseases. The main advantage of MRI of the lungs is its unique combination of morphological and functional assessment in a single imaging session. In this article, the authors review most technical aspects and suggest a protocol for performing chest MRI. The authors also describe the three major clinical indications for MRI of the lungs: staging of lung tumors; evaluation of pulmonary vascular diseases; and investigation of pulmonary abnormalities in patients who should not be exposed to radiation. PMID:26811555

  4. Telemetry Transmission over Internet Protocol (TMoIP) Standard

    Science.gov (United States)

    2010-10-01

    Gigabit Interface Converter (GBIC)/Small Form-factor Pluggable ( SFP ) connector interfaces be included in TMoIP equipment that implements fiber optic...Description Protocol: a format for describing streaming media parameters. SEQ NUMBER Sequence Number (field name reference) SFP Small Form-factor...Ethernet over twisted pair at 1000 Mbit/sec 802.3ab Optional Notes: a. To provide user flexibility, it is recommended that support for GBIC/ SFP

  5. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing

    Directory of Open Access Journals (Sweden)

    Bram Vrancken

    2016-01-01

    Full Text Available Genetic analyses play a central role in infectious disease research. Massively parallelized “mechanical cloning” and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™ with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure—from nucleic acid extraction to sequencing—should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping.

  6. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

    Directory of Open Access Journals (Sweden)

    Bass Ellen J

    2010-03-01

    Full Text Available Abstract Background While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments inferred from three-dimensional coordinates. Since sequence alignment algorithms produce optimal alignments, the best structural alignments must reflect suboptimal sequence alignment scores. Thus, we have examined a range of suboptimal sequence alignments and a range of scoring parameters to understand better which sequence alignments are likely to be more structurally accurate. Results We compared near-optimal protein sequence alignments produced by the Zuker algorithm and a set of probabilistic alignments produced by the probA program with structural alignments produced by four different structure alignment algorithms. There is significant overlap between the solution spaces of structural alignments and both the near-optimal sequence alignments produced by commonly used scoring parameters for sequences that share significant sequence similarity (E-values -5 and the ensemble of probA alignments. We constructed a logistic regression model incorporating three input variables derived from sets of near-optimal alignments: robustness, edge frequency, and maximum bits-per-position. A ROC analysis shows that this model more accurately classifies amino acid pairs (edges in the alignment path graph according to the likelihood of appearance in structural alignments than the robustness score alone. We investigated various trimming protocols for removing incorrect edges from the optimal sequence alignment; the most effective protocol is to remove matches from the semi-global optimal alignment that are outside the boundaries of the local alignment, although trimming according to the model-generated probabilities achieves a similar level of improvement. The

  7. Antibody engineering: methods and protocols

    National Research Council Canada - National Science Library

    Chames, Patrick

    2012-01-01

    "Antibody Engineering: Methods and Protocols, Second Edition was compiled to give complete and easy access to a variety of antibody engineering techniques, starting from the creation of antibody repertoires and efficient...

  8. Recommended protocols for sampling macrofungi

    Science.gov (United States)

    Gregory M. Mueller; John Paul Schmit; Sabine M. Hubndorf Leif Ryvarden; Thomas E. O' Dell; D. Jean Lodge; Patrick R. Leacock; Milagro Mata; Loengrin Umania; Qiuxin (Florence) Wu; Daniel L. Czederpiltz

    2004-01-01

    This chapter discusses several issues regarding reommended protocols for sampling macrofungi: Opportunistic sampling of macrofungi, sampling conspicuous macrofungi using fixed-size, sampling small Ascomycetes using microplots, and sampling a fixed number of downed logs.

  9. Automata-theoretic protocol programming

    NARCIS (Netherlands)

    Jongmans, Sung-Shik Theodorus Quirinus

    2016-01-01

    Parallel programming has become essential for writing scalable programs on general hardware. Conceptually, every parallel program consists of workers, which implement primary units of sequential computation, and protocols, which implement the rules of interaction that workers must abide by. As

  10. Protein sequence databases.

    Science.gov (United States)

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.

  11. Genome-scale validation of deep-sequencing libraries.

    Directory of Open Access Journals (Sweden)

    Dominic Schmidt

    Full Text Available Chromatin immunoprecipitation followed by high-throughput (HTP sequencing (ChIP-seq is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing.

  12. ACUTE EFFECTS OF THREE DIFFERENT CIRCUIT WEIGHT TRAINING PROTOCOLS ON BLOOD LACTATE, HEART RATE, AND RATING OF PERCEIVED EXERTION IN RECREATIONALLY ACTIVE WOMEN

    OpenAIRE

    Brook L. Skidmore; Margaret T. Jones; Mark Blegen; Tracey D. Matthews

    2012-01-01

    Interval and circuit weight training are popular training methods for maximizing time-efficiency, and are purported to deliver greater physiological benefits faster than traditional training methods. Adding interval training into a circuit weight-training workout may further enhance the benefits of circuit weight training by placing increased demands upon the cardiovascular system. Our purpose was to compare acute effects of three circuit weight training protocols 1) traditional circuit weigh...

  13. Monoclonal antibodies technology. Protocols

    International Nuclear Information System (INIS)

    Acevado Castro, B.E.

    1997-01-01

    Full text: Immunization. The first step in preparing useful monoclonal antibodies (MAbs) is to immunize an animal (Balb/c for example) with an appropriate antigen. Methods (only for soluble antigen): Solubilize selected antigen in Phosphate buffer solution (PBS) at pH 7.2-7.4, ideally at a final concentration per animal between 10 to 50 μg/ml. It is recommended that the antigen under consideration be incorporated into the emulsion adjuvants in 1:1 volumetric relation. We commonly use Frend's adjuvant (FA) to prepared immunized solution. The first immunization should be prepared with complete FA, and the another could be prepared with incomplete FA. It is recommended to inject mice with 0.2 ml intraperitoneal (ip) or subcutaneous (sc). Our experience suggests the sc route is the preferred route. A minimum protocol for immunizing mice to generate cells for preparing hybridomas is s follows: immunize sc on day 0, boost sc on day 21, take a trial bleeding on day 26; if antibody titters are satisfactory, boost ip on day 35 with antigen only, and remove the spleen to obtain cells for fusion on day 38. Fusion protocol. The myeloma cell line we are using is X63 Ag8.653. At the moment of fusion myeloma cells need a good viability (at least a 95%). 1. Remove the spleen cells from immunized mice using sterile conditions. An immune spleen should yield between 7 a 10x10 7 nucleated cells. 2. Place the spleen in 20 ml of serum-free RPMI 1640 in a Petri dish. Using a needle and syringe, inject the spleen with medium to distend and disrupt the spleen stroma and free the nucleated cells. 3. Flush the cell suspension with a Pasteur pipet to disperse clumps of cells. 4. Centrifuge the spleen cell suspension at 250g for 10 min. Resuspend the pellet in serum-free RPMI 1640. Determine cell concentration using Neuhabuer chamber. 5. Mix the myeloma cells and spleen cells in a conical 50-ml tube in serum-free RPMI 1640, 1 x10 7 spleen cells to 1x10 6 myeloma cells (ratio 10:1). Centrifuge

  14. Structural feature extraction protocol for classifying reversible membrane binding protein domains.

    Science.gov (United States)

    Källberg, Morten; Lu, Hui

    2009-01-01

    Machine learning based classification protocols for automated function annotation of protein structures have in many instances proven superior to simpler sequence based procedures. Here we present an automated method for extracting features from protein structures by construction of surface patches to be used in such protocols. The utility of the developed patch-growing procedure is exemplified by its ability to identify reversible membrane binding domains from the C1, C2, and PH families.

  15. The mesh network protocol evaluation and development

    OpenAIRE

    Pei, Ping; Petrenko, Y. N.

    2015-01-01

    In this paper, we introduce a Mesh network protocol evaluation and development. It has a special protocol. We could easily to understand that how different protocols are used in mesh network. In addition to our comprehension, Multi – hop routing protocol could provide robustness and load balancing to communication in wireless mesh networks.

  16. The Simplest Protocol for Oblivious Transfer

    DEFF Research Database (Denmark)

    Chou, Tung; Orlandi, Claudio

    2015-01-01

    Oblivious Transfer (OT) is the fundamental building block of cryptographic protocols. In this paper we describe the simplest and most efficient protocol for 1-out-of-n OT to date, which is obtained by tweaking the Diffie-Hellman key-exchange protocol. The protocol achieves UC-security against act...

  17. OTU analysis using metagenomic shotgun sequencing data.

    Directory of Open Access Journals (Sweden)

    Xiaolin Hao

    Full Text Available Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides 16S rRNA gene fragment data with natural immunity against the biases raised during priming and thus the potential of uncovering the true structure of microbial community by giving more accurate predictions of operational taxonomic units (OTUs. Nonetheless, the lack of statistically rigorous comparison between 16S rRNA gene fragments and other data types makes it difficult to interpret previously reported results using 16S rRNA gene fragments. Therefore, in the present work, we established a standard analysis pipeline that would help confirm if the differences in the data are true or are just due to potential technical bias. This pipeline is built by using simulated data to find optimal mapping and OTU prediction methods. The comparison between simulated datasets revealed a relationship between 16S rRNA gene fragments and full-length 16S rRNA sequences that a 16S rRNA gene fragment having a length >150 bp provides the same accuracy as a full-length 16S rRNA sequence using our proposed pipeline, which could serve as a good starting point for experimental design and making the comparison between 16S rRNA gene fragment-based and targeted 16S rRNA sequencing-based surveys possible.

  18. Epigenomics: sequencing the methylome.

    Science.gov (United States)

    Hirst, Martin

    2013-01-01

    DNA methylation patterns are increasingly surveyed through methods that utilize massively parallel sequencing. Sequence-based assays developed to detect DNA methylation can be broadly divided into those that depend on affinity enrichment, chemical conversion, or enzymatic restriction. The DNA fragments resulting from these methods are uniformly subjected to library construction and massively parallel sequencing. The sequence reads are subsequently aligned to a reference genome and subjected to specialized analytical tools to extract the underlying methylation signature. This chapter will outline these emerging techniques.

  19. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  20. Secret Public Key Protocols Revisited

    Science.gov (United States)

    Lim, Hoon Wei; Paterson, Kenneth G.

    Password-based protocols are important and popular means of providing human-to-machine authentication. The concept of secret public keys was proposed more than a decade ago as a means of securing password-based authentication protocols against off-line password guessing attacks, but was later found vulnerable to various attacks. In this paper, we revisit the concept and introduce the notion of identity-based secret public keys. Our new identity-based approach allows secret public keys to be constructed in a very natural way using arbitrary random strings, eliminating the structure found in, for example, RSA or ElGamal keys. We examine identity-based secret public key protocols and give informal security analyses, indicating that they are secure against off-line password guessing and other attacks.

  1. The Kyoto protocol development; La viabilite du protocole de Kyoto

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, R. [Harvard Univ., Barrow, AK (United States); Guesneris, R. [College de France, 75 - Paris (France)

    2002-04-01

    From the author R. Cooper point of view the Kyoto Protocol is a flawed concept. The reasons for dropping Kyoto are presented in this paper insisting that rejecting Kyoto not means to imply that global climate change is not a serious problem. After a presentation of the US policy facing the Climatic Change, some concluding propositions are proposed. (A.L.B.)

  2. Coverage statistics for sequence census methods

    Directory of Open Access Journals (Sweden)

    Evans Steven N

    2010-08-01

    Full Text Available Abstract Background We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how this can be used to detect regions with anomalous coverage. This modeling perspective is especially germane to current high-throughput sequencing experiments, where both sample preparation protocols and sequencing technology particulars can affect fragment length distributions. Results Under the mild assumptions that fragment start sites are Poisson distributed and successive fragment lengths are independent and identically distributed, we observe that, regardless of fragment length distribution, the fragments produced in a sequencing experiment can be viewed as resulting from a two-dimensional spatial Poisson process. We then study the successive jumps of the coverage function, and show that they can be encoded as a random tree that is approximately a Galton-Watson tree with generation-dependent geometric offspring distributions whose parameters can be computed. Conclusions We extend standard analyses of shotgun sequencing that focus on coverage statistics at individual sites, and provide a null model for detecting deviations from random coverage in high-throughput sequence census based experiments. Our approach leads to explicit determinations of the null distributions of certain test statistics, while for others it greatly simplifies the approximation of their null distributions by simulation. Our focus on fragments also leads to a new approach to visualizing sequencing data that is of independent interest.

  3. Time-efficient multidimensional threshold tracking method

    DEFF Research Database (Denmark)

    Fereczkowski, Michal; Kowalewski, Borys; Dau, Torsten

    2015-01-01

    Traditionally, adaptive methods have been used to reduce the time it takes to estimate psychoacoustic thresholds. However, even with adaptive methods, there are many cases where the testing time is too long to be clinically feasible, particularly when estimating thresholds as a function of anothe...

  4. Delayed Sequence Intubation

    DEFF Research Database (Denmark)

    Weingart, Scott D; Trueger, N Seth; Wong, Nelson

    2015-01-01

    assessed. RESULTS: A total of 62 patients were enrolled: 19 patients required delayed sequence intubation to allow nonrebreather mask, 39 patients required it to allow NIPPV, and 4 patients required it for nasogastric tube placement. Saturations increased from a mean of 89.9% before delayed sequence...

  5. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  6. 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…

  7. 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.

  8. Formalization in PVS of Balancing Properties Necessary for Proving Security of the Dolev-Yao Cascade Protocol Model

    Directory of Open Access Journals (Sweden)

    Mauricio Ayala-Rincón

    2013-01-01

    Full Text Available In this work, we present an algebraic approach for modeling the two-party cascade protocol of Dolev-Yao and for fully formalizing its security in the specification language of the Prototype Verification System PVS. Although cascade protocols could be argued to be a very limited model, it should be stressed here that they are the basis of more sophisticated protocols of great applicability, such as those which allow treatment of multiparty, tuples, nonces, name-stamps, signatures, etc. In the current algebraic approach, steps of the protocol are modeled in a monoid freely generated by the cryptographic operators. Words in this monoid are specified as finite sequences and the whole protocol as a finite sequence of protocol steps, that are functions from pairs of users to sequences of cryptographic operators. In a previous work, assuming that for balanced protocols admissible words produced by a potential intruder should be balanced, a formalization of the characterization of security of this kind of protocols was given in PVS. In this work, the previously assumed property is also formalized, obtaining in this way a complete formalization which mathematically guarantees the security of these protocols. Despite such property being relatively easy to specify, obtaining a complete formalization requires a great amount of effort, because several algebraic properties, that are related to the preservation of the balancing property of the admissible language of the intruder, should be formalized in the granularity of the underlying data structure (of finite sequences used in the specification. Among these properties, the most complex are related to the notion of linkage property, which allows for a systematic analysis of words of the admissible language of a potential saboteur, showing how he/she is unable to isolate private keys of other users under the assumption of balanced protocols. The difficulties that arose in conducting this formalization are

  9. Bundle Security Protocol for ION

    Science.gov (United States)

    Burleigh, Scott C.; Birrane, Edward J.; Krupiarz, Christopher

    2011-01-01

    This software implements bundle authentication, conforming to the Delay-Tolerant Networking (DTN) Internet Draft on Bundle Security Protocol (BSP), for the Interplanetary Overlay Network (ION) implementation of DTN. This is the only implementation of BSP that is integrated with ION.

  10. Superposition Attacks on Cryptographic Protocols

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Funder, Jakob Løvstad; Nielsen, Jesper Buus

    2011-01-01

    string model. While our protocol is classical, it is sound against a cheating unbounded quantum prover and computational zero-knowledge even if the verifier is allowed a superposition attack. Finally, we consider multiparty computation and show that for the most general type of attack, simulation based...

  11. Recursive Ping-Pong Protocols

    DEFF Research Database (Denmark)

    Huttel, Hans; Srba, Jiri

    2004-01-01

    This paper introduces a process calculus with recursion which allows us to express an unbounded number of runs of the ping-pong protocols introduced by Dolev and Yao. We study the decidability issues associated with two common approaches to checking security properties, namely reachability analysis...

  12. Affinity biosensors: techniques and protocols

    National Research Council Canada - National Science Library

    Rogers, Kim R; Mulchandani, Ashok

    1998-01-01

    ..., and government to begin or expand their biosensors research. This volume, Methods in Biotechnology vol. 7: Affinity Biosensors: Techniques and Protocols, describes a variety of classical and emerging transduction technologies that have been interfaced to bioaffinity elements (e.g., antibodies and receptors). Some of the reas...

  13. Implementation of postoperative handoff protocol

    African Journals Online (AJOL)

    Despite its importance, the practice of a structured postoperative ... the handoff protocol; limited nurse checklist to six items; added ... anticipatory guidance for the ICU team. Once the ICU team clarified any questions from the anaesthesiologist, the surgeon. (and then the theatre nursing staff) proceeded to report on the.

  14. Art. 1 Eerste Protocol EVRM

    NARCIS (Netherlands)

    Poelmann, E.

    2014-01-01

    Het recht op bezit is niet in het Europees Verdrag ter bescherming van de rechten van de mens en de fundamentele vrijheden (hierna: EVRM) neergelegd, maar in het Eerste Protocol daarbij (hierna: EP), dat in 1954 in werking is getreden. Het is van belang voor ogen te houden dat de Tweede Wereldoorlog

  15. Performance Evaluation of Security Protocols

    DEFF Research Database (Denmark)

    Bodei, Chiara; Buchholtz, Mikael; Curti, Michele

    2005-01-01

    We use a special operational semantics which drives us in inferring quantitative measures on systems describing cryptographis cryptographic protocols. We assign rates to transitions by only looking at these labels. The rates reflect the distributed architecture running applications and the use of...

  16. Combinatorial pooling enables selective sequencing of the barley gene space.

    Directory of Open Access Journals (Sweden)

    Stefano Lonardi

    2013-04-01

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

  17. 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.

  18. Evolution of DNA sequencing.

    Science.gov (United States)

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-03-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.

  19. Group covariant protocols for quantum string commitment

    International Nuclear Information System (INIS)

    Tsurumaru, Toyohiro

    2006-01-01

    We study the security of quantum string commitment (QSC) protocols with group covariant encoding scheme. First we consider a class of QSC protocol, which is general enough to incorporate all the QSC protocols given in the preceding literatures. Then among those protocols, we consider group covariant protocols and show that the exact upperbound on the binding condition can be calculated. Next using this result, we prove that for every irreducible representation of a finite group, there always exists a corresponding nontrivial QSC protocol which reaches a level of security impossible to achieve classically

  20. 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

  1. 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.

  2. Improvement In MAODV Protocol Using Location Based Routing Protocol

    Directory of Open Access Journals (Sweden)

    Kaur Sharnjeet

    2016-01-01

    Full Text Available Energy saving is difficult in wireless sensor network (WSN due to limited resources. Each node in WSN is constrained by their limited battery power for their energy. The energy is reduced as the time goes off due to the packet transmission and reception. Energy management techniques are necessary to minimize the total power consumption of all the nodes in the network in order to maximize its life span. Our proposed protocol Location based routing (LBR aimed to find a path which utilizes the minimum energy to transmit the packets between the source and the destination. The required energy for the transmission and reception of data is evaluated in MATLAB. LBR is implemented on Multicast Ad hoc On Demand Distance Vector Routing Protocol (MAODV to manage the energy consumption in the transmission and reception of data. Simulation results of LBR show the energy consumption has been reduced.

  3. Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

    Energy Technology Data Exchange (ETDEWEB)

    Chourey, Karuna [ORNL; Jansson, Janet [Lawrence Berkeley National Laboratory (LBNL); Verberkmoes, Nathan C [ORNL; Shah, Manesh B [ORNL; Chavarria, Krystle L. [Lawrence Berkeley National Laboratory (LBNL); Tom, Lauren M [Lawrence Berkeley National Laboratory (LBNL); Brodie, Eoin L. [Lawrence Berkeley National Laboratory (LBNL); Hettich, Robert {Bob} L [ORNL

    2010-01-01

    We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography-mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.

  4. Direct cellular lysis/protein extraction protocol for soil metaproteomics.

    Science.gov (United States)

    Chourey, Karuna; Jansson, Janet; VerBerkmoes, Nathan; Shah, Manesh; Chavarria, Krystle L; Tom, Lauren M; Brodie, Eoin L; Hettich, Robert L

    2010-12-03

    We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography-mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.

  5. Quantum Information Protocols with Gaussian States of Light

    DEFF Research Database (Denmark)

    Jacobsen, Christian Scheffmann

    Quantum cryptography is widely regarded as the most mature field within the context of quantum information in the sense that its application and development has produced companies that base their products on genuine quantum mechanical principles. Examples include quantum random number generators...... of Gaussian states. A quantum information protocol is essentially a sequence of state exchanges between some number of parties and a certain ordering of quantum mechanical unitary operators performed by these parties. An example of this is the famous BB84 protocol for secret key generation, where photons...... with Gaussian states is a promising avenue for the development of practical quantum key distribution with a relay network structure in environments where the distances are relatively short and there is a high number of users, such as an urban environment. In addition to this we consider various point...

  6. Improvement of methods for large scale sequencing; application to human Xq28

    Energy Technology Data Exchange (ETDEWEB)

    Gibbs, R.A.; Andersson, B.; Wentland, M.A. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    Sequencing of a one-metabase region of Xq28, spanning the FRAXA and IDS loci has been undertaken in order to investigate the practicality of the shotgun approach for large scale sequencing and as a platform to develop improved methods. The efficiency of several steps in the shotgun sequencing strategy has been increased using PCR-based approaches. An improved method for preparation of M13 libraries has been developed. This protocol combines a previously described adaptor-based protocol with the uracil DNA glycosylase (UDG)-cloning procedure. The efficiency of this procedure has been found to be up to 100-fold higher than that of previously used protocols. In addition the novel protocol is more reliable and thus easy to establish in a laboratory. The method has also been adapted for the simultaneous shotgun sequencing of multiple short fragments by concentrating them before library construction is presented. This protocol is suitable for rapid characterization of cDNA clones. A library was constructed from 15 PCR-amplified and concentrated human cDNA inserts, and the insert sequences could easily be identified as separate contigs during the assembly process and the sequence coverage was even along each fragment. Using this strategy, the fine structures of the FraxA and IDS loci have been revealed and several EST homologies indicating novel expressed sequences have been identified. Use of PCR to close repetitive regions that are difficult to clone was tested by determination of the sequence of a cosmid mapping DXS455 in Xq28, containing a polymorphic VNTR. The region containing the VNTR was not represented in the shotgun library, but by designing PCR primers in the sequences flanking the gap and by cloning and sequencing the PCR product, the fine structure of the VNTR has been determined. It was found to be an AT-rich VNTR with a repeated 25-mer at the center.

  7. Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory

    OpenAIRE

    Dheedene, Annelies; SANTE, TOM; De Smet, Matthias; Vanbellinghen, Jean-François; Grisart, Bernard; Vergult, Sarah; Janssens, Sandra; Menten, Björn

    2016-01-01

    Abstract Objectives To implement non?invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15?month experience on clinical samples. Methods We validated a NIPT protocol for cell?free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemen...

  8. Using Ovsynch protocol versus Cosynch protocol in dairy cows

    Directory of Open Access Journals (Sweden)

    Ion Valeriu Caraba

    2013-10-01

    Full Text Available As a research on the reproductive physiology and endocrinology surrounding the estrous cycle in dairy cattle has been compiled, several estrous synchronization programs have been developed for use with dairy cows. These include several programs that facilitate the mass breeding of all animals at a predetermined time (timed-AI rather than the detection of estrus. We studied on 15 dary cows which were synchronized by Ovsynch and Cosynch programs. The estrus response for cows in Ovsynch protocol was of 63%. Pregnancy per insemination at 60 days was of 25%. Estrus response for cow in Cosynch protocol was of 57%. Pregnancy per insemination at 60 days was of 57%. Synchronization of ovulation using Ovsynch protocols can provide an effective way to manage reproduction in lactating dairy cows by eliminating the need for estrus detection. These are really efficient management programs for TAI of dairy cows that are able to reduce both the labour costs and the extra handling to daily estrus detection and AI.

  9. 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...

  10. 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}.

  11. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene......This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis...

  12. 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.

  13. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

    Science.gov (United States)

    Matranga, Christian B; Andersen, Kristian G; Winnicki, Sarah; Busby, Michele; Gladden, Adrianne D; Tewhey, Ryan; Stremlau, Matthew; Berlin, Aaron; Gire, Stephen K; England, Eleina; Moses, Lina M; Mikkelsen, Tarjei S; Odia, Ikponmwonsa; Ehiane, Philomena E; Folarin, Onikepe; Goba, Augustine; Kahn, S Humarr; Grant, Donald S; Honko, Anna; Hensley, Lisa; Happi, Christian; Garry, Robert F; Malboeuf, Christine M; Birren, Bruce W; Gnirke, Andreas; Levin, Joshua Z; Sabeti, Pardis C

    2014-01-01

    We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.

  14. Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing.

    Science.gov (United States)

    Marais, Armelle; Faure, Chantal; Bergey, Bernard; Candresse, Thierry

    2018-01-01

    High-throughput sequencing (or next-generation sequencing-NGS) is an emerging technology that allows the detection of plant viruses without any prior knowledge. Various sequencing techniques and various templates can be used as substrate for NGS. This chapter describes an optimized protocol for the extraction of double-stranded RNAs (dsRNAs) from a wide range of plants and for their random amplification prior to NGS sequencing.

  15. Secure Multi-Player Protocols

    DEFF Research Database (Denmark)

    Fehr, Serge

    While classically cryptography is concerned with the problem of private communication among two entities, say players, in modern cryptography multi-player protocols play an important role. And among these, it is probably fair to say that secret sharing, and its stronger version verifiable secret......, MPC can be based on arbitrary finite rings. This is in sharp contrast to the literature where essentially all MPC protocols require a much stronger mathematical structure, namely a field. Apart from its theoretical value, this can lead to efficiency improvements since it allows a greater freedom...... of all known schemes follows as corollaries whose proofs are pure linear algebra arguments, in contrast to some hybrid arguments used in the literature. (4) We construct a new unconditionally secure VSS scheme with minimized reconstruction complexity in the setting of a dishonest minority. This improves...

  16. From protocol to published report

    DEFF Research Database (Denmark)

    Berendt, Louise; Callréus, Torbjörn; Petersen, Lene Grejs

    2016-01-01

    ), primary objective, primary endpoint, and--for confirmatory trials only--hypothesis and sample size calculation. We used logistic regression, χ(2), and Fisher's exact test. RESULTS: A total of 282 applications of academic clinical drug trials were submitted to the Danish Health and Medicines Authority......BACKGROUND: Unacknowledged inconsistencies in the reporting of clinical trials undermine the validity of the results of the trials. Little is known about inconsistency in the reporting of academic clinical drug trials. Therefore, we investigated the prevalence of consistency between protocols...... and published reports of academic clinical drug trials. METHODS: A comparison was made between study protocols and their corresponding published reports. We assessed the overall consistency, which was defined as the absence of discrepancy regarding study type (categorized as either exploratory or confirmatory...

  17. Enterprise Considerations for Ports and Protocols

    Science.gov (United States)

    2016-10-21

    Internet and similar networks . The Internet model is commonly known as TCP/IP, because of its most important protocols, the Transmission Control...according to the scope of the networking involved. IETF documents RFC 1122 [25] and RFC 1123 [26] describe the Internet Protocol suite and model ...An alternative model , the Open Systems Interconnection ( OSI ) model [27], is often used to describe protocols. The OSI model defines protocols in

  18. Data Integrity Protocol for Sensor Networks

    OpenAIRE

    Durresi, Arjan; Paruchuri, Vamsi; Kannan, Rajgopal; Iyengar, S. S.

    2005-01-01

    In this paper, we present a novel lightweight protocol for data integrity in wireless sensor networks. Our protocol is based on a leapfrog strategy in which each cluster head verifies if its previous node has preserved the integrity of the packet using the secret key it shares with two hop uptree nodes. The proposed protocol is simple. The analysis and simulation results show that the protocol needs very few header bits, as low as three bits, thus resulting in negligible bandwidth overhead; t...

  19. Bioinspired Security Analysis of Wireless Protocols

    DEFF Research Database (Denmark)

    Petrocchi, Marinella; Spognardi, Angelo; Santi, Paolo

    2016-01-01

    work, this paper investigates feasibility of adopting fraglets as model for specifying security protocols and analysing their properties. In particular, we give concrete sample analyses over a secure RFID protocol, showing evolution of the protocol run as chemical dynamics and simulating an adversary...... trying to circumvent the intended steps. The results of our analysis confirm the effectiveness of the cryptofraglets framework for the model and analysis of security properties and eventually show its potential to identify and uncover protocol flaws....

  20. Approaches to Formal Verification of Security Protocols

    OpenAIRE

    Lal, Suvansh; Jain, Mohit; Chaplot, Vikrant

    2011-01-01

    In recent times, many protocols have been proposed to provide security for various information and communication systems. Such protocols must be tested for their functional correctness before they are used in practice. Application of formal methods for verification of security protocols would enhance their reliability thereby, increasing the usability of systems that employ them. Thus, formal verification of security protocols has become a key issue in computer and communications security. In...

