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Sample records for alternative genotyping method

  1. Different genotypes of alternative small grains in organic farming

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    Kovačević Dušan Đ.

    2014-01-01

    Full Text Available The main objectives were to examine different genotypes of alternative small grains important for food technology in organic farming conditions on morphological and productive characteristics. Four genotypes of different alternative small grains were included in the trial. Three of them were chosen for specific usage in food technology compact wheat Bambi -Triticum aestivum L. ssp. compactum, spelt Nirvana (Triticum aestivum L. ssp. spelta, durum wheat Durumko-(Triticum durum L., and one which leads as a genotype for intensive conventional common wheat production in Serbia -NS 40S (Triticum aestivum L. ssp. vulgare. Plots were fertilized with biohumus "Royal ofert" (30 t ha-1 applied in autumn with basic tillage and microbial fertilizer "Slavol" ad as in spring foliar treatment in full tillering (5 l ha-1. Alternative small grains durum wheat and compact wheat except splet gives lower grain yield in organic condition compared with comercial cultivar for high-input NS-40S. [Projekat Ministarstva nauke Republike Srbije, br. TR-31066

  2. Alternation of cowpea genotypes affects the biology of Callosobruchus maculatus (fabr. (Coleoptera: Bruchidae

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    Lima Marcileyne Pessôa Leite de

    2004-01-01

    Full Text Available Callosobruchus maculatus (Fabr. is an important pest in stored cowpea, Vigna unguiculata (L. Walp., with ample distribution in tropical and subtropical regions. The effect of alternation of cowpea genotypes, susceptible (S and resistant (R, on the biology of (C. maculatus was studied after four generations. A no-choice test was carried out in a completely randomized design, factorial scheme, with five treatments, four host combinations (RR, RS, SR and SS and five replications. Each replication consisted of 30 grains of each genotype infested by two insect couples. The number of eggs per female was not different within or between combinations, evidencing that the genotypes and their alternation did not affect C. maculatus fecundity. Egg viability, however, varied between genotypes and between combinations. In combination RR, the longest duration of the immature stage was verified for genotype IT89KD-245; in addition, all genotypes presented the smallest survival for the same stage, resulting in a higher mortality of the pest. The resistance index categorized combination RR as moderately resistant for genotypes IT89KD-245, BR14-Mulato and BR17-Gurguéia, and as susceptible (S only for IT89KD-260, demonstrating that these combinations were not very adequate for the development of C. maculatus, a fact that was confirmed by the better performance of the pest on the genotype from combination SS, and because of a reduction in its performance when it returned to resistant genotypes.

  3. Comparison of two PCR-based human papillomavirus genotyping methods.

    Science.gov (United States)

    Castle, Philip E; Porras, Carolina; Quint, Wim G; Rodriguez, Ana Cecilia; Schiffman, Mark; Gravitt, Patti E; González, Paula; Katki, Hormuzd A; Silva, Sandra; Freer, Enrique; Van Doorn, Leen-Jan; Jiménez, Silvia; Herrero, Rolando; Hildesheim, Allan

    2008-10-01

    We compared two consensus primer PCR human papillomavirus (HPV) genotyping methods for the detection of individual HPV genotypes and carcinogenic HPV genotypes as a group, using a stratified sample of enrollment cervical specimens from sexually active women participating in the NCI/Costa Rica HPV16/18 Vaccine Efficacy Trial. For the SPF(10) method, DNA was extracted from 0.1% of the cervical specimen by using a MagNA Pure LC instrument, a 65-bp region of the HPV L1 gene was targeted for PCR amplification by using SPF(10) primers, and 25 genotypes were detected by reverse-line blot hybridization of the amplicons. For the Linear Array (LA) method, DNA was extracted from 0.5% of the cervical specimen by using an MDx robot, a 450-bp region of the HPV L1 gene was targeted for PCR amplification by using PGMY09/11 L1 primers, and 37 genotypes were detected by reverse-line blot hybridization of the amplicons. Specimens (n = 1,427) for testing by the LA method were randomly selected from strata defined on the basis of enrollment test results from the SPF(10) method, cytology, and Hybrid Capture 2. LA results were extrapolated to the trial cohort (n = 5,659). The LA and SPF(10) methods detected 21 genotypes in common; HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, and -73 were considered the carcinogenic HPV genotypes. There was no difference in the overall results for grouped detection of carcinogenic HPV by the SPF(10) and LA methods (35.3% versus 35.9%, respectively; P = 0.5), with a 91.8% overall agreement and a kappa value of 0.82. In comparisons of individual HPV genotypes, the LA method detected significantly more HPV16, HPV18, HPV39, HPV58, HPV59, HPV66, and HPV68/73 and less HPV31 and HPV52 than the SPF(10) method; inclusion of genotype-specific testing for HPV16 and HPV18 for those specimens testing positive for HPV by the SPF(10) method but for which no individual HPV genotype was detected abrogated any differences between the LA and SPF

  4. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

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    Moysés Nascimento

    2015-02-01

    Full Text Available This study aimed to evaluate the efficiency of multiple centroids to study the adaptability of alfalfa genotypes (Medicago sativa L.. In this method, the genotypes are compared with ideotypes defined by the bissegmented regression model, according to the researcher's interest. Thus, genotype classification is carried out as determined by the objective of the researcher and the proposed recommendation strategy. Despite the great potential of the method, it needs to be evaluated under the biological context (with real data. In this context, we used data on the evaluation of dry matter production of 92 alfalfa cultivars, with 20 cuttings, from an experiment in randomized blocks with two repetitions carried out from November 2004 to June 2006. The multiple centroid method proved efficient for classifying alfalfa genotypes. Moreover, it showed no unambiguous indications and provided that ideotypes were defined according to the researcher's interest, facilitating data interpretation.

  5. Molecular methods for bacterial genotyping and analyzed gene regions

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    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

    2011-06-01

    Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

  6. Genotyping of Rotavirus by Using RT-PCR Methods

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    Hera Nirwati

    2015-11-01

    Full Text Available There is a great diversity of rotavirus genotypes circulating worldwide, with dominant genotypes changing from year to year. Rotavirus genotyping was performed by using reverse transcription PCR with type-specifi c-primers. Since rotavirus is a RNA virus that has high mutation rate, there was a possibility of technical diffi culty in genotyping due to mutation in the primer binding sites. During Indonesian rotavirus surveillance study 2006-2009, it was reported that 17% of samples subjected for G type and 21% of samplessubjected for P type were untypeable. The objective of this study was to identify genotypes of the samples that were untypeable previously using RT-PCR based on the method described by Das et al. (1994 and Gentsch et al. (1992. There were 30 samples subjected to G type and 61 samples subjected to P type to be re-typed using method described by Gouvea et al. (1990 and Simmond et al. (2008 for G and P typing, respectively. By using another set of primer, the genotype of all samples was identifi ed. This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses.Key words: rotavirus, G typing, P typing

  7. Methods for Characterization of Alternative RNA Splicing.

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    Harvey, Samuel E; Cheng, Chonghui

    2016-01-01

    Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.

  8. Comparative analysis of minor histocompatibility antigens genotyping methods

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    A. S. Vdovin

    2016-01-01

    Full Text Available The wide range of techniques could be employed to find mismatches in minor histocompatibility antigens between transplant recipients and their donors. In the current study we compared three genotyping methods based on polymerase chain reaction (PCR for four minor antigens. Three of the tested methods: allele-specific PCR, restriction fragment length polymorphism and real-time PCR with TaqMan probes demonstrated 100% reliability when compared to Sanger sequencing for all of the studied polymorphisms. High resolution melting analysis was unsuitable for genotyping of one of the tested minor antigens (HA-1 as it has linked synonymous polymorphism. Obtained data could be used to select the strategy for large-scale clinical genotyping.

  9. Alternative methods in toxicology: pre-validated and validated methods

    OpenAIRE

    2011-01-01

    The development of alternative methods to animal experimentation has progressed rapidly over the last 20 years. Today, in vitro and in silico methods have an important role in the hazard identification and assessment of toxicology profile of compounds. Advanced alternative methods and their combinations are also used for safety assessment of final products. Several alternative methods, which were scientifically validated and accepted by competent regulatory bodies, can be used for regulatory ...

  10. Alternative methods in toxicology: pre-validated and validated methods.

    Science.gov (United States)

    Kandárová, Helena; Letašiová, Silvia

    2011-09-01

    The development of alternative methods to animal experimentation has progressed rapidly over the last 20 years. Today, in vitro and in silico methods have an important role in the hazard identification and assessment of toxicology profile of compounds. Advanced alternative methods and their combinations are also used for safety assessment of final products. Several alternative methods, which were scientifically validated and accepted by competent regulatory bodies, can be used for regulatory toxicology purposes, thus reducing or fully replacing living animals in toxicology experimentation. The acceptance of the alternative methods as valuable tools of modern toxicology has been recognized by regulators, including OECD, FDA and EPA.This paper provides a brief overview of the topic "alternative methods in toxicology" and focuses on pre-validated and validated alternative methods and their position in the modern toxicology.

  11. Methods for Characterization of Alternative RNA Splicing

    Science.gov (United States)

    Harvey, Samuel E.; Cheng, Chonghui

    2016-01-01

    Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing “minigene” in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest. PMID:26721495

  12. Comparing performance of modern genotype imputation methods in different ethnicities

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    Roshyara, Nab Raj; Horn, Katrin; Kirsten, Holger; Ahnert, Peter; Scholz, Markus

    2016-10-01

    A variety of modern software packages are available for genotype imputation relying on advanced concepts such as pre-phasing of the target dataset or utilization of admixed reference panels. In this study, we performed a comprehensive evaluation of the accuracy of modern imputation methods on the basis of the publicly available POPRES samples. Good quality genotypes were masked and re-imputed by different imputation frameworks: namely MaCH, IMPUTE2, MaCH-Minimac, SHAPEIT-IMPUTE2 and MaCH-Admix. Results were compared to evaluate the relative merit of pre-phasing and the usage of admixed references. We showed that the pre-phasing framework SHAPEIT-IMPUTE2 can overestimate the certainty of genotype distributions resulting in the lowest percentage of correctly imputed genotypes in our case. MaCH-Minimac performed better than SHAPEIT-IMPUTE2. Pre-phasing always reduced imputation accuracy. IMPUTE2 and MaCH-Admix, both relying on admixed-reference panels, showed comparable results. MaCH showed superior results if well-matched references were available (Nei’s GST ≤ 0.010). For small to medium datasets, frameworks using genetically closest reference panel are recommended if the genetic distance between target and reference data set is small. Our results are valid for small to medium data sets. As shown on a larger data set of population based German samples, the disadvantage of pre-phasing decreases for larger sample sizes.

  13. Assessing and comparison of different machine learning methods in parent-offspring trios for genotype imputation.

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    Mikhchi, Abbas; Honarvar, Mahmood; Kashan, Nasser Emam Jomeh; Aminafshar, Mehdi

    2016-06-21

    Genotype imputation is an important tool for prediction of unknown genotypes for both unrelated individuals and parent-offspring trios. Several imputation methods are available and can either employ universal machine learning methods, or deploy algorithms dedicated to infer missing genotypes. In this research the performance of eight machine learning methods: Support Vector Machine, K-Nearest Neighbors, Extreme Learning Machine, Radial Basis Function, Random Forest, AdaBoost, LogitBoost, and TotalBoost compared in terms of the imputation accuracy, computation time and the factors affecting imputation accuracy. The methods employed using real and simulated datasets to impute the un-typed SNPs in parent-offspring trios. The tested methods show that imputation of parent-offspring trios can be accurate. The Random Forest and Support Vector Machine were more accurate than the other machine learning methods. The TotalBoost performed slightly worse than the other methods.The running times were different between methods. The ELM was always most fast algorithm. In case of increasing the sample size, the RBF requires long imputation time.The tested methods in this research can be an alternative for imputation of un-typed SNPs in low missing rate of data. However, it is recommended that other machine learning methods to be used for imputation.

  14. [Molecular test Genotype® MTBDRplus, an alternative to rapid detection of multidrug resistance tuberculosis].

    Science.gov (United States)

    Asencios, Luis; Galarza, Marco; Quispe, Neyda; Vásquez, Lucy; Leo, Elena; Valencia, Eddy; Ramírez, Juan; Acurio, Margoth; Salazar, Rosario; Mendoza-Ticona, Alberto; Cáceres, Omar

    2012-03-01

    The Genotype®MTBDRplus molecular test is a method that allows identification of the most frequent mutations associated with resistance to major first-line antituberculosis drugs, Isoniazid (INH) and Rifampicin (RFP). The aim of this study was to evaluate the performance of the molecular test with culture and smear- positive sputum samples. We evaluated 95 cultures and 100 sputum samples with resistance profiles previously determined by the reference method "Agar Plate Proportions" (APP). The molecular test from cultures showed a sensitivity of 100 %, 97,5 % and 96,97 % for RIF, INH and MDR respectively while from sputums the sensitivity was 95,65 %, 96,77 % and 95,24 % for RIF, INH and MDR respectively. We conclude that the molecular test Genotype®MTBDRplus is a very useful tool to detect resistance to isoniazid and rifampicin simultaneously (MDR-TB) in up to 72 hours from sputum samples or cultures.

  15. Distributed Reconstruction via Alternating Direction Method

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    Linyuan Wang

    2013-01-01

    Full Text Available With the development of compressive sensing theory, image reconstruction from few-view projections has received considerable research attentions in the field of computed tomography (CT. Total-variation- (TV- based CT image reconstruction has been shown to be experimentally capable of producing accurate reconstructions from sparse-view data. In this study, a distributed reconstruction algorithm based on TV minimization has been developed. This algorithm is very simple as it uses the alternating direction method. The proposed method can accelerate the alternating direction total variation minimization (ADTVM algorithm without losing accuracy.

  16. Alternative methods of ophthalmic treatment in Russia.

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    Vader, L

    1994-04-01

    Russian ophthalmic nurses and physicians are using alternative methods of treatment to supplement traditional eye care. As acupuncture and iridology become more popular in the United States, ophthalmic nurses need to be more knowledgeable about these treatments and the implications for patients.

  17. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    Science.gov (United States)

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

  18. A novel hepatitis C virus genotyping method based on liquid microarray.

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    Cesar A B Duarte

    Full Text Available The strategy used to treat HCV infection depends on the genotype involved. An accurate and reliable genotyping method is therefore of paramount importance. We describe here, for the first time, the use of a liquid microarray for HCV genotyping. This liquid microarray is based on the 5'UTR - the most highly conserved region of HCV - and the variable region NS5B sequence. The simultaneous genotyping of two regions can be used to confirm findings and should detect inter-genotypic recombination. Plasma samples from 78 patients infected with viruses with genotypes and subtypes determined in the Versant™ HCV Genotype Assay LiPA (version I; Siemens Medical Solutions, Diagnostics Division, Fernwald, Germany were tested with our new liquid microarray method. This method successfully determined the genotypes of 74 of the 78 samples previously genotyped in the Versant™ HCV Genotype Assay LiPA (74/78, 95%. The concordance between the two methods was 100% for genotype determination (74/74. At the subtype level, all 3a and 2b samples gave identical results with both methods (17/17 and 7/7, respectively. Two 2c samples were correctly identified by microarray, but could only be determined to the genotype level with the Versant™ HCV assay. Genotype "1" subtypes (1a and 1b were correctly identified by the Versant™ HCV assay and the microarray in 68% and 40% of cases, respectively. No genotype discordance was found for any sample. HCV was successfully genotyped with both methods, and this is of prime importance for treatment planning. Liquid microarray assays may therefore be added to the list of methods suitable for HCV genotyping. It provides comparable results and may readily be adapted for the detection of other viruses frequently co-infecting HCV patients. Liquid array technology is thus a reliable and promising platform for HCV genotyping.

  19. Purification of Carbon Nanotubes: Alternative Methods

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    Files, Bradley; Scott, Carl; Gorelik, Olga; Nikolaev, Pasha; Hulse, Lou; Arepalli, Sivaram

    2000-01-01

    Traditional carbon nanotube purification process involves nitric acid refluxing and cross flow filtration using surfactant TritonX. This is believed to result in damage to nanotubes and surfactant residue on nanotube surface. Alternative purification procedures involving solvent extraction, thermal zone refining and nitric acid refiuxing are used in the current study. The effect of duration and type of solvent to dissolve impurities including fullerenes and P ACs (polyaromatic compounds) are monitored by nuclear magnetic reasonance, high performance liquid chromatography, and thermogravimetric analysis. Thermal zone refining yielded sample areas rich in nanotubes as seen by scanning electric microscopy. Refluxing in boiling nitric acid seem to improve the nanotube content. Different procedural steps are needed to purify samples produced by laser process compared to arc process. These alternative methods of nanotube purification will be presented along with results from supporting analytical techniques.

  20. 77 FR 43827 - International Workshop on Alternative Methods for Leptospira

    Science.gov (United States)

    2012-07-26

    ... Alternatives to Animal Testing (EURL ECVAM), the Japanese Center for the Validation of Alternative Methods, the... HUMAN SERVICES International Workshop on Alternative Methods for Leptospira Vaccine Potency Testing... Workshop on Alternative Methods for Leptospira Vaccine Potency Testing: State of the Science and the Way...

  1. An Alternative Method to Project Wind Patterns

    Science.gov (United States)

    Fadillioglu, Cagla; Kiyisuren, I. Cagatay; Collu, Kamil; Turp, M. Tufan; Kurnaz, M. Levent; Ozturk, Tugba

    2016-04-01

    Wind energy is one of the major clean and sustainable energy sources. Beside its various advantages, wind energy has a downside that its performance cannot be projected very accurately in the long-term. In this study, we offer an alternative method which can be used to determine the best location to install a wind turbine in a large area aiming maximum energy performance in the long run. For this purpose, a regional climate model (i.e. RegCM4.4) is combined with a software called Winds on Critical Streamline Surfaces (WOCSS) in order to identify wind patterns for any domains even in a changing climate. As a special case, Çanakkale region is examined due to the terrain profile having both coastal and mountainous features. WOCSS program was run twice for each month in the sample years in a double nested fashion, using the provisional RegCM4.4 wind data between years 2020 and 2040. Modified version of WOCSS provides terrain following flow surfaces and by processing those data, it makes a wind profile output for certain heights specified by the user. The computational time of WOCSS is also in reasonable range. Considering the lack of alternative methods for long-term wind performance projection, the model used in this study is a very good way for obtaining quick indications for wind performance taking the impact of the terrain effects into account. This research has been supported by Boǧaziçi University Research Fund Grant Number 10421.

  2. Comparison of methods for analysis of selective genotyping survival data

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    Dekkers Jack CM

    2006-11-01

    Full Text Available Abstract Survival traits and selective genotyping datasets are typically not normally distributed, thus common models used to identify QTL may not be statistically appropriate for their analysis. The objective of the present study was to compare models for identification of QTL associated with survival traits, in particular when combined with selective genotyping. Data were simulated to model the survival distribution of a population of chickens challenged with Marek disease virus. Cox proportional hazards (CPH, linear regression (LR, and Weibull models were compared for their appropriateness to analyze the data, ability to identify associations of marker alleles with survival, and estimation of effects when all individuals were genotyped (full genotyping and when selective genotyping was used. Little difference in power was found between the CPH and the LR model for low censoring cases for both full and selective genotyping. The simulated data were not transformed to follow a Weibull distribution and, as a result, the Weibull model generally resulted in less power than the other two models and overestimated effects. Effect estimates from LR and CPH were unbiased when all individuals were genotyped, but overestimated when selective genotyping was used. Thus, LR is preferred for analyzing survival data when the amount of censoring is low because of ease of implementation and interpretation. Including phenotypic data of non-genotyped individuals in selective genotyping analysis increased power, but resulted in LR having an inflated false positive rate, and therefore the CPH model is preferred for this scenario, although transformation of the data may also make the Weibull model appropriate for this case. The results from the research presented herein are directly applicable to interval mapping analyses.

  3. Alternative method of removing otoliths from sturgeon

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    Chalupnicki, Marc A.; Dittman, Dawn E.

    2016-01-01

    Extracting the otoliths (ear bones) from fish that have very thick skulls can be difficult and very time consuming. The common practice of making a transverse vertical incision on the top of the skull with a hand or electrical saw may damage the otolith if not performed correctly. Sturgeons (Acipenseridae) are one family in particular that have a very large and thick skull. A new laboratory method entering the brain cavity from the ventral side of the fish to expose the otoliths was easier than other otolith extraction methods found in the literature. Methods reviewed in the literature are designed for the field and are more efficient at processing large quantities of fish quickly. However, this new technique was designed to be more suited for a laboratory setting when time is not pressing and successful extraction from each specimen is critical. The success of finding and removing otoliths using this technique is very high and does not compromise the structure in any manner. This alternative technique is applicable to other similar fish species for extracting the otoliths.

  4. An alternative laboratory designed to address ethical concerns associated with traditional TAS2R38 student genotyping.

    Science.gov (United States)

    LaBonte, Michelle L; Beers, Melissa A

    2015-01-01

    The TAS2R38 alleles that code for the PAV/AVI T2R38 proteins have long been viewed as benign taste receptor variants. However, recent studies have demonstrated an expanding and medically relevant role for TAS2R38. The AVI variant of T2R38 is associated with an increased risk of both colorectal cancer and Pseudomonas aeruginosa-associated sinus infection and T2R38 variants have been implicated in off-target drug responses. To address ethical concerns associated with continued student TAS2R38 gene testing, we developed an alternative to the traditional laboratory genotyping exercise. Instead of determining their own genotype, introductory level students isolated plasmid DNA containing a section of the human TAS2R38 gene from Escherichia coli. Following PCR-mediated amplification of a section of the TAS2R38 gene spanning the SNP at position 785, students determined their assigned genotype by restriction enzyme digestion and agarose gel electrophoresis. Using the course wide genotype and phenotype data, students found that there was an association between TAS2R38 genotype and the age of persistent P. aeruginosa acquisition in cystic fibrosis "patients." Assessment data demonstrated that students taking part in this new TAS2R38 laboratory activity made clear learning gains.

  5. Molecular methods for genotyping complex copy number polymorphisms.

    Science.gov (United States)

    Cantsilieris, Stuart; Baird, Paul N; White, Stefan J

    2013-02-01

    Genome structural variation shows remarkable complexity with respect to copy number, sequence content and distribution. While the discovery of copy number polymorphisms (CNP) has increased exponentially in recent years, the transition from discovery to genotyping has proved challenging, particularly for CNPs embedded in complex regions of the genome. CNPs that are collectively common in the population and possess a dynamic range of copy numbers have proved the most difficult to genotype in association studies. This is in some part due to technical limitations of genotyping assays and the sequence properties of the genomic region being analyzed. Here we describe in detail the basis of a number of molecular techniques used to genotype complex CNPs, compare and contrast these approaches for determination of multi-allelic copy number, and discuss the potential application of these techniques in genetic studies.

  6. Alternative method for assessing coking coal plasticity

    Energy Technology Data Exchange (ETDEWEB)

    Dzuy Nguyen; Susan Woodhouse; Merrick Mahoney [University of Adelaide (Australia). BHP Billiton Newcastle Technology Centre

    2008-07-15

    Traditional plasticity measurements for coal have a number of limitations associated with the reproducibility of the tests and their use in predicting coking behaviour. This report reviews alternative rheological methods for characterising the plastic behaviour of coking coals. It reviews the application of more fundamental rheological measurements to the coal system as well as reviewing applications of rheology to other physical systems. These systems may act as potential models for the application of fundamental rheological measurements to cokemaking. The systems considered were polymer melts, coal ash melts, lava, bread making and ice cream. These systems were chosen because they exhibit some physically equivalent processes to the processes occurring during cokemaking, eg, the generation of bubbles within a softened system that then resolidifies. A number of recommendations were made; the steady and oscillatory shear squeeze flow techniques be further investigated to determine if the measured rheology characteristics are related to transformations within the coke oven and the characteristics of resultant coke; modification of Gieseler plastometers for more fundamental rheology measurements not be attempted.

  7. Methods and Strategies to Impute Missing Genotypes for Improving Genomic Prediction

    DEFF Research Database (Denmark)

    Ma, Peipei

    Genomic prediction has been widely used in dairy cattle breeding. Genotype imputation is a key procedure to efficently utilize marker data from different chips and obtain high density marker data with minimizing cost. This thesis investigated methods and strategies to genotype imputation for impr......Genomic prediction has been widely used in dairy cattle breeding. Genotype imputation is a key procedure to efficently utilize marker data from different chips and obtain high density marker data with minimizing cost. This thesis investigated methods and strategies to genotype imputation...

  8. From alternative methods to a new toxicology.

    Science.gov (United States)

    Hartung, Thomas

    2011-04-01

    Mechanistic toxicology has evolved by relying, to a large extent, on methodologies that substitute or complement traditional animal tests. The biotechnology and informatics revolutions of the last decades have made such technologies broadly available and useful, but regulatory toxicology has been slow to embrace these new approaches. Major validation efforts, however, have delivered the evidence that new approaches do not lower safety standards and can be integrated into regulatory safety assessments. Particularly in the EU, political pressures, such as the REACH legislation and the 7th Amendment to the cosmetic legislation, have prompted the need of new approaches. In the US, the NRC vision report calling for a toxicology for the 21st century (and its most recent adaptation by EPA for their toxicity testing strategy) have initiated a debate about how to create a novel approach based on human cell cultures, lower species, high-throughput testing, and modeling. Lessons learned from the development, validation, and acceptance of alternative methods support the creation of a new approach based on identified toxicity pathways. Conceptual steering and an objective assessment of current practices by evidence-based toxicology (EBT) are required. EBT is modeled on evidence-based medicine, which has demonstrated that rigorous systematic reviews of current practices and meta-analyses of studies provide powerful tools to provide health care professionals and patients with the current best scientific evidence. Similarly, a portal for high-quality reviews of toxicological approaches and tools for the quantitative meta-analyses of data promise to serve as door opener for a new regulatory toxicology.

  9. Alternate methods to teach history of anesthesia.

    Science.gov (United States)

    Desai, Manisha S; Desai, Sukumar P

    2014-02-01

    Residency programs in anesthesiology in the United States struggle to balance the conflicting needs of formal didactic sessions, clinical teaching, and clinical service obligations. As a consequence of the explosion in knowledge about basic and applied sciences related to our specialty, residents and fellows are expected to make substantial efforts to supplement formal lectures with self-study. There is strong evidence to suggest that members of the younger generation use nontraditional methods to acquire information. Although training programs are not required to include topics related to history of anesthesia (HOA) in the didactic curriculum, and despite the fact that such knowledge does not directly impact clinical care, many programs include such lectures and discussions. We describe and discuss our experience with 3 alternate modalities of teaching HOA.First, we provide brief descriptions of HOA-related historical narratives and novels within the domain of popular literature, rather than those that might be considered textbooks. Second, we analyze content in movies and videodiscs dealing with HOA and determine their utility as educational resources. Third, we describe HOA tours to sites in close proximity to our institutions, as well as those in locations elsewhere in the United States and abroad.We suggest that informal HOA teaching can be implemented by every residency program without much effort and without taking away from the traditional curriculum. Participating in this unique and enriching experience may be a means of academic advancement. It is our hope and expectation that graduates from programs that incorporate such exposure to HOA become advocates of history and may choose to devote a part of their academic career toward exploration of HOA.

  10. Methods for generating hydroelectric power development alternatives

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Shoou-yuh; Liaw, Shu-liang; Sale, M.J.; Railsback, S.F.

    1989-01-01

    Hydropower development on large rivers can result in a number of environmental impacts, including potential reductions in dissolved oxygen (DO) concentrations. This study presents a methodology for generating different hydropower development alternatives for evaluation. This methodology employs a Streeter-Phelps model to simulate DO, and the Bounded Implicit Enumeration algorithm to solve an optimization model formulated to maximize hydroelectric energy production subject to acceptable DO limits. The upper Ohio River basin was used to illustrate the use and characteristics of the methodology. The results indicate that several alternatives which meet the specified DO constraints can be generated efficiently, meeting both power and environmental objectives. 17 refs., 2 figs., 1 tab.

  11. Alternative genotyping method for the single nucleotide polymorphism A2959G (AF159246 of the bovine CAST gene Método alternativo de genotipagem do polimorfismo de nucleotídeo único A2959G (AF159246 do gene CAST bovino

    Directory of Open Access Journals (Sweden)

    Rogério Abdallah Curi

    2008-05-01

    Full Text Available The objective of this work was to genotype the single nucleotide polymorphism (SNP A2959G (AF159246 of bovine CAST gene by PCR-RFLP technique, and to report its use for the first time. For this, 147 Bos indicus and Bos taurus x Bos indicus animals were genotyped. The accuracy of the method was confirmed through the direct sequencing of PCR products of nine individuals. The lowest frequency of the meat tenderness favorable allele (A in Bos indicus was confirmed. The use of PCR-RFLP for the genotyping of the bovine CAST gene SNP was shown to be robust and inexpensive, which will greatly facilitate its analysis by laboratories with basic structure.O objetivo deste trabalho foi genotipar o polimorfismo de nucleotídeo único ("single nucleotide polymorphism" - SNP A2959G (AF159246 do gene CAST bovino, pela técnica de PCR-RFLP, e reportar a sua utilização pela primeira vez. Para tanto, 147 animais Bos indicus e Bos taurus x Bos indicus foram genotipados. A acurácia do método foi confirmada por meio do seqüenciamento direto de produtos de PCR de nove indivíduos. A menor freqüência do alelo A, favorável à maciez da carne, foi confirmada nos animais Bos indicus. O uso da PCR-RFLP, para a genotipagem do SNP do gene CAST bovino, mostrou-se consistente e de baixo custo, o que permite a sua análise por laboratórios dotados de estrutura básica.

  12. Deferring Elimination of Design Alternatives in Object Oriented Methods

    NARCIS (Netherlands)

    Aksit, Mehmet; Marcelloni, Francesco

    2001-01-01

    While developing systems, software engineers generally have to deal with a large number of design alternatives. Current object-oriented methods aim to eliminate design alternatives whenever they are generated. Alternatives, however, should be eliminated only when sufficient information to take such

  13. Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5'NCR PCR-RFLP, Core Type-Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India.

    Science.gov (United States)

    Daniel, Hubert D-J; David, Joel; Raghuraman, Sukanya; Gnanamony, Manu; Chandy, George M; Sridharan, Gopalan; Abraham, Priya

    2017-05-01

    Based on genetic heterogeneity, hepatitis C virus (HCV) is classified into seven major genotypes and 64 subtypes. In spite of the sequence heterogeneity, all genotypes share an identical complement of colinear genes within the large open reading frame. The genetic interrelationships between these genes are consistent among genotypes. Due to this property, complete sequencing of the HCV genome is not required. HCV genotypes along with subtypes are critical for planning antiviral therapy. Certain genotypes are also associated with higher progression to liver cirrhosis. In this study, 100 blood samples were collected from individuals who came for routine HCV genotype identification. These samples were used for the comparison of two different genotyping methods (5'NCR PCR-RFLP and HCV core type-specific PCR) with NS5b sequencing. Of the 100 samples genotyped using 5'NCR PCR-RFLP and HCV core type-specific PCR, 90% (κ = 0.913, P PCR-RFLP and HCV core type-specific PCR, respectively, belonged to genotype 6. All the HCV genotype 1 subtypes were classified accurately by both the methods. This study shows that the 5'NCR-based PCR-RFLP and the HCV core type-specific PCR-based assays correctly identified HCV genotypes except genotype 6 from this region. Direct sequencing of the HCV core region was able to identify all the genotype 6 from this region and serves as an alternative to NS5b sequencing. © 2016 Wiley Periodicals, Inc.

  14. Alternative parameter determination methods for a PMSG

    DEFF Research Database (Denmark)

    Kalogiannis, Theodoros; Malz, Elena; Llano, Enrique Muller

    2014-01-01

    One of the fundamental requirements for testing and analysing a Permanent Magnet Synchronous Generator (PMSG) is to obtain its electrical and mechanical parameters. This paper describes the test set up and the procedure for obtaining them. Stator resistance and flux linkage measurements follow IEEE...... standards. In the other hand a new approach for an alternative stator inductance and inertia measurement is analysed. More precisely, the former is obtained through laboratory work based on the locked rotor test, and the latter through a CAD software based on a 3D model. In order to assess and validate...

  15. Alternatives to radioimmunoassay: labels and methods

    Energy Technology Data Exchange (ETDEWEB)

    Schall, R.F. Jr.; Tenoso, H.J.

    1981-07-01

    The following labels used as substitutes for radioisotopes in immunoassay systems are reviewed bacteriophages, chemiluminescence precursors, fluorochromes, fluorogens, fluorescence quenchers, enzymes, coenzymes, inhibitors, substrates, various particulates, metal atoms, and stable free radicals. New methods for performing immunoassays with these labels are described where appropriate. Methods that require no separation steps and offer special promise for easy automation are noted. 69 references cited.

  16. Alternative Inspection Methods for Single Shell Tanks

    Energy Technology Data Exchange (ETDEWEB)

    Peters, Timothy J.; Alzheimer, James M.; Hurley, David E.

    2010-01-19

    This document was prepared to provide evaluations and recommendations regarding nondestructive evaluation methods that might be used to determine cracks and bowing in the ceiling of waste storage tanks on the Hanford site. The goal was to determine cracks as small as 1/16 in. wide in the ceiling, and bowing as small as 0.25 in. This report describes digital video camera methods that can be used to detect a crack in the ceiling of the dome, and methods for determining the surface topography of the ceiling in the waste storage tanks to detect localized movements in the surface. A literature search, combined with laboratory testing, comprised this study.

  17. PID Techniques: Alternatives to RICH Methods

    CERN Document Server

    Va'vra, Jerry

    2016-01-01

    In this review article we discuss new updates on PID techniques, other than the Cherenkov method. In particular, we discuss recent efforts to develop high resolution timing, placing an emphasis on small scale test results.

  18. Alternating Krylov subspace image restoration methods

    National Research Council Canada - National Science Library

    Abad, J.O; Morigi, S; Reichel, L; Sgallari, F

    2012-01-01

    ... of the Krylov subspace used. However, our solution methods, suitably modified, also can be applied when no bound for the norm of η δ is known. We determine an approximation of the desired image u ˆ by so...

  19. Alternative Therapy of Animals – Homeopathy and Other Alternative Methods of Therapy

    Directory of Open Access Journals (Sweden)

    Løken Torleiv

    2002-03-01

    Full Text Available Alternative therapy of animals is described, in the meaning of alternatives to veterinary therapy traditionally accepted by veterinary faculties and schools and included in their curricula. Alternative therapy composes of different disciplines, of which homeopathy is emphasised in this presentation. Information is given on the use and interest of such therapy among veterinarians and animal owners. Homeopathy as other alternative therapies, may offer great advances, if they induce any effect. Some of the disciplines are based on a scientifically accepted documentation. Others, and homeopathy in particular, are missing such a documentation of effect. The justification of including alternative therapy in treating animals is discussed. Research in alternative therapy of animals is greatly needed, in particular to evaluate therapeutic methods which are in extensive use without any documented effect. An ongoing research project in Norway on the effect of homeopathic treatment of mastitis in cows is shortly presented.

  20. Validation of a blood group genotyping method based on high-resolution melting curve analysis.

    Science.gov (United States)

    Gong, Tianxiang; Hong, Ying; Wang, Naihong; Fu, Xuemei; Zhou, Changhua

    2014-01-01

    The detection of polymorphism is the basis of blood group genotyping and phenotype prediction. Genotyping may be useful to determine blood groups when serologic results are unclear. The development and application of different methods for blood group genotyping may be needed as a substitute for blood group typing. The purpose of this study is to establish an approach for blood group genotyping based on a melting curve analysis of real-time polymerase chain reaction (PCR). Using DNA extracted from whole blood, we developed and validated a DNA typing method for detecting DO*01/DO*02, DO*01/DI*02, LU*01/LU*02, and GYPB*03/GYBP*04 alleles using a melting curve analysis. All assays were confirmed with a commercial reagent containing sequence-specific primers (PCR-SSP), and a cohort of the samples was confirmed with sequencing. Results for all blood groups were within the range of specificity and assay variability. Genotypes of 300 blood donors were fully consistent with PCR-SSP data. The obtained genotype distribution is in complete concordance with existing data for the Chinese population. There are several advantages for this approach of blood group genotyping: lower contamination rates with PCR products in this laboratory, ease of performance, automation potential, and rapid cycling time.

  1. HERBAL MEDICINE AMONG COMPLEMENTARY AND ALTERNATIVE MEDICINE METHODS

    OpenAIRE

    A. Ruban; Rodioniva, T.

    2012-01-01

    Alternative medicine methods may incorporate or base themselves on traditional medicine [1], folk knowledge [2], spiritual beliefs, or newly conceived approaches to healing. The major complementary and alternative medicine systems have many common characteristics, treating the whole person, including a focus on individualizing treatments, promoting self-care and self-healing, and recognizing the spiritual nature of each individual. Complementary and alternative medicine often lacks or has onl...

  2. Alternative methods for characterization of extracellular vesicles

    Directory of Open Access Journals (Sweden)

    Fatemeh eMomen-Heravi

    2012-09-01

    Full Text Available Extracellular vesicles are nano-sized vesicles released by all cells in vitro as well as in vivo. Their role has been implicated mainly in cell-cell communication, but also in disease biomarkers and more recently in gene delivery. They represent a snapshot of the cell status at the moment of release and carry bioreactive macromolecules such as nucleic acids, proteins and lipids. A major limitation in this emerging new field is the availability/awareness of techniques to isolate and properly characterize Extracellular vesicles. The lack of gold standards makes comparing different studies very difficult and may potentially hinder some Extracellular vesicles -specific evidence. Characterization of Extracellular vesicles has also recently seen many advances with the use of Nanoparticle Tracking Analysis (NTA, flow cytometry, cryo-EM instruments and proteomic technologies. In this review, we discuss the latest developments in translational technologies involving characterization methods including the facts in their support and the challenges they face.

  3. Analysis of Miami Blue Sampling Method and Potential Alternatives

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Alternatives are provided regarding methods to monitor the population of butterflies given limited staffing and what levels are needed to assess population trends.

  4. A quantitative method for evaluating alternatives. [aid to decision making

    Science.gov (United States)

    Forthofer, M. J.

    1981-01-01

    When faced with choosing between alternatives, people tend to use a number of criteria (often subjective, rather than objective) to decide which is the best alternative for them given their unique situation. The subjectivity inherent in the decision-making process can be reduced by the definition and use of a quantitative method for evaluating alternatives. This type of method can help decision makers achieve degree of uniformity and completeness in the evaluation process, as well as an increased sensitivity to the factors involved. Additional side-effects are better documentation and visibility of the rationale behind the resulting decisions. General guidelines for defining a quantitative method are presented and a particular method (called 'hierarchical weighted average') is defined and applied to the evaluation of design alternatives for a hypothetical computer system capability.

  5. Performance of Differents Genotyps of Brazilian Orchid Cultivation in Alternatives Substrates

    Directory of Open Access Journals (Sweden)

    Ricardo Tadeu de Faria

    2001-12-01

    Full Text Available Two native Brazilian orchid especies, Oncidium baueri and Maxillaria picta, were grown in different substrate mixtures. The plants were cultivated in ceramic pots in a greenhouse with 50% of shadind light and watered three times a week. The following substrates were used: 1 de-fibered xaxim; 2xaxim cubes; 3 vermiculite; 4 carbonized rice husk; 5 charcoal; 6 charcoal + carbonized rice husk; 7 crocks; 8 vermiculite and charcoal; 9 vermiculite + carbonized rice husks; 10 extruded polystyrene + charcoal; 11 pine bark + charcoal + extruded polystyrene; 12 vermiculite + carbonized rice husks + extruded polystyrene + charcoal; 13 pine bark. The substrate ratio was 1:1 in the mixture. NPK 10-10-10 leaf fertilizer was applied every thirty days and castor bean cake and bone powder organic fertilizer were applied every ninety days. A randomized complete block design was used with 10 replications. Growth and rooting were assessed after eight months. The best alternative substrate to O. baueri was vermiculie and the best alternatives substrates to M. picta were vermiculite and charcoal and vermiculite + carbonized rice husks.Diferentes misturas de substratos foram estudados para duas variedades de orquídeas nativas do Brasil: Oncidium baueri e Maxillaria pictea. As plantas foram cultivadas em vasos de cerâmica em casa de vegetação com 50% de luminosidade e regadas 3 vezes por semana. Os substratos utilizados foram os seguintes: 1xaxim desfibrado; 2xaxim e cubos; 3vermiculita; 4casca de arroz carbonizada; 5carvão; 6carvão + casca de arroz carbonizada; 7cacos de cerâmica; 8vermiculita + carvão; 9vermiculita + casca da arroz carbonizada; 10isopor + carvão; 11casca de pinus + carvão + isopor; 12 vermiculita + casca da arroz carbonizada + isopor + carvão; 13casca de pinus. A proporção dos substratos foi de 1:1na mistura. A cada trinta dias foi realizado uma adubação foliar com NPK: 10-10-10 e a cada 90 dias uma adubação orgânica com torta de

  6. Discriminative power of Campylobacter phenotypic and genotypic typing methods.

    Science.gov (United States)

    The aim of this study was to compare typing methods, individually and combined, to use in the routine surveillance of Campylobacter in broiler carcasses. C. jejuni (n=94) and C. coli (n=52) isolated from different broiler carcasses were characterized using different typing methods: multilocus sequen...

  7. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies

    Directory of Open Access Journals (Sweden)

    Charbonnel Nathalie

    2010-05-01

    Full Text Available Abstract Background High-throughput sequencing technologies offer new perspectives for biomedical, agronomical and evolutionary research. Promising progresses now concern the application of these technologies to large-scale studies of genetic variation. Such studies require the genotyping of high numbers of samples. This is theoretically possible using 454 pyrosequencing, which generates billions of base pairs of sequence data. However several challenges arise: first in the attribution of each read produced to its original sample, and second, in bioinformatic analyses to distinguish true from artifactual sequence variation. This pilot study proposes a new application for the 454 GS FLX platform, allowing the individual genotyping of thousands of samples in one run. A probabilistic model has been developed to demonstrate the reliability of this method. Results DNA amplicons from 1,710 rodent samples were individually barcoded using a combination of tags located in forward and reverse primers. Amplicons consisted in 222 bp fragments corresponding to DRB exon 2, a highly polymorphic gene in mammals. A total of 221,789 reads were obtained, of which 153,349 were finally assigned to original samples. Rules based on a probabilistic model and a four-step procedure, were developed to validate sequences and provide a confidence level for each genotype. The method gave promising results, with the genotyping of DRB exon 2 sequences for 1,407 samples from 24 different rodent species and the sequencing of 392 variants in one half of a 454 run. Using replicates, we estimated that the reproducibility of genotyping reached 95%. Conclusions This new approach is a promising alternative to classical methods involving electrophoresis-based techniques for variant separation and cloning-sequencing for sequence determination. The 454 system is less costly and time consuming and may enhance the reliability of genotypes obtained when high numbers of samples are studied

  8. Nucleic acid amplification: Alternative methods of polymerase chain reaction.

    Science.gov (United States)

    Fakruddin, Md; Mannan, Khanjada Shahnewaj Bin; Chowdhury, Abhijit; Mazumdar, Reaz Mohammad; Hossain, Md Nur; Islam, Sumaiya; Chowdhury, Md Alimuddin

    2013-10-01

    Nucleic acid amplification is a valuable molecular tool not only in basic research but also in application oriented fields, such as clinical medicine development, infectious diseases diagnosis, gene cloning and industrial quality control. A comperehensive review of the literature on the principles, applications, challenges and prospects of different alternative methods of polymerase chain reaction (PCR) was performed. PCR was the first nucleic acid amplification method. With the advancement of research, a no of alternative nucleic acid amplification methods has been developed such as loop mediated isothermal amplification, nucleic acid sequence based amplification, strand displacement amplification, multiple displacement amplification. Most of the alternative methods are isothermal obviating the need for thermal cyclers. Though principles of most of the alternate methods are relatively complex than that of PCR, they offer better applicability and sensitivity in cases where PCR has limitations. Most of the alternate methods still have to prove themselves through extensive validation studies and are not available in commercial form; they pose the potentiality to be used as replacements of PCR. Continuous research is going on in different parts of the world to make these methods viable technically and economically.

  9. Alternate Location Method of a Robot Team in Unknown Environment

    Institute of Scientific and Technical Information of China (English)

    WANG Jian-zhong; LIU Jing-jing

    2008-01-01

    The alternate location method of a robot team is proposed. Three of the robots are kept still as beacon robots, not always the same ones, while the others are regarded as mobile robots. The mobile robots alternatively measure the distance between one of them and three beacon robots with ultrasonic measurement module. The distance data are combined with its dead-reckoning information using iterated extended Kalman filter(IEKF) to realize the optimal estimate of its position. According to the condition the future beacon robots positions should be desired ones, the target function and the nonlinear constrain equations are set up which are used by nonlinear optimization algorithm to estimate the position of the future beacon robots. By alternately changing the robots roles as active beacon, the alternate location in unknown environment can be realized. Process and result of the simulation test are given and the position estimation error is within±10mm, which proves the validity of this method.

  10. Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus

    Directory of Open Access Journals (Sweden)

    Rogers Stephanie M

    2012-05-01

    Full Text Available Abstract Background The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV as a model plant virus. Method This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors. Result Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA. Conclusion The molecular typing method presented is one tool that could be

  11. Alternative methods in toxicity testing: the current approach

    OpenAIRE

    Araújo,Gabrielle Luck de; Campos,Maria Augusta Amaral; Valente,Maria Anete Santana; Silva,Sarah Cristina Teixeira; França,Flávia Dayrell; Chaves,Miriam Martins; Tagliati, Carlos Alberto

    2014-01-01

    Alternative methods are being developed to reduce, refine, and replace (3Rs) animals used in experiments, aimed at protecting animal welfare. The present study reports alternative tests which are based on the principles of the 3Rs and the efforts made to validate these tests. In Europe, several methodologies have already been implemented, such as tests of irritability, cell viability, and phototoxicity as well as in vitro mathematical models together with the use of in silico tools. This is a...

  12. Discriminative power of Campylobacter phenotypic and genotypic typing methods.

    Science.gov (United States)

    Duarte, Alexandra; Seliwiorstow, Tomasz; Miller, William G; De Zutter, Lieven; Uyttendaele, Mieke; Dierick, Katelijne; Botteldoorn, Nadine

    2016-06-01

    The aim of this study was to compare different typing methods, individually and combined, for use in the monitoring of Campylobacter in food. Campylobacter jejuni (n=94) and Campylobacter coli (n=52) isolated from different broiler meat carcasses were characterized using multilocus sequence typing (MLST), flagellin gene A restriction fragment length polymorphism typing (flaA-RFLP), antimicrobial resistance profiling (AMRp), the presence/absence of 5 putative virulence genes; and, exclusively for C. jejuni, the determination of lipooligosaccharide (LOS) class. Discriminatory power was calculated by the Simpson's index of diversity (SID) and the congruence was measured by the adjusted Rand index and adjusted Wallace coefficient. MLST was individually the most discriminative typing method for both C. jejuni (SID=0.981) and C. coli (SID=0.957). The most discriminative combination with a SID of 0.992 for both C. jejuni and C. coli was obtained by combining MLST with flaA-RFLP. The combination of MLST with flaA-RFLP is an easy and feasible typing method for short-term monitoring of Campylobacter in broiler meat carcass.

  13. Alternative methods for top quark mass measurements at the CMS

    CERN Document Server

    Kim, Ji Hyun

    2016-01-01

    The top quark mass is a fundamental parameter of the standard model and together with the W boson mass and the Higgs boson mass it provides a strong self-consistency check of the electroweak theory. Recently several new measurements of the top quark mass using alternative observables and reconstruction methods are performed by the CMS collaborations at the CERN LHC. Alternative methods can give a insight by providing different systematic sensitivities while standard ones are currently limited by jet energy uncertainties. We introduce various results from new methods including the one using a charmed meson, which are found to be consistent with what is obtained in standard measurements.

  14. A computational method for genotype calling in family-based sequencing data.

    Science.gov (United States)

    Chang, Lun-Ching; Li, Bingshan; Fang, Zhou; Vrieze, Scott; McGue, Matt; Iacono, William G; Tseng, George C; Chen, Wei

    2016-01-16

    As sequencing technologies can help researchers detect common and rare variants across the human genome in many individuals, it is known that jointly calling genotypes across multiple individuals based on linkage disequilibrium (LD) can facilitate the analysis of low to modest coverage sequence data. However, genotype-calling methods for family-based sequence data, particularly for complex families beyond parent-offspring trios, are still lacking. In this study, first, we proposed an algorithm that considers both linkage disequilibrium (LD) patterns and familial transmission in nuclear and multi-generational families while retaining the computational efficiency. Second, we extended our method to incorporate external reference panels to analyze family-based sequence data with a small sample size. In simulation studies, we show that modeling multiple offspring can dramatically increase genotype calling accuracy and reduce phasing and Mendelian errors, especially at low to modest coverage. In addition, we show that using external panels can greatly facilitate genotype calling of sequencing data with a small number of individuals. We applied our method to a whole genome sequencing study of 1339 individuals at ~10X coverage from the Minnesota Center for Twin and Family Research. The aggregated results show that our methods significantly outperform existing ones that ignore family constraints or LD information. We anticipate that our method will be useful for many ongoing family-based sequencing projects. We have implemented our methods efficiently in a C++ program FamLDCaller, which is available from http://www.pitt.edu/~wec47/famldcaller.html.

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

    Directory of Open Access Journals (Sweden)

    William E Stutz

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

  16. Evaluation of a Simple Method to Screen Soybean Genotypes for Salt Tolerance

    Science.gov (United States)

    Excessive salt can reduce soybean yield in grower fields. Salt tolerant cultivars are needed to prevent field yield losses where excess salt is a problem. Soybean genotypes have primarily been evaluated for reaction to salt in the greenhouse using a labor intensive and costly hydroponics method. ...

  17. An Alternative Surgical Method for Treatment of Osteoid Osteoma.

    Science.gov (United States)

    Gökalp, Mehmet Ata; Gözen, Abdurrahim; Ünsal, Seyyid Şerif; Önder, Haci; Güner, Savaş

    2016-02-22

    BACKGROUND An osteoid osteoma is a benign bone tumor that tends to be osteoma can be treated with various conservative and surgical methods, but these have some risks and difficulties. The purpose of the present study was to present an alternative treatment method for osteoid osteoma and the results we obtained. MATERIAL AND METHODS In the period from 2010 to 2014, 10 patients with osteoid osteoma underwent nidus excision by using a safe alternative method in an operating room (OR) with no computed tomography (CT). The localization of the tumor was determined by use of a CT-guided Kirschner wire in the radiology unit, then, in the OR the surgical intervention was performed without removing the Kirschner wire. RESULTS Following the alternative intervention, all the patients were completely relieved of pain. In the follow-up, no recurrence or complication occurred. CONCLUSIONS The presented alternative method for treating osteoid osteoma is an efficient and practical procedure for surgeons working in clinics that lack specialized equipment.

  18. An Alternative Surgical Method for Treatment of Osteoid Osteoma

    Science.gov (United States)

    Gökalp, Mehmet Ata; Gözen, Abdurrahim; Ünsal, Seyyid Şerif; Önder, Haci; Güner, Savaş

    2016-01-01

    Background An osteoid osteoma is a benign bone tumor that tends to be osteoma can be treated with various conservative and surgical methods, but these have some risks and difficulties. The purpose of the present study was to present an alternative treatment method for osteoid osteoma and the results we obtained. Material/Methods In the period from 2010 to 2014, 10 patients with osteoid osteoma underwent nidus excision by using a safe alternative method in an operating room (OR) with no computed tomography (CT). The localization of the tumor was determined by use of a CT-guided Kirschner wire in the radiology unit, then, in the OR the surgical intervention was performed without removing the Kirschner wire. Results Following the alternative intervention, all the patients were completely relieved of pain. In the follow-up, no recurrence or complication occurred. Conclusions The presented alternative method for treating osteoid osteoma is an efficient and practical procedure for surgeons working in clinics that lack specialized equipment. PMID:26898923

  19. 27 CFR 24.22 - Alternate method or procedure.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Alternate method or procedure. 24.22 Section 24.22 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS WINE Administrative and Miscellaneous Provisions...

  20. A fast alternating projection method for complex frequency estimation

    CERN Document Server

    Andersson, Fredrik; Ivert, Per-Anders

    2011-01-01

    The problem of approximating a sampled function using sums of a fixed number of complex exponentials is considered. We use alternating projections between fixed rank matrices and Hankel matrices to obtain such an approximation. Convergence, convergence rates and error estimates for this technique are proven, and fast algorithms are developed. We compare the numerical results obtain with the MUSIC and ESPRIT methods.

  1. Innovative Teaching Practice: Traditional and Alternative Methods (Challenges and Implications)

    Science.gov (United States)

    Nurutdinova, Aida R.; Perchatkina, Veronika G.; Zinatullina, Liliya M.; Zubkova, Guzel I.; Galeeva, Farida T.

    2016-01-01

    The relevance of the present issue is caused be the strong need in alternative methods of learning foreign language and the need in language training and retraining for the modern professionals. The aim of the article is to identify the basic techniques and skills in using various modern techniques in the context of modern educational tasks. The…

  2. 40 CFR 35.6315 - Alternative methods for obtaining property.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Alternative methods for obtaining property. 35.6315 Section 35.6315 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY GRANTS AND OTHER FEDERAL ASSISTANCE STATE AND LOCAL ASSISTANCE Cooperative Agreements and Superfund State Contracts for Superfund Response Actions...

  3. Alternative method of retesting UF{sub 6} cylinders

    Energy Technology Data Exchange (ETDEWEB)

    Christ, R. [Nuclear Crago + Service GmbH, Hanau (Germany)

    1991-12-31

    The paper describes an alternative method to perform the periodic inspection of UF{sub 6} cylinders. The hydraulic test is replaced by ultrasonic checking of wall thickness and by magnetic particle testing of all the weld seams. Information about the legal background, the air leak test and the qualification of inspectors is also given.

  4. Alternating Anderson-Richardson method: An efficient alternative to preconditioned Krylov methods for large, sparse linear systems

    CERN Document Server

    Suryanarayana, Phanish; Pask, John E

    2016-01-01

    We generalize the recently proposed Alternating Anderson-Jacobi (AAJ) method (Pratapa et al., J. Comput. Phys. (2016), 306, 43--54) to include preconditioning, and demonstrate its efficiency and scaling in the solution of large, sparse linear systems on parallel computers. The resulting preconditioned Alternating Anderson-Richardson (AAR) method reduces to the AAJ method for a particular choice of preconditioner. The AAR method employs Anderson extrapolation at periodic intervals within a preconditioned Richardson iteration to accelerate convergence. In this work, we develop a version of the method that is particularly well suited for scalable high-performance computing. In applications to Helmholtz and Poisson equations, we show that the strong and weak parallel scaling of AAR is superior to both Generalized Minimal Residual (GMRES) and Conjugate Gradient (CG) methods, using the same preconditioning, in large-scale parallel calculations employing up to 110,592 computational cores. Moreover, we find that the ...

  5. Methods on Identification and Screening of Rice Genotypes with High Nitrogen Efficiency

    Institute of Scientific and Technical Information of China (English)

    CHENG Jian-feng; JIANG Han-yan; LIU Yi-bai; DAI Ting-bo; CAO Wei-xing

    2011-01-01

    In order to establish methods for indentification and screening of rice genotypes with high nitrogen (N) efficiency,N absorption efficiency (NAE),N utilization efficiency (NUE) and N harvest index (NHI) in ten rice genotypes were investgated at the elongation,booting,heading and maturity stages under six N levels in a pot experiment with soil-sand mixtures at various ratios.NAE in various rice genotypes firstly increased,peaked under a medium nitrogen rate of 0.177 g/kg and then decreased,but NUE and NHI always decreased with increasing nitrogen levels.NAE in various rice genotypes ever increased with growing process and NUE indicated a descending tendency of elongation stage>heading stage>maturity stage>booting stage.N level influenced rice NAE,NUE and NHI most,followed by genotype,and the both effects were significant at 0.01 level.In addition,the interaction effects of genotype and nitrogen level on rice NAE and NUE were significant at 0.01 level,but not significant on rice NHI.Because the maximum differences of NAE and NUE were found at the elongation stage,it was thought to be the most suitable stage for identification and screening these two paremeters.Therefore,the optimum conditions for identification and screening of rice NAE,NUE and NHI in a pot experiment were the nitrogen rate of 0.157 g/kg at the elongation stage,low nitrogen at the elongation stage,and the nitrogen rate of 0.277 g/kg at the maturity stage,respectively.