  1. Quantum bit commitment protocol without quantum memory

    OpenAIRE

    Ramos, Rubens Viana; Mendonca, Fabio Alencar

    2008-01-01

    Quantum protocols for bit commitment have been proposed and it is largely accepted that unconditionally secure quantum bit commitment is not possible; however, it can be more secure than classical bit commitment. In despite of its usefulness, quantum bit commitment protocols have not been experimentally implemented. The main reason is the fact that all proposed quantum bit commitment protocols require quantum memory. In this work, we show a quantum bit commitment protocol that does not requir...

  2. Feasible quantum communication complexity protocol

    International Nuclear Information System (INIS)

    Galvao, Ernesto F.

    2002-01-01

    I show that a simple multiparty communication task can be performed more efficiently with quantum communication than with classical communication, even with low detection efficiency η. The task is a communication complexity problem in which distant parties need to compute a function of the distributed inputs, while minimizing the amount of communication between them. A realistic quantum optical setup is suggested that can demonstrate a five-party quantum protocol with higher-than-classical performance, provided η>0.33

  3. Building America House Simulation Protocols

    Energy Technology Data Exchange (ETDEWEB)

    Hendron, Robert [National Renewable Energy Lab. (NREL), Golden, CO (United States); Engebrecht, Cheryn [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2010-09-01

    The House Simulation Protocol document was developed to track and manage progress toward Building America's multi-year, average whole-building energy reduction research goals for new construction and existing homes, using a consistent analytical reference point. This report summarizes the guidelines for developing and reporting these analytical results in a consistent and meaningful manner for all home energy uses using standard operating conditions.

  4. Petri Nets in Cryptographic Protocols

    DEFF Research Database (Denmark)

    Crazzolara, Federico; Winskel, Glynn

    2001-01-01

    A process language for security protocols is presented together with a semantics in terms of sets of events. The denotation of process is a set of events, and as each event specifies a set of pre and postconditions, this denotation can be viewed as a Petri net. By means of an example we illustrate...... how the Petri-net semantics can be used to prove security properties....

  5. Universal Energy Supply Protocol (UESP)

    Energy Technology Data Exchange (ETDEWEB)

    Holz, F.; Meyer, T.; Roth, W.; Benz, J. [Fraunhofer-Institut fuer Solare Energiesysteme (ISE), Freiburg im Breisgau (Germany); Mueller, M. [Steca GmbH, Solar Electronics, Memmingen (Germany)

    2004-07-01

    The idea behind the Universal Energy Supply Protocol (UESP) is to equip all components (all kinds of generators, batteries and loads) with an identical and well-defined electrical DC connection as well as with intelligence and a communication interface, speaking a defined protocol (UESP). Power flow and information flow are separated, leading to more flexibility in system sizing and standardisation. A centralised control and energy management system administers the system as a whole. Its software is able to manage the energy generation and consumption and ensures the required level of reliability while reducing the operational cost to a minimum. In contrast to existing management concepts, the central idea behind UESP is to outsource the intelligence and the knowledge on the operational behaviour of the components out of the central management system into the components themselves. The components provide information about their current status of operation, current and future operation cost and constraints to the central management system. Here, using 'virtual stock exchange' algorithms, an optimised schedule for all components is determined and fed back to the components for implementation. The central management is thus very generic and can handle any component using the UESP protocol. It automatically adapts to new or changed system configurations, as these changes impact the optimisation only by additional 'players' on the virtual stock market. Eight German companies have teamed up with Fraunhofer ISE in a challenging project (funded by the German Ministry for the Environment, Nature Conservation and Nuclear Safety, BMU) to define the previously described protocol and interfaces and to elaborate the various implementations. The applications range form village power supply systems to telecommunication stations and signalling systems. It is foreseen to establish UESP as standardised interface in the future. (orig.)

  6. Heuristic Methods for Security Protocols

    Directory of Open Access Journals (Sweden)

    Qurat ul Ain Nizamani

    2009-10-01

    Full Text Available Model checking is an automatic verification technique to verify hardware and software systems. However it suffers from state-space explosion problem. In this paper we address this problem in the context of cryptographic protocols by proposing a security property-dependent heuristic. The heuristic weights the state space by exploiting the security formulae; the weights may then be used to explore the state space when searching for attacks.

  7. Cost estimation of Kyoto Protocol

    International Nuclear Information System (INIS)

    Di Giulio, Enzo

    2005-01-01

    This article proposes a reflection on important aspects in the costs determination performance of Kyoto Protocol. The evaluation of the main models evidence possible impacts on the economies. A key role in the determination of the cost is represented by the relative hypothesis to emission trading and the projects CDM-JI and from the political capacity at the cost negative or equal to zero [it

  8. Behavior Protocols for Software Components

    Czech Academy of Sciences Publication Activity Database

    Plášil, František; Višňovský, Stanislav

    2002-01-01

    Roč. 28, č. 11 (2002), s. 1056-1076 ISSN 0098-5589 R&D Projects: GA AV ČR IAA2030902; GA ČR GA201/99/0244 Grant - others:Eureka(XE) Pepita project no.2033 Institutional research plan: AV0Z1030915 Keywords : behavior protocols * component-based programming * software architecture Subject RIV: JC - Computer Hardware ; Software Impact factor: 1.170, year: 2002

  9. Desensitization protocols and their outcome.

    Science.gov (United States)

    Marfo, Kwaku; Lu, Amy; Ling, Min; Akalin, Enver

    2011-04-01

    In the last decade, transplantation across previously incompatible barriers has increasingly become popular because of organ donor shortage, availability of better methods of detecting and characterizing anti-HLA antibodies, ease of diagnosis, better understanding of antibody-mediated rejection, and the availability of effective regimens. This review summarizes all manuscripts published since the first publication in 2000 on desensitized patients and discusses clinical outcomes including acute and chronic antibody-mediated rejection rate, the new agents available, kidney paired exchange programs, and the future directions in sensitized patients. There were 21 studies published between 2000 and 2010, involving 725 patients with donor-specific anti-HLA antibodies (DSAs) who underwent kidney transplantation with different desensitization protocols. All studies were single center and retrospective. The patient and graft survival were 95% and 86%, respectively, at a 2-year median follow-up. Despite acceptable short-term patient and graft survivals, acute rejection rate was 36% and acute antibody-mediated rejection rate was 28%, which is significantly higher than in nonsensitized patients. Recent studies with longer follow-up of those patients raised concerns about long-term success of desensitization protocols. The studies utilizing protocol biopsies in desensitized patients also reported higher subclinical and chronic antibody-mediated rejection. An association between the strength of DSAs determined by median fluorescence intensity values of Luminex single-antigen beads and risk of rejection was observed. Two new agents, bortezomib, a proteasome inhibitor, and eculizumab, an anti-complement C5 antibody, were recently introduced to desensitization protocols. An alternative intervention is kidney paired exchange, which should be considered first for sensitized patients. © 2011 by the American Society of Nephrology

  10. Advanced dementia pain management protocols.

    Science.gov (United States)

    Montoro-Lorite, Mercedes; Canalias-Reverter, Montserrat

    2017-08-04

    Pain management in advanced dementia is complex because of neurological deficits present in these patients, and nurses are directly responsible for providing interventions for the evaluation, management and relief of pain for people suffering from this health problem. In order to facilitate and help decision-makers, pain experts recommend the use of standardized protocols to guide pain management, but in Spain, comprehensive pain management protocols have not yet been developed for advanced dementia. This article reflects the need for an integrated management of pain in advanced dementia. From the review and analysis of the most current and relevant studies in the literature, we performed an approximation of the scales for the determination of pain in these patients, with the observational scale PAINAD being the most recommended for the hospital setting. In addition, we provide an overview for comprehensive management of pain in advanced dementia through the conceptual framework «a hierarchy of pain assessment techniques by McCaffery and Pasero» for the development and implementation of standardized protocols, including a four-phase cyclical process (evaluation, planning/performance, revaluation and recording), which can facilitate the correct management of pain in these patients. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

  11. Static Validation of a Voting Protocol

    DEFF Research Database (Denmark)

    Nielsen, Christoffer Rosenkilde; Andersen, Esben Heltoft; Nielson, Hanne Riis

    2005-01-01

    The desired security properties of electronic voting protocols include verifiability, accuracy, democracy and fairness. In this paper we use a static program analysis tool to validate these properties for one of the classical voting protocols under appropriate assumptions. The protocol is formali...

  12. PCR protocols: current methods and applications

    National Research Council Canada - National Science Library

    White, Bruce Alan

    1993-01-01

    ..." between "small" and "big" labs, since its use makes certain projects, especially those related to molecular cloning, now far more feasible for the small lab with a modest budget. This new volume on PCR Protocols does not attempt the impossible task of representing all PCR-based protocols. Rather, it presents a range of protocols, both analytical ...

  13. IPv6: The Next Generation Internet Protocol

    Indian Academy of Sciences (India)

    internet. 2. New Features in IPv6. Harsha Srinath. IPv4, the workhorse protocol of the currently popular TePI. IP protocol suite, is fast becoming obsolete. The exponen- ... designers of this Internet Protocol (lPv4) never envisioned the scale of the ..... using multiple access providers across the same interface to have separate ...

  14. Timed Model Checking of Security Protocols

    NARCIS (Netherlands)

    Corin, R.J.; Etalle, Sandro; Hartel, Pieter H.; Mader, Angelika H.

    We propose a method for engineering security protocols that are aware of timing aspects. We study a simplified version of the well-known Needham Schroeder protocol and the complete Yahalom protocol. Timing information allows the study of different attack scenarios. We illustrate the attacks by model

  15. 21 CFR 1301.18 - Research protocols.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Research protocols. 1301.18 Section 1301.18 Food..., DISTRIBUTORS, AND DISPENSERS OF CONTROLLED SUBSTANCES Registration § 1301.18 Research protocols. (a) A protocol... have such submission approved by, the Food and Drug Administration as required in 21 U.S.C. 355(i) and...

  16. Crypto-Verifying Protocol Implementations in ML

    NARCIS (Netherlands)

    Bhargavan, K.; Corin, R.J.; Fournet, C.

    2007-01-01

    We intend to narrow the gap between concrete implementations and verified models of cryptographic protocols. We consider protocols implemented in F#, a variant of ML, and verified using CryptoVerif, Blanchet's protocol verifier for computational cryptography. We experiment with compilers from F#

  17. Formal Analysis of a Fair Payment Protocol

    NARCIS (Netherlands)

    Cederquist, J.G.; Dashti, Muhammad Torabi; Dimitrakos, Theo; Martinelli, Fabio

    We formally specify a payment protocol described by Vogt et al. This protocol is intended for fair exchange of time-sensitive data. Here the mCRL language is used to formalize the protocol. Fair exchange properties are expressed in the regular alternation-free mu-calculus. These properties are then

  18. Research of Video Steganalysis Algorithm Based on H265 Protocol

    Directory of Open Access Journals (Sweden)

    Wu Kaicheng

    2015-01-01

    This paper researches LSB matching VSA based on H265 protocol with the research background of 26 original Video sequences, it firstly extracts classification features out from training samples as input of SVM, and trains in SVM to obtain high-quality category classification model, and then tests whether there is suspicious information in the video sample. The experimental results show that VSA algorithm based on LSB matching can be more practical to obtain all frame embedded secret information and carrier and video of local frame embedded. In addition, VSA adopts the method of frame by frame with a strong robustness in resisting attack in the corresponding time domain.

  19. A new protocol for extraction of C 0 t-1 DNA from rice | Yan | African ...

    African Journals Online (AJOL)

    C0t-1 DNA, enriched for repetitive DNA sequences, has been proved to be valuable in the studies of plant species differentiation and genome evolution. A new protocol to steadily obtain the aimed range of DNA fragments has been developed by shearing the genomic DNA with the digest system containing DNase ...

  20. An extended protocol for usability validation of medical devices : Research design and reference model

    NARCIS (Netherlands)

    Schmettow, Martin; Schnittker, Raphaela; Schraagen, Jan Maarten

    2017-01-01

    This paper proposes and demonstrates an extended protocol for usability validation testing of medical devices. A review of currently used methods for the usability evaluation of medical devices revealed two main shortcomings. Firstly, the lack of methods to closely trace the interaction sequences

  1. 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.

  2. Sequencing of the Hepatitis C Virus: A Systematic Review.

    Directory of Open Access Journals (Sweden)

    Brendan Jacka

    Full Text Available Since the identification of hepatitis C virus (HCV, viral sequencing has been important in understanding HCV classification, epidemiology, evolution, transmission clustering, treatment response and natural history. The length and diversity of the HCV genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols. This systematic review was undertaken to map the location and frequency of sequencing on the HCV genome in peer reviewed publications, with the aim to produce a database of sequencing primers and amplicons to inform future research. Medline and Scopus databases were searched for English language publications based on keyword/MeSH terms related to sequence analysis (9 terms or HCV (3 terms, plus "primer" as a general search term. Exclusion criteria included non-HCV research, review articles, duplicate records, and incomplete description of HCV sequencing methods. The PCR primer locations of accepted publications were noted, and purpose of sequencing was determined. A total of 450 studies were accepted from the 2099 identified, with 629 HCV sequencing amplicons identified and mapped on the HCV genome. The most commonly sequenced region was the HVR-1 region, often utilised for studies of natural history, clustering/transmission, evolution and treatment response. Studies related to genotyping/classification or epidemiology of HCV genotype generally targeted the 5'UTR, Core and NS5B regions, while treatment response/resistance was assessed mainly in the NS3-NS5B region with emphasis on the Interferon sensitivity determining region (ISDR region of NS5A. While the sequencing of HCV is generally constricted to certain regions of the HCV genome there is little consistency in the positioning of sequencing primers, with the exception of a few highly referenced manuscripts. This study demonstrates the heterogeneity of HCV sequencing, providing a comprehensive database of previously

  3. Reactive broadcasting protocol for video on demand

    Science.gov (United States)

    Paris, Jehan-Francois; Carter, Steven W.; Long, Darrell D. E.

    1999-12-01

    We propose a reactive broadcasting protocol that addresses the problem of distributing moderately popular videos in a more efficient fashion. Like all efficient broadcasting protocols, reactive broadcasting assumes that the customer set-top box has enough local storage to store at least one half of each video being watched. Unlike other broadcasting protocols, reactive broadcasting only broadcasts the later portions of each video. the initial segment of each video is distributed on demand using a stream tapping protocol. Our simulations show that reactive broadcasting outperforms both conventional broadcasting protocols and pure stream tapping for a wide range of video request rates.

  4. Cardiovascular and Metabolic Demads of the Kettlebell Swing using Tabata Interval versus a Traditional Resistance Protocol

    Science.gov (United States)

    FORTNER, HOWARD A.; SALGADO, JEANETTE M.; HOLMSTRUP, ANGELICA M.; HOLMSTRUP, MICHAEL E.

    2014-01-01

    Tabata (TAB) training, consisting of eight cycles of 20 seconds of maximal exercise followed by 10 seconds of rest, is time-efficient, with aerobic and anaerobic benefit. This study investigated the cardiovascular and metabolic demands of a TAB versus traditional (TRAD) resistance protocol with the kettlebell swing. Fourteen young (18–25y), non-obese (BMI 25.7±0.8 kg/m2) participants reported on three occasions. All testing incorporated measurements of HR, oxygen consumption, and blood lactate accumulation. Each participant completed Tabata kettlebell swings (male- 8kg, female- 4.5kg; 8 intervals; 20s maximal repetitions, 10s rest). On a subsequent visit (TRAD), the total swings from the TAB protocol were evenly divided into 4 sets, with 90s rest between sets. Outcome measures were compared using paired t-tests. The TAB was completed more quickly than the TRAD protocol (240.0±0.0 v. 521.5±3.3 sec, PTRAD framework. Appropriate screening and risk stratification are advised before implementing kettlebell swings. PMID:27182402

  5. Cardiovascular and Metabolic Demads of the Kettlebell Swing using Tabata Interval versus a Traditional Resistance Protocol.

    Science.gov (United States)

    Fortner, Howard A; Salgado, Jeanette M; Holmstrup, Angelica M; Holmstrup, Michael E

    Tabata (TAB) training, consisting of eight cycles of 20 seconds of maximal exercise followed by 10 seconds of rest, is time-efficient, with aerobic and anaerobic benefit. This study investigated the cardiovascular and metabolic demands of a TAB versus traditional (TRAD) resistance protocol with the kettlebell swing. Fourteen young (18-25y), non-obese (BMI 25.7±0.8 kg/m 2 ) participants reported on three occasions. All testing incorporated measurements of HR, oxygen consumption, and blood lactate accumulation. Each participant completed Tabata kettlebell swings (male- 8kg, female- 4.5kg; 8 intervals; 20s maximal repetitions, 10s rest). On a subsequent visit (TRAD), the total swings from the TAB protocol were evenly divided into 4 sets, with 90s rest between sets. Outcome measures were compared using paired t-tests. The TAB was completed more quickly than the TRAD protocol (240.0±0.0 v. 521.5±3.3 sec, Pkettlebell swing demonstrated significantly greater cardiovascular and metabolic responses within a TAB vs. TRAD framework. Appropriate screening and risk stratification are advised before implementing kettlebell swings.

  6. PHARMACOGENETIC TESTING OPPORTUNITIES IN CARDIOLOGY BASED ON EXOME SEQUENCING

    Directory of Open Access Journals (Sweden)

    N. V. Shcherbakova

    2014-01-01

    Full Text Available Aim. To study what cardiac drugs currently have any comments on biomarkers and what information can be obtained by pharmacogenetic testing using data exome sequencing in patients with cardiac diseases.Material and methods. Exome sequencing in random participant of the ATEROGEN IVANOVO study and bioinformatics analysis of the data were performed. Point mutations were annotated using ANNOVAR program, as well as comparison with a number of specialized databases was done on the basis of user protocols.Results. 11 cardiac drugs and 7 genes which variants can influence cardiac drug metabolism were analyzed. According to exome sequencing of the participant we did not reveal allelic variants that require dose regime correction and careful efficacy control.Conclusion. The exome sequencing application is the next step to a wide range of personalized therapy. Future opportunities for improvement of the risk-benefit ratio in each patient are the main purpose of the collection and analysis of pharmacogenetic data.

  7. 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...... that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison...... 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...

  8. Phylogenetic Heatmaps Highlight Composition Biases in Sequenced Reads

    Directory of Open Access Journals (Sweden)

    Sulbha Choudhari

    2017-01-01

    Full Text Available Due to advancements in sequencing technology, sequence data production is no longer a constraint in the field of microbiology and has made it possible to study uncultured microbes or whole environments using metagenomics. However, these new technologies introduce different biases in metagenomic sequencing, affecting the nucleotide distribution of resulting sequence reads. Here, we illustrate such biases using two methods. One is based on phylogenetic heatmaps (PGHMs, a novel approach for compact visualization of sequence composition differences between two groups of sequences containing the same phylogenetic groups. This method is well suited for finding noise and biases when comparing metagenomics samples. We apply PGHMs to detect noise and bias in the data produced with different DNA extraction protocols, different sequencing platforms and different experimental frameworks. In parallel, we use principal component analysis displaying different clustering of sequences from each sample to support our findings and illustrate the utility of PGHMs. We considered contributions of the read length and GC-content variation and observed that in most cases biases were generally due to the GC-content of the reads.

  9. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  10. Neural mechanisms of sequence generation in songbirds

    Science.gov (United States)

    Langford, Bruce

    Animal models in research are useful for studying more complex behavior. For example, motor sequence generation of actions requiring good muscle coordination such as writing with a pen, playing an instrument, or speaking, may involve the interaction of many areas in the brain, each a complex system in itself; thus it can be difficult to determine causal relationships between neural behavior and the behavior being studied. Birdsong, however, provides an excellent model behavior for motor sequence learning, memory, and generation. The song consists of learned sequences of notes that are spectrographically stereotyped over multiple renditions of the song, similar to syllables in human speech. The main areas of the songbird brain involve in singing are known, however, the mechanisms by which these systems store and produce song are not well understood. We used a custom built, head-mounted, miniature motorized microdrive to chronically record the neural firing patterns of identified neurons in HVC, a pre-motor cortical nucleus which has been shown to be important in song timing. These were done in Bengalese finch which generate a song made up of stereotyped notes but variable note sequences. We observed song related bursting in neurons projecting to Area X, a homologue to basal ganglia, and tonic firing in HVC interneurons. Interneuron had firing rate patterns that were consistent over multiple renditions of the same note sequence. We also designed and built a light-weight, low-powered wireless programmable neural stimulator using Bluetooth Low Energy Protocol. It was able to generate perturbations in the song when current pulses were administered to RA, which projects to the brainstem nucleus responsible for syringeal muscle control.

  11. Language, Semantics, and Methods for Security Protocols

    DEFF Research Database (Denmark)

    Crazzolara, Federico

    Security protocols help in establishing secure channels between communicating systems. Great care needs therefore to be taken in developing and implementing robust protocols. The complexity of security-protocol interactions can hide, however, security weaknesses that only a formal analysis can...... to a transition semantics which can easily be implemented. (An existing SPL implementation bridges the gap that often exists between abstract protocol models on which verification of security properties is carried out and the implemented protocol.) SPL-nets are a particular kind of contextual Petri...... reveal. The last few years have seen the emergence of successful intensional, event-based, formal approaches to reasoning about security protocols. The methods are concerned with reasoning about the events that a security protocol can perform, and make use of a causal dependency that exists between...

  12. Effective Protocols for Mobile Communications and Networking

    Energy Technology Data Exchange (ETDEWEB)

    Espinoza, J.; Sholander, P.; Van Leeuwen, B,

    1998-12-01

    This report examines methods of mobile communications with an emphasis on mobile computing and wireless communications. Many of the advances in communications involve the use of Internet Protocol (IP), Asynchronous Transfer Mode (ATM), and ad hoc network protocols. However, many of the advances in these protocols have been focused on wired communications. Recently much focus has been directed at advancing communication technology in the area of mobile wireless networks. This report discusses various protocols used in mobile communications and proposes a number of extensions to existing protocols. A detailed discussion is also included on desirable protocol characteristics and evaluation criteria. In addition, the report includes a discussion on several network simulation tools that maybe used to evaluate network protocols.

  13. Generalized routing protocols for multihop relay networks

    KAUST Repository

    Khan, Fahd Ahmed

    2011-07-01

    Performance of multihop cooperative networks depends on the routing protocols employed. In this paper we propose the last-n-hop selection protocol, the dual path protocol, the forward-backward last-n-hop selection protocol and the forward-backward dual path protocol for the routing of data through multihop relay networks. The average symbol error probability performance of the schemes is analysed by simulations. It is shown that close to optimal performance can be achieved by using the last-n-hop selection protocol and its forward-backward variant. Furthermore we also compute the complexity of the protocols in terms of number of channel state information required and the number of comparisons required for routing the signal through the network. © 2011 IEEE.

  14. Developing security protocols in χ-Spaces

    DEFF Research Database (Denmark)

    Crazzolara, Federico; Milicia, Giuseppe

    2002-01-01

    It is of paramount importance that a security protocol effectively enforces the desired security requirements. The apparent simplicity of informal protocol descriptions hides the inherent complexity of their interactions which, often, invalidate informal correctness arguments and justify the effort...... of formal protocol verification. Verification, however, is usually carried out on an abstract model not at all related with a protocol’s implementation. Experience shows that security breaches introduced in implementations of successfully verified models are rather common. The χ-Spaces framework...... is an implementation of SPL (Security Protocol Language), a formal model for studying security protocols. In this paper we discuss the use of χ-Spaces as a tool for developing robust security protocol implementations. To make the case, we take a family of key-translation protocols due to Woo and Lam and show how χ...

  15. Security Protocols: Specification, Verification, Implementation, and Composition

    DEFF Research Database (Denmark)

    Almousa, Omar

    An important aspect of Internet security is the security of cryptographic protocols that it deploys. We need to make sure that such protocols achieve their goals, whether in isolation or in composition, i.e., security protocols must not suffer from any aw that enables hostile intruders to break...... their security. Among others, tools like OFMC [MV09b] and Proverif [Bla01] are quite efficient for the automatic formal verification of a large class of protocols. These tools use different approaches such as symbolic model checking or static analysis. Either approach has its own pros and cons, and therefore, we...... called SPS (Security Protocol Specification) language, that enables users, without requiring deep expertise in formal models from them, to specify a wide range of real-world protocols in a simple and intuitive way. Thus, SPS allows users to verify their protocols using different tools, and generate...

  16. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules.

    Science.gov (United States)

    Mayjonade, Baptiste; Gouzy, Jérôme; Donnadieu, Cécile; Pouilly, Nicolas; Marande, William; Callot, Caroline; Langlade, Nicolas; Muños, Stéphane

    2016-10-01

    De novo sequencing of complex genomes is one of the main challenges for researchers seeking high-quality reference sequences. Many de novo assemblies are based on short reads, producing fragmented genome sequences. Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.

  17. Crestal bone remodeling around implants placed using a short drilling protocol.

    Science.gov (United States)

    Bratu, Emanuel; Mihali, Sorin; Shapira, Lior; Bratu, Dana Cristina; Wang, Hom-Lay

    2015-01-01

    The aim of the study was to examine the influence of a short drilling protocol on peri-implant crestal bone levels. Forty implants were placed in the posterior mandibles of 20 patients. The implants (diameter, 4.2 mm; length, 10 to 11.5 mm) were inserted in pairs: one implant was inserted using the standard drilling protocol (five drills in sequence), while the other was inserted using the short drilling protocol sequence (three drills). All implants received healing abutments and were restored with single-unit restorations after 3 months of healing. Analysis of crestal bone level was based on radiographs taken at insertion and at 3, 6, and 12 months after insertion. The results were analyzed using software Image J 1.46r (National Institutes of Health). Crestal bone level was measured in millimeters at the distal aspect of each implant. None of the implants in either group was lost during the 12-month follow-up period, and all patients completed the follow-up examination. The drilling time for the insertion of one implant with the short drilling protocol was 1.03 ± 3.63 minutes compared to 1.57 ± 2.88 minutes for the standard protocol. The mean values of crestal bone loss at 12 months were 0.94 ± 0.43 mm for implants placed using the standard protocol and 0.90 ± 0.33 mm for implants placed using the short drilling protocol. No statistically significant differences were noted. Using the short drilling protocol reduced the surgery time by approximately 50% and did not affect crestal bone remodeling during the first year postinsertion.

  18. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

  19. An implementation of the SNR high speed network communication protocol (Receiver part)

    Science.gov (United States)

    Wan, Wen-Jyh

    1995-03-01

    This thesis work is to implement the receiver pan of the SNR high speed network transport protocol. The approach was to use the Systems of Communicating Machines (SCM) as the formal definition of the protocol. Programs were developed on top of the Unix system using C programming language. The Unix system features that were adopted for this implementation were multitasking, signals, shared memory, semaphores, sockets, timers and process control. The problems encountered, and solved, were signal loss, shared memory conflicts, process synchronization, scheduling, data alignment and errors in the SCM specification itself. The result was a correctly functioning program which implemented the SNR protocol. The system was tested using different connection modes, lost packets, duplicate packets and large data transfers. The contributions of this thesis are: (1) implementation of the receiver part of the SNR high speed transport protocol; (2) testing and integration with the transmitter part of the SNR transport protocol on an FDDI data link layered network; (3) demonstration of the functions of the SNR transport protocol such as connection management, sequenced delivery, flow control and error recovery using selective repeat methods of retransmission; and (4) modifications to the SNR transport protocol specification such as corrections for incorrect predicate conditions, defining of additional packet types formats, solutions for signal lost and processes contention problems etc.

  20. An Efficient Causal Group Communication Protocol for Free Scale Peer-to-Peer Networks

    Directory of Open Access Journals (Sweden)

    Grigory Evropeytsev

    2016-08-01

    Full Text Available In peer-to-peer (P2P overlay networks, a group of n (≥2 peer processes have to cooperate with each other. Each peer sends messages to every peer and receives messages from every peer in a group. In group communications, each message sent by a peer is required to be causally delivered to every peer. Most of the protocols designed to ensure causal message order are designed for networks with a plain architecture. These protocols can be adapted to use in free scale and hierarchical topologies; however, the amount of control information is O(n, where n is the number of peers in the system. Some protocols are designed for a free scale or hierarchical networks, but in general they force the whole system to accomplish the same order viewed by a super peer. In this paper, we present a protocol that is specifically designed to work with a free scale peer-to-peer network. By using the information about the network’s architecture and by representing message dependencies on a bit level, the proposed protocol ensures causal message ordering without enforcing super peers order. The designed protocol is simulated and compared with the Immediate Dependency Relation and the Dependency Sequences protocols to show its lower overhead.

  1. Analyzing the effect of routing protocols on media access control protocols in radio networks

    Energy Technology Data Exchange (ETDEWEB)

    Barrett, C. L. (Christopher L.); Drozda, M. (Martin); Marathe, A. (Achla); Marathe, M. V. (Madhav V.)

    2002-01-01

    We study the effect of routing protocols on the performance of media access control (MAC) protocols in wireless radio networks. Three well known MAC protocols: 802.11, CSMA, and MACA are considered. Similarly three recently proposed routing protocols: AODV, DSR and LAR scheme 1 are considered. The experimental analysis was carried out using GloMoSim: a tool for simulating wireless networks. The main focus of our experiments was to study how the routing protocols affect the performance of the MAC protocols when the underlying network and traffic parameters are varied. The performance of the protocols was measured w.r.t. five important parameters: (i) number of received packets, (ii) average latency of each packet, (iii) throughput (iv) long term fairness and (v) number of control packets at the MAC layer level. Our results show that combinations of routing and MAC protocols yield varying performance under varying network topology and traffic situations. The result has an important implication; no combination of routing protocol and MAC protocol is the best over all situations. Also, the performance analysis of protocols at a given level in the protocol stack needs to be studied not locally in isolation but as a part of the complete protocol stack. A novel aspect of our work is the use of statistical technique, ANOVA (Analysis of Variance) to characterize the effect of routing protocols on MAC protocols. This technique is of independent interest and can be utilized in several other simulation and empirical studies.