  6. The use of imputed sibling genotypes in sibship-based association analysis: On modeling alternatives, power and model misspecification

    NARCIS (Netherlands)

    Minica, C.C.; Dolan, C.V.; Hottenga, J.J.; Willemsen, G.; Vink, J.M.; Boomsma, D.I.

    2013-01-01

    When phenotypic, but no genotypic data are available for relatives of participants in genetic association studies, previous research has shown that family-based imputed genotypes can boost the statistical power when included in such studies. Here, using simulations, we compared the performance of tw

  7. International Harmonization and Cooperation in the Validation of Alternative Methods.

    Science.gov (United States)

    Barroso, João; Ahn, Il Young; Caldeira, Cristiane; Carmichael, Paul L; Casey, Warren; Coecke, Sandra; Curren, Rodger; Desprez, Bertrand; Eskes, Chantra; Griesinger, Claudius; Guo, Jiabin; Hill, Erin; Roi, Annett Janusch; Kojima, Hajime; Li, Jin; Lim, Chae Hyung; Moura, Wlamir; Nishikawa, Akiyoshi; Park, HyeKyung; Peng, Shuangqing; Presgrave, Octavio; Singer, Tim; Sohn, Soo Jung; Westmoreland, Carl; Whelan, Maurice; Yang, Xingfen; Yang, Ying; Zuang, Valérie

    The development and validation of scientific alternatives to animal testing is important not only from an ethical perspective (implementation of 3Rs), but also to improve safety assessment decision making with the use of mechanistic information of higher relevance to humans. To be effective in these efforts, it is however imperative that validation centres, industry, regulatory bodies, academia and other interested parties ensure a strong international cooperation, cross-sector collaboration and intense communication in the design, execution, and peer review of validation studies. Such an approach is critical to achieve harmonized and more transparent approaches to method validation, peer-review and recommendation, which will ultimately expedite the international acceptance of valid alternative methods or strategies by regulatory authorities and their implementation and use by stakeholders. It also allows achieving greater efficiency and effectiveness by avoiding duplication of effort and leveraging limited resources. In view of achieving these goals, the International Cooperation on Alternative Test Methods (ICATM) was established in 2009 by validation centres from Europe, USA, Canada and Japan. ICATM was later joined by Korea in 2011 and currently also counts with Brazil and China as observers. This chapter describes the existing differences across world regions and major efforts carried out for achieving consistent international cooperation and harmonization in the validation and adoption of alternative approaches to animal testing.

  8. Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry.

    Science.gov (United States)

    Viollet, Louis; Glusman, Gustavo; Murphy, Kelley J; Newcomb, Tara M; Reyna, Sandra P; Sweney, Matthew; Nelson, Benjamin; Andermann, Frederick; Andermann, Eva; Acsadi, Gyula; Barbano, Richard L; Brown, Candida; Brunkow, Mary E; Chugani, Harry T; Cheyette, Sarah R; Collins, Abigail; DeBrosse, Suzanne D; Galas, David; Friedman, Jennifer; Hood, Lee; Huff, Chad; Jorde, Lynn B; King, Mary D; LaSalle, Bernie; Leventer, Richard J; Lewelt, Aga J; Massart, Mylynda B; Mérida, Mario R; Ptáček, Louis J; Roach, Jared C; Rust, Robert S; Renault, Francis; Sanger, Terry D; Sotero de Menezes, Marcio A; Tennyson, Rachel; Uldall, Peter; Zhang, Yue; Zupanc, Mary; Xin, Winnie; Silver, Kenneth; Swoboda, Kathryn J

    2015-01-01

    Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clusteredin exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K(26%) and 11 had G947R (8%) mutations [corrected].Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.

  9. Development of T m -shift genotyping method for detection of cat-derived Giardia lamblia.

    Science.gov (United States)

    Pan, Weida; Fu, Yeqi; Abdullahi, Auwalu Yusuf; Wang, Mingwei; Shi, Xianli; Yang, Fang; Yu, Xingang; Yan, Xinxin; Zhang, Pan; Hang, Jianxiong; Li, Guoqing

    2017-04-01

    To develop T m -shift genotyping method for detection of cat-derived Giardia lamblia, two sets of primers with two GC-rich tails of unequal length attached to their 5'-end were designed according to two SNPs (BG434 and BG170) of β-giardin (bg) gene, and specific PCR products were identified by inspection of a melting curve on real-time PCR thermocycler. A series of experiments on the stability, sensitivity, and accuracy of T m -shift method was tested, and clinical samples were also detected. The results showed that two sets of primers based on SNP could distinguish accurately between assemblages A and F. Coefficient of variation of T m values of assemblage A and F was 0.14 and 0.07% in BG434 and 0.10 and 0.11% in BG170, respectively. The lowest detection concentration was 4.52 × 10(-5) and 4.88 × 10(-5) ng/μL samples of assemblage A and F standard plasmids. The T m -shift genotyping results of ten DNA samples from the cat-derived G. lamblia were consistent with their known genotypes. The detection rate of clinical samples by T m -shift was higher than that by microscopy, and their genotyping results were in complete accordance with sequencing results. It is concluded that the T m -shift genotyping method is rapid, specific, and sensitive and may provide a new technological mean for molecular detection and epidemiological investigation of the cat-derived G. lamblia.

  10. Application of Method of Multicriteria Alternatives for Land Assessment

    Directory of Open Access Journals (Sweden)

    Pavel V. Grigorev

    2017-06-01

    Full Text Available This article discusses the use of the multicriteria alternatives method for the assessment of a real estate object taking into account the concept of a system of standards, rules and requirements in the field of valuation activities, considering international standards for valuation. The main means for work and costs associated with allotment and development of the built-up area are indicated. In the work, the assessment of four sites is carried out taking into account three parameters: the distance from the construction site to the center by car; cost of 1 ha of land of each of the plots; deterioration of the centralized heat supply networks. The results show that the method of multicriteria alternatives is objective and optimal when comparing land sites on the criteria with different units of measurements. The advantage of this method is the possibility to apply it to evaluation in different areas of the economy.

  11. SLA-DRB1 and -DQB1 genotyping by the PCR-SSOP-Luminex method.

    Science.gov (United States)

    Ando, A; Shigenari, A; Ota, M; Sada, M; Kawata, H; Azuma, F; Kojima-Shibata, C; Nakajoh, M; Suzuki, K; Uenishi, H; Kulski, J K; Inoko, H

    2011-07-01

    A simple and novel genotyping method was developed to detect alleles at the swine leukocyte antigen (SLA)-DRB1 and -DQB1 class II loci by using polymerase chain reaction (PCR)-fluorescently labeled sequence-specific oligonucleotide probes (SSOPs) and Luminex 100 xMAP detection. The PCR-SSOP-Luminex method exhibited accuracy of 95% for both SLA-DRB1 and -DQB1 in 6 homozygous and 16 heterozygous pig samples as confirmed by sequencing the PCR products of the same samples. In addition, 12 low-resolution SLA class II haplotypes consisting of 7 and 9 DRB1 and DQB1 alleles were identified, respectively, in one population of 283 Landrace pigs. This genotyping method facilitates the rapid and accurate identification of two- or four-digit alleles at the SLA-DRB1 and -DQB1 loci. © 2011 John Wiley & Sons A/S.

  12. Optimization of a method for the profiling and quantification of saponins in different green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodriguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-07-01

    The main goal of this study was the optimization of a HPLC-MS method for the qualitative and quantitative analysis of asparagus saponins. The method includes extraction with aqueous ethanol, cleanup by solid phase extraction, separation by reverse phase chromatography, electrospray ionization, and detection in a single quadrupole mass analyzer. The method was used for the comparison of selected genotypes of Huétor-Tájar asparagus landrace and selected varieties of commercial diploid hybrids of green asparagus. The results showed that while protodioscin was almost the only saponin detected in the commercial hybrids, eight different saponins were detected in the Huétor-Tájar asparagus genotypes. The mass spectra indicated that HT saponins are derived from a furostan type steroidal genin having a single bond between carbons 5 and 6 of the B ring. The total concentration of saponins was found to be higher in triguero asparagus than in commercial hybrids.

  13. HPV detection methods and genotyping techniques in screening for cervical cancer.

    Science.gov (United States)

    Eide, Maj Liv; Debaque, Hervé

    2012-12-01

    Human papillomaviruses (HPV), double-stranded DNA viruses, are causing many mucocutaneous diseases, benign or malignant, ranging from common warts to malignancies involving the upper aerodigestive tract and the anogenital sphere. The diagnosis of HPV infection is based primarily on the viral genome detection by molecular biological methods, given the difficulty in routine cultivation of these viruses. The current trend in screening against cervical cancer is to improve the sensitivity of screening with new methods and to propose new algorithms for diagnostic and therapeutic decisions. The development of liquid-based cytology facilitates the cytologic diagnosis and molecular assays from the same sample. There are two main types of HPV detection methods used on uterine cervical samples: signal amplification methods (hybridization techniques in liquid phase) and target amplification methods (the techniques of gene amplification or Polymerase Chain Reaction [PCR]). Genotyping techniques are also developed: they are based on an amplification technique followed by hybridization with probe specific types. In addition to the detection, genotyping techniques allow quantitative detection of viral DNA of HPV genotype and so monitor changes in viral load over time. Another approach relies on the detection of messenger RNA (mRNA) of HPV proteins E6 and E7 oncogenes, which would appear to be a relevant marker to identify and monitor women at risk of progression to a precancerous lesion or cervical cancer.

  14. Methods of analysis and number of replicates for trials with large numbers of soybean genotypes

    Directory of Open Access Journals (Sweden)

    Gilvani Matei

    Full Text Available ABSTRACT: The aim of this study was to evaluate the experimental precision of different methods of statistical analysis for trials with large numbers of soybean genotypes, and their relationship with the number of replicates. Soybean yield data (nine trials; 324 genotypes; 46 cultivars; 278 lines; agricultural harvest of 2014/15 were used. Two of these trials were performed at the same location, side by side, forming a trial with six replicates. Each trial was analyzed by the randomized complete block, triple lattice design, and use of the Papadakis method. The selective accuracy, least significant difference, and Fasoulas differentiation index were estimated, and model assumptions were tested. The resampling method was used to study the influence of the number of replicates, by varying the number of blocks and estimating the precision measurements. The experimental precision indicators of the Papadakis method are more favorable as compared to the randomized complete block design and triple lattice. To obtain selective accuracy above the high experimental precision range in trials with 324 soybean genotypes, two repetitions can be used, and data can be analyzed using the randomized complete block design or Papadakis method.

  15. Alternative methods for the control of postharvest citrus diseases.

    Science.gov (United States)

    Talibi, I; Boubaker, H; Boudyach, E H; Ait Ben Aoumar, A

    2014-07-01

    The postharvest diseases of citrus fruit cause considerable losses during storage and transportation. These diseases are managed principally by the application of synthetic fungicides. However, the increasing concern for health hazards and environmental pollution due to chemical use has required the development of alternative strategies for the control of postharvest citrus diseases. Management of postharvest diseases using microbial antagonists, natural plant-derived products and Generally Recognized As Safe compounds has been demonstrated to be most suitable to replace the synthetic fungicides, which are either being banned or recommended for limited use. However, application of these alternatives by themselves may not always provide a commercially acceptable level of control of postharvest citrus diseases comparable to that obtained with synthetic fungicides. To provide more effective disease control, a multifaceted approach based on the combination of different postharvest treatments has been adopted. Actually, despite the distinctive features of these alternative methods, several reasons hinder the commercial use of such treatments. Consequently, research should emphasize the development of appropriate tools to effectively implement these alternative methods to commercial citrus production.

  16. Alternative statistical methods for cytogenetic radiation biological dosimetry

    CERN Document Server

    Fornalski, Krzysztof Wojciech

    2014-01-01

    The paper presents alternative statistical methods for biological dosimetry, such as the Bayesian and Monte Carlo method. The classical Gaussian and robust Bayesian fit algorithms for the linear, linear-quadratic as well as saturated and critical calibration curves are described. The Bayesian model selection algorithm for those curves is also presented. In addition, five methods of dose estimation for a mixed neutron and gamma irradiation field were described: two classical methods, two Bayesian methods and one Monte Carlo method. Bayesian methods were also enhanced and generalized for situations with many types of mixed radiation. All algorithms were presented in easy-to-use form, which can be applied to any computational programming language. The presented algorithm is universal, although it was originally dedicated to cytogenetic biological dosimetry of victims of a nuclear reactor accident.

  17. AN ALTERNATIVE GREEN SCREEN KEYING METHOD FOR FILM VISUAL EFFECTS

    Directory of Open Access Journals (Sweden)

    Jin Zhi

    2015-04-01

    Full Text Available This study focuses on a green screen keying method developed especially for film visual effects. There are a series of ways of using existing tools for creating mattes from green or blue screen plates. However, it is still a time-consuming process, and the results vary especially when it comes to retaining tiny details, such as hair and fur. This paper introduces an alternative concept and method for retaining edge details of characters on a green screen plate, also, a number of connected mathematical equations are explored. At the end of this study, a simplified process of applying this method in real productions is also tested.

  18. Top-quark mass measurements at the LHC: alternative methods

    CERN Document Server

    Vos, Marcel

    2016-01-01

    Alternative top quark mass determinations can provide inputs to the world average with orthogonal systematic uncertainties and may help to refine the interpretation of the standard method. Among a number of recent results I focus on the extractions by ATLAS and CMS of the top quark pole mass from the top quark pair and tt + 1 jet production cross-section, which have now reached a precision of 1%.

  19. Top-quark mass measurements at the LHC: alternative methods

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00240580; The ATLAS collaboration

    2016-01-01

    Alternative top quark mass determinations can provide inputs to the world average with orthogonal systematic uncertainties and may help to refine the interpretation of the standard method. Among a number of recent results I focus on the extractions by ATLAS and CMS of the top quark pole mass from the \\ttbar{} pair and \\ttbar{} + 1 jet production cross-section, which have now reached a precision of 1\\%.

  20. ALTERNATING DIRECTION FINITE ELEMENT METHOD FOR SOME REACTION DIFFUSION MODELS

    Institute of Scientific and Technical Information of China (English)

    江成顺; 刘蕴贤; 沈永明

    2004-01-01

    This paper is concerned with some nonlinear reaction - diffusion models. To solve this kind of models, the modified Laplace finite element scheme and the alternating direction finite element scheme are established for the system of patrical differential equations. Besides, the finite difference method is utilized for the ordinary differential equation in the models. Moreover, by the theory and technique of prior estimates for the differential equations, the convergence analyses and the optimal L2- norm error estimates are demonstrated.

  1. A novel high-resolution melting analysis-based method for Yersinia enterocolitica genotyping.

    Science.gov (United States)

    Souza, Roberto A; Falcão, Juliana P

    2014-11-01

    Pathogenic Yersinia enterocolitica strains are associated with biotypes 1B, 2-5, while environmental strains with biotype 1A. In this work a method for Y. enterocolitica genotyping based on HRMA to determine SNPs was developed and the genetic diversity of 50 strains was determined. The strains were clustered into three groups consistent with the pathogenic profile of each biotype. The results provided a better understanding of the Y. enterocolitica genetic variability.

  2. Development of a bead-based multiplex genotyping method for diagnostic characterization of HPV infection.

    Directory of Open Access Journals (Sweden)

    Mee Young Chung

    Full Text Available The accurate genotyping of human papillomavirus (HPV is clinically important because the oncogenic potential of HPV is dependent on specific genotypes. Here, we described the development of a bead-based multiplex HPV genotyping (MPG method which is able to detect 20 types of HPV (15 high-risk HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68 and 5 low-risk HPV types 6, 11, 40, 55, 70 and evaluated its accuracy with sequencing. A total of 890 clinical samples were studied. Among these samples, 484 were HPV positive and 406 were HPV negative by consensus primer (PGMY09/11 directed PCR. The genotyping of 484 HPV positive samples was carried out by the bead-based MPG method. The accuracy was 93.5% (95% CI, 91.0-96.0, 80.1% (95% CI, 72.3-87.9 for single and multiple infections, respectively, while a complete type mismatch was observed only in one sample. The MPG method indiscriminately detected dysplasia of several cytological grades including 71.8% (95% CI, 61.5-82.3 of ASCUS (atypical squamous cells of undetermined significance and more specific for high grade lesions. For women with HSIL (high grade squamous intraepithelial lesion and SCC diagnosis, 32 women showed a PPV (positive predictive value of 77.3% (95% CI, 64.8-89.8. Among women >40 years of age, 22 women with histological cervical cancer lesions showed a PPV of 88% (95% CI, 75.3-100. Of the highest risk HPV types including HPV-16, 18 and 31 positive women of the same age groups, 34 women with histological cervical cancer lesions showed a PPV of 77.3% (95% CI, 65.0-89.6. Taken together, the bead-based MPG method could successfully detect high-grade lesions and high-risk HPV types with a high degree of accuracy in clinical samples.

  3. Integrated Parasite Management for Livestock - Alternative control methods

    Directory of Open Access Journals (Sweden)

    Souvik Paul1

    Full Text Available Internal parasites are considered by some to be one of the most economically important constraints in raising livestock. The growing concern about the resistance of internal parasites to all classes of dewormers has caused people to look for alternatives. As dewormers lose their effectiveness, the livestock community fears increasing economic losses from worms. There is no one thing that can be given or done to replace chemical dewormers. It will take a combination of extremely good management techniques and possibly some alternative therapies. It is not wise to think that one can just stop deworming animals with chemical dewormers. It is something one will need to change gradually, observing and testing animals and soil, in order to monitor the progress. Alternative parasite control is an area that is receiving a lot of interest and attention. Programs and research will continue in the pursuit of parasite control, using alternative and more management-intensive methods. [Veterinary World 2010; 3(9.000: 431-435

  4. Dry matter genotypes of Cynodon by microwave and conventional oven methods

    Directory of Open Access Journals (Sweden)

    Euclides Reuter de Oliveira

    2013-02-01

    Full Text Available The aimed of this work was to comparing the drying process in a microwave oven and forced air ventilation, as well as their effects on the chemical composition of different genotypes of the genus Cynodon (Tifton 85, Jiggs, Russell, Tifton 68 and Vaquero collected at different ages cutting (28, 48, 63 and 79 days. The experimental design was a randomized block in a split-plot design, with 4 replicates. There was no difference (P>0.05 between the methods analyzed on the chemical composition of the genotypes studied. Increasing age cutoff negatively influenced (P<0.05 the crude protein content of the different plant parts. A significant increase (P<0.05 of dry matter, neutral detergent fiber, acid detergent fiber and dry matter production was observed with increasing age cut. The use of the microwave oven is a quick and precise method obtain the dry matter content of the fodder showing efficiency similar to the method of drying in an oven with forced air circulation. The genotypes showed better chemical composition results when handled at age 28 days.

  5. Development of a rapid HRM genotyping method for detection of dog-derived Giardia lamblia.

    Science.gov (United States)

    Tan, Liping; Yu, Xingang; Abdullahi, Auwalu Yusuf; Wu, Sheng; Zheng, Guochao; Hu, Wei; Song, Meiran; Wang, Zhen; Jiang, Biao; Li, Guoqing

    2015-11-01

    Giardia lamblia is a zoonotic flagellate protozoan in the intestine of human and many mammals including dogs. To assess a threat of dog-derived G. lamblia to humans, the common dog-derived G. lamblia assemblages A, C, and D were genotyped by high-resolution melting (HRM) technology. According to β-giardin gene sequence, the qPCR-HRM primers BG5 and BG7 were designed. A series of experiments on the stability, sensitivity, and accuracy of the HRM method were also tested. Results showed that the primers BG5 and BG7 could distinguish among three assemblages A, C, and D, which Tm value differences were about 1 °C to each other. The melting curves of intra-assay reproducibility were almost coincided, and those of inter-assay reproducibility were much the same shape. The lowest detection concentration was about 5 × 10(-6)-ng/μL sample. The genotyping results from 21 G. lamblia samples by the HRM method were in complete accordance with sequencing results. It is concluded that the HRM genotyping method is rapid, stable, specific, highly sensitive, and suitable for clinical detection and molecular epidemiological survey of dog-derived G. lamblia.

  6. A multicenter evaluation of genotypic methods for the epidemiologic typing of Legionella pneumophila serogroup 1

    DEFF Research Database (Denmark)

    Fry, Norman K.; Alexiou-Daniel, Stella; Bangsborg, Jette Marie

    1999-01-01

    OBJECTIVES: To compare genotypic methods for epidemiologic typing of Legionella pneumophila serogroup (sg) 1, in order to determine the best available method within Europe for implementation and standardization by members of the European Working Group on Legionella Infections. METHODS: Coded.......990 for PFGE using Sfil: E ranged from 0.06 for AP- and AP/rep-PCR to 1.00 for ribotyping using Pstl/EcoRI and AFLP: in general, E was inversely related to D. Although offering only limited discrimination (D=0.838), mAb typing was both rapid and highly epidemiologically concordant (E=1.00). CONCLUSIONS: Two...

  7. Hypoplastic thumb type IIIB: An alternative method for surgical repair

    Directory of Open Access Journals (Sweden)

    Salih Onur Basat

    2014-08-01

    Full Text Available Hypoplastic thumb is the second most common congenital deformity of the thumb. Thumb hypoplasia is characterized by diminished thumb size, metacarpal adduction, metacarpophalangeal joint instability, and thenar muscle hypoplasia. In the literature, different classification types of hypoplastic thumb have been used and different treatment methods described. In this case we presented an alternative palliative treatment method for a ten-year-old patient with modified Blauth's classification type IIIB hypoplastic thumb and one-year follow-up results. [Hand Microsurg 2014; 3(2.000: 59-61

  8. The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods

    NARCIS (Netherlands)

    Mulder, H.A.; Meuwissen, T.H.E.; Calus, M.P.L.; Veerkamp, R.F.

    2010-01-01

    In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing geneassisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-as

  9. A microsatellite-based method for genotyping diploid and triploid water frogs of the Rana esculenta hybrid complex

    DEFF Research Database (Denmark)

    Christiansen, Ditte Guldager

    2005-01-01

    Rana esculenta is a hybrid between Rana lessonae (LL) and Rana ridibunda (RR), and hybrids may be diploid (LR) or triploid (LLR or LRR). Genotypes can be roughly determined from erythrocyte size and morphometry in adult frogs, but accurate genotyping requires more labourious methods. Here I...

  10. Prediction of skin sensitizers using alternative methods to animal experimentation.

    Science.gov (United States)

    Johansson, Henrik; Lindstedt, Malin

    2014-07-01

    Regulatory frameworks within the European Union demand that chemical substances are investigated for their ability to induce sensitization, an adverse health effect caused by the human immune system in response to chemical exposure. A recent ban on the use of animal tests within the cosmetics industry has led to an urgent need for alternative animal-free test methods that can be used for assessment of chemical sensitizers. To date, no such alternative assay has yet completed formal validation. However, a number of assays are in development and the understanding of the biological mechanisms of chemical sensitization has greatly increased during the last decade. In this MiniReview, we aim to summarize and give our view on the recent progress of method development for alternative assessment of chemical sensitizers. We propose that integrated testing strategies should comprise complementary assays, providing measurements of a wide range of mechanistic events, to perform well-educated risk assessments based on weight of evidence. © 2014 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

  11. Osmotic shock as alternative method to control Acanthaster planci

    Institute of Scientific and Technical Information of China (English)

    Jairo Rivera-Posada; Leigh Owens

    2014-01-01

    Objective:To test six osmotic stressors as alternative methods to control Acanthaster planci (A. planci) outbreaks by exploiting their incapacity to tolerate drastic changes in osmolarity. Finding more effective ways to control A. planci outbreaks is one of the most immediate and effective ways by which to reverse rapid declines in the abundance of live coral cover in the Indo-Pacific. Methods: A total of 10 mL of each of the following chemicals: sodium chloride, ethylenediaminetetraacetic acid, sodium carbonate, sodium cholate, sodium deoxycholate, urea and mannitol were injected into individual healthy sea stars to examine which chemicals induced disease and death. Results:Four out of six chemicals used in this study induced disease. Sodium chloride, sodium cholate, sodium deoxycholate and ethylenediaminetetraacetic acid are capable of inducing death in injected sea stars offering an alternative option to control A. planci outbreaks. Conclusions: Hyperosmotic stress is a viable alternative to control A. planci outbreaks as massive cell death results when acute hypertonicity exceeds a certain level.

  12. An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test

    KAUST Repository

    Rodriguez, Jesse M.

    2013-01-01

    Studies that map disease genes rely on accurate annotations that indicate whether individuals in the studied cohorts are related to each other or not. For example, in genome-wide association studies, the cohort members are assumed to be unrelated to one another. Investigators can correct for individuals in a cohort with previously-unknown shared familial descent by detecting genomic segments that are shared between them, which are considered to be identical by descent (IBD). Alternatively, elevated frequencies of IBD segments near a particular locus among affected individuals can be indicative of a disease-associated gene. As genotyping studies grow to use increasingly large sample sizes and meta-analyses begin to include many data sets, accurate and efficient detection of hidden relatedness becomes a challenge. To enable disease-mapping studies of increasingly large cohorts, a fast and accurate method to detect IBD segments is required. We present PARENTE, a novel method for detecting related pairs of individuals and shared haplotypic segments within these pairs. PARENTE is a computationally-efficient method based on an embedded likelihood ratio test. As demonstrated by the results of our simulations, our method exhibits better accuracy than the current state of the art, and can be used for the analysis of large genotyped cohorts. PARENTE\\'s higher accuracy becomes even more significant in more challenging scenarios, such as detecting shorter IBD segments or when an extremely low false-positive rate is required. PARENTE is publicly and freely available at http://parente.stanford.edu/. © 2013 Springer-Verlag.

  13. Hysterectomy—Current Methods and Alternatives for Benign Indications

    Directory of Open Access Journals (Sweden)

    Michail S. Papadopoulos

    2010-01-01

    Full Text Available Hysterectomy is the commonest gynecologic operation performed not only for malignant disease but also for many benign conditions such as fibroids, endometrial hyperplasia, adenomyosis, uterine prolapse, dysfunctional uterine bleeding, and cervical intraepithelial neoplasia. There are many approaches to hysterectomy for benign disease: abdominal hysterectomy, vaginal hysterectomy, laparoscopic assisted vaginal hysterectomy (LAVH where a vaginal hysterectomy is assisted by laparoscopic procedures that do not include uterine artery ligation, total laparoscopic hysterectomy (TLH where the laparoscopic procedures include uterine artery ligation, and subtotal laparoscopic hysterectomy (STLH where there is no vaginal component and the uterine body is removed using a morcelator. In the last decades, many new techniques, alternative to hysterectomy with conservation of the uterus have been developed. They use modern technologies and their results are promising and in many cases comparable with hysterectomy. This paper is a review of all the existing hysterectomy techniques and the alternative methods for benign indications.

  14. Alternative Methods for Measuring Obesity in African American Women

    Science.gov (United States)

    Clark, Ashley E.; Taylor, Jacquelyn Y.; Wu, Chun Yi; Smith, Jennifer A.

    2013-01-01

    The use of body mass index (BMI) may not be the most appropriate measurement tool in determining obesity in diverse populations. We studied a convenience sample of 108 African American (AA) women to determine the best method for measuring obesity in this at-risk population. The purpose of this study was to determine if percent body fat (PBF) and percent body water (PBW) could be used as alternatives to BMI in predicting obesity and risk for hypertension (HTN) among AA women. After accounting for age, BMI, and the use of anti-hypertensive medication, PBF (p = 0.0125) and PBW (p = 0.0297) were significantly associated with systolic blood pressure, while BMI was not. Likewise, PBF (p = 0.0316) was significantly associated with diastolic blood pressure, while PBW and BMI were not. Thus, health care practitioners should consider alternative anthropometric measurements such as PBF when assessing obesity in AA women. PMID:23483836

  15. Highly multiplex and sensitive SNP genotyping method using a three-color fluorescence-labeled ligase detection reaction coupled with conformation-sensitive CE.

    Science.gov (United States)

    Choi, Woong; Jung, Gyoo Yeol

    2017-02-01

    For the development of clinically useful genotyping methods for SNPs, accuracy, simplicity, sensitivity, and cost-effectiveness are the most important criteria. Among the methods currently being developed for SNP genotyping technology, the ligation-dependent method is considered the simplest for clinical diagnosis. However, sensitivity is not guaranteed by the ligation reaction alone, and analysis of multiple targets is limited by the detection method. Although CE is an attractive alternative to error-prone hybridization-based detection, the multiplex assay process is complicated because of the size-based DNA separation principle. In this study, we employed the ligase detection reaction coupled with high-resolution CE-SSCP to develop an accurate, sensitive, and simple multiplex genotyping method. Ligase detection reaction could amplify ligated products through recurrence of denaturation and ligation reaction, and SSCP could separate these products according to each different structure conformation without size variation. Thus, simple and sensitive SNP analysis can be performed using this method involving the use of similar-sized probes, without complex probe design steps. We found that this method could not only accurately discriminate base mismatches but also quantitatively detect 37 SNPs of the tp53 gene, which are used as targets in multiplex analysis, using three-color fluorescence-labeled probes.

  16. A rapid genotyping method for an obligate fungal pathogen, Puccinia striiformis f.sp. tritici, based on DNA extraction from infected leaf and Multiplex PCR genotyping

    Directory of Open Access Journals (Sweden)

    Enjalbert Jérôme

    2011-07-01

    Full Text Available Abstract Background Puccinia striiformis f.sp. tritici (PST, an obligate fungal pathogen causing wheat yellow/stripe rust, a serious disease, has been used to understand the evolution of crop pathogen using molecular markers. However, numerous questions regarding its evolutionary history and recent migration routes still remains to be addressed, which need the genotyping of a large number of isolates, a process that is limited by both DNA extraction and genotyping methods. To address the two issues, we developed here a method for direct DNA extraction from infected leaves combined with optimized SSR multiplexing. Findings We report here an efficient protocol for direct fungal DNA extraction from infected leaves, avoiding the costly and time consuming step of spore multiplication. The genotyping strategy we propose, amplified a total of 20 SSRs in three Multiplex PCR reactions, which were highly polymorphic and were able to differentiate different PST populations with high efficiency and accuracy. Conclusion These two developments enabled a genotyping strategy that could contribute to the development of molecular epidemiology of yellow rust disease, both at a regional or worldwide scale.

  17. 48 CFR 32.503-9 - Liquidation rates-alternate method.

    Science.gov (United States)

    2010-10-01

    ...-alternate method. 32.503-9 Section 32.503-9 Federal Acquisition Regulations System FEDERAL ACQUISITION... Liquidation rates—alternate method. (a) The liquidation rate determined under 32.503-8 shall apply throughout... the alternate method in this 32.503-9. The objective of the alternate liquidation rate method is...

  18. Nonequilibrium relaxation method – An alternative simulation strategy

    Indian Academy of Sciences (India)

    Nobuyasu Ito

    2005-06-01

    One well-established simulation strategy to study the thermal phases and transitions of a given microscopic model system is the so-called equilibrium method, in which one first realizes the equilibrium ensemble of a finite system and then extrapolates the results to infinite system. This equilibrium method traces over the standard theory of the thermal statistical mechanics, and over the idea of the thermodynamic limit. Recently, an alternative simulation strategy has been developed, which analyzes the nonequilibrium relaxation (NER) process. It is called the NER method. NER method has some advantages over the equilibrium method. The NER method provides a simpler analyzing procedure. This implies less systematic error which is inevitable in the simulation and provides efficient resource usage. The NER method easily treats not only the thermodynamic limit but also other limits, for example, non-Gibbsian nonequilibrium steady states. So the NER method is also relevant for new fields of the statistical physics. Application of the NER method have been expanding to various problems: from basic first- and second-order transitions to advanced and exotic phases like chiral, KT spin-glass and quantum phases. These studies have provided, not only better estimations of transition point and exponents, but also qualitative developments. For example, the universality class of a random system, the nature of the two-dimensional melting and the scaling behavior of spin-glass aging phenomena have been clarified.

  19. Impact of Three Illumina Library Construction Methods on GC Bias and HLA Genotype Calling

    Science.gov (United States)

    Lan, James H; Yin, Yuxin; Reed, Elaine F; Moua, Kevin; Thomas, Kimberly; Zhang, Qiuheng

    2016-01-01

    Next-generation sequencing (NGS) is increasingly recognized for its ability to overcome allele ambiguity and deliver high-resolution typing in the human leukocyte antigen (HLA) system. Using this technology, non-uniform read distribution can impede the reliability of variant detection, which renders high-confidence genotype calling particularly difficult to achieve in the polymorphic HLA complex. Recently, library construction has been implicated as the dominant factor in instigating coverage bias. To study the impact of this phenomenon on HLA genotyping, we performed long-range PCR on 12 samples to amplify HLA-A, -B, -C, -DRB1, and -DQB1, and compared the relative contribution of three Illumina library construction methods (TruSeq Nano, Nextera, Nextera XT) in generating downstream bias. Here, we show high GC% to be a good predictor of low sequencing depth. Compared to standard TruSeq Nano, GC bias was more prominent in transposase-based protocols, particularly Nextera XT, likely through a combination of transposase insertion bias being coupled with a high number of PCR enrichment cycles. Importantly, our findings demonstrate non-uniform read depth can have a direct and negative impact on the robustness of HLA genotyping, which has clinical implications for users when choosing a library construction strategy that aims to balance cost and throughput with data quality. PMID:25543015

  20. Complementary and Alternative Medicine Methods in Chronic Renal Failure

    Directory of Open Access Journals (Sweden)

    Zeynep Erdogan

    2014-08-01

    Full Text Available Despite its long history, use of complementary and alternative medicine (CAM methods has increased dramatically only after 1990s. Up to 57% of patients with chronic renal use CAM methods.These patienys use CAM methods to overcome hypertension, fatigue, constipation, leg edema, pain, cramps, anxiety, depression, sleep disorders, to cope with symptoms such as itching, to stop the progression of kidney disease and to improve their quality of life. Methods used are herbal products and food supplements, acupressure, acupuncture, homeopathy, exercise, aromatherapy, yoga and reflexology. Nephrotoxic effect of several CAM therapies used in patients with renal impairment could disturb hemodynamics by reducing the glomerular filtration rate. For this reason, health care providers should question patients about used of CAM, methods. Communication with patients should be clear and should not act judgmental. Health care personnel should learn more about CAM methods in order to avoid unwanted situations that could develop after the application of CAM methods. Patients should be informed correctly and scientifically about these methods to avoid harmful and unnecessary uses. [Archives Medical Review Journal 2014; 23(4.000: 770-786

  1. Phenotyping and genotyping methods applied to investigate the relatedness of Brazilian isolates of Enterobacter cloacae

    Directory of Open Access Journals (Sweden)

    A.L.C. Darini

    1999-09-01

    Full Text Available In order to evaluate the resolving power of several typing methods to identify relatedness among Brazilian strains of Enterobacter cloacae, we selected twenty isolates from different patients on three wards of a University Hospital (Orthopedics, Nephrology, and Hematology. Traditional phenotyping methods applied to isolates included biotyping, antibiotic sensitivity, phage-typing, and O-serotyping. Plasmid profile analysis, ribotyping, and macrorestriction analysis by pulsed-field gel electrophoresis (PFGE were used as genotyping methods. Sero- and phage-typing were not useful since the majority of isolates could not be subtyped by these methods. Biotyping, antibiogram and plasmid profile permitted us to classify the samples into different groups depending on the method used, and consequently were not reliable. Ribotyping and PFGE were significantly correlated with the clinical epidemiological analysis. PFGE did not type strains containing nonspecific DNase. Ribotyping was the most discriminative method for typing Brazilian isolates of E. cloacae.

  2. Fast alternating projection methods for constrained tomographic reconstruction.

    Science.gov (United States)

    Liu, Li; Han, Yongxin; Jin, Mingwu

    2017-01-01

    The alternating projection algorithms are easy to implement and effective for large-scale complex optimization problems, such as constrained reconstruction of X-ray computed tomography (CT). A typical method is to use projection onto convex sets (POCS) for data fidelity, nonnegative constraints combined with total variation (TV) minimization (so called TV-POCS) for sparse-view CT reconstruction. However, this type of method relies on empirically selected parameters for satisfactory reconstruction and is generally slow and lack of convergence analysis. In this work, we use a convex feasibility set approach to address the problems associated with TV-POCS and propose a framework using full sequential alternating projections or POCS (FS-POCS) to find the solution in the intersection of convex constraints of bounded TV function, bounded data fidelity error and non-negativity. The rationale behind FS-POCS is that the mathematically optimal solution of the constrained objective function may not be the physically optimal solution. The breakdown of constrained reconstruction into an intersection of several feasible sets can lead to faster convergence and better quantification of reconstruction parameters in a physical meaningful way than that in an empirical way of trial-and-error. In addition, for large-scale optimization problems, first order methods are usually used. Not only is the condition for convergence of gradient-based methods derived, but also a primal-dual hybrid gradient (PDHG) method is used for fast convergence of bounded TV. The newly proposed FS-POCS is evaluated and compared with TV-POCS and another convex feasibility projection method (CPTV) using both digital phantom and pseudo-real CT data to show its superior performance on reconstruction speed, image quality and quantification.

  3. Self-assessment: an alternative method of assessing speaking skills

    Directory of Open Access Journals (Sweden)

    Ekaterini Chalkia

    2012-02-01

    Full Text Available The present study focuses on self-assessment as an alternative method of assessing the speaking skills of a group of sixth graders of a Greek State Primary School. The paper consists of two parts. In the first part, traditional and alternative assessment approaches are compared and a literature review on self-assessment is presented. In the second part the methodology and the findings of the study are presented. The study was carried out by means of a questionnaire and observation notes. This was done in order to draw conclusions on the benefits of self-assessment, the difficulties students faced while carrying out self-assessment as well as to reveal the extent to which students improved their speaking skills after being involved in self-assessment. The findings revealed that the students were positive towards self-assessment. Although self-assessment was of limited duration, it turned out to be a worthwhile activity as it fostered motivation and sensitized the students to take a more active role in the learning process. It also enabled them to notice their strengths and weaknesses and improve their speaking skills. The study also revealed the practical difficulties the students faced in carrying out their self-assessment. Finally, the study concludes with recommendations for further research into this specific assessment method.

  4. An Alternating Iterative Method and Its Application in Statistical Inference

    Institute of Scientific and Technical Information of China (English)

    Ning Zhong SHI; Guo Rong HU; Qing CUI

    2008-01-01

    This paper studies non-convex programming problems. It is known that, in statistical inference, many constrained estimation problems may be expressed as convex programming problems. However, in many practical problems, the objective functions are not convex. In this paper, we give a definition of a semi-convex objective function and discuss the corresponding non-convex programming problems. A two-step iterative algorithm called the alternating iterative method is proposed for finding solutions for such problems. The method is illustrated by three examples in constrained estimation problems given in Sasabuchi et al. (Biometrika, 72, 465–472 (1983)), Shi N. Z. (J. Multivariate Anal.,50, 282–293 (1994)) and El Barmi H. and Dykstra R. (Ann. Statist., 26, 1878–1893 (1998)).

  5. An alternative method to specify the degree of resonator stability

    Indian Academy of Sciences (India)

    Jogy George; K Ranganathan; T P S Nathan

    2007-04-01

    We present an alternative method to specify the stability of real stable resonators. We introduce the degree of optical stability or the parameter, which specify the stability of resonators in a numerical scale ranging from 0 to 100%. The value of zero corresponds to marginally stable resonator and < 0 corresponds to unstable resonator. Also, three definitions of the S parameter are provided: in terms of &, & R0 and 12. It may be noticed from the present formalism that the maximum degree of stability with = 1 automatically corresponds to 12 = 1/2. We also describe the method to measure the parameter from the output beam characteristics and parameter. A possible correlation between the parameter and the misalignment tolerance is also discussed.

  6. Outcome modelling strategies in epidemiology: traditional methods and basic alternatives.

    Science.gov (United States)

    Greenland, Sander; Daniel, Rhian; Pearce, Neil

    2016-04-01

    Controlling for too many potential confounders can lead to or aggravate problems of data sparsity or multicollinearity, particularly when the number of covariates is large in relation to the study size. As a result, methods to reduce the number of modelled covariates are often deployed. We review several traditional modelling strategies, including stepwise regression and the 'change-in-estimate' (CIE) approach to deciding which potential confounders to include in an outcome-regression model for estimating effects of a targeted exposure. We discuss their shortcomings, and then provide some basic alternatives and refinements that do not require special macros or programming. Throughout, we assume the main goal is to derive the most accurate effect estimates obtainable from the data and commercial software. Allowing that most users must stay within standard software packages, this goal can be roughly approximated using basic methods to assess, and thereby minimize, mean squared error (MSE).

  7. Alternative remedies for insomnia: a proposed method for personalized therapeutic trials

    Directory of Open Access Journals (Sweden)

    Romero K

    2017-03-01

    Full Text Available Kate Romero,1,2 Balaji Goparaju,1,2 Kathryn Russo,1,2 M Brandon Westover,1 Matt T Bianchi1,2 1Neurology Department, Massachusetts General Hospital, 2Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA Abstract: Insomnia is a common symptom, with chronic insomnia being diagnosed in 5–10% of adults. Although many insomnia patients use prescription therapy for insomnia, the health benefits remain uncertain and adverse risks remain a concern. While similar effectiveness and risk concerns exist for herbal remedies, many individuals turn to such alternatives to prescriptions for insomnia. Like prescription hypnotics, herbal remedies that have undergone clinical testing often show subjective sleep improvements that exceed objective measures, which may relate to interindividual heterogeneity and/or placebo effects. Response heterogeneity can undermine traditional randomized trial approaches, which in some fields has prompted a shift toward stratified trials based on genotype or phenotype, or the so-called n-of-1 method of testing placebo versus active drug in within-person alternating blocks. We reviewed six independent compendiums of herbal agents to assemble a group of over 70 reported to benefit sleep. To bridge the gap between the unfeasible expectation of formal evidence in this space and the reality of common self-medication by those with insomnia, we propose a method for guided self-testing that overcomes certain operational barriers related to inter- and intraindividual sources of phenotypic variability. Patient-chosen outcomes drive a general statistical model that allows personalized self-assessment that can augment the open-label nature of routine practice. The potential advantages of this method include flexibility to implement for other (nonherbal insomnia interventions. Keywords: insomnia, over the counter, alternative remedy, herbal, supplement

  8. A high-throughput method for genotyping S-RNase alleles in apple

    DEFF Research Database (Denmark)

    Larsen, Bjarne; Ørgaard, Marian; Toldam-Andersen, Torben Bo

    2016-01-01

    We present a new efficient screening tool for detection of S-alleles in apple. The protocol using general and multiplexed primers for PCR reaction and fragment detection on an automatized capillary DNA sequencer exposed a higher number of alleles than any previous studies. Analysis of alleles...... is made on basis of three individual fragment sizes making the allele interpretation highly accurate. The method was employed to genotype 432 Malus accessions and exposed 25 different S-alleles in a selection of Malus domestica cultivars of mainly Danish origin (402 accessions) as well as a selection...

  9. Graphical genotyping as a method to map Ny (o,n)sto and Gpa5 using a reference panel of tetraploid potato cultivars.

    Science.gov (United States)

    van Eck, Herman J; Vos, Peter G; Valkonen, Jari P T; Uitdewilligen, Jan G A M L; Lensing, Hellen; de Vetten, Nick; Visser, Richard G F

    2017-03-01

    The method of graphical genotyping is applied to a panel of tetraploid potato cultivars to visualize haplotype sharing. The method allowed to map genes involved in virus and nematode resistance. The physical coordinates of the amount of linkage drag surrounding these genes are easily interpretable. Graphical genotyping is a visually attractive and easily interpretable method to represent genetic marker data. In this paper, the method is extended from diploids to a panel of tetraploid potato cultivars. Application of filters to select a subset of SNPs allows one to visualize haplotype sharing between individuals that also share a specific locus. The method is illustrated with cultivars resistant to Potato virus Y (PVY), while simultaneously selecting for the absence of the SNPs in susceptible clones. SNP data will then merge into an image which displays the coordinates of a distal genomic region on the northern arm of chromosome 11 where a specific haplotype is introgressed from the wild potato species S. stoloniferum (CPC 2093) carrying a gene (Ny (o,n)sto ) conferring resistance to two PVY strains, PVY(O) and PVY(NTN). Graphical genotyping was also successful in showing the haplotypes on chromosome 12 carrying Ry-f sto , another resistance gene derived from S. stoloniferum conferring broad-spectrum resistance to PVY, as well as chromosome 5 haplotypes from S. vernei, with the Gpa5 locus involved in resistance against Globodera pallida cyst nematodes. The image also shows shortening of linkage drag by meiotic recombination of the introgression segment in more recent breeding material. Identity-by-descent was found to be a requirement for using graphical genotyping, which is proposed as a non-statistical alternative method for gene discovery, as compared with genome-wide association studies. The potential and limitations of the method are discussed.

  10. Evaluation of alternative methods for the disinfection of toothbrushes

    Directory of Open Access Journals (Sweden)

    Edson Yukio Komiyama

    2010-03-01

    Full Text Available The aim of this study was to evaluate alternative methods for the disinfection of toothbrushes considering that most of the previously proposed methods are expensive and cannot be easily implemented. Two-hundred toothbrushes with standardized dimensions and bristles were included in the study. The toothbrushes were divided into 20 experimental groups (n = 10, according to microorganism considered and chemical agent used. The toothbrushes were contaminated in vitro by standardized suspensions of Streptococcus mutans, Streptococcus pyogenes, Staphylococcus aureus or Candida albicans. The following disinfectants were tested: 0.12% chlorhexidine digluconate, 50% white vinegar, a triclosan-containing dentifrice solution, and a perborate-based tablet solution. The disinfection method was immersion in the disinfectant for 10 min. After the disinfection procedure, the number of remaining microbial cells was evaluated. The values of cfu/toothbrush of each group of microorganism after disinfection were compared by Kruskal-Wallis ANOVA and Dunn's test for multiple comparisons (5%. The chlorhexidine digluconate solution was the most effective disinfectant. The triclosan-based dentifrice solution promoted a significant reduction of all microorganisms' counts in relation to the control group. As to the disinfection with 50% vinegar, a significant reduction was observed for all the microorganisms, except for C. albicans. The sodium perborate solution was the less effective against the tested microorganisms. Solutions based on triclosan-containing dentifrice may be considered effective, nontoxic, cost-effective, and an easily applicable alternative for the disinfection of toothbrushes. The vinegar solution reduced the presence of S. aureus, S. mutans and S. pyogenes on toothbrushes.

  11. Alternative Testing Methods for Predicting Health Risk from Environmental Exposures

    Directory of Open Access Journals (Sweden)

    Annamaria Colacci

    2014-08-01

    Full Text Available Alternative methods to animal testing are considered as promising tools to support the prediction of toxicological risks from environmental exposure. Among the alternative testing methods, the cell transformation assay (CTA appears to be one of the most appropriate approaches to predict the carcinogenic properties of single chemicals, complex mixtures and environmental pollutants. The BALB/c 3T3 CTA shows a good degree of concordance with the in vivo rodent carcinogenesis tests. Whole-genome transcriptomic profiling is performed to identify genes that are transcriptionally regulated by different kinds of exposures. Its use in cell models representative of target organs may help in understanding the mode of action and predicting the risk for human health. Aiming at associating the environmental exposure to health-adverse outcomes, we used an integrated approach including the 3T3 CTA and transcriptomics on target cells, in order to evaluate the effects of airborne particulate matter (PM on toxicological complex endpoints. Organic extracts obtained from PM2.5 and PM1 samples were evaluated in the 3T3 CTA in order to identify effects possibly associated with different aerodynamic diameters or airborne chemical components. The effects of the PM2.5 extracts on human health were assessed by using whole-genome 44 K oligo-microarray slides. Statistical analysis by GeneSpring GX identified genes whose expression was modulated in response to the cell treatment. Then, modulated genes were associated with pathways, biological processes and diseases through an extensive biological analysis. Data derived from in vitro methods and omics techniques could be valuable for monitoring the exposure to toxicants, understanding the modes of action via exposure-associated gene expression patterns and to highlight the role of genes in key events related to adversity.

  12. The European Partnership for Alternative Approaches to Animal Testing (EPAA): Promoting Alternative Methods in Europe and Beyond

    OpenAIRE

    COZIGOU, Gwenole; Crozier, Jonathan; Hendriksen, Coenraad; Manou, Irene; Ramirez-Hernandez, Tzutzuy; Weissenhorn, Renate

    2015-01-01

    Here in we introduce the European Partnership for Alternative Approaches to Animal Testing (EPAA) and its activities, which are focused on international cooperation toward alternative methods. The EPAA is one of the leading organizations in Europe for the promotion of alternative approaches to animal testing. Its innovative public–private partnership structure enables a consensus-driven dialogue across 7 industry sectors to facilitate interaction between regulators and regulated stakeholders....

  13. Constructivist Pedagogy and Alternative Teaching Methods for Intercultural Education

    Directory of Open Access Journals (Sweden)

    Ramona Lupu

    2014-05-01

    Full Text Available Our research proposes to underline the role of the constructivist pedagogy in the formative accomplishing of the intercultural education objectives, starting from the premise that the intuitive learning and the use of active-participative teaching-learning methods cover in a greater measure this discipline‟s cognitive, affective and psychomotor dimensions. The research design is made up of: 2 homogenous lots of intentionality composed of 70 and 60 students. There were used quantitative and qualitative research methods: structured questionnaire, semi-structured interview, focus-group method, evaluative techniques and statistics applied on a 2 years period. The discovery theory applied in teaching and learning increases the acknowledgement degree regarding the existence of ethnic groups and possible discriminatory actions; the mediator role assumed by the professor stimulates the formation and sedimentation of attitudes envisaged by the intercultural education, respecting with great fidelity the principle of conscious appropriation of knowledge; the use of alternative evaluative methods illustrate an increase of the students‟ school efficaciousness at this discipline and in the same time of their enthusiasm; the principles underlined by the constructivist pedagogy apply with great success in intercultural education.

  14. An alternative method for order tracking using autopower spectrum

    Directory of Open Access Journals (Sweden)

    Guido R Guercioni

    2015-11-01

    Full Text Available Order tracking is a method of analysis used by engineers in the diagnosis of rotating machinery. In many applications, order analysis of non-stationary signals is required. The direct extraction of the amplitude information from the short-time Fourier transform may lead to inaccurate vibration-level estimation in the case of fast changes in the signal frequency content. This article discusses spectral smearing, which is the main reason of the problem, and its sensitivity to the characteristics of the signal (frequency and amplitude variations and to the input parameters of discrete Fourier transform analysis (window size and type. Through the years, many different approaches to perform order analysis have been developed; this article introduces a novel method for order tracking based on the short-time Fourier transform, which applies a compensation of the smearing effect based on an invariant information contained in autopower spectrum. The limitations and capabilities of the proposed method with respect to other existing techniques are discussed: considering the accuracy of the results, low requirements of computational resources, and ease of implementation, this method proves a valid alternative to currently used techniques.

  15. Epidemiological typing of clinical isolates of Achromobacter xylosoxidans: comparison of phenotypic and genotypic methods.

    Science.gov (United States)

    Kaur, M; Ray, P; Bhatty, M; Sharma, M

    2009-09-01

    The purpose of this paper is to evaluate the utility of different typing methods for Achromobacter xylosoxidans clinical isolates. Ninety-two blood culture isolates of A. xylosoxidans subsp. xylosoxidans were collected over a 25-month period. The typeability, discriminatory power and reproducibility of commonly used phenotypic and genotypic methods, such as resistotyping, plasmid profiling, whole-cell protein fingerprinting, random amplification of polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE), were compared. All 92 isolates were typeable by all of the methods used, with comparable reproducibility. PFGE showed the highest discriminatory power (98.9%), but whole-cell protein profiling showed better correlation with epidemiological data without significant loss in discriminatory power (94%). Whole-cell protein profiling is a reliable epidemiological tool for the analysis of A. xylosoxidans; PFGE is the most discriminatory.

  16. Evaluation of DNA Extraction Methods Suitable for PCR-based Detection and Genotyping of Clostridium botulinum

    DEFF Research Database (Denmark)

    Auricchio, Bruna; Anniballi, Fabrizio; Fiore, Alfonsina

    2013-01-01

    Sufficient quality and quantity of extracted DNA is critical to detecting and performing genotyping of Clostridium botulinum by means of PCR-based methods. An ideal extraction method has to optimize DNA yield, minimize DNA degradation, allow multiple samples to be extracted, and be efficient...... in terms of cost, time, labor, and supplies. Eleven botulinum toxin–producing clostridia strains and 25 samples (10 food, 13 clinical, and 2 environmental samples) naturally contaminated with botulinum toxin–producing clostridia were used to compare 4 DNA extraction procedures: Chelex® 100 matrix, Phenol......-Cloroform-Isoamyl alcohol, NucliSENS® magnetic extraction kit, and DNeasy® Blood & Tissue kit. Integrity, purity, and amount of amplifiable DNA were evaluated. The results show that the DNeasy® Blood & Tissue kit is the best extraction method evaluated because it provided the most pure, intact, and amplifiable DNA. However...

  17. Sparse Inverse Covariance Selection via Alternating Linearization Methods

    CERN Document Server

    Scheinberg, Katya; Goldfarb, Donald

    2010-01-01

    Gaussian graphical models are of great interest in statistical learning. Because the conditional independencies between different nodes correspond to zero entries in the inverse covariance matrix of the Gaussian distribution, one can learn the structure of the graph by estimating a sparse inverse covariance matrix from sample data, by solving a convex maximum likelihood problem with an $\\ell_1$-regularization term. In this paper, we propose a first-order method based on an alternating linearization technique that exploits the problem's special structure; in particular, the subproblems solved in each iteration have closed-form solutions. Moreover, our algorithm obtains an $\\epsilon$-optimal solution in $O(1/\\epsilon)$ iterations. Numerical experiments on both synthetic and real data from gene association networks show that a practical version of this algorithm outperforms other competitive algorithms.

  18. A likelihood-based method for haplotype association studies of case-control data with genotyping uncertainty

    Institute of Scientific and Technical Information of China (English)

    ZHU; Wensheng; GUO; Jianhua

    2006-01-01

    This paper discusses the associations between traits and haplotypes based on Fl (fluorescent intensity) data sets, We consider a clustering algorithm based on mixtures of t distributions to obtain all possible genotypes of each individual (i.e. "GenoSpectrum"). We then propose a likelihood-based approach that incorporates the genotyping uncertainty to assessing the associations between traits and haplotypes through a haplotypebased logistic regression model, Simulation studies show that our likelihood-based method can reduce the impact induced by genotyping errors.

  19. An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing.

    Directory of Open Access Journals (Sweden)

    Rongrong Liao

    Full Text Available Single nucleotide polymorphisms (SNPs are essential for identifying the genetic mechanisms of complex traits. In the present study, we applied genotyping by genome reducing and sequencing (GGRS method to construct a 252-plex sequencing library for SNP discovery and genotyping in chicken. The library was successfully sequenced on an Illumina HiSeq 2500 sequencer with a paired-end pattern; approximately 400 million raw reads were generated, and an average of approximately 1.4 million good reads per sample were generated. A total of 91,767 SNPs were identified after strict filtering, and all of the 252 samples and all of the chromosomes were well represented. Compared with the Illumina 60K chicken SNP chip data, approximately 34,131 more SNPs were identified using GGRS, and a higher SNP density was found using GGRS, which could be beneficial for downstream analysis. Using the GGRS method, more than 3528 samples can be sequenced simultaneously, and the cost is reduced to $18 per sample. To the best of our knowledge, this study describes the first report of such highly multiplexed sequencing in chicken, indicating potential applications for genome-wide association and genomic selection in chicken.

  20. ALTERNATIVE FIELD METHODS TO TREAT MERCURY IN SOIL

    Energy Technology Data Exchange (ETDEWEB)

    Ernest F. Stine Jr; Steven T. Downey

    2002-08-14

    U.S. Department of Energy (DOE) used large quantities of mercury in the uranium separating process from the 1950s until the late 1980s in support of national defense. Some of this mercury, as well as other hazardous metals and radionuclides, found its way into, and under, several buildings, soil and subsurface soils and into some of the surface waters. Several of these areas may pose potential health or environmental risks and must be dealt with under current environmental regulations. DOE's National Energy Technology Laboratory (NETL) awarded a contract ''Alternative Field Methods to Treat Mercury in Soil'' to IT Group, Knoxville TN (IT) and its subcontractor NFS, Erwin, TN to identify remedial methods to clean up mercury-contaminated high-clay content soils using proven treatment chemistries. The sites of interest were the Y-12 National Security Complex located in Oak Ridge, Tennessee, the David Witherspoon properties located in Knoxville, Tennessee, and at other similarly contaminated sites. The primary laboratory-scale contract objectives were (1) to safely retrieve and test samples of contaminated soil in an approved laboratory and (2) to determine an acceptable treatment method to ensure that the mercury does not leach from the soil above regulatory levels. The leaching requirements were to meet the TC (0.2 mg/l) and UTS (0.025 mg/l) TCLP criteria. In-situ treatments were preferred to control potential mercury vapors emissions and liquid mercury spills associated with ex-situ treatments. All laboratory work was conducted in IT's and NFS laboratories. Mercury contaminated nonradioactive soil from under the Alpha 2 building in the Y-12 complex was used. This soils contained insufficient levels of leachable mercury and resulted in TCLP mercury concentrations that were similar to the applicable LDR limits. The soil was spiked at multiple levels with metallic (up to 6000 mg/l) and soluble mercury compounds (up to 500 mg/kg) to

  1. An alternative method for centrifugal compressor loading factor modelling

    Science.gov (United States)

    Galerkin, Y.; Drozdov, A.; Rekstin, A.; Soldatova, K.

    2017-08-01

    The loading factor at design point is calculated by one or other empirical formula in classical design methods. Performance modelling as a whole is out of consideration. Test data of compressor stages demonstrates that loading factor versus flow coefficient at the impeller exit has a linear character independent of compressibility. Known Universal Modelling Method exploits this fact. Two points define the function – loading factor at design point and at zero flow rate. The proper formulae include empirical coefficients. A good modelling result is possible if the choice of coefficients is based on experience and close analogs. Earlier Y. Galerkin and K. Soldatova had proposed to define loading factor performance by the angle of its inclination to the ordinate axis and by the loading factor at zero flow rate. Simple and definite equations with four geometry parameters were proposed for loading factor performance calculated for inviscid flow. The authors of this publication have studied the test performance of thirteen stages of different types. The equations are proposed with universal empirical coefficients. The calculation error lies in the range of plus to minus 1,5%. The alternative model of a loading factor performance modelling is included in new versions of the Universal Modelling Method.

  2. Selection of Superior Genotypes of Coffea Canephora Pierre on ControlledHybrid Population Using Cluster Analysis Method

    Directory of Open Access Journals (Sweden)

    Ucu Sumirat

    2007-05-01

    Full Text Available Selection of superior genotypes of robusta coffee (Coffea canephora to improve its important agronomic characters should be conducted continuously to get better planting productivity. The aim of this research was to select superior genotypes of Robusta coffee for high yield and high proportion of large bean. Selection was conducted on controlled hybrid populations, developed from three crossing parental clones, i.e. BP 961 x Q 121 (A, BP 409 x Q 121 (B and BP 961 x BP 409 (C. Selection was done by applying cluster analysis with complete linkage and Euclidean distance as the clustering method. The result of the research showed that the selection was successful to identify superior genotypes of Robusta coffee for high yield and high proportion of large bean. The parameters used (cherries weight/tree, bean weight/tree, bean size percentage > 6.5 mm and 100 cherries weight were effective in clustering the superior genotypes, indicated by increased minimum and average value of population. Yield potential and percentage of bean size > 6.5 mm of those genotypes were having better performance than the control genotype and its parent. The selection code A 95, B 28, B 62, B 66, B 74 and C 38 were considered  as promising superior genotypes of Robusta coffee, respectively. Key words: Coffea canephora, selection, bean size, yield, cluster analysis

  3. ALTERNATIVE FIELD METHODS TO TREAT MERCURY IN SOIL

    Energy Technology Data Exchange (ETDEWEB)

    Ernie F. Stine

    2002-08-14

    The Department of Energy (DOE) currently has mercury (Hg) contaminated materials and soils at the various sites. Figure 1-1 (from http://www.ct.ornl.gov/stcg.hg/) shows the estimated distribution of mercury contaminated waste at the various DOE sites. Oak Ridge and Idaho sites have the largest deposits of contaminated materials. The majorities of these contaminated materials are soils, sludges, debris, and waste waters. This project concerns treatment of mercury contaminated soils. The technology is applicable to many DOE sites, in-particular, the Y-12 National Security Complex in Oak Ridge Tennessee and Idaho National Engineering and Environmental Laboratory (INEEL). These sites have the majority of the soils and sediments contaminated with mercury. The soils may also be contaminated with other hazardous metals and radionuclides. At the Y12 plant, the baseline treatment method for mercury contaminated soil is low temperature thermal desorption (LTTD), followed by on-site landfill disposal. LTTD is relatively expensive (estimated cost of treatment which exclude disposal cost for the collect mercury is greater than $740/per cubic yard [cy] at Y-12), does not treat any of the metal or radionuclides. DOE is seeking a less costly alternative to the baseline technology. As described in the solicitation (DE-RA-01NT41030), this project initially focused on evaluating cost-effective in-situ alternatives to stabilize or remove the mercury (Hg) contamination from high-clay content soil. It was believed that ex-situ treatment of soil contaminated with significant quantities of free-liquid mercury might pose challenges during excavation and handling. Such challenges may include controlling potential mercury vapors and containing liquid mercury beads. As described below, the focus of this project was expanded to include consideration of ex-situ treatment after award of the contract to International Technology Corporation (IT). After award of the contract, IT became part of Shaw

  4. Selection of mango rosa genotypes in a breeding population using the multivariate-biplot method

    Directory of Open Access Journals (Sweden)

    Maria Clideana Cabral Maia

    Full Text Available ABSTRACT: Mango ( Mangifera indica L. trees stand out among the main fruit trees cultivated in Brazil. The mango rosa fruit is a very popular local variety (landrace, especially because of their superior technological characteristics such as high contents of Vitamin C and soluble solids (SS, as well as attractive taste and color. The objective of this study was to select a breeding population of mango rosa (polyclonal variety; ≥5 individuals that can simultaneously meet the fresh and processed fruit markets, using the multivariate method of principal components and the biplot graphic. The principal components, biplot graphic, and phenotype correlations were obtained using the R (2012 software. Pulp percentage and the pulp, skin, and seed mass variables can be indirectly selected using the smallest fruit diameter, which allowed an easier measurement. The P23R AREA3, P30R AREA3, and P32R AREA3 genotypes are selection candidates due to the presence of alleles, which are important agro-technological traits for mango breeding. This study showed that the biplot analysis is a valuable tool for decision making and visualization of interrelationships between variables and genotypes, facilitating the mango selection process.

  5. Understanding Alternative Education: A Mixed Methods Examination of Student Experiences

    Science.gov (United States)

    Farrelly, Susan Glassett; Daniels, Erika

    2014-01-01

    Alternative education plays a critical role in the opportunity gap that persists in the US public education system. However, there has been little research on alternative schools. Scaffolded by a theoretical framework constructed from critical theory, self-determination theory (SDT) and student voice, this research examined how well students in…

  6. 77 FR 8865 - Recent Postings of Broadly Applicable Alternative Test Methods

    Science.gov (United States)

    2012-02-15

    ... AGENCY Recent Postings of Broadly Applicable Alternative Test Methods AGENCY: Environmental Protection.... Background Broadly applicable alternative test method approval decisions made by the EPA in 2011 under the...). Source owners and operators may voluntarily use these broadly applicable alternative test methods subject...

  7. An alternative calibration method for counting P-32 reactor monitors

    Energy Technology Data Exchange (ETDEWEB)

    Quirk, T.J. [Applied Nuclear Technologies, Sandia National Laboratories, MS 1143, PO Box 5800, Albuquerque, NM 87185-1143 (United States); Vehar, D.W. [Sandia National Laboratories, Albuquerque, NM 87185-1143 (United States)

    2011-07-01

    Radioactivation of sulfur is a common technique used to measure fast neutron fluences in test and research reactors. Elemental sulfur can be pressed into pellets and used as monitors. The {sup 32}S(n, p) {sup 32}P reaction has a practical threshold of about 3 MeV and its cross section and associated uncertainties are well characterized [1]. The product {sup 32P} emits a beta particle with a maximum energy of 1710 keV [2]. This energetic beta particle allows pellets to be counted intact. ASTM Standard Test Method for Measuring Reaction Rates and Fast-Neutron Fluences by Radioactivation of Sulfur-32 (E265) [3] details a method of calibration for counting systems and subsequent analysis of results. This method requires irradiation of sulfur monitors in a fast-neutron field whose spectrum and intensity are well known. The resultant decay-corrected count rate is then correlated to the known fast neutron fluence. The Radiation Metrology Laboratory (RML) at Sandia has traditionally performed calibration irradiations of sulfur pellets using the {sup 252}Cf spontaneous fission neutron source at the National Inst. of Standards and Technology (NIST) [4] as a transfer standard. However, decay has reduced the intensity of NIST's source; thus lowering the practical upper limits of available fluence. As of May 2010, neutron emission rates have decayed to approximately 3 e8 n/s. In practice, this degradation of capabilities precludes calibrations at the highest fluence levels produced at test reactors and limits the useful range of count rates that can be measured. Furthermore, the reduced availability of replacement {sup 252}Cf threatens the long-term viability of the NIST {sup 252}Cf facility for sulfur pellet calibrations. In lieu of correlating count rate to neutron fluence in a reference field the total quantity of {sup 32}P produced in a pellet can be determined by absolute counting methods. This offers an attractive alternative to extended {sup 252}Cf exposures because

  8. Alternative production methods to face global molybdenum-99 supply shortage.

    Science.gov (United States)

    Lyra, Maria; Charalambatou, Paraskevi; Roussou, Eirini; Fytros, Stavros; Baka, Irini

    2011-01-01

    The sleeping giant of molybdenum-99 ((99)Mo) production is grinding to a halt and the world is wondering how this happened. Fewer than 10 reactors in the world are capable of producing radio nuclides for medicine; approximately 50% of the world's supply of raw material comes from National Research Universal (NRU) reactor in Canada. Many of these reactors, like the NRU, are old and aging. No one of these reactors, and probably not even all of them in combination, can replace the production of NRU. As the healthcare industry faces an aging population and the demand for diagnostic services using (99m)Tc continues to rise, the need for a consistent, reliable supply of (99)Mo has become increasingly important, so alternative methods to produce (99)Mo or even directly (99m)Tc had to be considered to avoid a supply shortage in the coming years. This need guides to the production of (99)Mo by replacing the Highly Enriched Uranium (HEU) target in a nuclear reactor with Low Enriched Uranium (LEU) and furthermore to the use of accelerators for manufacturing (99)Mo or for directly producing (99m)Tc.

  9. Assessing Partnership Alternatives in an IT Network Employing Analytical Methods

    Directory of Open Access Journals (Sweden)

    Vahid Reza Salamat

    2016-01-01

    Full Text Available One of the main critical success factors for the companies is their ability to build and maintain an effective collaborative network. This is more critical in the IT industry where the development of sustainable competitive advantage requires an integration of various resources, platforms, and capabilities provided by various actors. Employing such a collaborative network will dramatically change the operations management and promote flexibility and agility. Despite its importance, there is a lack of an analytical tool on collaborative network building process. In this paper, we propose an optimization model employing AHP and multiobjective programming for collaborative network building process based on two interorganizational relationships’ theories, namely, (i transaction cost theory and (ii resource-based view, which are representative of short-term and long-term considerations. The five different methods were employed to solve the formulation and their performances were compared. The model is implemented in an IT company who was in process of developing a large-scale enterprise resource planning (ERP system. The results show that the collaborative network formed through this selection process was more efficient in terms of cost, time, and development speed. The framework offers novel theoretical underpinning and analytical solutions and can be used as an effective tool in selecting network alternatives.

  10. The European Partnership for Alternative Approaches to Animal Testing (EPAA): promoting alternative methods in Europe and beyond.

    Science.gov (United States)

    Cozigou, Gwenole; Crozier, Jonathan; Hendriksen, Coenraad; Manou, Irene; Ramirez-Hernandez, Tzutzuy; Weissenhorn, Renate

    2015-03-01

    Here in we introduce the European Partnership for Alternative Approaches to Animal Testing (EPAA) and its activities, which are focused on international cooperation toward alternative methods. The EPAA is one of the leading organizations in Europe for the promotion of alternative approaches to animal testing. Its innovative public-private partnership structure enables a consensus-driven dialogue across 7 industry sectors to facilitate interaction between regulators and regulated stakeholders. Through a brief description of EPAA's activities and organizational structure, we first articulate the value of this collaboration; we then focus on 2 key projects driven by EPAA. The first project aims to address research gaps on stem cells for safety testing, whereas the second project strives for an approach toward demonstration of consistency in vaccine batch release testing. We highlight the growing need for harmonization of international acceptance and implementation of alternative approaches and for increased international collaboration to foster progress on nonanimal alternatives.

  11. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species.

    Directory of Open Access Journals (Sweden)

    Brant K Peterson

    Full Text Available The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via "SNP chip" microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotype-phenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more of individuals for a range of markers (hundreds to hundreds of thousands. Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.

  12. An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system.

    Science.gov (United States)

    Zhu, Xiaoxiao; Xu, Yajie; Yu, Shanshan; Lu, Lu; Ding, Mingqin; Cheng, Jing; Song, Guoxu; Gao, Xing; Yao, Liangming; Fan, Dongdong; Meng, Shu; Zhang, Xuewen; Hu, Shengdi; Tian, Yong

    2014-09-19

    The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system, and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.

  13. Comparing simple root phenotyping methods on a core set of rice genotypes.

    Science.gov (United States)

    Shrestha, R; Al-Shugeairy, Z; Al-Ogaidi, F; Munasinghe, M; Radermacher, M; Vandenhirtz, J; Price, A H

    2014-05-01

    Interest in belowground plant growth is increasing, especially in relation to arguments that shallow-rooted cultivars are efficient at exploiting soil phosphorus while deep-rooted ones will access water at depth. However, methods for assessing roots in large numbers of plants are diverse and direct comparisons of methods are rare. Three methods for measuring root growth traits were evaluated for utility in discriminating rice cultivars: soil-filled rhizotrons, hydroponics and soil-filled pots whose bottom was sealed with a non-woven fabric (a potential method for assessing root penetration ability). A set of 38 rice genotypes including the OryzaSNP set of 20 cultivars, additional parents of mapping populations and products of marker-assisted selection for root QTLs were assessed. A novel method of image analysis for assessing rooting angles from rhizotron photographs was employed. The non-woven fabric was the easiest yet least discriminatory method, while the rhizotron was highly discriminatory and allowed the most traits to be measured but required more than three times the labour of the other methods. The hydroponics was both easy and discriminatory, allowed temporal measurements, but is most likely to suffer from artefacts. Image analysis of rhizotrons compared favourably to manual methods for discriminating between cultivars. Previous observations that cultivars from the indica subpopulation have shallower rooting angles than aus or japonica cultivars were confirmed in the rhizotrons, and indica and temperate japonicas had lower maximum root lengths in rhizotrons and hydroponics. It is concluded that rhizotrons are the preferred method for root screening, particularly since root angles can be assessed.

  14. Yield and nutritional quality of greenhouse lettuce (Lactuca sativa L. as affected by genotype and production methods

    Directory of Open Access Journals (Sweden)

    Govedarica-Lučić Aleksandra

    2014-01-01

    Full Text Available Greenhouse experiments were conducted in winter growing seasons in order to evaluate the effects of genotype and production methods on yield and nutritional quality of lettuce (Lactuca sativa L.. A three-year (2009-2011 study was conducted by randomized block system in a greenhouse without additional heating. The trial included three genotypes of lettuce (Archimedes RZ, Santoro RZ, Kibou RZ. Each row with these genotypes was exposed to the following variants of covering: control-planting on bare soil, mulching before sowing with PE-black foil, agro textile-covering plants after planting with agro textile (17 g, a combination of mulching + agro textile. Throughout of all the three years of the trial, it was continuously evidenced that the genotype “Santoro RZ” had the biggest heads and the highest yield (15.33 kg 10 m-2, which leads to conclusion that the yield of lettuce is a genotype characteristics. Moreover, the nutritional value (ascorbic acid concentration has shown that, depending on the method of production, in average, the combination of mulching + agro textile (26.77 mg 100 g-1 had the highest content while the control variant had significantly lower vitamin C content (21.10 mg 100 g-1. The three-year researches have shown that the production method and genotype significantly affect the nitrate content. An average nitrate content was 2196.33 mg kg-1 on the control variant, and 2526.24 mg kg-1 on agro textile. Leafy lettuce of genotyp „Kibou RZ“ had lower nitrate content (2176.85 mg kg-1 compared to „Archimedes RZ“ (2843.05 mg kg-1 and „Santoro RZ“ (2221.37 mg kg-1. However nitrate concentration in all treatments remained within the European Union’s permissible levels.

  15. Some thoughts on alternative methods and their scientific implications

    NARCIS (Netherlands)

    Mansvelt, van J.D.

    1983-01-01

    Reflections upon our agricultural problems cannot be limitated to those problems itself, but should incorporate a reflection upon our social and scientific traditions. An alternative agriculture asks for participating nature research

  16. The Budget Scoring Alternatives Financing Methods for Defense Requirements

    Science.gov (United States)

    2007-04-30

    programs, the Department of Defense (DoD) must consider alternative forms of financing, including leases and public - private partnerships (PPPs), to...Åèìáëáíáçå=oÉëÉ~êÅÜW=`ob^qfkd=pvkbodv=clo=fkclojba=`e^kdb====- 4 - = = leases, share-in-savings contracts, and public private partnerships (PPPs), have...to meet the requirements. Alternative Financing Agreements: Public - private Partnerships In August 2003, the Government Accountability Office (GAO

  17. Alternative methods for the treatment of post-menopausal troubles [Alternative Methoden zur Behandlung postmenopausaler Beschwerden

    Directory of Open Access Journals (Sweden)

    Wasem, Jürgen

    2012-05-01

    Full Text Available [english] Menopause is described as the transition from the reproductive phase of a women to the non reproductive. Changes in hormone levels might lead to complaints and health consequences especially during peri- and postmenopause. Hormone therapy has a potential damaging health risk profile and is recommended for temporal limited therapy for acute vasomotor symptoms only.The present HTA-report aims to assess the effectiveness and the cost-effectiveness of alternative treatment methods for women with postmenopausal symptoms in Germany regarding patient relevant endpoints (reduction of symptoms and frequency of adverse events and improvement of quality of life.A systematic literature search was carried out in 33 relevant databases in September 2010. Citations were selected according to pre-defined criteria and were extracted and evaluated.In the systematic research 22 studies are identified for the effectiveness evaluation, 22 primary studies and one review.High doses of isolated genistein reduce the frequency/intensity of hot flashes while low doses of genistein show no significant effect. Intake of isoflavone extract such as genistein, daidzein, glycitein in various combinations does not have an effect on improvement of cognitive function or vaginal dryness. The effect of black cohosh and hop extract for menopausal complaints cannot be determined since results are heterogenous. The combination of isoflavone, black cohosh, monk’s pepper, valerian and vitamin E has a positive effect on menopause symptoms. Ginkgo biloba shows no significant effect on menopause symptoms and cognitive improvement beside mental flexibility. Acupuncture has a significant influence on hot flashes especially in severe cases.No final statement can be drawn regarding the effectiveness of alter­ne treatment methods due to qualitative shortcomings of included studies and a general limited availability of studies in this field. Furthermore, the generalization of the

  18. Which alternative methods to the iridium gamma-graphy?; Quelles methodes alternatives a la gammagraphie a l'iridium?

    Energy Technology Data Exchange (ETDEWEB)

    Hatsch, J.; Chauveau, D.; Blettner, A. [Institut de Soudure, 93 - Villepinte (France)

    2009-05-15

    Gamma-graphy is a very widely used process for testing welded steel constructions, pipings, pressure vessels, frameworks and particularly welds in them. The major disadvantage of this NDT method lies in the risks due to ionizing radiations requiring the setting up of a safety perimeter being a constraint to the owner or involving a shift system for the personnel and thus heavy indirect expenditures. In addition, the recent French regulatory pressure as for transport, storage, and radioactive sources management make their use still more complicated under industrial conditions and their setting up more and more expensive. It seems difficult that only one NDT technique could a substitute for gamma-graphy. Various alternative solutions are possible. Their setting up depends on the type of component to be inspected, on the nature of material, on the type of welding (butt weld, nozzle), on the orientation and position of the defects to be detected as well as their environment. This conference surveys the techniques liable to substitute for gamma-graphy as well as their scope of application and the hindrances limiting their development. (authors)

  19. An Alternative Method for Identifying Interplanetary Magnetic Cloud Regions

    Science.gov (United States)

    Ojeda-Gonzalez, A.; Mendes, O.; Calzadilla, A.; Domingues, M. O.; Prestes, A.; Klausner, V.

    2017-03-01

    Spatio-temporal entropy (STE) analysis is used as an alternative mathematical tool to identify possible magnetic cloud (MC) candidates. We analyze Interplanetary Magnetic Field (IMF) data using a time interval of only 10 days. We select a convenient data interval of 2500 records moving forward by 200 record steps until the end of the time series. For every data segment, the STE is calculated at each step. During an MC event, the STE reaches values close to zero. This extremely low value of STE is due to MC structure features. However, not all of the magnetic components in MCs have STE values close to zero at the same time. For this reason, we create a standardization index (the so-called Interplanetary Entropy, IE, index). This index is a worthwhile effort to develop new tools to help diagnose ICME structures. The IE was calculated using a time window of one year (1999), and it has a success rate of 70% over other identifiers of MCs. The unsuccessful cases (30%) are caused by small and weak MCs. The results show that the IE methodology identified 9 of 13 MCs, and emitted nine false alarm cases. In 1999, a total of 788 windows of 2500 values existed, meaning that the percentage of false alarms was 1.14%, which can be considered a good result. In addition, four time windows, each of 10 days, are studied, where the IE method was effective in finding MC candidates. As a novel result, two new MCs are identified in these time windows.

  20. Mendel Meets CSI: Forensic Genotyping as a Method to Teach Genetics & DNA Science

    Science.gov (United States)

    Kurowski, Scotia; Reiss, Rebecca

    2007-01-01

    This article describes a forensic DNA science laboratory exercise for advanced high school and introductory college level biology courses. Students use a commercial genotyping kit and genetic analyzer or gene sequencer to analyze DNA recovered from a fictitious crime scene. DNA profiling and STR genotyping are outlined. DNA extraction, PCR, and…

  1. NordVal: A Nordic system for validation of alternative microbiological methods

    DEFF Research Database (Denmark)

    Qvist, Sven

    2007-01-01

    Val validated and certified methods for meat intended for Finland and Sweden. NordVal has at present 25 validated and certified alternative microbiological methods registered. The methods comprise ELISA, PCR and DNA based methods for Salmonella, Listeria and Campylobacter. Alternative culture based methods...

  2. Prueba molecular Genotype® MTBDRplus, una alternativa para la detección rápida de tuberculosis multidrogorresistente Molecular test Genotype® MTBDRplus, an alternative to rapid detection of multidrug resistance tuberculosis

    Directory of Open Access Journals (Sweden)

    Luis Asencios

    2012-03-01

    Full Text Available La prueba molecular Genotype®MTBDRplus, es un método que permite identificar las mutaciones más frecuentes asociadas con la resistencia a las drogas antituberculosas de primera línea: isoniacida (INH y rifampicina (RIF. El objetivo de este estudio fue evaluar el desempeño de la prueba molecular con cultivos y muestras de esputo con baciloscopía positiva. Se evaluó 95 cultivos y 100 esputos con perfiles de resistencia previamente determinados por el método de referencia "proporciones agar en placa" (APP. La prueba molecular a partir de cultivos mostró una sensibilidad de 100%; 97,5% y 96,9% para RIF, INH y multidrogorresistente (MDR respectivamente; mientras que para esputo la sensibilidad fue de 95,7%; 96,8% y 95,2% para RIF, INH y MDR respectivamente. Se concluye que Genotype®MTBDRplus es una herramienta muy útil para la detección rápida de la resistencia a INH y RIF simultáneamente (MDR en un máximo de 72 h a partir de esputo o de cultivo.The Genotype®MTBDRplus molecular test is a method that allows identification of the most frequent mutations associated with resistance to major first-line antituberculosis drugs, Isoniazid (INH and Rifampicin (RFP. The aim of this study was to evaluate the performance of the molecular test with culture and smear- positive sputum samples. We evaluated 95 cultures and 100 sputum samples with resistance profiles previously determined by the reference method "Agar Plate Proportions" (APP. The molecular test from cultures showed a sensitivity of 100 %, 97,5 % and 96,97 % for RIF, INH and MDR respectively while from sputums the sensitivity was 95,65 %, 96,77 % and 95,24 % for RIF, INH and MDR respectively. We conclude that the molecular test Genotype®MTBDRplus is a very useful tool to detect resistance to isoniazid and rifampicin simultaneously (MDR-TB in up to 72 hours from sputum samples or cultures.

  3. Simple and rapid human papillomavirus genotyping method by restriction fragment length polymorphism analysis with two restriction enzymes.

    Science.gov (United States)

    Chen, Linghan; Watanabe, Ken; Haruyama, Takahiro; Kobayashi, Nobuyuki

    2013-07-01

    Cervical cancer, the third most common cancer that affects women worldwide, is caused by the human papillomavirus (HPV) and is treatable when detected at an early stage. To date, more than 100 different HPV types have been described, and the development of simple, low-cost, and accurate methods to distinguish HPV genotypes is highly warranted. In this study, an HPV genotyping assay based on polymerase chain reaction (PCR) was evaluated. This method involved the use of MY09/11 primers followed by restriction fragment length polymorphism (RFLP) analysis with the restriction enzymes HpyCH4V and NlaIII. Cervical specimens preserved using CytoRich Blue fluid were collected from 1,134 female volunteers for HPV detection, and 1,111 valid samples were amplified using PCR. The PCR method was sensitive enough to detect 25 copies of HPV18, and three copies of HPV16. Out of 202 PCR-positive samples, HPV genotypes were determined in 189 samples (93.6%) by this RFLP method. Results were then evaluated further by capillary sequencing method. Concordant results between the two tests were as high as 96.0%. Thirteen samples, which tested negative with RFLP, were verified as non-specific amplifications with PCR. In conclusion, this PCR-RFLP method using restriction enzymes HpyCH4V and NlaIII is simple, non-labor intensive, and is applicable for the inexpensive determination of HPV genotypes in clinical samples.

  4. Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping.

    Science.gov (United States)

    Mehta, Bhavik; Venables, Samantha; Roffey, Paul

    2017-04-18

    Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample. The library preparation procedure involves a series of steps including target amplification, library purification and library normalisation. This study highlights the comparison between the manufacturer recommended magnetic bead normalisation and quantitative polymerase chain reaction (qPCR) methods. Furthermore, two qPCR chemistries, KAPA® (KAPA Biosystems) and NEBNext® (New England Bio Inc.), have also been compared. The qPCR outperformed the bead normalisation method, while the NEBNext® kit obtained higher genotype concordance than KAPA®. The study also established an MPS workflow that can be utilised in any operational forensic laboratory.

  5. Alternative modeling methods for plasma-based Rf ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Veitzer, Seth A., E-mail: veitzer@txcorp.com; Kundrapu, Madhusudhan, E-mail: madhusnk@txcorp.com; Stoltz, Peter H., E-mail: phstoltz@txcorp.com; Beckwith, Kristian R. C., E-mail: beckwith@txcorp.com [Tech-X Corporation, Boulder, Colorado 80303 (United States)

    2016-02-15

    Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H{sup −} source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. In particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H{sup −} ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two

  6. Alternative modeling methods for plasma-based Rf ion sources

    Science.gov (United States)

    Veitzer, Seth A.; Kundrapu, Madhusudhan; Stoltz, Peter H.; Beckwith, Kristian R. C.

    2016-02-01

    Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H- source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. In particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H- ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two-temperature MHD models

  7. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Bryan N Howie

    2009-06-01

    Full Text Available Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 Genomes Project will soon allow a broader range of SNPs to be imputed with higher accuracy, thereby increasing power. We describe a genotype imputation method (IMPUTE version 2 that is designed to address the challenges presented by these new datasets. The main innovation of our approach is a flexible modelling framework that increases accuracy and combines information across multiple reference panels while remaining computationally feasible. We find that IMPUTE v2 attains higher accuracy than other methods when the HapMap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made. We also find that imputation accuracy can be greatly enhanced by expanding the reference panel to contain thousands of chromosomes and that IMPUTE v2 outperforms other methods in this setting at both rare and common SNPs, with overall error rates that are 15%-20% lower than those of the closest competing method. One particularly challenging aspect of next-generation association studies is to integrate information across multiple reference panels genotyped on different sets of SNPs; we show that our approach to this problem has practical advantages over other suggested solutions.

  8. Comparison of alternative improved perturbative methods for nonlinear oscillations

    Energy Technology Data Exchange (ETDEWEB)

    Amore, Paolo [Facultad de Ciencias, Universidad de Colima, Bernal Diaz del Castillo 340, Colima (Mexico)]. E-mail: paolo@ucol.mx; Raya, Alfredo [Facultad de Ciencias, Universidad de Colima, Bernal Diaz del Castillo 340, Colima (Mexico); Fernandez, Francisco M. [INIFTA (Conicet, UNLP), Diag. 113 y 64 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)

    2005-06-06

    We discuss and compare two alternative perturbation approaches for the calculation of the period of nonlinear systems based on the Lindstedt-Poincare technique. As illustrative examples we choose one-dimensional anharmonic oscillators and the Van der Pol equation. Our results show that each approach is better for just one type of model considered here.

  9. Alternatives in Medical Education: Non-Animal Methods.

    Science.gov (United States)

    Carlson, Peggy, Ed.

    The technology explosion in medical education has led to the use of computer models, videotapes, interactive videos, and state-of-the-art simulators in medical training. This booklet describes alternatives to using animals in medical education. Although it is mainly intended to describe products applicable to medical school courses, high-quality,…

  10. Tracing the sources of human salmonellosis: a multi-model comparison of phenotyping and genotyping methods.

    Science.gov (United States)

    Mughini-Gras, Lapo; Smid, Joost; Enserink, Remko; Franz, Eelco; Schouls, Leo; Heck, Max; van Pelt, Wilfrid

    2014-12-01

    Salmonella source attribution is usually performed using frequency-matched models, such as the (modified) Dutch and Hald models, based on phenotyping data, i.e. serotyping, phage typing, and antimicrobial resistance profiling. However, for practical and economic reasons, genotyping methods such as Multi-locus Variable Number of Tandem Repeats Analysis (MLVA) are gradually replacing traditional phenotyping of salmonellas beyond the serovar level. As MLVA-based source attribution of human salmonellosis using frequency-matched models is problematic due to the high variability of the genetic targets investigated, other models need to be explored. Using a comprehensive data set from the Netherlands in 2005-2013, this study aimed at attributing sporadic and domestic cases of Salmonella Typhimurium/4,[5],12:i:- and Salmonella Enteritidis to four putative food-producing animal sources (pigs, cattle, broilers, and layers/eggs) using the modified Dutch and Hald models (based on sero/phage typing data) in comparison with a widely applied population genetics model - the asymmetric island model (AIM) - supplied with MLVA data. This allowed us to compare model outcomes and to corroborate whether MLVA-based Salmonella source attribution using the AIM is able to provide sound, comparable results. All three models provided very similar results, confirming once more that most S. Typhimurium/4,[5],12:i:- and S. Enteritidis cases are attributable to pigs and layers/eggs, respectively. We concluded that MLVA-based source attribution using the AIM is a feasible option, at least for S. Typhimurium/4,[5],12:i:- and S. Enteritidis. Enough information seems to be contained in the MLVA profiles to trace the sources of human salmonellosis even in presence of imperfect temporal overlap between human and source isolates. Besides Salmonella, the AIM might also be applicable to other pathogens that do not always comply to clonal models. This would add further value to current surveillance

  11. Genetic diversity of Bacillus anthracis in Europe: genotyping methods in forensic and epidemiologic investigations.

    Science.gov (United States)

    Derzelle, Sylviane; Thierry, Simon

    2013-09-01

    Bacillus anthracis, the etiological agent of anthrax, a zoonosis relatively common throughout the world, can be used as an agent of bioterrorism. In naturally occurring outbreaks and in criminal release of this pathogen, a fast and accurate diagnosis is crucial to an effective response. Microbiological forensics and epidemiologic investigations increasingly rely on molecular markers, such as polymorphisms in DNA sequence, to obtain reliable information regarding the identification or source of a suspicious strain. Over the past decade, significant research efforts have been undertaken to develop genotyping methods with increased power to differentiate B. anthracis strains. A growing number of DNA signatures have been identified and used to survey B. anthracis diversity in nature, leading to rapid advances in our understanding of the global population of this pathogen. This article provides an overview of the different phylogenetic subgroups distributed across the world, with a particular focus on Europe. Updated information on the anthrax situation in Europe is reported. A brief description of some of the work in progress in the work package 5.1 of the AniBioThreat project is also presented, including (1) the development of a robust typing tool based on a suspension array technology and multiplexed single nucleotide polymorphisms scoring and (2) the typing of a collection of DNA from European isolates exchanged between the partners of the project. The know-how acquired will contribute to improving the EU's ability to react rapidly when the identity and real origin of a strain need to be established.

  12. Alternative and Efficient Extraction Methods for Marine-Derived Compounds

    OpenAIRE

    Clara Grosso; Patrícia Valentão; Federico Ferreres; Paula B. Andrade

    2015-01-01

    Marine ecosystems cover more than 70% of the globe’s surface. These habitats are occupied by a great diversity of marine organisms that produce highly structural diverse metabolites as a defense mechanism. In the last decades, these metabolites have been extracted and isolated in order to test them in different bioassays and assess their potential to fight human diseases. Since traditional extraction techniques are both solvent- and time-consuming, this review emphasizes alternative extracti...

  13. Alternative Methods for Field Corrections in Helical Solenoids

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, M. L. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Krave, S. T. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Tompkins, J. C. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Yonehara, K. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Flanagan, G. [Muons Inc., Batavia, IL (United States); Kahn, S. A. [Muons Inc., Batavia, IL (United States); Melconian, K. [Texas A & M Univ., College Station, TX (United States)

    2015-05-01

    Helical cooling channels have been proposed for highly efficient 6D muon cooling. Helical solenoids produce solenoidal, helical dipole, and helical gradient field components. Previous studies explored the geometric tunability limits on these main field components. In this paper we present two alternative correction schemes, tilting the solenoids and the addition of helical lines, to reduce the required strength of the anti-solenoid and add an additional tuning knob.

  14. Alternative Methods of Collective Disputes Resolution in the Czech Republic

    Directory of Open Access Journals (Sweden)

    Hamuľáková Klára

    2016-10-01

    Full Text Available On 11 June 2013, the Commission issued the Recommendation on common principles for injunctive and compensatory collective redress mechanisms in the Member States concerning the violations of rights granted under Union law. The main areas where private enforcement of rights granted under Union law in the form of collective redress is of value are consumer protection, competition, environment protection, protection of personal data, financial services legislation and protection of investments. Point 13 of the Recommendation concurrently emphasises that the principles it puts forward relate both to judicial and out-of-court collective redress. The Member States should ensure that judicial collective redress mechanisms are accompanied by appropriate means of collective alternative dispute resolution available to the parties before and throughout the litigation. Point 25 et seq. of the Recommendation then contains special regulations concerning collective alternative dispute resolution and settlements. The purpose of this article is to evaluate if the current legislation on alternative dispute resolution in the Czech Republic meets the principles encompassed in the Recommendation or if radical legal changes need to be adopted.

  15. Development of a candidate method for forensic microbial genotyping using multiplex pyrosequencing combined with a universal biotinylated primer.

    Science.gov (United States)

    Gu, Yan; Mao, Xuhu; Zha, Lagabaiyila; Hou, Yiping; Yun, Libing

    2015-01-01

    Bacterial genotyping can be used for crime scene investigations and contribute to the attribution of biological attacks for microbial forensics. PyroMark ID Pyrosequencer as an accurate detection platform for single nucleotide polymorphisms (SNPs) has been applied to identify and resolve microorganisms involved in closely Escherichia coli O157:H7 (E. coli O157:H7). To explore more applications and improve the efficiency for pyrosequencing in this field, we developed a method integrated multiplex pyrosequencing with a universal primer. Two multiplex pyrosequencing assays with a universal biotinylated primer were designed to analyze five SNPs located in four gene of E. coli O157:H7 strain. The accuracy of the established assays was validated by genotyping reference strain E. coli O157:H7 EDL933 and E. coli K-12. We also demonstrated that two multiplex pyrosequencing assays were specific and sensitive for genotyping closely related E. coli O157 strains. Reproducibility of results and multiplexing capability were evaluated by a comparison of this method with the monoplex pyrosequencing. Furthermore, these two multiplex pyrosequencing assays have been successfully applied to detect 11 E. coli O157 strains isolated from 1504 Chinese livestock samples. This method reduces costs and time consumption in the process of pyrosequencing analysis, and potentially serves as a rapid tool and reliable candidate strategy for the microbial identification and other genotyping application.

  16. Effects of ractopamine administration and castration method on the response to preslaughter stress and carcass and meat quality in pigs of two Piétrain genotypes.

    Science.gov (United States)

    Rocha, L M; Bridi, A M; Foury, A; Mormède, P; Weschenfelder, A V; Devillers, N; Bertoloni, W; Faucitano, L

    2013-08-01

    The objective of this study was to evaluate the effects of ractopamine supplementation, castration method, and their interaction on the behavioral and physiological response to preslaughter stress and carcass and meat quality of 2 Piétrain genotypes. A total of 1,488 male pigs (115 ± 5 kg BW) were distributed according to a 2 × 2 × 2 factorial arrangement of treatments. The first factor was ractopamine supplementation with 2 groups of pigs (376 and 380 pigs each) receiving 7.5 mg/kg of ractopamine (RAC) or not (NRAC) in their diet during the last 28 d of the finishing period. The second factor was castration method, with 744 surgical castrates (SC) and 744 immunized males (IM), and the third factor was the genotype with 2 crossbreeds containing 50% (genotype A, GA; n = 744) or 25% (genotype B, GB; n = 744) Piétrain genetics. Surgical castration took place at 2 d of age, whereas immunization against gonadotropin-releasing factor (GnRF) was performed through 2 subcutaneous injections of GnRF analog (Improvest, 2 mL) at 10 and 4 wk before slaughter. At loading more vocal stimulation was needed by the handler to drive GB pigs forward through the farm alley (P = 0.01) and RAC-fed GB pigs through the ramp (P = 0.02). Feeding RAC to IM increased the number of fights in lairage compared with SC (P = 0.03). Feeding RAC shortened fighting bouts compared with NRAC pigs (P = 0.05). The SC-GA pigs showed a greater gastrointestinal tract temperature during unloading (P = 0.05) and lairage time (P = 0.03). Blood creatine kinase (CK) concentrations were greater (P = 0.04) in SC compared with IM, and no difference was found in the concentrations of stress hormones in urine collected postmortem. Dressing yield was greater (P = 0.01) in RAC and SC-GB pigs. Carcasses from RAC pigs and IM were leaner than those from NRAC and SC pigs (P pigs and from IM compared with SC (P = 0.01 and P pigs (P = 0.006). In conclusion, immunization against GnRF more than the use of Pi

  17. The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods.

    Science.gov (United States)

    Mulder, H A; Meuwissen, T H E; Calus, M P L; Veerkamp, R F

    2010-01-01

    In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing gene-assisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-assisted breeding value estimation for identified bi-allelic genes using Monte Carlo simulation. A nested full-sib half-sib structure was simulated with a mixed inheritance model with one bi-allelic quantitative trait loci (QTL) and a polygenic effect due to infinite number of polygenes. The effect of the QTL was included in gene-assisted BLUP either by random regression on predicted gene content, i.e. the number of positive alleles, or including haplotype effects in the model with an inverse IBD matrix to account for identity-by-descent relationships between haplotypes using linkage analysis information (IBD-LA). The inverse IBD matrix was constructed using segregation indicator probabilities obtained from multiple marker iterative peeling. Gene contents for unknown genotypes were predicted using either multiple marker iterative peeling or mixed model methodology. For both methods, gene-assisted breeding value estimation increased accuracies of total estimated breeding value (EBV) with 0% to 22% for genotyped animals in comparison to conventional breeding value estimation. For animals that were not genotyped, the increase in accuracy was much lower (0% to 5%), but still substantial when the heritability was 0.1 and when the QTL explained at least 15% of the genetic variance. Regression on predicted gene content yielded higher accuracies than IBD-LA. Allele substitution effects were, however, overestimated, especially when only sires and males in the last generation were genotyped. For juveniles without phenotypic records and traits measured only on females, the superiority of regression on gene content over IBD-LA was larger than when all animals had phenotypes. Missing

  18. An Alternate Method for Computation of Transfer Function Matrix

    Directory of Open Access Journals (Sweden)

    Appukuttan K. K.

    2010-01-01

    Full Text Available A direct and simple numerical method is presented for calculating the transfer function matrix of a linear time invariant multivariable system (A, B, C. The method is based on the matrix-determinant identity, and it involves operations with an auxiliary vector on the matrices. The method is computationally faster compared to Liverrier and Danilevsky methods.

  19. Single nucleotide polymorphism (SNP-strings: an alternative method for assessing genetic associations.

    Directory of Open Access Journals (Sweden)

    Douglas S Goodin

    Full Text Available BACKGROUND: Genome-wide association studies (GWAS identify disease-associations for single-nucleotide-polymorphisms (SNPs from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association. METHODOLOGY/PRINCIPAL FINDINGS: Here we develop a method to identify the two SNP-haplotypes, which combine to produce each person's SNP-genotype over specified chromosomal segments. Two multiple sclerosis (MS-associated genetic regions were modeled; DRB1 (a Class II molecule of the major histocompatibility complex and MMEL1 (an endopeptidase that degrades both neuropeptides and β-amyloid. For each locus, we considered sets of eleven adjacent SNPs, surrounding the putative disease-associated gene and spanning ∼200 kb of DNA. The SNP-information was converted into an ordered-set of eleven-numbers (subject-vectors based on whether a person had zero, one, or two copies of particular SNP-variant at each sequential SNP-location. SNP-strings were defined as those ordered-combinations of eleven-numbers (0 or 1, representing a haplotype, two of which combined to form the observed subject-vector. Subject-vectors were resolved using probabilistic methods. In both regions, only a small number of SNP-strings were present. We compared our method to the SHAPEIT-2 phasing-algorithm. When the SNP-information spanning 200 kb was used, SHAPEIT-2 was inaccurate. When the SHAPEIT-2 window was increased to 2,000 kb, the concordance between the two methods, in both of these eleven-SNP regions, was over 99%, suggesting that, in these regions, both methods were quite accurate. Nevertheless, correspondence was not uniformly high over the entire DNA-span but, rather, was characterized by alternating peaks and valleys of concordance. Moreover, in the valleys of poor-correspondence, SHAPEIT-2 was also inconsistent with itself

  20. A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders.

    Science.gov (United States)

    King, Daniel A; Fitzgerald, Tomas W; Miller, Ray; Canham, Natalie; Clayton-Smith, Jill; Johnson, Diana; Mansour, Sahar; Stewart, Fiona; Vasudevan, Pradeep; Hurles, Matthew E

    2014-04-01

    Exome sequencing of parent-offspring trios is a popular strategy for identifying causative genetic variants in children with rare diseases. This method owes its strength to the leveraging of inheritance information, which facilitates de novo variant calling, inference of compound heterozygosity, and the identification of inheritance anomalies. Uniparental disomy describes the inheritance of a homologous chromosome pair from only one parent. This aberration is important to detect in genetic disease studies because it can result in imprinting disorders and recessive diseases. We have developed a software tool to detect uniparental disomy from child-mother-father genotype data that uses a binomial test to identify chromosomes with a significant burden of uniparentally inherited genotypes. This tool is the first to read VCF-formatted genotypes, to perform integrated copy number filtering, and to use a statistical test inherently robust for use in platforms of varying genotyping density and noise characteristics. Simulations demonstrated superior accuracy compared with previously developed approaches. We implemented the method on 1057 trios from the Deciphering Developmental Disorders project, a trio-based rare disease study, and detected six validated events, a significant enrichment compared with the population prevalence of UPD (1 in 3500), suggesting that most of these events are pathogenic. One of these events represents a known imprinting disorder, and exome analyses have identified rare homozygous candidate variants, mainly in the isodisomic regions of UPD chromosomes, which, among other variants, provide targets for further genetic and functional evaluation.

  1. Practical methods for generating alternating magnetic fields for biomedical research

    Science.gov (United States)

    Christiansen, Michael G.; Howe, Christina M.; Bono, David C.; Perreault, David J.; Anikeeva, Polina

    2017-08-01

    Alternating magnetic fields (AMFs) cause magnetic nanoparticles (MNPs) to dissipate heat while leaving surrounding tissue unharmed, a mechanism that serves as the basis for a variety of emerging biomedical technologies. Unfortunately, the challenges and costs of developing experimental setups commonly used to produce AMFs with suitable field amplitudes and frequencies present a barrier to researchers. This paper first presents a simple, cost-effective, and robust alternative for small AMF working volumes that uses soft ferromagnetic cores to focus the flux into a gap. As the experimental length scale increases to accommodate animal models (working volumes of 100s of cm3 or greater), poor thermal conductivity and volumetrically scaled core losses render that strategy ineffective. Comparatively feasible strategies for these larger volumes instead use low loss resonant tank circuits to generate circulating currents of 1 kA or greater in order to produce the comparable field amplitudes. These principles can be extended to the problem of identifying practical routes for scaling AMF setups to humans, an infrequently acknowledged challenge that influences the extent to which many applications of MNPs may ever become clinically relevant.

  2. Alternative microbial methods: An overview and selection criteria.

    NARCIS (Netherlands)

    Jasson, V.; Jacxsens, L.; Luning, P.A.; Rajkovic, A.; Uyttendaele, M.

    2010-01-01

    This study provides an overview and criteria for the selection of a method, other than the reference method, for microbial analysis of foods. In a first part an overview of the general characteristics of rapid methods available, both for enumeration and detection, is given with reference to relevant

  3. Alternative microbial methods: An overview and selection criteria.

    NARCIS (Netherlands)

    Jasson, V.; Jacxsens, L.; Luning, P.A.; Rajkovic, A.; Uyttendaele, M.

    2010-01-01

    This study provides an overview and criteria for the selection of a method, other than the reference method, for microbial analysis of foods. In a first part an overview of the general characteristics of rapid methods available, both for enumeration and detection, is given with reference to relevant

  4. Alternative and Efficient Extraction Methods for Marine-Derived Compounds

    Directory of Open Access Journals (Sweden)

    Clara Grosso

    2015-05-01

    Full Text Available Marine ecosystems cover more than 70% of the globe’s surface. These habitats are occupied by a great diversity of marine organisms that produce highly structural diverse metabolites as a defense mechanism. In the last decades, these metabolites have been extracted and isolated in order to test them in different bioassays and assess their potential to fight human diseases. Since traditional extraction techniques are both solvent- and time-consuming, this review emphasizes alternative extraction techniques, such as supercritical fluid extraction, pressurized solvent extraction, microwave-assisted extraction, ultrasound-assisted extraction, pulsed electric field-assisted extraction, enzyme-assisted extraction, and extraction with switchable solvents and ionic liquids, applied in the search for marine compounds. Only studies published in the 21st century are considered.

  5. Alternative and efficient extraction methods for marine-derived compounds.

    Science.gov (United States)

    Grosso, Clara; Valentão, Patrícia; Ferreres, Federico; Andrade, Paula B

    2015-05-01

    Marine ecosystems cover more than 70% of the globe's surface. These habitats are occupied by a great diversity of marine organisms that produce highly structural diverse metabolites as a defense mechanism. In the last decades, these metabolites have been extracted and isolated in order to test them in different bioassays and assess their potential to fight human diseases. Since traditional extraction techniques are both solvent- and time-consuming, this review emphasizes alternative extraction techniques, such as supercritical fluid extraction, pressurized solvent extraction, microwave-assisted extraction, ultrasound-assisted extraction, pulsed electric field-assisted extraction, enzyme-assisted extraction, and extraction with switchable solvents and ionic liquids, applied in the search for marine compounds. Only studies published in the 21st century are considered.

  6. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

    DEFF Research Database (Denmark)

    Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer;

    2013-01-01

    genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types. Results: A total of 3051 different phenotypic tests were performed; 482 led......-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures. Methods: Antimicrobial susceptibility tests were performed...... on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used to identify acquired antimicrobial resistance...

  7. A maximum likelihood method for studying gene-environment interactions under conditional independence of genotype and exposure.

    Science.gov (United States)

    Cheng, K F

    2006-09-30

    Given the biomedical interest in gene-environment interactions along with the difficulties inherent in gathering genetic data from controls, epidemiologists need methodologies that can increase precision of estimating interactions while minimizing the genotyping of controls. To achieve this purpose, many epidemiologists suggested that one can use case-only design. In this paper, we present a maximum likelihood method for making inference about gene-environment interactions using case-only data. The probability of disease development is described by a logistic risk model. Thus the interactions are model parameters measuring the departure of joint effects of exposure and genotype from multiplicative odds ratios. We extend the typical inference method derived under the assumption of independence between genotype and exposure to that under a more general assumption of conditional independence. Our maximum likelihood method can be applied to analyse both categorical and continuous environmental factors, and generalized to make inference about gene-gene-environment interactions. Moreover, the application of this method can be reduced to simply fitting a multinomial logistic model when we have case-only data. As a consequence, the maximum likelihood estimates of interactions and likelihood ratio tests for hypotheses concerning interactions can be easily computed. The methodology is illustrated through an example based on a study about the joint effects of XRCC1 polymorphisms and smoking on bladder cancer. We also give two simulation studies to show that the proposed method is reliable in finite sample situation.

  8. Development of Alternative Methods for Determining Soil Organic Matter

    Directory of Open Access Journals (Sweden)

    Diego Mendes de Souza

    2016-01-01

    Full Text Available ABSTRACT Soil organic matter (SOM is important to fertility, since it performs several functions such as cycling, water and nutrient retention and soil aggregation, in addition to being an energy requirement for biological activity. This study proposes new trends to the Embrapa, Walkley-Black, and Mebius methods that allowed the determination of SOM by spectrophotometry, increasing functionality. The mass of 500 mg was reduced to 200 mg, generating a mean of 60 % saving of reagents and a decrease of 91 % in the volume of residue generated for the three methods without compromising accuracy and precision. We were able to optimize conditions for the Mebius method and establish the digestion time of maximum recovery of SOM by factorial design and response surface. The methods were validated by the estimate of figures of merits. Between the methods investigated, the optimized Mebius method was best suited for determining SOM, showing near 100 % recovery.

  9. A critical review of alternate methods of Purex solvent treatment

    Energy Technology Data Exchange (ETDEWEB)

    Gordon, N.R.

    1957-09-20

    This document is a HAPO report dated September 20, 1957. At the time of this report, there had been many different methods suggested for improving the Purex organic recovery system. Some of these suggestions been tried in the plant and others had not. Information concerning this system and, particularly, methods for improving it were wide spread. At the time of this report was no immediate source of information available on the proposed and investigated methods for improving the Purex solvent recovery system.

  10. The Sine Method: An Alternative Height Measurement Technique

    Science.gov (United States)

    Don C. Bragg; Lee E. Frelich; Robert T. Leverett; Will Blozan; Dale J. Luthringer

    2011-01-01

    Height is one of the most important dimensions of trees, but few observers are fully aware of the consequences of the misapplication of conventional height measurement techniques. A new approach, the sine method, can improve height measurement by being less sensitive to the requirements of conventional techniques (similar triangles and the tangent method). We studied...

  11. Evaluating an alternative method for rapid urinary creatinine determination

    Science.gov (United States)

    Creatinine (CR) is an endogenously-produced chemical routinely assayed in urine specimens to assess kidney function, sample dilution. The industry-standard method for CR determination, known as the kinetic Jaffe (KJ) method, relies on an exponential rate of a colorimetric change,...

  12. Effectiveness of Alternative Extension Methods through Radio Broadcasting in West Africa

    Science.gov (United States)

    Moussa, Bokar; Otoo, Miriam; Fulton, Joan; Lowenberg-DeBoer, James

    2011-01-01

    There is an urgent need to quantify which extension methods are most effective in Africa. The objective of this study was to determine the impact of alternative extension methods on adoption of the triple bagging cowpea storage technology in Niger and Burkina Faso. This study was designed as a quasi-experiment with two alternative extension…

  13. 76 FR 50221 - International Workshop on Alternative Methods for Human and Veterinary Rabies Vaccine Testing...

    Science.gov (United States)

    2011-08-12

    ... HUMAN SERVICES International Workshop on Alternative Methods for Human and Veterinary Rabies Vaccine... ``International Workshop on Alternative Methods for Human and Veterinary Rabies Vaccine Testing: State of the... approaches that may reduce, refine, or replace animal use in human and veterinary rabies vaccine...

  14. 77 FR 17457 - Work Group on Alternative Test Methods for Commercial Measuring Devices

    Science.gov (United States)

    2012-03-26

    ... National Institute of Standards and Technology Work Group on Alternative Test Methods for Commercial...: The National Institute of Standards and Technology (NIST) is forming a Work Group (WG) to examine alternative methods for testing the accuracy of commercial measuring devices including, but not limited...

  15. 76 FR 65382 - Regulation of Fuel and Fuel Additives: Alternative Test Method for Olefins in Gasoline

    Science.gov (United States)

    2011-10-21

    ... Olefins in Gasoline AGENCY: Environmental Protection Agency (EPA). ACTION: Final rule. SUMMARY: The... alternative test method for olefin content in gasoline. This final rule will provide flexibility to the... to me? II. Rule Change A. Alternative Test Method for Olefins in Gasoline III. Statutory...

  16. Effectiveness of Alternative Extension Methods through Radio Broadcasting in West Africa

    Science.gov (United States)

    Moussa, Bokar; Otoo, Miriam; Fulton, Joan; Lowenberg-DeBoer, James

    2011-01-01

    There is an urgent need to quantify which extension methods are most effective in Africa. The objective of this study was to determine the impact of alternative extension methods on adoption of the triple bagging cowpea storage technology in Niger and Burkina Faso. This study was designed as a quasi-experiment with two alternative extension…

  17. Inference of antibiotic resistance and virulence among diverse group A Streptococcus strains using emm sequencing and multilocus genotyping methods.

    Directory of Open Access Journals (Sweden)

    David Metzgar

    Full Text Available BACKGROUND: Group A Streptococcus pyogenes (GAS exhibits a high degree of clinically relevant phenotypic diversity. Strains vary widely in terms of antibiotic resistance (AbR, clinical severity, and transmission rate. Currently, strain identification is achieved by emm typing (direct sequencing of the genomic segment coding for the antigenic portion of the M protein or by multilocus genotyping methods. Phenotype analysis, including critical AbR typing, is generally achieved by much slower and more laborious direct culture-based methods. METHODOLOGY/PRINCIPAL FINDINGS: We compare genotype identification (by emm typing and PCR/ESI-MS with directly measured phenotypes (AbR and outbreak associations for 802 clinical isolates of GAS collected from symptomatic patients over a period of 6 years at 10 military facilities in the United States. All independent strain characterization methods are highly correlated. This shows that recombination, horizontal transfer, and other forms of reassortment are rare in GAS insofar as housekeeping genes, primary virulence and antibiotic resistance determinants, and the emm gene are concerned. Therefore, genotyping methods offer an efficient way to predict emm type and the associated AbR and virulence phenotypes. CONCLUSIONS/SIGNIFICANCE: The data presented here, combined with much historical data, suggest that emm typing assays and faster molecular methods that infer emm type from genomic signatures could be used to efficiently infer critical phenotypic characteristics based on robust genotype: phenotype correlations. This, in turn, would enable faster and better-targeted responses during identified outbreaks of constitutively resistant or particularly virulent emm types.