  2. Publication trends of study protocols in rehabilitation.

    Science.gov (United States)

    Jesus, Tiago S; Colquhoun, Heather L

    2017-09-04

    Growing evidence points for the need to publish study protocols in the health field. To observe whether the growing interest in publishing study protocols in the broader health field has been translated into increased publications of rehabilitation study protocols. Observational study using publication data and its indexation in PubMed. Not applicable. Not applicable. PubMed was searched with appropriate combinations of Medical Subject Headings up to December 2014. The effective presence of study protocols was manually screened. Regression models analyzed the yearly growth of publications. Two-sample Z-tests analyzed whether the proportion of Systematic Reviews (SRs) and Randomized Controlled Trials (RCTs) among study protocols differed from that of the same designs for the broader rehabilitation research. Up to December 2014, 746 publications of rehabilitation study protocols were identified, with an exponential growth since 2005 (r2=0.981; p<0.001). RCT protocols were the most common among rehabilitation study protocols (83%), while RCTs were significantly more prevalent among study protocols than among the broader rehabilitation research (83% vs. 35.8%; p<0.001). For SRs, the picture was reversed: significantly less common among study protocols (2.8% vs. 9.3%; p<0.001). Funding was more often reported by rehabilitation study protocols than the broader rehabilitation research (90% vs. 53.1%; p<0.001). Rehabilitation journals published a significantly lower share of rehabilitation study protocols than they did for the broader rehabilitation research (1.8% vs.16.7%; p<0.001). Identifying the reasons for these discrepancies and reverting unwarranted disparities (e.g. low rate of publication for rehabilitation SR protocols) are likely new avenues for rehabilitation research and its publication. SRs, particularly those aggregating RCT results, are considered the best standard of evidence to guide rehabilitation clinical practice; however, that standard can be improved

  3. Palindromic sequence impedes sequencing-by-ligation mechanism.

    Science.gov (United States)

    Huang, Yu-Feng; Chen, Sheng-Chung; Chiang, Yih-Shien; Chen, Tzu-Han; Chiu, Kuo-Ping

    2012-01-01

    Current next-generation sequencing (NGS) platforms adopt two types of sequencing mechanisms: by synthesis or by ligation. The former is employed by 454 and Solexa systems, while the latter by SOLiD system. Although the pros and cons for each sequencing mechanism have more or less been discussed in a number of occasions, the potential obstacle imposed by palindromic sequences has not yet been addressed. To test the effect of the palindromic region on sequencing efficacy, we clonally amplified a paired-end ditag sequence composed of a 24-bp palindromic sequence flanked by a pair of tags from the E. coli genome. We used the near homogeneous fragments produced from MmeI digestion of the amplified clone to generate a sequencing library for SOLiD 5500xl sequencer. Results showed that, traditional ABI sequencers, which adopt sequencing-by-synthesis mechanism, were able to read through the palindromic region. However, SOLiD 5500xl was unable to do so. Instead, the palindromic region was read as miscellaneous random sequences. Moreover, readable tag sequence turned obscure ~2 bp prior to the palindromic region. Taken together, we demonstrate that SOLiD machines, which employ sequencing-by-ligation mechanism, are unable to read through the palindromic region. On the other hand, sequencing-by-synthesis sequencers had no difficulty in doing so.

  4. INEEL AIR MODELING PROTOCOL ext

    Energy Technology Data Exchange (ETDEWEB)

    C. S. Staley; M. L. Abbott; P. D. Ritter

    2004-12-01

    Various laws stemming from the Clean Air Act of 1970 and the Clean Air Act amendments of 1990 require air emissions modeling. Modeling is used to ensure that air emissions from new projects and from modifications to existing facilities do not exceed certain standards. For radionuclides, any new airborne release must be modeled to show that downwind receptors do not receive exposures exceeding the dose limits and to determine the requirements for emissions monitoring. For criteria and toxic pollutants, emissions usually must first exceed threshold values before modeling of downwind concentrations is required. This document was prepared to provide guidance for performing environmental compliance-driven air modeling of emissions from Idaho National Engineering and Environmental Laboratory facilities. This document assumes that the user has experience in air modeling and dose and risk assessment. It is not intended to be a "cookbook," nor should all recommendations herein be construed as requirements. However, there are certain procedures that are required by law, and these are pointed out. It is also important to understand that air emissions modeling is a constantly evolving process. This document should, therefore, be reviewed periodically and revised as needed. The document is divided into two parts. Part A is the protocol for radiological assessments, and Part B is for nonradiological assessments. This document is an update of and supersedes document INEEL/INT-98-00236, Rev. 0, INEEL Air Modeling Protocol. This updated document incorporates changes in some of the rules, procedures, and air modeling codes that have occurred since the protocol was first published in 1998.

  5. Robust QKD-based private database queries based on alternative sequences of single-qubit measurements

    Science.gov (United States)

    Yang, YuGuang; Liu, ZhiChao; Chen, XiuBo; Zhou, YiHua; Shi, WeiMin

    2017-12-01

    Quantum channel noise may cause the user to obtain a wrong answer and thus misunderstand the database holder for existing QKD-based quantum private query (QPQ) protocols. In addition, an outside attacker may conceal his attack by exploiting the channel noise. We propose a new, robust QPQ protocol based on four-qubit decoherence-free (DF) states. In contrast to existing QPQ protocols against channel noise, only an alternative fixed sequence of single-qubit measurements is needed by the user (Alice) to measure the received DF states. This property makes it easy to implement the proposed protocol by exploiting current technologies. Moreover, to retain the advantage of flexible database queries, we reconstruct Alice's measurement operators so that Alice needs only conditioned sequences of single-qubit measurements.

  6. A Genome Sequencing Program for Novel Undiagnosed Diseases

    OpenAIRE

    Bloss, Cinnamon S.; Scott-Van Zeeland, Ashley A.; Topol, Sarah E.; Darst, Burcu F.; Boeldt, Debra L.; Erikson, Galina A.; Bethel, Kelly J.; Bjork, Robert L.; Friedman, Jennifer R.; Hwynn, Nelson; Patay, Bradley A.; Pockros, Paul J.; Scott, Erick R.; Simon, Ronald A.; Williams, Gary W.

    2015-01-01

    Purpose The Scripps Idiopathic Diseases of huMan (IDIOM) study aims to discover novel gene-disease relationships and provide molecular genetic diagnosis and treatment guidance for individuals with novel diseases using genome sequencing integrated with clinical assessment and multidisciplinary case review. Methods Here we describe the IDIOM study operational protocol and initial results. Results 121 cases underwent first tier review by the principal investigators to determine if the primary in...

  7. Optical protocols for terabit networks

    Science.gov (United States)

    Chua, P. L.; Lambert, J. L.; Morookian, J. M.; Bergman, L. A.

    1991-01-01

    This paper describes a new fiber-optic local area network technology providing 100X improvement over current technology, has full crossbar funtionality, and inherent data security. Based on optical code-division multiple access (CDMA), using spectral phase encoding/decoding of optical pulses, networking protocols are implemented entirely in the optical domain and thus conventional networking bottlenecks are avoided. Component and system issues for a proof-of-concept demonstration are discussed, as well as issues for a more practical and commercially exploitable system. Possible terrestrial and aerospace applications of this technology, and its impact on other technologies are explored. Some initial results toward realization of this concept are also included.

  8. Estimation of radiation exposure for brain perfusion CT: standard protocol compared with deviations in protocol.

    Science.gov (United States)

    Hoang, Jenny K; Wang, Chu; Frush, Donald P; Enterline, David S; Samei, Ehsan; Toncheva, Greta; Lowry, Carolyn; Yoshizumi, Terry T

    2013-11-01

    The purpose of this study was to measure the organ doses and estimate the effective dose for the standard brain perfusion CT protocol and erroneous protocols. An anthropomorphic phantom with metal oxide semiconductor field effect transistor (MOSFET) detectors was scanned on a 64-MDCT scanner. Protocol 1 used a standard brain perfusion protocol with 80 kVp and fixed tube current of 200 mA. Protocol 2 used 120 kVp and fixed tube current of 200 mA. Protocol 3 used 120 kVp with automatic tube current modulation (noise index, 2.4; minimum, 100 mA; maximum, 520 mA). Compared with protocol 1, the effective dose was 2.8 times higher with protocol 2 and 7.8 times higher with protocol 3. For all protocols, the peak dose was highest in the skin, followed by the brain and calvarial marrow. Compared with protocol 1, the peak skin dose was 2.6 times higher with protocol 2 and 6.7 times higher with protocol 3. The peak skin dose for protocol 3 exceeded 3 Gy. The ocular lens received significant scatter radiation: 177 mGy for protocol 2 and 435 mGy for protocol 3, which were 4.6 and 11.3 times the dose for protocol 1, respectively. Compared with the standard protocol, erroneous protocols of increasing the tube potential from 80 kVp to 120 kVp will lead to a three- to fivefold increase in organ doses, and concurrent use of high peak kilovoltage with incorrectly programmed tube current modulation can increase dose to organs by 7- to 11-fold. Tube current modulation with a low noise index can lead to doses to the skin and ocular lens that are close to thresholds for tissue reactions.

  9. A Practical and Scalable Tool to Find Overlaps between Sequences

    Directory of Open Access Journals (Sweden)

    Maan Haj Rachid

    2015-01-01

    Full Text Available The evolution of the next generation sequencing technology increases the demand for efficient solutions, in terms of space and time, for several bioinformatics problems. This paper presents a practical and easy-to-implement solution for one of these problems, namely, the all-pairs suffix-prefix problem, using a compact prefix tree. The paper demonstrates an efficient construction of this time-efficient and space-economical tree data structure. The paper presents techniques for parallel implementations of the proposed solution. Experimental evaluation indicates superior results in terms of space and time over existing solutions. Results also show that the proposed technique is highly scalable in a parallel execution environment.

  10. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 11. Goldbach Partitions and Sequences. Subhash Kak. General Article Volume 19 Issue 11 November 2014 pp 1028-1037. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/019/11/1028-1037 ...

  11. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  12. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    IAS Admin

    Properties of Goldbach partitions of numbers, as sums of primes, are presented and their potential applications to cryptography are described. The sequence of the number of partitions has excel- lent randomness properties. Goldbach partitions can be used to create ellipses and circles on the number line and they can also ...

  13. Protocols in human molecular genetics

    National Research Council Canada - National Science Library

    Mathew, Christopher G

    1991-01-01

    ... sequences has led to the development of DNA fingerprinting. The application of these techniques to the study of the human genome has culminated in major advances such as the cloning of the cystic fibrosis gene, the construction of genetic linkage maps of each human chromosome, the mapping of many genes responsible for human inherited disorders, genet...

  14. Cacades: A reliable dissemination protocol for data collection sensor network

    Science.gov (United States)

    Peng, Y.; Song, W.; Huang, R.; Xu, M.; Shirazi, B.; LaHusen, R.; Pei, G.

    2009-01-01

    In this paper, we propose a fast and reliable data dissemination protocol Cascades to disseminate data from the sink(base station) to all or a subset of nodes in a data collection sensor network. Cascades makes use of the parentmonitor-children analogy to ensure reliable dissemination. Each node monitors whether or not its children have received the broadcast messages through snooping children's rebroadcasts or waiting for explicit ACKs. If a node detects a gap in its message sequences, it can fetch the missing messages from its neighbours reactively. Cascades also considers many practical issues for field deployment, such as dynamic topology, link/node failure, etc.. It therefore guarantees that a disseminated message from the sink will reach all intended receivers and the dissemination is terminated in a short time period. Notice that, all existing dissemination protocols either do not guarantee reliability or do not terminate [1, 2], which does not meet the requirement of real-time command control. We conducted experiment evaluations in both TOSSIM simulator and a sensor network testbed to compare Cascades with those existing dissemination protocols in TinyOS sensor networks, which show that Cascades achieves a higher degree of reliability, lower communication cost, and less delivery delay. ??2009 IEEE.

  15. Genetic mutation analysis of human gastric adenocarcinomas using ion torrent sequencing platform.

    Directory of Open Access Journals (Sweden)

    Zhi Xu

    Full Text Available Gastric cancer is the one of the major causes of cancer-related death, especially in Asia. Gastric adenocarcinoma, the most common type of gastric cancer, is heterogeneous and its incidence and cause varies widely with geographical regions, gender, ethnicity, and diet. Since unique mutations have been observed in individual human cancer samples, identification and characterization of the molecular alterations underlying individual gastric adenocarcinomas is a critical step for developing more effective, personalized therapies. Until recently, identifying genetic mutations on an individual basis by DNA sequencing remained a daunting task. Recent advances in new next-generation DNA sequencing technologies, such as the semiconductor-based Ion Torrent sequencing platform, makes DNA sequencing cheaper, faster, and more reliable. In this study, we aim to identify genetic mutations in the genes which are targeted by drugs in clinical use or are under development in individual human gastric adenocarcinoma samples using Ion Torrent sequencing. We sequenced 737 loci from 45 cancer-related genes in 238 human gastric adenocarcinoma samples using the Ion Torrent Ampliseq Cancer Panel. The sequencing analysis revealed a high occurrence of mutations along the TP53 locus (9.7% in our sample set. Thus, this study indicates the utility of a cost and time efficient tool such as Ion Torrent sequencing to screen cancer mutations for the development of personalized cancer therapy.

  16. A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae).

    Science.gov (United States)

    Françoso, Elaine; Gomes, Fernando; Arias, Maria Cristina

    2016-07-01

    Nuclear mitochondrial DNA insertions (NUMTs) are mitochondrial DNA sequences that have been transferred into the nucleus and are recognized by the presence of indels and stop codons. Although NUMTs have been identified in a diverse range of species, their discovery was frequently accidental. Here, our initial goal was to develop and standardize a simple method for isolating NUMTs from the nuclear genome of a single bee. Subsequently, we tested our new protocol by determining whether the indels and stop codons of the cytochrome c oxidase subunit I (COI) sequence of Melipona flavolineata are of nuclear origin. The new protocol successfully demonstrated the presence of a COI NUMT. In addition to NUMT investigations, the protocol described here will also be very useful for studying mitochondrial mutations related to diseases and for sequencing complete mitochondrial genomes with high read coverage by Next-Generation technology.

  17. Metric representation of DNA sequences.

    Science.gov (United States)

    Wu, Z B

    2000-07-01

    A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

  18. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

  19. Latest approaches of Kyoto protocol

    International Nuclear Information System (INIS)

    Matei, M.; Matei, L.

    2005-01-01

    Recently EURELECTRIC welcome the proposal of new EC Directive concerning the inclusion in the EU Emissions Trading Scheme (ETS) of credits from the project mechanisms - Joint Implementation (JI) and Clean Development Mechanism (CDM). The proposed Directive is an amendment to the EU Emissions Trading Directive adopted in June 2003. EURELECTRIC calls for unlimited use of credits in ETS. The draft Directive provides for the application of these mechanisms to begin as of 2008, on condition that the Kyoto Protocol does actually enter into force, an event which is still dependent on Russia's ratification. Such ratification has been subject to contradictory statements from the Russian Government, and the question of whether their signature to the Protocol is forthcoming is still fraught with uncertainty. Although it is not anticipated that significant quantities of JI or CDM certified credits will be available in the period 2005-2007, those that do become available would provide some additional liquidity in the emissions trading market. There is a direct relation between the coming ETS and electricity pricing: environmental policy is the driver, based on the need to switch to a low-carbon future and manage the necessary investments in a rational manner - and emissions trading is the best solution available. Romania has good opportunities to be involved in the greenhouse gases market, both in ETS and JI mechanisms. Some JI projects between Romanian and The Netherlands are already done or underway. (author)

  20. DAQ architecture and read-out protocole

    CERN Document Server

    Harris, F; Jost, B; Mato, P; Mato, Pere

    1998-01-01

    The proposed LHCb readout architecture is overviewed, followed by discussion and comparison of two candidate readout protocols, namely the 'Full Readout' and'Phased Readout' protocols.The philosophy of the Full Readout protocol is to send all of the event data to a processor before commencing the high level trigger algorithms.This results in simplicity in the protocol at the cost of the bandwidth requirement for the readout network. This is our preferred approach if the network costs are not prohibitive. Using the Phased Readout protocol the event data is sent in portions according to the demands of the trigger algorithms. This results in a more complex protocol, but in a reduction on the readout network bandwidth requirement.The effect of transmission errors on the behaviour of the system, and the implementation of system partitioning, are also discussed.1

  1. Merging Multiparty Protocols in Multiparty Choreographies

    Directory of Open Access Journals (Sweden)

    Fabrizio Montesi

    2013-02-01

    Full Text Available Choreography-based programming is a powerful paradigm for defining communication-based systems from a global viewpoint. A choreography can be checked against multiparty protocol specifications, given as behavioural types, that may be instantiated indefinitely at runtime. Each protocol instance is started with a synchronisation among the involved peers. We analyse a simple transformation from a choreography with a possibly unbounded number of protocol instantiations to a choreography instantiating a single protocol, which is the merge of the original ones. This gives an effective methodology for obtaining new protocols by composing existing ones. Moreover, by removing all synchronisations required for starting protocol instances, our transformation reduces the number of communications and resources needed to execute a choreography.

  2. In-memory interconnect protocol configuration registers

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Kevin Y.; Roberts, David A.

    2017-09-19

    Systems, apparatuses, and methods for moving the interconnect protocol configuration registers into the main memory space of a node. The region of memory used for storing the interconnect protocol configuration registers may also be made cacheable to reduce the latency of accesses to the interconnect protocol configuration registers. Interconnect protocol configuration registers which are used during a startup routine may be prefetched into the host's cache to make the startup routine more efficient. The interconnect protocol configuration registers for various interconnect protocols may include one or more of device capability tables, memory-side statistics (e.g., to support two-level memory data mapping decisions), advanced memory and interconnect features such as repair resources and routing tables, prefetching hints, error correcting code (ECC) bits, lists of device capabilities, set and store base address, capability, device ID, status, configuration, capabilities, and other settings.

  3. In-memory interconnect protocol configuration registers

    Science.gov (United States)

    Cheng, Kevin Y.; Roberts, David A.

    2017-09-19

    Systems, apparatuses, and methods for moving the interconnect protocol configuration registers into the main memory space of a node. The region of memory used for storing the interconnect protocol configuration registers may also be made cacheable to reduce the latency of accesses to the interconnect protocol configuration registers. Interconnect protocol configuration registers which are used during a startup routine may be prefetched into the host's cache to make the startup routine more efficient. The interconnect protocol configuration registers for various interconnect protocols may include one or more of device capability tables, memory-side statistics (e.g., to support two-level memory data mapping decisions), advanced memory and interconnect features such as repair resources and routing tables, prefetching hints, error correcting code (ECC) bits, lists of device capabilities, set and store base address, capability, device ID, status, configuration, capabilities, and other settings.

  4. Optimized workflow and imaging protocols for whole-body oncologic PET/MRI.

    Science.gov (United States)

    Ishii, Shirou; Hara, Takamitsu; Nanbu, Takeyuki; Suenaga, Hiroki; Sugawara, Shigeyasu; Kuroiwa, Daichi; Sekino, Hirofumi; Miyajima, Masayuki; Kubo, Hitoshi; Oriuchi, Noboru; Ito, Hiroshi

    2016-11-01

    Although PET/MRI has the advantages of a simultaneous acquisition of PET and MRI, high soft-tissue contrast of the MRI images, and reduction of radiation exposure, its low profitability and long acquisition time are significant problems in clinical settings. Thus, MRI protocols that meet oncological purposes need to be used in order to reduce examination time while securing detectability. Currently, half-Fourier acquisition single-shot turbo spin echo and 3D-T1 volumetric interpolated breath-hold examination may be the most commonly used sequences for whole-body imaging due to their shorter acquisition time and higher diagnostic accuracy. Although there have been several reports that adding diffusion weighted image (DWI) to PET/MRI protocol has had no effect on tumor detection to date, in cases of liver, kidney, bladder, and prostate cancer, the use of DWI may be beneficial in detecting lesions. Another possible option is to scan each region with different MRI sequences instead of scanning the whole body using one sequence continuously. We herein report a workflow and imaging protocols for whole-body oncologic PET/MRI using an integrated system in the clinical routine, designed for the detection, for example by cancer screening, of metastatic lesions, in order to help future users optimize their workflow and imaging protocols.

  5. Evaluation of ddRADseq for reduced representation metagenome sequencing

    Directory of Open Access Journals (Sweden)

    Michael Y. Liu

    2017-09-01

    Full Text Available Background Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq protocol for reduced representation metagenome profiling. Methods This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data. Results The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Discussion Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

  6. Evaluation of ddRADseq for reduced representation metagenome sequencing.

    Science.gov (United States)

    Liu, Michael Y; Worden, Paul; Monahan, Leigh G; DeMaere, Matthew Z; Burke, Catherine M; Djordjevic, Steven P; Charles, Ian G; Darling, Aaron E

    2017-01-01

    Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data. The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

  7. QPLOT: a quality assessment tool for next generation sequencing data.

    Science.gov (United States)

    Li, Bingshan; Zhan, Xiaowei; Wing, Mary-Kate; Anderson, Paul; Kang, Hyun Min; Abecasis, Goncalo R

    2013-01-01

    Next generation sequencing (NGS) is being widely used to identify genetic variants associated with human disease. Although the approach is cost effective, the underlying data is susceptible to many types of error. Importantly, since NGS technologies and protocols are rapidly evolving, with constantly changing steps ranging from sample preparation to data processing software updates, it is important to enable researchers to routinely assess the quality of sequencing and alignment data prior to downstream analyses. Here we describe QPLOT, an automated tool that can facilitate the quality assessment of sequencing run performance. Taking standard sequence alignments as input, QPLOT generates a series of diagnostic metrics summarizing run quality and produces convenient graphical summaries for these metrics. QPLOT is computationally efficient, generates webpages for interactive exploration of detailed results, and can handle the joint output of many sequencing runs. QPLOT is an automated tool that facilitates assessment of sequence run quality. We routinely apply QPLOT to ensure quick detection of diagnostic of sequencing run problems. We hope that QPLOT will be useful to the community as well.

  8. QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data

    Directory of Open Access Journals (Sweden)

    Bingshan Li

    2013-01-01

    Full Text Available Background. Next generation sequencing (NGS is being widely used to identify genetic variants associated with human disease. Although the approach is cost effective, the underlying data is susceptible to many types of error. Importantly, since NGS technologies and protocols are rapidly evolving, with constantly changing steps ranging from sample preparation to data processing software updates, it is important to enable researchers to routinely assess the quality of sequencing and alignment data prior to downstream analyses. Results. Here we describe QPLOT, an automated tool that can facilitate the quality assessment of sequencing run performance. Taking standard sequence alignments as input, QPLOT generates a series of diagnostic metrics summarizing run quality and produces convenient graphical summaries for these metrics. QPLOT is computationally efficient, generates webpages for interactive exploration of detailed results, and can handle the joint output of many sequencing runs. Conclusion. QPLOT is an automated tool that facilitates assessment of sequence run quality. We routinely apply QPLOT to ensure quick detection of diagnostic of sequencing run problems. We hope that QPLOT will be useful to the community as well.

  9. VANET Routing Protocols: Pros and Cons

    OpenAIRE

    Paul, Bijan; Ibrahim, Md.; Bikas, Md. Abu Naser

    2012-01-01

    VANET (Vehicular Ad-hoc Network) is a new technology which has taken enormous attention in the recent years. Due to rapid topology changing and frequent disconnection makes it difficult to design an efficient routing protocol for routing data among vehicles, called V2V or vehicle to vehicle communication and vehicle to road side infrastructure, called V2I. The existing routing protocols for VANET are not efficient to meet every traffic scenarios. Thus design of an efficient routing protocol h...

  10. Merging Multiparty Protocols in Multiparty Choreographies

    OpenAIRE

    Fabrizio Montesi; Marco Carbone

    2013-01-01

    Choreography-based programming is a powerful paradigm for defining communication-based systems from a global viewpoint. A choreography can be checked against multiparty protocol specifications, given as behavioural types, that may be instantiated indefinitely at runtime. Each protocol instance is started with a synchronisation among the involved peers. We analyse a simple transformation from a choreography with a possibly unbounded number of protocol instantiations to a choreography instantia...

  11. Composing security protocols: from confidentiality to privacy

    OpenAIRE

    Arapinis, Myrto; Cheval, Vincent; Delaune, Stéphanie

    2015-01-01

    Security protocols are used in many of our daily-life applications, and our privacy largely depends on their design. Formal verification techniques have proved their usefulness to analyse these protocols, but they become so complex that modular techniques have to be developed. We propose several results to safely compose security protocols. We consider arbitrary primitives modeled using an equational theory, and a rich process algebra close to the applied pi calculus. Relying on these composi...

  12. New Models for Protocol Security

    Science.gov (United States)

    2015-06-18

    the premier Cryptography conferences (CRYPTO, EuroCrypt, TCC ); 5 of these papers were selected for special issues on best papers. 15. SUBJECT TERMS...prestigious Cryptography conferences (CRYPTO, EuroCrypt, TCC ); 5 of these papers were selected for special issues on best papers. 2 Concurrent Security...sequence of works appearing in STOC 2013, FOCS 2013 (2 on this topic), and TCC 2014, we resolved some of central outstanding open questions in this

  13. 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 ...

  14. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  15. Tool Supported Analysis of Web Services Protocols

    DEFF Research Database (Denmark)

    Marques, Abinoam P.; Ravn, Anders Peter; Srba, Jiri

    2011-01-01

    We describe an abstract protocol model suitable for modelling of web services and other protocols communicating via unreliable, asynchronous communication channels. The model is supported by a tool chain where the first step translates tables with state/transition protocol descriptions, often used...... e.g. in the design of web services protocols, into an intermediate XML format. We further translate this format into a network of communicating state machines directly suitable for verification in the model checking tool UPPAAL. We introduce two types of communication media abstractions in order...

  16. Efficient secure two-party protocols

    CERN Document Server

    Hazay, Carmit

    2010-01-01

    The authors present a comprehensive study of efficient protocols and techniques for secure two-party computation -- both general constructions that can be used to securely compute any functionality, and protocols for specific problems of interest. The book focuses on techniques for constructing efficient protocols and proving them secure. In addition, the authors study different definitional paradigms and compare the efficiency of protocols achieved under these different definitions.The book opens with a general introduction to secure computation and then presents definitions of security for a

  17. Search and nonsearch protocols for radiographic consultation

    International Nuclear Information System (INIS)

    Swensson, R.G.; Theodore, G.H.

    1989-01-01

    Six radiologists, acting as film reviewers, used two different consultation protocols to differentiate among 292 ambiguous findings on chest films: 120 simulated nodules and 172 normal findings (previous readers' false-positive reports of nodules). The non-search protocol identified each finding (by location), and reviewers rated its likelihood as a nodule. The search protocol, which asked reviewers to report and rate all locations regarded as possible nodules on each film, assigned a default negative rating to any unreported finding (nodule or normal). Receiver operator characteristic analyses demonstrated a significantly higher accuracy for each reviewer's search- protocol discriminations between these nodules and confusing normal findings

  18. A new quantum private comparison protocol

    Science.gov (United States)

    Xu, Ling; Wang, Jing; Ahmed, Hafeez; Zhao, Zhiwen

    2017-10-01

    For two participants to compare the equality of their private information without revealing them, a new quantum private protocol with the help of semi-honest third party TP is proposed. Different from previous protocols, the four particle |Wf⟩ state and the |χ+⟩ state are utilized in this protocol as the carriers of quantum information and form the entanglement swapping as basic principle. The simple measurement of quantum states and exclusive-or operation are only required to conduct in this protocol. What's more, this protocol can compare two bits of two participants' private information in every comparison time. Meanwhile, it needs no unitary operation to fulfill this protocol. This protocol is feasible and efficient to execute through these aspects. In the end, the security of this protocol is analyzed at great length from two kinds of attacks including the outside attack and the participant attack. And the analysis result shows that this protocol can withstand various kinds of attacks and be secure to perform efficiently.

  19. Mac protocols for cyber-physical systems

    CERN Document Server

    Xia, Feng

    2015-01-01

    This book provides a literature review of various wireless MAC protocols and techniques for achieving real-time and reliable communications in the context of cyber-physical systems (CPS). The evaluation analysis of IEEE 802.15.4 for CPS therein will give insights into configuration and optimization of critical design parameters of MAC protocols. In addition, this book also presents the design and evaluation of an adaptive MAC protocol for medical CPS, which exemplifies how to facilitate real-time and reliable communications in CPS by exploiting IEEE 802.15.4 based MAC protocols. This book wil

  20. Multimode Communication Protocols Enabling Reconfigurable Radios

    Directory of Open Access Journals (Sweden)

    Berlemann Lars

    2005-01-01

    Full Text Available This paper focuses on the realization and application of a generic protocol stack for reconfigurable wireless communication systems. This focus extends the field of software-defined radios which usually concentrates on the physical layer. The generic protocol stack comprises common protocol functionality and behavior which are extended through specific parts of the targeted radio access technology. This paper considers parameterizable modules of basic protocol functions residing in the data link layer of the ISO/OSI model. System-specific functionality of the protocol software is realized through adequate parameterization and composition of the generic modules. The generic protocol stack allows an efficient realization of reconfigurable protocol software and enables a completely reconfigurable wireless communication system. It is a first step from side-by-side realized, preinstalled modes in a terminal towards a dynamic reconfigurable anymode terminal. The presented modules of the generic protocol stack can also be regarded as a toolbox for the accelerated and cost-efficient development of future communication protocols.