  18. Empirical Evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds

    NARCIS (Netherlands)

    Rosenberg, N.A.; Burke, T.; Elo, K.; Feldman, M.W.; Friedlin, P.J.; Groenen, M.A.M.; Hillel, J.; Maki-Tanila, A.; Tixier-Boichard, M.; Vignal, A.; Wimmers, K.

    2001-01-01

    We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus

  19. Computer-assisted analysis and epidemiological value of genotyping methods for Campylobacter jejuni and Campylobacter coli

    NARCIS (Netherlands)

    Boer, P. de; Duim, B.; Rigter, A.; Plas, J. van der; Jacobs-Reitsma, W.F.; Wagenaar, J.A.

    2000-01-01

    For epidemiological tracing of the thermotolerant Campylobacter species C. jejuni and C. coli, reliable and highly discriminatory typing techniques are necessary. In this study the genotyping techniques of flagellin typing (flaA typing), pulsed-field gel electrophoresis (PFGE), automated ribotyping,

  20. Computer-assisted analysis and epidemiological value of genotyping methods for Campylobacter jejuni and Campylobacter coli

    NARCIS (Netherlands)

    Boer, P. de; Duim, B.; Rigter, A.; Plas, J. van der; Jacobs-Reitsma, W.F.; Wagenaar, J.A.

    2000-01-01

    For epidemiological tracing of the thermotolerant Campylobacter species C. jejuni and C. coli, reliable and highly discriminatory typing techniques are necessary. In this study the genotyping techniques of flagellin typing (flaA typing), pulsed-field gel electrophoresis (PFGE), automated ribotyping,

  1. Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods

    NARCIS (Netherlands)

    Bayjanov, J.; Starrenburg, M.J.; Sijde, M.R. van der; Siezen, R.J.; Hijum, S.A.F.T. van

    2013-01-01

    BACKGROUND: Lactococcus lactis is used in dairy food fermentation and for the efficient production of industrially relevant enzymes. The genome content and different phenotypes have been determined for multiple L. lactis strains in order to understand intra-species genotype and phenotype diversity a

  2. Methods Matter: Tracking Health Disparities in Alternative High Schools.

    Science.gov (United States)

    Johnson, Karen E; Goyal, Mohit; Simonton, Amanda J; Richardson, Rebecca; Morris, Marian; Rew, Lynn

    2017-05-01

    Alternative high school (AHS) students are at-risk for school dropout and engage in high levels of health-risk behaviors that should be monitored over time. They are excluded from most public health surveillance efforts (e.g., Youth Risk Behavior Survey; YRBS), hindering our ability to monitor health disparities and allocate scarce resources to the areas of greatest need. Using active parental consent, we recruited 515 students from 14 AHSs in Texas to take a modified YRBS. We calculated three different participation rates, tracked participation by age of legal consent (≥18 and rate among students students, cooperation rates may be more accurate than participation rates based off of enrollment or attendance. Requiring active consent and not having accurate participation rates may result in surveillance data that are of disparate quality. This threatens to mask the needs of AHS students and perpetuate disparities because we are likely missing the highest-risk students within a high-risk sample and cannot generalize findings. © 2017 Wiley Periodicals, Inc.

  3. Alternative Methods to Treat Nausea and Vomiting from Cancer Chemotherapy

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Sheikhi

    2015-01-01

    Full Text Available Chemotherapy Induced Nausea and Vomiting (CINV is among the most intensive side effects and critical concerns for patients with cancer. Most of these patients experience nausea and vomiting after chemotherapy. Sometimes, this is so annoying that it may prevent them from continuing the therapy. With the recent advances, a variety of therapeutic methods are innovated and applied to control CINV. Among them, the main methods include medicinal therapy, relaxation, and herbal therapy. Yet, using dexamethasone together with massage therapy and ginger is identified as the most effective method.

  4. Back to basics: an evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding, genotyping, and disease diagnostics from fungal and oomycete samples.

    Science.gov (United States)

    Osmundson, Todd W; Eyre, Catherine A; Hayden, Katherine M; Dhillon, Jaskirn; Garbelotto, Matteo M

    2013-01-01

    The ubiquity, high diversity and often-cryptic manifestations of fungi and oomycetes frequently necessitate molecular tools for detecting and identifying them in the environment. In applications including DNA barcoding, pathogen detection from plant samples, and genotyping for population genetics and epidemiology, rapid and dependable DNA extraction methods scalable from one to hundreds of samples are desirable. We evaluated several rapid extraction methods (NaOH, Rapid one-step extraction (ROSE), Chelex 100, proteinase K) for their ability to obtain DNA of quantity and quality suitable for the following applications: PCR amplification of the multicopy barcoding locus ITS1/5.8S/ITS2 from various fungal cultures and sporocarps; single-copy microsatellite amplification from cultures of the phytopathogenic oomycete Phytophthora ramorum; probe-based P. ramorum detection from leaves. Several methods were effective for most of the applications, with NaOH extraction favored in terms of success rate, cost, speed and simplicity. Frozen dilutions of ROSE and NaOH extracts maintained PCR viability for over 32 months. DNA from rapid extractions performed poorly compared to CTAB/phenol-chloroform extracts for TaqMan diagnostics from tanoak leaves, suggesting that incomplete removal of PCR inhibitors is an issue for sensitive diagnostic procedures, especially from plants with recalcitrant leaf chemistry. NaOH extracts exhibited lower yield and size than CTAB/phenol-chloroform extracts; however, NaOH extraction facilitated obtaining clean sequence data from sporocarps contaminated by other fungi, perhaps due to dilution resulting from low DNA yield. We conclude that conventional extractions are often unnecessary for routine DNA sequencing or genotyping of fungi and oomycetes, and recommend simpler strategies where source materials and intended applications warrant such use.

  5. Alternative method for reconstruction of antihydrogen annihilation vertices

    Science.gov (United States)

    Amole, C.; Ashkezari, M. D.; Andresen, G. B.; Baquero-Ruiz, M.; Bertsche, W.; Bowe, P. D.; Butler, E.; Cesar, C. L.; Chapman, S.; Charlton, M.; Deller, A.; Eriksson, S.; Fajans, J.; Friesen, T.; Fujiwara, M. C.; Gill, D. R.; Gutierrez, A.; Hangst, J. S.; Hardy, W. N.; Hayano, R. S.; Hayden, M. E.; Humphries, A. J.; Hydomako, R.; Jonsell, S.; Kurchaninov, L.; Madsen, N.; Menary, S.; Nolan, P.; Olchanski, K.; Olin, A.; Povilus, A.; Pusa, P.; Robicheaux, F.; Sarid, E.; Silveira, D. M.; So, C.; Storey, J. W.; Thompson, R. I.; van der Werf, D. P.; Wurtele, J. S.; Yamazaki, Y.

    The ALPHA experiment, located at CERN, aims to compare the properties of antihydrogen atoms with those of hydrogen atoms. The neutral antihydrogen atoms are trapped using an octupole magnetic trap. The trap region is surrounded by a three layered silicon detector used to reconstruct the antiproton annihilation vertices. This paper describes a method we have devised that can be used for reconstructing annihilation vertices with a good resolution and is more efficient than the standard method currently used for the same purpose.

  6. Alternative method for reconstruction of antihydrogen annihilation vertices

    CERN Document Server

    Amole, C; Andresen , G B; Baquero-Ruiz, M; Bertsche, W; Bowe, P D; Butler, E; Cesar, C L; Chapman, S; Charlton, M; Deller, A; Eriksson, S; Fajans, J; Friesen, T; Fujiwara, M C; Gill, D R; Gutierrez, A; Hangst, J S; Hardy, W N; Hayano, R S; Hayden, M E; Humphries, A J; Hydomako, R; Jonsell, S; Kurchaninov, L; Madsen, N; Menary, S; Nolan, P; Olchanski, K; Olin, A; Povilus, A; Pusa, P; Robicheaux, F; Sarid, E; Silveira, D M; So, C; Storey, J W; Thompson, R I; van der Werf, D P; Wurtele, J S; Yamazaki,Y

    2012-01-01

    The ALPHA experiment, located at CERN, aims to compare the properties of antihydrogen atoms with those of hydrogen atoms. The neutral antihydrogen atoms are trapped using an octupole magnetic trap. The trap region is surrounded by a three layered silicon detector used to reconstruct the antiproton annihilation vertices. This paper describes a method we have devised that can be used for reconstructing annihilation vertices with a good resolution and is more efficient than the standard method currently used for the same purpose.

  7. Feasibility and acceptability of alternate methods of postnatal data collection.

    Science.gov (United States)

    McCormack, Lacey A; Friedrich, Christa; Fahrenwald, Nancy; Specker, Bonny

    2014-05-01

    This study was done in preparation for the launch of the National Children's Study (NCS) main study. The goal of this study was to examine the feasibility (completion rates and completeness of data), acceptability, staff time and cost-effectiveness of three methods of data collection for the postnatal 3- and 9-month questionnaires completed as part of NCS protocol. Eligible NCS participants who were scheduled to complete a postnatal questionnaire at three and nine months were randomly assigned to receive either: (a) telephone data collection (b) web-based data collection, or (c) self-administered (mailed) questionnaires. Event completion rates and satisfaction across the three data collection methods were compared and the influence of socio-demographic factors on completion rates and satisfaction rates was examined. Cost data were compared to data for completion and satisfaction for each of the delivery methods. Completion rates and satisfaction did not differ significantly by method, but completeness of data did, with odds of data completeness higher among web than phone (p data collection methods were seen. Mail and phone data collection were the least complete of the three methods and were the most expensive. Mailed data collection was neither complete nor exceptionally economical. Web-based data collection was the least costly and provided the most complete data. Participants without web access could complete the questionnaire over the phone.

  8. An alternative method for the measurement of the mechanical impulse of a vertically directed blast

    CSIR Research Space (South Africa)

    Turner, GR

    2008-01-01

    Full Text Available An alternative method for the measurement of the total mechanical impulse of a vertically directed blast due to an explosive charge is presented. The method differs from apparatus that employ a vertically displaced mass (similar in principle...

  9. An alternative method for assessing early mortality in contemporary populations.

    Science.gov (United States)

    Wiley, A S; Pike, I L

    1998-11-01

    Biological anthropologists are interested in a population's early mortality rates for a variety of reasons. Early mortality (infant or juvenile) is of obvious importance to those interested in demography, but early mortality statistics are useful for life history analysis, paleodemography, and human adaptability studies, among others. In general, the form of mortality statistics is derived from demography, where chronological age is the gold standard for statistical calculation and comparison. However, there are numerous problems associated with the collection, analysis, and interpretation of early mortality statistics based on age, particularly for anthropological research, which is often conducted in small or non-calendrical-age numerate populations. The infant mortality rate (IMR), for example, is notoriously difficult to determine in populations where accurate accounting of age is not routine, and yet it is widely used in demography, public health, medicine, and social science research. Here we offer an alternative to age-based early mortality statistics that makes use of human biologists' interest in, and skill at, assessing human growth and development. Our proposal is to use developmental stages of juveniles instead of relying exclusively on age as the basis for mortality statistics. Death or survival according to a developmental stage (such as crawling or weaning) may provide more accurate data that are also more closely related to the cause of death. Developmental stages have the added advantage of putting infants and children back at the center of the discussion of early mortality by focusing on their activities in relation to their environment. A case study from the Turkana population of Kenya illustrates the use of developmental stages in describing early mortality.

  10. Alternative sample preparation methods for MALDI-MS

    Energy Technology Data Exchange (ETDEWEB)

    Hurst, G.B.; Buchanan, M.V. [Oak Ridge National Lab., TN (United States); Czartoski, T.J. [Kenyon College, Gambier, OH (United States)

    1994-12-31

    Since the introduction of matrix-assisted laser desorption and ionization (MALDI), sample preparation has been a limiting step in the applicability of this important technique for mass spectrometric analysis of biomolecules. A number of variations on the original sample preparation method for have been described. The {open_quotes}standard{close_quotes} method of MALDI sample preparation requires mixing a solution containing the analyte and a large excess of matrix, and allowing a small volume of this solution to dry on a probe tip before insertion into the mass spectrometer. The resulting sample can fairly inhomogeneous. As a result, the process of aiming the desorption laser at a favorable spot on the dried sample can be tedious and time-consuming. The authors are evaluating several approaches to MALDI sample preparation, with the goal of developing a faster and more reproducible method.

  11. Alternative methods for determining shrinkage in restorative resin composites.

    Science.gov (United States)

    de Melo Monteiro, Gabriela Queiroz; Montes, Marcos Antonio Japiassú Resende; Rolim, Tiago Vieira; de Oliveira Mota, Cláudia Cristina Brainer; de Barros Correia Kyotoku, Bernardo; Gomes, Anderson Stevens Leônidas; de Freitas, Anderson Zanardi

    2011-08-01

    The purpose of this study was to evaluate polymerization shrinkage of resin composites using a coordinate measuring machine, optical coherence tomography and a more widely known method, such as Archimedes Principle. Two null hypothesis were tested: (1) there are no differences between the materials tested; (2) there are no differences between the methods used for polymerization shrinkage measurements. Polymerization shrinkage of seven resin-based dental composites (Filtek Z250™, Filtek Z350™, Filtek P90™/3M ESPE, Esthet-X™, TPH Spectrum™/Dentsply 4 Seasons™, Tetric Ceram™/Ivoclar-Vivadent) was measured. For coordinate measuring machine measurements, composites were applied to a cylindrical Teflon mold (7 mm × 2 mm), polymerized and removed from the mold. The difference between the volume of the mold and the volume of the specimen was calculated as a percentage. Optical coherence tomography was also used for linear shrinkage evaluations. The thickness of the specimens was measured before and after photoactivation. Polymerization shrinkage was also measured using Archimedes Principle of buoyancy (n=5). Statistical analysis of the data was performed with ANOVA and the Games-Howell test. The results show that polymerization shrinkage values vary with the method used. Despite numerical differences the ranking of the resins was very similar with Filtek P90 presenting the lowest shrinkage values. Because of the variations in the results, reported values could only be used to compare materials within the same method. However, it is possible rank composites for polymerization shrinkage and to relate these data from different test methods. Independently of the method used, reduced polymerization shrinkage was found for silorane resin-based composite. Copyright © 2011 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  12. Conceptual Approaches to Alternate Methods in Toxicological Testing

    Directory of Open Access Journals (Sweden)

    Alan M. Goldberg

    1987-04-01

    Full Text Available Due to public pressure, in vivo methods of toxicity testing is being attempted to be replaced by in vitro methods, such as cell and organ culture, computer modelling and modified LD50 tests using lesser number of animals. Specifically in the case of Draize eye irritancy test using rabbits, a number of refinements have been incorporated by different workers, mainly use of a local anaesthetic which will reduce animal distress without vitiating the test results. The author recommends exploration of new avenues for testing based on the advances in cell biology.

  13. Alternative correction equations in the Jacobi-Davidson method

    NARCIS (Netherlands)

    Genseberger, M.; Sleijpen, G.L.G.

    1998-01-01

    The correction equation in the Jacobi-Davidson method is effective in a subspace orthogonal to the current eigenvector approximation, whereas for the continuation of the process only vectors orthogonal to the search subspace are of importance. Such a vector is obtained by orthogonalizing the

  14. Alternative correction equations in the Jacobi-Davidson method

    NARCIS (Netherlands)

    Genseberger, M.; Sleijpen, G.L.G.

    2001-01-01

    The correction equation in the Jacobi-Davidson method is effective in a subspace orthogonal to the current eigenvector approximation, whereas for the continuation of the process only vectors orthogonal to the search subspace are of importance. Such a vector is obtained by orthogonalizing the (approx

  15. An alternative method for neonatal cerebro-myocardial perfusion

    Science.gov (United States)

    Luciani, Giovanni Battista; De Rita, Fabrizio; Faggian, Giuseppe; Mazzucco, Alessandro

    2012-01-01

    Several techniques have already been described for selective cerebral perfusion during repair of aortic arch pathology in children. One method combining cerebral with myocardial perfusion has also been proposed. A novel technique is reported here for selective and independent cerebro-myocardial perfusion for neonatal and infant arch surgery. Technical aspects and potential advantages are discussed. PMID:22307393

  16. ALTERNATIVE METHODS FOR CONDUCTING COMPARATIVE ANALYSES OF CADASTRAL SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The conception of an efficient cadastral system is an important element in the development of each coun-try. It is crucial for the efficient operation of the real estate market-the security and liberty of making transactions, register-ing a property, planning operations, the introduction of an ad valorem tax on property and more rational use of space. InEurope there are different types of cadastral systems, because the countries in Europe have different cultural back-grounds, different economical and social backgrounds. Through the centuries, many types of cadastral systems evolvedand their differences often depend upon local cultural heritage, physical geography, land use, technology, etc. Compara-tive analyses of cadastral systems have been the subjects of many publications and studies in world literature. It was as-sessed that the useful tools in conducting comparative analyses of various cadastral systems include the procedures of statisti-cal inference. This paper presents the results of a project to compare the performance of ten cadastral systems international-ly by creating appropriate integrated indicators of a cadastral system using statistical technique. Such indicators willmake it possible to compare different cadastral systems and present them hierarchically in relation to their quality, struc-ture, as well as legal, organizational and technological solutions. From a good number of methods available, techniquesoriginating from two spheres of statistic inference were selected: distribution free methods and multivariate analysis meth-ods. For analyses with the distribution free methods, FRIEDMAN's test (FRIENDMAN's non-parametric variance analy-sis) as well as KENDALL's test (KENDALL's compatibility ratio) were selected. For analyses with the multivariate analy-sis methods, factor analysis was selected.

  17. An Accelerated Linearized Alternating Direction Method of Multipliers

    Science.gov (United States)

    2014-02-01

    Obozinski, and J.-P. Vert. Group lasso with overlap and graph lasso. In Proceedings of the 26th Annual International Conference on Machine Learning...the 30th International Conference on Machine Learning (ICML-13), pages 80–88, 2013. [43] J. Pena. Nash equilibria computation via smoothing techniques...Optima, 78:12–13, 2008. [44] M. J. D. Powell. A method for nonlinear constraints in minimization problems. In Optimization (Sympos., Univ. Keele

  18. Alternative method for quantification of alfa-amylase activity

    Directory of Open Access Journals (Sweden)

    DF. Farias

    Full Text Available A modification of the sensitive agar diffusion method was developed for macro-scale determination of alfa-amylase. The proposed modifications lower costs with the utilisation of starch as substrate and agar as supporting medium. Thus, a standard curve was built using alfa-amylase solution from Aspergillus oryzae, with concentrations ranging from 2.4 to 7,500 U.mL-1. Clear radial diffusion zones were measured after 4 hours of incubation at 20 °C. A linear relationship between the logarithm of enzyme activities and the area of clear zones was obtained. The method was validated by testing α-amylase from barley at the concentrations of 2.4; 60; 300 and 1,500 U.mL-1. The proposed method turned out to be simpler, faster, less expensive and able to determine on a macro-scale α-amylase over a wide range (2.4 to 7,500 U.mL-1 in scientific investigation as well as in teaching laboratory activities.

  19. OZONE: ALTERNATIVE METHOD FOR MITE CONTROL ON SPECK

    Directory of Open Access Journals (Sweden)

    C. Cantoni

    2013-02-01

    Full Text Available This study is aimed at the development of a method for integrated mite control in the industrial production of speck. The investigation were carried out on the premises of five factories in the north-east of Italy. Tyrophagus putrescentiae and T. longior were predominant. The gaseous ozone treatment at low level (0.4 ppm was able to kill mites in a period within 15 days and 1 month. The characteristic layer of mould on the product surface reappears within 1 month from the end of treatment with ozone.

  20. Proximal Alternating Direction Method with Relaxed Proximal Parameters for the Least Squares Covariance Adjustment Problem

    Directory of Open Access Journals (Sweden)

    Minghua Xu

    2014-01-01

    Full Text Available We consider the problem of seeking a symmetric positive semidefinite matrix in a closed convex set to approximate a given matrix. This problem may arise in several areas of numerical linear algebra or come from finance industry or statistics and thus has many applications. For solving this class of matrix optimization problems, many methods have been proposed in the literature. The proximal alternating direction method is one of those methods which can be easily applied to solve these matrix optimization problems. Generally, the proximal parameters of the proximal alternating direction method are greater than zero. In this paper, we conclude that the restriction on the proximal parameters can be relaxed for solving this kind of matrix optimization problems. Numerical experiments also show that the proximal alternating direction method with the relaxed proximal parameters is convergent and generally has a better performance than the classical proximal alternating direction method.

  1. Haplotypes versus genotypes on pedigrees

    Directory of Open Access Journals (Sweden)

    Kirkpatrick Bonnie B

    2011-04-01

    Full Text Available Abstract Background Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysis with haplotype data have not yet been developed, and the computational complexity of such problems has been an open question. Furthermore, it is not clear in which scenarios haplotype data would provide better estimates than genotype data for quantities such as recombination rates. Results To answer these questions, a reduction is given from genotype problem instances to haplotype problem instances, and it is shown that solving the haplotype problem yields the solution to the genotype problem, up to constant factors or coefficients. The pedigree analysis problems we will consider are the likelihood, maximum probability haplotype, and minimum recombination haplotype problems. Conclusions Two algorithms are introduced: an exponential-time hidden Markov model (HMM for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data.

  2. Alternative method for direct measurement of tibial slope

    Directory of Open Access Journals (Sweden)

    Stijak Lazar

    2014-01-01

    Full Text Available Background/Aim. The tibial slope is one of the most frequently cited anatomical causes of anterior cruciate ligament trauma. The aim of this study was to determine the possibility of direct measuring of the tibial slope of the knee without prior soft tissue dissection in cadavers. Methods. Measurement was performed on the two groups of samples: osteological and cadaveric. The osteological group consisted of 102 matured tibiae and measurement was performed: indirectly by sagittal photographing of the tibia, and directly by a set of parallel bars. The cadaveric group consisted of 50 cadaveric knees and measurement was performed directly by a set of parallel bars. The difference and correlation between indirect and the direct measurements were observed, which included also measuring of the difference and correlation of the tibial slope on the medial and lateral condyles. Results. A statistically significant difference between the direct and indirect method of measuring (p 0.05. However, the slope on the medial condyle, as well as indirect measurement showed a statistically significant difference (p < 0.01. Conclusion. By the use of a set of parallel bars it is possible to measure the tibial slope directly without removal of the soft tissue. The results of indirect, photographic measurement did not statistically differ from the results of direct measurement of the tibial slope.

  3. An alternative method for smartphone input using AR markers

    Directory of Open Access Journals (Sweden)

    Yuna Kang

    2014-07-01

    Full Text Available As smartphones came into wide use recently, it has become increasingly popular not only among young people, but among middle-aged people as well. Most smartphones adopt capacitive full touch screen, so touch commands are made by fingers unlike the PDAs in the past that use touch pens. In this case, a significant portion of the smartphone’s screen is blocked by the finger so it is impossible to see the screens around the finger touching the screen; this causes difficulties in making precise inputs. To solve this problem, this research proposes a method of using simple AR markers to improve the interface of smartphones. A marker is placed in front of the smartphone camera. Then, the camera image of the marker is analyzed to determine the position of the marker as the position of the mouse cursor. This method can enable click, double-click, drag-and-drop used in PCs as well as touch, slide, long-touch-input in smartphones. Through this research, smartphone inputs can be made more precise and simple, and show the possibility of the application of a new concept of smartphone interface.

  4. Alternative Method for Solving Traveling Salesman Problem by Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    Zuzana Čičková

    2008-06-01

    Full Text Available This article describes the application of Self Organizing Migrating Algorithm (SOMA to the well-known optimization problem - Traveling Salesman Problem (TSP. SOMA is a relatively new optimization method that is based on Evolutionary Algorithms that are originally focused on solving non-linear programming problems that contain continuous variables. The TSP has model character in many branches of Operation Research because of its computational complexity; therefore the use of Evolutionary Algorithm requires some special approaches to guarantee feasibility of solutions. In this article two concrete examples of TSP as 8 cities set and 25 cities set are given to demonstrate the practical use of SOMA. Firstly, the penalty approach is applied as a simple way to guarantee feasibility of solution. Then, new approach that works only on feasible solutions is presented.

  5. An alternative method for the measurement of neutron flux

    Indian Academy of Sciences (India)

    Rupa Sarkar; Prasanna Kumar Mondal; Barun Kumar Chatterjee

    2015-10-01

    A simple and easy method for measuring the neutron flux is presented. This paper deals with the experimental verification of neutron dose rate–flux relationship for a non-dissipative medium. Though the neutron flux cannot be obtained from the dose rate in a dissipative medium, experimental result shows that for non-dissipative medium one can obtain the neutron flux from dose rate. We have used a 241 AmBe neutron source for neutron irradiation, and the neutron dose rate and count rate were measured using a NM2B neutron monitor and R-12 superheated droplet detector (SDD), respectively. Here, the neutron flux inferred from the neutron count rate obtained with R-12 SDD shows an excellent agreement with the flux inferred from the neutron dose rate in a non-dissipative medium.

  6. ALTERNATING METHOD STUDY ON STRESS ANALYSIS OF SURROUNDING ROCK FOR TWO RANDOM GEOMETRY TUNNELS

    Institute of Scientific and Technical Information of China (English)

    吕爱钟; 张路青

    1997-01-01

    The stress analysis of surrounding rock for two random geometry tunnels is studied inthis paper by using Schwarz's alternating method. The simple and effective alternating algorithm is found, in which the surplus surface force is approximated by Fourier series, thus the iteration derivation can be conducted according to the precision required, finally, the stress results with high precision are obtained.

  7. Alternative sintering methods compared to conventional thermal sintering for inkjet printed silver nanoparticle ink

    NARCIS (Netherlands)

    Niittynen, J.; Abbel, R.; Mäntysalo, M.; Perelaer, J.; Schubert, U.S.; Lupo, D.

    2014-01-01

    In this contribution several alternative sintering methods are compared to traditional thermal sintering as high temperature and long process time of thermal sintering are increasing the costs of inkjet-printing and preventing the use of this technology in large scale manufacturing. Alternative sint

  8. Innovative Solutions for Words with Emphasis: Alternative Methods of Braille Transcription

    Science.gov (United States)

    Kamei-Hannan, Cheryl

    2009-01-01

    The author of this study proposed two alternative methods for transcribing words with emphasis into braille and compared the use of the symbols for emphasis with the current braille code. The results showed that students were faster at locating words presented in one of the alternate formats, but that there was no difference in students' accuracy…

  9. A von Neumann Alternating Method for Finding Common Solutions to Variational Inequalities

    CERN Document Server

    Censor, Yair; Reich, Simeon

    2012-01-01

    Modifying von Neumann's alternating projections algorithm, we obtain an alternating method for solving the recently introduced Common Solutions to Variational Inequalities Problem (CSVIP). For simplicity, we mainly confine our attention to the two-set CSVIP, which entails finding common solutions to two unrelated variational inequalities in Hilbert space.

  10. NEW POSSIBILITIES OF RAISING RABBIT YOUNG BY ALTERNATIVE NURSING METHODS

    Directory of Open Access Journals (Sweden)

    Tünde Gyarmati

    2000-06-01

    Full Text Available In the first experiment 360 Pannon White kits from 45 litters were divided into 3 groups. The kits in group SS were suckled once a day during the first 35 days of life (traditional method of nursing. Group DD was raised by 2 does and the kits were suckled both in the morning and in the evening until 35 days of age. The kits of the 3 rd group (D0 were suckled twice a day for 23 days, after which they were weaned. Rabbits which were suckled twice a day consumed 89 % more milk until 23 days of age than those of the SS kits. In the second experiment authors used different management systems, to investigate the possibilities of “double-suckling”. Both nulliparous as multiparous does were treated to induce pseudopregnancy (by means of GnRH. They were used as second doe and suckled the kits in the afternoon. Pseudopregnant does produced milk (nulliparous does less than does which had previously produced litters, but in conditions of controlled suckling they were not willing to suckle the young. In a third experiment, does (n=44 were inseminated 11 days after kindling. Weaning was performed at the age of 21 days and does could systematically serve as second mother for the litters born at the same day. The “additional” does that nursed the young in the afternoon produced 65 % of the milk quantity produced by the natural mother between days 0 and 21.

  11. A non-invasive, rapid method to genotype late-onset Alzheimer’s disease-related apolipoprotein E gene polymorphisms

    Institute of Scientific and Technical Information of China (English)

    Li Yi; Ting Wu; Wenyuan Luo; Wen Zhou; Jun Wu

    2014-01-01

    The apolipoprotein E geneε4 allele is considered a negative factor for neural regeneration in late-onset Alzheimer’s disease cases. The aim of this study was to establish a non-invasive, rapid method to genotype apolipoprotein E gene polymorphisms. Genomic DNA from mouth swab specimens was extracted using magnetic nanoparticles, and genotyping was performed by real-time PCR using TaqMan-BHQ probes. Genotyping accuracy was validated by DNA se-quencing. Our results demonstrate 100%correlation to DNA sequencing, indicating reliability of our protocol. Thus, the method we have developed for apolipoprotein E genotyping is accurate and reliable, and also suitable for genotyping large samples, which may help determine the role of the apolipoprotein Eε4 allele in neural regeneration in late-onset Alzheimer’s disease cases.

  12. High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods

    Science.gov (United States)

    Gregori, Josep; Rodríguez-Frias, Francisco; Buti, Maria; Madejon, Antonio; Perez-del-Pulgar, Sofia; Garcia-Cehic, Damir; Casillas, Rosario; Blasi, Maria; Homs, Maria; Tabernero, David; Alvarez-Tejado, Miguel; Muñoz, Jose Manuel; Cubero, Maria; Caballero, Andrea; delCampo, Jose Antonio; Domingo, Esteban; Belmonte, Irene; Nieto, Leonardo; Lens, Sabela; Muñoz-de-Rueda, Paloma; Sanz-Cameno, Paloma; Sauleda, Silvia; Bes, Marta; Gomez, Jordi; Briones, Carlos; Perales, Celia; Sheldon, Julie; Castells, Lluis; Viladomiu, Lluis; Salmeron, Javier; Ruiz-Extremera, Angela; Quiles-Pérez, Rosa; Moreno-Otero, Ricardo; López-Rodríguez, Rosario; Allende, Helena; Romero-Gómez, Manuel; Guardia, Jaume; Esteban, Rafael; Garcia-Samaniego, Javier; Forns, Xavier

    2014-01-01

    Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes. PMID:25378574

  13. Developmental neurotoxicity testing: recommendations for developing alternative methods for the screening and prioritization of chemicals.

    Science.gov (United States)

    Crofton, Kevin M; Mundy, William R; Lein, Pamela J; Bal-Price, Anna; Coecke, Sandra; Seiler, Andrea E M; Knaut, Holger; Buzanska, Leonora; Goldberg, Alan

    2011-01-01

    Developmental neurotoxicity testing (DNT) is perceived by many stakeholders to be an area in critical need of alternative methods to current animal testing protocols and guidelines. An immediate goal is to develop test methods that are capable of screening large numbers of chemicals. This document provides recommendations for developing alternative DNT approaches that will generate the type of data required for evaluating and comparing predictive capacity and efficiency across test methods and laboratories. These recommendations were originally drafted to stimulate and focus discussions of alternative testing methods and models for DNT at the TestSmart DNT II meeting (http://caat.jhsph.edu/programs/workshops/dnt2.html) and this document reflects critical feedback from all stakeholders that participated in this meeting. The intent of this document is to serve as a catalyst for engaging the research community in the development of DNT alternatives and it is expected that these recommendations will continue to evolve with the science.

  14. 27 CFR 22.22 - Alternate methods or procedures; and emergency variations from requirements.

    Science.gov (United States)

    2010-04-01

    ... OF TAX-FREE ALCOHOL Administrative Provisions Authorities § 22.22 Alternate methods or procedures..., conditions or limitations set forth in the approval, authority for the variation from requirements...

  15. 27 CFR 20.22 - Alternate methods or procedures; and emergency variations from requirements.

    Science.gov (United States)

    2010-04-01

    ... OF DENATURED ALCOHOL AND RUM Administrative Provisions Authorities § 20.22 Alternate methods or... forth in the approval, authority for the variation from requirements is automatically terminated and...

  16. Notification: Notification Memo for Evaluation of Management Controls for Alternative Asbestos Control Method Experiments

    Science.gov (United States)

    Project #OPE-FY12-0011, February 27, 2012. This memorandum is to notify you that the Office of Inspector General (OIG) is initiating an evaluation on the Alternative Asbestos Control Method (AACM) experiments.

  17. Allergic Contact Dermatitis to Ophthalmic Medications: Relevant Allergens and Alternative Testing Methods.

    Science.gov (United States)

    Grey, Katherine R; Warshaw, Erin M

    Allergic contact dermatitis is an important cause of periorbital dermatitis. Topical ophthalmic agents are relevant sensitizers. Contact dermatitis to ophthalmic medications can be challenging to diagnose and manage given the numerous possible offending agents, including both active and inactive ingredients. Furthermore, a substantial body of literature reports false-negative patch test results to ophthalmic agents. Subsequently, numerous alternative testing methods have been described. This review outlines the periorbital manifestations, causative agents, and alternative testing methods of allergic contact dermatitis to ophthalmic medications.

  18. The Pharmacogenomic HLA Biomarker Associated to Adverse Abacavir Reactions: Comparative Analysis of Different Genotyping Methods

    Science.gov (United States)

    Stocchi, Laura; Cascella, Raffaella; Zampatti, Stefania; Pirazzoli, Antonella; Novelli, Giuseppe; Giardina, Emiliano

    2012-01-01

    Many pharmacogenomic biomarkers (PGBM) were identified and translated into clinical practice, affecting the usage of drugs via label updates. In this context, abacavir is one of the most brilliant examples of pharmacogenetic studies translated into clinical practice. Pharmacogenetic studies have revealed that abacavir HSRs are highly associated with the major histocompatibility complex class I. Large studies established the effectiveness of prospective HLA-B*57:01 screening to prevent HSRs to abacavir. Accordingly to these results the abacavir label has been modified: the European Medicines Agency (EMA) and the FDA recommend/suggested that the administration of abacavir must be preceded by a specific genotyping test. The HLA locus is extremely polymorphic, exhibiting many closely related alleles, making it difficult to discriminate HLA-B*57:01 from other related alleles, and a number of different molecular techniques have been developed recently to detect the presence of HLA-B*57:01. In this review, we provide a summary of the available techniques used by laboratories to genotype HLA-B*57:01, outlining the scientific and pharmacoeconomics pros and cons. PMID:23204921

  19. The Continuized Log-Linear Method: An Alternative to the Kernel Method of Continuization in Test Equating

    Science.gov (United States)

    Wang, Tianyou

    2008-01-01

    Von Davier, Holland, and Thayer (2004) laid out a five-step framework of test equating that can be applied to various data collection designs and equating methods. In the continuization step, they presented an adjusted Gaussian kernel method that preserves the first two moments. This article proposes an alternative continuization method that…

  20. Optimal Alternative to the Akima's Method of Smooth Interpolation Applied in Diabetology

    Directory of Open Access Journals (Sweden)

    Emanuel Paul

    2006-12-01

    Full Text Available It is presented a new method of cubic piecewise smooth interpolation applied to experimental data obtained by glycemic profile for diabetics. This method is applied to create a soft useful in clinical diabetology. The method give an alternative to the Akima's procedure of the derivatives computation on the knots from [Akima, J. Assoc. Comput. Mach., 1970] and have an optimal property.

  1. Alternative sintering methods compared to conventional thermal sintering for inkjet printed silver nanoparticle ink

    Energy Technology Data Exchange (ETDEWEB)

    Niittynen, Juha, E-mail: juha.niittynen@tut.fi [Department of Electronics and Communications Engineering, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere (Finland); Abbel, Robert [Holst Centre, High Tech Campus 31, 5656 AE Eindhoven (Netherlands); Mäntysalo, Matti [Department of Electronics and Communications Engineering, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere (Finland); Perelaer, Jolke; Schubert, Ulrich S. [Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich-Schiller-University Jena, Humboldtstrasse 10, D-07743 Jena (Germany); Jena Center for Soft Matter (JCSM), Friedrich-Schiller-University Jena, Humboldtstrasse 10, D-07743 Jena (Germany); Lupo, Donald [Department of Electronics and Communications Engineering, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere (Finland)

    2014-04-01

    In this contribution several alternative sintering methods are compared to traditional thermal sintering as high temperature and long process time of thermal sintering are increasing the costs of inkjet-printing and preventing the use of this technology in large scale manufacturing. Alternative sintering techniques are evaluated based on the electrical and mechanical performance they enable on inkjet-printed structures as well as their potential feasibility for large scale manufacturing. Photonic sintering was identified as the most promising alternative to thermal sintering. - Highlights: • Comparison of alternative sintering techniques for large-scale electronics manufacturing • Laser, plasma and photonic sintering of nanoparticle silver ink tested • Electrical and mechanical properties of sintered inks tested • Microstructure analysis used to explain the different electrical and mechanical properties • Photonic sintering identified as the most promising alternative technique.

  2. Evaluation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples.

    Directory of Open Access Journals (Sweden)

    Devidas N Chaturbhuj

    Full Text Available OBJECTIVES: Validation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. DESIGN: The validation includes the establishment of analytical performance characteristics such as accuracy, reproducibility, precision and sensitivity. METHODS: The accuracy was assessed by comparing 26 paired Virological Quality Assessment (VQA proficiency testing panel sequences generated by in-house and ViroSeq Genotyping System 2.0 (Celera Diagnostics, US as a gold standard. The reproducibility and precision were carried out on five samples with five replicates representing multiple HIV-1 subtypes (A, B, C and resistance patterns. The amplification sensitivity was evaluated on HIV-1 positive plasma samples (n = 88 with known viral loads ranges from 1000-1.8 million RNA copies/ml. RESULTS: Comparison of the nucleotide sequences generated by ViroSeq and in-house method showed 99.41±0.46 and 99.68±0.35% mean nucleotide and amino acid identity respectively. Out of 135 Stanford HIVdb listed HIV-1 drug resistance mutations, partial discordance was observed at 15 positions and complete discordance was absent. The reproducibility and precision study showed high nucleotide sequence identities i.e. 99.88±0.10 and 99.82±0.20 respectively. The in-house method showed 100% analytical sensitivity on the samples with HIV-1 viral load >1000 RNA copies/ml. The cost of running the in-house method is only 50% of that for ViroSeq method (112$ vs 300$, thus making it cost effective. CONCLUSIONS: The validated cost effective in-house method may be used to collect surveillance data on the emergence and transmission of HIV-1 drug resistance in resource limited countries. Moreover, the wide applications of a cost effective and validated in-house method for HIV-1 drug resistance testing will facilitate the decision making for the appropriate management of HIV infected patients.

  3. HPV Direct Flow CHIP: a new human papillomavirus genotyping method based on direct PCR from crude-cell extracts.

    Science.gov (United States)

    Herraez-Hernandez, Elsa; Alvarez-Perez, Martina; Navarro-Bustos, Gloria; Esquivias, Javier; Alonso, Sonia; Aneiros-Fernandez, Jose; Lacruz-Pelea, Cesar; Sanchez-Aguera, Magdalena; Santamaria, Javier Saenz; de Antonio, Jesus Chacon; Rodriguez-Peralto, Jose Luis

    2013-10-01

    HPV Direct Flow CHIP is a newly developed test for identifying 18 high-risk and 18 low-risk human papillomavirus (HPV) genotypes. It is based on direct PCR from crude-cell extracts, automatic flow-through hybridization, and colorimetric detection. The aim of this study was to evaluate the performance of HPV Direct Flow CHIP in the analysis of 947 samples from routine cervical screening or the follow-up of abnormal Pap smears. The specimens were dry swab samples, liquid-based cytology samples, or formalin-fixed paraffin-embedded tissues. The genotype distribution was in agreement with known epidemiological data for the Spanish population. Three different subgroups of the samples were also tested by Linear Array (LA) HPV Genotyping Test (n=108), CLART HPV2 (n=82), or Digene Hybrid Capture 2 (HC2) HPV DNA Test (n=101). HPV positivity was 73.6% by HPV Direct Flow CHIP versus 67% by LA, 65.9% by HPV Direct Flow CHIP versus 59.8% by CLART, and 62.4% by HPV Direct Flow CHIP versus 42.6% by HC2. HPV Direct Flow CHIP showed a positive agreement of 88.6% with LA (k=0.798), 87.3% with CLART (k=0.818), and 68.2% with HC2 (k=0.618). In conclusion, HPV Direct Flow CHIP results were comparable with those of the other methods tested. Although further investigation is needed to compare the performance of this new test with a gold-standard reference method, these preliminary findings evidence the potential value of HPV Direct Flow CHIP in HPV vaccinology and epidemiology studies.

  4. PROBLEMS CONCERNING ALTERNATIVE EVALUATION METHODS: THE CASE OF SCIENCE AND TEHNOLOGY TEACHERS

    Directory of Open Access Journals (Sweden)

    Yasemin DEVECİOĞLU-KAYMAKÇI

    2009-11-01

    Full Text Available Recent changes on the Science and Tehnology (ST curriculum have required using alternative evaluation methods in learning and teaching process. The aim of this study is to determine the ST teachers’ problems while using the alternative evaluation methods during their courses. To achieve this, semi-structured interviews have been conducted with 10 ST teachers from different parts of Trabzon during the academic year 2008-2009. The data, analyzed qualitatively, reveals that the teachers have important difficulties in determining, using and evaluating these methods. At the end of the research, it has been concluded that besides the lack of physical infrastructure, labs and libraries, computer and other technologies in their schools, most of the teachers lack the knowledge and skills to implement these methods. The result of the study has shown that ST teachers need an adaptation process to appropriate the aims and importance of alternative evaluation methods effectively.

  5. Unfolding the mystery of alternative splicing through a unique method of in vivo selection.

    Science.gov (United States)

    Singh, Ravindra N

    2007-05-01

    Alternative splicing of pre-messenger RNA (pre-mRNA) is a fundamental mechanism of gene regulation in higher eukaryotes. In addition to creating protein diversity, alternative splicing provides the safest mode of gene evolution. Of late, more and more forms of alternatively spliced transcripts (mRNAs) are being discovered for key genes. Some of the alternatively spliced transcripts are also associated with major human diseases. This has created a sense of urgency to find the methods by which regulation of alternative splicing of specific exons could be best understood. Here I review a powerful in vivo selection method that uses a combinatorial library of partially random sequences. Several advantages of this method include in vivo analysis of large sequences, identification of unique sequence motifs, determination of relative strength of splice sites and identification of long-distance interactions including role of RNA structures. This unique method could be applied to identify tissue-specific cis-elements. Similarly, the method is suitable to find cis-elements that become active in response to specific treatments of cells. Considering this unbiased method uses in vivo conditions, it has potential to identify critical regulatory elements as therapeutic targets for a growing number of splicing-associated diseases.

  6. The Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM): a review of the ICCVAM test method evaluation process and current international collaborations with the European Centre for the Validation of Alternative Methods (ECVAM).

    Science.gov (United States)

    Stokes, William S; Schechtman, Leonard M; Hill, Richard N

    2002-12-01

    Over the last decade, national authorities in the USA and Europe have launched initiatives to validate new and improved toxicological test methods. In the USA, the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) and its supporting National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM) were established by the Federal Government to work with test developers and Federal agencies to facilitate the validation, review, and adoption of new scientifically sound test methods, including alternatives that can refine, reduce, and replace animal use. In Europe, the European Centre for the Validation of Alternative Methods (ECVAM) was established to conduct validation studies on alternative test methods. Despite differences in organisational structure and processes, both organisations seek to achieve the adoption and use of alternative test methods. Accordingly, both have adopted similar validation and regulatory acceptance criteria. Collaborations and processes have also evolved to facilitate the international adoption of new test methods recommended by ECVAM and ICCVAM. These collaborations involve the sharing of expertise and data for test-method workshops and independent scientific peer reviews, and the adoption of processes to expedite the consideration of test methods already reviewed by the other organisation. More recently, NICEATM and ECVAM initiated a joint international validation study on in vitro methods for assessing acute systemic toxicity. These collaborations are expected to contribute to accelerated international adoption of harmonised new test methods that will support improved public health and provide for reduced and more-humane use of laboratory animals.

  7. Biodiesel production by biocatalysis using alternative method for lipase immobilization in hydrogel

    OpenAIRE

    Fernanda Marder; Mariéli Milanesi Ceolin; Mariele da Silva Mazuim; Rosana de Cassia de Souza Schneider; Marilda Teixeira Macagnan; Valeriano Antonio Corbellini

    2009-01-01

    The society has been looking for alternatives in order to stop the process of environmental destruction installed in the world, however, starting from last century, a new vision on the indiscriminate use of the environmental resources started to be discussed leading to the use of new technologies of production of cleaner fuel, as the biodiesel, produced from vegetable oils. The enzymatic processes are a production alternative, for they are methods with losses reduction and larger efficiency, ...

  8. Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes.

    Science.gov (United States)

    Simcox, Amanda; Mitra, Sayan; Truesdell, Sharon; Paul, Litty; Chen, Ting; Butchar, Jonathan P; Justiniano, Steven

    2008-08-01

    Analysis of cells in culture has made substantial contributions to biological research. The versatility and scale of in vitro manipulation and new applications such as high-throughput gene silencing screens ensure the continued importance of cell-culture studies. In comparison to mammalian systems, Drosophila cell culture is underdeveloped, primarily because there is no general genetic method for deriving new cell lines. Here we found expression of the conserved oncogene Ras(V12) (a constitutively activated form of Ras) profoundly influences the development of primary cultures derived from embryos. The cultures become confluent in about three weeks and can be passaged with great success. The lines have undergone more than 90 population doublings and therefore constitute continuous cell lines. Most lines are composed of spindle-shaped cells of mesodermal type. We tested the use of the method for deriving Drosophila cell lines of a specific genotype by establishing cultures from embryos in which the warts (wts) tumor suppressor gene was targeted. We successfully created several cell lines and found that these differ from controls because they are primarily polyploid. This phenotype likely reflects the known role for the mammalian wts counterparts in the tetraploidy checkpoint. We conclude that expression of Ras(V12) is a powerful genetic mechanism to promote proliferation in Drosophila primary culture cells and serves as an efficient means to generate continuous cell lines of a given genotype.

  9. Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes.

    Directory of Open Access Journals (Sweden)

    Amanda Simcox

    2008-08-01

    Full Text Available Analysis of cells in culture has made substantial contributions to biological research. The versatility and scale of in vitro manipulation and new applications such as high-throughput gene silencing screens ensure the continued importance of cell-culture studies. In comparison to mammalian systems, Drosophila cell culture is underdeveloped, primarily because there is no general genetic method for deriving new cell lines. Here we found expression of the conserved oncogene Ras(V12 (a constitutively activated form of Ras profoundly influences the development of primary cultures derived from embryos. The cultures become confluent in about three weeks and can be passaged with great success. The lines have undergone more than 90 population doublings and therefore constitute continuous cell lines. Most lines are composed of spindle-shaped cells of mesodermal type. We tested the use of the method for deriving Drosophila cell lines of a specific genotype by establishing cultures from embryos in which the warts (wts tumor suppressor gene was targeted. We successfully created several cell lines and found that these differ from controls because they are primarily polyploid. This phenotype likely reflects the known role for the mammalian wts counterparts in the tetraploidy checkpoint. We conclude that expression of Ras(V12 is a powerful genetic mechanism to promote proliferation in Drosophila primary culture cells and serves as an efficient means to generate continuous cell lines of a given genotype.

  10. A Web-based Alternative Non-animal Method Database for Safety Cosmetic Evaluations.

    Science.gov (United States)

    Kim, Seung Won; Kim, Bae-Hwan

    2016-07-01

    Animal testing was used traditionally in the cosmetics industry to confirm product safety, but has begun to be banned; alternative methods to replace animal experiments are either in development, or are being validated, worldwide. Research data related to test substances are critical for developing novel alternative tests. Moreover, safety information on cosmetic materials has neither been collected in a database nor shared among researchers. Therefore, it is imperative to build and share a database of safety information on toxicological mechanisms and pathways collected through in vivo, in vitro, and in silico methods. We developed the CAMSEC database (named after the research team; the Consortium of Alternative Methods for Safety Evaluation of Cosmetics) to fulfill this purpose. On the same website, our aim is to provide updates on current alternative research methods in Korea. The database will not be used directly to conduct safety evaluations, but researchers or regulatory individuals can use it to facilitate their work in formulating safety evaluations for cosmetic materials. We hope this database will help establish new alternative research methods to conduct efficient safety evaluations of cosmetic materials.

  11. Evaluating imputation algorithms for low-depth genotyping-by-sequencing (GBS) data

    Science.gov (United States)

    Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordabl...

  12. An Alternative Method to Gauss-Jordan Elimination: Minimizing Fraction Arithmetic

    Science.gov (United States)

    Smith, Luke; Powell, Joan

    2011-01-01

    When solving systems of equations by using matrices, many teachers present a Gauss-Jordan elimination approach to row reducing matrices that can involve painfully tedious operations with fractions (which I will call the traditional method). In this essay, I present an alternative method to row reduce matrices that does not introduce additional…

  13. 76 FR 5319 - Regulation of Fuel and Fuel Additives: Alternative Test Method for Olefins in Gasoline

    Science.gov (United States)

    2011-01-31

    ... Olefins in Gasoline AGENCY: Environmental Protection Agency (EPA). ACTION: Proposed rule. SUMMARY: The... method for olefin content in gasoline. This proposed rule will provide flexibility to the regulated... A. Alternative Test Method for Olefins in Gasoline III. Statutory and Executive Order Reviews...

  14. Validation of Alternative In Vitro Methods to Animal Testing: Concepts, Challenges, Processes and Tools.

    Science.gov (United States)

    Griesinger, Claudius; Desprez, Bertrand; Coecke, Sandra; Casey, Warren; Zuang, Valérie

    This chapter explores the concepts, processes, tools and challenges relating to the validation of alternative methods for toxicity and safety testing. In general terms, validation is the process of assessing the appropriateness and usefulness of a tool for its intended purpose. Validation is routinely used in various contexts in science, technology, the manufacturing and services sectors. It serves to assess the fitness-for-purpose of devices, systems, software up to entire methodologies. In the area of toxicity testing, validation plays an indispensable role: "alternative approaches" are increasingly replacing animal models as predictive tools and it needs to be demonstrated that these novel methods are fit for purpose. Alternative approaches include in vitro test methods, non-testing approaches such as predictive computer models up to entire testing and assessment strategies composed of method suites, data sources and decision-aiding tools. Data generated with alternative approaches are ultimately used for decision-making on public health and the protection of the environment. It is therefore essential that the underlying methods and methodologies are thoroughly characterised, assessed and transparently documented through validation studies involving impartial actors. Importantly, validation serves as a filter to ensure that only test methods able to produce data that help to address legislative requirements (e.g. EU's REACH legislation) are accepted as official testing tools and, owing to the globalisation of markets, recognised on international level (e.g. through inclusion in OECD test guidelines). Since validation creates a credible and transparent evidence base on test methods, it provides a quality stamp, supporting companies developing and marketing alternative methods and creating considerable business opportunities. Validation of alternative methods is conducted through scientific studies assessing two key hypotheses, reliability and relevance of the

  15. An Exploratory Study of a Subspace Iteration Method as an Alternative to the QR Method for Floquet Eigenanalysis

    Science.gov (United States)

    Achar, N. S.; Gaonkar, G. H.

    1994-01-01

    Floquet eigenanalysis requires a few dominant eigenvalues of the Floquet transition matrix (FTM). Although the QR method is used almost exclusively, it is expensive for such partial eigenanalysis; the operation counts and, thereby, the approximate machine-time grow cubically with the matrix order. Accordingly, for Floquet eigenanalysis, the Arnold-Saad method, a subspace iteration method, is investigated as an alternative to the QR method. The two methods are compared for machine-time efficiency and the residual errors of the corresponding eigenpairs. The Arnolds-Saad method takes much less machine-time than the QR method with comparable computational reliability and offers promise fpr large-scale Floquet eigenanalysis.

  16. A Line-Search-Based Partial Proximal Alternating Directions Method for Separable Convex Optimization

    Directory of Open Access Journals (Sweden)

    Yu-hua Zeng

    2014-01-01

    Full Text Available We propose an appealing line-search-based partial proximal alternating directions (LSPPAD method for solving a class of separable convex optimization problems. These problems under consideration are common in practice. The proposed method solves two subproblems at each iteration: one is solved by a proximal point method, while the proximal term is absent from the other. Both subproblems admit inexact solutions. A line search technique is used to guarantee the convergence. The convergence of the LSPPAD method is established under some suitable conditions. The advantage of the proposed method is that it provides the tractability of the subproblem in which the proximal term is absent. Numerical tests show that the LSPPAD method has better performance compared with the existing alternating projection based prediction-correction (APBPC method if both are employed to solve the described problem.

  17. Study of alternative strategies and methods for conserving energy. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1977-04-01

    Objectives of the study were: (1) to identify and analyze alternative methods, means, and techniques, for controlling and moderating the consumption of energy; (2) to evaluate the impact of regulatory actions, taxes, incentives, subsidies or other strategies and methods on alternative physical technologies for energy conservation; and (3) to evaluate, macro- and micro-economic impacts and consequences of alternative energy conservation methods, means and techniques on work, leisure, life styles, and institutions on a local, regional, and national level. The study excludes automobile and related road vehicle energy consumption control strategies, but includes those for residential, commercial, industrial, and other energy end-use sectors. The time frame is from 1973 to 1990/2000, with emphasis on the period 1973-1980.

  18. Rep-PCR--a variant to RAPD or an independent technique of bacteria genotyping? A comparison of the typing properties of rep-PCR with other recognised methods of genotyping of microorganisms.

    Science.gov (United States)

    Baldy-Chudzik, K

    2001-01-01

    The paper presents technical aspects of rep-PCR fingerprinting technique and compares its typing abilities, differentiation power and reproducibility with other recognised and recommended genotyping methods. Although rep-PCR fingerprinting is similar to MAAP techniques, it demonstrates some essentially different elements. The data presented in this review, indicate a rep-PCR genomic fingerprinting technique as a highly discriminating, independent screening method for determining the taxonomical diversity of bacterial population.

  19. A methodology to quantify the differences between alternative methods of heart rate variability measurement.

    Science.gov (United States)

    García-González, M A; Fernández-Chimeno, M; Guede-Fernández, F; Ferrer-Mileo, V; Argelagós-Palau, A; Álvarez-Gómez, L; Parrado, E; Moreno, J; Capdevila, L; Ramos-Castro, J

    2016-01-01

    This work proposes a systematic procedure to report the differences between heart rate variability time series obtained from alternative measurements reporting the spread and mean of the differences as well as the agreement between measuring procedures and quantifying how stationary, random and normal the differences between alternative measurements are. A description of the complete automatic procedure to obtain a differences time series (DTS) from two alternative methods, a proposal of a battery of statistical tests, and a set of statistical indicators to better describe the differences in RR interval estimation are also provided. Results show that the spread and agreement depend on the choice of alternative measurements and that the DTS cannot be considered generally as a white or as a normally distributed process. Nevertheless, in controlled measurements the DTS can be considered as a stationary process.

  20. Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods.

    Science.gov (United States)

    Satish, Lakkakula; Shilpha, Jayabalan; Pandian, Subramani; Rency, Arockiam Sagina; Rathinapriya, Periyasamy; Ceasar, Stanislaus Antony; Largia, Muthiah Joe Virgin; Kumar, Are Ashok; Ramesh, Manikandan

    2016-01-15

    Genetic variation among 45 genotypes of sorghum (Sorghum bicolor L.) representing seven subpopulations was assessed using three single primer amplification reaction (SPAR) methods viz., inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and directed amplification of minisatellite-region DNA (DAMD). Totally 15 ISSR, 8 RAPD and 7 DAMD primers generated 263 amplification products, accounting for 84.6% polymorphism across all the genotypes. The Mantel's test of correlation revealed the best correlation between ISSR and cumulative data with a correlation coefficient (r) of 0.84. Assessment of population diversity indicated that the maximum intra population genetic diversity was recorded among high FeZn lines (HFL) having maximum values of Nei's genetic diversity (h) (0.244), Shannon information index (I) (0.368) and the percentage of polymorphic loci (Pp) (72.65%) while the corresponding lowest values of 0.074, 0.109 and 17.95% respectively were observed among the members of MDT subpopulation. The mean coefficient of gene differentiation (GST) and the gene flow (Nm) between populations were observed to be 0.396 and 0.7680 respectively. The analysis of molecular variance (AMOVA) suggested that maximum genetic variation exists within populations (95%) than among populations (5%). Thus the information obtained from this study could be utilized in sorghum breeding programmes for the development of varieties with improved nutrition and agronomic values in future.

  1. Methods and Algorythms of Alternatives Ranging in Managing the Telecommunication Services Guality.

    Directory of Open Access Journals (Sweden)

    Pham Quang Hiep

    2015-07-01

    Full Text Available The article deals with methods of solving the problem of ranging of alternatives in information-analytical system of managing the quality of telecommunication services rendering process. Tasks of choice are determined, in which the alternatives are as follows: states of quality of different objects in the structure of telecommunication company management. An algorithm of ranging of objects is elaborated for the case of using unstructured set of indices. The algorithm enables to determine the objects priorities and to select the best ones among them. The suggested methods may be used while elaborating the programs of improvement of telecommunication companies competitiveness.

  2. THE ALTERNATING SEGMENT CRANK-NICOLSON METHOD FOR SOLVING CONVECTION-DIFFUSION EQUATION WITH VARIABLE COEFFICIENT

    Institute of Scientific and Technical Information of China (English)

    王文洽

    2003-01-01

    A new discrete approximation to the convection term of the covection-diffusionequation was constructed in Saul' yev type difference scheme, then the alternating segmentCrank-Nicolson( ASC-N) method for solving the convection-diffusion equation with variablecoefficient was developed. The ASC-N method is unconditionally stable. Numericalexperiment shows that this method has the obvious property of parallelism and accuracy. Themethod can be used directly on parallel computers.

  3. Solution of nonlinear Volterra-Hammerstein integral equations using alternative Legendre collocation method

    Directory of Open Access Journals (Sweden)

    Sohrab Bazm

    2016-11-01

    Full Text Available Alternative Legendre polynomials (ALPs are used to approximate the solution of a class of nonlinear Volterra-Hammerstein integral equations. For this purpose, the operational matrices of integration and the product for ALPs are derived. Then, using the collocation method, the considered problem is reduced into a set of nonlinear algebraic equations. The error analysis of the method is given and the efficiency and accuracy are illustrated by applying the method to some examples.

  4. Evaluation of an Array-Based Method for Human Papillomavirus Detection and Genotyping in Comparison with Conventional Methods Used in Cervical Cancer Screening▿

    Science.gov (United States)

    García-Sierra, Nerea; Martró, Elisa; Castellà, Eva; Llatjós, Mariona; Tarrats, Antoni; Bascuñana, Elisabet; Díaz, Rosana; Carrasco, María; Sirera, Guillem; Matas, Lurdes; Ausina, Vicente

    2009-01-01

    Cervical cancer is the second-most prevalent cancer in young women around the world. Infection with human papillomavirus (HPV), especially high-risk HPV types (HR-HPV), is necessary for the development of this cancer. HPV-DNA detection is increasingly being used in cervical cancer screening programs, together with the Papanicolau smear test. We evaluated the usefulness of introducing this new array-based HPV genotyping method (i.e., Clinical Arrays Papillomavirus Humano) in the cervical cancer screening algorithm in our center. The results obtained using this method were compared to those obtained by the hybrid capture II high-risk HPV DNA test (HC-II) and Papanicolau in a selected group of 408 women. The array-based assay was performed in women that were HC-II positive or presented cytological alterations. Among 246 array-positive patients, 123 (50%) presented infection with ≥2 types, and HR-HPV types were detected in 206 (83.7%), mainly HPV-16 (24.0%). Up to 132 (33.2%) specimens were classified as ASCUS (for atypical squamous cells of undetermined significance), and only 48 (36.4%) of them were HPV-DNA positive by either assay; however, 78.7% of these cases were caused by HR-HPV types. The agreement between both HPV-DNA detection techniques was fairly good (n = 367). Screening with Papanicolau smear and HC-II tests, followed by HPV detection and genotyping, provided an optimal identification of women at risk for the development of cervical cancer. Furthermore, with the identification of specific genotypes, either in single or multiple infections, a better prediction of disease progression was achieved. The array method also made allowed us to determine the possible contribution of the available vaccines in our setting. PMID:19439534

  5. Evaluation of an array-based method for human papillomavirus detection and genotyping in comparison with conventional methods used in cervical cancer screening.

    Science.gov (United States)

    García-Sierra, Nerea; Martró, Elisa; Castellà, Eva; Llatjós, Mariona; Tarrats, Antoni; Bascuñana, Elisabet; Díaz, Rosana; Carrasco, María; Sirera, Guillem; Matas, Lurdes; Ausina, Vicente

    2009-07-01

    Cervical cancer is the second-most prevalent cancer in young women around the world. Infection with human papillomavirus (HPV), especially high-risk HPV types (HR-HPV), is necessary for the development of this cancer. HPV-DNA detection is increasingly being used in cervical cancer screening programs, together with the Papanicolau smear test. We evaluated the usefulness of introducing this new array-based HPV genotyping method (i.e., Clinical Arrays Papillomavirus Humano) in the cervical cancer screening algorithm in our center. The results obtained using this method were compared to those obtained by the hybrid capture II high-risk HPV DNA test (HC-II) and Papanicolau in a selected group of 408 women. The array-based assay was performed in women that were HC-II positive or presented cytological alterations. Among 246 array-positive patients, 123 (50%) presented infection with >or=2 types, and HR-HPV types were detected in 206 (83.7%), mainly HPV-16 (24.0%). Up to 132 (33.2%) specimens were classified as ASCUS (for atypical squamous cells of undetermined significance), and only 48 (36.4%) of them were HPV-DNA positive by either assay; however, 78.7% of these cases were caused by HR-HPV types. The agreement between both HPV-DNA detection techniques was fairly good (n = 367). Screening with Papanicolau smear and HC-II tests, followed by HPV detection and genotyping, provided an optimal identification of women at risk for the development of cervical cancer. Furthermore, with the identification of specific genotypes, either in single or multiple infections, a better prediction of disease progression was achieved. The array method also made allowed us to determine the possible contribution of the available vaccines in our setting.

  6. Modeling alternatives for basin-level hydropower development: 1. Optimization methods and applications

    Science.gov (United States)

    Chang, Shoou-Yuh; Liaw, Shu-Liang; Railsback, Steven F.; Sale, Michael J.

    1992-10-01

    Development of multiple hydroelectric projects at navigation dams on large river systems can result in a number of environmental impacts, including potential reductions in dissolved oxygen (DO) concentrations. This study presents a method for generating hydropower development alternatives for evaluation by planners by quantifying the trade-offs between water quality and power generation. This method employs a Streeter-Phelps model to simulate DO and the bounded implicit enumeration algorithm to solve an optimization model formulated to maximize hydroelectric energy production. A portion of the upper Ohio River basin was selected to illustrate the methodology. The results indicate that various alternatives that meet the specified DO constraints can be generated efficiently. These alternatives are nearly optimal solutions with respect to the modeled objectives but are different with respect to decision variables.

  7. Attributed Goal-Oriented Analysis Method for Selecting Alternatives of Software Requirements

    Science.gov (United States)

    Yamamoto, Kazuma; Saeki, Motoshi

    During software requirements analysis, developers and stakeholders have many alternatives of requirements to be achieved and should make decisions to select an alternative out of them. There are two significant points to be considered for supporting these decision making processes in requirements analysis; 1) dependencies among alternatives and 2) evaluation based on multi-criteria and their trade-off. This paper proposes the technique to address the above two issues by using an extended version of goal-oriented analysis. In goal-oriented analysis, elicited goals and their dependencies are represented with an AND-OR acyclic directed graph. We use this technique to model the dependencies of the alternatives. Furthermore we associate attribute values and their propagation rules with nodes and edges in a goal graph in order to evaluate the alternatives with them. The attributes and their calculation rules greatly depend on the characteristics of a development project. Thus, in our approach, we select and use the attributes and their rules that can be appropriate for the project. TOPSIS method is adopted to show alternatives and their resulting attribute values.

  8. An Alternative Method to Compute the Bit Error Probability of Modulation Schemes Subject to Nakagami- Fading

    Directory of Open Access Journals (Sweden)

    Madeiro Francisco

    2010-01-01

    Full Text Available Abstract This paper presents an alternative method for determining exact expressions for the bit error probability (BEP of modulation schemes subject to Nakagami- fading. In this method, the Nakagami- fading channel is seen as an additive noise channel whose noise is modeled as the ratio between Gaussian and Nakagami- random variables. The method consists of using the cumulative density function of the resulting noise to obtain closed-form expressions for the BEP of modulation schemes subject to Nakagami- fading. In particular, the proposed method is used to obtain closed-form expressions for the BEP of -ary quadrature amplitude modulation ( -QAM, -ary pulse amplitude modulation ( -PAM, and rectangular quadrature amplitude modulation ( -QAM under Nakagami- fading. The main contribution of this paper is to show that this alternative method can be used to reduce the computational complexity for detecting signals in the presence of fading.

  9. Using a Forensic Research Method for Establishing an Alternative Method for Audience Measurement in Print Advertising

    DEFF Research Database (Denmark)

    Schmidt, Marcus; Krause, Niels; Solgaard, Hans Stubbe

    2012-01-01

    Advantages and disadvantages of the survey approach are discussed. It is hypothesized that observational methods sometimes constitute reasonable and powerful substitute to traditional survey methods. Under certain circumstances, unobtrusive methods may even outperform traditional techniques. Non-...

  10. Using a Forensic Research Method for Establishing an Alternative Method for Audience Measurement in Print Advertising

    DEFF Research Database (Denmark)

    Schmidt, Marcus; Krause, Niels; Solgaard, Hans Stubbe

    2012-01-01

    Advantages and disadvantages of the survey approach are discussed. It is hypothesized that observational methods sometimes constitute reasonable and powerful substitute to traditional survey methods. Under certain circumstances, unobtrusive methods may even outperform traditional techniques. Non...

  11. Evaluation of phenotypic and genotypic methods for subtyping Campylobacter jejuni isolates from humans, poultry, and cattle

    DEFF Research Database (Denmark)

    Nielsen, Eva Møller; Engberg, J.; Fussing, V.

    2000-01-01

    Six methods for subtyping of Campylobacter jejuni were compared and evaluated with a collection of 90 isolates from poultry, cattle, and sporadic human clinical cases as well as from a waterborne outbreak. The applied methods were Penner heat-stable serotyping; automated ribotyping (Ribo...

  12. Consequences for welfare and pension buffers of alternative methods of discounting future pensions

    NARCIS (Netherlands)

    A. Bucciol; R.M.W.J. Beetsma

    2011-01-01

    We explore the implications of alternative methods of discounting future pension outlays for the valuation of funded pension liabilities. Measured liabilities affect the asset-liability ratio of pension funds and, thereby, their policies. Our framework for analysis is an applied many-generation OLG

  13. The Duplicate-Replacement System: An Alternative Method of Handling Book Duplicates.

    Science.gov (United States)

    Clement, Russell T.

    This report studied the alternative method of using book duplicates as replacement copies for worn or missing stack items. The simple operational procedure which is proposed and evaluated could be adapted to virtually any library setting. When tested in Brigham Young University's Lee Library, it was found that such a procedure cost an estimated…

  14. Alternating Renewal Process Models for Behavioral Observation: Simulation Methods, Software, and Validity Illustrations

    Science.gov (United States)

    Pustejovsky, James E.; Runyon, Christopher

    2014-01-01

    Direct observation recording procedures produce reductive summary measurements of an underlying stream of behavior. Previous methodological studies of these recording procedures have employed simulation methods for generating random behavior streams, many of which amount to special cases of a statistical model known as the alternating renewal…

  15. 29 CFR 2520.104-4 - Alternative method of compliance for certain successor pension plans.

    Science.gov (United States)

    2010-07-01

    ... pension plans. 2520.104-4 Section 2520.104-4 Labor Regulations Relating to Labor (Continued) EMPLOYEE... certain successor pension plans. (a) General. Under the authority of section 110 of the Act, this section sets forth an alternative method of compliance for certain successor pension plans in which some...

  16. Comparison of DNA Pyrosequencing with Alternative Methods for Identification of Mycobacteria▿

    OpenAIRE

    2008-01-01

    Identification of mycobacterial clinical isolates by pyrosequencing within the hypervariable A region of the 16S rRNA gene was compared to other identification methods. For >90% of isolates, these identifications correlated to the level of complex or species. For identification of many mycobacteria, pyrosequencing offers an inexpensive alternative to traditional sequencing.

  17. Communicative Approach: An Alternative Method Used in Improving Students' Academic Reading Achievement

    Science.gov (United States)

    Irmawati, Noer Doddy

    2012-01-01

    Academic reading is a difficult subject to be mastered. It is needed because most of books or references are written in English. The emphasis is on academic reading which becomes a compulsory subject that must be taught and understood in Faculty of Letters UAD Yogyakarta. Communicative approach is used and applied as an alternative method in the…

  18. Method and apparatus for detecting cyber attacks on an alternating current power grid

    Energy Technology Data Exchange (ETDEWEB)

    McEachern, Alexander; Hofmann, Ronald

    2017-04-11

    A method and apparatus for detecting cyber attacks on remotely-operable elements of an alternating current distribution grid. Two state estimates of the distribution grid are prepared, one of which uses micro-synchrophasors. A difference between the two state estimates indicates a possible cyber attack.

  19. Report to the Congress on alternative methods for the Strategic Petroleum Reserve

    Energy Technology Data Exchange (ETDEWEB)

    1990-02-01

    The purpose of this study is to fulfill the requirements of Public Law No. 101-46, approved June 30, 1989. The study describes and evaluates alternative methods for financing the future expansion of the Strategic petroleum Reserve (SPR), both to the current target level of 750 million barrels and to potential future levels of up to one billion barrels.

  20. Accelerating the Use of Weblogs as an Alternative Method to Deliver Case-Based Learning

    Science.gov (United States)

    Chen, Charlie; Wu, Jiinpo; Yang, Samuel C.

    2008-01-01

    Weblog technology is an alternative medium to deliver the case-based method of learning business concepts. The social nature of this technology can potentially promote active learning and enhance analytical ability of students. The present research investigates the primary factors contributing to the adoption of Weblog technology by students to…

  1. Record-keeping as an Alternative Method οf Assessment

    Directory of Open Access Journals (Sweden)

    Androniki Kouvdou

    2010-02-01

    Full Text Available The basic topic of this chapter is the description of an alternative method of assessment which supplements traditional objective techniques (i.e. testing, while counterbalancing their limitations. This alternative method, known as ‘record-keeping’, involves the systematic collection and recording of information about learner progress and aims at providing a more complete and valid formative assessment of their developmental abilities in specified areas. More particularly, this chapter presents a small-scale case study, which was carried out in the sixth grade of a primary school and lasted three months. The subjects of this case study were four twelve-year-old learners and its purpose was to investigate the potential of ‘record-keeping’ as an alternative method of assessing oracy skills in the foreign language. The data that derived from the case study reinforce the usefulness and validity of the particular method of assessment. The goals of the experimental assessment design, which entailed the recording and gradual development of learner oracy skills as well as the enhancement of motivation and awareness of their relevant sub-skills, were accomplished to a considerable degree. Additionally, the learners responded positively to the implemented assessment project, while being actively involved in it, which further substantiates its effectiveness. Alternative assessment, however, is a large area, whose full potential of implementation calls for further investigation.

  2. Surveying immigrants without sampling frames - evaluating the success of alternative field methods.

    Science.gov (United States)

    Reichel, David; Morales, Laura

    2017-01-01

    This paper evaluates the sampling methods of an international survey, the Immigrant Citizens Survey, which aimed at surveying immigrants from outside the European Union (EU) in 15 cities in seven EU countries. In five countries, no sample frame was available for the target population. Consequently, alternative ways to obtain a representative sample had to be found. In three countries 'location sampling' was employed, while in two countries traditional methods were used with adaptations to reach the target population. The paper assesses the main methodological challenges of carrying out a survey among a group of immigrants for whom no sampling frame exists. The samples of the survey in these five countries are compared to results of official statistics in order to assess the accuracy of the samples obtained through the different sampling methods. It can be shown that alternative sampling methods can provide meaningful results in terms of core demographic characteristics although some estimates differ to some extent from the census results.

  3. An evaluation of alternative cleaning methods for removing an organic contaminant from a stainless steel part

    Energy Technology Data Exchange (ETDEWEB)

    Boyd, J.L.

    1996-08-01

    As of December 1995, the manufacture of Freon, along with many other chlorofluorocarbons (CFCs), was prohibited by the Clean Air Act of 1990 (CAA). The ban of CFC solvents has forced manufacturers across the country to search for alternative metal cleaning techniques. The objective of this study was to develop a thorough, scientific based approach for resolving one specific manufacturer`s problem of removing organic contamination from a stainless steel part. This objective was accomplished with an approach that involved: (1) defining the problem, (2) identifying the process constraints, (3) researching alternate cleaning methods, (4) researching applicable government regulations, (5) performing a scientific evaluation and (6) drawing conclusions.

  4. An alternative method for modeling the size distribution of top wealth

    Science.gov (United States)

    Wang, Yuanjun; You, Shibing

    2016-09-01

    The Pareto distribution has been widely applied in modeling the distribution of wealth, as well as top incomes, cities and firms. However, recent evidence has shown that the Pareto distribution is not consistent with many situations in which it was previously considered applicable. We propose an alternative method for estimating the upper tail distribution of wealth and suggest a new Lorenz curve for building models to provide such estimates. Applying our new models to the Forbes World's Billionaire Lists, we show that they significantly outperform the Pareto Lorenz curve as well as some other popular alternatives.

  5. The Worldsheet Formulation as an Alternative Method for Simulating Dynamical Fermions

    CERN Document Server

    Fort, H

    1998-01-01

    The recently proposed worldsheet formulation of lattice fermions is tested for the first time carrying out a simulation for the simplest model: the one-flavor, strictly massless lattice Schwinger model. A main advantage of this alternative method for simulating dynamical fermions consists in its economy: it involves many fewer degrees of freedom than the ordinary Kogut-Susskind formulation. The known continuum limit is reproduced by the method for relatively small lattices.

  6. A Study of Alternative Quantile Estimation Methods in Newsboy-Type Problems

    Science.gov (United States)

    1980-03-01

    early in 1950 [1]. This problem has been presented in the literature under a variety of names, including newsvendor problem , Christmas tree problem ...quantile estimation methods in newsboy-type problems . Sok, Yong-u Monterey, California. Naval Postgraduate School http://hdl.handle.net/10945/19069...Downloaded from NPS Archive: Calhoun A STUDY OF ALTERNATIVE QUANTILE ESTIMATION METHODS IN NEWSBOY-TYPE PROBLEMS Yong-u Sok sss- 939434 NAVAL POSTGRADUATE

  7. An Alternating Direction Method for Convex Quadratic Second-Order Cone Programming with Bounded Constraints

    OpenAIRE

    Xuewen Mu; Yaling Zhang

    2015-01-01

    An alternating direction method is proposed for convex quadratic second-order cone programming problems with bounded constraints. In the algorithm, the primal problem is equivalent to a separate structure convex quadratic programming over second-order cones and a bounded set. At each iteration, we only need to compute the metric projection onto the second-order cones and the projection onto the bound set. The result of convergence is given. Numerical results demonstrate that our method is ...

  8. Direct PCR: Alternative Diagnostic Method for Diagnosis of Diphtheria Rapidly, Easily and Cost Effective

    Directory of Open Access Journals (Sweden)

    Sunarno Sunarno

    2013-12-01

    Full Text Available Some diseases require immediate and appropriate treatment to decrease the fatality risk patients incident, for example diphtheria. Time to help patients is very crucial since delay of therapy may increase the mortality cases up to 20 times. In other hands, conventional diagnostic methods (the gold standard for diagnosis of diphtheria is time consuming and laborious. Therefore, an alternative diagnostic method which is rapid, easy and inexpensive is needed. In this case, direct PCR has been proved to reduce time and cost in laboratory examination. This study aimed to develop direct PCR as alternative diagnostic method for diagnosis of diphtheria rapidly, easily, and inexpensive. Fifteen samples include 10 isolates of Corynebacterium diphtheriae (toxigenic and 3 isolates of Corynebacterium non- diphtheriae (nontoxigenic and 2 clinical specimens (throat swab was examined by performing direct PCR method and a standard PCR method was used for optimizing the protocols. Result showed that direct PCR can be used to amplify target genes correctly as well as standard PCR. All of C. diphtheriae samples showed bands at 168 bp (dtxR gene marker and 551 bp (tox gene marker while no band appeared in others. Direct PCR detected at least 71 CFU/uL of bacterial cells in samples. We concluded that direct PCR can be used for alternative diagnostic method for diagnosis of diphtheria which is rapid, easy and cost effective.

  9. Biodiesel production by biocatalysis using alternative method for lipase immobilization in hydrogel

    Directory of Open Access Journals (Sweden)

    Fernanda Marder

    2009-03-01

    Full Text Available The society has been looking for alternatives in order to stop the process of environmental destruction installed in the world, however, starting from last century, a new vision on the indiscriminate use of the environmental resources started to be discussed leading to the use of new technologies of production of cleaner fuel, as the biodiesel, produced from vegetable oils. The enzymatic processes are a production alternative, for they are methods with losses reduction and larger efficiency, presenting however, high production cost. With the objective of reducing costs and increasing the efficiency we have searched the enzymes immobilization through alternative method and to use them as biocatalysts in the biodiesel production. The immobilization of the lipase PS Amano was accomplished in spheres formed by the hydration of commercial hydrogel in aqueous solution containing the enzyme. With the immobilized enzyme it was accomplished the transesterification, in which it was obtained conversions in methyl esters of up to 70%, in organic solvent, with 24h, 55°C, 100 rpm and 40 hydrogel spheres with immobilized enzyme. The method comes as a promising alternative technology for the biodiesel obtaining.

  10. A fast and easy real-time PCR genotyping method for the HLA-G 14-bp insertion/deletion polymorphism in the 3' untranslated region

    DEFF Research Database (Denmark)

    Djurisic, S; Sørensen, A E; Hviid, T V F

    2012-01-01

    and reliable method to screen for the HLA-G 14-bp insertion/deletion polymorphism using an optimized real-time polymerase chain reaction protocol. The genotyping assay has been validated by comparison with conventional methods. As results can be obtained within a few hours, the assay will have a potential...

  11. Methods of adaptability and stability analysis in irrigated rice genotypes in Minas Gerais, Brazil

    Directory of Open Access Journals (Sweden)

    Felipe Lopes da Silva

    2008-01-01

    Full Text Available The objective of this study was to compare different estimation methods of adaptability and stability in ninegenotypes of irrigated rice. The experiment was conducted at three sites in the state of Minas Gerais in the growing seasonsfrom 2000/2001 to 2005/2006, totaling 11 environments. The adaptability and stability were analyzed by the methods proposedby Eberhart and Russel (1966, Cruz et al. (1989, Carneiro (1998 and Annicchiarico (1992. The methods proposed byCarneiro (1998 and by Annicchiarico (1992 were more satisfactory due to the measure of behavioral adaptability andstability, which combined adaptation, adaptability and stability concepts in just one parameter. General adaptability wasobserved in the lines CNAi 8872 and CNAi 8874 and specific adaptability to favorable conditions in cultivar Rio Grande.

  12. Evaluation of Genotypic and Phenotypic Methods to Detect Carbapenemase Production in Gram-Negative Bacilli.

    Science.gov (United States)

    McMullen, Allison R; Yarbrough, Melanie L; Wallace, Meghan A; Shupe, Angela; Burnham, Carey-Ann D

    2017-03-01

    Carbapenemase-producing gram-negative bacteria (CP-GNB) are an urgent and expanding public health threat. Rapid and accurate identification of these organisms facilitates infection prevention efforts in healthcare facilities. The objective of our study was to evaluate methods to detect and identify CP-GNB. We examined 189 carbapenem-resistant GNB(CR-GNB), including Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii complex, using 3 different methods: 2 methods to screen isolates of GNB for carbapenemase production [the carbapenem inactivation method (CIM) and 2 chromogenic agars] and a molecular method (Cepheid GeneXpert Carba-R) to identify the mechanism of carbapenem resistance and the associated resistance genes (blaKPC, blaNDM, blaIMP, blaOXA-48-like, and blaVIM). The CIM was a simple and inexpensive phenotypic screen to differentiate between CR-GNB and CP-GNB, with improved analytical performance characteristics and inter-reader correlation compared to the modified Hodge test. Both chromogenic agars evaluated (HardyCHROM CRE and chromID CARBA) were able to support growth of most of the organisms tested, including isolates possessing the blaOXA-48-like gene. However, these media had a low analytical specificity for carbapenemase production, with breakthrough of CR-GNB that did not produce a carbapenemase. The Xpert Carba-R assay was rapid and easy to perform, and demonstrated 100% positive and negative agreement for characterization of genetic determinants of carbapenem resistance. Screening by CIM followed by the Xpert Carba-R PCR is an accurate method for detecting and characterizing CP-GNB, including Enterobacteriaceae, P. aeruginosa, and A. baumannii complex. © 2016 American Association for Clinical Chemistry.

  13. An evaluation of alternate production methods for Pu-238 general purpose heat source pellets

    Energy Technology Data Exchange (ETDEWEB)

    Mark Borland; Steve Frank

    2009-06-01

    For the past half century, the National Aeronautics and Space Administration (NASA) has used Radioisotope Thermoelectric Generators (RTG) to power deep space satellites. Fabricating heat sources for RTGs, specifically General Purpose Heat Sources (GPHSs), has remained essentially unchanged since their development in the 1970s. Meanwhile, 30 years of technological advancements have been made in the applicable fields of chemistry, manufacturing and control systems. This paper evaluates alternative processes that could be used to produce Pu 238 fueled heat sources. Specifically, this paper discusses the production of the plutonium-oxide granules, which are the input stream to the ceramic pressing and sintering processes. Alternate chemical processes are compared to current methods to determine if alternative fabrication processes could reduce the hazards, especially the production of respirable fines, while producing an equivalent GPHS product.

  14. Use of Biosensors as Alternatives to Current Regulatory Methods for Marine Biotoxins

    Directory of Open Access Journals (Sweden)

    Luis M. Botana

    2009-11-01

    Full Text Available Marine toxins are currently monitored by means of a bioassay that requires the use of many mice, which poses a technical and ethical problem in many countries. With the exception of domoic acid, there is a legal requirement for the presence of other toxins (yessotoxin, saxitoxin and analogs, okadaic acid and analogs, pectenotoxins and azaspiracids in seafood to be controlled by bioassay, but other toxins, such as palytoxin, cyclic imines, ciguatera and tetrodotoxin are potentially present in European food and there are no legal requirements or technical approaches available to identify their presence. The need for alternative methods to the bioassay is clearly important, and biosensors have become in recent years a feasible alternative to animal sacrifice. This review will discuss the advantages and disadvantages of using biosensors as alternatives to animal assays for marine toxins, with particular focus on surface plasmon resonance (SPR technology.

  15. Method for exploiting bias in factor analysis using constrained alternating least squares algorithms

    Science.gov (United States)

    Keenan, Michael R.

    2008-12-30

    Bias plays an important role in factor analysis and is often implicitly made use of, for example, to constrain solutions to factors that conform to physical reality. However, when components are collinear, a large range of solutions may exist that satisfy the basic constraints and fit the data equally well. In such cases, the introduction of mathematical bias through the application of constraints may select solutions that are less than optimal. The biased alternating least squares algorithm of the present invention can offset mathematical bias introduced by constraints in the standard alternating least squares analysis to achieve factor solutions that are most consistent with physical reality. In addition, these methods can be used to explicitly exploit bias to provide alternative views and provide additional insights into spectral data sets.

  16. Prediction-correction alternating direction method for a class of constrained rain-max problems

    Institute of Scientific and Technical Information of China (English)

    LI Min; HE Bingsheng

    2007-01-01

    The problems concerned in this paper are a class of constrained min-max problems. By introducing the Lagrange multipliers to the linearconstraints, such problems can be solved by some projection type prediction-correction methods. However, to obtain components of the predictor one by one, we use an alternating direction method. And then the new iterate is generated by a minor correction. Global convergence of the proposed method is proved. Finally, numerical results for a constrained single-facility location problem are provided to verify that the new method is effective for some practical problems.

  17. Evaluation of phenotypic and genotypic methods for subtyping Campylobacter jejuni isolates from humans, poultry, and cattle

    DEFF Research Database (Denmark)

    Nielsen, Eva Møller; Engberg, J.; Fussing, V.;

    2000-01-01

    Printing); random amplified polymorphic DNA typing (RAPD); pulsed-field gel electrophoresis (PFGE); restriction fragment length polymorphisms of the flagellin gene,flaA (fla-RFLP); and denaturing gradient gel electrophoresis of flaA (fla-DGGE). The methods were evaluated and compared on the basis of their abilities...

  18. COMPARISON OF FOUR GENOTYPING METHODS FOR P.AERUGINODA: IN SILICO STUDY.

    Science.gov (United States)

    Babenko, D

    2016-05-01

    Many molecular typing methods have been employed as major tools in epidemiological investigation for identifying clonal relatedness of P.aeruginosa isolates. Having own application points and principles they have certain advantages and disadvantages. The aim of this study was the estimation of discriminatory power and concordance between four different typing methods: PFGE, MLVA, MLST and wgMLST. 58 P.aeruginosa genome were analyzed in silico to determine PFGE, MLVA, MLST and wgMLST types and their cluster/clonal complexes. These data were estimated in term of discriminatory power and concordance. All four typing approaches demonstrated high resolution power (Simpson's ID): wgMLST (1.0), PFGE (0.999), MLVA (0.997) and MLST (0.983). Concordance between PFGE, MLVA, MLST was weak/moderate and was no more 74.1%. WgMLST demonstrated high concordance between wgMLST clusters and clonal complex/groups/clusters determined by MLST (AR=0.938), PFGE (AR=0.952) and MLVA (AR=0.798) typing methods after choosing appropriate cut-off value for wgMLST. wgMLST with more than 5100 target genes showed the highest index diversity and high concordance with other typing methods.

  19. Alternative methods for dispoal of low-level radioactive wastes. Task 1. Description of methods and assessment of criteria. [Alternative methods are belowground vaults, aboveground vaults; earth mounded concrete bunkers, mined cavities, augered holes

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, R.D.; Miller, W.O.; Warriner, J.B.; Malone, P.G.; McAneny, C.C.

    1984-04-01

    The study reported herein contains the results of Task 1 of a four-task study entitled Criteria for Evaluating Engineered Facilities. The overall objective of this study is to ensure that the criteria needed to evaluate five alternative low-level radioactive waste (LLW) disposal methods are available to the Nuclear Regulatory Commission (NRC) and the Agreement States. The alternative methods considered are belowground vaults, aboveground vaults, earth mounded concrete bunkers, mined cavities, and augered holes. Each of these alternatives is either being used by other countries for low-level radioactive waste (LLW) disposal or is being considered by other countries or US agencies. In this report the performance requirements are listed, each alternative is described, the experience gained with its use is discussed, and the performance capabilities of each method are addressed. Next, the existing 10 CFR Part 61 Subpart D criteria with respect to paragraphs 61.50 through 61.53, pertaining to site suitability, design, operations and closure, and monitoring are assessed for applicability to evaluation of each alternative. Preliminary conclusions and recommendations are offered on each method's suitability as an LLW disposal alternative, the applicability of the criteria, and the need for supplemental or modified criteria.

  20. Fast ℓ1-regularized space-time adaptive processing using alternating direction method of multipliers

    Science.gov (United States)

    Qin, Lilong; Wu, Manqing; Wang, Xuan; Dong, Zhen

    2017-04-01

    Motivated by the sparsity of filter coefficients in full-dimension space-time adaptive processing (STAP) algorithms, this paper proposes a fast ℓ1-regularized STAP algorithm based on the alternating direction method of multipliers to accelerate the convergence and reduce the calculations. The proposed algorithm uses a splitting variable to obtain an equivalent optimization formulation, which is addressed with an augmented Lagrangian method. Using the alternating recursive algorithm, the method can rapidly result in a low minimum mean-square error without a large number of calculations. Through theoretical analysis and experimental verification, we demonstrate that the proposed algorithm provides a better output signal-to-clutter-noise ratio performance than other algorithms.

  1. Parents' attitude toward multiple vaccinations at a single visit with alternative delivery methods.

    Science.gov (United States)

    Kaaijk, Patricia; Kleijne, Deborah E; Knol, Mirjam J; Harmsen, Irene A; Ophorst, Olga J A E; Rots, Nynke Y

    2014-01-01

    Last decades, the number of routine childhood vaccinations has increased considerably, which consequently has led to multiple vaccine injections per consultation. Implementation of additional vaccines will probably lead to more than 2 vaccine injections per consult, which might be a barrier for parents to vaccinate their child. A decrease in vaccination coverage, however, increases the risk of disease outbreaks. Less stressful alternative methods for vaccine delivery might lead to an increased acceptance of multiple childhood vaccinations by parents. The present questionnaire study was set up to explore the maximum number of vaccine injections per visit that is acceptable for parents, as well as to gauge parents' attitude toward alternative needle-free methods for vaccine delivery. For this purpose, the parents' opinion toward a jet injector, a patch, a microneedle system, and nasal spray device as methods for vaccine delivery was assessed. The majority of the 1154 participating parents indicated that 3 vaccine injections per visit was perceived as too much. Most participants had a positive attitude with respect to the jet injector and the patch as alternative vaccine delivery method, whereas the microneedle device and an intranasal spray device were not perceived as better than the conventional syringe by the parents. Parents indicated that both the jet injector and the patch might increase their acceptance of giving their children more than 2 vaccinations at the same time. This should encourage vaccine developers and manufacturers to put efforts in developing these delivery methods for their vaccines.

  2. A high throughput and sensitive method correlates neuronal disorder genotypes to Drosophila larvae crawling phenotypes.

    Science.gov (United States)

    Jakubowski, Brandon R; Longoria, Rafael A; Shubeita, George T

    2012-01-01

    Drosophila melanogaster is widely used as a model system for development and disease. Due to the homology between Drosophila and human genes, as well as the tractable genetics of the fly, its use as a model for neurologic disorders, in particular, has been rising. Locomotive impairment is a commonly used diagnostic for screening and characterization of these models, yet a fast, sensitive and model-free method to compare behavior is lacking. Here, we present a high throughput method to quantify the crawling behavior of larvae. We use the mean squared displacement as well as the direction autocorrelation of the crawling larvae as descriptors of their motion. By tracking larvae from wild-type strains and models of the Fragile X mental retardation as well as Alzheimer disease, we show these mutants exhibit impaired crawling. We further show that the magnitude of impairment correlates with the severity of the mutation, demonstrating the sensitivity and the dynamic range of the method. Finally, we study larvae with altered expression of the shaggy gene, a homolog of Glycogen Synthase Kinase-3 (GSK-3), which has been implicated in Alzheimer disease. Surprisingly, we find that both increased and decreased expression of dGSK-3 lead to similar larval crawling impairment. These findings have implications for the use of GSK-3 inhibitors recently proposed for Alzheimer treatment.

  3. Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

    Science.gov (United States)

    Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

    2015-11-01

    Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years.

  4. Testing alternative ground water models using cross-validation and other methods

    Science.gov (United States)

    Foglia, L.; Mehl, S.W.; Hill, M.C.; Perona, P.; Burlando, P.

    2007-01-01

    Many methods can be used to test alternative ground water models. Of concern in this work are methods able to (1) rank alternative models (also called model discrimination) and (2) identify observations important to parameter estimates and predictions (equivalent to the purpose served by some types of sensitivity analysis). Some of the measures investigated are computationally efficient; others are computationally demanding. The latter are generally needed to account for model nonlinearity. The efficient model discrimination methods investigated include the information criteria: the corrected Akaike information criterion, Bayesian information criterion, and generalized cross-validation. The efficient sensitivity analysis measures used are dimensionless scaled sensitivity (DSS), composite scaled sensitivity, and parameter correlation coefficient (PCC); the other statistics are DFBETAS, Cook's D, and observation-prediction statistic. Acronyms are explained in the introduction. Cross-validation (CV) is a computationally intensive nonlinear method that is used for both model discrimination and sensitivity analysis. The methods are tested using up to five alternative parsimoniously constructed models of the ground water system of the Maggia Valley in southern Switzerland. The alternative models differ in their representation of hydraulic conductivity. A new method for graphically representing CV and sensitivity analysis results for complex models is presented and used to evaluate the utility of the efficient statistics. The results indicate that for model selection, the information criteria produce similar results at much smaller computational cost than CV. For identifying important observations, the only obviously inferior linear measure is DSS; the poor performance was expected because DSS does not include the effects of parameter correlation and PCC reveals large parameter correlations. ?? 2007 National Ground Water Association.

  5. Alternative methods for the use of non-human primates in biomedical research.

    Science.gov (United States)

    Burm, Saskia M; Prins, Jan-Bas; Langermans, Jan; Bajramovic, Jeffrey J

    2014-01-01

    The experimental use of non-human primates (NHP) in Europe is tightly regulated and is only permitted when there are no alternatives available. As a result, NHP are most often used in late, pre-clinical phases of biomedical research. Although the impetus for scientists, politicians and the general public to replace, reduce and refine NHP in biomedical research is strong, the development of 3Rs technology for NHP poses specific challenges. In February 2014 a workshop on "Alternative methods for the use of NHP in biomedical research" was organized within the international exchange program of EUPRIM-Net II, a European infrastructure initiative that links biomedical primate research centers. The workshop included lectures by key scientists in the field of alternatives as well as by experts from governmental and non-governmental organizations. Furthermore, parallel sessions were organized to stimulate discussion on the challenges of advancing the use of alternative methods for NHP. Subgroups voted on four statements and together composed a list with opportunities and priorities. This report summarizes the presentations that were held, the content of the discussion sessions and concludes with recommendations on 3Rs development for NHP specifically. These include technical, conceptual as well as political topics.

  6. Evaluation of Alternatives to the Ontario Hydro Method as a Reference Method for CAMR

    Energy Technology Data Exchange (ETDEWEB)

    Dennis L. Laudal

    2007-03-31

    In June 2005, the U.S. Environmental Protection Agency (EPA) finalized the Clean Air Mercury Rule (CAMR). As part of the rule, all coal-fired power plants will be required to do continuous mercury measurements. To complete the required relative accuracy test assessment (RATA), the only reference methods allowed are the wet-chemistry methods: the Ontario Hydro (OH) mercury speciation method (ASTM International D6784-02) and EPA Method 29. Either method will be a challenge and expensive. It would be much more desirable to use an instrumental reference method (IRM) or use sorbent traps as a reference method so that the results can be obtained quickly and cheaply. This report presents the results from testing at Reliant Energy, Inc.'s, Portland Station. The project was designed to compare mercury concentrations measured using sorbent traps to those obtained using the OH method. The tests were done using a RATA scenario and at three different conditions. In addition, as part of the project, limited IRM testing was also completed. The results from the testing show that the sorbent traps compared very well with the OH method and, therefore, must be considered as a potential reference method. Although the IRM testing using manual injection of elemental and oxidized mercury for dynamic spiking showed some promise, it was clear that additional testing was needed. However, this method of dynamic spiking may not be acceptable to EPA, as it does not consider vapor pressure curves for elemental mercury a National Institute of Standards Technology traceable standard.

  7. Capsular serotyping of Pasteurella multocida from various animal hosts - a comparison of phenotypic and genotypic methods.

    Science.gov (United States)

    Arumugam, N D; Ajam, N; Blackall, P J; Asiah, N M; Ramlan, M; Maria, J; Yuslan, S; Thong, K L

    2011-04-01

    One hundred and fourteen strains of Pasteurella multocida were isolated from different domestic animals species (cattle, buffalo, sheep, goat, pig, rabbit, dog, cat), avian species (chicken, duck, turkey) and wild animals (deer, tiger, orang utan, marmoset). The serogroups of P. multocida were determined by both conventional capsular serotyping and a multiplex PCR assay targeting specific capsular genes. Based on the conventional serotyping method, the 114 strains of P. multocida were subtyped into 55 species-specific (untypeable strains) P. multocida, 15 serogroup A, 23 serogroup B and 21 serogroup D. Based on the multiplex PCR assay on the specific capsular genes associated with each serogroup, the 114 strains were further divided to 22 species-specific P. multocida (KMT1 - 460 bp), 53 serogroup A (A - 1,044 bp), 33 serogroup B (B - 760 bp) and 6 serogroup D (D - 657 bp). No serogroup E (511 bp) or F (851 bp) was detected among the Malaysian P. multocida. PCR-based typing was more discriminative and could further subtype the previously untypeable strains. Overall, there was a significant and positive correlation between both methods in serogrouping P. multocida (r = 0.7935; pmultocida were present among the livestock with 75% of the strains belonging to serogroups A or B. PCR serotyping was therefore a highly species-specific, sensitive and robust method for detection and differentiation of P. multocida serogroups compared to conventional serotyping. To the best of our knowledge, this is the first report from Malaysia of the application of a PCR to rapidly define the species-specific P. multocida and its serogroups as an important zoonotic pathogen in Malaysia.

  8. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering.

    Science.gov (United States)

    Wang, Harris H; Church, George M

    2011-01-01

    Engineering at the scale of whole genomes requires fundamentally new molecular biology tools. Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale. With these techniques, libraries of mutants can be generated, from which individuals with functionally useful phenotypes can be isolated. Furthermore, populations of cells can be evolved in situ by directed evolution using complex pools of oligonucleotides. Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation.

  9. ezRAD: a simplified method for genomic genotyping in non-model organisms

    Directory of Open Access Journals (Sweden)

    Robert J. Toonen

    2013-11-01

    Full Text Available Here, we introduce ezRAD, a novel strategy for restriction site–associated DNA (RAD that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.

  10. ezRAD: a simplified method for genomic genotyping in non-model organisms.

    Science.gov (United States)

    Toonen, Robert J; Puritz, Jonathan B; Forsman, Zac H; Whitney, Jonathan L; Fernandez-Silva, Iria; Andrews, Kimberly R; Bird, Christopher E

    2013-01-01

    Here, we introduce ezRAD, a novel strategy for restriction site-associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes) that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.

  11. Performance of two alternative methods for Listeria detection throughout Serro Minas cheese ripening.

    Science.gov (United States)

    Mata, Gardênia Márcia Silva Campos; Martins, Evandro; Machado, Solimar Gonçalves; Pinto, Maximiliano Soares; de Carvalho, Antônio Fernandes; Vanetti, Maria Cristina Dantas

    2016-01-01

    The ability of pathogens to survive cheese ripening is a food-security concern. Therefore, this study aimed to evaluate the performance of two alternative methods of analysis of Listeria during the ripening of artisanal Minas cheese. These methods were tested and compared with the conventional method: Lateral Flow System™, in cheeses produced on laboratory scale using raw milk collected from different farms and inoculated with Listeria innocua; and VIDAS(®)-LMO, in cheese samples collected from different manufacturers in Serro, Minas Gerais, Brazil. These samples were also characterized in terms of lactic acid bacteria, coliforms and physical-chemical analysis. In the inoculated samples, L. innocua was detected by Lateral Flow System™ method with 33% false-negative and 68% accuracy results. L. innocua was only detected in the inoculated samples by the conventional method at 60-days of cheese ripening. L. monocytogenes was not detected by the conventional and the VIDAS(®)-LMO methods in cheese samples collected from different manufacturers, which impairs evaluating the performance of this alternative method. We concluded that the conventional method provided a better recovery of L. innocua throughout cheese ripening, being able to detect L. innocua at 60-day, aging period which is required by the current legislation.

  12. Performance of two alternative methods for Listeria detection throughout Serro Minas cheese ripening

    Directory of Open Access Journals (Sweden)

    Gardênia Márcia Silva Campos Mata

    Full Text Available ABSTRACT The ability of pathogens to survive cheese ripening is a food-security concern. Therefore, this study aimed to evaluate the performance of two alternative methods of analysis of Listeria during the ripening of artisanal Minas cheese. These methods were tested and compared with the conventional method: Lateral Flow System™, in cheeses produced on laboratory scale using raw milk collected from different farms and inoculated with Listeria innocua; and VIDAS®-LMO, in cheese samples collected from different manufacturers in Serro, Minas Gerais, Brazil. These samples were also characterized in terms of lactic acid bacteria, coliforms and physical-chemical analysis. In the inoculated samples, L. innocua was detected by Lateral Flow System™ method with 33% false-negative and 68% accuracy results. L. innocua was only detected in the inoculated samples by the conventional method at 60-days of cheese ripening. L. monocytogenes was not detected by the conventional and the VIDAS®-LMO methods in cheese samples collected from different manufacturers, which impairs evaluating the performance of this alternative method. We concluded that the conventional method provided a better recovery of L. innocua throughout cheese ripening, being able to detect L. innocua at 60-day, aging period which is required by the current legislation.

  13. Optimized genotyping method for identification of bacterial contaminants in pharmaceutical industry.

    Science.gov (United States)

    Stamatoski, Borche; Ilievska, Miroslava; Babunovska, Hristina; Sekulovski, Nikola; Panov, Sasho

    2016-06-01

    Microbiological control is of crucial importance in the pharmaceutical industry regarding the possible bacterial contamination of the environment, water, raw materials and finished products. Molecular identification of bacterial contaminants based on DNA sequencing of the hypervariable 16SrRNA gene has been introduced recently. The aim of this study is to investigate the suitability of gene sequencing using our selection of PCR primers and conditions for rapid and accurate bacterial identification in pharmaceutical industry quality control. DNA was extracted from overnight incubated colonies from 10 bacterial ATCC strains, which are common contaminants in the pharmaceutical industry. A region of bacterial 16SrRNA gene was analyzed by bidirectional DNA sequencing. Bacterial identification based on partial sequencing of the 16SrRNA gene is the appropriate method that could be used in the pharmaceutical industry after adequate validations. We have successfully identified all tested bacteria with more than 99 % similarity to the already published sequences.

  14. Input-constrained model predictive control via the alternating direction method of multipliers

    DEFF Research Database (Denmark)

    Sokoler, Leo Emil; Frison, Gianluca; Andersen, Martin S.

    2014-01-01

    This paper presents an algorithm, based on the alternating direction method of multipliers, for the convex optimal control problem arising in input-constrained model predictive control. We develop an efficient implementation of the algorithm for the extended linear quadratic control problem (LQCP......) with input and input-rate limits. The algorithm alternates between solving an extended LQCP and a highly structured quadratic program. These quadratic programs are solved using a Riccati iteration procedure, and a structure-exploiting interior-point method, respectively. The computational cost per iteration...... is quadratic in the dimensions of the controlled system, and linear in the length of the prediction horizon. Simulations show that the approach proposed in this paper is more than an order of magnitude faster than several state-of-the-art quadratic programming algorithms, and that the difference in computation...

  15. Alternative (non-animal) methods for cosmetics testing: current status and future prospects-2010

    DEFF Research Database (Denmark)

    Adler, Sarah; Basketter, David; Creton, Stuart

    2011-01-01

    The 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodies (industry, non-governmental organisations, EU Member States, and the Commission's Scientific Committee...... methods would not be available in time. The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing. In summary, the experts confirmed that it will take...... on Consumer Safety) to identify scientific experts in five toxicological areas, i.e. toxicokinetics, repeated dose toxicity, carcinogenicity, skin sensitisation, and reproductive toxicity for which the Directive foresees that the 2013 deadline could be further extended in case alternative and validated...

  16. Design of Optimal Sparse Feedback Gains via the Alternating Direction Method of Multipliers

    CERN Document Server

    Lin, Fu; Jovanović, Mihailo R

    2011-01-01

    We design sparse and block sparse feedback gains that minimize the $H_2$ norm of distributed systems. Our approach consists of two steps. First, we identify sparsity patterns of the feedback gains by incorporating sparsity-promoting penalty functions into the $H_2$ problem, where the added terms penalize the number of communication links in the distributed controller. Second, we optimize the state feedback gains subject to the structural constraints determined by the identified sparsity patterns. This polishing step improves the $H_2$ performance of the distributed controllers. In the first step, we identify sparsity structure of the feedback gains using the alternating direction method of multipliers, which is a powerful algorithm well-suited to large optimization problems. This method alternates between optimizing the sparsity and optimizing the closed-loop $H_2$ norm, which allows us to exploit the structure of the corresponding objective functions. In particular, we take advantage of the separability of t...

  17. Investigation in vivo of Enterococcus faecalis in endodontic retreatment by phenotypic and genotypic methods

    Directory of Open Access Journals (Sweden)

    Marcos Sergio Endo

    2015-06-01

    Full Text Available This study aimed to investigate the prevalence of E. faecalis in root-filled canals using culture and molecular approaches. It was evaluated the antimicrobial susceptibility to different antibiotics and the virulence factors of E. faecalis isolates. Microbial samples were taken from thirty root-filled canals. Culture methods and 16S rDNA assay were used to identify E. faecalis. The antimicrobial susceptibility of E. faecalis was determined by MIC values using the E test. Cultivable strains of E. faecalis were investigated for virulence factors by PCR technique. E. faecalis were detected by culture (7/30, traditional PCR assay (13/30 and nested PCR (23/30. Both PCR were significantly more effective than culture in detecting  E. faecalis (p < 0.05. All tested E. faecalis were highly sensitive to amoxicillin. Some strains of E. faecalis were resistant to antibiotics such as rifampicin (4/12, erythromycin (3/12 and azythromycin (8/12. The genes efaA and ace were detected in all isolates. The other virulence genes were found in 91.6 (gelE, 83.3 (asa, 25 (esp and 16.6% (cylA. Strains of E. faecalis isolated from root-filled canals showed virulence factors related to adherence. They also showed resistance to some antibiotics commonly used in dentistry.

  18. Measurement of the resistivity of porous materials with an alternating air-flow method.

    Science.gov (United States)

    Dragonetti, Raffaele; Ianniello, Carmine; Romano, Rosario A

    2011-02-01

    Air-flow resistivity is a main parameter governing the acoustic behavior of porous materials for sound absorption. The international standard ISO 9053 specifies two different methods to measure the air-flow resistivity, namely a steady-state air-flow method and an alternating air-flow method. The latter is realized by the measurement of the sound pressure at 2 Hz in a small rigid volume closed partially by the test sample. This cavity is excited with a known volume-velocity sound source implemented often with a motor-driven piston oscillating with prescribed area and displacement magnitude. Measurements at 2 Hz require special instrumentation and care. The authors suggest an alternating air-flow method based on the ratio of sound pressures measured at frequencies higher than 2 Hz inside two cavities coupled through a conventional loudspeaker. The basic method showed that the imaginary part of the sound pressure ratio is useful for the evaluation of the air-flow resistance. Criteria are discussed about the choice of a frequency range suitable to perform simplified calculations with respect to the basic method. These criteria depend on the sample thickness, its nonacoustic parameters, and the measurement apparatus as well. The proposed measurement method was tested successfully with various types of acoustic materials.

  19. Facile fabrication of controllable zinc oxide nanorod clusters on polyacrylonitrile nanofibers via repeatedly alternating immersion method

    Science.gov (United States)

    Zhou, Ying; Li, Xia; Yu, Hou-Yong; Hu, Guo-Liang; Yao, Ju-Ming

    2016-12-01

    Polyacrylonitrile/zinc oxide (PAN/ZnO) composite nanofiber membranes with different ZnO morphologies were fabricated by repeatedly alternating hot-cold immersion and single alternating hot-cold immersion methods. The influence of the PAN/ZnCl2 ratio and different immersion methods on the morphology, microstructure, and properties of the nanofiber membranes was investigated by using field-emission scanning electron microscopy (FE-SEM), Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD) analysis, thermogravimetric analysis (TGA), and ultraviolet-visible (UV-Vis) spectroscopy. A possible mechanism for different morphologies of PAN/ZnO nanofiber membranes with different PAN/ZnCl2 ratio through different immersion processes was presented, and well-dispersed ZnO nanorod clusters with smallest average dimeter of 115 nm and hexagonal wurtzite structure were successfully anchored onto the PAN nanofiber surface for R-7/1 nanofiber membrane. Compared to S-5/1 prepared by single alternating hot-cold immersion method, the PAN/ZnO nanofiber membrane fabricated by repeatedly alternating hot-cold immersion method (especially for R-7/1) showed improved thermal stability and high photocatalytic activity for methylene blue (MB). Compared to S-5/1, decomposition temperature at 5% weight loss ( T 5%) was increased by 43 °C from 282 to 325 °C for R-7/1; meanwhile, R-7/1 showed higher photocatalytic degradation ratio of approximately 100% (after UV light irradiation for 8 h) than 65% for S-5/1 even after irradiation for 14 h. Moreover, the degradation efficiency of R-7/1 with good reuse stability remained above 94% after 3 cycles.

  20. An alternative method to estimate WiP inventory for cultivated assets

    OpenAIRE

    野村, 浩二

    2006-01-01

    The objectives of this paper are to describe the problems with the current estimates for WiP inventories of cultivated assets in Japan's system of national accounts and to propose an alternative method of dealing with these assets. There is a huge di erence between inventory stock measurement that are compiled according to the 1968 SNA versus the 1993 SNA for Japan's national accounts. This leads to non-negligible di erences for productivity measures when inventories are treated as a capital ...

  1. The viability of alternative assessment methods in the Greek upper secondary school: the oral portfolio

    OpenAIRE

    Angeliki Daphni

    2012-01-01

    Τhe final examination of the English language subject, in the context of the Greek state upper secondary education, is a traditional paper-and-pencil test which does not include any assessment of oracy skills. This article explores the viability of the oral portfolio as an alternative assessment and pedagogic method that can facilitate the assessment of speaking and listening skills and create a more motivating learning environment. To this effect, three methodological tools were designed, na...

  2. A molecular method for typing Herpes simplex virus isolates as an alternative to immunofluorescence methods

    Directory of Open Access Journals (Sweden)

    Abraham A

    2009-01-01

    Full Text Available Background: Typing of Herpes simplex virus (HSV isolates is required to identify the virus isolated in culture. The methods available for this include antigen detection by immunofluorescence (IF assays and polymerase chain reaction (PCR. This study was undertaken to standardize a molecular method for typing of HSV and compare it with a commercial IF reagent for typing. Objectives: To compare a molecular method for typing HSV isolates with a monoclonal antibody (MAb based IF test. Study design : This cross-sectional study utilized four reference strains and 42 HSV isolates obtained from patients between September 1998 and September 2004. These were subjected to testing using an MAb-based IF test and a PCR that detects the polymerase ( pol gene of HSV isolates. Results: The observed agreement of the MAb IF assay with the pol PCR was 95.7%. Fifty four point eight percent (23/42 of isolates tested by IF typing were found to be HSV-1, 40.5% (17/42 were HSV-2, and two (4.8% were untypable using the MAb IF assay. The two untypable isolates were found to be HSV-2 using the pol PCR. In addition, the cost per PCR test for typing is estimated to be around Rs 1,300 (USD 30, whereas the cost per MAb IF test is about Rs 1,500 (USD 35 including all overheads (reagents, instruments, personnel time, and consumables. Conclusion: The pol PCR is a cheaper and more easily reproducible method for typing HSV isolates as compared to the IF test. It could replace the IF-based method for routine typing of HSV isolates as availability of PCR machines (thermal cyclers is now more widespread than fluorescence microscopes in a country like India.

  3. Genetic diversification of methicillin-resistant Staphylococcus aureus as a function of prolonged geographic dissemination and as measured by binary typing and other genotyping methods.