  1. [Climate change and Kyoto protocol].

    Science.gov (United States)

    Ergasti, G; Pippia, V; Murzilli, G; De Luca D'Alessandro, E

    2009-01-01

    Due to industrial revolution and the heavy use of fossil fuels, the concentration of greenhouse gases in the atmosphere has increased dramatically during the last hundred years, and this has lead to an increase in mean global temperature. The environmental consequences of this are: the melting of the ice caps, an increase in mean sea-levels, catastrophic events such as floodings, hurricanes and earthquakes, changes to the animal and vegetable kingdoms, a growth in vectors and bacteria in water thus increasing the risk of infectious diseases and damage to agriculture. The toxic effects of the pollution on human health are both acute and chronic. The Kyoto Protocol is an important step in the campaign against climatic changes but it is not sufficient. A possible solution might be for the States which produce the most of pollution to adopt a better political stance for the environment and to use renewable resources for the production of energy.

  2. Natural disturbances and Kyoto protocol

    Directory of Open Access Journals (Sweden)

    Teobaldelli M

    2008-06-01

    Full Text Available A recent letter published in Nature (Kurz et al. 2008a reports an outbreak of mountain pine beetles in British Columbia, destroying millions of trees; according to the authors, by 2020, the beetles will have done so much damage that the forest is expected to release more carbon dioxide than it absorbs. All those natural disturbances could overwhelmed all the efforts made by Canada to influence the carbon balance through forest management. Considering that Canada decided not to elect forest management within the Kyoto Protocol, it is clear that future climate mitigation agreements, aimed to encourage changes in forest management, should account for and protect against the impacts of natural disturbances.

  3. Protocol Monitoring Passive Solar Energy

    International Nuclear Information System (INIS)

    Van den Ham, E.R.; Bosselaar, L.

    1998-01-01

    A method has been developed by means of which the contribution of passive solar energy to the Dutch energy balance can be quantified univocally. The contribution was 57 PJ in 1990 and also 57 PJ in 1995. The efficiency of passive solar energy systems increased from -31.5% to -28.1% in the period 1990-1995, mainly as a result of the use of extra insulating glazing. As a result of the reduction of energy consumption for heating in houses it is expected that the extra contribution of 2 PJ will not be realized in the year 2010. It is suggested that the method to determine the absolute contribution of passive solar energy to the energy demand of dwellings is to be included in the protocol monitoring renewable energy. For the method to be included in the energy statistics of Statistics Netherlands (CBS) it can be considered only to take into account the difference compared to 1990. 11 refs

  4. GENERIC VERIFICATION PROTOCOL: DISTRIBUTED GENERATION AND COMBINED HEAT AND POWER FIELD TESTING PROTOCOL

    Science.gov (United States)

    This report is a generic verification protocol by which EPA’s Environmental Technology Verification program tests newly developed equipment for distributed generation of electric power, usually micro-turbine generators and internal combustion engine generators. The protocol will ...

  5. A computational protocol for the discovery of lead molecules targeting DNA unique to pathogens.

    Science.gov (United States)

    Mishra, Akhilesh; Pant, Pradeep; Mrinal, Nirotpal; Jayaram, B

    2017-12-01

    With the rapid emergence of drug resistant pathogens, it has become imperative to develop alternative medications as well as find new drug targets to overcome this crisis. Hence, this has become prime focus of several academic laboratories and pharmaceutical companies. Here, we report a computational protocol for identifying unique DNA sequence(s) in the pathogen which is absent in human and related non-pathogenic strains of the microbe. In order to use the unique sequence as drug target, the protocol, in the second step, uses virtual screening against a million compound library to identify candidate small molecules which can bind to these unique DNA targets in the pathogen only. Theoretically the molecules identified after screening should not bind to human DNA. This methodology is demonstrated on Mycobacterium tuberculosis H37Rv, wherein a new octamer sequence present only in H37Rv has been identified and a few candidate small molecules as potential drug have been proposed. Being fast and cost effective, this protocol could be of importance in generating new potential drug candidates against infectious organisms for further experimental studies. This methodology is freely available at http://www.scfbio-iitd.res.in/PSDDF/. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. A vision for ubiquitous sequencing.

    Science.gov (United States)

    Erlich, Yaniv

    2015-10-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. © 2015 Erlich; Published by Cold Spring Harbor Laboratory Press.

  7. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  8. In vitro HIV-1 selective integration into the target sequence and decoy-effect of the modified sequence.

    Directory of Open Access Journals (Sweden)

    Tatsuaki Tsuruyama

    Full Text Available Although there have been a few reports that the HIV-1 genome can be selectively integrated into the genomic DNA of cultured host cell, the biochemistry of integration selectivity has not been fully understood. We modified the in vitro integration reaction protocol and developed a reaction system with higher efficiency. We used a substrate repeat, 5'-(GTCCCTTCCCAGT(n(ACTGGGAAGGGAC(n-3', and a modified sequence DNA ligated into a circular plasmid. CAGT and ACTG (shown in italics in the above sequence in the repeat units originated from the HIV-1 proviral genome ends. Following the incubation of the HIV-1 genome end cDNA and recombinant integrase for the formation of the pre-integration (PI complex, substrate DNA was reacted with this complex. It was confirmed that the integration selectively occurred in the middle segment of the repeat sequence. In addition, integration frequency and selectivity were positively correlated with repeat number n. On the other hand, both frequency and selectivity decreased markedly when using sequences with deletion of CAGT in the middle position of the original target sequence. Moreover, on incubation with the deleted DNAs and original sequence, the integration efficiency and selectivity for the original target sequence were significantly reduced, which indicated interference effects by the deleted sequence DNAs. Efficiency and selectivity were also found to vary discontinuously with changes in manganese dichloride concentration in the reaction buffer, probably due to its influence on the secondary structure of substrate DNA. Finally, integrase was found to form oligomers on the binding site and substrate DNA formed a loop-like structure. In conclusion, there is a considerable selectivity in HIV-integration into the specified sequence; however, similar DNA sequences can interfere with the integration process, and it is therefore difficult for in vivo integration to occur selectively in the actual host genome DNA.

  9. Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.

    Directory of Open Access Journals (Sweden)

    Fan Gao

    Full Text Available In human immune system, V(DJ recombination produces an enormously large repertoire of immunoglobulins (Ig so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of immunoglobulins. However, these techniques typically require separation of B cell population from whole blood and require a few weeks for running the sequencers, so it may not be practical to implement them in clinical settings. Recently, the Ion Torrent personal genome sequencer has emerged as a tabletop personal genome sequencer that can be operated in a time-efficient and cost-effective manner. In this study, we explored the technical feasibility to use multiplex PCR for amplifying V(DJ recombination for IgH, directly from whole blood, then sequence the amplicons by the Ion Torrent sequencer. The whole process including data generation and analysis can be completed in one day. We tested the method in a pilot study on patients with benign, atypical and malignant meningiomas. Despite the noisy data, we were able to compare the samples by their usage frequencies of the V segment, as well as their somatic hypermutation rates. In summary, our study suggested that it is technically feasible to perform clinical monitoring of V(DJ recombination within a day by personal genome sequencers.

  10. OPM Scheme Editor 2: A graphical editor for specifying object-protocol structures

    Energy Technology Data Exchange (ETDEWEB)

    Chen, I-Min A.; Markowitz, V.M.; Pang, F.; Ben-Shachar, O.

    1993-07-01

    This document describes an X-window based Schema Editor for the Object-Protocol Model (OPM). OPM is a data model that supports the specification of complex object and protocol classes. objects and protocols are qualified in OPM by attributes that are defined over (associated with) value classes. Connections of object and protocol classes are expressed in OPM via attributes. OPM supports the specification (expansion) of protocols in terms of alternative and sequences of component (sub) protocols. The OPM Schema Editor allows specifying, displaying, modifying, and browsing through OPM schemas. The OPM Schema Editor generates an output file that can be used as input to an OPM schema translation tool that maps OPM schemas into definitions for relational database management systems. The OPM Schema Editor was implemented using C++ and the X11 based Motif toolkit, on Sun SPARCstation under Sun Unix OS 4.1. This document consists of the following parts: (1) A tutorial consisting of seven introductory lessons for the OPM Schema Editor. (2) A reference manual describing all the windows and functions of the OPM Schema Editor. (3) An appendix with an overview of OPM.

  11. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  12. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

    Science.gov (United States)

    Mitra, Abhishek; Skrzypczak, Magdalena; Ginalski, Krzysztof; Rowicka, Maga

    2015-01-01

    Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer's, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how

  13. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

    Directory of Open Access Journals (Sweden)

    Abhishek Mitra

    Full Text Available Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding. Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants. Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer's, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively

  14. Wind power agreement protocol; Protocole d'accord eolien

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-10-01

    The aim of this protocol of agreement is to propose to wind turbine fitters some models of contracts allowing the setting up of wind turbines on agricultural lots. These documents, which make an indissociable ensemble, apply to both phases of development of a wind power project: the feasibility study phase, for a duration comprised between 2 and 5 years (studies, administrative procedures, precise definition of the project), and the construction, exploitation and dismantling phase. These documents will serve as common guidelines for both the farmers and the wind turbine designers. Both parties agree to meet together in the future to propose some modifications of these texts if necessary. The four models of contracts are attached to the document: contract for the feasibility study phase, first contract between the landlord and the farmer for the cancellation of the rural lease, second contract between the landlord and the wind power exploitation company for the common right lease, and the third contract between the farmer and the wind power company for the indemnification convention. (J.S.)

  15. Platyrrhine dental eruption sequences.

    Science.gov (United States)

    Henderson, Emily

    2007-10-01

    To determine dental eruption sequences of extant platyrrhines, 367 mandibles and maxillae of informative juvenile specimens from all 16 genera were scored for presence of permanent teeth including three intermediate eruption stages following Harvati (Am J Phys Anthropol 112 (2000) 69-85). The timing of molar eruption relative to that of the anterior dentition is variable in platyrrhines. Aotus is precocious, with all molars erupting in succession before replacement of any deciduous teeth, while Cebus is delayed in M2-3 eruption relative to I1-2. Callitrichines have a distinct tendency toward delayed canine and premolar development. Platyrrhine eruption sequences presented here show some evidence of conformity to Schultz's Rule, with relatively early replacement of deciduous dentition in "slower"-growing animals. The relationship of dental eruption sequences to degree of folivory, body mass, brain mass, and dietary quality is also examined. The early eruption of molars relative to anterior teeth in Pithecia, Chiropotes, and Cacajao, in comparison to genera such as Ateles, Lagothrix, and Alouatta, showing relatively later eruption of the molars, appears to be consistent with current phylogenetic hypotheses. Schultz (Am J Phys Anthropol 19 (1935) 489-581) postulated early relative molar eruption as the primitive dental eruption schedule for primates. The extremely early molar eruption of Aotus versus Callicebus (where both incisors erupt before M2 and M3, with M3 usually last) may lend support to the status of Aotus as a basal taxon. The early relative molar eruption of the fossil platyrrhine species Branisella boliviana is also consistent with this hypothesis (Takai et al.: Am J Phys Anthropol 111 (2000) 263-281). (c) 2007 Wiley-Liss, Inc.

  16. Human genome and genetic sequencing research and informed consent

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi

    2003-01-01

    On March 29, 2001, the Ethical Guidelines for Human Genome and Genetic Sequencing Research were established. They have intended to serve as ethical guidelines for all human genome and genetic sequencing research practice, for the purpose of upholding respect for human dignity and rights and enforcing use of proper methods in the pursuit of human genome and genetic sequencing research, with the understanding and cooperation of the public. The RadGenomics Project has prepared a research protocol and informed consent document that follow these ethical guidelines. We have endeavored to protect the privacy of individual information, and have established a procedure for examination of research practices by an ethics committee. Here we report our procedure in order to offer this concept to the patients. (authors)

  17. High throughput 16S rRNA gene amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Jørgensen, Mads Koustrup

    S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. In this study we show how 16S r......RNA gene amplicon sequencing can be used to reveal factors of importance for the operation of full-scale nutrient removal plants related to settling problems and floc properties. Using optimized DNA extraction protocols, indexed primers and our in-house Illumina platform, we prepared multiple samples...... be correlated to the presence of the species that are regarded as “strong” and “weak” floc formers. In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling of activated sludge that in combination with multivariate statistics can be used...

  18. DNA Sequencing apparatus

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  19. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  20. Model checking the HAVi leader election protocol

    NARCIS (Netherlands)

    J.M.T. Romijn (Judi)

    1999-01-01

    textabstractThe HAVi specification proposes an architecture for audio/video interoperability in home networks. Part of the HAVi specification is a distributed leader election protocol. We have modelled this leader election protocol in Promela and Lotos and have checked several properties with the

  1. Kyoto Protocol: trade versus the environment

    International Nuclear Information System (INIS)

    Loose, H.

    2001-01-01

    Could the signatories to the Kyoto Protocol find themselves up against the WTO? This paper examines how the climate change agreement could conflict with trade rules, and shows that there are potentially serious conflicts in the interface between the WTO and the Kyoto Protocol. It argues for dialogue and debate before it is too late. (author)

  2. Climate Change And The Kyoto Protocol

    International Nuclear Information System (INIS)

    Comsan, M.N.H.

    2007-01-01

    The problem of global warming is addressed. Changes in earth surface temperature, emission of CO 2 and other four major green house gases are presented. Effect of global warming on weather, ocean, and ecosystem is discussed. A brief history of the Kyoto protocol starting from the 151 Earth Summit in 1972 is outlined. An overview of the protocol and a brief summary are given

  3. Welfare monitoring system : assessment protocol for horses

    OpenAIRE

    Livestock Research

    2012-01-01

    This document describes the protocol for horses in more detail. For the development of the protocol the Welfare Quality® framework was used. For each measure there is a description how to assess the measure including the method of classification.

  4. Protocols | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Each reagent on the Antibody Portal has been characterized by a combination of methods specific for that antibody. To view the customized antibody methods and protocols (Standard Operating Procedures) used to generate and characterize each reagent, select an antibody of interest and open the protocols associated with their respective characterization methods along with characterization data.

  5. Efficient Communication Protocols for Deciding Edit Distance

    DEFF Research Database (Denmark)

    Jowhari, Hossein

    2012-01-01

    In this paper we present two communication protocols on computing edit distance. In our first result, we give a one-way protocol for the following Document Exchange problem. Namely given x ∈ Σn to Alice and y ∈ Σn to Bob and integer k to both, Alice sends a message to Bob so that he learns x...

  6. Taking an idea to a research protocol

    African Journals Online (AJOL)

    2013-11-13

    Nov 13, 2013 ... have been identified as an effective therapy as early as. 1977. Instead, multiple ... The fifth step entails writing a study one-page summary which provides a succinct summary of what is intended. The sixth step involves writing the protocol. The rigid process of protocol writing will ensure that a number of ...

  7. Statistical principles for prospective study protocols:

    DEFF Research Database (Denmark)

    Christensen, Robin; Langberg, Henning

    2012-01-01

    (rigorous) protocol writing too troublesome, will realize that they have already written the first half of the final paper if they follow these recommendations; authors simply need to change the protocols future tense into past tense. Thus, the aim of this clinical commentary is to describe and explain...

  8. Analysis of a security protocol in ?CRL

    NARCIS (Netherlands)

    J. Pang

    2002-01-01

    textabstractNeedham-Schroeder public-key protocol; With the growth and commercialization of the Internet, the security of communication between computers becomes a crucial point. A variety of security protocols based on cryptographic primitives are used to establish secure communication over

  9. Algebraic techniques for low communication secure protocols

    NARCIS (Netherlands)

    Haan, Robbert de

    2009-01-01

    This thesis discusses new results in two areas within cryptography; securely transmitting a message between two parties and securely computing a function on the inputs of multiple parties. For both of these areas we mainly consider perfectly secure protocols, which are protocols that have a zero

  10. How to write a research protocol

    African Journals Online (AJOL)

    MMed degree. Although occasional reference will be made to qualitative approaches, it is likely that the majority of these studies will be quantitative designs and these form the focus of this paper. Keywords: MMed, protocol, protocol design, research, research design. Introduction. The introduction of compulsory research for ...

  11. 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 and com...... 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....... and complex genomes. Recent developments in strategies for target-enrichment, transcriptome re-sequencing, and partial genome re-sequencing allows for enrichment for regions of interest at a scale that is matched to the throughput of next-generation sequencing platforms, and has emerged as a promising...

  12. Spaces of ideal convergent sequences.

    Science.gov (United States)

    Mursaleen, M; Sharma, Sunil K

    2014-01-01

    In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ = (M(k)). We also examine some topological properties of the resulting sequence spaces.

  13. Nucleic acid protocols: Extraction and optimization

    Directory of Open Access Journals (Sweden)

    Saeed El-Ashram

    2016-12-01

    Full Text Available Yield and quality are fundamental features for any researchers during nucleic acid extraction. Here, we describe a simplified, semi-unified, effective, and toxic material free protocol for extracting DNA and RNA from different prokaryotic and eukaryotic sources exploiting the physical and chemical properties of nucleic acids. Furthermore, this protocol showed that DNA and RNA are under triple protection (i.e. EDTA, SDS and NaCl during lysis step, and this environment is improper for RNase to have DNA liberated of RNA and even for DNase to degrade the DNA. Therefore, the complete removal of RNA under RNase influence is achieved when RNase is added after DNA extraction, which gives optimal quality with any protocols. Similarly, DNA contamination in an isolated RNA is degraded by DNase to obtain high-quality RNA. Our protocol is the protocol of choice in terms of simplicity, recovery time, environmental safety, amount, purity, PCR and RT-PCR applicability.

  14. Quantum Communication Attacks on Classical Cryptographic Protocols

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre

    , one can show that the protocol remains secure even under such an attack. However, there are also cases where the honest players are quantum as well, even if the protocol uses classical communication. For instance, this is the case when classical multiparty computation is used as a “subroutine......” in quantum multiparty computation. Furthermore, in the future, players in a protocol may employ quantum computing simply to improve efficiency of their local computation, even if the communication is supposed to be classical. In such cases, it no longer seems clear that a quantum adversary must be limited......In the literature on cryptographic protocols, it has been studied several times what happens if a classical protocol is attacked by a quantum adversary. Usually, this is taken to mean that the adversary runs a quantum algorithm, but communicates classically with the honest players. In several cases...

  15. Summary Report on Unconditionally Secure Protocols

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Salvail, Louis; Cachin, Christian

    level. In noisy-channel cryptography security proofs are based on the assumption that a given physical means of communication is at a sufficiently low level inherently noisy. In bounded-storage cryptography security proofs are based on the assumption that there exists streams of information, generated...... above mentioned research areas.   This report focuses on unconditionally secure cryptographic protocols. Such protocols are based on a limitation of the adversary's knowledge in an information-theoretic or quantum- theoretic sense. They provide a very strong form of security because they cannot even......This document describes the state of the art snd some of the main open problems in the area of unconditionally secure cryptographic protocols. The most essential part of a cryptographic protocol is not its being secure. Imagine a cryptographic protocol which is secure, but where we do not know...

  16. Accuracy of NHANES periodontal examination protocols.

    Science.gov (United States)

    Eke, P I; Thornton-Evans, G O; Wei, L; Borgnakke, W S; Dye, B A

    2010-11-01

    This study evaluates the accuracy of periodontitis prevalence determined by the National Health and Nutrition Examination Survey (NHANES) partial-mouth periodontal examination protocols. True periodontitis prevalence was determined in a new convenience sample of 454 adults ≥ 35 years old, by a full-mouth "gold standard" periodontal examination. This actual prevalence was compared with prevalence resulting from analysis of the data according to the protocols of NHANES III and NHANES 2001-2004, respectively. Both NHANES protocols substantially underestimated the prevalence of periodontitis by 50% or more, depending on the periodontitis case definition used, and thus performed below threshold levels for moderate-to-high levels of validity for surveillance. Adding measurements from lingual or interproximal sites to the NHANES 2001-2004 protocol did not improve the accuracy sufficiently to reach acceptable sensitivity thresholds. These findings suggest that NHANES protocols produce high levels of misclassification of periodontitis cases and thus have low validity for surveillance and research.

  17. Cryptanalysis of the arbitrated quantum signature protocols

    Energy Technology Data Exchange (ETDEWEB)

    Gao Fei; Qin Sujuan; Guo Fenzhuo; Wen Qiaoyan [State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876 (China)

    2011-08-15

    As a new model for signing quantum messages, arbitrated quantum signature (AQS) has recently received a lot of attention. In this paper we study the cryptanalysis of previous AQS protocols from the aspects of forgery and disavowal. We show that in these protocols the receiver, Bob, can realize existential forgery of the sender's signature under known message attack. Bob can even achieve universal forgery when the protocols are used to sign a classical message. Furthermore, the sender, Alice, can successfully disavow any of her signatures by simple attack. The attack strategies are described in detail and some discussions about the potential improvements of the protocols are given. Finally we also present several interesting topics on AQS protocols that can be studied in future.

  18. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl......The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... inositol-anchored proteins....

  19. High Interlaboratory Reprocucibility of DNA Sequence-based Typing of Bacteria in a Multicenter Study

    DEFF Research Database (Denmark)

    Sousa, MA de; Boye, Kit; Lencastre, H de

    2006-01-01

    Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without...... extensive harmonization of protocols for 30 blind-coded S. aureus DNA samples sent to 10 laboratories. Specialized software for automated sequence analysis ensured a common typing nomenclature....

  20. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries.

    Science.gov (United States)

    Fisher, Sheila; Barry, Andrew; Abreu, Justin; Minie, Brian; Nolan, Jillian; Delorey, Toni M; Young, Geneva; Fennell, Timothy J; Allen, Alexander; Ambrogio, Lauren; Berlin, Aaron M; Blumenstiel, Brendan; Cibulskis, Kristian; Friedrich, Dennis; Johnson, Ryan; Juhn, Frank; Reilly, Brian; Shammas, Ramy; Stalker, John; Sykes, Sean M; Thompson, Jon; Walsh, John; Zimmer, Andrew; Zwirko, Zac; Gabriel, Stacey; Nicol, Robert; Nusbaum, Chad

    2011-01-01

    Genome targeting methods enable cost-effective capture of specific subsets of the genome for sequencing. We present here an automated, highly scalable method for carrying out the Solution Hybrid Selection capture approach that provides a dramatic increase in scale and throughput of sequence-ready libraries produced. Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol.

  1. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  2. MRI Sequences in Head & Neck Radiology - State of the Art.

    Science.gov (United States)

    Widmann, Gerlig; Henninger, Benjamin; Kremser, Christian; Jaschke, Werner

    2017-05-01

    Background  Magnetic resonance imaging (MRI) has become an essential imaging modality for the evaluation of head & neck pathologies. However, the diagnostic power of MRI is strongly related to the appropriate selection and interpretation of imaging protocols and sequences. The aim of this article is to review state-of-the-art sequences for the clinical routine in head & neck MRI and to describe the evidence for which medical question these sequences and techniques are useful. Method  Literature review of state-of-the-art sequences in head & neck MRI. Results and Conclusion  Basic sequences (T1w, T2w, T1wC+) and fat suppression techniques (TIRM/STIR, Dixon, Spectral Fat sat) are important tools in the diagnostic workup of inflammation, congenital lesions and tumors including staging. Additional sequences (SSFP (CISS, FIESTA), SPACE, VISTA, 3D-FLAIR) are used for pathologies of the cranial nerves, labyrinth and evaluation of endolymphatic hydrops in Menière's disease. Vessel and perfusion sequences (3D-TOF, TWIST/TRICKS angiography, DCE) are used in vascular contact syndromes, vascular malformations and analysis of microvascular parameters of tissue perfusion. Diffusion-weighted imaging (EPI-DWI, non-EPI-DWI, RESOLVE) is helpful in cholesteatoma imaging, estimation of malignancy, and evaluation of treatment response and posttreatment recurrence in head & neck cancer. Understanding of MRI sequences and close collaboration with referring physicians improves the diagnostic confidence of MRI in the daily routine and drives further research in this fascinating image modality. Key Points:   · Understanding of MRI sequences is essential for the correct and reliable interpretation of MRI findings.. · MRI protocols have to be carefully selected based on relevant clinical information.. · Close collaboration with referring physicians improves the output obtained from the diagnostic possibilities of MRI.. Citation Format · Widmann G, Henninger B, Kremser C et

  3. A Pan-HIV Strategy for Complete Genome Sequencing

    Science.gov (United States)

    Yamaguchi, Julie; Alessandri-Gradt, Elodie; Tell, Robert W.; Brennan, Catherine A.

    2015-01-01

    Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e., switching mechanism at 5′ end of RNA transcript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance. PMID:26699702

  4. Event sequence variability in healthy swallowing: building on previous findings.

    Science.gov (United States)

    Molfenter, Sonja M; Leigh, Chelsea; Steele, Catriona M

    2014-04-01

    This study builds on previous work by Kendall, Leonard, and McKenzie, which investigated event sequence variability for 12 paired events during swallowing by healthy volunteers. They identified four event pairs that always occurred in a stereotyped order and a most common occurring overall order of events during swallowing. In the current study, we investigated overall event sequencing and the same four paired events in a sample of swallows by healthy young (under 45 years old) volunteers. Data were collected during a 16-swallow lateral videofluoroscopy protocol, which included manipulations of bolus volume, barium density, bolus viscosity, and swallow cueing. Our results agreed with previous findings that variable event sequencing is found in healthy swallowing, and, in regard to obligatory sequencing of two paired events, movement of the arytenoids toward the base of the epiglottis begins prior to upper esophageal sphincter (UES) opening and maximum hyolaryngeal approximation occurs after UES opening. However, our data failed to replicate the previous findings that there is obligatory sequencing of maximum pharyngeal constriction after maximal UES distension and the UES opens before bolus arrival at the UES. The most common observed overall event sequence reported by Kendall et al. was observed in only 4/293 swallows in our dataset. Manipulations of bolus volume, bolus viscosity, barium concentration, swallow cueing, and swallow repetitions could not completely account for the differences observed between the two studies.

  5. A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data

    Directory of Open Access Journals (Sweden)

    Masanori Kakuta

    2017-10-01

    Full Text Available Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses. To analyze large-scale metagenomic data, such as those found in the human oral microbiome, we developed GHOST-MP (Genome-wide HOmology Search Tool on Massively Parallel system, a parallel sequence similarity search tool for massively parallel computing systems. This tool uses a fast search algorithm based on suffix arrays of query and database sequences and a hierarchical parallel search to accelerate the large-scale sequence similarity search of metagenomic sequencing data. The parallel computing efficiency and the search speed of this tool were evaluated. GHOST-MP was shown to be scalable over 10,000 CPU (Central Processing Unit cores, and achieved over 80-fold acceleration compared with mpiBLAST using the same computational resources. We applied this tool to human oral metagenomic data, and the results indicate that the oral cavity, the oral vestibule, and plaque have different characteristics based on the functional gene category.

  6. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  7. Sequencing Games with Repeated Players

    NARCIS (Netherlands)

    Estevez Fernandez, M.A.; Borm, P.; Calleja, P.; Hamers, H.

    2008-01-01

    Two classes of one machine sequencing situations are considered in which each job corresponds to exactly one player but a player may have more than one job to be processed, so called RP(repeated player) sequencing situations. In max-RP sequencing situations it is assumed that each player's cost

  8. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... 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 ...

  9. A Comparison Between Inter-Asterisk eXchange Protocol and Jingle Protocol: Session Time

    Directory of Open Access Journals (Sweden)

    H. S. Haj Aliwi

    2016-08-01

    Full Text Available Over the last few years, many multimedia conferencing and Voice over Internet Protocol (VoIP applications have been developed due to the use of signaling protocols in providing video, audio and text chatting services between at least two participants. This paper compares between two widely common signaling protocols: InterAsterisk eXchange Protocol (IAX and the extension of the eXtensible Messaging and Presence Protocol (Jingle in terms of delay time during call setup, call teardown, and media sessions.

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

    Science.gov (United States)

    DeMaere, Matthew Z; Darling, Aaron E

    2017-11-15

    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 (TADs) 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. © The Authors 2017. Published by Oxford University Press.

  11. Emergency contraceptive pills (ECP) protocol.

    Science.gov (United States)

    1994-05-01

    Outlined is a protocol for the administration of emergency contraceptive pills. The indication for such treatment is unprotected intercourse within the past 72 hours. Absolute contraindications include the possibility of an existing pregnancy and a family history of stroke, heart attack, thrombophlebitis, breast or endometrial cancer, or liver tumor. Possibly excluded, depending on evaluation by a physician, are women with abnormal vaginal bleeding, active hepatitis, active gallbladder disease, high blood pressure, acute focal migraine, breastfeeding women, and those unable to understand instructions. The recommended regimen consists of six tablets of Ovral (two taken immediately, two more in 12 hours) or 12 tablets of Lo/Ovral, Nordette, or Levlen (four taken immediately, repeat dosage in 12 hours). The extra pills are to be used in cases of vomiting within three hours of pill ingestion. Women with a history of oral contraceptive-related nausea and vomiting should be provided with Compazine. Women should be informed that this method is effective in only about 92% of cases. All women who receive emergency contraception should be counseled that this is strictly a back-up method and helped to formulate a long-term birth control strategy.