    Science.gov (United States)

    van Leeuwen, W; van Belkum, A; Kreiswirth, B; Verbrugh, H

    1998-01-01

    The aim of the present study was to determine the extent of genome evolution among methicillin-resistant Staghylococcus aureus (MRSA) strains. Three different collections of strains were analysed, comprising locally, nationally and internationally disseminated genotypes. Various genotyping assays displaying different levels of resolution were used. Geographically and temporally diverse MRSA strains comprised the international group. MRSA strains recovered during an outbreak in a New York City hospital and Portuguese MRSA isolates, all resembling the so-called Iberian clone, were included in the local and national collections, respectively. Genotypes were determined by genome scanning typing techniques and procedures which analyse specific DNA elements only. The outbreak strains showed subclonal variation, whereas the Portuguese isolates displayed an increased number of genotypes. Among the epidemiologically unrelated MRSA strains, the different genotyping techniques revealed a wide heterogeneity of types. Different typing techniques appeared to show different levels of resolution, which could be correlated with the extent of geographic spread; the more pronounced the spread, the higher the degree of genome evolution. Binary typing and randomly amplified polymorphic DNA analysis are the typing methods of choice for determining (non)identity among strains that have a recent common ancestor and have undergone yet limited dissemination.

  4. Development and evaluation of an off-the-slide genotyping technique for identifying Giardia cysts and Cryptosporidium oocysts directly from US EPA Method 1623 slides

    Science.gov (United States)

    ABSTRACT Aims This study developed and systematically evaluated performance and limit of detection of an off-the-slide genotyping procedure for both Cryptosporidium oocysts and Giardia cysts. Methods and Results Slide standards containing flow sorted (oo)cysts were used to e...

  5. The Dialectic Method: A Critical and Postmodern Alternative to the Scientific Method

    OpenAIRE

    Phillip Dybicz; Loretta Pyles

    2011-01-01

    This paper introduces Hans-Georg Gadamer's dialectic method and elaborates upon its application to social work inquiry. Its strengths lie in its ability to uncover social constructed truths, to explain human behavior in a non-deterministic manner that emphasizes personal agency and empowerment, and to foster a consciousness-raising process that leads to praxis. This makes it ideally suited for knowledge gathering by practitioners in the field who seek to apply postmodern practice approaches...

  6. ALTERNATING PROJECTION BASED PREDICTION-CORRECTION METHODS FOR STRUCTURED VARIATIONAL INEQUALITIES

    Institute of Scientific and Technical Information of China (English)

    Bing-sheng He; Li-zhi Liao; Mai-jian Qian

    2006-01-01

    The monotone variational inequalities Ⅵ(Ω, F) have vast applications, including optimal controls and convex programming. In this paper we focus on the Ⅵ problems that have a particular splitting structure and in which the mapping F does not have an explicit form, therefore only its function values can be employed in the numerical methods for solving such problems. We study a set of numerical methods that are easily implementable.Each iteration of the proposed methods consists of two procedures. The first (prediction) procedure utilizes alternating projections to produce a predictor. The second (correction) procedure generates the new iterate via some minor computations. Convergence of the proposed methods is proved under mild conditions. Preliminary numerical experiments for some traffic equilibrium problems illustrate the effectiveness of the proposed methods.

  7. Alternating Direction Finite Volume Element Methods for Three-Dimensional Parabolic Equations

    Institute of Scientific and Technical Information of China (English)

    Tongke

    2010-01-01

    This paper presents alternating direction finite volume element methods for three-dimensional parabolic partial differential equations and gives four computational schemes, one is analogous to Douglas finite difference scheme with second-order splitting error, the other two schemes have third-order splitting error, and the last one is an extended LOD scheme. The L2 norm and H1 semi-norm error estimates are obtained for the first scheme and second one, respectively. Finally, two numerical examples are provided to illustrate the efficiency and accuracy of the methods.

  8. An alternative method for the measurement of the mechanical impulse of a vertically directed blast

    Science.gov (United States)

    Turner, Geoffrey R.

    2008-07-01

    An alternative method for the measurement of the total mechanical impulse of a vertically directed blast due to an explosive charge is presented. The method differs from apparatus that employ a vertically displaced mass (similar in principle to the ballistic pendulum) in that a relatively compact spring-damper system is employed to constrain the movement of the mass. The mechanical impulse is determined by integrating, with respect to time, the net force applied to the spring-damper system. The details of an explosive impulse measuring instrument rated to 12kNs are presented.

  9. Method of estimation of selected hens welfare elements in an alternative maintenance system

    Directory of Open Access Journals (Sweden)

    Zbigniew Domagalski

    2012-09-01

    Full Text Available Broody hens welfare in an alternative maintenance system was the focus of the undertaken attempt. Both behavioural and health aspects, as well as numerous physiological indicators are taken into consideration while applying animal welfare estimation methods. The described evaluation complies with the EU recommendations for the applied spot method TG-200. It serves to evaluate the conformity of both buildings and technology of breeding with the requirements of regulations and those defined in the process of the carried out hens research. The following functional areas were focused on while assessing the welfare: terms of mobility, feed intake, herding behaviour, resting conditions, comfort of living, nesting conditions, herd health and care.

  10. A Modified T-test Feature Selection Method and Its Application on the HapMap Genotype Data

    Institute of Scientific and Technical Information of China (English)

    Nina Zhou; Lipo Wang

    2007-01-01

    Single nucleotide polymorphisms (SNPs) are genetic variations that determine the differences between any two unrelated individuals. Various population groups can be distinguished from each other using SNPs. For instance, the HapMap dataset has four population groups with about ten million SNPs. For more insights on human evolution, ethnic variation, and population assignment, we propose to find out which SNPs are significant in determining the population groups and then to classify different populations using these relevant SNPs as input features. In this study, we developed a modified t-test ranking measure and applied it to the HapMap genotype data. Firstly, we rank all SNPs in comparison with other feature importance measures including F-statistics and the informativeness for assignment. Secondly, we select different numbers of the most highly ranked SNPs as the input to a classifier, such as the support vector machine, so as to find the best feature subset corresponding to the best classification accuracy. Experimental results showed that the proposed method is very effective in finding SNPs that are significant in determining the population groups, with reduced computational burden and better classification accuracy.

  11. Detection of Fetomaternal Genotype Associations in Early-Onset Disorders: Evaluation of Different Methods and Their Application to Childhood Leukemia

    Directory of Open Access Journals (Sweden)

    Jasmine Healy

    2010-01-01

    Full Text Available Several designs and analytical approaches have been proposed to dissect offspring from maternal genetic contributions to early-onset diseases. However, lack of parental controls halts the direct verification of the assumption of mating symmetry (MS required to assess maternally-mediated effects. In this study, we used simulations to investigate the performance of existing methods under mating asymmetry (MA when parents of controls are missing. Our results show that the log-linear, likelihood-based framework using a case-triad/case-control hybrid design provides valid tests for maternal genetic effects even under MA. Using this approach, we examined fetomaternal associations between 29 SNPs in 12 cell-cycle genes and childhood pre-B acute lymphoblastic leukemia (ALL. We identified putative fetomaternal effects at loci CDKN2A rs36228834 (P=.017 and CDKN2B rs36229158 (P=.022 that modulate the risk of childhood ALL. These data further corroborate the importance of the mother's genotype on the susceptibility to early-onset diseases.

  12. Short communication: appropriate and alternative methods to determine viable bacterial counts in cow milk samples.

    Science.gov (United States)

    Loss, G; Apprich, S; Kneifel, W; von Mutius, E; Genuneit, J; Braun-Fahrländer, C

    2012-06-01

    Farm milk consumption is reported to be inversely related to the development of asthma and atopy in children and it has been hypothesized that microorganisms in milk might contribute to this protective effect. The GABRIEL study was designed to investigate this hypothesis in a large population of European children, calling for a rapid alternative to classical culture techniques to determine bacteriological properties of milk samples. One objective was to evaluate 2 different rapid methods to determine bacteriological properties in a large number of cow milk samples collected under field conditions. BactoScan (Foss Analytical, Hillerød, Denmark), an automated standard flow cytometric method utilized for routine testing of milk quality, and TEMPO (bioMérieux, Marcy l'Etoile, France), an automated most-probable-number method, were used to assess the total viable bacterial count in farm and commercial milk samples. Both methods were compared with standard plate count method and each other. Measurements based on the TEMPO method were in good agreement with the standard plate count method and showed reliable results, whereas BactoScan results did not correlate with standard plate count measurements and yielded higher bacteria counts in heat-treated milk samples compared with raw milk samples. Most likely, these discrepant results were due to inferences with staining reactions and detection of bacteria in heat-treated milk samples. We conclude that, in contrast to the routinely used BactoScan method, the TEMPO method is an inexpensive and rapid alternative to standard culture methods suitable to assess total bacterial counts in processed and raw milk samples.

  13. Application of Microarray-Based Method for Functional SNP Genotyping in the Risk of Gastric Carcinoma in Chinese Population

    Institute of Scientific and Technical Information of China (English)

    Song Li; Meiju Ji; Peng Hou; Nongyue He; Hong Chen

    2006-01-01

    High-throughput SNP detection microarrays were used here to explore the relationship between 5,10-methylenetetrahydrofolate reductase (MTHFR) gene polymorphism C677T and the risk of gastric carcinoma among population in Jiangsu region, by genotyping the specimens from 170 patients with gastric carcinoma and 140 age- and sexmatched control subjects. PCR products were spotted onto a 3-aminopropyltriethoxysilane coated glass slide to fabricate a microarray, then interrogated by hybridization with dual-color probes (Cy3, Cy5) to determine the SNP genotype of each sample, and the relation between the genotypes and the risk of gastric carcinoma was analyzed. The frequencies of C677T genotype were CC(47.9%), CT(40%), CT(12.1%) in control group and CC(35.9%), CT(45.9%), TT(18.2%) in gastric carcinoma group, respectively. The individuals with 677CT+TT genotype group or 677TT had a 1.67-fold (95% CI: 1.06-2.64)or 2.67-fold (95% CI: 1.382-5.341) increased risk to develop gastric carcinoma compared with those having 677CC genotype.It was shown that the single nucleotide polymorphisms in the MTHFR gene are associated with the risk of gastric carcinoma in the Chinese population.

  14. Comparison of genotypic and phenotypic characterization methods for Pasteurella multocida isolates from fatal cases of bovine respiratory disease.

    Science.gov (United States)

    Taylor, Jared D; Fulton, Robert W; Dabo, S Mady; Lehenbauer, Terry W; Confer, Anthony W

    2010-05-01

    Bovine respiratory disease (BRD) is the most costly disease of beef cattle in North America. Because Pasteurella multocida is a commensal of the upper respiratory tract, it is generally considered an opportunistic pathogen. However, studies in swine indicated that there may be a limited number of strains associated with disease, suggesting that some are more virulent than others. Although this may also be true of isolates from cattle, appropriate typing methods must be established before this possibility can be investigated. The purpose of this study was to compare effectiveness of polymerase chain reaction (PCR) fingerprinting to more traditional approaches for typing bovine P. multocida isolates. Isolates were obtained from 41 cases of fatal BRD and subjected to random amplified polymorphic DNA PCR (RAPD-PCR), whole cell protein (WCP) profiles, outer membrane protein (OMP) profiles, and serotyping. The discrimination index was calculated for each typing method and combinations of each using Simpson's index of diversity. Correlation coefficients were calculated to assess concordance between classification results achieved through genotypic (RAPD-PCR) and phenotypic (WCP, OMP, and serotyping) approaches. All characterization methods were capable of discriminating between isolates. However, there was poor concordance between techniques. There were also few significant associations between typing results and epidemiologic data. Random amplified polymorphic DNA PCR was validated as being a repeatable and reliable means of discriminating between P. multocida isolates obtained from cattle. Isolates obtained from fatal cases of BRD in calves in a commercial feedlot demonstrated significant diversity, justifying additional investigation into whether P. multocida is a strictly opportunistic pathogen in cattle.

  15. Typing of Campylobacter jejuni Isolated from Turkey by Genotypic Methods, Antimicrobial Susceptibility, and Virulence Gene Patterns: A Retrospective Study.

    Science.gov (United States)

    Manfreda, Gerardo; Parisi, Antonio; De Cesare, Alessandra; Mion, Domenico; Piva, Silvia; Zanoni, Renato G

    2016-02-01

    In this retrospective study, typing ability, discriminatory power, and concordance between typing results obtained on 123 Campylobacter jejuni turkey isolates, collected in 1998, within 14 different farms, applying multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), antibiotic resistance profile, and virulence gene pattern, were assessed and compared. Overall, 33 sequence types, 28 pulsotypes, 10 resistotypes, and 5 pathotypes were identified. MLST and PFGE showed the better discriminatory ability (i.e., Simpson's diversity index >0.90) as well as unidirectional (i.e., Wallace and adjusted Wallace coefficients >0.86) and bidirectional (i.e., adjusted Rand coefficient >0.60) concordance. Moreover, both methods showed a good unidirectional and bidirectional concordance with the resistotype. On the contrary, the congruence of both genotyping methods and resistotype with the pathotype seemed due to chance alone. A clonal relationship was identified among 66.7% of the isolates. Furthermore, 59.7% of the investigated isolates were resistant to two or more antimicrobials and 92% to tetracycline. All the isolates harbored cadF and pldA genes, whereas a flaA gene product and a cdtB gene product were amplified from 85.4% and 79.7% of the isolates, respectively, using the primers designed by Bang et al. (2003). The results of this study clarify the level of genetic diversity among the C. jejuni originating from turkeys. MLST level of correlation with PFGE, resistotype, and pathotype is assessed. This result supports the selection of type and number of typing methods to use in epidemiological studies. Finally, the identification of clonal complexes (i.e., groups of profiles differing by no more than one gene from at least one other profile of the group using the entire Campylobacter MLST database) shared between turkey and human isolates suggests that turkeys could be a possible source of Campylobacter infection.

  16. A framework program for the teaching of alternative methods (replacement, reduction, refinement) to animal experimentation.

    Science.gov (United States)

    Daneshian, Mardas; Akbarsha, Mohammad A; Blaauboer, Bas; Caloni, Francesca; Cosson, Pierre; Curren, Rodger; Goldberg, Alan; Gruber, Franz; Ohl, Frauke; Pfaller, Walter; van der Valk, Jan; Vinardell, Pilar; Zurlo, Joanne; Hartung, Thomas; Leist, Marcel

    2011-01-01

    Development of improved communication and education strategies is important to make alternatives to the use of animals, and the broad range of applications of the 3Rs concept better known and understood by different audiences. For this purpose, the Center for Alternatives to Animal Testing in Europe (CAAT-Europe) together with the Transatlantic Think Tank for Toxicology (t(4)) hosted a three-day workshop on "Teaching Alternative Methods to Animal Experimentation". A compilation of the recommendations by a group of international specialists in the field is summarized in this report. Initially, the workshop participants identified the different audience groups to be addressed and also the communication media that may be used. The main outcome of the workshop was a framework for a comprehensive educational program. The modular structure of the teaching program presented here allows adaptation to different audiences with their specific needs; different time schedules can be easily accommodated on this basis. The topics cover the 3Rs principle, basic research, toxicological applications, method development and validation, regulatory aspects, case studies and ethical aspects of 3Rs approaches. This expert consortium agreed to generating teaching materials covering all modules and providing them in an open access online repository.

  17. Analytical methods for the determination of DEHP plasticizer alternatives present in medical devices: a review.

    Science.gov (United States)

    Bernard, L; Décaudin, B; Lecoeur, M; Richard, D; Bourdeaux, D; Cueff, R; Sautou, V

    2014-11-01

    Until 2010, diethylhexylphthalate (DEHP) was the plasticizer most commonly used to soften PVC medical devices (MDs), because of a good efficiency/cost ratio. In flexible plasticized PVC, phthalates are not chemically bound to PVC and they are released into the environment and thus may come into contact with patients. The European Directive 2007/47/CE, classified DEHP as a product with a toxicity risk and restricted its use in MDs. MD manufacturers were therefore forced to quickly find alternatives to DEHP to maintain the elasticity of PVC nutrition tubings, infusion sets and hemodialysis lines. Several replacement plasticizers, so-called "alternative to DEHP plasticizers" were incorporated into the MDs. Nowadays, the risk of exposure to these compounds for hospitalized patients, particularly in situations classified "at risk", has not yet been evaluated, because migrations studies, providing sufficient exposure and human toxicity data have not been performed. To assess the risk to patients of DEHP plasticizer alternatives, reliable analytical methods must be first developed in order to generate data that supports clinical studies being conducted in this area. After a brief introduction of the characteristics and toxicity of the selected plasticizers used currently in MDs, this review outlines recently analytical methods available to determine and quantify these plasticizers in several matrices, allowing the evaluation of potential risk and so risk management.

  18. TREATMENT BY ALTERNATIVE METHODS OF REGRESSION GAS CHROMATOGRAPHIC RETENTION INDICES OF 35 PYRAZINES

    Directory of Open Access Journals (Sweden)

    Fatiha Mebarki

    2016-02-01

    Full Text Available The study treated two closer alternative methods of which the principal characteristic: a non-parametric method (the least absolute deviation (LAD and a traditional method of diagnosis OLS.This was applied to model, separately, the indices of retention of the same whole of 35 pyrazines (27 pyrazines with 8 other pyrazines in the same unit eluted to the columns OV-101 and Carbowax-20M, by using theoretical molecular descriptors calculated using the software DRAGON. The detection of influential observations for non-parametric method (LAD is a problem which has been extensively studied and offers alternative dicapproaches whose main feature is the robustness.here is presented and compared with the standard least squares regression .The comparison between methods LAD and OLS is based on the equation of the hyperplane, in order to confirm the robustness thus to detect by the meaningless statements and the points of lever and validated results in the state approached by the tests statistics: Test of Anderson-Darling, shapiro-wilk, Agostino, Jarque-Bera, graphic test (histogram of frequency and the confidence interval thanks to the concept of robustness to check if the distribution of the errors is really approximate.

  19. Geobacter strains that use alternate organic compounds, methods of making, and methods of use thereof

    Science.gov (United States)

    Lovley, Derek R; Summers, Zarath Morgan; Haveman, Shelley Annette; Izallalen, Mounir

    2013-12-03

    In preferred embodiments, the present invention provides new isolated strains of Geobacter species that are capable of using a carbon source that is selected from C.sub.3 to C.sub.12 organic compounds selected from pyruvate or metabolic precursors of pyruvate as an electron donor in metabolism and in subsequent energy production. In other aspects, other preferred embodiments of the present invention include methods of making such strains and methods of using such strains. In general, the wild type strain of the microorganisms has been shown to be unable to use these C.sub.3 to C.sub.12 organic compounds as electron donors in metabolic steps such as the reduction of metallic ions. The inventive strains of microorganisms are useful improving bioremediation applications, including in situ bioremediation (including uranium bioremediation and halogenated solvent bioremediation), microbial fuel cells, power generation from small and large-scale waste facilities (e.g., biomass waste from dairy, agriculture, food processing, brewery, or vintner industries, etc.) using microbial fuel cells, and other applications of microbial fuel cells, including, but not limited to, improved electrical power supplies for environmental sensors, electronic sensors, and electric vehicles.

  20. Alternative normalization methods demonstrate widespread cortical hypometabolism in untreated de novo Parkinson's disease

    DEFF Research Database (Denmark)

    Berti, Valentina; Polito, C; Borghammer, Per

    2012-01-01

    , recent studies suggested that conventional data normalization procedures may not always be valid, and demonstrated that alternative normalization strategies better allow detection of low magnitude changes. We hypothesized that these alternative normalization procedures would disclose more widespread...... metabolic alterations in de novo PD. METHODS: [18F]FDG PET scans of 26 untreated de novo PD patients (Hoehn & Yahr stage I-II) and 21 age-matched controls were compared using voxel-based analysis. Normalization was performed using gray matter (GM), white matter (WM) reference regions and Yakushev...... normalization. RESULTS: Compared to GM normalization, WM and Yakushev normalization procedures disclosed much larger cortical regions of relative hypometabolism in the PD group with extensive involvement of frontal and parieto-temporal-occipital cortices, and several subcortical structures. Furthermore...

  1. An alternative method of gas boriding applied to the formation of borocarburized layer

    Energy Technology Data Exchange (ETDEWEB)

    Kulka, M., E-mail: michal.kulka@put.poznan.pl; Makuch, N.; Pertek, A.; Piasecki, A.

    2012-10-15

    The borocarburized layers were produced by tandem diffusion processes: carburizing followed by boriding. An alternative method of gas boriding was proposed. Two-stage gas boronizing in N{sub 2}-H{sub 2}-BCl{sub 3} atmosphere was applied to the formation of iron borides on a carburized substrate. This process consisted in two stages, which were alternately repeated: saturation by boron and diffusion annealing. The microstructure and microhardness of produced layer were compared to those-obtained in case of continuous gas boriding in H{sub 2}-BCl{sub 3} atmosphere, earlier used. The first objective of two-stage boronizing, consisting in acceleration of boron diffusion, has been efficiently implemented. Despite the lower temperature and shorter duration of boronizing, about 1.5 times larger iron borides' zone has been formed on carburized steel. Second objective, the absolute elimination of brittle FeB phase, has failed. However, the amount of FeB phase has been considerably limited. Longer diffusion annealing should provide the boride layer with single-phase microstructure, without FeB phase. - Highlights: Black-Right-Pointing-Pointer Alternative method of gas boriding in H{sub 2}-N{sub 2}-BCl{sub 3} atmosphere was proposed. Black-Right-Pointing-Pointer The process consisted in two stages: saturation by boron and diffusion annealing. Black-Right-Pointing-Pointer These stages of short duration were alternately repeated. Black-Right-Pointing-Pointer The acceleration of boron diffusion was efficiently implemented. Black-Right-Pointing-Pointer The amount of FeB phase in the boride zone was limited.

  2. 29 CFR 2520.104-48 - Alternative method of compliance for model simplified employee pensions-IRS Form 5305-SEP.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Alternative method of compliance for model simplified employee pensions-IRS Form 5305-SEP. 2520.104-48 Section 2520.104-48 Labor Regulations Relating to Labor... Provisions Applicable to Both Reporting and Disclosure Requirements § 2520.104-48 Alternative method...

  3. Report and recommendations of the international workshop "Retrieval approaches for information on alternative methods to animal experiments".

    Science.gov (United States)

    Grune, Barbara; Fallon, Michael; Howard, Carol; Hudson, Vera; Kulpa-Eddy, Jodie A; Larson, Jean; Leary, Sue; Roi, Annett; van der Valk, Jan; Wood, Mary; Dörendahl, Antje; Köhler-Hahn, Dorothea; Box, Rainer; Spielmann, Horst

    2004-01-01

    In the member states of the EU and in the USA, scientists are obliged by animal welfare legislation not to conduct an animal experiment if another scientifically satisfactory method is reasonably and practicably available. To meet the regulatory obligation to use alternatives to animal experiments, scientists should consult literature and other relevant sources on alternatives prior to any experimental study on laboratory animals. It is the responsibility of the individual scientist to select the most appropriate database to obtain information on alternatives, which have been defined as methods that refine, reduce or replace animal experiments (the 3 Rs concept of Russell and Burch (1959)). Specialised information services provide support to scientists searching for publications on alternative methods. On occasion of a workshop in Berlin in November 2003, representatives of animal welfare information centres discussed currently available information sources on alternative methods, index terms for alternative methods, and search strategies based on index terms for alternative methods. ZEBET presented an investigation on the current status of indexing systems on alternative methods in established literature databases. The project analysed how the results of a search for publications on alternatives was influenced by the indexing procedure. The results of the study were exemplified by a typical search result. The results of the study indicated that the current indexing systems do not provide the required information, since not all of the relevant information is indexed under "alternative methods". The workshop participants developed recommendations for ad hoc working groups and research projects, e.g. development of suitable search strategies on alternative methods for scientists.

  4. An alternative method based on enzymatic fat hydrolysis to quantify volatile compounds in wheat bread crumb.

    Science.gov (United States)

    Pico, Joana; Nozal, María Jesús; Gómez, Manuel; Bernal, José Luis

    2016-09-01

    An alternative method to quantify 40 volatile compounds in wheat bread crumb is proposed. It consists of a Soxhlet extraction with a mixture of dichloromethane and diethyl ether containing lipases and a subsequent concentration with Vigreux column. It is the first time that lipases are added to transform the fat into free fatty acids and glycerol, which elute at the end of the chromatogram after the analytes, avoiding problems in the chromatography due to fat residues, such as dirtiness in the injector, column clogging or overlapping peaks. The extract is most easily analysed by GC/MS, using a standard addition method to correct matrix effect. The method was fully validated, with extraction efficiencies between 70% and 100% and precision RSD lower than 15%. The method was applied to a commercial crumb, with acetoin, phenylethyl alcohol and acetic acid as highly abundant compounds, which are considered main volatiles in crumb.

  5. L0-based sparse approximation: two alternative methods and some applications

    Science.gov (United States)

    Portilla, Javier; Mancera, Luis

    2007-09-01

    We propose two methods for sparse approximation of images under l II error metric. First one performs an approximation error minimization given a l p-norm of the representation through alternated orthogonal projections onto two sets. We study the cases p = 0 (sub-optimal) and p = 1 (optimal), and find that the l 0-AP method is neatly superior, for typical images and overcomplete oriented pyramids. Given that l I-AP is optimal, this shows that it is not equivalent in practical image processing conditions to minimize one or the other norm, contrarily to what is often assumed. The second method is more powerful, and it performs gradient descent onto decreasingly smoothed versions of the sparse approximation cost function, yielding a method previously proposed as a heuristic. We adapt these techniques for being applied to image restoration, with very positive results.

  6. Timing of Peripheral Blood Stem Cell Yield: Comparison of Alternative Methods with the Classic Method for CD34+ Cell Determination

    Directory of Open Access Journals (Sweden)

    I. Fatorova

    2014-01-01

    Full Text Available Hematopoietic stem cells (HSCs, still represent a certain mystery in biology, have a unique property of dividing into equal cells and repopulating the hematopoietic tissue. This potential enables their use in transplantation treatments. The quality of the HSC grafts for transplantation is evaluated by flow cytometric determination of the CD34+ cells, which enables optimal timing of the first apheresis and the acquisition of maximal yield of the peripheral blood stem cells (PBSCs. To identify a more efficient method for evaluating CD34+ cells, we compared the following alternative methods with the reference method: hematopoietic progenitor cells (HPC enumeration (using the Sysmex XE-2100 analyser, detection of CD133+ cells, and quantification of aldehyde dehydrogenase activity in the PBSCs. 266 aphereses (84 patients were evaluated. In the preapheretic blood, the new methods produced data that were in agreement with the reference method. The ROC curves have shown that for the first-day apheresis target, the optimal predictive cut-off value was 0.032 cells/mL for the HPC method (sensitivity 73.4%, specificity 69.3%. HPC method exhibited a definite practical superiority as compared to other methods tested. HPC enumeration could serve as a supplementary method for the optimal timing of the first apheresis; it is simple, rapid, and cheap.

  7. Alternative (non-animal) methods for cosmetics testing: current status and future prospects-2010.

    Science.gov (United States)

    Adler, Sarah; Basketter, David; Creton, Stuart; Pelkonen, Olavi; van Benthem, Jan; Zuang, Valérie; Andersen, Klaus Ejner; Angers-Loustau, Alexandre; Aptula, Aynur; Bal-Price, Anna; Benfenati, Emilio; Bernauer, Ulrike; Bessems, Jos; Bois, Frederic Y; Boobis, Alan; Brandon, Esther; Bremer, Susanne; Broschard, Thomas; Casati, Silvia; Coecke, Sandra; Corvi, Raffaella; Cronin, Mark; Daston, George; Dekant, Wolfgang; Felter, Susan; Grignard, Elise; Gundert-Remy, Ursula; Heinonen, Tuula; Kimber, Ian; Kleinjans, Jos; Komulainen, Hannu; Kreiling, Reinhard; Kreysa, Joachim; Leite, Sofia Batista; Loizou, George; Maxwell, Gavin; Mazzatorta, Paolo; Munn, Sharon; Pfuhler, Stefan; Phrakonkham, Pascal; Piersma, Aldert; Poth, Albrecht; Prieto, Pilar; Repetto, Guillermo; Rogiers, Vera; Schoeters, Greet; Schwarz, Michael; Serafimova, Rositsa; Tähti, Hanna; Testai, Emanuela; van Delft, Joost; van Loveren, Henk; Vinken, Mathieu; Worth, Andrew; Zaldivar, José-Manuel

    2011-05-01

    The 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodies (industry, non-governmental organisations, EU Member States, and the Commission's Scientific Committee on Consumer Safety) to identify scientific experts in five toxicological areas, i.e. toxicokinetics, repeated dose toxicity, carcinogenicity, skin sensitisation, and reproductive toxicity for which the Directive foresees that the 2013 deadline could be further extended in case alternative and validated methods would not be available in time. The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing. In summary, the experts confirmed that it will take at least another 7-9 years for the replacement of the current in vivo animal tests used for the safety assessment of cosmetic ingredients for skin sensitisation. However, the experts were also of the opinion that alternative methods may be able to give hazard information, i.e. to differentiate between sensitisers and non-sensitisers, ahead of 2017. This would, however, not provide the complete picture of what is a safe exposure because the relative potency of a sensitiser would not be known. For toxicokinetics, the timeframe was 5-7 years to develop the models still lacking to predict lung absorption and renal/biliary excretion, and even longer to integrate the methods to fully replace the animal toxicokinetic models. For the systemic toxicological endpoints of repeated dose toxicity, carcinogenicity and reproductive toxicity, the time horizon for full replacement could not be estimated.

  8. Comparative evaluation of different DNA extraction methods for HPV genotyping by linear array and INNO-LiPA.

    Science.gov (United States)

    Donà, Maria Gabriella; Benevolo, Maria; Pimpinelli, Fulvia; Battista, Mara; Rollo, Francesca; Stivali, Francesca; Moscarelli, Antonella; Giuliani, Massimo; Di Carlo, Aldo; Vocaturo, Amina

    2011-06-01

    In order to investigate the influence of DNA extraction on two PCR-based HPV genotyping tests (Linear Array, Roche and INNO-LiPA Extra, Innogenetics), three different procedures were used to purify DNA from 28 cervico-vaginal samples tested previously by the Hybrid Capture 2: the AmpliLute Liquid Media Extraction kit (Roche), the QIAamp DNA Blood mini kit (QIAGEN), and the NucliSENS EasyMAG automated platform (bioMérieux). All HC2-positive samples were found positive by both assays, independently of the extract used. Type-specific concordance (i.e., identical HPV type-specific profile in all the extracts of the same sample) was observed in 55% and 75% of the cases testing samples by the Linear Array and the INNO-LiPA, respectively. Using the DNA extracted with the two manual methods the results were concordant in 75% of the cases both for the Linear Array and the INNO-LiPA. When comparing the Linear Array results obtained on either of the two manual extracts with those obtained following automated extraction, 65% of the samples showed type-specific concordance in both cases. The INNO-LiPA results were concordant in 80% of the cases comparing the AmpliLute versus the automated extract, while concordant results were observed in 90% of the cases when comparing the QIAGEN versus the automated extract. In conclusion, the Linear Array and INNO-LiPA results are affected by the method of DNA extraction. Consequently, different HPV type-specific profiles may be observed using different extracts of the same sample. The use of consistent protocols for DNA purification is a priority to guarantee intra-assay reproducibility over time.

  9. Spectral fitting of NMR spectra using an alternating optimization method with a priori knowledge.

    Science.gov (United States)

    Bi, Z; Bruner, A P; Li, J; Scott, K N; Liu, Z S; Stopka, C B; Kim, H W; Wilson, D C

    1999-09-01

    As alternatives to the fast Fourier transform, advanced parametric methods based on the damped sinusoidal data model have been devised to better quantify the nuclear magnetic resonance (NMR) spectroscopy time-domain data. Previously, linear prediction (LP) fitting methods using Householder triangularization and singular value decomposition (SVD) techniques have been applied to the NMR spectroscopy data analysis. In this paper, we propose an alternating optimization method to quantify the time-domain NMR spectroscopy data. The proposed algorithm uses the a priori knowledge of the possible frequency intervals of the damped sinusoids to obtain more accurate parameter estimates when the NMR spectroscopy data are obtained under low signal-to-noise ratio conditions and the peaks are close together. None of the LP and SVD type of methods can use such approximate a priori knowledge. We have shown with measured NMR spectroscopy data that the proposed algorithm can be used to obtain accurate parameter estimates of frequencies, amplitudes, and damping ratios of the damped sinusoids and therefore the ultimate fit of the spectrum by using the a priori knowledge about the possible frequency intervals of the damped sinusoids. Copyright 1999 Academic Press.

  10. Development of a cost-efficient novel method for rapid, concurrent genotyping of five common single nucleotide polymorphisms of the brain derived neurotrophic factor (BDNF) gene by tetra-primer amplification refractory mutation system.

    Science.gov (United States)

    Wang, Cathy K; Xu, Michael S; Ross, Colin J; Lo, Ryan; Procyshyn, Ric M; Vila-Rodriguez, Fidel; White, Randall F; Honer, William G; Barr, Alasdair M

    2015-09-01

    Brain derived neurotrophic factor (BDNF) is a molecular trophic factor that plays a key role in neuronal survival and plasticity. Single nucleotide polymorphisms (SNPs) of the BDNF gene have been associated with specific phenotypic traits in a large number of neuropsychiatric disorders and the response to psychotherapeutic medications in patient populations. Nevertheless, due to study differences and occasionally contrasting findings, substantial further research is required to understand in better detail the association between specific BDNF SNPs and these psychiatric disorders. While considerable progress has been made recently in developing advanced genotyping platforms of SNPs, many high-throughput probe- or array-based detection methods currently available are limited by high costs, slow processing times or access to advanced instrumentation. The polymerase chain reaction (PCR)-based, tetra-primer amplification refractory mutation system (T-ARMS) method is a potential alternative technique for detecting SNP genotypes efficiently, quickly, easily, and cheaply. As a tool in psychopathology research, T-ARMS was shown to be capable of detecting five common SNPs in the BDNF gene (rs6265, rs988748, rs11030104, 11757G/C and rs7103411), which are all SNPs with previously demonstrated clinical relevance to schizophrenia and depression. The present technique therefore represents a suitable protocol for many research laboratories to study the genetic correlates of BDNF in psychiatric disorders. Copyright Copyright © 2015 John Wiley & Sons, Ltd.

  11. Short communication: Establishment of a new polymerase chain reaction-sequence-based typing method for genotyping cattle major histocompatibility complex class II DRB3.

    Science.gov (United States)

    Takeshima, S-N; Matsumoto, Y; Aida, Y

    2009-06-01

    Sequence-based typing (SBT) is the most comprehensive method for characterizing major histocompatibility complex (MHC) gene polymorphisms. We report here a new PCR-SBT method for genotyping cattle MHC (BoLA) class II DRB3 using the Assign 400ATF ver. 1.0.2.41 software (Conexio Genomics, Fremantle, Australia), which detects alleles in a semiautomated manner. We examined 12 sets of PCR reactions for their ability to amplify BoLA-DRB3 exon 2 and selected an optimal primer set, which used ERB3N-HL031 for first-round PCR and ALL-DRB3B for second-round PCR. Next, we constructed a BoLA-DRB3 allele database using the reference sequences of the Assign 400ATF software and successfully assigned heterozygous samples (including those with deletion alleles) using bidirectional sequencing, unlike our previously described method, which used unidirectional sequencing for detecting of deletion alleles. Next, blood samples of 128 Holstein cattle were used to correlate the results of our modified PCR-SBT method with those of our previously described PCR-SBT method. Each new PCR-SBT result corresponded completely with the DRB3 allele that was genotyped by our previously described PCR-SBT method. Moreover, we confirmed the accuracy of our modified PCR-SBT method by genotyping 7 sire cattle and their 22 calves using Japanese Black cattle. This new method will contribute to high-throughput genotyping of BoLA-DRB3 by sequence-based typing.

  12. A simple DNA recombination screening method by RT-PCR as an alternative to Southern blot.

    Science.gov (United States)

    Albers, Eliene; Sbroggiò, Mauro; Martin-Gonzalez, Javier; Avram, Alexandra; Munk, Stephanie; Lopez-Contreras, Andres J

    2017-01-19

    The generation of genetically engineered mouse models (GEMMs), including knock-out (KO) and knock-in (KI) models, often requires genomic screening of many mouse ES cell (mESC) clones by Southern blot. The use of large targeting constructs facilitates the recombination of exogenous DNA in a specific genomic locus, but limits the detection of its correct genomic integration by standard PCR methods. Genomic Long Range PCR (LR-PCR), using primers adjacent to the homology arms, has been used as an alternative to radioactive-based Southern blot screenings. However, LR-PCRs are often difficult and render many false positive and false negative results. Here, we propose an alternative screening method based on the detection of a genetic modification at the mRNA level, which we successfully optimized in two mouse models. This screening method consists of a reverse-transcription PCR (RT-PCR) using primers that match exons flanking the targeting construct. The detection of the expected modification in this PCR product confirms the integration at the correct genomic location and shows that the mutant mRNA is expressed. This is a simple and sensitive strategy to screen locus-specific recombination of targeting constructs which can also be useful to screen KO and KI mutant mice or cell lines including those generated by CRISPR/Cas9.

  13. Limitations in small artisanal gold mining addressed by educational components paired with alternative mining methods.

    Science.gov (United States)

    Zolnikov, Tara R

    2012-03-01

    Current solutions continue to be inadequate in addressing the longstanding, worldwide problem of mercury emissions from small artisanal gold mining. Mercury, an inexpensive and easily accessible heavy metal, is used in the process of extracting gold from ore. Mercury emissions disperse, affecting human populations by causing adverse health effects and environmental and social ramifications. Many developing nations have sizable gold ore deposits, making small artisanal gold mining a major source of employment in the world. Poverty drives vulnerable, rural populations into gold mining because of social and economic instabilities. Educational programs responding to this environmental hazard have been implemented in the past, but have had low positive results due to lack of governmental support and little economic incentive. Educational and enforced intervention programs must be developed in conjunction with governmental agencies in order to successfully eliminate this ongoing problem. Industry leaders offered hopeful suggestions, but revealed limitations when trying to develop encompassing solutions to halt mercury emissions. This research highlights potential options that have been attempted in the past and suggests alternative solutions to improve upon these methods. Some methods include buyer impact recognition, risk assessment proposals exposing a cost-benefit analysis and toxicokinetic modeling, public health awareness campaigns, and the education of miners, healthcare workers, and locals within hazardous areas of mercury exposure. These methods, paired with the implementation of alternative mining techniques, propose a substantial reduction of mercury emissions.

  14. Comprehensive Review of Foam Application during Foam Assisted Water Alternating Gas (FAWAG Method

    Directory of Open Access Journals (Sweden)

    A. Shabib-asl

    2014-11-01

    Full Text Available In the last few decades, much focus has been placed on enhancing oil recovery from existing fields. This is accomplished by the study and application of various methods. As for recent cases, the Study of fluid mobility control and sweep efficiency in gas injection process as well as Water Alternating Gas (WAG method have demonstrated positive results on oil recovery and thus gained wide interest in petroleum industry. WAG injection application results in an increased oil recovery. Its mechanism consists in reduction of Gas Oil Ratio (GOR. However, there are some problems associated with this which includes poor volumetric sweep efficiency due to its low density and high mobility when compared with oil. This has led to the introduction of Foam Assisted Water Alternating Gas (FAWAG technique, which in contrast with WAG injection, acts in improving the sweep efficiency and reducing the gas oil ration therefore maximizing the production rate from the producer wells. This study presents a comprehensive review of FAWAG process from perspective of Snorre field experience. In addition some comparative results between FAWAG and the other EOR methods are presented including their setbacks. The main aim is to provide a solid background for future laboratory research and successful field application-extend.

  15. Alternative methods for ray tracing in uniaxial media. Application to negative refraction

    Science.gov (United States)

    Bellver-Cebreros, Consuelo; Rodriguez-Danta, Marcelo

    2007-03-01

    In previous papers [C. Bellver-Cebreros, M. Rodriguez-Danta, Eikonal equation, alternative expression of Fresnel's equation and Mohr's construction in optical anisotropic media, Opt. Commun. 189 (2001) 193; C. Bellver-Cebreros, M. Rodriguez-Danta, Internal conical refraction in biaxial media and graphical plane constructions deduced from Mohr's method, Opt. Commun. 212 (2002) 199; C. Bellver-Cebreros, M. Rodriguez-Danta, Refraccion conica externa en medios biaxicos a partir de la construccion de Mohr, Opt. Pura AppliE 36 (2003) 33], the authors have developed a method based on the local properties of dielectric permittivity tensor and on Mohr's plane graphical construction in order to study the behaviour of locally plane light waves in anisotropic media. In this paper, this alternative methodology is compared with the traditional one, by emphasizing the simplicity of the former when studying ray propagation through uniaxial media (comparison is possible since, in this case, traditional construction becomes also plane). An original and simple graphical method is proposed in order to determine the direction of propagation given by the wave vector from the knowledge of the extraordinary ray direction (given by Poynting vector). Some properties of light rays in these media not described in the literature are obtained. Finally, two applications are considered: a description of optical birefringence under normal incidence and the study of negative refraction in uniaxial media.

  16. Linearized Alternating Direction Method with Adaptive Penalty for Low-Rank Representation

    CERN Document Server

    Lin, Zhouchen; Su, Zhixun

    2011-01-01

    Low-rank representation (LRR) is an effective method for subspace clustering and has found wide applications in computer vision and machine learning. The existing LRR solver is based on the alternating direction method (ADM). It suffers from $O(n^3)$ computation complexity due to the matrix-matrix multiplications and matrix inversions, even if partial SVD is used. Moreover, introducing auxiliary variables also slows down the convergence. Such a heavy computation load prevents LRR from large scale applications. In this paper, we generalize ADM by linearizing the quadratic penalty term and allowing the penalty to change adaptively. We also propose a novel rule to update the penalty such that the convergence is fast. With our linearized ADM with adaptive penalty (LADMAP) method, it is unnecessary to introduce auxiliary variables and invert matrices. The matrix-matrix multiplications are further alleviated by using the skinny SVD representation technique. As a result, we arrive at an algorithm for LRR with comple...

  17. Use of nicarbazin, salinomycin and zinc oxide as alternative molting methods for commercial laying hens

    Directory of Open Access Journals (Sweden)

    C H de F Domingues

    2014-06-01

    Full Text Available An experiment was carried out to evaluate the performance, egg quality and morphometry of the reproductive tract, liver, pancreas and tongue of laying hens submitted to different molting methods. Two hundred and eighty eight 72-week-old Isa brown layers were distributed according to a completely randomized design with six treatments (molting methods and six replicates of eight birds each. Layers were fed diets containing 3000 ppm zinc oxide, 60 ppm or 120 ppm nicarbazin, 30 ppm or 60 ppm salinomycin, or were submitted to feed fasting. Data were submitted to analysis of variance and means were compared by the test of Tukey at 5% probability level. Molting methods alternative to feed fasting were effective to induce molting in layer and provided good performance results in the second laying cycle.

  18. Potential Use of Lime as Nitric Acid Source for Alternative Electrolyte Fuel-Cell Method

    Science.gov (United States)

    Christianto, V.; Smarandache, Florentin

    2011-04-01

    Despite growing popularity for the use of biofuel and other similar methods to generate renewable energy sources from natural plantation in recent years, there is also growing concern over its disadvantage, i.e. that the energy use of edible plants may cause unwanted effects, because the plantation price tends to increase following the oil price. Therefore an alternative solution to this problem is to find `natural plantation' which have no direct link to `food chain' (for basic foods, such as palm oil etc.).

  19. Acoustic rhinometry (AR): An Alternative Method to Image Nasal Airway Geometry

    DEFF Research Database (Denmark)

    Straszek, Sune; Pedersen, O.F.

      ACOUSTIC RHINOMETRY (AR): AN ALTERNATIVE METHOD TO IMAGE NASAL AIRWAY GEOMETRY.  INTRODUCTION AND BACKGROUND:  In human studies the acoustic reflection technique was first applied to describe the area-distance relationship of the lower airways, but later the acoustic reflection technique appeared...... studies in laboratory animals more reliable. To accomplish this we hope to receive new input from adjacent fields of research.  [OFP1] Det er ikke nogen piezoelektrisk mikrofon. Det er en ganske billig kondensator mikrofon. [OFP2] Jeg tror du kan nøjes med små figurer1) Indfaldende og reflekteret kurve...

  20. A general method for nested RT-PCR amplification and sequencing the complete HCV genotype 1 open reading frame

    Directory of Open Access Journals (Sweden)

    Tavis John E

    2005-12-01

    Full Text Available Abstract Background Hepatitis C virus (HCV is a pathogenic hepatic flavivirus with a single stranded RNA genome. It has a high genetic variability and is classified into six major genotypes. Genotype 1a and 1b cause the majority of infections in the USA. Viral genomic sequence information is needed to correlate viral variation with pathology or response to therapy. However, reverse transcription-polymerase chain reaction (RT-PCR of the HCV genome must overcome low template concentration and high target sequence diversity. Amplification conditions must hence have both high sensitivity and specificity yet recognize a heterogeneous target population to permit general amplification with minimal bias. This places divergent demands of the amplification conditions that can be very difficult to reconcile. Results RT and nested PCR conditions were optimized independently and systematically for amplifying the complete open reading frame (ORF from HCV genotype 1a and 1b using several overlapping amplicons. For each amplicon, multiple pairs of nested PCR primers were optimized. Using these primers, the success rate (defined as the rate of production of sufficient DNA for sequencing with any one of the primer pairs for a given amplicon for amplification of 72 genotype 1a and 1b patient plasma samples averaged over 95% for all amplicons. In addition, two sets of sequencing primers were optimized for each genotype 1a and 1b. Viral consensus sequences were determined by directly sequencing the amplicons. HCV ORFs from 72 patients have been sequenced using these primers. Sequencing errors were negligible because sequencing depth was over 4-fold and both strands were sequenced. Primer bias was controlled and monitored through careful primer design and control experiments. Conclusion Optimized RT-PCR and sequencing conditions are useful for rapid and reliable amplification and sequencing of HCV genotype 1a and 1b ORFs.

  1. Genotyping of coeliac-specific human leucocyte antigen in children with type 1 diabetes: does this screening method make sense?

    Science.gov (United States)

    Binder, Elisabeth; Loinger, Martina; Mühlbacher, Annelies; Edlinger, Michael; Steichen, Elisabeth; Meraner, Dagmar; Loacker, Lorin; Weigel, Guenter; Müller, Thomas; Fröhlich-Reiterer, Elke; Hofer, Sabine E

    2017-07-01

    Due to a high linkage disequilibrium of diabetes and coeliac-specific human leucocyte antigen (HLA) genotypes, the prevalence of coeliac disease (CD) in children and adolescents with diabetes mellitus type 1 (T1D) is much higher than in the general population. Recently, the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) revised new screening guidelines in which genotyping for coeliac-specific HLA alleles is recommended for high-risk patients as patients with T1D. The aim of our study was to investigate the frequency and distribution of coeliac-specific HLA genotypes in paediatric patients with T1D. HLA genotyping was performed on paediatric patients with T1D, recruited at the Medical University Hospital of Innsbruck and Graz. The test was done by PCR. Statistical analysis was performed with IBM-SPSS V.20. In 121 paediatric patients with T1D (52% male), mean age 13.3 (SD 3.9) years, mean age at diabetes diagnosis 7.4 (SD 3.8) and mean diabetes duration of 5.9 (SD 3.3) years, HLA genotyping was conducted. Ninety-two per cent showed positive HLA DQ2 and/or HLA DQ8 genotypes. Thirty-four per cent carried HLA DQ2, 33% were HLA DQ2+DQ8 positive and 25% of the patients showed positive results for HLA DQ8 alone. Only 8% had no coeliac-specific HLA markers. Four (3%) patients were diagnosed with CD. The majority of paediatric patients with T1D has positive coeliac-specific HLA genotypes DQ2 and/or DQ8. Therefore, genotyping for coeliac-specific HLA alleles as a first-line test in patients with T1D as recommended in the ESPGHAN guidelines does not seem reasonable. Screening for coeliac-specific antibodies needs to be performed on a regular basis for patients with T1D. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  2. Giardia duodenalis in Damascus, Syria: Identification of Giardia genotypes in a sample of human fecal isolates using polymerase chain reaction and restriction fragment length polymorphism analyzing method.

    Science.gov (United States)

    Skhal, Dania; Aboualchamat, Ghalia; Al Nahhas, Samar

    2016-02-01

    Giardia duodenalis is a common gastrointestinal parasite that infects humans and many other mammals. It is most prevalent in many developing and industrialized countries. G. duodenalis is considered to be a complex species. While no morphological distinction among different assemblages exist, it can be genetically differentiated into eight major assemblages: A to H. The aim of this study was to determine the genetic heterogeneity of G. duodenalis in human isolates (a study conducted for the first time in Syria). 40 fecal samples were collected from three different hospitals during the hot summer season of 2014. Extraction of genomic DNA from all Giardia positive samples (based on a microscopic examination) was performed using QIAamp DNA Stool Mini Kit. β-giardin gene was used to differentiate between different Giardia assemblages. The 514 bp fragment was amplified using the Polymerase Chain Reaction method, followed by digestion in HaeIII restriction enzyme. Our result showed that genotype A was more frequent than genotype B, 27/40 (67.5%); 4/40 (10%) respectively. A mixed genotype of A+B was only detected in 9 isolates (22.5%). This is the first molecular study performed on G. duodenalis isolates in Syria in order to discriminate among the different genotypes. Further expanded studies using more genes are needed to detect and identify the Giardia parasite at the level of assemblage and sub-assemblage.

  3. Novel, Non-Radioactive, Simple and Multiplex PCR-cRFLP Methods for Genotyping Human SP-A and SP-D Marker Alleles

    Directory of Open Access Journals (Sweden)

    Susan DiAngelo

    1999-01-01

    Full Text Available We have previously identified an allele of the human SP-A2 gene that occurs with greater frequency in an RDS population [12]. Because of the importance of SP-A in normal lung function and its newly emerging role in innate host defense and regu-lation of inflammatory processes, we wish to better characterize genotypes of both SP-A1 and SP-A2 genes. It has been determined that SP-D shares similar roles in immune response. Therefore, in this report we 1 describe a novel, non radioactive PCR based-cRFLP method for genotyping both SP-A and SP-D; 2 describe two previously unpublished biallelic polymorphisms within the SP-D gene; 3 present the partial sequence of one new SP-A1 allele (6A14 and describe other new SP-A1 and SP-A2 alleles; and 4 describe additional methodologies for SP-A genotype assessment. The ability to more accurately and efficiently genotype samples from individuals with various pulmonary diseases will facilitate population and family based association studies. Genetic poly-morphisms may be identified that partially explain individual disease susceptibility and/or treatment effectiveness.

  4. Single-Case Research Methods: History and Suitability for a Psychological Science in Need of Alternatives.

    Science.gov (United States)

    Hurtado-Parrado, Camilo; López-López, Wilson

    2015-09-01

    This paper presents a historical and conceptual analysis of a group of research strategies known as the Single-Case Methods (SCMs). First, we present an overview of the SCMs, their history, and their major proponents. We will argue that the philosophical roots of SCMs can be found in the ideas of authors who recognized the importance of understanding both the generality and individuality of psychological functioning. Second, we will discuss the influence that the natural sciences' attitude toward measurement and experimentation has had on SCMs. Although this influence can be traced back to the early days of experimental psychology, during which incipient forms of SCMs appeared, SCMs reached full development during the subsequent advent of Behavior Analysis (BA). Third, we will show that despite the success of SCMs in BA and other (mainly applied) disciplines, these designs are currently not prominent in psychology. More importantly, they have been neglected as a possible alternative to one of the mainstream approaches in psychology, the Null Hypothesis Significance Testing (NHST), despite serious controversies about the limitations of this prevailing method. Our thesis throughout this section will be that SCMs should be considered as an alternative to NHST because many of the recommendations for improving the use of significance testing (Wilkinson & the TFSI, 1999) are main characteristics of SCMs. The paper finishes with a discussion of a number of the possible reasons why SCMs have been neglected.

  5. An alternative method to determine maximal accumulated O2 deficit in runners.

    Science.gov (United States)

    Hill, D W; Ferguson, C S; Ehler, K L

    1998-12-01

    An accepted measure of anaerobic capacity is the maximal O2 deficit. But it is not feasible to use O2 deficit if > or =10 submaximal runs are needed to extrapolate the O2 demand of high velocity running (Medbø et al. 1988). Recently, an alternative method to determine O2 deficit was proposed (Hill 1996) using only results of supramaximal cycle ergometer tests. The purpose of this study was to evaluate this alternative method with data from treadmill tests. Twenty-six runners ran at 95%, 100%, 105%, and 110% of their velocity at VO2max. Times to exhaustion, velocity, and accumulated oxygen uptake (VO2) from each individual's four tests were fit to the following equation using iterative nonlinear regression: accumulated VO2 = (O2 demand x velocity x time)-O2 deficit. The mean value s derived for O2 demand and O2 deficit were 0.198+/-0.031 ml x kg(-1) x m(-1) and 42+/-22 ml x kg(-1). SEE for the parameters were 0.007+/-0.007 ml x kg(-1) x m(-1) and 8+/-10 ml x kg(-1), respectively. Mean R2 was 0.998+/-0.003. It was concluded that O2 deficit can be determined from all-out treadmill tests without the need to perform submaximal tests.

  6. Computer Simulation Modeling: A Method for Predicting the Utilities of Alternative Computer-Aided Treat Evaluation Algorithms

    Science.gov (United States)

    1990-09-01

    0 Technical Report 911 D~i. FiLE COPY Computer Simulation Modeling : A Method for Predicting the Utilities of Alternative Computer-Aided Threat...63007A 793 1202 HI 11. TITLE (Include Security Classification) Computer Simulation Modeling : A Method for Predicting the Utilities of Alternative...SECURITY CLASSIFICATION OF THIS PAGE("wn Data Entered) ii Technical Report 911 Computer Simulation Modeling : A Method for Predicting the Utilities of

  7. Biomechanical comparison of sinus floor elevation and alternative treatment methods for dental implant placement.

    Science.gov (United States)

    Küçükkurt, Sercan; Alpaslan, Gökhan; Kurt, Ahmet

    2017-02-01

    In this study, we compared the success of sinus lifting and alternative treatment methods in applying dental implants in cases lacking adequate bone due to pneumatization of the maxillary sinus. In a computer environment, 3D models were created using computerized tomography data from a patient. Additionally, implants and abutments were scanned at the macroscopic level, and the resulting images were transferred to the 3D models. Five different models were examined: a control model, lateral sinus lifting (LSL), short dental implant placement (SIP), tilted implant placement (TIP) and distal prosthetic cantilever (DC) use. Vertical and oblique forces were applied in each model. The compression, tension and von Mises stresses in each model were analyzed by implementing a finite element analysis method. In our study, the LSL method was observed to be the closest to the control model. The TIP model showed high stress values under conditions of oblique forces but showed successful results under conditions of vertical forces, and the opposite results were observed in the SIP model. The DC model provided the least successful results among all models. Based on the results of this study, the LSL method should be the first choice among treatment options. Considering its successful results under conditions of oblique forces, the SIP method may be preferable to the TIP method. In contrast, every effort should be made to avoid the use of DCs.

  8. Low Rank Alternating Direction Method of Multipliers Reconstruction for MR Fingerprinting

    CERN Document Server

    Assländer, Jakob; Knoll, Florian; Sodickson, Daniel K; Hennig, Jürgen; Lattanzi, Riccardo

    2016-01-01

    Purpose The proposed reconstruction framework addresses the reconstruction accuracy, noise propagation and computation time for Magnetic Resonance Fingerprinting (MRF). Methods Based on a singular value decomposition (SVD) of the signal evolution, MRF is formulated as a low rank inverse problem in which one image is reconstructed for each singular value under consideration. This low rank approximation of the signal evolution reduces the computational burden by reducing the number of Fourier transformations. Also, the low rank approximation improves the conditioning of the problem, which is further improved by extending the low rank inverse problem to an augmented Lagrangian that is solved by the alternating direction method of multipliers (ADMM). The root mean square error and the noise propagation are analyzed in simulations. For verification, an in vivo example is provided. Results The proposed low rank ADMM approach shows a reduced root mean square error compared to the original fingerprinting reconstructi...