  12. Genomic DNA extraction protocols from ovine hair

    Directory of Open Access Journals (Sweden)

    Jennifer Nonato da Silva Prate

    2013-12-01

    Full Text Available Genomic DNA extracted from animal cells can be used for several purposes, for example, to know genetic variability and genetic relationships between individuals, breeds and/or species, paternity tests, to describe the genetic profile for registration of the animal at association of breeders, detect genetic polymorphisms (SNP related to characteristics of commercial interest, disease diagnose, assess resistance or susceptibility to pathogens, etc. For such evaluations, in general, DNA is amplified by PCR (polymerase chain reaction, and then subjected to various techniques as RFLP (restriction fragments length polymorphism, SSCP (single strand conformation polymorphism, and sequencing. The DNA may be obtained from blood, buccal swabs, meat, cartilage or hair bulb. Among all, the last biological material has been preferred by farmers for its ease acquisition. Several methods for extracting DNA from hair bulb were reported without any consensus for its implementation. This study aimed to optimize a protocol for efficient DNA extraction for use in PCR-RFLP analysis of the Prion gene. For this study, were collected hair samples containing hair bulb from 131 Santa Inês sheep belonging to the Institute of Zootechny, Nova Odessa - SP. Two DNA extraction protocols were evaluated. The first, called phenol-chloroform-isoamyl alcohol (PCIA has long been used by Animal Genetic Laboratories, whose procedures are described below: in each microtube (1.5 mL containing 500 µL of TE-Tween solution (Tris-HCl 50 mM, EDTA 1 mM and 0.5% Tween 20 were added to approximately 30 hair bulb per animal which was incubated at 65°C with shaking at 170 rpm for 2 hours. Then was added 15 µL of proteinase K [10 mg mL-1] and incubated at 55°C at 170 rpm for 6-12 hours. At the end of digestion was added 1 volume of solution phenol-chloroform-isoamyl alcohol (25:24:1 followed by vigorous shaking for 10 seconds and centrifuged at 8000 rpm and 4°C for 10 minutes. The upper phase

  13. Protocol for a systematic review of N-of-1 trial protocol guidelines and protocol reporting guidelines.

    Science.gov (United States)

    Porcino, Antony J; Punja, Salima; Chan, An-Wen; Kravitz, Richard; Orkin, Aaron; Ravaud, Philippe; Schmid, Christopher H; Vohra, Sunita

    2017-07-06

    N-of-1 trials are multiple cross-over trials done in individual participants, generating individual treatment effect information. While reporting guidelines for the CONSORT Extension for N-of-1 trials (CENT) and the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) already exist, there is no standardized recommendation for the reporting of N-of-1 trial protocols. The objective of this study is to evaluate current literature on N-of-1 design and reporting to identify key elements of rigorous N-of-1 protocol design. We will conduct a systematic search for all N-of-1 trial guidelines and protocol-reporting guidelines published in peer-reviewed literature. We will search Medline, Embase, PsycINFO, CINAHL, the Cochrane Methodology Register, CENTRAL, and the NHS Economic Evaluation Database. Eligible articles will contain explicit guidance on N-of-1 protocol construction or reporting. Two reviewers will independently screen all titles and abstracts and then undertake full-text reviews of potential articles to determine eligibility. One reviewer will perform data extraction of selected articles, checked by the second reviewer. Data analysis will ascertain common features of N-of-1 trial protocols and compare them to the SPIRIT and CENT items. This systematic review assesses recommendations on the design and reporting of N-of-1 trial protocols. These findings will inform an international Delphi development process for an N-of-1 trial protocol reporting guideline. The development of this guideline is critical for improving the quality of N-of-1 protocols, leading to improvements in the quality of published N-of-1 trial research.

  14. Universally composable protocols with relaxed set-up assumptions

    DEFF Research Database (Denmark)

    Barak, Boaz; Canetti, Ran; Nielsen, Jesper Buus

    2004-01-01

    A desirable goal for cryptographic protocols is to guarantee security when the protocol is composed with other protocol instances. Universally composable (UC) protocols provide this guarantee in a strong sense: A protocol remains secure even when composed concurrently with an unbounded number...

  15. CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.

    Science.gov (United States)

    Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

    2017-05-15

    B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study. Copyright © 2017 by The American Association of Immunologists, Inc.

  16. SU-G-TeP4-09: Development of a Plan Data Aggregator for Time Efficient Physics Second-Checks of Machine Parameters for External Beam Treatment Plans

    Energy Technology Data Exchange (ETDEWEB)

    Belley, M; Schmidt, M; Knutson, N [Rhode Island Hospital, Providence RI (United States); University of Rhode Island, Kingston, RI (United States); Price, M [Rhode Island Hospital, Providence RI (United States); University of Rhode Island, Kingston, RI (United States); Alpert Medical School of Brown University, Providence, RI (United States)

    2016-06-15

    Purpose: Physics second-checks for external beam radiation therapy are performed, in-part, to verify that the machine parameters in the Record-and-Verify (R&V) system that will ultimately be sent to the LINAC exactly match the values initially calculated by the Treatment Planning System (TPS). While performing the second-check, a large portion of the physicists’ time is spent navigating and arranging display windows to locate and compare the relevant numerical values (MLC position, collimator rotation, field size, MU, etc.). Here, we describe the development of a software tool that guides the physicist by aggregating and succinctly displaying machine parameter data relevant to the physics second-check process. Methods: A data retrieval software tool was developed using Python to aggregate data and generate a list of machine parameters that are commonly verified during the physics second-check process. This software tool imported values from (i) the TPS RT Plan DICOM file and (ii) the MOSAIQ (R&V) Structured Query Language (SQL) database. The machine parameters aggregated for this study included: MLC positions, X&Y jaw positions, collimator rotation, gantry rotation, MU, dose rate, wedges and accessories, cumulative dose, energy, machine name, couch angle, and more. Results: A GUI interface was developed to generate a side-by-side display of the aggregated machine parameter values for each field, and presented to the physicist for direct visual comparison. This software tool was tested for 3D conformal, static IMRT, sliding window IMRT, and VMAT treatment plans. Conclusion: This software tool facilitated the data collection process needed in order for the physicist to conduct a second-check, thus yielding an optimized second-check workflow that was both more user friendly and time-efficient. Utilizing this software tool, the physicist was able to spend less time searching through the TPS PDF plan document and the R&V system and focus the second-check efforts on

  17. Large scale library generation for high throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Erik Borgström

    Full Text Available BACKGROUND: Large efforts have recently been made to automate the sample preparation protocols for massively parallel sequencing in order to match the increasing instrument throughput. Still, the size selection through agarose gel electrophoresis separation is a labor-intensive bottleneck of these protocols. METHODOLOGY/PRINCIPAL FINDINGS: In this study a method for automatic library preparation and size selection on a liquid handling robot is presented. The method utilizes selective precipitation of certain sizes of DNA molecules on to paramagnetic beads for cleanup and selection after standard enzymatic reactions. CONCLUSIONS/SIGNIFICANCE: The method is used to generate libraries for de novo and re-sequencing on the Illumina HiSeq 2000 instrument with a throughput of 12 samples per instrument in approximately 4 hours. The resulting output data show quality scores and pass filter rates comparable to manually prepared samples. The sample size distribution can be adjusted for each application, and are suitable for all high throughput DNA processing protocols seeking to control size intervals.

  18. A Simple XML Producer-Consumer Protocol

    Science.gov (United States)

    Smith, Warren; Gunter, Dan; Quesnel, Darcy; Biegel, Bryan (Technical Monitor)

    2001-01-01

    There are many different projects from government, academia, and industry that provide services for delivering events in distributed environments. The problem with these event services is that they are not general enough to support all uses and they speak different protocols so that they cannot interoperate. We require such interoperability when we, for example, wish to analyze the performance of an application in a distributed environment. Such an analysis might require performance information from the application, computer systems, networks, and scientific instruments. In this work we propose and evaluate a standard XML-based protocol for the transmission of events in distributed systems. One recent trend in government and academic research is the development and deployment of computational grids. Computational grids are large-scale distributed systems that typically consist of high-performance compute, storage, and networking resources. Examples of such computational grids are the DOE Science Grid, the NASA Information Power Grid (IPG), and the NSF Partnerships for Advanced Computing Infrastructure (PACIs). The major effort to deploy these grids is in the area of developing the software services to allow users to execute applications on these large and diverse sets of resources. These services include security, execution of remote applications, managing remote data, access to information about resources and services, and so on. There are several toolkits for providing these services such as Globus, Legion, and Condor. As part of these efforts to develop computational grids, the Global Grid Forum is working to standardize the protocols and APIs used by various grid services. This standardization will allow interoperability between the client and server software of the toolkits that are providing the grid services. The goal of the Performance Working Group of the Grid Forum is to standardize protocols and representations related to the storage and distribution of

  19. Sequence analysis on microcomputers.

    Science.gov (United States)

    Cannon, G C

    1987-10-02

    Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further

  20. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  1. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  2. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  3. Blending protocol effect in structural properties of PA6/ABS nanocomposites compatibilized with SAN-MA

    International Nuclear Information System (INIS)

    Castro, Lucas D.C. de; Oliveira, Amanda D.; Pessan, Luiz Antonio

    2015-01-01

    Nanocomposites based on polyamide 6 (PA6) and acrylonitrile-butadiene-styrene (ABS) compatibilized with styrene acrylonitrile-co-maleic anhydride were prepared using different blending protocols in a twin screw extruder. Specimen were prepared though injection molding. The organoclay (OMMT) incorporation and blending sequence effect on structural properties were investigated. X-ray diffraction analysis (XRD) indicates a complete exfoliated structure for all samples. Rheological measurements show an increasing in nanocomposites complex viscosities and storage modulus values when compared with the ternary blend. However, no significant effects in the rheological behavior were observed due the blending sequence. Differential scanning calorimetry (DSC) measurements suggests the incorporation of OMMT and different blending protocols may influence the polyamide polymorphism and degree of crystallinity. (author)

  4. The evolution of nanopore sequencing

    Science.gov (United States)

    Wang, Yue; Yang, Qiuping; Wang, Zhimin

    2014-01-01

    The “$1000 Genome” project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the “$1000 Genome” while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards. PMID:25610451

  5. The Evolution of Nanopore Sequencing

    Directory of Open Access Journals (Sweden)

    Yue eWang

    2015-01-01

    Full Text Available The $1,000 Genome project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the $1,000 Genome while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

  6. New logistics protocols for distributed interactive simulation

    Science.gov (United States)

    Taylor, Darrin; Morrison, John; Katz, Warren; Felton, Erik; Herman, Deborah A.

    1995-06-01

    In today's environment, the transportation and maintenance of military forces is nearly as important as combat operations. Rapid deployment to regions of low-intensity conflict will become a very common training scenario for the U.S. military. Thus it is desirable to apply distributed simulation technology to train logistics personnel in their combat support roles. Currently, distributed interactive simulation (DIS) only contains rudimentary logistics protocols. This paper introduces new protocols designed to handle the logistics problem. The Newtonian protocol takes a physics-based approach to modeling interactions on the simulation network. This protocol consists of a family of protocol data units (PDUs) which are used to communicate forces in different circumstances. The protocol implements a small set of physical relations. This represents a flexible and general mechanism to describe battlefield interactions between network entities. The migratory object protocol (MOP) family addresses the transfer of control. General mechanisms provide the means to simulate resupply, repair, and maintenance of entities at any level of abstraction (individual soldier to division). It can also increase the fidelity of mine laying, enable handover of weapons for terminal guidance, allow for the distribution of aggregate-level simulation entities, provide capabilities for the simulation of personnel, etc.

  7. Applications of 3D CISS sequence for problem solving in neuroimaging

    International Nuclear Information System (INIS)

    Hingwala, Divyata; Chatterjee, Somnath; Kesavadas, Chandrasekharan; Thomas, Bejoy; Kapilamoorthy, Tirur Raman

    2011-01-01

    Three-dimensional (3D) constructive interference in steady state (CISS) is a gradient-echo MRI sequence that is used to investigate a wide range of pathologies when routine MRI sequences do not provide the desired anatomic information. The increased sensitivity of the 3D CISS sequence is an outcome of the accentuation of the T2 values between cerebrospinal fluid (CSF) and pathological structures. Apart from its well-recognized applications in the evaluation of the cranial nerves, CSF rhinorrhea and aqueduct stenosis, we have found the CISS sequence to be useful for the cisternal spaces, cavernous sinuses and the ventricular system, where it is useful for detecting subtle CSF-intensity lesions that may be missed on routine spin-echo sequences. This information helps in the management of these conditions. After a brief overview of the physics behind this sequence, we illustrate its clinical applications with representative cases and discuss its potential role in imaging protocols

  8. Whole exome and whole genome sequencing with dried blood spot DNA without whole genome amplification.

    Science.gov (United States)

    Bassaganyas, Laia; Freedman, George; Vaka, Dedeepya; Wan, Eunice; Lao, Richard; Chen, Flavia; Kvale, Mark; Currier, Robert J; Puck, Jennifer M; Kwok, Pui-Yan

    2018-01-01

    Newborn screening (NBS) for rare conditions is performed in all 50 states in the USA. We have partnered with the California Department of Public Health Genetic Disease Laboratory to determine whether sufficient DNA can be extracted from archived dried blood spots (DBS) for next-generation sequencing in the hopes that next-generation sequencing can play a role in NBS. We optimized the DNA extraction and sequencing library preparation protocols for residual infant DBS archived over 20 years ago and successfully obtained acceptable whole exome and whole genome sequencing data. This sequencing study using DBS DNA without whole genome amplification prior to sequencing library preparation provides evidence that properly stored residual newborn DBS are a satisfactory source of DNA for genetic studies. © 2017 Wiley Periodicals, Inc.

  9. Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

    Science.gov (United States)

    Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

    2017-11-13

    A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

  10. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.

    Science.gov (United States)

    Welch, John S; Westervelt, Peter; Ding, Li; Larson, David E; Klco, Jeffery M; Kulkarni, Shashikant; Wallis, John; Chen, Ken; Payton, Jacqueline E; Fulton, Robert S; Veizer, Joelle; Schmidt, Heather; Vickery, Tammi L; Heath, Sharon; Watson, Mark A; Tomasson, Michael H; Link, Daniel C; Graubert, Timothy A; DiPersio, John F; Mardis, Elaine R; Ley, Timothy J; Wilson, Richard K

    2011-04-20

    Whole-genome sequencing is becoming increasingly available for research purposes, but it has not yet been routinely used for clinical diagnosis. To determine whether whole-genome sequencing can identify cryptic, actionable mutations in a clinically relevant time frame. We were referred a difficult diagnostic case of acute promyelocytic leukemia with no pathogenic X-RARA fusion identified by routine metaphase cytogenetics or interphase fluorescence in situ hybridization (FISH). The case patient was enrolled in an institutional review board-approved protocol, with consent specifically tailored to the implications of whole-genome sequencing. The protocol uses a "movable firewall" that maintains patient anonymity within the entire research team but allows the research team to communicate medically relevant information to the treating physician. Clinical relevance of whole-genome sequencing and time to communicate validated results to the treating physician. Massively parallel paired-end sequencing allowed identification of a cytogenetically cryptic event: a 77-kilobase segment from chromosome 15 was inserted en bloc into the second intron of the RARA gene on chromosome 17, resulting in a classic bcr3 PML-RARA fusion gene. Reverse transcription polymerase chain reaction sequencing subsequently validated the expression of the fusion transcript. Novel FISH probes identified 2 additional cases of t(15;17)-negative acute promyelocytic leukemia that had cytogenetically invisible insertions. Whole-genome sequencing and validation were completed in 7 weeks and changed the treatment plan for the patient. Whole-genome sequencing can identify cytogenetically invisible oncogenes in a clinically relevant time frame.

  11. An Authentication Protocol for Future Sensor Networks.

    Science.gov (United States)

    Bilal, Muhammad; Kang, Shin-Gak

    2017-04-28

    Authentication is one of the essential security services in Wireless Sensor Networks (WSNs) for ensuring secure data sessions. Sensor node authentication ensures the confidentiality and validity of data collected by the sensor node, whereas user authentication guarantees that only legitimate users can access the sensor data. In a mobile WSN, sensor and user nodes move across the network and exchange data with multiple nodes, thus experiencing the authentication process multiple times. The integration of WSNs with Internet of Things (IoT) brings forth a new kind of WSN architecture along with stricter security requirements; for instance, a sensor node or a user node may need to establish multiple concurrent secure data sessions. With concurrent data sessions, the frequency of the re-authentication process increases in proportion to the number of concurrent connections. Moreover, to establish multiple data sessions, it is essential that a protocol participant have the capability of running multiple instances of the protocol run, which makes the security issue even more challenging. The currently available authentication protocols were designed for the autonomous WSN and do not account for the above requirements. Hence, ensuring a lightweight and efficient authentication protocol has become more crucial. In this paper, we present a novel, lightweight and efficient key exchange and authentication protocol suite called the Secure Mobile Sensor Network (SMSN) Authentication Protocol. In the SMSN a mobile node goes through an initial authentication procedure and receives a re-authentication ticket from the base station. Later a mobile node can use this re-authentication ticket when establishing multiple data exchange sessions and/or when moving across the network. This scheme reduces the communication and computational complexity of the authentication process. We proved the strength of our protocol with rigorous security analysis (including formal analysis using the BAN

  12. Protocolized hyperventilation enhances electroconvulsive therapy.

    Science.gov (United States)

    de Arriba-Arnau, Aida; Dalmau, Antonia; Soria, Virginia; Salvat-Pujol, Neus; Ribes, Carmina; Sánchez-Allueva, Ana; Menchón, José Manuel; Urretavizcaya, Mikel

    2017-08-01

    Hyperventilation is recommended in electroconvulsive therapy (ECT) to enhance seizures and to increase patients' safety. However, more evidence is needed regarding its effects and the optimum method of application. This prospective study involving 21 subjects compared two procedures, protocolized hyperventilation (PHV) and hyperventilation as usual (HVau), applied to the same patient in two consecutive sessions. Transcutaneous partial pressure of carbon dioxide (TcPCO 2 ) was measured throughout all sessions. Ventilation parameters, hemodynamic measures, seizure characteristics, and side effects were also explored. PHV resulted in lower TcPCO 2 after hyperventilation (p=.008) and over the whole session (p=.035). The lowest TcPCO 2 was achieved after voluntary hyperventilation. Changes in TcPCO 2 from baseline showed differences between HVau and PHV at each session time-point (all p<.05). Between- and within-subjects factors were statistically significant in a general linear model. Seizure duration was greater in PHV sessions (p=.028), without differences in other seizure quality parameters or adverse effects. Correlations were found between hypocapnia induction and seizure quality indexes. Secondary outcomes could be underpowered. PHV produces hypocapnia before the stimulus, modifies patients' TcPCO 2 values throughout the ECT session and lengthens seizure duration. Voluntary hyperventilation is the most important part of the PHV procedure with respect to achieving hypocapnia. A specific ventilation approach, CO 2 quantification and monitoring may be advisable in ECT. PHV is easy to apply in daily clinical practice and does not imply added costs. Ventilation management has promising effects in terms of optimizing ECT technique. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Analyzing security protocols in hierarchical networks

    DEFF Research Database (Denmark)

    Zhang, Ye; Nielson, Hanne Riis

    2006-01-01

    Validating security protocols is a well-known hard problem even in a simple setting of a single global network. But a real network often consists of, besides the public-accessed part, several sub-networks and thereby forms a hierarchical structure. In this paper we first present a process calculus...... capturing the characteristics of hierarchical networks and describe the behavior of protocols on such networks. We then develop a static analysis to automate the validation. Finally we demonstrate how the technique can benefit the protocol development and the design of network systems by presenting a series...

  14. Micromobility protocols performance in differentiated services networks

    Science.gov (United States)

    Mariz, Denio; Fernandes, Stenio F.; Santos, Klebson; Kelner, Judith; Sadok, Djamel

    2003-08-01

    This work analyses and compares the performance of the recently proposed micro-mobility protocols HAWAII and Hierarchical MIP when submitted to several levels of traffic load and scenarios that effectively degrade the low packet loss feature of these protocols. Furthermore, it is shown that the use of differentiated services within a given domain infrastructure results in a considerable increase of performance for mobile nodes. The preferential treatment offered to such mobile nodes protects micro-mobility protocols traffic from the fluctuations of background traffic with losses only occurring as a result of handoff events.

  15. A Logical Analysis of Quantum Voting Protocols

    Science.gov (United States)

    Rad, Soroush Rafiee; Shirinkalam, Elahe; Smets, Sonja

    2017-12-01

    In this paper we provide a logical analysis of the Quantum Voting Protocol for Anonymous Surveying as developed by Horoshko and Kilin in (Phys. Lett. A 375, 1172-1175 2011). In particular we make use of the probabilistic logic of quantum programs as developed in (Int. J. Theor. Phys. 53, 3628-3647 2014) to provide a formal specification of the protocol and to derive its correctness. Our analysis is part of a wider program on the application of quantum logics to the formal verification of protocols in quantum communication and quantum computation.

  16. Security Protocol Review Method Analyzer(SPRMAN)

    OpenAIRE

    Navaz, A. S. Syed; Narayanan, H. Iyyappa; Vinoth, R.

    2013-01-01

    This Paper is designed using J2EE (JSP, SERVLET), HTML as front end and a Oracle 9i is back end. SPRMAN is been developed for the client British Telecom (BT) UK., Telecom company. Actually the requirement of BT is, they are providing Network Security Related Products to their IT customers like Virtusa,Wipro,HCL etc., This product is framed out by set of protocols and these protocols are been associated with set of components. By grouping all these protocols and components together, product is...

  17. Advanced Internet Protocols, Services, and Applications

    CERN Document Server

    Oki, Eiji; Tatipamula, Mallikarjun; Vogt, Christian

    2012-01-01

    Today, the internet and computer networking are essential parts of business, learning, and personal communications and entertainment. Virtually all messages or transactions sent over the internet are carried using internet infrastructure- based on advanced internet protocols. Advanced internet protocols ensure that both public and private networks operate with maximum performance, security, and flexibility. This book is intended to provide a comprehensive technical overview and survey of advanced internet protocols, first providing a solid introduction and going on to discu

  18. The protocol amending the 1963 Vienna Convention

    International Nuclear Information System (INIS)

    Lamm, V.

    2006-01-01

    Technically the Vienna Convention was revised by the adoption of the protocol to amend the instrument. and according to Article 19 of the protocol 'A State which is Party to this Protocol but not to the 1963 Vienna Convention shall be bound by the provisions of that Convention as amended by this Protocol in relation to other States Parties hereto, and failing an expression of a different intention by that State at the time of deposit of an instrument referred to in Article 20 shall be bound by the provisions of the 1963 Vienna Convention in relation to States which are only Parties thereto'. This solution has created a special situation, because after the entry into force of the protocol there will be living together or operating in practice 'two' Vienna Conventions, notably the convention's original text of 1963 and its new version as amended by the protocol. After the protocol has come into force, a state may only accede to the amended version, but in the inter se relations of the States Party to the 'old' Vienna Convention the provisions of that convention will remain in force until such time as they have acceded to the new protocol. This rather complicated situation is nevertheless understandable and is fully in accord with Article 40 of the 1969 Vienna Convention on the Law of Treaties, which provides for the amendment of multilateral treaties. In 1989 the negotiations on the revision of the Vienna Convention had begun with the aim of strengthening the existing nuclear liability regime and of improving the situation of potential victims of nuclear accidents. The Protocol to Amend the Vienna Convention serves those purposes; it also reflects a good compromise, since it is the outcome of a negotiation process in which experts from both nuclear and non-nuclear states, from Contacting Parties and non-Contracting Parties were very active. That affords some assurance that the compromise solution reached is acceptable to all States participating in the adoption of

  19. Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples.

    Science.gov (United States)

    Rehimi, Rizwan; Bartusel, Michaela; Solinas, Francesca; Altmüller, Janine; Rada-Iglesias, Alvaro

    2017-08-29

    Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies. In order to make the ChIP assay compatible with the amount of biological material that can typically be obtained in vivo during early vertebrate embryogenesis, we describe here a simplified ChIP protocol in which the number of steps required to complete the assay were reduced to minimize sample loss. This ChIP protocol has been successfully used to investigate different histone modifications in various embryonic chicken and adult mouse tissues using low to medium cell numbers (5 x 10 4 - 5 x 10 5 cells). Importantly, this protocol is compatible with ChIP-seq technology using standard library preparation methods, thus providing global epigenomic maps in highly relevant embryonic tissues.

  20. Developing daisy chain receivers for light-emitting diode illumination adopting the digital multiplex-512 protocol.

    Science.gov (United States)

    Um, Keehong; Yoo, Sooyeup

    2013-10-01

    Protocol for digital multiplex with 512 pieces of information is increasingly adopted in the design of illumination systems. In conventional light-emitting diode systems, the receivers are connected in parallel and each of the receiving units receives all the data from the master dimmer console, but each receiving unit operates by recognizing as its own data that which corresponds to the assigned number of the receiver. Because the serial numbers of illumination devices are transmitted in binary code, synchronization is too complicated to be used properly. In order to improve the protocol of illumination control systems, we propose an algorithm of protocol reception to install and manage the system in a simpler and more convenient way. We propose the systems for controlling the light-emitting diode illumination of simplified receiver slaves adopting the digital multiplex-512 protocol where master console and multiple receiver slaves are connected in a daisy chain fashion. The digital multiplex-512 data packet is received according to the sequence order of their locations from the console, without assigning the sequence number of each channel at the receiving device. The purpose of this paper is to design a simple and small-sized controller for the control systems of lamps and lighting adopting the digital multiplex-512 network.

  1. Modification of the GS LT Paired-end Library Protocol for Constructing Longer Insert Size Libraries

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ze; Peng, Ze; Hamilton, Matthew; Ting, Sara; Tu, Hank; Goltsman, Eugene; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang

    2008-05-22

    Paired-end library sequencing has been proven useful in scaffold construction during de novo assembly of genomic sequences. The ability of generating mate pairs with 8 Kb or greater insert sizes is especially important for genomes containing long repeats. While the current 454 GS LT Paired-end library preparation protocol can successfully construct libraries with 3 Kb insert size, it fails to generate longer insert sizes because the protocol is optimized to purify shorter fragments. We have made several changes in the protocol in order to increase the fragment length. These changes include the use of Promega column to increase the yield of large size DNA fragments, two gel purification steps to remove contaminated short fragments, and a large reaction volume in the circularization step to decrease the formation of chimeras. We have also made additional changes in the protocol to increase the overall quality of the libraries. The quality of the libraries are measured by a set of metrics, which include levels of redundant reads, linker positive, linker negative, half linker reads, and driver DNA contamination, and read length distribution, were used to measure the primary quality of these libraries. We have also assessed the quality of the resulted mate pairs including levels of chimera, distribution of insert sizes, and genome coverage after the assemblies are completed. Our data indicated that all these changes have improved the quality of the longer insert size libraries.

  2. Event-by-event simulation of quantum cryptography protocols

    NARCIS (Netherlands)

    Zhao, S.; Raedt, H. De

    We present a new approach to simulate quantum cryptography protocols using event-based processes. The method is validated by simulating the BB84 protocol and the Ekert protocol, both without and with the presence of an eavesdropper.

  3. A Black Hole Attack Model for Reactive Ad-Hoc Protocols

    Science.gov (United States)

    2012-03-01

    metric value may be easily detected by more secure versions of the protocol. In 17 [DhS08], the authors used the fact that sequence numbers generally...analytical model is presented to calculate network throughput under denial of service attacks; specifically these attacks are Jellyfish and Black Hole...things of interest to point out using Table 1. First, it is easy to see the recursive relationship between n-cubes. Any element at row n and column

  4. Evaluation of Adherence to a Convulsion management Protocol for Children in Rwanda

    OpenAIRE

    kaputu-kalal-malu, Célestin; D'Amour Birindabagabo, Jean; Walker, Timothy David; Mafuta-Musalu, Eric; Ntumba-Tshitenge, Olga; Preux, Pierre-Marie; MISSON, Jean-Paul

    2014-01-01

    Inappropriate seizure management may result in high morbidity and mortality. We assessed the adherence of health professionals in southern Rwanda to a national protocol for pharmacological management of seizures in children. A questionnaire featuring a 5-year-old child with generalized prolonged seizures was administered. The questions focused on the choice of initial treatment and the sequence of management following failure of the initial treatment choice. Benzodiazepine was cho...

  5. Identification of cut-rose (Rosa hybrida) and rootstock varieties using robust Sequence Tagged Microsatellite markers

    NARCIS (Netherlands)

    Esselink, D.; Smulders, M.J.M.; Vosman, B.

    2003-01-01

    In this study a DNA fingerprinting protocol was developed for the identification of rose varieties based on the variability of microsatellites. Microsatellites were isolated from Rosa hybrida L. using enriched small insert libraries. In total 24 polymorphic sequenced tagged microsatellite site

  6. The Impact of RLC Delivery Sequence on FTP Performance in UMTS

    DEFF Research Database (Denmark)

    Teyeb, Oumer; Boussif, Malek; Sørensen, Troels Bundgaard

    2005-01-01

    is investigated. The investigations are carried out using a real-time emulation platform, and Transmission Control Protocol (TCP) with and without Selective Acknowledgement/Forward Acknowledgment (SACK/FACK) options. The results show that out-of-sequence delivery has a negative impact at higher bandwidths and TCP...

  7. Generation, Analysis and Functional Annotation of Expressed Sequence Tags from the Sheepshead Minnow (Cyprinodon variegatus)

    Science.gov (United States)

    2010-01-01

    CA) were cloned using the pGEM-T Easy Vector System (Promega, Madison, WI) and Electromax DH10B T1 Phage Resistant Cells (Invitrogen, Carlsbad, CA...reactions were performed using 75ng of plasmid DNA template and a M13 (-40) forward primer according to the manufac- turer’s protocol for DNA sequencing of

  8. Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes

    NARCIS (Netherlands)

    Cornelissen, Marion; Gall, Astrid; van der Kuyl, Antoinette; Wymant, Chris; Blanquart, François; Fraser, Christophe; Berkhout, Ben

    2018-01-01

    We describe a detailed protocol for the manual workup of blood (plasma/serum) samples from individuals infected with the human immunodeficiency virus type 1 (HIV-1) for deep sequence analysis of the viral genome. The study optimizing the assay was performed in the context of the BEEHIVE (Bridging

  9. 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.

  10. A Hybrid Collision Resolution Protocol for Passive RFID Tag Identification

    OpenAIRE

    Xin-qing, Yan; Zhou-ping, Yin; You-lun, Xiong

    2009-01-01

    Wireless communication channel collision of RFID system is a key issue that affects the pervasive application of the system, especially for passive RFID system due to the constrained communication ability and energy supply of tags. The collision resolution protocols suggested can be categorized into deterministic tree based protocols and probabilistic frame slot ALOHA based protocols. A hybrid protocol, which combines the query tree protocol and dynamic framed slotted ALOHA protocol, is prese...

  11. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    International Nuclear Information System (INIS)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja; Espinosa, Norman

    2017-01-01

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  12. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    Energy Technology Data Exchange (ETDEWEB)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Department of Radiology, Zurich (Switzerland); Espinosa, Norman [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Orthopedic Surgery, Zurich (Switzerland)

    2017-08-15

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  13. Whole-genome sequencing and assembly with high-throughput, short-read technologies.

    Directory of Open Access Journals (Sweden)

    Andreas Sundquist

    Full Text Available While recently developed short-read sequencing technologies may dramatically reduce the sequencing cost and eventually achieve the $1000 goal for re-sequencing, their limitations prevent the de novo sequencing of eukaryotic genomes with the standard shotgun sequencing protocol. We present SHRAP (SHort Read Assembly Protocol, a sequencing protocol and assembly methodology that utilizes high-throughput short-read technologies. We describe a variation on hierarchical sequencing with two crucial differences: (1 we select a clone library from the genome randomly rather than as a tiling path and (2 we sample clones from the genome at high coverage and reads from the clones at low coverage. We assume that 200 bp read lengths with a 1% error rate and inexpensive random fragment cloning on whole mammalian genomes is feasible. Our assembly methodology is based on first ordering the clones and subsequently performing read assembly in three stages: (1 local assemblies of regions significantly smaller than a clone size, (2 clone-sized assemblies of the results of stage 1, and (3 chromosome-sized assemblies. By aggressively localizing the assembly problem during the first stage, our method succeeds in assembling short, unpaired reads sampled from repetitive genomes. We tested our assembler using simulated reads from D. melanogaster and human chromosomes 1, 11, and 21, and produced assemblies with large sets of contiguous sequence and a misassembly rate comparable to other draft assemblies. Tested on D. melanogaster and the entire human genome, our clone-ordering method produces accurate maps, thereby localizing fragment assembly and enabling the parallelization of the subsequent steps of our pipeline. Thus, we have demonstrated that truly inexpensive de novo sequencing of mammalian genomes will soon be possible with high-throughput, short-read technologies using our methodology.

  14. BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation

    Science.gov (United States)

    Schomburg, Dietmar

    2017-01-01

    The prediction of gene functions is crucial for a large number of different life science areas. Faster high throughput sequencing techniques generate more and larger datasets. The manual annotation by classical wet-lab experiments is not suitable for these large amounts of data. We showed earlier that the automatic sequence pattern-based BrEPS protocol, based on manually curated sequences, can be used for the prediction of enzymatic functions of genes. The growing sequence databases provide the opportunity for more reliable patterns, but are also a challenge for the implementation of automatic protocols. We reimplemented and optimized the BrEPS pattern generation to be applicable for larger datasets in an acceptable timescale. Primary improvement of the new BrEPS protocol is the enhanced data selection step. Manually curated annotations from Swiss-Prot are used as reliable source for function prediction of enzymes observed on protein level. The pool of sequences is extended by highly similar sequences from TrEMBL and SwissProt. This allows us to restrict the selection of Swiss-Prot entries, without losing the diversity of sequences needed to generate significant patterns. Additionally, a supporting pattern type was introduced by extending the patterns at semi-conserved positions with highly similar amino acids. Extended patterns have an increased complexity, increasing the chance to match more sequences, without losing the essential structural information of the pattern. To enhance the usability of the database, we introduced enzyme function prediction based on consensus EC numbers and IUBMB enzyme nomenclature. BrEPS is part of the Braunschweig Enzyme Database (BRENDA) and is available on a completely redesigned website and as download. The database can be downloaded and used with the BrEPScmd command line tool for large scale sequence analysis. The BrEPS website and downloads for the database creation tool, command line tool and database are freely accessible at

  15. Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol.

    Science.gov (United States)

    Seetin, Matthew G; Kladwang, Wipapat; Bida, John P; Das, Rhiju

    2014-01-01

    Chemical mapping methods probe RNA structure by revealing and leveraging correlations of a nucleotide's structural accessibility or flexibility with its reactivity to various chemical probes. Pioneering work by Lucks and colleagues has expanded this method to probe hundreds of molecules at once on an Illumina sequencing platform, obviating the use of slab gels or capillary electrophoresis on one molecule at a time. Here, we describe optimizations to this method from our lab, resulting in the MAP-seq protocol (Multiplexed Accessibility Probing read out through sequencing), version 1.0. The protocol permits the quantitative probing of thousands of RNAs at once, by several chemical modification reagents, on the time scale of a day using a tabletop Illumina machine. This method and a software package MAPseeker ( http://simtk.org/home/map_seeker ) address several potential sources of bias, by eliminating PCR steps, improving ligation efficiencies of ssDNA adapters, and avoiding problematic heuristics in prior algorithms. We hope that the step-by-step description of MAP-seq 1.0 will help other RNA mapping laboratories to transition from electrophoretic to next-generation sequencing methods and to further reduce the turnaround time and any remaining biases of the protocol.

  16. Postexercise hypotension during different water-based concurrent training intrasession sequences in young women.

    Science.gov (United States)

    Pinto, Stephanie Santana; Umpierre, Daniel; Ferreira, Hector Kerchirne; Nunes, Gabriela Neves; Ferrari, Rodrigo; Alberton, Cristine Lima

    2017-10-01

    The purpose of the study was to compare the acute effects of water-based resistance-aerobic (RA) and aerobic-resistance (AR) sequences on systolic blood pressure, diastolic blood pressure (DBP), and mean blood pressure (MBP) in young women. Thirteen active women participated in four sessions: (1) exercises familiarization, (2) aquatic maximal test to determine the heart rate (HR) corresponding to the anaerobic threshold (HR AT ), (3) concurrent protocol RA, and (4) concurrent protocol AR. Both protocols were initiated with the blood pressure measurements at rest in supine position. After that, either RA or AR concurrent protocol was performed. At the end of both protocols, blood pressure was measured throughout 60 minutes (every 10 minutes). The water-based resistance protocol was made up by exercises at maximal velocity, and the water-based aerobic protocol was performed at ±5 bpm of HR AT continuously. Two-way analysis of variance with repeated measures was used to analyze the data (α = 0.05). There was no hypotensive effect on systolic blood pressure among the time points (P = .235) in both water-based intrasession exercise sequences (P = .423). Regarding the DBP and MBP, both intrasession exercise sequences presented similar (DBP: P = .980; MBP: P = .796) hypotensive effects in the first 10 minutes (DBP: P = .003; MBP: P = .008) at the end of RA and AR sessions (DBP: -4 vs. -13 mm Hg; MBP: -3 vs. -10 mm Hg). It was concluded that both RA and AR water-based concurrent training sessions resulted in postexercise hypotension (DBP and MBP) in normotensive young women. Copyright © 2017 American Society of Hypertension. Published by Elsevier Inc. All rights reserved.

  17. Standardization of DNA extraction from sand flies: Application to genotyping by next generation sequencing.

    Science.gov (United States)

    Casaril, Aline Etelvina; de Oliveira, Liliane Prado; Alonso, Diego Peres; de Oliveira, Everton Falcão; Gomes Barrios, Suellem Petilim; de Oliveira Moura Infran, Jucelei; Fernandes, Wagner de Souza; Oshiro, Elisa Teruya; Ferreira, Alda Maria Teixeira; Ribolla, Paulo Eduardo Martins; de Oliveira, Alessandra Gutierrez

    2017-06-01

    Standardization of the methods for extraction of DNA from sand flies is essential for obtaining high efficiency during subsequent molecular analyses, such as the new sequencing methods. Information obtained using these methods may contribute substantially to taxonomic, evolutionary, and eco-epidemiological studies. The aim of the present study was to standardize and compare two methods for the extraction of genomic DNA from sand flies for obtaining DNA in sufficient quantities for next-generation sequencing. Sand flies were collected from the municipalities of Campo Grande, Camapuã, Corumbá and Miranda, state of Mato Grosso do Sul, Brazil. Three protocols using a silica column-based commercial kit (ReliaPrep™ Blood gDNA Miniprep System kit, Promega ® ), and three protocols based on the classical phenol-chloroform extraction method (Uliana et al., 1991), were compared with respect to the yield and quality of the extracted DNA. DNA was quantified using a Qubit 2.0 fluorometer. The presence of sand fly DNA was confirmed by PCR amplification of the IVS6 region (constitutive gene), followed by electrophoresis on a 1.5% agarose gel. A total of 144 male specimens were analyzed, 72 per method. Significant differences were observed between the two methods tested. Protocols 2 and 3 of phenol-chloroform extraction presented significantly better performance than all commercial kit extraction protocols tested. For phenol-chloroform extraction, protocol 3 presented significantly better performance than protocols 1 and 2. The IVS6 region was detected in 70 of 72 (97.22%) samples extracted with phenol, including all samples for protocols 2 and 3. This is the first study on the standardization of methods for the extraction of DNA from sand flies for application to next-generation sequencing, which is a promising tool for entomological and molecular studies of sand flies. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. [New protocol combining orthodontics and implant therapy for partially edentulous adult patients. Part I: Description of the Decker protocol].

    Science.gov (United States)

    Davarpanah, K; Decker, A; Sache, M P; Deffrennes, D; Demurashvili, G; Szmukler-Moncler, S

    2014-12-01

    The treatment of adult malocclusion is usually complex and pluridisciplinary. Its prognosis is not reliable. We present a new clinical protocol to improve the management and final result. We use a specific software (Simplant®, OMS®, Materialise Dental) and its accessory modules. It allows visualization of the expected final clinical result of the orthodontic treatment. Combined with guided-surgery, it allows placing implants at the beginning of treatment in a position that is compatible with the final position. The implants serve as absolute anchorage for dental motions during the orthodontic step; it is also used to support the final prosthesis. The treatment is thus optimized and its prognosis is improved. Finally, the reversed surgical sequences shorten the treatment thus promoting the compliance of patients. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  19. Evolution of a C2 protocol gateway

    CSIR Research Space (South Africa)

    Duvenhage, A

    2008-06-01

    Full Text Available Live, Virtual and Constructive (LVC) simulations can share tactical awareness data using command and control (C2) protocol gateways as bridges: Multiple training simulations can be linked to create large scale collaborative environments; simulations...

  20. Real-Time Fault Tolerant Networking Protocols

    National Research Council Canada - National Science Library

    Henzinger, Thomas A

    2004-01-01

    We made significant progress in the areas of video streaming, wireless protocols, mobile ad-hoc and sensor networks, peer-to-peer systems, fault tolerant algorithms, dependability and timing analysis...

  1. UK Biobank's cardiovascular magnetic resonance protocol.

    Science.gov (United States)

    Petersen, Steffen E; Matthews, Paul M; Francis, Jane M; Robson, Matthew D; Zemrak, Filip; Boubertakh, Redha; Young, Alistair A; Hudson, Sarah; Weale, Peter; Garratt, Steve; Collins, Rory; Piechnik, Stefan; Neubauer, Stefan

    2016-02-01

    UK Biobank's ambitious aim is to perform cardiovascular magnetic resonance (CMR) in 100,000 people previously recruited into this prospective cohort study of half a million 40-69 year-olds. We describe the CMR protocol applied in UK Biobank's pilot phase, which will be extended into the main phase with three centres using the same equipment and protocols. The CMR protocol includes white blood CMR (sagittal anatomy, coronary and transverse anatomy), cine CMR (long axis cines, short axis cines of the ventricles, coronal LVOT cine), strain CMR (tagging), flow CMR (aortic valve flow) and parametric CMR (native T1 map). This report will serve as a reference to researchers intending to use the UK Biobank resource or to replicate the UK Biobank cardiovascular magnetic resonance protocol in different settings.

  2. Protocol to Exploit Waiting Resources for UASNs

    Directory of Open Access Journals (Sweden)

    Li-Ling Hung

    2016-03-01

    Full Text Available The transmission speed of acoustic waves in water is much slower than that of radio waves in terrestrial wireless sensor networks. Thus, the propagation delay in underwater acoustic sensor networks (UASN is much greater. Longer propagation delay leads to complicated communication and collision problems. To solve collision problems, some studies have proposed waiting mechanisms; however, long waiting mechanisms result in low bandwidth utilization. To improve throughput, this study proposes a slotted medium access control protocol to enhance bandwidth utilization in UASNs. The proposed mechanism increases communication by exploiting temporal and spatial resources that are typically idle in order to protect communication against interference. By reducing wait time, network performance and energy consumption can be improved. A performance evaluation demonstrates that when the data packets are large or sensor deployment is dense, the energy consumption of proposed protocol is less than that of existing protocols as well as the throughput is higher than that of existing protocols.

  3. Entanglement distillation protocols and number theory

    International Nuclear Information System (INIS)

    Bombin, H.; Martin-Delgado, M.A.

    2005-01-01

    We show that the analysis of entanglement distillation protocols for qudits of arbitrary dimension D benefits from applying basic concepts from number theory, since the set Z D n associated with Bell diagonal states is a module rather than a vector space. We find that a partition of Z D n into divisor classes characterizes the invariant properties of mixed Bell diagonal states under local permutations. We construct a very general class of recursion protocols by means of unitary operations implementing these local permutations. We study these distillation protocols depending on whether we use twirling operations in the intermediate steps or not, and we study them both analytically and numerically with Monte Carlo methods. In the absence of twirling operations, we construct extensions of the quantum privacy algorithms valid for secure communications with qudits of any dimension D. When D is a prime number, we show that distillation protocols are optimal both qualitatively and quantitatively

  4. Implementation of the Additional Protocol in Japan

    International Nuclear Information System (INIS)

    Ogawa, T.

    2001-01-01

    The Additional Protocol between Japan and the IAEA entered into force in December 1999. To come into force a series of implementation trials of Additional Protocol was carried out at two Japanese representative nuclear research centers, i.e. Tokai Research Establishment of Japan Atomic Energy Research Institute (JAERI) and Oarai Engineering Center of Japan Nuclear Fuel Cycle Development Institute (JNC). These trials were proposed by Japan and were conducted in cooperation with the IAEA Secretariat. In addition, Japan amended 'the Law for the Regulation of Reactors etc.', to collect adequate information to submit to the IAEA, to arrange the surrounding for the complementary access, etc. In addition, Japan Submitted the Initial Declaration of the Additional Protocol within 180 days of the entry into force of the Protocol, in the middle of June, 2000

  5. ARC Code TI: Geometry Manipulation Protocol (GMP)

    Data.gov (United States)

    National Aeronautics and Space Administration — The Geometry Manipulation Protocol (GMP) is a library which serializes datatypes between XML and ANSI C data structures to support CFD applications. This library...

  6. Technical Analysis of SSP-21 Protocol

    Energy Technology Data Exchange (ETDEWEB)

    Bromberger, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-06-09

    As part of the California Energy Systems for the Twenty-First Century (CES-21) program, in December 2016 San Diego Gas and Electric (SDG&E) contracted with Lawrence Livermore National Laboratory (LLNL) to perform an independent verification and validation (IV&V) of a white paper describing their Secure SCADA Protocol for the Twenty-First Century (SSP-21) in order to analyze the effectiveness and propriety of cryptographic protocol use within the SSP-21 specification. SSP-21 is designed to use cryptographic protocols to provide (optional) encryption, authentication, and nonrepudiation, among other capabilities. The cryptographic protocols to be used reflect current industry standards; future versions of SSP-21 will use other advanced technologies to provide a subset of security services.

  7. Routing protocols in wireless sensor networks.

    Science.gov (United States)

    Villalba, Luis Javier García; Orozco, Ana Lucila Sandoval; Cabrera, Alicia Triviño; Abbas, Cláudia Jacy Barenco

    2009-01-01

    The applications of wireless sensor networks comprise a wide variety of scenarios. In most of them, the network is composed of a significant number of nodes deployed in an extensive area in which not all nodes are directly connected. Then, the data exchange is supported by multihop communications. Routing protocols are in charge of discovering and maintaining the routes in the network. However, the appropriateness of a particular routing protocol mainly depends on the capabilities of the nodes and on the application requirements. This paper presents a review of the main routing protocols proposed for wireless sensor networks. Additionally, the paper includes the efforts carried out by Spanish universities on developing optimization techniques in the area of routing protocols for wireless sensor networks.

  8. Protocol Coordinator | Center for Cancer Research

    Science.gov (United States)

    PROGRAM DESCRIPTION Within the Leidos Biomedical Research Inc.’s Clinical Research Directorate, the Clinical Monitoring Research Program (CMRP) provides high-quality comprehensive and strategic operational support to the high-profile domestic and international clinical research initiatives of the National Cancer Institute (NCI), National Institute of Allergy and Infectious Diseases (NIAID), Clinical Center (CC), National Institute of Heart, Lung and Blood Institute (NHLBI), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Center for Advancing Translational Sciences (NCATS), National Institute of Neurological Disorders and Stroke (NINDS), and the National Institute of Mental Health (NIMH). Since its inception in 2001, CMRP’s ability to provide rapid responses, high-quality solutions, and to recruit and retain experts with a variety of backgrounds to meet the growing research portfolios of NCI, NIAID, CC, NHLBI, NIAMS, NCATS, NINDS, and NIMH has led to the consid erable expansion of the program and its repertoire of support services. CMRP’s support services are strategically aligned with the program’s mission to provide comprehensive, dedicated support to assist National Institutes of Health researchers in providing the highest quality of clinical research in compliance with applicable regulations and guidelines, maintaining data integrity, and protecting human subjects. For the scientific advancement of clinical research, CMRP services include comprehensive clinical trials, regulatory, pharmacovigilance, protocol navigation and development, and programmatic and project management support for facilitating the conduct of 400+ Phase I, II, and III domestic and international trials on a yearly basis. These trials investigate the prevention, diagnosis, treatment of, and therapies for cancer, influenza, HIV, and other infectious diseases and viruses such as hepatitis C, tuberculosis, malaria, and Ebola virus; heart, lung, and

  9. Saudi Arabia and CERN sign protocol

    CERN Multimedia

    2008-01-01

    On 9 May 2008, Mohammed I. Al Suwaiyel, President of the King Abdulaziz City of Science and Technology, representing the Government of Saudi Arabia, and CERN Director-General, Robert Aymar, signed a protocol to the 2006 cooperation agreement between CERN and Saudi Arabia. Members of the Saudi Arabian Government visit ATLAS.The purpose of the protocol is to define the operational framework needed to carry out various specific tasks provided for in the cooperation agreement in order to promote the development of a high energy particle physics community in Saudi Arabia and its ultimate visible participation as a member of the global CERN community. Signing the protocol, Mohammed I. Al-Suwaiyel said: "The Saudi Arabian Government has taken a number of initiatives to promote R&D in the interests of our country’s development and the advancement of science. Thanks to this protocol, Saudi scientists will be able to work towards this go...

  10. Purification of sequence-specific DNA-binding proteins by affinity chromatography.

    Science.gov (United States)

    Kerrigan, L A; Kadonaga, J T

    2001-05-01

    Affinity chromatography is a very effective and straightforward means of purifying a protein based on its sequence-specific DNA-binding properties. The affinity chromatography procedure described in this unit uses DNA containing specific recognition sites for the desired protein that has been covalently linked to a solid support. The first basic protocol describes preparation of a DNA affinity resin, including cyanogen bromide (CNBr) activation of the agarose support. An provides a method to couple DNA to commercially available CNBr-activated Sepharose, and a support protocol describes how to purify crude synthetic oligonucleotides by gel electrophoresis prior to preparation of the affinity resin. The second basic protocol outlines the affinity chromatography procedure. A second support protocol describes determination of the appropriate type and quantity of nonspecific competitor DNA that should be used in the procedure and its preparation. Parameters essential to the success of an affinity chromatography experiment are discussed in detail in the Commentary.

  11. SPION: Secure Protocols in OSI Networks

    OpenAIRE

    Ahlgren, Bengt; Lindgren, Per; Sirotkin, Teet

    1989-01-01

    SPION: Secure Protocols in OSI Networks This report describes how security services can be realized in a computer network using the protocols of the Open Systems Interconnection (OSI) reference model for communication. The report starts with defining security requirements for a "typical" local area network in a company, university or similar organization. It is assumed that the organization does not use the network for transfer of extremely sensitive information, such a...

  12. Topology Discovery Using Cisco Discovery Protocol

    OpenAIRE

    Rodriguez, Sergio R.

    2009-01-01

    In this paper we address the problem of discovering network topology in proprietary networks. Namely, we investigate topology discovery in Cisco-based networks. Cisco devices run Cisco Discovery Protocol (CDP) which holds information about these devices. We first compare properties of topologies that can be obtained from networks deploying CDP versus Spanning Tree Protocol (STP) and Management Information Base (MIB) Forwarding Database (FDB). Then we describe a method of discovering topology ...

  13. Field Monitoring Protocol. Heat Pump Water Heaters

    Energy Technology Data Exchange (ETDEWEB)

    Sparn, B. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Earle, L. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Christensen, D. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Maguire, J. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Wilson, E. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Hancock, C. E. [Mountain Energy Partnership, Longmont, CO (United States)

    2013-02-01

    This document provides a standard field monitoring protocol for evaluating the installed performance of Heat Pump Water Heaters in residential buildings. The report is organized to be consistent with the chronology of field test planning and execution. Research questions are identified first, followed by a discussion of analysis methods, and then the details of measuring the required information are laid out. A field validation of the protocol at a house near the NREL campus is included for reference.

  14. Field Monitoring Protocol: Heat Pump Water Heaters

    Energy Technology Data Exchange (ETDEWEB)

    Sparn, B.; Earle, L.; Christensen, D.; Maguire, J.; Wilson, E.; Hancock, E.

    2013-02-01

    This document provides a standard field monitoring protocol for evaluating the installed performance of Heat Pump Water Heaters in residential buildings. The report is organized to be consistent with the chronology of field test planning and execution. Research questions are identified first, followed by a discussion of analysis methods, and then the details of measuring the required information are laid out. A field validation of the protocol at a house near the NREL campus is included for reference.

  15. Protocol for communications in potentially noisy environments

    Energy Technology Data Exchange (ETDEWEB)

    Boyd, Gerlad M.; Farrow, Jeffrey

    2016-02-09

    A communications protocol that is designed for transmission of data in networks that are subjected to harsh conditions is described herein. A network includes a plurality of devices, where the devices comprise respective nodes. The nodes are in communication with one another by way of a central network hub. The protocol causes the nodes to transmit data over a network bus at different data rates depending upon whether the nodes are operating normally or an arbitration procedure has been invoked.

  16. Robust Routing Protocol For Digital Messages

    Science.gov (United States)

    Marvit, Maclen

    1994-01-01

    Refinement of ditigal-message-routing protocol increases fault tolerance of polled networks. AbNET-3 is latest of generic AbNET protocols for transmission of messages among computing nodes. AbNET concept described in "Multiple-Ring Digital Communication Network" (NPO-18133). Specifically aimed at increasing fault tolerance of network in broadcast mode, in which one node broadcasts message to and receives responses from all other nodes. Communication in network of computers maintained even when links fail.

  17. A Review of Fair Exchange Protocols

    OpenAIRE

    Abdullah AlOtaibi; Hamza Aldabbas

    2012-01-01

    Recently, the Internet has become an essential business platform, aiding trading, distribution and sales between organisations, consumers and even between consumers themselves. This technology revolution has brought e-commerce to an entirely new level, which therefore has raised some new security issues. Security protocols in e-commerce are required to manage the transactions between buyers and sellers. In order to engage customers in e-commerce, these protocols should be well formulated and ...

  18. Network Coding Protocols for Smart Grid Communications

    DEFF Research Database (Denmark)

    Prior, Rui; Roetter, Daniel Enrique Lucani; Phulpin, Yannick

    2014-01-01

    but then switches to a denser coding structure towards the end. Our systematic mechanism maintains the sparse structure during the recombination of packets at the intermediate nodes. The performance of our protocol is compared by means of simulations of IEEE reference grids against standard master-slave protocols...... used in real systems. Our results show that network coding achieves 100% reliability, even for hostile network conditions, while gathering data 10 times faster than standard master-slave schemes....

  19. Hybrid Long-Distance Entanglement Distribution Protocol

    DEFF Research Database (Denmark)

    Brask, J.B.; Rigas, I.; Polzik, E.S.

    2010-01-01

    We propose a hybrid (continuous-discrete variable) quantum repeater protocol for long-distance entanglement distribution. Starting from states created by single-photon detection, we show how entangled coherent state superpositions can be generated by means of homodyne detection. We show that near......-deterministic entanglement swapping with such states is possible using only linear optics and homodyne detectors, and we evaluate the performance of our protocol combining these elements....

  20. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    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 nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  1. High Interlaboratory Reprocucibility of DNA Sequence-based Typing of Bacteria in a Multicenter Study

    DEFF Research Database (Denmark)

    Sousa, MA de; Boye, Kit; Lencastre, H de

    2006-01-01

    Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without...... extensive harmonization of protocols for 30 blind-coded S. aureus DNA samples sent to 10 laboratories. Specialized software for automated sequence analysis ensured a common typing nomenclature.......Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without...

  2. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  3. Energy Consumption Research of Mobile Data Collection Protocol for Underwater Nodes Using an USV

    Directory of Open Access Journals (Sweden)

    Zhichao Lv

    2018-04-01

    Full Text Available The Unmanned Surface Vehicle (USV integrated with an acoustic modem is a novel mobile vehicle for data collection, which has an advantage in terms of mobility, efficiency, and collection cost. In the scenario of data collection, the USV is controlled autonomously along the planning trajectory and the data of underwater nodes are dynamically collected. In order to improve the efficiency of data collection and extend the life of the underwater nodes, a mobile data collection protocol for underwater nodes using the USV was proposed. In the protocol, the stop-and-wait ARQ transmission mechanism is adopted, where the duty cycle is designed considering the ratio between the sleep mode and the detection mode, and the transmission ratio is defined by the duty cycle, wake-up signal cycles, and USV’s speed. According to protocol, the evaluation index for energy consumption is constructed based on the duty cycle and the transmission ratio. The energy consumption of the protocol is simulated and analyzed using the mobile communication experiment data of USV, taking into consideration USV’s speed, data sequence length, and duty cycle. Optimized protocol parameters are identified, which in turn denotes the proposed protocol’s feasibility and effectiveness.

  4. A new communication protocol family for a distributed spacecraft control system

    Science.gov (United States)

    Baldi, Andrea; Pace, Marco

    1994-01-01

    In this paper we describe the concepts behind and architecture of a communication protocol family, which was designed to fulfill the communication requirements of ESOC's new distributed spacecraft control system SCOS 2. A distributed spacecraft control system needs a data delivery subsystem to be used for telemetry (TLM) distribution, telecommand (TLC) dispatch and inter-application communication, characterized by the following properties: reliability, so that any operational workstation is guaranteed to receive the data it needs to accomplish its role; efficiency, so that the telemetry distribution, even for missions with high telemetry rates, does not cause a degradation of the overall control system performance; scalability, so that the network is not the bottleneck both in terms of bandwidth and reconfiguration; flexibility, so that it can be efficiently used in many different situations. The new protocol family which satisfies the above requirements is built on top of widely used communication protocols (UDP and TCP), provides reliable point-to-point and broadcast communication (UDP+) and is implemented in C++. Reliability is achieved using a retransmission mechanism based on a sequence numbering scheme. Such a scheme allows to have cost-effective performances compared to the traditional protocols, because retransmission is only triggered by applications which explicitly need reliability. This flexibility enables applications with different profiles to take advantage of the available protocols, so that the best rate between sped and reliability can be achieved case by case.