  9. Foveation: an alternative method to simultaneously preserve privacy and information in face images

    Science.gov (United States)

    Alonso, Víctor E.; Enríquez-Caldera, Rogerio; Sucar, Luis Enrique

    2017-03-01

    This paper presents a real-time foveation technique proposed as an alternative method for image obfuscation while simultaneously preserving privacy in face deidentification. Relevance of the proposed technique is discussed through a comparative study of the most common distortions methods in face images and an assessment on performance and effectiveness of privacy protection. All the different techniques presented here are evaluated when they go through a face recognition software. Evaluating the data utility preservation was carried out under gender and facial expression classification. Results on quantifying the tradeoff between privacy protection and image information preservation at different obfuscation levels are presented. Comparative results using the facial expression subset of the FERET database show that the technique achieves a good tradeoff between privacy and awareness with 30% of recognition rate and a classification accuracy as high as 88% obtained from the common figures of merit using the privacy-awareness map.

  10. An alternative method of constructing axisymmetric toroidal equilibria with nonparallel flow

    Science.gov (United States)

    Kuiroukidis, Ap; Throumoulopoulos, G. N.

    2016-11-01

    An alternative method based on an inverse aspect ratio (ɛ) expansion which reduces the axisymmetric equilibrium problem to a set of ODEs containing terms of arbitrary order in ɛ is employed to solve a generalized Grad-Shafranov equation with incompressible sheared flow nonparallel to the magnetic field. The method is applied to construct equilibria with either circular magnetic surfaces and reversed magnetic shear or D-shaped magnetic surfaces and normal magnetic shear. From the former equilibrium, it turns out that the electric field results in an increase of the reversed magnetic shear, thus indicating potential synergetic effects of the sheared flow and the magnetic shear in the formation of an internal transport barrier in consistent with experimental evidence.

  11. Medical savings accounts - in search of an alternative method of health care financing in European countries

    Directory of Open Access Journals (Sweden)

    Marta Borda

    2011-09-01

    Full Text Available In times of increasing health care expenditure and insufficient cover provided by publicly financed health systems additional, alternative methods of health care financing become more and more considerable. The purpose of the paper is to present the concept of Medical Savings Accounts (MSAs and possibilities of their application in the health care systems of European countries. First, the author describes the idea of MSAs and reviews positive and negative findings about the effects of implementing this method into the health systems. Next, two main approaches to the application of MSAs in health care financing are considered. In the last part of the paper, the possibilities of introducing MSAs into health care systems in European countries are discussed. The author takes into consideration the existing health care financing conditions and other specific institutional, socio-economic and cultural factors as the main determinants for successful designing and implementation of the MSA scheme in a given country.

  12. USAGE OF PICTOGRAMS TO INTRODUCE MUSICAL INSTRUMENTS TO EDUCABLE MENTALLY RETARDED CHILDREN AS AN ALTERNATIVE METHOD

    Directory of Open Access Journals (Sweden)

    Gunsu YILMA

    2014-01-01

    Full Text Available The purpose of this research is to examine and investigate the perception ability of musical instruments of educable mentally retarded children with the support of visual elements. The research is conducted for every children individually in a special education and rehabilitation centre. The problematic of this research is the level of perception ability of musical instruments with visual support on mild mentally retarded children. In this research, perception ability of defining pictograms by music is introduced as an alternative method. It is researched that how educable mentally retarded children perceive pictograms by music tools. In this case, it is aimed to introduce musical instruments to educable mentally retarded children by pictograms with music. The research is applied with a qualitative approach. Data were obtained with the recorder, then they were turned into texts and analyzed with content analysis method.

  13. Fast gain calibration in radio astronomy using alternating direction implicit methods: Analysis and applications

    CERN Document Server

    Salvini, Stefano

    2014-01-01

    Context. Modern radio astronomical arrays have (or will have) more than one order of magnitude more receivers than classical synthesis arrays, such as the VLA and the WSRT. This makes gain calibration a computationally demanding task. Several alternating direction implicit (ADI) approaches have therefore been proposed that reduce numerical complexity for this task from $\\mathcal{O}(P^3)$ to $\\mathcal{O}(P^2)$, where $P$ is the number of receive paths to be calibrated. Aims. We present an ADI method, show that it converges to the optimal solution, and assess its numerical, computational and statistical performance. We also discuss its suitability for application in self-calibration and report on its successful application in LOFAR standard pipelines. Methods. Convergence is proved by rigorous mathematical analysis using a contraction mapping. Its numerical, algorithmic, and statistical performance, as well as its suitability for application in self-calibration, are assessed using simulations. Results. Our simu...

  14. A method of genotyping by pedigree-based training-set for identification of QTLs associated with cucumber fruit size

    Science.gov (United States)

    Large sets of genomic data are becoming available for cucumber (Cucumis sativus), yet there is no tool for whole genome genotyping. Creation of saturated genetic maps depends on development of good markers. The present cucumber genetic maps are based on several hundreds of markers. However they are ...

  15. Report of an ISRTP workshop: progress and barriers to incorporating alternative toxicological methods in the U.S.

    Science.gov (United States)

    Becker, Richard A; Borgert, Christopher J; Webb, Simon; Ansell, Jay; Amundson, Sara; Portier, Christopher J; Goldberg, Alan; Bruner, Leon H; Rowan, Andrew; Curren, Rodger D; Stott, William T

    2006-10-01

    The workshop objectives were to explore progress in implementing new, revised and alternative toxicological test methods across regulatory evaluation frameworks and decision-making programs in the United States, to identify barriers and to develop recommendations to further promote adoption of approaches that reduce, refine, or replace the use of animal methods. The workshop included sessions on: (1) current research, development, and validation of alternative methods within the U.S. federal government; (2) emerging alternative methodologies with potential applications to a broad spectrum of toxicity evaluation strategies; (3) tiered evaluation ("intelligent testing") strategies; and (4) identification of, and recommendations to address, critical barriers that affect adoption and use of new, revised alternative toxicological test methods by U.S. regulatory agencies. Through facilitated discussion, a list of barriers and recommendations were developed and grouped into categories of economic/financial, scientific/technical, and regulatory/policy. Overall, participants from all sectors collectively supported catalyzing actions to promote more meaningful and rapid progress for research to develop alternative methods focused for use in regulatory programs, accelerated lab investigations to validate such alternative methods and adoption of regulatory frameworks which embrace and incorporate these validated alternatives.

  16. Update and Improve Subsection NH –– Alternative Simplified Creep-Fatigue Design Methods

    Energy Technology Data Exchange (ETDEWEB)

    Tai Asayama

    2009-10-26

    This report described the results of investigation on Task 10 of DOE/ASME Materials NGNP/Generation IV Project based on a contract between ASME Standards Technology, LLC (ASME ST-LLC) and Japan Atomic Energy Agency (JAEA). Task 10 is to Update and Improve Subsection NH -- Alternative Simplified Creep-Fatigue Design Methods. Five newly proposed promising creep-fatigue evaluation methods were investigated. Those are (1) modified ductility exhaustion method, (2) strain range separation method, (3) approach for pressure vessel application, (4) hybrid method of time fraction and ductility exhaustion, and (5) simplified model test approach. The outlines of those methods are presented first, and predictability of experimental results of these methods is demonstrated using the creep-fatigue data collected in previous Tasks 3 and 5. All the methods (except the simplified model test approach which is not ready for application) predicted experimental results fairly accurately. On the other hand, predicted creep-fatigue life in long-term regions showed considerable differences among the methodologies. These differences come from the concepts each method is based on. All the new methods investigated in this report have advantages over the currently employed time fraction rule and offer technical insights that should be thought much of in the improvement of creep-fatigue evaluation procedures. The main points of the modified ductility exhaustion method, the strain range separation method, the approach for pressure vessel application and the hybrid method can be reflected in the improvement of the current time fraction rule. The simplified mode test approach would offer a whole new advantage including robustness and simplicity which are definitely attractive but this approach is yet to be validated for implementation at this point. Therefore, this report recommends the following two steps as a course of improvement of NH based on newly proposed creep-fatigue evaluation

  17. Alternative sanitization methods for minimally processed lettuce in comparison to sodium hypochlorite

    Directory of Open Access Journals (Sweden)

    Mara Lígia Biazotto Bachelli

    2013-09-01

    Full Text Available Lettuce is a leafy vegetable widely used in industry for minimally processed products, in which the step of sanitization is the crucial moment for ensuring a safe food for consumption. Chlorinated compounds, mainly sodium hypochlorite, are the most used in Brazil, but the formation of trihalomethanes from this sanitizer is a drawback. Then, the search for alternative methods to sodium hypochlorite has been emerging as a matter of great interest. The suitability of chlorine dioxide (60 mg L-1/10 min, peracetic acid (100 mg L-1/15 min and ozonated water (1.2 mg L-1 /1 min as alternative sanitizers to sodium hypochlorite (150 mg L-1 free chlorine/15 min were evaluated. Minimally processed lettuce washed with tap water for 1 min was used as a control. Microbiological analyses were performed in triplicate, before and after sanitization, and at 3, 6, 9 and 12 days of storage at 2 ± 1 ºC with the product packaged on LDPE bags of 60 µm. It was evaluated total coliforms, Escherichia coli, Salmonella spp., psicrotrophic and mesophilic bacteria, yeasts and molds. All samples of minimally processed lettuce showed absence of E. coli and Salmonella spp. The treatments of chlorine dioxide, peracetic acid and ozonated water promoted reduction of 2.5, 1.1 and 0.7 log cycle, respectively, on count of microbial load of minimally processed product and can be used as substitutes for sodium hypochlorite. These alternative compounds promoted a shelf-life of six days to minimally processed lettuce, while the shelf-life with sodium hypochlorite was 12 days.

  18. Alternative method for identification of the dynamic properties of bolted joints

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Tieneng [Beijing Univ. of Technology, Beijing (China); Li, Ling; Cai, Ligang; Zhao, Yong Sheng [Xi' an Univ. of Architecture Technology, Xi' an (China)

    2012-10-15

    Bolted joints often have a significant effect on the dynamical behavior of assembled mechanical structures. An accurate model of an assembled structure depends on correctly determining and identifying the dynamic parameters of bolted joints. This paper presents an alternative method for identifying these dynamic parameters using structure's natural frequency and damping. A novel experiment is designed with a test piece consisting of only bolted joints, with the governing equations of the test piece established using the analytical method. The relationships between the equivalent dynamic parameters of the bolted joints and the natural frequencies and damping ratios of the test piece are determined for both the normal and tangential directions. The parameter identification problem for bolted joints is thus transformed into a test of the natural frequency and the damping ratio of the test piece. In order to check the accuracy of the proposed identification method, the test piece and bolted joints are modeled using the finite element method (FEM) and the dynamic properties of the test piece are analyzed. The maximum error between the natural frequencies of the FEM result and the experimental values in the normal and tangential models are 4.73% and 0.34%, respectively. The result indicates that the proposed method is valid for the dynamic parameter identification of bolted joints.

  19. Evaluation of the long-term performance of six alternative disposal methods for LLRW

    Energy Technology Data Exchange (ETDEWEB)

    Kossik, R.; Sharp, G. [Golder Associates, Inc., Redmond, WA (United States); Chau, T. [Rogers & Associates Engineering Corp., Salt Lake City, UT (United States)

    1995-12-31

    The State of New York has carried out a comparison of six alternative disposal methods for low-level radioactive waste (LLRW). An important part of these evaluations involved quantitatively analyzing the long-term (10,000 yr) performance of the methods with respect to dose to humans, radionuclide concentrations in the environment, and cumulative release from the facility. Four near-surface methods (covered above-grade vault, uncovered above-grade vault, below-grade vault, augered holes) and two mine methods (vertical shaft mine and drift mine) were evaluated. Each method was analyzed for several generic site conditions applicable for the state. The evaluations were carried out using RIP (Repository Integration Program), an integrated, total system performance assessment computer code which has been applied to radioactive waste disposal facilities both in the U.S. (Yucca Mountain, WIPP) and worldwide. The evaluations indicate that mines in intact low-permeability rock and near-surface facilities with engineered covers generally have a high potential to perform well (within regulatory limits). Uncovered above-grade vaults and mines in highly fractured crystalline rock, however, have a high potential to perform poorly, exceeding regulatory limits.

  20. Desmanthus GENOTYPES

    Directory of Open Access Journals (Sweden)

    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  1. A rapid and robust sequence-based genotyping method for BoLA-DRB3 alleles in large numbers of heterozygous cattle.

    Science.gov (United States)

    Baxter, R; Hastings, N; Law, A; Glass, E J

    2008-10-01

    The BoLA-DRB3 gene is a highly polymorphic major histocompatibility complex class II gene of cattle with over one hundred alleles reported. Most of the polymorphisms are located in exon 2, which encodes the peptide-binding cleft, and these sequence differences play a role in variability of immune responsiveness and disease resistance. However, the high degree of polymorphism in exon 2 leads to difficulty in accurately genotyping cattle, especially heterozygous animals. In this study, we have improved and simplified an earlier sequence-based typing method to easily and reliably genotype cattle for BoLA-DRB3. In contrast to the earlier method, which used a nested primer set to amplify exon 2 followed by sequencing with internal primers, the new method uses only internal primers for both amplification and sequencing, which results in high-quality sequence across the entire exon. The haplofinder software, which assigns alleles from the heterozygous sequence, now has a pre-processing step that uses a consensus of all known alleles and checks for errors in base calling, thus improving the ability to process large numbers of samples. In addition, advances in sequencing technology have reduced the requirement for manual editing and improved the clarity of heterozygous base calls, resulting in longer and clearer sequence reads. Taken together, this has resulted in a rapid and robust method for genotyping large numbers of heterozygous samples for BoLA-DRB3 polymorphisms. Over 400 Holstein-Charolais cattle have now been genotyped for BoLA-DRB3 using this approach.

  2. Susceptibility of biallelic haplotype and genotype frequencies to genotyping error.

    Science.gov (United States)

    Moskvina, Valentina; Schmidt, Karl Michael

    2006-12-01

    With the availability of fast genotyping methods and genomic databases, the search for statistical association of single nucleotide polymorphisms with a complex trait has become an important methodology in medical genetics. However, even fairly rare errors occurring during the genotyping process can lead to spurious association results and decrease in statistical power. We develop a systematic approach to study how genotyping errors change the genotype distribution in a sample. The general M-marker case is reduced to that of a single-marker locus by recognizing the underlying tensor-product structure of the error matrix. Both method and general conclusions apply to the general error model; we give detailed results for allele-based errors of size depending both on the marker locus and the allele present. Multiple errors are treated in terms of the associated diffusion process on the space of genotype distributions. We find that certain genotype and haplotype distributions remain unchanged under genotyping errors, and that genotyping errors generally render the distribution more similar to the stable one. In case-control association studies, this will lead to loss of statistical power for nondifferential genotyping errors and increase in type I error for differential genotyping errors. Moreover, we show that allele-based genotyping errors do not disturb Hardy-Weinberg equilibrium in the genotype distribution. In this setting we also identify maximally affected distributions. As they correspond to situations with rare alleles and marker loci in high linkage disequilibrium, careful checking for genotyping errors is advisable when significant association based on such alleles/haplotypes is observed in association studies.

  3. Optimizing tridiagonal solvers for alternating direction methods on Boolean cube multiprocessors

    Energy Technology Data Exchange (ETDEWEB)

    Ho, C.T. (IBM Almaden Research Center, San Jose, CA (US)); Johnsson, S.L. (Dept. of Computer Science and Electrical Engineering, Yale Univ., New Haven, CT (US))

    1990-05-01

    Sets of tridiagonal systems occur in many applications. Fast Poisson solvers and Alternate Direction Methods make use of tridiagonal system solvers. Network-based multiprocessors provide a cost-effective alternative to traditional supercomputer architectures. The complexity of concurrent algorithms for the solution of multiple tridiagonal systems on Boolean-cube-configured multiprocessors with distributed memory are investigated. Variations of odd-even cyclic reduction, parallel cyclic reduction, and algorithms making use of data transposition with or without substructuring and local elimination, or pipelined elimination, are considered. A simple performance model is used for algorithm comparison, and the validity of the model is verified on an Intel iPSC/1. For many combinations of machine and system parameters, pipelined elimination, or equation transposition with or without substructuring is optimum. Hybrid algorithms that at any stage choose the best algorithm among the considered ones for the remainder of the problem are presented. It is shown that the optimum partitioning of a set of independent tridiagonal systems among a set of processors yields the embarrassingly parallel case.

  4. Musical training as an alternative and effective method for neuro-education and neuro-rehabilitation.

    Science.gov (United States)

    François, Clément; Grau-Sánchez, Jennifer; Duarte, Esther; Rodriguez-Fornells, Antoni

    2015-01-01

    In the last decade, important advances in the field of cognitive science, psychology, and neuroscience have largely contributed to improve our knowledge on brain functioning. More recently, a line of research has been developed that aims at using musical training and practice as alternative tools for boosting specific perceptual, motor, cognitive, and emotional skills both in healthy population and in neurologic patients. These findings are of great hope for a better treatment of language-based learning disorders or motor impairment in chronic non-communicative diseases. In the first part of this review, we highlight several studies showing that learning to play a musical instrument can induce substantial neuroplastic changes in cortical and subcortical regions of motor, auditory and speech processing networks in healthy population. In a second part, we provide an overview of the evidence showing that musical training can be an alternative, low-cost and effective method for the treatment of language-based learning impaired populations. We then report results of the few studies showing that training with musical instruments can have positive effects on motor, emotional, and cognitive deficits observed in patients with non-communicable diseases such as stroke or Parkinson Disease. Despite inherent differences between musical training in educational and rehabilitation contexts, these results favor the idea that the structural, multimodal, and emotional properties of musical training can play an important role in developing new, creative and cost-effective intervention programs for education and rehabilitation in the next future.

  5. Pretrial detention and alternate methods of securing the presence of the accused during the criminal procedure

    Directory of Open Access Journals (Sweden)

    Perišić Jelena

    2009-01-01

    Full Text Available In this paper, the author discusses pretrial detention and alternate methods of securing the presence of the accused during the criminal procedure. Except issues of terminology, in the introduction to this paper, the author deals with the current status of our criminal justice system, the readiness of both the state and the criminal justice system to accept innovations. Further, the author examines the accordance of pretrial detention with international sources, then its correlations with the Constitution, Criminal Procedure Codes from 2001 and 2006, and types of pretrial detention. As the paper continues, it describes institutes that are alternatives of pretrial detention: home detention and other restriction orders, and bail. The paper follows with the definition and content of the reasonable doubt concept as a mandatory condition for pronouncing pretrial detention. The major part of the paper deals is dedicated to the discussion of legal regulations of pretrial detention and its misinterpretation by judicial apparatus, and the effort to explain some undefined parts of those regulations.

  6. Social Benefits of Energy Conservation in Hungary. An examination of alternative methods of evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Aaheim, H.A.; Aunan, K.; Seip, H.M.

    1997-12-31

    This report compares alternative methods for valuation of the social benefits of less air pollution. One can estimate such benefits by the economic consequences of less damage caused by pollution or by the willingness to pay for less pollution. As a case study, the report examines an energy conservation programme in Hungary, in which 64 PJ of fossil energy was conserved per year. According to the damage cost approach, the benefits corresponds to 75 million USD per year, divided into 41 mill for health and 33 mill in material damage. The willingness to pay approach yielded a value of 1.9 bill. USD. Most of the difference is attributed to different estimates for chronic distresses and early death. One should not regard the results of the different approaches as alternative answers to the same question. Instead, damage cost and willingness to pay assessments can be considered as necessary components of a macro economic study of environmental policy. 23 refs., 9 figs., 5 tabs.

  7. Musical training as an alternative and effective method for neuro-education and neuro-rehabilitation

    Science.gov (United States)

    François, Clément; Grau-Sánchez, Jennifer; Duarte, Esther; Rodriguez-Fornells, Antoni

    2015-01-01

    In the last decade, important advances in the field of cognitive science, psychology, and neuroscience have largely contributed to improve our knowledge on brain functioning. More recently, a line of research has been developed that aims at using musical training and practice as alternative tools for boosting specific perceptual, motor, cognitive, and emotional skills both in healthy population and in neurologic patients. These findings are of great hope for a better treatment of language-based learning disorders or motor impairment in chronic non-communicative diseases. In the first part of this review, we highlight several studies showing that learning to play a musical instrument can induce substantial neuroplastic changes in cortical and subcortical regions of motor, auditory and speech processing networks in healthy population. In a second part, we provide an overview of the evidence showing that musical training can be an alternative, low-cost and effective method for the treatment of language-based learning impaired populations. We then report results of the few studies showing that training with musical instruments can have positive effects on motor, emotional, and cognitive deficits observed in patients with non-communicable diseases such as stroke or Parkinson Disease. Despite inherent differences between musical training in educational and rehabilitation contexts, these results favor the idea that the structural, multimodal, and emotional properties of musical training can play an important role in developing new, creative and cost-effective intervention programs for education and rehabilitation in the next future. PMID:25972820

  8. MUSICAL TRAINING AS AN ALTERNATIVE AND EFFECTIVE METHOD FOR NEURO-EDUCATION AND NEURO-REHABILITATION

    Directory of Open Access Journals (Sweden)

    Clément eFrançois

    2015-04-01

    Full Text Available In the last decade, important advances in the field of cognitive science, psychology and neuroscience have largely contributed to improve our knowledge on brain functioning. More recently, a line of research has been developed that aims at using musical training and practice as alternative tools for boosting specific perceptual, motor, cognitive and emotional skills both in healthy population and in neurologic patients. These findings are of great hope for a better treatment of language-based learning disorders or motor impairment in chronic non-communicative diseases. In the first part of this review, we highlight several studies showing that learning to play a musical instrument can induce substantial neuroplastic changes in cortical and subcortical regions of motor, auditory and speech processing networks in healthy population. In a second part, we provide an overview of the evidence showing that musical training can be an alternative, low-cost and effective method for the treatment of language-based learning impaired populations. We then report results of the few studies showing that training with musical instruments can have positive effects on motor, emotional and cognitive deficits observed in patients with noncommunicable diseases such as stroke or Parkinson Disease. Despite inherent differences between musical training in educational and rehabilitation contexts, these results favour the idea that the structural, multimodal and emotional properties of musical training can play an important role in developing new, creative and cost-effective intervention programs for education and rehabilitation in the next future.

  9. Nonlinear projection trick in kernel methods: an alternative to the kernel trick.

    Science.gov (United States)

    Kwak, Nojun

    2013-12-01

    In kernel methods such as kernel principal component analysis (PCA) and support vector machines, the so called kernel trick is used to avoid direct calculations in a high (virtually infinite) dimensional kernel space. In this brief, based on the fact that the effective dimensionality of a kernel space is less than the number of training samples, we propose an alternative to the kernel trick that explicitly maps the input data into a reduced dimensional kernel space. This is easily obtained by the eigenvalue decomposition of the kernel matrix. The proposed method is named as the nonlinear projection trick in contrast to the kernel trick. With this technique, the applicability of the kernel methods is widened to arbitrary algorithms that do not use the dot product. The equivalence between the kernel trick and the nonlinear projection trick is shown for several conventional kernel methods. In addition, we extend PCA-L1, which uses L1-norm instead of L2-norm (or dot product), into a kernel version and show the effectiveness of the proposed approach.

  10. Robust fluence map optimization via alternating direction method of multipliers with empirical parameter optimization

    Science.gov (United States)

    Gao, Hao

    2016-04-01

    For the treatment planning during intensity modulated radiation therapy (IMRT) or volumetric modulated arc therapy (VMAT), beam fluence maps can be first optimized via fluence map optimization (FMO) under the given dose prescriptions and constraints to conformally deliver the radiation dose to the targets while sparing the organs-at-risk, and then segmented into deliverable MLC apertures via leaf or arc sequencing algorithms. This work is to develop an efficient algorithm for FMO based on alternating direction method of multipliers (ADMM). Here we consider FMO with the least-square cost function and non-negative fluence constraints, and its solution algorithm is based on ADMM, which is efficient and simple-to-implement. In addition, an empirical method for optimizing the ADMM parameter is developed to improve the robustness of the ADMM algorithm. The ADMM based FMO solver was benchmarked with the quadratic programming method based on the interior-point (IP) method using the CORT dataset. The comparison results suggested the ADMM solver had a similar plan quality with slightly smaller total objective function value than IP. A simple-to-implement ADMM based FMO solver with empirical parameter optimization is proposed for IMRT or VMAT.

  11. An alternative empirical likelihood method in missing response problems and causal inference.

    Science.gov (United States)

    Ren, Kaili; Drummond, Christopher A; Brewster, Pamela S; Haller, Steven T; Tian, Jiang; Cooper, Christopher J; Zhang, Biao

    2016-11-30

    Missing responses are common problems in medical, social, and economic studies. When responses are missing at random, a complete case data analysis may result in biases. A popular debias method is inverse probability weighting proposed by Horvitz and Thompson. To improve efficiency, Robins et al. proposed an augmented inverse probability weighting method. The augmented inverse probability weighting estimator has a double-robustness property and achieves the semiparametric efficiency lower bound when the regression model and propensity score model are both correctly specified. In this paper, we introduce an empirical likelihood-based estimator as an alternative to Qin and Zhang (2007). Our proposed estimator is also doubly robust and locally efficient. Simulation results show that the proposed estimator has better performance when the propensity score is correctly modeled. Moreover, the proposed method can be applied in the estimation of average treatment effect in observational causal inferences. Finally, we apply our method to an observational study of smoking, using data from the Cardiovascular Outcomes in Renal Atherosclerotic Lesions clinical trial. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Effectiveness of Alternative Methods for Toothbrush Disinfection: An In Vitro Study

    Directory of Open Access Journals (Sweden)

    Ilkay Peker

    2014-01-01

    Full Text Available Objective. This study aimed to evaluate the effectiveness of alternative methods for toothbrush disinfection. Methods. Two-hundred eighty toothbrushes were included in the study. The toothbrushes were divided into 7 groups and were contaminated by standardized suspensions of Lactobacillus rhamnosus (L. rhamnosus, Streptococcus mutans (S. mutans, Staphylococcus aureus (S. aureus, and Escherichia coli (E. coli. The following disinfectants were tested: 1% sodium hypochlorite (NaOCl, 100% and 50% white vinegar, microwave (MW oven, ultraviolet (UV sanitizer, and mouth rinse-containing propolis (MCP. Data were analyzed with Kruskal Wallis and Dunn’s tests. Results. Statistically significant differences were found between different methods and control group for all tested bacteria. There were statistically significant differences between all test groups for all microorganisms. MW was the most effective for L. rhamnosus and 100% white vinegar was the most effective method for S. mutans and S. aureus. NaOCl was the most effective for E. coli. Conclusion. This study showed that 100% white vinegar was considered to be effective for tested microorganisms. Similarly, 1% NaOCl is cost-effective, easily accessible, and comparatively effective for toothbrush disinfection. Because these agents are nontoxic, cost-effective and easily accessible, they may be appropriate for household use.

  13. Effective Alternating Direction Optimization Methods for Sparsity-Constrained Blind Image Deblurring.

    Science.gov (United States)

    Xiong, Naixue; Liu, Ryan Wen; Liang, Maohan; Wu, Di; Liu, Zhao; Wu, Huisi

    2017-01-18

    Single-image blind deblurring for imaging sensors in the Internet of Things (IoT) is a challenging ill-conditioned inverse problem, which requires regularization techniques to stabilize the image restoration process. The purpose is to recover the underlying blur kernel and latent sharp image from only one blurred image. Under many degraded imaging conditions, the blur kernel could be considered not only spatially sparse, but also piecewise smooth with the support of a continuous curve. By taking advantage of the hybrid sparse properties of the blur kernel, a hybrid regularization method is proposed in this paper to robustly and accurately estimate the blur kernel. The effectiveness of the proposed blur kernel estimation method is enhanced by incorporating both the L 1 -norm of kernel intensity and the squared L 2 -norm of the intensity derivative. Once the accurate estimation of the blur kernel is obtained, the original blind deblurring can be simplified to the direct deconvolution of blurred images. To guarantee robust non-blind deconvolution, a variational image restoration model is presented based on the L 1 -norm data-fidelity term and the total generalized variation (TGV) regularizer of second-order. All non-smooth optimization problems related to blur kernel estimation and non-blind deconvolution are effectively handled by using the alternating direction method of multipliers (ADMM)-based numerical methods. Comprehensive experiments on both synthetic and realistic datasets have been implemented to compare the proposed method with several state-of-the-art methods. The experimental comparisons have illustrated the satisfactory imaging performance of the proposed method in terms of quantitative and qualitative evaluations.

  14. Effective Alternating Direction Optimization Methods for Sparsity-Constrained Blind Image Deblurring

    Directory of Open Access Journals (Sweden)

    Naixue Xiong

    2017-01-01

    Full Text Available Single-image blind deblurring for imaging sensors in the Internet of Things (IoT is a challenging ill-conditioned inverse problem, which requires regularization techniques to stabilize the image restoration process. The purpose is to recover the underlying blur kernel and latent sharp image from only one blurred image. Under many degraded imaging conditions, the blur kernel could be considered not only spatially sparse, but also piecewise smooth with the support of a continuous curve. By taking advantage of the hybrid sparse properties of the blur kernel, a hybrid regularization method is proposed in this paper to robustly and accurately estimate the blur kernel. The effectiveness of the proposed blur kernel estimation method is enhanced by incorporating both the L 1 -norm of kernel intensity and the squared L 2 -norm of the intensity derivative. Once the accurate estimation of the blur kernel is obtained, the original blind deblurring can be simplified to the direct deconvolution of blurred images. To guarantee robust non-blind deconvolution, a variational image restoration model is presented based on the L 1 -norm data-fidelity term and the total generalized variation (TGV regularizer of second-order. All non-smooth optimization problems related to blur kernel estimation and non-blind deconvolution are effectively handled by using the alternating direction method of multipliers (ADMM-based numerical methods. Comprehensive experiments on both synthetic and realistic datasets have been implemented to compare the proposed method with several state-of-the-art methods. The experimental comparisons have illustrated the satisfactory imaging performance of the proposed method in terms of quantitative and qualitative evaluations.

  15. Comparison of marine spatial planning methods in Madagascar demonstrates value of alternative approaches.

    Science.gov (United States)

    Allnutt, Thomas F; McClanahan, Timothy R; Andréfouët, Serge; Baker, Merrill; Lagabrielle, Erwann; McClennen, Caleb; Rakotomanjaka, Andry J M; Tianarisoa, Tantely F; Watson, Reg; Kremen, Claire

    2012-01-01

    The Government of Madagascar plans to increase marine protected area coverage by over one million hectares. To assist this process, we compare four methods for marine spatial planning of Madagascar's west coast. Input data for each method was drawn from the same variables: fishing pressure, exposure to climate change, and biodiversity (habitats, species distributions, biological richness, and biodiversity value). The first method compares visual color classifications of primary variables, the second uses binary combinations of these variables to produce a categorical classification of management actions, the third is a target-based optimization using Marxan, and the fourth is conservation ranking with Zonation. We present results from each method, and compare the latter three approaches for spatial coverage, biodiversity representation, fishing cost and persistence probability. All results included large areas in the north, central, and southern parts of western Madagascar. Achieving 30% representation targets with Marxan required twice the fish catch loss than the categorical method. The categorical classification and Zonation do not consider targets for conservation features. However, when we reduced Marxan targets to 16.3%, matching the representation level of the "strict protection" class of the categorical result, the methods show similar catch losses. The management category portfolio has complete coverage, and presents several management recommendations including strict protection. Zonation produces rapid conservation rankings across large, diverse datasets. Marxan is useful for identifying strict protected areas that meet representation targets, and minimize exposure probabilities for conservation features at low economic cost. We show that methods based on Zonation and a simple combination of variables can produce results comparable to Marxan for species representation and catch losses, demonstrating the value of comparing alternative approaches during

  16. Comparison of marine spatial planning methods in Madagascar demonstrates value of alternative approaches.

    Directory of Open Access Journals (Sweden)

    Thomas F Allnutt

    Full Text Available The Government of Madagascar plans to increase marine protected area coverage by over one million hectares. To assist this process, we compare four methods for marine spatial planning of Madagascar's west coast. Input data for each method was drawn from the same variables: fishing pressure, exposure to climate change, and biodiversity (habitats, species distributions, biological richness, and biodiversity value. The first method compares visual color classifications of primary variables, the second uses binary combinations of these variables to produce a categorical classification of management actions, the third is a target-based optimization using Marxan, and the fourth is conservation ranking with Zonation. We present results from each method, and compare the latter three approaches for spatial coverage, biodiversity representation, fishing cost and persistence probability. All results included large areas in the north, central, and southern parts of western Madagascar. Achieving 30% representation targets with Marxan required twice the fish catch loss than the categorical method. The categorical classification and Zonation do not consider targets for conservation features. However, when we reduced Marxan targets to 16.3%, matching the representation level of the "strict protection" class of the categorical result, the methods show similar catch losses. The management category portfolio has complete coverage, and presents several management recommendations including strict protection. Zonation produces rapid conservation rankings across large, diverse datasets. Marxan is useful for identifying strict protected areas that meet representation targets, and minimize exposure probabilities for conservation features at low economic cost. We show that methods based on Zonation and a simple combination of variables can produce results comparable to Marxan for species representation and catch losses, demonstrating the value of comparing alternative

  17. Effective Alternating Direction Optimization Methods for Sparsity-Constrained Blind Image Deblurring

    Science.gov (United States)

    Xiong, Naixue; Liu, Ryan Wen; Liang, Maohan; Wu, Di; Liu, Zhao; Wu, Huisi

    2017-01-01

    Single-image blind deblurring for imaging sensors in the Internet of Things (IoT) is a challenging ill-conditioned inverse problem, which requires regularization techniques to stabilize the image restoration process. The purpose is to recover the underlying blur kernel and latent sharp image from only one blurred image. Under many degraded imaging conditions, the blur kernel could be considered not only spatially sparse, but also piecewise smooth with the support of a continuous curve. By taking advantage of the hybrid sparse properties of the blur kernel, a hybrid regularization method is proposed in this paper to robustly and accurately estimate the blur kernel. The effectiveness of the proposed blur kernel estimation method is enhanced by incorporating both the L1-norm of kernel intensity and the squared L2-norm of the intensity derivative. Once the accurate estimation of the blur kernel is obtained, the original blind deblurring can be simplified to the direct deconvolution of blurred images. To guarantee robust non-blind deconvolution, a variational image restoration model is presented based on the L1-norm data-fidelity term and the total generalized variation (TGV) regularizer of second-order. All non-smooth optimization problems related to blur kernel estimation and non-blind deconvolution are effectively handled by using the alternating direction method of multipliers (ADMM)-based numerical methods. Comprehensive experiments on both synthetic and realistic datasets have been implemented to compare the proposed method with several state-of-the-art methods. The experimental comparisons have illustrated the satisfactory imaging performance of the proposed method in terms of quantitative and qualitative evaluations. PMID:28106764

  18. Feeling blue, going green and finding other attractive alternatives: a case of biphasic anaphylaxis to patent blue and a literature review of alternative sentinel node localisation methods.

    Science.gov (United States)

    Iqbal, Fahad Mujtaba; Basit, Abdul; Salem, Fathi; Vidya, Raghavan

    2015-12-15

    Patent blue dye is used for sentinel lymph node localisation in order to stage the axilla in patients with breast cancer. Patent blue is one of the most common dyes used across the UK, however, the incidence of adverse effects seems to be increasing. This case highlights our experience of a biphasic anaphylactic reaction to patent blue dye, and we conduct a brief literature review of alternative and more novel methods to adequately visualise the lymphatics for sentinel lymph node biopsy.

  19. Designing Alternative Transport Methods for the Distributed Data Collection of ATLAS EventIndex Project

    CERN Document Server

    Fernandez Casani, Alvaro; The ATLAS collaboration

    2016-01-01

    One of the key and challenging tasks of the ATLAS EventIndex project is to index and catalog all the produced events not only at CERN but also at hundreds of worldwide grid sites, and convey the data in real time to a central Hadoop instance at CERN. While this distributed data collection is currently operating correctly in production, there are some issues that might impose performance bottlenecks in the future, with an expected rise in the event production and reprocessing rates. In this work, we first describe the current approach based on a messaging system, which conveys the data from the sources to the central catalog, and we identify some weaknesses of this system. Then, we study a promising alternative transport method based on an object store, presenting a performance comparison with the current approach, and the architectural design changes needed to adapt the system to the next run of the ATLAS experiment at CERN.

  20. Valuation of imaging centers: alternative methods and detailed description of the discounted cash flow approach.

    Science.gov (United States)

    Russell, Philip J

    2007-01-01

    Medical imaging centers are an increasingly integral part of the medical services landscape in America. There are many instances in which owners and potential buyers of these enterprises want to ascertain the value of the businesses. There is an industry of professionals who provide expert valuation services for many types of businesses using various recognized alternative methods, some of which are more appropriate than others when valuing an imaging center. The federal government has prescribed parameters for all valuations if they lead to transactions in which fair market value is mandated, and it also expects transactions to adhere to more generalized laws relating to entities that provide services to Medicare patients. Radiologists who own, or who are contemplating ownership of, imaging center operations need to understand the principles of valuation, specifically the factors that are involved in a discounted cash flow determination of fair market value.

  1. Poorly understood and often miscategorized congenital umbilical cord hernia: an alternative repair method.

    Science.gov (United States)

    İnce, E; Temiz, A; Ezer, S S; Gezer, H Ö; Hiçsönmez, A

    2017-06-01

    Umbilical cord hernia is poorly understood and often miscategorized as "omphalocele minor". Careless clamping of the cord leads to iatrogenic gut injury in the situation of umbilical cord hernia. This study aimed to determine the characteristics and outcomes of umbilical cord hernias. We also highlight an alternative repair method for umbilical cord hernias. We recorded 15 cases of umbilical cord hernias over 10 years. The patients' data were retrospectively reviewed, and preoperative preparation of the newborn, gestational age, birth weight, other associated malformations, surgical technique used, enteral nutrition, and length of hospitalization were recorded. This study included 15 neonates with umbilical cord hernias. The mean gestational age at the time of referral was 38.2 ± 2.1 umbilical cord hernia, the body folds develop normally and form the umbilical ring. The double purse-string technique is easy to apply and produces satisfactory cosmetic results in neonates with umbilical cord hernias.

  2. Evaluation of Alternate Materials and Methods for Strontium and Alpha Removal from Savannah River Site High-Level Waste Solutions

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, D.T.

    2000-11-07

    A literature survey indicated a number of alternate materials and methods for the removal of strontium and alpha-emitting radionuclides (actinides). We evaluated the use of alternate materials versus proposed flowsheets for salt processing at the Savannah River Site (SRS). From this evaluation we recommend the following materials for further testing to determine the rate and extent of removal. We do not recommend testing of liquid/liquid extraction and polymer filtration methods at this time.

  3. Using Writing Portfolios as an Alternative Assessment Method in the Greek Primary School

    Directory of Open Access Journals (Sweden)

    Angeliki Panou

    2010-02-01

    Full Text Available The purpose of this study is to present and analyze the use of writing portfolios as an alternative method of assessing the writing skill in a group of young learners who attend the 6th grade of a Greek State Primary School. In order for this research to be carried out successfully and to provide enlightening results, a systematic and purposeful collection and observation of these learners’ writing samples was conducted over a period of 4 months and further data was basically collected by means of questionnaires before, during and after the completion of the study. There are two major parts in this paper: the theoretical and the practical one. In the first one the following issues are considered: contrasts between traditional testing and alternative assessment and reasons for the selection of the latter as more preferable concerning the positive and very promising outcomes it provides to learners; current portfolio pedagogy and the benefits deriving in relation to the most profound theories underpinning young learners’ cognitive and linguistic development; and the process-writing approach in combination with the use of writing portfolios. The second part presents the actual implementation of the research, analyzing the whole process of the portfolio stages followed from the very beginning of the ‘journey’ to the end. Τhe outcomes and results of this research are discussed and evaluated, whether positive or even negative, and the implications of the present classroom-based study are outlined. Finally, the study concludes with suggestions for further research in order for possible revisions and/or improvements to the specific assessment method to be looked into in future.

  4. Full-vectorial finite-difference beam propagation method based on the modified alternating direction implicit method

    Institute of Scientific and Technical Information of China (English)

    Xiao Jin-Biao; Sun Xiao-Han

    2006-01-01

    A modified alternating direction implicit algorithm is proposed to solve the full-vectorial finite-difference beam propagation method formulation based on H fields. The cross-coupling terms are neglected in the first sub-step, but evaluated and doubly used in the second sub-step. The order of two sub-steps is reversed for each transverse magnetic field component so that the cross-coupling terms are always expressed in implicit form, thus the calculation is very efficient and stable. Moreover, an improved six-point finite-difference scheme with high accuracy independent of specific structures of waveguide is also constructed to approximate the cross-coupling terms along the transverse directions. The imaginary-distance procedure is used to assess the validity and utility of the present method. The field patterns and the normalized propagation constants of the fundamental mode for a buried rectangular waveguide and a rib waveguide are presented. Solutions are in excellent agreement with the benchmark results from the modal transverse resonance method.

  5. GROWTH HORMONE GENE GENOTYPING BY Msp I RESTRICTION ENZYME AND PCR-RFLP METHODS IN ACEH CATTLE BREED AT INDRAPURI DISTRICT OF ACEH PROVINCE

    Directory of Open Access Journals (Sweden)

    W.P.B. Putra

    2014-10-01

    Full Text Available The objective of this research was to identify growth hormone (GH genes genotype in selectedAceh cattle at Indrapuri’s Breeding and Forage Centre (IBFC of Aceh Cattle. Fourty one cattleconsisting of 21 male and 20 female cattle were used in this study. The genomic DNA was extractedfrom blood using Sambrook et al. (1989 methods. Polymerase Chain Reaction - Restriction FragmentLength Polymorphism (PCR-RFLP and mehod of sequencing was used to detect MspI site on GH gene.Based on sequencing results, it can be concluded that all cattle were monomorphism. The frequency ofTT genotype were 1.00 and same as T allele frequency. The transition of C (cytosine into T (thymineon 1548 bp caused the lost of restriction site.

  6. PHOTOPROBER® Biotin: An Alternative Method for Labeling Archival DNA for Comparative Genomic Hybridization

    Directory of Open Access Journals (Sweden)

    Dirk Korinth

    2004-01-01

    Full Text Available Comparative genomic hybridization (CGH represents a powerful method for screening the entire genome of solid tumors for chromosomal imbalances. Particularly it enabled the molecular cytogenetic analysis of archival, formalin‐fixed, paraffin‐embedded (FFPE tissue. A well‐known dilemma, however, is the poor DNA quality of this material with fragment sizes below 1000 bp. Nick translation, the conventionally used enzymatic DNA labeling method in CGH, leads to even shorter fragments often below a critical limit for successful analysis. In this study we report the alternative application of non‐enzymatic, PHOTOPROBE® biotin labeling for conjugation of the hapten to the DNA prior to in situ hybridization and fluorescence detection. We analyzed 51 FFPE tumor samples mainly from the upper respiratory tract by both labeling methods. In 19 cases, both approaches were successful. The comparison of hybridized metaphases showed a distinct higher fluorescence signal of the PHOTOPROBE® samples sometimes with a discrete cytoplasm background which however did not interfere with specificity and sensitivity of the detected chromosomal imbalances. For further 32 cases characterized by an average DNA fragment size below 1000 bp, PHOTOPROBE® biotin was the only successful labeling technique thus offering a new option for CGH analysis of highly degraded DNA from archival material.

  7. ALTERNATIVE METHODS OF TECHNOLOGICAL PROCESSING TO REDUCE SALT IN MEAT PRODUCTS

    Directory of Open Access Journals (Sweden)

    E. K. Tunieva

    2017-01-01

    Full Text Available The world trends in table salt reduction in meat products contemplate the use of different methods for preservation of taste and consistency in finished products as well as shelf life prolongation. There are several approaches to a sodium chloride reduction in meat products. The paper presents a review of the foreign studies that give evidence of the possibility to maintain quality of traditional meat products produced with the reduced salt content. The studies in the field of salty taste perception established that a decrease in a salt crystal size to 20 µm enabled reducing an amount of added table salt due to an increase in the salty taste intensity in food products. Investigation of the compatibility of different taste directions is also interesting as one of the approaches to a sodium chloride reduction in food products. The use of water-in-oil-in-water (w/o/w double emulsions allows controlling a release of encapsulated ingredients (salt, which enables enhancement of salty taste. The other alternative method of technological processing of meat raw material for reducing salt in meat products is the use of high pressure processing. This method has several advantages and allows not only an increase in the salty taste intensity, but also formation of a stable emulsion, an increase in water binding capacity of minced meat and extension of shelf-life.

  8. A novel method to assist the detection of the Cyclic Alternating Pattern (CAP).

    Science.gov (United States)

    Tenorio, J M; Alba, A; Mendez, M O; Bianchi, A M; Grassi, A; Arce-Santana, E; Chouvarda, I; Mariani, S; Rosso, V; Terzano, M G; Parrino, L

    2012-01-01

    This study proposes a novel method to assist the detection of the components that build up the Cyclic Alternating Pattern (CAP). CAP is a sleep phenomenon formed by consecutive sequences of activations (A1, A2, A3) and non-activations during nonREM sleep. The main importance of CAP evaluation is the possibility of defining the sleep process more accurately. Ten recordings from healthy and good sleepers were included in this study. The method is based on inferential statistics to define the initial and ending points of the CAP components based only on an initialization point given by the expert. The results show concordance up to 95% for A1, 85% for A2 and 60% for A3, together with an overestimation of 1.5 s in A1, 1.3 s in A2 and 0 s in A3. The total CAP rate presents a total underestimation of 7 min. Those results suggest that the method is able to accurately detect the initial and ending points of the activations, and may be helpful for the physicians by reducing the time dedicated to the manual inspection task.

  9. Between Contemporary Art and Cultural Analysis: Alternative Methods for Knowledge Production

    Directory of Open Access Journals (Sweden)

    Billy Ehn

    2012-03-01

    Full Text Available Artistic research suggests alternative methods for producing various kinds of knowledge, whether within or without the confines of academe. These methods may involve either the production of investigative artworks or the writing by the artist of a doctoral dissertation about his or her own work. For cultural researchers, the methods employed by artists engaged in these processes are both familiar and challenging, as conventional ethnography is mixed with more unpredictable experiments. This article presents several contemporary artworks, including sculpture, film, dance, installation and performance that explore various aspects of reality. What can be learnt from these works? And what could be achieved by an open exchange between artists and academic researchers? Four methodological approaches are highlighted as being of particular interest. The first relates to artists’ tendency to live experimentally, using themselves both as actors and as research objects. The second arises from the very tangible ways in which contemporary artworks approach the theme of materiality. The third relates to the emotional nature of much of contemporary art – even when it is categorised as conceptual – in its creation, forms of presentation, and influence on the spectator. Finally, many artists are gifted with the ability to find and communicate surprising meanings in ordinary life. How do they do this? Part of the answer seems to be that although artists are open to the implementation of “wild whims”, they exploit their spontaneity in a highly professional manner.

  10. The characteristic function, a method-specific alternative to the Horwitz function.

    Science.gov (United States)

    Thompson, Michael

    2012-01-01

    The Horwitz function is compared with the characteristic function as a descriptor of the precision of individual analytical methods. The Horwitz function describes the trend of reproducibility SDs observed in collaborative trials in the food sector over a wide range of concentrations of the analyte. However, it is imperfectly adaptable for describing the precision of individual methods, which is the role of the characteristic function. An essential difference between the two functions is that the characteristic function can accommodate a detection limit. This makes it a useful alternative when the precision of a method down to a detection limit is of interest. Many characteristic functions have a simple mathematical form, the parameters of which can be estimated with the usual resources. The Horwitz function serves an additional role as a fitness-for-purpose criterion in the form of the Horwitz ratio (HorRat). This use also has some shortcomings. The functional form of the characteristic function (with suitable prescribed parameters) is better adapted to this task.

  11. USING COMPUTER-BASED TESTING AS ALTERNATIVE ASSESSMENT METHOD OF STUDENT LEARNING IN DISTANCE EDUCATION

    Directory of Open Access Journals (Sweden)

    Amalia SAPRIATI

    2010-04-01

    Full Text Available This paper addresses the use of computer-based testing in distance education, based on the experience of Universitas Terbuka (UT, Indonesia. Computer-based testing has been developed at UT for reasons of meeting the specific needs of distance students as the following: Ø students’ inability to sit for the scheduled test, Ø conflicting test schedules, and Ø students’ flexibility to take examination to improve their grades. In 2004, UT initiated a pilot project in the development of system and program for computer-based testing method. Then in 2005 and 2006 tryouts in the use of computer-based testing methods were conducted in 7 Regional Offices that were considered as having sufficient supporting recourses. The results of the tryouts revealed that students were enthusiastic in taking computer-based tests and they expected that the test method would be provided by UT as alternative to the traditional paper and pencil test method. UT then implemented computer-based testing method in 6 and 12 Regional Offices in 2007 and 2008 respectively. The computer-based testing was administered in the city of the designated Regional Office and was supervised by the Regional Office staff. The development of the computer-based testing was initiated with conducting tests using computers in networked configuration. The system has been continually improved, and it currently uses devices linked to the internet or the World Wide Web. The construction of the test involves the generation and selection of the test items from the item bank collection of the UT Examination Center. Thus the combination of the selected items compromises the test specification. Currently UT has offered 250 courses involving the use of computer-based testing. Students expect that more courses are offered with computer-based testing in Regional Offices within easy access by students.

  12. Modeling the impacts of alternative fertilization methods on nitrogen loading in rice production in Shanghai.

    Science.gov (United States)

    Zhao, Zheng; Sha, Zhimin; Liu, Yibo; Wu, Shuhang; Zhang, Hanlin; Li, Changsheng; Zhao, Qi; Cao, Linkui

    2016-10-01

    Nitrogen (N) loss from paddy fields is an important source of agricultural non-point source pollution that leads to eutrophication of water bodies and degradation of water quality. The impacts of alternative N fertilizer management practices on N loading (N loss through runoff and leaching) from paddy fields in Shanghai were assessed using a process-based biogeochemical model, DNDC. The results indicated that the current fertilization rate in paddy fields of Shanghai (300kgN/ha) exceeds the actual rice demand and has led to substantial N loading of 1142±276kg. The combined application of urea at 150kgN/ha and organic manure at 100kgN/ha was identified as the best fertilization method for rice cultivation in Shanghai; this application maintained optimal rice yields and significantly reduced N loading to 714±151kg in comparison with the current fertilization rate. A sensitivity test was conducted with various input parameters, and the results indicated that fertilization, precipitation and soil properties were the most sensitive factors that regulate N loss from paddy fields. The variability of soil properties, especially SOC led to high uncertainties in the simulated results. Therefore, the local climate conditions and soil properties should be taken into account in the identification of the best management practice (BMP) for rice cultivation, given the high spatially heterogeneous N loading values across all towns used in the simulation. The DNDC model is an effective approach for simulating and predicting N loading in paddy fields under alternative agricultural management practices.

  13. Comparing five alternative methods of breast reconstruction surgery: a cost-effectiveness analysis.

    Science.gov (United States)

    Grover, Ritwik; Padula, William V; Van Vliet, Michael; Ridgway, Emily B

    2013-11-01

    The purpose of this study was to assess the cost-effectiveness of five standardized procedures for breast reconstruction to delineate the best reconstructive approach in postmastectomy patients in the settings of nonirradiated and irradiated chest walls. A decision tree was used to model five breast reconstruction procedures from the provider perspective to evaluate cost-effectiveness. Procedures included autologous flaps with pedicled tissue, autologous flaps with free tissue, latissimus dorsi flaps with breast implants, expanders with implant exchange, and immediate implant placement. All methods were compared with a "do-nothing" alternative. Data for model parameters were collected through a systematic review, and patient health utilities were calculated from an ad hoc survey of reconstructive surgeons. Results were measured in cost (2011 U.S. dollars) per quality-adjusted life-year. Univariate sensitivity analyses and Bayesian multivariate probabilistic sensitivity analysis were conducted. Pedicled autologous tissue and free autologous tissue reconstruction were cost-effective compared with the do-nothing alternative. Pedicled autologous tissue was the slightly more cost-effective of the two. The other procedures were not found to be cost-effective. The results were robust to a number of sensitivity analyses, although the margin between pedicled and free autologous tissue reconstruction is small and affected by some parameter values. Autologous pedicled tissue was slightly more cost-effective than free tissue reconstruction in irradiated and nonirradiated patients. Implant-based techniques were not cost-effective. This is in agreement with the growing trend at academic institutions to encourage autologous tissue reconstruction because of its natural recreation of the breast contour, suppleness, and resiliency in the setting of irradiated recipient beds.

  14. Alternative methods for specification of observed forcing in single-column models and cloud system models

    Science.gov (United States)

    Randall, David A.; Cripe, Douglas G.

    1999-10-01

    We discuss alternative methods for prescribing advective tendencies in single-column models (SCMs) and cloud system models. These include "revealed forcing," in which the total advective tendency is prescribed from observations; "horizontal advective forcing," in which the horizontal advective tendencies are prescribed, together with the observed vertical motion which is combined with the predicted sounding to determine the tendencies due to vertical advection; and "relaxation forcing," in which the horizontal advective tendencies are computed by relaxing the sounding toward the observed upstream sounding, with a relaxation timescale determined by the time required for the wind to carry parcels across the grid column. When relaxation forcing is used, the horizontal advective tendencies can be diagnosed from the model output and compared with the corresponding observed tendencies. We present SCM results to illustrate these three forcing methods, based on data from several field experiments in both the tropics and the midlatitudes. Each method is shown to have its strengths and weaknesses. Overall, the results presented here do not show unambiguous differences between revealed forcing and horizontal advective forcing. The two methods appear to be generally comparable. Revealed forcing may therefore be preferred for its simplicity. Relaxation forcing guarantees realistic soundings of the state variables but can produce large errors in parameterized processes which are driven by rates (e.g., fluxes) rather than states. In particular, relaxation forcing gives large errors in the precipitation rate in this model. We demonstrate that relaxation forcing leads to unrealistically high (low) precipitation in versions of the model which tend to produce unrealistically dry (humid) soundings. The observed horizontal advective tendencies in the tropics are so weak, especially for temperature, that small absolute errors in the diabatic tendencies diagnosed with relaxation forcing

  15. Go3R - semantic Internet search engine for alternative methods to animal testing.

    Science.gov (United States)

    Sauer, Ursula G; Wächter, Thomas; Grune, Barbara; Doms, Andreas; Alvers, Michael R; Spielmann, Horst; Schroeder, Michael

    2009-01-01

    Consideration and incorporation of all available scientific information is an important part of the planning of any scientific project. As regards research with sentient animals, EU Directive 86/609/EEC for the protection of laboratory animals requires scientists to consider whether any planned animal experiment can be substituted by other scientifically satisfactory methods not entailing the use of animals or entailing less animals or less animal suffering, before performing the experiment. Thus, collection of relevant information is indispensable in order to meet this legal obligation. However, no standard procedures or services exist to provide convenient access to the information required to reliably determine whether it is possible to replace, reduce or refine a planned animal experiment in accordance with the 3Rs principle. The search engine Go3R, which is available free of charge under http://Go3R.org, runs up to become such a standard service. Go3R is the world-wide first search engine on alternative methods building on new semantic technologies that use an expert-knowledge based ontology to identify relevant documents. Due to Go3R's concept and design, the search engine can be used without lengthy instructions. It enables all those involved in the planning, authorisation and performance of animal experiments to determine the availability of non-animal methodologies in a fast, comprehensive and transparent manner. Thereby, Go3R strives to significantly contribute to the avoidance and replacement of animal experiments.