  5. Time- and Cost-Efficient Identification of T-DNA Insertion Sites through Targeted Genomic Sequencing

    Science.gov (United States)

    Lepage, Étienne; Zampini, Éric; Boyle, Brian; Brisson, Normand

    2013-01-01

    Forward genetic screens enable the unbiased identification of genes involved in biological processes. In Arabidopsis, several mutant collections are publicly available, which greatly facilitates such practice. Most of these collections were generated by agrotransformation of a T-DNA at random sites in the plant genome. However, precise mapping of T-DNA insertion sites in mutants isolated from such screens is a laborious and time-consuming task. Here we report a simple, low-cost and time efficient approach to precisely map T-DNA insertions simultaneously in many different mutants. By combining sequence capture, next-generation sequencing and 2D-PCR pooling, we developed a new method that allowed the rapid localization of T-DNA insertion sites in 55 out of 64 mutant plants isolated in a screen for gyrase inhibition hypersensitivity. PMID:23951038

  6. Network-topology-adaptive quantum conference protocols

    International Nuclear Information System (INIS)

    Zhang Sheng; Wang Jian; Tang Chao-Jing; Zhang Quan

    2011-01-01

    As an important application of the quantum network communication, quantum multiparty conference has made multiparty secret communication possible. Previous quantum multiparty conference schemes based on quantum data encryption are insensitive to network topology. However, the topology of the quantum network significantly affects the communication efficiency, e.g., parallel transmission in a channel with limited bandwidth. We have proposed two distinctive protocols, which work in two basic network topologies with efficiency higher than the existing ones. We first present a protocol which works in the reticulate network using Greeberger—Horne—Zeilinger states and entanglement swapping. Another protocol, based on quantum multicasting with quantum data compression, which can improve the efficiency of the network, works in the star-like network. The security of our protocols is guaranteed by quantum key distribution and one-time-pad encryption. In general, the two protocols can be applied to any quantum network where the topology can be equivalently transformed to one of the two structures we propose in our protocols. (general)

  7. Content evidence of a spectrographic analysis protocol

    Directory of Open Access Journals (Sweden)

    Leonardo Wanderley Lopes

    Full Text Available ABSTRACT Objective: to verify the content evidence of a spectrographic analysis protocol. Methods: a methodological study in which five speech therapists who assessed the clarity and the relevance of the protocol were selected. The Content Validity Index (CVI was used to investigate the level of agreement among judges regarding overall aspects, items and domains of the protocol. Results: most judges considered the overall aspects of the protocol as comprehensive. As for clarity, 17 items showed an excellent content validity (CVI ≥ 0.78, three showed a good content validity (0.60 ≤ CVI ≤ 0.77 and two items were judged as poor (CVI ≤ 0.59. As for relevance, 19 items obtained an excellent content validity (CVI ≥ 0.78 and three had a good content validity (0.60 ≤ CVI ≤ 0.77. The judges suggested adding items related to vocal signal normality in all domains. After the analysis, 18 items required no reformulation, five items were added, three were reformulated and one was excluded. Conclusion: the proposed protocol was regarded as a comprehensive one. The items presented a good to excellent content validity as for clarity and relevance. After this validation step, the protocol ended up presenting 25 items distributed into five domains.

  8. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  9. 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.

  10. An improved protocol for efficient transformation and regeneration of diverse indica rice cultivars

    Directory of Open Access Journals (Sweden)

    Sahoo Khirod K

    2011-12-01

    Full Text Available Abstract Background Rice genome sequencing projects have generated remarkable amount of information about genes and genome architecture having tremendous potential to be utilized in both basic and applied research. Success in transgenics is paving the way for preparing a road map of functional genomics which is expected to correlate action of a gene to a trait in cellular and organismal context. However, the lack of a simple and efficient method for transformation and regeneration is a major constraint for such studies in this important cereal crop. Results In the present study, we have developed an easy, rapid and highly efficient transformation and regeneration protocol using mature seeds as explants and found its successful applicability to a choice of elite indica rice genotypes. We have optimized various steps of transformation and standardized different components of the regeneration medium including growth hormones and the gelling agent. The modified regeneration medium triggers production of large number of shoots from smaller number of calli and promotes their faster growth, hence significantly advantageous over the existing protocols where the regeneration step requires maximum time. Using this protocol, significantly higher transformation efficiency (up to 46% and regeneration frequency (up to 92% for the untransformed calli and 59% for the transformed calli were achieved for the four tested cultivars. We have used this protocol to produce hundreds of independent transgenic lines of different indica rice genotypes. Upon maturity, these transgenic lines were fertile thereby indicating that faster regeneration during tissue culture did not affect their reproductive potential. Conclusions This speedy, yet less labor-intensive, protocol overcomes major limitations associated with genetic manipulation in rice. Moreover, our protocol uses mature seeds as the explant, which can easily be obtained in quantity throughout the year and kept

  11. Method-centered digital communities on protocols.io for fast-paced scientific innovation.

    Science.gov (United States)

    Kindler, Lori; Stoliartchouk, Alexei; Teytelman, Leonid; Hurwitz, Bonnie L

    2016-01-01

    The Internet has enabled online social interaction for scientists beyond physical meetings and conferences. Yet despite these innovations in communication, dissemination of methods is often relegated to just academic publishing. Further, these methods remain static, with subsequent advances published elsewhere and unlinked. For communities undergoing fast-paced innovation, researchers need new capabilities to share, obtain feedback, and publish methods at the forefront of scientific development. For example, a renaissance in virology is now underway given the new metagenomic methods to sequence viral DNA directly from an environment. Metagenomics makes it possible to "see" natural viral communities that could not be previously studied through culturing methods. Yet, the knowledge of specialized techniques for the production and analysis of viral metagenomes remains in a subset of labs.  This problem is common to any community using and developing emerging technologies and techniques. We developed new capabilities to create virtual communities in protocols.io, an open access platform, for disseminating protocols and knowledge at the forefront of scientific development. To demonstrate these capabilities, we present a virology community forum called VERVENet. These new features allow virology researchers to share protocols and their annotations and optimizations, connect with the broader virtual community to share knowledge, job postings, conference announcements through a common online forum, and discover the current literature through personalized recommendations to promote discussion of cutting edge research. Virtual communities in protocols.io enhance a researcher's ability to: discuss and share protocols, connect with fellow community members, and learn about new and innovative research in the field.  The web-based software for developing virtual communities is free to use on protocols.io. Data are available through public APIs at protocols.io.

  12. From human monocytes to genome-wide binding sites--a protocol for small amounts of blood: monocyte isolation/ChIP-protocol/library amplification/genome wide computational data analysis.

    Directory of Open Access Journals (Sweden)

    Sebastian Weiterer

    Full Text Available Chromatin immunoprecipitation in combination with a genome-wide analysis via high-throughput sequencing is the state of the art method to gain genome-wide representation of histone modification or transcription factor binding profiles. However, chromatin immunoprecipitation analysis in the context of human experimental samples is limited, especially in the case of blood cells. The typically extremely low yields of precipitated DNA are usually not compatible with library amplification for next generation sequencing. We developed a highly reproducible protocol to present a guideline from the first step of isolating monocytes from a blood sample to analyse the distribution of histone modifications in a genome-wide manner.The protocol describes the whole work flow from isolating monocytes from human blood samples followed by a high-sensitivity and small-scale chromatin immunoprecipitation assay with guidance for generating libraries compatible with next generation sequencing from small amounts of immunoprecipitated DNA.

  13. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  14. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  15. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  16. Simulation and Evaluation of CTP and Secure-CTP Protocols

    Directory of Open Access Journals (Sweden)

    P. Pecho

    2010-04-01

    Full Text Available The paper discusses characteristics and qualities of two routing protocols – Collection Tree Protocol and its secure modification. The original protocol, as well as other protocols for wireless sensors, solves only problems of ra- dio communication and limited resources. Our design of the secure protocol tries to solve also the essential security ob- jectives. For the evaluation of properties of our protocol in large networks, a TOSSIM simulator was used. Our effort was to show the influence of the modification of the routing protocol to its behavior and quality of routing trees. We have proved that adding security into protocol design does not necessarily mean higher demands for data transfer, power consumption or worse protocol efficiency. In the paper, we manifest that security in the protocol may be achieved with low cost and may offer similar performance as the original protocol.

  17. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

  18. HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

    Science.gov (United States)

    Wan, Shixiang; Zou, Quan

    2017-01-01

    Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

  19. Epidemic Protocols for Pervasive Computing Systems - Moving Focus from Architecture to Protocol

    DEFF Research Database (Denmark)

    Mogensen, Martin

    2009-01-01

    Pervasive computing systems are inherently running on unstable networks and devices, subject to constant topology changes, network failures, and high churn. For this reason, pervasive computing infrastructures need to handle these issues as part of their design. This is, however, not feasible...... epidemic protocols as distribution mechanism for pervasive systems. The nature of epidemic protocols make them easy to implement, easy to deploy, and resilient to failures. By using epidemic protocols, it is possible to mitigate a wide range of the potential issues on the protocol layer. The result...... is lower complexity of building pervasive systems and higher robustness....

  20. An Abbreviated Protocol for High-risk Screening Breast Magnetic Resonance Imaging: Impact on Performance Metrics and BI-RADS Assessment.

    Science.gov (United States)

    Panigrahi, Babita; Mullen, Lisa; Falomo, Eniola; Panigrahi, Benita; Harvey, Susan

    2017-09-01

    Annual breast magnetic resonance imaging (MRI) is recommended to screen high-risk populations for breast cancer, although costs are significant. This study assesses the performance of an abbreviated MRI protocol as a resource-efficient approach for screening patients at high-risk of breast cancer, and assesses whether the abbreviated protocol alters the assigned Breast Imaging Reporting and Data System (BI-RADS) category. This is a prospective paired cohort study performed in an academic ambulatory setting. MRI images of women at high risk of breast cancer were reviewed using an abbreviated MRI protocol, followed by an immediate review of additional sequences included in a full diagnostic protocol. BI-RADS assessments, including all changes and interpretation times, were recorded for both the abbreviated and full protocol reviews. Cancer detection rate, positive predictive value 3 (PPV3), sensitivity, and specificity were calculated. A total of 1052 MRI cases were reviewed. The cancer detection rate was 13.3 per 1000 with a PPV3 of 30.4% based on the full protocol. Review of sequences included in the full protocol resulted in a change in the final BI-RADS assessments in 3.4% of the cases, the majority of which did not change clinical management with respect to biopsy. The sensitivity and specificity of the abbreviated and full protocols were not significantly different. This pilot study of an abbreviated MRI protocol demonstrates effective performance in cancer detection. BI-RADS assessments were rarely altered with the additional information afforded by the full protocol. The abbreviated protocol holds promise for resource-efficient breast cancer screening in high-risk women. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

  1. Sequencing of hepatitis C virus for detection of resistance to direct‐acting antiviral therapy: A systematic review

    Science.gov (United States)

    Grebely, Jason; Eltahla, Auda A.; Reeves, Jacqueline D.; Howe, Anita Y.M.; Miller, Veronica; Ceccherini‐Silberstein, Francesca; Bull, Rowena A.; Douglas, Mark W.; Dore, Gregory J.; Harrington, Patrick; Lloyd, Andrew R.; Jacka, Brendan; Matthews, Gail V.; Wang, Gary P.; Pawlotsky, Jean‐Michel; Feld, Jordan J.; Schinkel, Janke; Garcia, Federico; Lennerstrand, Johan; Applegate, Tanya L.

    2017-01-01

    The significance of the clinical impact of direct‐acting antiviral (DAA) resistance‐associated substitutions (RASs) in hepatitis C virus (HCV) on treatment failure is unclear. No standardized methods or guidelines for detection of DAA RASs in HCV exist. To facilitate further evaluations of the impact of DAA RASs in HCV, we conducted a systematic review of RAS sequencing protocols, compiled a comprehensive public library of sequencing primers, and provided expert guidance on the most appropriate methods to screen and identify RASs. The development of standardized RAS sequencing protocols is complicated due to a high genetic variability and the need for genotype‐ and subtype‐specific protocols for multiple regions. We have identified several limitations of the available methods and have highlighted areas requiring further research and development. The development, validation, and sharing of standardized methods for all genotypes and subtypes should be a priority. (Hepatology Communications 2017;1:379–390) PMID:29404466

  2. RNA isolation for small RNA Next-Generation Sequencing from acellular biofluids.

    Science.gov (United States)

    Burgos, Kasandra L; Van Keuren-Jensen, Kendall

    2014-01-01

    There are a number of considerations when choosing protocols both upstream and downstream of Next-Generation Sequencing experiments. On the front end, purification methods, additives, and residuum can often inhibit the sensitive chemistries by which sequencing-by-synthesis is performed. On the back end, data handling, analysis software packages, and pipelines can also impact sequencing outcomes. The current chapter will describe stepwise how acellular biofluid samples are prepared for small RNA sequencing. With regard to purification methods, we found that small RNA yield can be improved considerably by following the total RNA isolation protocol included with Ambion's mirVana PARIS Kit but modifying the organic extraction step. Specifically, after transferring the upper aqueous phase to a fresh tube, water is added to the residual material (interphase and lower organic layer) and again phase-separated. In contrast, all the protocols provided with the commercially available kits at the time of this chapter publication require only one organic extraction. This simple yet, as it turns out, quite useful modification allows access to previously inaccessible material. Potential benefits from these changes are a more comprehensive sample profiling of small RNA, as well as wider access to small volume samples, such as is typically available for acellular biofluids, which now can be prepared for small RNA sequencing on the Illumina platform.

  3. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  4. Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform.

    Science.gov (United States)

    Vanni, Irene; Coco, Simona; Truini, Anna; Rusmini, Marta; Dal Bello, Maria Giovanna; Alama, Angela; Banelli, Barbara; Mora, Marco; Rijavec, Erika; Barletta, Giulia; Genova, Carlo; Biello, Federica; Maggioni, Claudia; Grossi, Francesco

    2015-12-03

    Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.

  5. Whole-Genome Sequencing: Automated, Indexed Library Preparation.

    Science.gov (United States)

    Mardis, Elaine; McCombie, W Richard

    2017-03-01

    This protocol describes an automated procedure for constructing an indexed Illumina DNA library. With this method, genomic DNA fragments are produced by sonication, using high-frequency acoustic energy to shear DNA. Double-stranded DNA (dsDNA) will fragment when exposed to the energy of adaptive focused acoustic shearing (AFA). The resulting DNA fragments are ligated to adaptors, amplified by polymer chain reaction (PCR), and subjected to size selection using magnetic beads. The product is suitable for use as template in whole-genome sequencing. © 2017 Cold Spring Harbor Laboratory Press.

  6. Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides

    Directory of Open Access Journals (Sweden)

    Ho Antoine

    2011-12-01

    Full Text Available Abstract Background Sequencing-by-ligation (SBL is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons. SBL has the advantage of being easy to implement and accessible to all because it can be performed with off-the-shelf reagents. However, SBL has the limitation of very short read lengths. Results To overcome the read length limitation, research groups have developed complex library preparation processes, which can be time-consuming, difficult, and result in low complexity libraries. Herein we describe a variation on traditional SBL protocols that extends the number of sequential bases that can be sequenced by using Endonuclease V to nick a query primer, thus leaving a ligatable end extended into the unknown sequence for further SBL cycles. To demonstrate the protocol, we constructed a known DNA sequence and utilized our SBL variation, cyclic SBL (cSBL, to resequence this region. Using our method, we were able to read thirteen contiguous bases in the 3' - 5' direction. Conclusions Combining this read length with sequencing in the 5' - 3' direction would allow a read length of over twenty bases on a single tage. Implementing mate-paired tags and this SBL variation could enable > 95% coverage of the genome.

  7. Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms.

    Science.gov (United States)

    Recknagel, Hans; Jacobs, Arne; Herzyk, Pawel; Elmer, Kathryn R

    2015-11-01

    Research in evolutionary biology involving nonmodel organisms is rapidly shifting from using traditional molecular markers such as mtDNA and microsatellites to higher throughput SNP genotyping methodologies to address questions in population genetics, phylogenetics and genetic mapping. Restriction site associated DNA sequencing (RAD sequencing or RADseq) has become an established method for SNP genotyping on Illumina sequencing platforms. Here, we developed a protocol and adapters for double-digest RAD sequencing for Ion Torrent (Life Technologies; Ion Proton, Ion PGM) semiconductor sequencing. We sequenced thirteen genomic libraries of three different nonmodel vertebrate species on Ion Proton with PI chips: Arctic charr Salvelinus alpinus, European whitefish Coregonus lavaretus and common lizard Zootoca vivipara. This resulted in ~962 million single-end reads overall and a mean of ~74 million reads per library. We filtered the genomic data using Stacks, a bioinformatic tool to process RAD sequencing data. On average, we obtained ~11,000 polymorphic loci per library of 6-30 individuals. We validate our new method by technical and biological replication, by reconstructing phylogenetic relationships, and using a hybrid genetic cross to track genomic variants. Finally, we discuss the differences between using the different sequencing platforms in the context of RAD sequencing, assessing possible advantages and disadvantages. We show that our protocol can be used for Ion semiconductor sequencing platforms for the rapid and cost-effective generation of variable and reproducible genetic markers. © 2015 John Wiley & Sons Ltd.

  8. Protocol for Communication Networking for Formation Flying

    Science.gov (United States)

    Jennings, Esther; Okino, Clayton; Gao, Jay; Clare, Loren

    2009-01-01

    An application-layer protocol and a network architecture have been proposed for data communications among multiple autonomous spacecraft that are required to fly in a precise formation in order to perform scientific observations. The protocol could also be applied to other autonomous vehicles operating in formation, including robotic aircraft, robotic land vehicles, and robotic underwater vehicles. A group of spacecraft or other vehicles to which the protocol applies could be characterized as a precision-formation- flying (PFF) network, and each vehicle could be characterized as a node in the PFF network. In order to support precise formation flying, it would be necessary to establish a corresponding communication network, through which the vehicles could exchange position and orientation data and formation-control commands. The communication network must enable communication during early phases of a mission, when little positional knowledge is available. Particularly during early mission phases, the distances among vehicles may be so large that communication could be achieved only by relaying across multiple links. The large distances and need for omnidirectional coverage would limit communication links to operation at low bandwidth during these mission phases. Once the vehicles were in formation and distances were shorter, the communication network would be required to provide high-bandwidth, low-jitter service to support tight formation-control loops. The proposed protocol and architecture, intended to satisfy the aforementioned and other requirements, are based on a standard layered-reference-model concept. The proposed application protocol would be used in conjunction with conventional network, data-link, and physical-layer protocols. The proposed protocol includes the ubiquitous Institute of Electrical and Electronics Engineers (IEEE) 802.11 medium access control (MAC) protocol to be used in the datalink layer. In addition to its widespread and proven use in

  9. Diesel Mechanics: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a diesel mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  10. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    c Indian Academy of Sciences. Farey sequences and resistor networks. SAMEEN AHMED KHAN. Department of Engineering, Salalah College of Technology, Post Box No. 608, ..... 2.61n, strictly fixed by the Farey sequence method. For n ≥ 7, all the three basic sets have odd number of elements since A(n) is odd for n ≥ 6.

  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. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  13. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  14. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Combinatorial representations of token sequences

    NARCIS (Netherlands)

    Elzinga, C.H.

    2005-01-01

    This paper presents new representations of token sequences, with and without associated quantities, in Euclidean space. The representations are free of assumptions about the nature of the sequences or the processes that generate them. Algorithms and applications from the domains of structured

  16. A criterion for regular sequences

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Note that every sequence is a strongly regular as well as regular sequence on the zero ... following statement given in Chapter II, 6.1 of [4]. .... for financial support. The authors sincerely thank Harmut Wiebe for stimulating discus- sions. References. [1] Bruns W and Herzog J, Cohen–Macaulay rings (Cambridge Studies in ...

  17. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  18. 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

  19. MiSeq: A Next Generation Sequencing Platform for Genomic Analysis.

    Science.gov (United States)

    Ravi, Rupesh Kanchi; Walton, Kendra; Khosroheidari, Mahdieh

    2018-01-01

    MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.

  20. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  1. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  2. Poisson process approximation for sequence repeats, and sequencing by hybridization.

    Science.gov (United States)

    Arratia, R; Martin, D; Reinert, G; Waterman, M S

    1996-01-01

    Sequencing by hybridization is a tool to determine a DNA sequence from the unordered list of all l-tuples contained in this sequence; typical numbers for l are l = 8, 10, 12. For theoretical purposes we assume that the multiset of all l-tuples is known. This multiset determines the DNA sequence uniquely if none of the so-called Ukkonen transformations are possible. These transformations require repeats of (l-1)-tuples in the sequence, with these repeats occurring in certain spatial patterns. We model DNA as an i.i.d. sequence. We first prove Poisson process approximations for the process of indicators of all leftmost long repeats allowing self-overlap and for the process of indicators of all left-most long repeats without self-overlap. Using the Chen-Stein method, we get bounds on the error of these approximations. As a corollary, we approximate the distribution of longest repeats. In the second step we analyze the spatial patterns of the repeats. Finally we combine these two steps to prove an approximation for the probability that a random sequence is uniquely recoverable from its list of l-tuples. For all our results we give some numerical examples including error bounds.

  3. Global Run-On Sequencing (GRO-Seq).

    Science.gov (United States)

    Gardini, Alessandro

    2017-01-01

    Transcription occurring at gene loci results in accumulation of mature RNA molecules (i.e., mRNAs) that can be easily assayed by RT-PCR or RNA sequencing. However, the steady-state level of RNA does not accurately mirror transcriptional activity per se. In fact, RNA stability plays a major role in determining the relative abundance of any given RNA molecule. Here, I describe a protocol of Nuclear Run-On assay coupled to deep sequencing to assess real-time transcription from engaged RNA polymerase. Mapping nascent transcripts at the genome-wide scale provides a reliable measure of transcriptional activity in mammalian cells and delivers a high-resolution map of coding and noncoding transcripts that is especially useful for annotation and quantification of short-lived RNA molecules.

  4. EEG changes during sequences of visual and kinesthetic motor imagery.

    Science.gov (United States)

    Stecklow, Marcus Vinicius; Infantosi, Antonio Fernando Catelli; Cagy, Maurício

    2010-08-01

    The evoked cerebral electric response when sequences of complex motor imagery (MI) task are executed several times is still unclear. This work aims at investigating the existence of habituation in the cortical response, more specifically in the alpha band peak of parietal and occipital areas (10-20 international system electroencephalogram, EEG, protocol). The EEG signals were acquired during sequences of MI of volleyball spike movement in kinesthetic and visual modalities and also at control condition. Thirty right-handed male subjects (18 to 40 years) were assigned to either an 'athlete' or a 'non-athlete' group, both containing 15 volunteers. Paired Wilcoxon tests (with alpha=0.05) indicates that sequential MI of complex tasks promotes cortical changes, mainly in the power vicinity of the alpha peak. This finding is more pronounced along the initial trials and also for the athletes during the modality of kinesthetic motor imagery.

  5. Assessment of metagenomic assembly using simulated next generation sequencing data

    DEFF Research Database (Denmark)

    Mende, Daniel R; Waller, Alison S; Sunagawa, Shinichi

    2012-01-01

    the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition......Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators...... with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved...

  6. Differential phase-time shifting protocol for QKD (DPTS)

    DEFF Research Database (Denmark)

    Usuga Castaneda, Mario A.; Bacco, Davide; Christensen, Jesper Bjerge

    2016-01-01

    We explore the implementation of a novel protocol for fiber-based high-dimensional quantum key distribution (QKD) which improves over the traditional DPS-QKD and COW protocols.......We explore the implementation of a novel protocol for fiber-based high-dimensional quantum key distribution (QKD) which improves over the traditional DPS-QKD and COW protocols....

  7. The iceLogo web server and SOAP service for determining protein consensus sequences.

    Science.gov (United States)

    Maddelein, Davy; Colaert, Niklaas; Buchanan, Iain; Hulstaert, Niels; Gevaert, Kris; Martens, Lennart

    2015-07-01

    The iceLogo web server and SOAP service implement the previously published iceLogo algorithm. iceLogo builds on probability theory to visualize protein consensus sequences in a format resembling sequence logos. Peptide sequences are compared against a reference sequence set that can be tailored to the studied system and the used protocol. As such, not only over- but also underrepresented residues can be visualized in a statistically sound manner, which further allows the user to easily analyse and interpret conserved sequence patterns in proteins. The web application and SOAP service can be found free and open to all users without the need for a login on http://iomics.ugent.be/icelogoserver/main.html. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing.

    Science.gov (United States)

    Chatterjee, Aniruddha; Rodger, Euan J; Stockwell, Peter A; Le Mée, Gwenn; Morison, Ian M

    2017-01-01

    Reduced representation bisulfite sequencing (RRBS) is an effective technique for profiling genome-wide DNA methylation patterns in eukaryotes. RRBS couples size selection, bisulfite conversion, and second-generation sequencing to enrich for CpG-dense regions of the genome. The progressive improvement of second-generation sequencing technologies and reduction in cost provided an opportunity to examine the DNA methylation patterns of multiple genomes. Here, we describe a protocol for sequencing multiple RRBS libraries in a single sequencing reaction to generate base-resolution methylomes. Furthermore, we provide a brief guideline for base-calling and data analysis of multiplexed RRBS libraries. These strategies will be useful to perform large-scale, genome-wide DNA methylation analysis.

  9. The challenges of additional protocol implementation

    International Nuclear Information System (INIS)

    Renis, Therese

    2001-01-01

    Full text: The IAEA Board of Governors approved the Model Protocol Additional to Safeguards Agreements, INFCIRC/540, (referred to as the Additional Protocol) in May 1997. The Additional Protocol provides for new mechanisms that include expanded information on State's nuclear activities to be declared to the IAEA and increased physical access to locations for IAEA inspectors. The objective is to provide the basis for gaining assurance of the absence of undeclared nuclear material and activities in a State. Although the Agency conducted field trials of various aspects of implementation of the Additional Protocol, the first actual implementation experience began with the entry into force of Australia's additional protocol in December of 1997. As of late August 2001,21 states have entered into force an additional protocol and another 35 states have signed the additional protocol but not yet entered the agreement into force. Because implementation of the Additional Protocol requires new activities to be carried out by the IAEA, new procedures, guidelines and training have been developed to support these activities. As more experience is gained these documents are being refined and additional ones developed to meet unforeseen needs. In addition, evaluation and follow-up of the expanded information and the results of increased access has required the Safeguards Department to expand and adapt its procedures and mode of operation. The challenge has been in establishing sufficient measures and the necessary infrastructure for consistent application of the additional protocol in such a way that they can be adapted as needed based on Agency experience. Initial development focused on the logistical aspects of implementing these new activities. These activities include the processing, handling and review of additional protocol declarations; planning, conducting and reporting on complementary access activities; and follow-up activities arising from information review or

  10. Modelling passive margin sequence stratigraphy

    Science.gov (United States)

    Steckler, M.S.; Reynolds, D.; Coakley, B.; Swift, B.A.; Jarrard, R.D.

    1993-01-01

    We have modelled stratigraphic sequences to aid in deciphering the sedimentary response to sea-level change. Sequence geometry is found to be most sensitive to sea level, but other factors, including subsidence rate and sediment supply, can produce similar changes. Sediment loading and compaction also play a major role in generating accommodation, a factor often neglected in sequence-stratigraphic models. All of these parameters can control whether a type 1 or type 2 sequence boundary is produced. The models indicate that variations in margin characteristics produce systematic shifts in sequence boundary timing and systems tract distribution. The timing of the sequence boundary formation and systems tracts may differ by up to one-half of a sea-level cycle. Thus correlative sequence boundaries will not be synchronous. While rates of sea-level change may exceed the rate of thermal subsidence, isostasy and compaction may amplify the rate of total subsidence to several times greater than the thermal subsidence. Thus, total subsidence does not vary uniformly across the margin since it is modified by the sediment load. The amplitude of sea-level changes cannot be determined accurately without accounting for the major processes that affect sediment accumulation. Backstripping of a seismic line on the New Jersey margin is used to reconstruct continental margin geometry. The reconstructions show that the pre-existing ramp-margin geometry, rather than sea level, controls clinoform heights and slopes and sedimentary bypass. Backstripping also reveals progressive deformation of sequences due to compaction. Further work is still needed to understand quantitatively the role of sea level and the tectonic and sedimentary processes controlling sequence formation and influencing sequence architecture.

  11. Standardized North American marsh bird monitoring protocol

    Science.gov (United States)

    Conway, Courtney J.

    2011-01-01

    Little is known about the population status of many marsh-dependent birds in North America but recent efforts have focused on collecting more reliable information and estimates of population trends. As part of that effort, a standardized survey protocol was developed in 1999 that provided guidance for conducting marsh bird surveys throughout North America such that data would be consistent among locations. The original survey protocol has been revised to provide greater clarification on many issues as the number of individuals using the protocol has grown. The Standardized North American Marsh Bird Monitoring Protocol instructs surveyors to conduct an initial 5-minute passive point-count survey followed by a series of 1-minute segments during which marsh bird calls are broadcast into the marsh following a standardized approach. Surveyors are instructed to record each individual bird from the suite of 26 focal species that are present in their local area on separate lines of a datasheet and estimate the distance to each bird. Also, surveyors are required to record whether each individual bird was detected within each 1-minute subsegment of the survey. These data allow analysts to use several different approaches for estimating detection probability. The Standardized North American Marsh Bird Monitoring Protocol provides detailed instructions that explain the field methods used to monitor marsh birds in North America.

  12. A Lightweight Buyer-Seller Watermarking Protocol

    Directory of Open Access Journals (Sweden)

    Yongdong Wu

    2008-01-01

    Full Text Available The buyer-seller watermarking protocol enables a seller to successfully identify a traitor from a pirated copy, while preventing the seller from framing an innocent buyer. Based on finite field theory and the homomorphic property of public key cryptosystems such as RSA, several buyer-seller watermarking protocols (N. Memon and P. W. Wong (2001 and C.-L. Lei et al. (2004 have been proposed previously. However, those protocols require not only large computational power but also substantial network bandwidth. In this paper, we introduce a new buyer-seller protocol that overcomes those weaknesses by managing the watermarks. Compared with the earlier protocols, ours is n times faster in terms of computation, where n is the number of watermark elements, while incurring only O(1/lN times communication overhead given the finite field parameter lN. In addition, the quality of the watermarked image generated with our method is better, using the same watermark strength.

  13. Information Flow in Secret Sharing Protocols

    Directory of Open Access Journals (Sweden)

    Elham Kashefi

    2009-11-01

    Full Text Available The entangled graph states have emerged as an elegant and powerful quantum resource, indeed almost all multiparty protocols can be written in terms of graph states including measurement based quantum computation (MBQC, error correction and secret sharing amongst others. In addition they are at the forefront in terms of implementations. As such they represent an excellent opportunity to move towards integrated protocols involving many of these elements. In this paper we look at expressing and extending graph state secret sharing and MBQC in a common framework and graphical language related to flow. We do so with two main contributions. First we express in entirely graphical terms which set of players can access which information in graph state secret sharing protocols. These succinct graphical descriptions of access allow us to take known results from graph theory to make statements on the generalisation of the previous schemes to present new secret sharing protocols. Second, we give a set of necessary conditions as to when a graph with flow, i.e. capable of performing a class of unitary operations, can be extended to include vertices which can be ignored, pointless measurements, and hence considered as unauthorised players in terms of secret sharing, or error qubits in terms of fault tolerance. This offers a way to extend existing MBQC patterns to secret sharing protocols. Our characterisation of pointless measurements is believed also to be a useful tool for further integrated measurement based schemes, for example in constructing fault tolerant MBQC schemes.

  14. Decellularization of placentas: establishing a protocol

    Directory of Open Access Journals (Sweden)

    L.C.P.C. Leonel

    2017-11-01

    Full Text Available Biological biomaterials for tissue engineering purposes can be produced through tissue and/or organ decellularization. The remaining extracellular matrix (ECM must be acellular and preserve its proteins and physical features. Placentas are organs of great interest because they are discarded after birth and present large amounts of ECM. Protocols for decellularization are tissue-specific and have not been established for canine placentas yet. This study aimed at analyzing a favorable method for decellularization of maternal and fetal portions of canine placentas. Canine placentas were subjected to ten preliminary tests to analyze the efficacy of parameters such as the type of detergents, freezing temperatures and perfusion. Two protocols were chosen for further analyses using histology, scanning electron microscopy, immunofluorescence and DNA quantification. Sodium dodecyl sulfate (SDS was the most effective detergent for cell removal. Freezing placentas before decellularization required longer periods of incubation in different detergents. Both perfusion and immersion methods were capable of removing cells. Placentas decellularized using Protocol I (1% SDS, 5 mM EDTA, 50 mM TRIS, and 0.5% antibiotic preserved the ECM structure better, but Protocol I was less efficient to remove cells and DNA content from the ECM than Protocol II (1% SDS, 5 mM EDTA, 0.05% trypsin, and 0.5% antibiotic.

  15. Supporting Adaptation of Wireless Communication Protocols

    Directory of Open Access Journals (Sweden)

    LACHHMAN DAS DHOMEJA

    2016-10-01

    Full Text Available Pervasive devices such as mobile phones and PDAs (Personal Digital Assistants come with different wireless communication capabilities, for example, WiFi (Wireless Fidelity, Bluetooth, IrDA (Infrared, etc. In order for pervasive devices to interact with each other, they need to have matching (alike communication capabilities, otherwise such heterogeneous devices would not be able to interact with each other. In this paper we address this issue and propose a system that makes devices with heterogeneous wireless communication capabilities communicate with each other. The proposed system supports adaptation of wireless communication protocols through a proxy, which sits between a client and a server, and supports adaptation of wireless communication protocols. Its functionality involves intercepting a request made by a client with a different wireless communication capability (e.g. Bluetooth from what the server has (e.g. WiFi, connecting to the server and then sending results back to the client. We have tested the system by implementing a messaging service application and running it on the system. The proxy supports all Bluetooth protocols, i.e. OBEX (Object Exchange, L2CAP (Logical Link Control and Adaptation Protocol, RFCOM (Radio Frequency Communication and WiFi protocol and can run on (J2MW (Java 2 Micro Edition enabled mobile phones which support both Bluetooth and WiFi capabilities

  16. Controlled Delegation Protocol in Mobile RFID Networks

    Directory of Open Access Journals (Sweden)

    Yang MingHour

    2010-01-01

    Full Text Available To achieve off-line delegation for mobile readers, we propose a delegation protocol for mobile RFID allowing its readers access to specific tags through back-end server. That is to say, reader-tag mutual authentication can be performed without readers being connected to back-end server. Readers are also allowed off-line access to tags' data. Compared with other delegation protocols, our scheme uniquely enables back-end server to limit each reader's reading times during delegation. Even in a multireader situation, our protocol can limit reading times and reading time periods for each of them and therefore makes back-end server's delegation more flexible. Besides, our protocol can prevent authorized readers from transferring their authority to the unauthorized, declining invalid access to tags. Our scheme is proved viable and secure with GNY logic; it is against certain security threats, such as replay attacks, denial of service (DoS attacks, Man-in-the-Middle attacks, counterfeit tags, and breaches of location and data privacy. Also, the performance analysis of our protocol proves that current tags can afford the computation load required in this scheme.

  17. Supporting Adaptation of Wireless Communication Protocols

    International Nuclear Information System (INIS)

    Dhomeja, L.D.; Soomro, I.A.; Malkani, Y.A.

    2016-01-01

    Pervasive devices such as mobile phones and PDAs (Personal Digital Assistants) come with different wireless communication capabilities, for example, WiFi (Wireless Fidelity), Bluetooth, IrDA (Infrared), etc. In order for pervasive devices to interact with each other, they need to have matching (alike) communication capabilities, otherwise such heterogeneous devices would not be able to interact with each other. In this paper we address this issue and propose a system that makes devices with heterogeneous wireless communication capabilities communicate with each other. The proposed system supports adaptation of wireless communication protocols through a proxy, which sits between a client and a server, and supports adaptation of wireless communication protocols. Its functionality involves intercepting a request made by a client with a different wireless communication capability (e.g. Bluetooth) from what the server has (e.g. WiFi), connecting to the server and then sending results back to the client. We have tested the system by implementing a messaging service application and running it on the system. The proxy supports all Bluetooth protocols, i.e. OBEX (Object Exchange), L2CAP (Logical Link Control and Adaptation Protocol), RFCOM (Radio Frequency Communication) and WiFi protocol and can run on (J2MW (Java 2 Micro Edition) enabled mobile phones which support both Bluetooth and WiFi capabilities. (author)

  18. Evaluation of counterfactuality in counterfactual communication protocols

    Science.gov (United States)

    Arvidsson-Shukur, D. R. M.; Barnes, C. H. W.; Gottfries, A. N. O.

    2017-12-01

    We provide an in-depth investigation of parameter estimation in nested Mach-Zehnder interferometers (NMZIs) using two information measures: the Fisher information and the Shannon mutual information. Protocols for counterfactual communication have, so far, been based on two different definitions of counterfactuality. In particular, some schemes have been based on NMZI devices, and have recently been subject to criticism. We provide a methodology for evaluating the counterfactuality of these protocols, based on an information-theoretical framework. More specifically, we make the assumption that any realistic quantum channel in MZI structures will have some weak uncontrolled interaction. We then use the Fisher information of this interaction to measure counterfactual violations. The measure is used to evaluate the suggested counterfactual communication protocol of H. Salih et al. [Phys. Rev. Lett. 110, 170502 (2013), 10.1103/PhysRevLett.110.170502]. The protocol of D. R. M. Arvidsson-Shukur and C. H. W. Barnes [Phys. Rev. A 94, 062303 (2016), 10.1103/PhysRevA.94.062303], based on a different definition, is evaluated with a probability measure. Our results show that the definition of Arvidsson-Shukur and Barnes is satisfied by their scheme, while that of Salih et al. is only satisfied by perfect quantum channels. For realistic devices the latter protocol does not achieve its objective.

  19. Two Cheers for the Trafficking Protocol

    Directory of Open Access Journals (Sweden)

    Anne T Gallagher

    2015-04-01

    Full Text Available The Trafficking Protocol makes an easy target for attack. Its origins lie in an attempt to control a particularly exploitative form of migration that was challenging the ability of States to control their own borders. Its parent instrument is a framework agreement to address transnational organised crime. While paying fleeting attention to the rights of victims, the Protocol, with its emphasis on criminalisation and border protection is nowhere near being a human rights treaty. On top of all that it does not even have a credible enforcement mechanism, allowing states parties wide latitude in interpreting and applying their obligations. Strangely, these seemingly insurmountable flaws have not stopped the Protocol’s emergence as perhaps the single most important development in the fight against human trafficking. Without the Protocol, arguments around definitions would have continued to block the evolution of principles and rules. Without the Protocol it is likely that the human rights system would have continued its shameful tradition of sidelining issues such as forced labour, forced sex, forced marriage and the ritual exploitation of migrant workers through debt. Most critically, the Protocol provided the impetus and template for a series of legal and political developments that, over time, have served to ameliorate some of its greatest weaknesses, including the lack of human rights protections and of a credible oversight mechanism.

  20. A More Efficient Contextuality Distillation Protocol

    Science.gov (United States)

    Meng, Hui-xian; Cao, Huai-xin; Wang, Wen-hua; Fan, Ya-jing; Chen, Liang

    2017-12-01

    Based on the fact that both nonlocality and contextuality are resource theories, it is natural to ask how to amplify them more efficiently. In this paper, we present a contextuality distillation protocol which produces an n-cycle box B ∗ B ' from two given n-cycle boxes B and B '. It works efficiently for a class of contextual n-cycle (n ≥ 4) boxes which we termed as "the generalized correlated contextual n-cycle boxes". For any two generalized correlated contextual n-cycle boxes B and B ', B ∗ B ' is more contextual than both B and B '. Moreover, they can be distilled toward to the maximally contextual box C H n as the times of iteration goes to infinity. Among the known protocols, our protocol has the strongest approximate ability and is optimal in terms of its distillation rate. What is worth noting is that our protocol can witness a larger set of nonlocal boxes that make communication complexity trivial than the protocol in Brunner and Skrzypczyk (Phys. Rev. Lett. 102, 160403 2009), this might be helpful for exploring the problem that why quantum nonlocality is limited.

  1. Nursing Music Protocol and Postoperative Pain.

    Science.gov (United States)

    Poulsen, Michael J; Coto, Jeffrey

    2018-04-01

    Pain has always been a major concern for patients and nurses during the postoperative period. Therapies, medicines, and protocols have been developed to improve pain and anxiety but have undesirable risks to the patient. Complementary and alternative medicine therapies have been studied but have not been applied as regular protocols in the hospital setting. Music is one type of complementary and alternative medicine therapy that has been reported to have favorable results on reducing postoperative pain, anxiety, and opioid usage. However, music lacks a protocol that nurses can implement during the perioperative process. This paper is an in-depth literature review assessing a best practice recommendation and protocol that establishes a consensus in the use of music therapy. The results suggest that music therapy may consist of calming, soft tones of 60-80 beats per minute for at least 15-30 minutes at least twice daily during the pre- and postoperative periods. It is suggested that music only be used in conjunction with standards of care and not as the primary intervention of pain or anxiety. This evidence suggests that proper use of music therapy can significantly reduce surgical pain. Implementing these protocols and allowing the freedom of nursing staff to use them may lead to greater reductions in surgical pain and anxiety and a reduction in opioid use. Copyright © 2017 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

  2. Semen cryopreservation protocols of Mangalarga Marchador stallions

    Directory of Open Access Journals (Sweden)

    Marcela Leite Candeias

    2012-09-01

    Full Text Available The effect of the utilization of three semen protocols (Inra 82®, Merck Gema and Botu-crio® and two filling techniques (0.25 and 0.50 mL straws in Mangalarga Marchador stallions were studied in this experiment. Sperm parameters were assessed during processing and post-freezing. No interactions between the protocols and type of filling were observed, so they were assessed separately. Sperm parameters were not altered when the extender was added to the centrifugation; however, there was reduction of motility and strength when freezing extenders were added. The Botu-crio® protocol preserved the parameters of total and progressive sperm motility, smoothed path velocity (µm/s, straight line velocity (µm/s, track velocity (µm/s and the average and fast spermatozoa percentage better than the others. No difference between the extenders for the percentage of sperm integrity was observed. There was no difference in the responses studied on the filling techniques. The stallions presented better freezing with the use of the Botu-crio® protocol. The best post-freezing viability results were found for semen frozen using the Botu-crio® protocol and there were no differences concerning the sperm quality comparing 0.25 and 0.50 mL straws.

  3. Welfare Quality assessment protocol for laying hens = Welfare Quality assessment protocol voor leghennen

    NARCIS (Netherlands)

    Niekerk, van T.G.C.M.; Gunnink, H.; Reenen, van C.G.

    2012-01-01

    Results of a study on the Welfare Quality® assessment protocol for laying hens. It reports the development of the integration of welfare assessment as scores per criteria as well as simplification of the Welfare Quality® assessment protocol. Results are given from assessment of 122 farms.

  4. A Cryptographic Moving-Knife Cake-Cutting Protocol

    Directory of Open Access Journals (Sweden)

    Yoshifumi Manabe

    2012-02-01

    Full Text Available This paper proposes a cake-cutting protocol using cryptography when the cake is a heterogeneous good that is represented by an interval on a real line. Although the Dubins-Spanier moving-knife protocol with one knife achieves simple fairness, all players must execute the protocol synchronously. Thus, the protocol cannot be executed on asynchronous networks such as the Internet. We show that the moving-knife protocol can be executed asynchronously by a discrete protocol using a secure auction protocol. The number of cuts is n-1 where n is the number of players, which is the minimum.

  5. A class-chest for deriving transport protocols

    Energy Technology Data Exchange (ETDEWEB)

    Strayer, W.T.

    1996-10-01

    Development of new transport protocols or protocol algorithms suffers from the complexity of the environment in which they are intended to run. Modeling techniques attempt to avoid this by simulating the environment. Another approach to promoting rapid prototyping of protocols and protocol algorithms is to provide a pre-built infrastructure that is common to transport protocols, so that the focus is placed on the protocol-specific aspects. The Meta-Transport Library is a library of C++ base classes that implement or abstract out the mundane functions of a protocol, new protocol implementations are derived from base classes. The result is a fully viable user- level transport protocol implementation, with emphasis on modularity. The collection of base classes form a ``class-chest`` of tools .from which protocols can be developed and studied with as little change to a normal UNIX environment as possible.

  6. Myelin protein zero gene sequencing diagnoses Charcot-Marie-Tooth Type 1B disease

    Energy Technology Data Exchange (ETDEWEB)

    Su, Y.; Zhang, H.; Madrid, R. [Univ. of California, San Francisco, CA (United States)] [and others

    1994-09-01

    Charcot-Marie-Tooth disease (CMT), the most common genetic neuropathy, affects about 1 in 2600 people in Norway and is found worldwide. CMT Type 1 (CMT1) has slow nerve conduction with demyelinated Schwann cells. Autosomal dominant CMT Type 1B (CMT1B) results from mutations in the myelin protein zero gene which directs the synthesis of more than half of all Schwann cell protein. This gene was mapped to the chromosome 1q22-1q23.1 borderline by fluorescence in situ hybridization. The first 7 of 7 reported CMT1B mutations are unique. Thus the most effective means to identify CMT1B mutations in at-risk family members and fetuses is to sequence the entire coding sequence in dominant or sporadic CMT patients without the CMT1A duplication. Of the 19 primers used in 16 pars to uniquely amplify the entire MPZ coding sequence, 6 primer pairs were used to amplify and sequence the 6 exons. The DyeDeoxy Terminator cycle sequencing method used with four different color fluorescent lables was superior to manual sequencing because it sequences more bases unambiguously from extracted genomic DNA samples within 24 hours. This protocol was used to test 28 CMT and Dejerine-Sottas patients without CMT1A gene duplication. Sequencing MPZ gene-specific amplified fragments identified 9 polymorphic sites within the 6 exons that encode the 248 amino acid MPZ protein. The large number of major CMT1B mutations identified by single strand sequencing are being verified by reverse strand sequencing and when possible, by restriction enzyme analysis. This protocol can be used to distringuish CMT1B patients from othre CMT phenotypes and to determine the CMT1B status of relatives both presymptomatically and prenatally.

  7. Energy Consumption in Location Sharing Protocols for Android Applications

    OpenAIRE

    Prihodko, Mihails

    2012-01-01

    This thesis studies the Message Queue Telemetry Transport protocol (MQTT) as an application layer protocol in geographical location sharing applications using third generation cellular communication (3G). The MQTT protocol is compared in terms of energy efficiency and amount of data generated with the Hypertext Transfer Protocol (HTTP), which is currently used in typical location sharing applications. In order to compare the communication energy efficiency of both protocols a location sharing...

  8. Privacy-preserving audit mechanisms for multi-party protocols

    OpenAIRE

    Cuvelier, Édouard

    2015-01-01

    This thesis sets as goal the study and development of cryptographic multi-party protocols offering the properties of verifiability and privacy. The verifiability property guarantees the protocols participants and/or observers that the result of the execution of the protocol is exactly what is expected from a honest execution of the protocol. On the other hand, the privacy property ensures the participants that their private information is not leaked by executing the protocol. The thesis targe...

  9. Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols.

    Science.gov (United States)

    Campagne, Fabien

    2008-02-29

    The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications. We describe two protocols for evaluating biomedical information retrieval techniques without human relevance judgments. We call these protocols No Title Evaluation (NT Evaluation). The first protocol measures performance for focused searches, where only one relevant document exists for each query. The second protocol measures performance for queries expected to have potentially many relevant documents per query (high-recall searches). Both protocols take advantage of the clear separation of titles and abstracts found in Medline. We compare the performance obtained with these evaluation protocols to results obtained by reusing the relevance judgments produced in the 2004 and 2005 TREC Genomics Track and observe significant correlations between performance rankings generated by our approach and TREC. Spearman's correlation coefficients in the range of 0.79-0.92 are observed comparing bpref measured with NT Evaluation or with TREC evaluations. For comparison, coefficients in the range 0.86-0.94 can be observed when evaluating the same set of methods with data from two independent TREC Genomics Track evaluations. We discuss the advantages of NT Evaluation over the TRels and the data fusion evaluation protocols introduced recently. Our results suggest that the NT Evaluation protocols described here could be used to optimize some search engine parameters before human evaluation. Further research is needed to determine if NT Evaluation or variants of these protocols can fully substitute

  10. Network protocols for real-time applications

    Science.gov (United States)

    Johnson, Marjory J.

    1987-01-01

    The Fiber Distributed Data Interface (FDDI) and the SAE AE-9B High Speed Ring Bus (HSRB) are emerging standards for high-performance token ring local area networks. FDDI was designed to be a general-purpose high-performance network. HSRB was designed specifically for military real-time applications. A workshop was conducted at NASA Ames Research Center in January, 1987 to compare and contrast these protocols with respect to their ability to support real-time applications. This report summarizes workshop presentations and includes an independent comparison of the two protocols. A conclusion reached at the workshop was that current protocols for the upper layers of the Open Systems Interconnection (OSI) network model are inadequate for real-time applications.

  11. Changeable HA to improve MIPv6 protocol

    Science.gov (United States)

    Hu, Qing-gui

    2015-12-01

    For mobile IPv6, home agent (HA) plays an important role. Each mobile node (MN) has a home IP address, it will be not changeable. Also, the home agent (HA) of MN is not changeable. This rule provides the convenient for the ongoing communication without interruption. But it has some obvious drawbacks. Here, the new variable HA scheme is proposed. Every MN has a dynamic cache table, recording the information such as its home address, care-of address, and history address etc. If the accumulated time in one region exceeds that in the hometown, the foreign agent (FA) could become home agent (HA), the home agent could become history agent. Later, the performance of the new protocol is simulated with OPNET software, whose result shows the performance of the new protocol works better than that of the traditional protocol.

  12. Analysis of Security Protocols by Annotations

    DEFF Research Database (Denmark)

    Gao, Han

    The trend in Information Technology is that distributed systems and networks are becoming increasingly important, as most of the services and opportunities that characterise the modern society are based on these technologies. Communication among agents over networks has therefore acquired a great...... deal of research interest. In order to provide effective and reliable means of communication, more and more communication protocols are invented, and for most of them, security is a significant goal. It has long been a challenge to determine conclusively whether a given protocol is secure or not....... The development of formal techniques, e.g. control flow analyses, that can check various security properties, is an important tool to meet this challenge. This dissertation contributes to the development of such techniques. In this dissertation, security protocols are modelled in the process calculus LYSA...

  13. Will OPEC lose from the Kyoto Protocol?

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, Jon E-mail: jbarn@unimelb.edu.au; Dessai, Suraje E-mail: s.dessai@uea.ac.uk; Webber, Michael E-mail: mjwebber@unimelb.edu.au

    2004-12-01

    A range of energy-economy models forecast losses to members of the Organisation of Petroleum Exporting Countries (OPEC) should the Kyoto Protocol come into force. These forecasts are a powerful influence in the United Nations Framework Convention on Climate Change negotiations. They are used by OPEC to advance the agenda on the impacts of response measures, covertly arguing for compensation for lost oil revenues arising from implementation of the Protocol. This paper discusses this issue, and explores the key assumptions of these models and their uncertainties. Assumptions about carbon leakage, future availability of oil reserves, substitution, innovation, and capital turnover are considered. The paper suggests that losses will not affect OPEC countries equally, and that these losses are not likely to be as substantial as the models forecast. A range of policy measures are proposed to lessen any impact the Protocol may have on OPEC.

  14. A template for writing radiotherapy protocols.

    Science.gov (United States)

    Nilsson, Per; Ceberg, Crister; Kjellén, Elisabeth; Gagliardi, Giovanna; Blomgren, Klas; Nilsson, Sten; Johansson, Mikael; Glimelius, Bengt

    2015-02-01

    Well-specified and unambiguous treatment protocols are essential both for current practice and for the future development of radiation therapy. In order to provide assistance for writing good protocols, irrespective of treatment intention and complexity, up-to-date guidelines are highly desirable. We have analysed the radiotherapy work-flow, including clinical and physical aspects, such as preparatory imaging, treatment planning, delivery and evaluation, with the aim to outline a consistent framework covering the entire radiotherapy process. Based on the analysis, a recipe-style template for specifying the description of the radiotherapy process has been designed. The template is written in a general format, which allows for modified phrasing, and should be customised for the specific clinical situation and diagnosis, as well as facility resources. The template can be used as a tool to ensure a consistent and comprehensive description of the radiotherapy section of clinical guidelines, care programmes and clinical trial protocols.

  15. Structured Transition Protocol for Children with Cystinosis

    Directory of Open Access Journals (Sweden)

    Rupesh Raina

    2017-08-01

    Full Text Available The transition from pediatric to adult medical services has a greater impact on the care of adolescents or young adults with chronic diseases such as cystinosis. This transition period is a time of psychosocial development and new responsibilities placing these patients at increased risk of non-adherence. This can lead to serious adverse effects such as graft loss and progression of the disease. Our transition protocol will provide patients, families, physicians, and all those involved a structured guide to transitioning cystinosis patients. This structured protocol depends on four areas of competency: Recognition, Insight, Self-reliance, and Establishment of healthy habits (RISE. This protocol has not been tested and therefore challenges not realized. With a focus on medical, social, and educational/vocational aspects, we aim to improve transition for cystinosis patients in all aspects of their lives.

  16. Breaking Megrelishvili protocol using matrix diagonalization

    Science.gov (United States)

    Arzaki, Muhammad; Triantoro Murdiansyah, Danang; Adi Prabowo, Satrio

    2018-03-01

    In this article we conduct a theoretical security analysis of Megrelishvili protocol—a linear algebra-based key agreement between two participants. We study the computational complexity of Megrelishvili vector-matrix problem (MVMP) as a mathematical problem that strongly relates to the security of Megrelishvili protocol. In particular, we investigate the asymptotic upper bounds for the running time and memory requirement of the MVMP that involves diagonalizable public matrix. Specifically, we devise a diagonalization method for solving the MVMP that is asymptotically faster than all of the previously existing algorithms. We also found an important counterintuitive result: the utilization of primitive matrix in Megrelishvili protocol makes the protocol more vulnerable to attacks.

  17. Automatic Generation of Network Protocol Gateways

    DEFF Research Database (Denmark)

    Bromberg, Yérom-David; Réveillère, Laurent; Lawall, Julia

    2009-01-01

    for describing protocol behaviors, message structures, and the gateway logic.  Z2z includes a compiler that checks essential correctness properties and produces efficient code. We have used z2z to develop a number of gateways, including SIP to RTSP, SLP to UPnP, and SMTP to SMTP via HTTP, involving a range......The emergence of networked devices in the home has made it possible to develop applications that control a variety of household functions. However, current devices communicate via a multitude of incompatible protocols, and thus gateways are needed to translate between them.  Gateway construction......, however, requires an intimate knowledge of the relevant protocols and a substantial understanding of low-level network programming, which can be a challenge for many application programmers. This paper presents a generative approach to gateway construction, z2z, based on a domain-specific language...

  18. Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models.

    Science.gov (United States)

    Liu, Bowen; Ramsundar, Bharath; Kawthekar, Prasad; Shi, Jade; Gomes, Joseph; Luu Nguyen, Quang; Ho, Stephen; Sloane, Jack; Wender, Paul; Pande, Vijay

    2017-10-25

    We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis.

  19. Newborn hearing screening protocol in tuscany region.

    Science.gov (United States)

    Berrettini, Stefano; Ghirri, Paolo; Lazzerini, Francesco; Lenzi, Giovanni; Forli, Francesca

    2017-09-20

    Newborn hearing screening has to be considered the first step of a program for the identification, diagnosis, treatment and habilitation/rehabilitation of children with hearing impairment. In Tuscany Region of Italy, the universal newborn hearing screening is mandatory since november 2007. The first guidelines for the execution of the screening have been released in June 2008; then many other Italian regions partially or totally adopted these guidelines. On the basis of the experience from 2008 and according to the recent evidences in the scientific literature, a new screening protocol was released in Tuscany region. The new protocol is an evolution of the previous one. Some issues reported in the previous protocol and in the Joint Committee on Infant Hearing statement published in 2007 were revised, such as the risk factors for auditory neuropathy and for late onset, progressive or acquired hearing loss. The new updated guidelines were submitted to the Sanitary Regional Council and then they have been approved in August 2016. The updated screening protocol is mainly aimed to identify newborns with a congenital moderate-to-profound hearing loss, but it also provides indications for the audiological follow-up of children with risk's factor for progressive or late onset hearing loss; further it provides indications for the audiological surveillance of children at risk for acquired hearing impairment. Then, in the new guidelines the role of the family paediatrician in the newborn hearing screening and audiological follow-up and surveillance is underscored. Finally the new guidelines provide indications for the treatment with hearing aids and cochlear implant, in accordance with the recent Italian Health Technology Assessment (HTA) guidelines. In the paper we report the modality of execution of the universal newborn hearing screening in the Tuscany Region, according to the recently updated protocol. The main features of the protocol and the critical issues are

  20. Adherence to MRI protocol consensus guidelines in multiple sclerosis: an Australian multi-centre study

    International Nuclear Information System (INIS)

    Curley, Michael; Josey, Lawrence; Lucas, Robyn; Dear, Keith; Taylor, Bruce V.; Coulthard, Alan; Ausimmune Investigator Group

    2012-01-01

    Multiple sclerosis (MS) is a debilitating disease that causes significant morbidity within a young demographic. Diagnostic guidelines for MS have evolved, and imaging has played an increasingly important role in diagnosis over the last two decades. For imaging to contribute to diagnosis in a meaningful way, it must be reproducible. Consensus guidelines for MRI in MS exist to define correct sequence type and imaging technique, but it is not clear to what extent they are followed. This study reviewed MRI studies performed on Australian individuals presenting with a first clinical diagnosis of central nervous system demyelination (FCD) for adherence to published guidelines and discussed practical implementation of MS guidelines in light of recent updates. The Ausimmune study was a prospective case control study of Australian participants presenting with FCD from 2003 to 2006. Baseline cranial and spinal cord MRI studies of 226 case participants from four separate Australian regions were reviewed. MRI sequences were classified according to anatomical location, slice plane, tissue weighting and use of gadolinium-containing contrast media. Results were compared with the 2003 Consortium of Multiple Sclerosis Centres MRI protocol for the diagnosis of MS. The composition of core cranial MRI sequences performed varied across the 226 scans. Of the studies, 91% included sagittal fluid attenuated inversion recovery (FLAIR) sequences. Cranial axial T2-weighted, axial FLAIR and axial proton density-weighted sequences were performed in 88%, 60% and 16% (respectively) of scans. Only 25% of the studies included a T1-weighted contrast-enhanced sequence. Concordance with the guidelines in all sequences was very low (2). Only a small number of MRI investigations performed included all of the sequences stipulated by consensus guidelines. This is likely due to poor awareness in the imaging community of the guidelines and the rationale behind certain sequences. Radiologists with a sub