  16. Alternative Chemical Cleaning Methods for High Level Waste Tanks: Simulant Studies

    Energy Technology Data Exchange (ETDEWEB)

    Rudisill, T. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); King, W. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hay, M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Jones, D. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-11-19

    Solubility testing with simulated High Level Waste tank heel solids has been conducted in order to evaluate two alternative chemical cleaning technologies for the dissolution of sludge residuals remaining in the tanks after the exhaustion of mechanical cleaning and sludge washing efforts. Tests were conducted with non-radioactive pure phase metal reagents, binary mixtures of reagents, and a Savannah River Site PUREX heel simulant to determine the effectiveness of an optimized, dilute oxalic/nitric acid cleaning reagent and pure, dilute nitric acid toward dissolving the bulk non-radioactive waste components. A focus of this testing was on minimization of oxalic acid additions during tank cleaning. For comparison purposes, separate samples were also contacted with pure, concentrated oxalic acid which is the current baseline chemical cleaning reagent. In a separate study, solubility tests were conducted with radioactive tank heel simulants using acidic and caustic permanganate-based methods focused on the “targeted” dissolution of actinide species known to be drivers for Savannah River Site tank closure Performance Assessments. Permanganate-based cleaning methods were evaluated prior to and after oxalic acid contact.

  17. The convergence rate of the proximal alternating direction method of multipliers with indefinite proximal regularization

    Directory of Open Access Journals (Sweden)

    Min Sun

    2017-01-01

    Full Text Available Abstract The proximal alternating direction method of multipliers (P-ADMM is an efficient first-order method for solving the separable convex minimization problems. Recently, He et al. have further studied the P-ADMM and relaxed the proximal regularization matrix of its second subproblem to be indefinite. This is especially significant in practical applications since the indefinite proximal matrix can result in a larger step size for the corresponding subproblem and thus can often accelerate the overall convergence speed of the P-ADMM. In this paper, without the assumptions that the feasible set of the studied problem is bounded or the objective function’s component θ i ( ⋅ $\\theta_{i}(\\cdot$ of the studied problem is strongly convex, we prove the worst-case O ( 1 / t $\\mathcal{O}(1/t$ convergence rate in an ergodic sense of the P-ADMM with a general Glowinski relaxation factor γ ∈ ( 0 , 1 + 5 2 $\\gamma\\in(0,\\frac{1+\\sqrt{5}}{2}$ , which is a supplement of the previously known results in this area. Furthermore, some numerical results on compressive sensing are reported to illustrate the effectiveness of the P-ADMM with indefinite proximal regularization.

  18. Alternative method for design and optimization of the ring resonator used in micro-optic gyro.

    Science.gov (United States)

    Wang, Kunbo; Feng, Lishuang; Wang, Junjie; Lei, Ming

    2013-03-01

    The ring resonator is one of the key elements in the micro-optic gyro system, but there is not a uniform method for designing the parameters of a ring resonator, especially for its size. In this paper, an alternative method is presented for designing the ring resonator used in micro-optic gyro. Maximization of the resonator output is proposed to be the principle in design and optimization for the first time to our knowledge. The scale factor accuracy and the full range of the gyro system are taken into account to obtain the optimum diameter of the ring. A theoretical optimal diameter of 0.25 m is achieved for SiO(2) waveguide resonator with a dynamic range of ±500°/s by analyzing the influence of resonator parameters on the output in detail, and the corresponding sensitivity of the gyro is less than 1.28°/h, which can meet the demands of a tactical inertia system.

  19. Alternative sorptive extraction method for gas chromatography determination of halogenated anisoles in water and wine samples

    Energy Technology Data Exchange (ETDEWEB)

    Montes, R. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Instituto de Investigacion y Analisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela 15782 (Spain); Rodriguez, I. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Instituto de Investigacion y Analisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela 15782 (Spain)], E-mail: qnisaac@usc.es; Rubi, E.; Bollain, M.H.; Cela, R. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Instituto de Investigacion y Analisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela 15782 (Spain)

    2007-09-05

    An alternative sorptive microextraction method for the determination of five halogenated anisoles in water and wine matrices is proposed. Analytes were concentrated in an inexpensive and disposable piece of bulk polydimethylsiloxane (PDMS), desorbed with a small volume of organic solvent, and determined by gas chromatography with electron-capture detection (GC-ECD) or tandem mass spectrometry (GC-MS/MS). The influence of several factors on the efficiency of extraction and desorption steps was investigated in detail and the observed behaviour justified on the basis of thermodynamics and kinetics of the solid-phase microextraction technique. Under optimised conditions, analytes were first extracted in the headspace (HS) mode, at room temperature, for 2.5 h and then desorbed with 1 mL of n-pentane. This extract was further evaporated to 50 {mu}L. The overall extraction yield of the procedure ranged from 40 to 55% and the limits of quantification remained between 0.5 and 20 ng L{sup -1}, depending on the compound considered and the detection technique. Precision and linearity of the method were excellent for all species with both GC-ECD and GC-MS/MS detection. Matrix effects were evaluated with different water and wine samples; moreover, the suitability of the PDMS sorbent for storage of analytes, under different conditions, was demonstrated.

  20. Alternate calibration method of radiochromic EBT3 film for quality assurance verification of clinical radiotherapy treatments

    Science.gov (United States)

    Park, Soah; Kang, Sei-Kwon; Cheong, Kwang-Ho; Hwang, Taejin; Yoon, Jai-Woong; Koo, Taeryool; Han, Tae Jin; Kim, Haeyoung; Lee, Me Yeon; Bae, Hoonsik; Kim, Kyoung Ju

    2016-07-01

    EBT3 film is utilized as a dosimetry quality assurance tool for the verification of clinical radiotherapy treatments. In this work, we suggest a percentage-depth-dose (PDD) calibration method that can calibrate several EBT3 film pieces together at different dose levels because photon beams provide different dose levels at different depths along the axis of the beam. We investigated the feasibility of the film PDD calibration method based on PDD data and compared the results those from the traditional film calibration method. Photon beams at 6 MV were delivered to EBT3 film pieces for both calibration methods. For the PDD-based calibration, the film pieces were placed on solid phantoms at the depth of maximum dose (dmax) and at depths of 3, 5, 8, 12, 17, and 22 cm, and a photon beam was delivered twice, at 100 cGy and 400 cGy, to extend the calibration dose range under the same conditions. Fourteen film pieces, to maintain their consistency, were irradiated at doses ranging from approximately 30 to 400 cGy for both film calibrations. The film pieces were located at the center position on the scan bed of an Epson 1680 flatbed scanner in the parallel direction. Intensity-modulated radiation therapy (IMRT) plans were created, and their dose distributions were delivered to the film. The dose distributions for the traditional method and those for the PDD-based calibration method were evaluated using a Gamma analysis. The PDD dose values using a CC13 ion chamber and those obtained by using a FC65-G Farmer chamber and measured at the depth of interest produced very similar results. With the objective test criterion of a 1% dosage agreement at 1 mm, the passing rates for the four cases of the three IMRT plans were essentially identical. The traditional and the PDD-based calibrations provided similar plan verification results. We also describe another alternative for calibrating EBT3 films, i.e., a PDD-based calibration method that provides an easy and time-saving approach

  1. Repeated measurement sampling in genetic association analysis with genotyping errors.

    Science.gov (United States)

    Lai, Renzhen; Zhang, Hong; Yang, Yaning

    2007-02-01

    Genotype misclassification occurs frequently in human genetic association studies. When cases and controls are subject to the same misclassification model, Pearson's chi-square test has the correct type I error but may lose power. Most current methods adjusting for genotyping errors assume that the misclassification model is known a priori or can be assessed by a gold standard instrument. But in practical applications, the misclassification probabilities may not be completely known or the gold standard method can be too costly to be available. The repeated measurement design provides an alternative approach for identifying misclassification probabilities. With this design, a proportion of the subjects are measured repeatedly (five or more repeats) for the genotypes when the error model is completely unknown. We investigate the applications of the repeated measurement method in genetic association analysis. Cost-effectiveness study shows that if the phenotyping-to-genotyping cost ratio or the misclassification rates are relatively large, the repeat sampling can gain power over the regular case-control design. We also show that the power gain is not sensitive to the genetic model, genetic relative risk and the population high-risk allele frequency, all of which are typically important ingredients in association studies. An important implication of this result is that whatever the genetic factors are, the repeated measurement method can be applied if the genotyping errors must be accounted for or the phenotyping cost is high.

  2. A Comprehensive Study of Internal Distraction Plating, an Alternative Method for Distal Radius Fractures

    Science.gov (United States)

    Mavani, Kinjal J

    2016-01-01

    Introduction The management of highly comminuted distal radius fractures still remains a major treatment challenge. Articular comminution and compromised bone quality are the culprits. One novel approach is the technique of Internal Distraction Plating which involves “bridging” the fracture with the use of a standard 3.5mm plate applied dorsally in distraction from the radius, proximal to the fracture, to the long finger metacarpal distally, bypassing the comminuted segment. The plate is removed once fracture union has been achieved. Aim The present study was conducted with the aim to evaluate the role of internal dorsal distraction plating as an alternative method in the treatment of fracture distal radius in terms of special indications, technique and outcome. Materials and Methods This study was a prospective longitudinal study on 20 patients (mean age 62 years) treated with internal distraction plating for comminuted distal radius fractures with specific indications. Regular follow-ups with standard radiographs and analysis were done upto 24 months. Functional outcome were assessed by DASH Score and the Gartland and Werley demerit score. Results At final follow-up, all fractures had united and X-rays showed mean palmar tilt of 7°, positive ulnar variance of 0.5mm, radial inclination of 18° and average loss of 2mm of radial height. Mean range of motion values for wrist flexion 46°, extension 50°, pronation 79° and supination 77° At final follow-up, the mean DASH score was 32. 85% patient had excellent to good result as per Gartland and Werley demerit score. This construct has yield satisfactory clinical and radiographic results with these very challenging injuries. Conclusion The purpose of this study was to report the radiographic and the functional outcomes of treatment with this technique. External fixator and volar plating in communited distal end radius fractures are not always satisfactory in old age with osteoporotic bone because of

  3. Dental movement acceleration: Literature review by an alternative scientific evidence method

    Science.gov (United States)

    Camacho, Angela Domínguez; Cujar, Sergio Andres Velásquez

    2014-01-01

    The aim of this study was to analyze the majority of publications using effective methods to speed up orthodontic treatment and determine which publications carry high evidence-based value. The literature published in Pubmed from 1984 to 2013 was reviewed, in addition to well-known reports that were not classified under this database. To facilitate evidence-based decision making, guidelines such as the Consolidation Standards of Reporting Trials, Preferred Reporting items for systematic Reviews and Meta-analyses, and Transparent Reporting of Evaluations with Non-randomized Designs check list were used. The studies were initially divided into three groups: local application of cell mediators, physical stimuli, and techniques that took advantage of the regional acceleration phenomena. The articles were classified according to their level of evidence using an alternative method for orthodontic scientific article classification. 1a: Systematic Reviews (SR) of randomized clinical trials (RCTs), 1b: Individual RCT, 2a: SR of cohort studies, 2b: Individual cohort study, controlled clinical trials and low quality RCT, 3a: SR of case-control studies, 3b: Individual case-control study, low quality cohort study and short time following split mouth designs. 4: Case-series, low quality case-control study and non-systematic review, and 5: Expert opinion. The highest level of evidence for each group was: (1) local application of cell mediators: the highest level of evidence corresponds to a 3B level in Prostaglandins and Vitamin D; (2) physical stimuli: vibratory forces and low level laser irradiation have evidence level 2b, Electrical current is classified as 3b evidence-based level, Pulsed Electromagnetic Field is placed on the 4th level on the evidence scale; and (3) regional acceleration phenomena related techniques: for corticotomy the majority of the reports belong to level 4. Piezocision, dentoalveolar distraction, alveocentesis, monocortical tooth dislocation and ligament

  4. Application of sensitivity analysis for assessment of de-desertification alternatives in the central Iran by using Triantaphyllou method.

    Science.gov (United States)

    Sadeghi Ravesh, Mohammad Hassan; Ahmadi, Hassan; Zehtabian, Gholamreza

    2011-08-01

    Desertification, land degradation in arid, semi-arid, and dry sub-humid regions, is a global environmental problem. With respect to increasing importance of desertification and its complexity, the necessity of attention to the optimal de-desertification alternatives is essential. Therefore, this work presents an analytic hierarchy process (AHP) method to objectively select the optimal de-desertification alternatives based on the results of interviews with experts in Khezr Abad region, central Iran as the case study. This model was used in Yazd Khezr Abad region to evaluate the efficiency in presentation of better alternatives related to personal and environmental situations. Obtained results indicate that the criterion "proportion and adaptation to the environment" with the weighted average of 33.6% is the most important criterion from experts viewpoints. While prevention alternatives of land usage unsuitable of reveres and conversion with 22.88% mean weight and vegetation cover development and reclamation with 21.9% mean weight are recognized ordinarily as the most important de-desertification alternatives in region. Finally, sensitivity analysis is performed in detail by varying the objective factor decision weight, the priority weight of subjective factors, and the gain factors. After the fulfillment of sensitivity analysis and determination of the most sensitive criteria and alternatives, the former classification and ranking of alternatives does not change so much, and it was observed that unsuitable land use alternative with the preference degree of 22.7% was still in the first order of priority. The final priority of livestock grazing control alternative was replaced with the alternative of modification of ground water harvesting.

  5. 75 FR 71155 - Market Test of Experimental Product: “Alternative Postage Payment Method for Greeting Cards”

    Science.gov (United States)

    2010-11-22

    ... of Experimental Product: ``Alternative Postage Payment Method for Greeting Cards'' AGENCY: Postal Service TM . ACTION: Notice. SUMMARY: The Postal Service gives notice of a market test of an experimental... Postage Payment Method for Greeting Cards'' experimental product on January 2, 2011. The Postal...

  6. Estimating Rumen Degradable Protein in Forage Legume Hays and Silages by In Situ Disappearance Kinetics vs. Alternative Methods

    Science.gov (United States)

    Currently, the in situ kinetic method is considered the “gold standard” for estimating rumen degradable protein (RDP) in forages. When such estimates are impractical (e.g. numerous samples, limited sample quantities, or lack of ruminally fistulated cattle) alternative RDP methods are used, but their...

  7. Transcervical double-balloon catheter as an alternative and salvage method for medical termination of pregnancy in midtrimester

    Directory of Open Access Journals (Sweden)

    Yi-An Tu

    2017-02-01

    Conclusion: There was no significant additional benefit of using a double-balloon catheter in midtrimester termination of pregnancy, although the technique was considered simple and generally well-tolerated. Placing a transcervical double-balloon catheter could be the primary method, or one of the alternative medical methods if the patient and/or obstetrician prefers no operation.

  8. Alternative method of highway traffic safety analysis for developing countries using delphi technique and Bayesian network.

    Science.gov (United States)

    Mbakwe, Anthony C; Saka, Anthony A; Choi, Keechoo; Lee, Young-Jae

    2016-08-01

    Highway traffic accidents all over the world result in more than 1.3 million fatalities annually. An alarming number of these fatalities occurs in developing countries. There are many risk factors that are associated with frequent accidents, heavy loss of lives, and property damage in developing countries. Unfortunately, poor record keeping practices are very difficult obstacle to overcome in striving to obtain a near accurate casualty and safety data. In light of the fact that there are numerous accident causes, any attempts to curb the escalating death and injury rates in developing countries must include the identification of the primary accident causes. This paper, therefore, seeks to show that the Delphi Technique is a suitable alternative method that can be exploited in generating highway traffic accident data through which the major accident causes can be identified. In order to authenticate the technique used, Korea, a country that underwent similar problems when it was in its early stages of development in addition to the availability of excellent highway safety records in its database, is chosen and utilized for this purpose. Validation of the methodology confirms the technique is suitable for application in developing countries. Furthermore, the Delphi Technique, in combination with the Bayesian Network Model, is utilized in modeling highway traffic accidents and forecasting accident rates in the countries of research.

  9. Relationship between DAPI-fluorescence fading and nuclear DNA content: An alternative method to DNA quantification?

    Science.gov (United States)

    Gallardo-Escárate, Cristian; Alvarez-Borrego, Josué; Von Brand, Elisabeth; Dupré, Enrique; Del Río-Portilla, Miguel Angel

    2007-01-01

    In observations by confocal or conventional fluorescence microscopy, important factors should be considered in order to obtain accurate images. One of them, such as the fluorescence bleaching from highest intensity to lowest signal of fluorescence is a common problem with several DNA fluorochromes and especially for DAPI stain. The fluorescence of DAPI fades rapidly when it is exposed to UV light, under optimal conditions of observation. Although the fading process can be retarded using a mounting medium with antifading reagents, the photochemical process underlying the fluorescence decay has not yet been fully explained. In addition, no relationship between fluorescence fading and nuclear DNA content has been tested. In order to test this relationship, we measured by means of image analysis the DAPI-fluorescence intensity in several cellular types (spermatozoa, erythrocytes and haemocytes) during their fluorescence bleaching. An algorithm specifically built in MATLAB software was used for this approach. The correlation coefficient between nuclear DNA content and DAPI-fluorescence fading was found equal to 99%. This study demonstrates the feasibility to measure nuclear DNA content by fluorescence fading quantification, as an alternative method concurrently with image analysis procedures.

  10. Equine tracheal epithelial membrane strips - An alternate method for examining epithelial cell arachidonic acid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Gray, P.R.; Derksen, F.J.; Robinson, N.E.; Peter-Golden, M.L. (Michigan State Univ., East Lansing (United States) Univ. of Michigan, Ann Arbor (United States))

    1990-02-26

    Arachidonic acid metabolism by tracheal epithelium can be studied using enzymatically dispersed cell suspensions or cell cultures. Both techniques require considerable tissue disruption and manipulation and may not accurately represent in vivo activity. The authors have developed an alternate method for obtaining strips of equine tracheal epithelium without enzymatic digestion. In the horse, a prominent elastic lamina supports the tracheal epithelium. By physical splitting this lamina, they obtained strips ({le}12 x 1.5 cm) of pseudostratified columnar epithelium attached to a layer of elastic tissue 30-100 {mu}m thick. Epithelial strips (1.2 x 0.5 cm) were attached to plexiglass rods and incubated with ({sup 3}H)arachidonic acid in M199 medium (0.5 {mu}Ci/ml) for 24 hours at 37C. The strips incorporated 36{+-}4% (mean {+-} SEM) of the total radioactivity and released 8.0{+-}1.2% of incorporated radioactivity when stimulated by 5.0 {mu}M calcium ionophore A23187. The extracted supernatant was processed using HPLC, resulting in peaks of radioactivity that co-eluted with authentic PGE{sub 2}, PGF{sub 2}{alpha}, and 12-HETE standards. The greatest activity corresponded to the PGE{sub 2} and PGF{sub 2}{alpha} standards, which is a similar pattern to that reported for cultured human tracheal epithelium.

  11. The viability of alternative assessment methods in the Greek upper secondary school: the oral portfolio

    Directory of Open Access Journals (Sweden)

    Angeliki Daphni

    2012-02-01

    Full Text Available Τhe final examination of the English language subject, in the context of the Greek state upper secondary education, is a traditional paper-and-pencil test which does not include any assessment of oracy skills. This article explores the viability of the oral portfolio as an alternative assessment and pedagogic method that can facilitate the assessment of speaking and listening skills and create a more motivating learning environment. To this effect, three methodological tools were designed, namely, a questionnaire addressing upper secondary English teachers in Greek state schools, a case study involving an oral portfolio implementation and finally, a questionnaire for students to record their experience. The study demonstrates that implementation of the portfolio contributed to a successful assessment of oracy skills and that it was a stimulating experience for students. The results of the study also showed that the pedagogical value of the portfolio counterbalanced its practical constraints. The paper concludes by putting forward recommendations for the future application of this assessment technique in state school education.

  12. Support vector machine as an alternative method for lithology classification of crystalline rocks

    Science.gov (United States)

    Deng, Chengxiang; Pan, Heping; Fang, Sinan; Amara Konaté, Ahmed; Qin, Ruidong

    2017-03-01

    With the expansion of machine learning algorithms, automatic lithology classification that uses well logging data is becoming significant in formation evaluation and reservoir characterization. In fact, the complicated composition and structural variations of metamorphic rocks result in more nonlinear features in well logging data and elevate requirements to algorithms. Herein, the application of the support vector machine (SVM) in classifying crystalline rocks from Chinese Continental Scientific Drilling Main Hole (CCSD-MH) data was reported. We found that the SVM performs poorly on the lithology classification of crystalline rocks when training samples are imbalanced. The fact is that training samples are generally limited and imbalanced as cores cannot be obtained balanced and at 100 percent. In this paper, we introduced the synthetic minority over-sampling technique (SMOTE) and Borderline-SMOTE to deal with imbalanced data. After experiments generating different quantities of training samples by SMOTE and Borderline-SMOTE, the most suitable classifier was selected to overcome the disadvantage of the SVM. Then, the popular supervised classifier back-propagation neural networks (BPNN), which has been proved competent for lithology classification of crystalline rocks in previous studies, was compared to evaluate the performance of the SVM. Results show that Borderline-SMOTE can improve the SVM with substantially increased accuracy even for minority classes in a reasonable manner, while the SVM outperforms BPNN in aspects of lithology prediction and CCSD-MH data generalization. We demonstrate the potential of the SVM as an alternative to current methods for lithology identification of crystalline rocks.

  13. An Alternative Method of Spatial Autocorrelation for Chlorophyll Detection in Water Bodies Using Remote Sensing

    Directory of Open Access Journals (Sweden)

    Tainá T. Guimarães

    2017-03-01

    Full Text Available Additional measures of in situ water quality monitoring in natural environments can be obtained through remote sensing because certain elements in water modify its spectral behavior. One of the indicators of water quality is the presence of algae, and the aim of this study was to propose an alternative method for the quantification of chlorophyll in water by correlating spectral data, infrared images, and limnology data. The object of study was an artificial lake located at Unisinos University, São Leopoldo/RS, Brazil. The area has been mapped with a modified NGB (near infrared (N, green (G and blue (B camera coupled to an unmanned aerial vehicle (UAV. From the orthorectified and georeferenced images, a modified normalized difference vegetation index (NDVImod image has been generated. Additionally, 20 sampling points have been established on the lake. At these points, in situ spectral analysis with a spectroradiometer has been performed, and water samples have been collected for laboratory determination of chlorophyll concentrations. The correlation resulted in two models. The first model, based on the multivariate analysis of spectral data, and the second model, based on polynomial equations from NDVI, had coefficients of determination (R2 of 0.86 and 0.51, respectively. This study confirmed the applicability of remote sensing for water resource management using UAVs, which can be characterized as a quick and easy methodology.

  14. Hepatotoxic microcystin removal using pumice embedded monolithic composite cryogel as an alternative water treatment method.

    Science.gov (United States)

    Gurbuz, Fatma; Ceylan, Şeyda; Odabaşı, Mehmet; Codd, Geoffrey A

    2016-03-01

    Microcystins are the most commonly encountered water-borne cyanotoxins which present short- and long-term risks to human health. Guidelines at international and national level, and legislation in some countries, have been introduced for the effective health risk management of these potent hepatotoxic, tumour-promoters. The stable cyclic structure of microcystins and their common production by cyanobacteria in waterbodies at times of high total dissolved organic carbon content presents challenges to drinking water treatment facilities, with conventional, advanced and novel strategies under evaluation. Here, we have studied the removal of microcystins using three different forms of pumice particles (PPs), which are embedded into macroporous cryogel columns. Macroporous composite cryogel columns (MCCs) are a new generation of separation media designed to face this challenging task. Three different MCCs were prepared by adding plain PPs, Cu(2+)-attached PPs and Fe(3+)-attached PPs to reaction media before the cryogelation step. Column studies showed that MCCs could be successfully used as an alternative water treatment method for successful microcystin removal.

  15. a Study on the Alternative Technology Using Unsm Instead of the Presetting Method for Torsion Bar

    Science.gov (United States)

    Suh, Chang-Min; Kim, Min-Ho; Baek, Un-Bong; Pyoun, Young-Sik; Kim, Chang-Sik; Chi, Chong-Ho

    The torsion bar must be changed periodically due to its lack of durability and a phenomenon related to stress relaxation. Therefore technical development regarding the torsion bar's durability is urgently needed. In order to improve the fatigue life and durability of the dynamic components, new surface treatment technology such as ultrasonic shot peening, deep rolling, laser shock peening, etc. are developing widely. In this study, Ultrasonic Nanocrystal Surface Modification (UNSM) technology is applied as an advanced one to replace the presetting method (PM). UNSM and PM technology also induced the compressive residual stress on the surface layer of the torsion bar, which is the main improvement factor of fatigue life. DIN17221 material as a new MIL specification of torsion bar and SCM440 (as an alternative one to a old MIL-DTL-62567C) were processed with the UNSM technology to obtain the basic data and compare it between two, and then torsion fatigue tests of two materials were carried out to obtain the characteristics of torsion fatigue in this study.

  16. Alternative Methods of Classifying Eating Disorders: Models Incorporating Comorbid Psychopathology and Associated Features

    Science.gov (United States)

    Wildes, Jennifer E.; Marcus, Marsha D.

    2013-01-01

    There is increasing recognition of the limitations of current approaches to psychiatric classification. Nowhere is this more apparent than in the eating disorders (EDs). Several alternative methods of classifying EDs have been proposed, which can be divided into two major groups: 1) those that have classified individuals on the basis of disordered eating symptoms; and, 2) those that have classified individuals on the basis of comorbid psychopathology and associated features. Several reviews have addressed symptom-based approaches to ED classification, but we are aware of no paper that has critically examined comorbidity-based systems. Thus, in this paper, we review models of classifying EDs that incorporate information about comorbid psychopathology and associated features. Early approaches are described first, followed by more recent scholarly contributions to comorbidity-based ED classification. Importantly, several areas of overlap among the classification schemes are identified that may have implications for future research. In particular, we note similarities between early models and newer studies in the salience of impulsivity, compulsivity, distress, and inhibition versus risk taking. Finally, we close with directions for future work, with an emphasis on neurobiologically-informed research to elucidate basic behavioral and neuropsychological correlates of comorbidity-based ED classes, as well as implications for treatment. PMID:23416343

  17. Skills based evaluation of alternative input methods to command a semi-autonomous electric wheelchair.

    Science.gov (United States)

    Rojas, Mario; Ponce, Pedro; Molina, Arturo

    2016-08-01

    This paper presents the evaluation, under standardized metrics, of alternative input methods to steer and maneuver a semi-autonomous electric wheelchair. The Human-Machine Interface (HMI), which includes a virtual joystick, head movements and speech recognition controls, was designed to facilitate mobility skills for severely disabled people. Thirteen tasks, which are common to all the wheelchair users, were attempted five times by controlling it with the virtual joystick and the hands-free interfaces in different areas for disabled and non-disabled people. Even though the prototype has an intelligent navigation control, based on fuzzy logic and ultrasonic sensors, the evaluation was done without assistance. The scored values showed that both controls, the head movements and the virtual joystick have similar capabilities, 92.3% and 100%, respectively. However, the 54.6% capacity score obtained for the speech control interface indicates the needs of the navigation assistance to accomplish some of the goals. Furthermore, the evaluation time indicates those skills which require more user's training with the interface and specifications to improve the total performance of the wheelchair.

  18. Gene expression in human skeletal muscle: alternative normalization method and effect of repeated biopsies.

    Science.gov (United States)

    Lundby, Carsten; Nordsborg, Nikolai; Kusuhara, Keiko; Kristensen, Kristina Møller; Neufer, P Darrell; Pilegaard, Henriette

    2005-10-01

    The reverse transcriptase-polymerase chain reaction (RT-PCR) method has lately become widely used to determine transcription and mRNA content in rodent and human muscle samples. However, the common use of endogenous controls for correcting for variance in cDNA between samples is not optimal. Specifically, we investigated (1) a new normalization method based on determining the cDNA content by the flourophores PicoGreen and OliGreen, (2) effect of repeated muscle biopsies on mRNA gene expression, and (3) the spatial heterogeneity in mRNA expression across the muscle. Standard curves using oligo standards revealed a high degree of sensitivity and linearity (2.5-45 ng; R2>0.99) with OliGreen reagent, as was the case for OliGreen analyses with standard curves constructed from serial dilutions of representative RT samples (R2 >0.99 for a ten times dilution range of a representative reversed transcribed (RT) sample). Likewise, PicoGreen reagent detected the RNA:DNA hybrid content in RT samples with great sensitivity. Standard curves constructed from both double-stranded lambda DNA (1-10 ng) and from serial dilutions of representative RT samples consistently resulted in linearity with R2 >0.99. The present determination of cDNA content in reversed transcribed human skeletal muscle RNA samples by both PicoGreen and OliGreen analyses suggests that these fluorophores provide a potential alternative normalization procedure for human gene expression studies. In addition, the present study shows that multiple muscle biopsies obtained from the same muscle do not influence the mRNA response induced by an acute exercise bout for any of the genes examined.

  19. HIPPOTHERAPY SIMULATOR AS ALTERNATIVE METHOD FOR HIPPOTHERAPY TREATMENT IN HEMIPLEGIC CHILDREN

    Directory of Open Access Journals (Sweden)

    Mohamed Ali Elshafey

    2014-04-01

    Full Text Available Background: Hippotherapy considered as worldwide techniques used in rehabilitation of children with neurological disorders as it improved gait pattern, balance, postural control, strengthen, range of motion and gross and fine motor skills development but it encounter some technical problems. Purpose: The purpose of the current study was to compare between hippotherapy and hippotherapy simulators effect on back geometry and balance in hemiplegic children. Materials and Methods: Thirty ambulant hemiplegic children, their age ranges from four to six years old participated in this study. They were randomly divided into two matched groups (control and study. The control group treated with hippotherapy for half hour in addition to the selected physical therapy program, while the study group treated with hippotherapy simulators for half hour in addition to the selected physical therapy program also. All children received the treatment three times weekly for three successive months. Spinal geometry were evaluated by Formatric instrumentation systems and balance were evaluated by pediatric balance scale before and after treatment Results: There was significant improvement in all the measured variables for both groups after comparing of their pre and post-treatment mean values with non-significant difference between both groups post treatment. Conclusion: Hippotherapy simulators is an alternative method for hippotherapy could be used for modulation of back geometry and for improving balance in hemiplegic children. Brief summary and potential implication: Hippotherapy simulator was used in treatment of back geometry and balance in hemiplegic children, all the measurements were compared with hippotherapy. The results were nearly the same in both groups.

  20. Alternative Therapeutic Method for Type Two Diabetes: Whole Body Vibration Therapy: A Mini-Review

    Directory of Open Access Journals (Sweden)

    Erika L Simmerman

    2016-05-01

    Full Text Available Context As the prevalence of obesity and diabetes continues to increase there is a need for new interventions to control this epidemic. Multiple alternative treatment methods exist for type 2 diabetes mellitus such as acupuncture, bariatric surgery, yoga, aromatherapy, herbal remedies, etc. Whole Body Vibration is a relatively new area of interest recently utilized as an adjunctive therapy in type 2 diabetes mellitus, representing a potentially new and novel treatment for type 2 diabetes mellitus. Objective The primary objective of this study was to summarize current literature regarding the effects of whole body vibration on type 2 diabetes mellitus. This review details the effect of whole body vibration on areas of high clinical impact in the treatment of type 2 diabetes mellitus such as glycemic control, body composition, renal function, inflammatory indices, peripheral neuropathy, and wound healing. Methods Reviewers independently screened abstracts and full texts in journal articles and books to extract data from multiple studies and literature to compile a current review on the topic of whole body vibration and diabetes mellitus. Results Current literature in murine and human models reported an overall improvement in glycemic control, renal function, inflammatory indices, and peripheral neuropathy following whole body vibration therapy. Whole body vibration effect on body mass composition is controversial with inconsistent reports of the effect on lean mass, bone density, and fat mass. Conclusions Whole body vibration has demonstrated significant promise in improving multiple systems related to the sequela of type 2 diabetes mellitus, thereby suggesting a new and novel treatment modification in this patient population. Subsequent studies are needed to further analyze the effect of whole body vibration on type 2 diabetes mellitus.

  1. Detection of Leptospira spp. in wildlife reservoir hosts in Ontario through comparison of immunohistochemical and polymerase chain reaction genotyping methods.

    Science.gov (United States)

    Shearer, Karen E; Harte, Michael J; Ojkic, Davor; Delay, Josepha; Campbell, Douglas

    2014-03-01

    A total of 460 kidney samples from wildlife (beavers, coyotes, deer, foxes, opossums, otters, raccoons, skunks) were obtained from road-kill and hunter/trapper donations in Ontario between January 2010 and November 2012. The objectives of the study were to detect Leptospira spp. by immunohistochemistry and polymerase chain reaction (PCR), to map presence of leptospires in wildlife relative to livestock and human populations, and to characterize positive samples by sequencing and comparison to leptospires known to affect domestic animals and humans. The proportion of samples that tested positive ranged from 0% to 42%, with the highest rates in skunks and raccoons. Leptospira spp. were present in kidneys of wildlife across Ontario, particularly in areas of high human density, and areas in which livestock populations are abundant. The PCR was too weak in most samples to permit genotyping and examination of the relationship between the leptospires found in this study and those affecting domestic animals and humans.

  2. Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples

    Science.gov (United States)

    Psifidi, Androniki; Dovas, Chrysostomos I.; Bramis, Georgios; Lazou, Thomai; Russel, Claire L.; Arsenos, Georgios; Banos, Georgios

    2015-01-01

    Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals. PMID:25635817

  3. Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples.

    Science.gov (United States)

    Psifidi, Androniki; Dovas, Chrysostomos I; Bramis, Georgios; Lazou, Thomai; Russel, Claire L; Arsenos, Georgios; Banos, Georgios

    2015-01-01

    Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.

  4. Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples.

    Directory of Open Access Journals (Sweden)

    Androniki Psifidi

    Full Text Available Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.

  5. Friction stir welding - an alternative method for sealing nuclear waste storage canisters

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, R.E. [TWI Ltd, Cambridge (United Kingdom)

    2004-12-01

    When welding 50 mm thick copper a very high heat input is required to combat the high thermal diffusivity and only the Electron Beam Welding (EBW) process had this capability when this copper canister concept was conceived. Despite the encouraging results achieved using EBW with thick section copper, SKB felt that it would be prudent to assess other joining methods. This assessment concluded that friction welding, could also provide very high quality welds to satisfy the service life requirements of the SKB canister design. A friction welding variant called Friction Stir Welding (FSW) was shown to have the capability of welding 3 mm thick copper sheet with excellent integrity and reproducibility. This later provided sufficient encouragement for SKB to consider the potential of FSW as a method for joining thick section copper, using relatively simple machine tool based technology. It was thought that FSW might provide an alternative or complementary method for welding lids, or bases to canisters. In 1997 an FSW development programme started at TWI, focussed on the feasibility of welding 10 mm thick copper plate. Once this task was successfully completed, work continued to demonstrate that progressively thicker plate, up to 50 mm thick, could be joined. At this stage, with process viability established, a full size experimental FSW canister machine was designed and built. Work with this machine finished in January 2003, when it had been shown that FSW could definitely be used to weld lids to full size canisters. This report summarises the TWI development of FSW for SKB from 1997 to January 2003. It also highlights the important aspects of the process and the project milestones that will help to ensure that SKB has a welding technology that can be used with confidence for production fabrication of copper waste storage canisters in the future. The overall conclusion to this FSW development is that there is no doubt that the FSW process could be used to produce full

  6. An alternant method to the traditional NASA hindlimb unloading model in mice.

    Science.gov (United States)

    Ferreira, J Andries; Crissey, Jacqueline M; Brown, Marybeth

    2011-03-10

    The Morey-Holton hindlimb unloading (HU) method is a widely accepted National Aeronautics and Space Administration (NASA) ground-based model for studying disuse-atrophy in rodents. Our study evaluated an alternant method to the gold-standard Morey-Holton HU tail-traction technique in mice. Fifty-four female mice (4-8 mo.) were HU for 14 days (n=34) or 28 days (n=20). Recovery from HU was assessed after 3 days of normal cage ambulation following HU (n=22). Aged matched mice (n=76) served as weight-bearing controls. Prior to HU a tail ring was formed with a 2-0 sterile surgical steel wire that was passed through the 5(th), 6(th), or 7(th) inter-vertebral disc space and shaped into a ring from which the mice were suspended. Vertebral location for the tail-ring was selected to appropriately balance animal body weight without interfering with defecation. We determined the success of this novel HU technique by assessing body weight before and after HU, degree of soleus atrophy, and adrenal mass following HU. Body weight of the mice prior to HU (24.3 ± 2.9g) did not significantly decline immediately after 14d of HU (22.7 ± 1.9g), 28d of HU (21.3 + 2.1g) or after 3 days recovery (24.0 ± 1.8g). Soleus muscle mass significantly declined (-39.1%, and -46.6%) following HU for 14 days and 28 days respectively (pmaintenance of animal body weight, comparable adrenal gland weights, and soleus atrophy following HU, corresponding to expected literature values. The primary advantages of this HU method include: 1) ease of tail examination during suspension; 2) decreased likelihood of cyanotic, inflamed, and/or necrotic tails frequently observed with tail-taping and HU; 3) no possibility of mice chewing the traction tape and coming out of the suspension apparatus; and 4) rapid recovery and normal cage activity immediately after HU.

  7. Protocol: An improved high-throughput method for generating tissue samples in 96-well format for plant genotyping (Ice-Cap 2.0

    Directory of Open Access Journals (Sweden)

    Krysan Patrick J

    2007-06-01

    Full Text Available Abstract Background We previously developed a high-throughput system called 'Ice-Cap' for growing Arabidopsis seedlings in a 96-well format and rapidly collecting tissue for subsequent DNA extraction and genotyping. While the originally described Ice-Cap method is an effective tool for high-throughput genotyping, one shortcoming of the first version of Ice-Cap is that optimal seedling growth is highly dependent on specific environmental conditions. Here we describe several technical improvements to the Ice-Cap method that make it much more robust and provide a detailed protocol for implementing the method. Results The key innovation underlying Ice-Cap 2.0 is the development of a continuous watering system. The addition of the watering system allows the seedling growth plates to be incubated without a lid for the duration of the growth period, which in turn allows for much more uniform and robust seedling growth than was observed using the original method. We also determined that inserting wooden skewers between the upper and lower plates prior to tissue harvest made it easier to separate the plates following freezing. Seedlings grown using the Ice-Cap 2.0 method remain viable in the Ice-Cap plates twice as long as seedlings grown using the original method. Conclusion The continuous watering system that we have developed provides an effective solution to the problem of sub-optimal seedling growth that can be encountered when using the originally described Ice-Cap system. This novel watering system and several additional modifications to the Ice-Cap procedure have improved the robustness and utility of the method.

  8. "Tectonic Petrameter," An Alternative Method to Teaching the Geologic Time Scale

    Science.gov (United States)

    Posner, E. S.

    2011-12-01

    I have over a decade of experience as a performance poet and am now a graduate student in the geosciences. I have created a performance poem / play script, "Tectonic Petrameter," as an alternative method of teaching the geologic time scale. "The Archean came next and it was a blast. Tectonic plates were smaller and they moved pretty fast. In an enthusiastic flash of ash, volcanic islands smashed together." The use of rhyme and rhythm presents a different and interdisciplinary approach to teaching Earth history that appeals to a wide range of learning styles and makes science fun, while clearly describing important concepts in geology and events in Earth history. "Now it's time to get down with the Coal Swamp Stomp! Tap your feet to the beat of the formation of peat like a plant plantation soaking up the bright heat." "Tectonic Petrameter" by itself is an illustrated spoken-word poem that leads audiences from all levels of scientific background on an excitingly educational journey through geologic time. I will perform my 10-minute memorized poem and present results from my ongoing study to assess the effectiveness of "Tectonic Petrameter" as a teaching tool in K-12 and introductory undergraduate classroom curricula. I propose that using "Tectonic Petrameter" as a performance piece and theatrical play script in K-12 and introductory undergraduate classrooms, as well as in broader community venues, may be an avenue for breaking down barriers related to teaching about Earth's long and complex history. Digital copies of "Tectonic Petrameter" will be made available to interested parties.

  9. Alternative Process Flow for Underground Mining Operations: Analysis of Conceptual Transport Methods Using Discrete Event Simulation

    Directory of Open Access Journals (Sweden)

    Jenny Greberg

    2016-06-01

    Full Text Available As the near surface deposits are being mined out, underground mines will increasingly operate at greater depths. This will increase the challenges related to transporting materials from deeper levels to the surface. For many years, the ore and waste transportation from most deep underground mines has depended on some or all of the following: truck haulage, conveyor belts, shafts, rails, and ore pass systems. In sub-level caving, and where ore passes are used, trains operating on the main lower level transport the ore from ore passes to a crusher, for subsequent hoisting to the surface through the shaft system. In many mines, the use of the ore pass system has led to several problems related to the ore pass availability, causing production disturbances and incurred cost and time for ore pass rehabilitation. These production disturbances have an impact on the mining activities since they increase the operational costs, and lower the mine throughput. A continued dependency on rock mass transportation using ore passes will generate high capital costs for various supporting structures such as rail tracks, shaft extensions, and crushers for every new main level. This study was conducted at an existing underground mine and analyzed the transport of ore from loading areas at the lower levels up to the existing shaft points using trucks without employing ore passes. The results show that, when the costs of extending ore passes to lower levels become too great or ore passes cannot be used for production, haul trucks can be a feasible alternative method for transport of ore and waste up the ramp to the existing crusher located at the previous main level. The use of trucks will avoid installing infrastructure at the next main level and extending the ore passes to lower levels, hence reducing costs.

  10. Earnings Management of Firms Reporting Long Term Debt: An Alternative Method

    Directory of Open Access Journals (Sweden)

    Yulius Jogi Christiawan

    2014-01-01

    Full Text Available This study aims to apply an alternative detection model to prove that the earnings management will be occured when a company has long-term debts as well as the pressure of operating income. Generally, the literature study of earnings management indicates that the detection of earnings management can be grouped into two objectives, 1] to find variables for detecting earnings management (accruals, real activity and classification shifting and 2] to use some advanced statistical or mathematical models to detect earnings management. This study applies a quantitative approach using secondary data of financial statements. The study was conducted on 50 companies with the largest market capitalization, 50 of the most active companies based on trading volume, 50 of the most active companies based on the value of trade and 50 of the most active companies by frequency trading. All of them are 200  public company (listed in the Indonesia Stock Exchange-ID based on IDX statistical report 2013. The results of this study are expected to provide a new method to detect earnings management and its application in the context of positive accounting theory (PAT. The results of the study proves that the model is able to detect earnings management by utilizing foreign exchange transaction losses and use these models to support PAT (particularly on debt covenant hypothesis. These results contribute that earnings management can be done by using the foreign exchange gain / loss. However, the limitation of this study is the model has not been able to capture the phenomenon of earnings management if a company does not report any long-term debt nor foreign exchange gain/ loss.

  11. Establishment of alternative culture method for spermatogonial stem cells using knockout serum replacement.

    Directory of Open Access Journals (Sweden)

    Keisuke Aoshima

    Full Text Available Since spermatogonial stem cells (SSCs are capable of both self-renewal and differentiation to daughter cells for subsequent spermatogenesis, the development of an efficient in vitro culture system is essential for studies related to spermatogenesis. Although the currently available system is serum-free and contains only chemically-defined components, it highly relies upon bovine serum albumin (BSA, a component with batch-to-batch quality variations similar to those of fetal bovine serum. Thus, we searched for an alternative BSA-free culture system that preserved the properties of SSCs. In this study, we utilized Knockout Serum Replacement (KSR in the SSC culture medium, as a substitute for BSA. The results demonstrated that KSR supported the continuous growth of SSCs in vitro and the SSC activity in vivo without BSA, in a feeder-cell combination with mouse embryonic fibroblasts. The addition of BSA to KSR further facilitated cell cycle progression, whereas a transplantation assay revealed that the addition of BSA did not affect the number of SSCs in vivo. The combination of KSR with BSA also allowed the elimination of GFRA1 and FGF2, and the reduction of the GDNF concentration from 20 ng/ml to 5 ng/ml, while maintaining the growth rate and the expression of SSC markers. Furthermore, KSR was also useful with SSCs from non-DBA/2 strains, such as C57BL/6 and ICR. These results suggested that KSR is an effective substitute for BSA for long-term in vitro cultures of SSCs. Therefore, this method is practical for various studies related to SSCs, including spermatogenesis and germ stem cell biology.

  12. Growth hormone genotyping by MspI restriction enzyme and PCR-RFLP method in Aceh cattle breed at Indrapuri District, Aceh Province, Indonesia

    Directory of Open Access Journals (Sweden)

    WIDYA PINTAKA BAYU PUTRA

    2014-04-01

    Full Text Available Putra WPB, Hartatik T, Sumadi. 2014. Growth hormone genotyping by MspI restriction enzyme and PCR-RFLP method in Aceh cattle breed at Indrapuri District, Aceh Province, Indonesia. Biodiversitas 15: 1-5. The objective of this research was to identify growth hormone (GH gene in Aceh cattle at Indrapuri’s Breeding and Forage Centre (IBFC of Aceh Cattle. Fourty one cattle consisting of 21 male and 20 female cattle were used in this study. Polymerase Chain Reaction (PCR - Restriction Fragment Length Polymorphism (RFLP and sequencing method was used to detect MspI site on GH gene. Based on the sequencing, it can be concluded that all cattle were monomorphic. The frequency of TT genotype and T allele were 1.00 relatively. The transition of C (cytosine into T (thymine on 1549 position caused the lost of restriction site. The insertion of T and G (guanine on 1542 and 1552 position caused the length of GH gene were 329 bp in Aceh cattle.

  13. Genotypic difference in canopy diffusive conductance measured by a new remote-sensing method and its association with the difference in rice yield potential.

    Science.gov (United States)

    Horie, Takeshi; Matsuura, Shoji; Takai, Toshiyuki; Kuwasaki, Kouhei; Ohsumi, Akihiro; Shiraiwa, Tatsuhiko

    2006-04-01

    There have been few practical ways of measuring physiological determinants of rice yield. Rapid evaluation of yield determination traits may expedite breeding of high-yielding rice. Here, we report a new remote-sensing technique for the evaluation of canopy ecophysiological status under field conditions developed based on simultaneous measurements of sunlit and suddenly shaded canopy temperatures. This technique has the advantage of instantaneous estimation of aerodynamic resistance (r(a)) and canopy diffusive resistance (r(c) without measuring wind velocity. Canopy diffusive conductance (1 / r(c)) estimated by the remote sensing method was closely related to leaf stomatal conductance (g(s)) measured with a portable gas exchange system. This result supported the validity of this new method for quantitative estimation of canopy physiological characteristics. Significant genotypic differences were obtained in canopy-air temperature difference (Tc-Ta), r(c) and 1 / r(c) during the 2-week period preceding full heading for two years, and 1 / r(c) was highly correlated with crop growth rate (CGR), which was closely related to the final yield. These results suggest that 1 / r(c) can be an effective criterion for the selection of high-yielding rice genotypes, and the remote sensing technique proposed here can be a powerful tool for the rapid evaluation of 1 / r(c) under field conditions.

  14. An alternative method for calibration of narrow band radiometer using a radiative transfer model

    Energy Technology Data Exchange (ETDEWEB)

    Salvador, J; Wolfram, E; D' Elia, R [Centro de Investigaciones en Laseres y Aplicaciones, CEILAP (CITEFA-CONICET), Juan B. de La Salle 4397 (B1603ALO), Villa Martelli, Buenos Aires (Argentina); Zamorano, F; Casiccia, C [Laboratorio de Ozono y Radiacion UV, Universidad de Magallanes, Punta Arenas (Chile) (Chile); Rosales, A [Universidad Nacional de la Patagonia San Juan Bosco, UNPSJB, Facultad de Ingenieria, Trelew (Argentina) (Argentina); Quel, E, E-mail: jsalvador@citefa.gov.ar [Universidad Nacional de la Patagonia Austral, Unidad Academica Rio Gallegos Avda. Lisandro de la Torre 1070 ciudad de Rio Gallegos-Sta Cruz (Argentina) (Argentina)

    2011-01-01

    city of Punta Arenas, Chile using the sun as a source. These results show us that the proposed method is a viable alternative for developing countries that use instrumentation of this type and find it difficult to apply calibration programs on a regular basis.

  15. Analysis of an alternative method for the study of bromeliad-associated fauna in plants with different foliar organization.

    Science.gov (United States)

    Müller, Gerson A; Name, Fernando T; Pacheco, Frederico C L; Marcondes, Carlos B

    2010-12-01

    The efficiency of an alternative method of collection (by suction of water) for the study of Culicidae and Chironomidae (Diptera), Scirtidae (Coleoptera) and Coenagrionidae (Odonata) in bromeliads with different foliar architecture in a restinga at Florianópolis, SC, Brazil, was studied. The alternative method was less efficient to collect Culicidae and Chironomidae (Wilcoxon test p 0.05) from Aechmea lindenii. This method was less efficient to collect insects of all groups from Vriesea friburgensis (Wilcoxon test p insects in both species of bromeliads. The higher mobility of immature forms of beetles and dragonflies, and the availability of only one tank in Aechea lindenii, contrasting to several tanks in Vriesea friburgensis that help the suction of these immature, probably influenced the results, which indicated that the suction method should not replace the dismantling in the study of Culicidae and Chironomidae. This method can be useful to get immature forms of Scirtidae and Coenagrionidae in one-tank bromeliads.

  16. Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data.

    Science.gov (United States)

    Kogelman, Lisette J A; Kadarmideen, Haja N

    2014-01-01

    High-throughput genotype (HTG) data has been used primarily in genome-wide association (GWA) studies; however, GWA results explain only a limited part of the complete genetic variation of traits. In systems genetics, network approaches have been shown to be able to identify pathways and their underlying causal genes to unravel the biological and genetic background of complex diseases and traits, e.g., the Weighted Gene Co-expression Network Analysis (WGCNA) method based on microarray gene expression data. The main objective of this study was to develop a scale-free weighted genetic interaction network method using whole genome HTG data in order to detect biologically relevant pathways and potential genetic biomarkers for complex diseases and traits. We developed the Weighted Interaction SNP Hub (WISH) network method that uses HTG data to detect genome-wide interactions between single nucleotide polymorphism (SNPs) and its relationship with complex traits. Data dimensionality reduction was achieved by selecting SNPs based on its: 1) degree of genome-wide significance and 2) degree of genetic variation in a population. Network construction was based on pairwise Pearson's correlation between SNP genotypes or the epistatic interaction effect between SNP pairs. To identify modules the Topological Overlap Measure (TOM) was calculated, reflecting the degree of overlap in shared neighbours between SNP pairs. Modules, clusters of highly interconnected SNPs, were defined using a tree-cutting algorithm on the SNP dendrogram created from the dissimilarity TOM (1-TOM). Modules were selected for functional annotation based on their association with the trait of interest, defined by the Genome-wide Module Association Test (GMAT). We successfully tested the established WISH network method using simulated and real SNP interaction data and GWA study results for carcass weight in a pig resource population; this resulted in detecting modules and key functional and biological pathways

  17. Exploring alternative wind vulnerability and loss modeling methods - application to Europe extra-tropical cyclones

    Science.gov (United States)

    Peiris, N.

    2009-04-01

    Catastrophe models are used to assess the economic and insured loss to the built environment due to natural hazards such as earthquakes, windstorms, floods, storm surges, tsunamis, etc. A conventional catastrophe model estimating direct economic loss could be divided into three basic components; hazard, vulnerability and exposure. For a single event, the hazard component represents the best estimate realization of the hazard footprint over a region at the modeling resolution, i.e. variable grid, postalcode, cresta, etc. The vulnerability component represents the response of the buildings or any modeled structure to the hazard, quantified in terms of a loss ratio. The exposure component represents the value of the buildings in a portfolio covering a region or those underwritten by an insurer or a re-insurer. The exposure together with the vulnerability functions produces the expected economic loss of the hazard footprint for a given hazard event. In the case of estimating indirect economic losses and insured losses financial models are utilized with various financial structures applied on the economic loss estimates. The commonly used method of characterizing wind vulnerability of buildings is to develop functions of mean loss ratio or mean damage ratio (MDR) vs wind speed where the wind speed is often defined as the peak gust measured at a height of 10m above the ground elevation. The uncertainty associated with MDR due to the likelihood of the building experiencing a range of damage states and hence loss ratios at a given wind speed is quantified by a continuous statistical distribution with a mean (which is the MDR) and a standard deviation, SD. For a given event footprint a conventional catastrophe model calculates an MDR and associated SD for each location of a building portfolio. This together with the location exposure or insured value results in the location loss. The location losses are then aggregated together with their SDs to obtain the total expected

  18. How can we improve crop genotypes to increase stress resilience and productivity in a future climate? A new crop screening method based on productivity and resistance to abiotic stress

    Science.gov (United States)

    Thiry, Arnauld A.; Chavez Dulanto, Perla N.; Reynolds, Matthew P.; Davies, William J.

    2016-01-01

    The need to accelerate the selection of crop genotypes that are both resistant to and productive under abiotic stress is enhanced by global warming and the increase in demand for food by a growing world population. In this paper, we propose a new method for evaluation of wheat genotypes in terms of their resilience to stress and their production capacity. The method quantifies the components of a new index related to yield under abiotic stress based on previously developed stress indices, namely the stress susceptibility index, the stress tolerance index, the mean production index, the geometric mean production index, and the tolerance index, which were created originally to evaluate drought adaptation. The method, based on a scoring scale, offers simple and easy visualization and identification of resilient, productive and/or contrasting genotypes according to grain yield. This new selection method could help breeders and researchers by defining clear and strong criteria to identify genotypes with high resilience and high productivity and provide a clear visualization of contrasts in terms of grain yield production under stress. It is also expected that this methodology will reduce the time required for first selection and the number of first-selected genotypes for further evaluation by breeders and provide a basis for appropriate comparisons of genotypes that would help reveal the biology behind high stress productivity of crops. PMID:27677299

  19. Treatment for chronic daily headache by using auxiliary and alternative methods

    Directory of Open Access Journals (Sweden)

    V. A. Golovacheva

    2015-01-01

    Full Text Available Chronic daily headache (CDH is one of the top 10 causes of adult disability and one of the 5 most common causes of female disability. To treat patients with CDH is one of the most difficult tasks in neurological practice. Difficulties in managing patients with CHD are associated with the high prevalence of comorbid mental disorders, analgesic abuse, pain syndromes at another site, and misconceptions of a patient about his/her disease. A combination of drug and non-drug therapies is the mainstay of the current approach to treating patients with CDH. Standard, alternative, and auxiliary therapies are identified. The paper describes different types of current auxiliary and alternative therapy used in the world’s leading headache centers and clinics. It describes experience with cerebrolysin used as auxiliary and alternative pharmacotherapies for CDH.

  20. EURL ECVAM Status Report on the Development, Validation and Regulatory Acceptance of Alternative Methods and Approaches (2016)

    OpenAIRE

    ZUANG Valerie; ASTURIOL BOFILL DAVID; VIEGAS BARROSO JOAO FILIPE; BELZ SUSANNE; BERGGREN ELISABET; Bernasconi, Camilla; BOPP Stephanie; BOSTROEM Ann-Charlotte; BOUHIFD Mounir; Casati, Silvia; Coecke, Sandra; Cole, Thomas; Corvi, Raffaella; HALDER MARIA ELISABETH; HOLLEY TRACEY

    2016-01-01

    Replacement, Reduction and Refinement of animal testing is anchored in EU legislation. Alternative non-animal approaches facilitate a shift away from animal testing. Cell-based methods and computational technologies are integrated to translate molecular mechanistic understanding of toxicity into safety testing strategies.

  1. Pre-Service Mathematics Teachers' Views on the Use of Portfolios in Their Education as an Alternative Assessment Method

    Science.gov (United States)

    Birgin, Osman

    2011-01-01

    The purpose of this study was to ascertain the views of pre-service mathematics (PSM) teachers on the use of portfolios as an alternative assessment method. This study was conducted with 146 Turkish PSM teachers participating in a semester-long portfolio assessment application. Data were collected with a questionnaire comprising 34 items on a…

  2. 29 CFR 2520.104-23 - Alternative method of compliance for pension plans for certain selected employees.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Alternative method of compliance for pension plans for... pension plans for certain selected employees. (a) Purpose and scope. (1) This section contains an... Employee Retirement Income Security Act of 1974 for unfunded or insured pension plans maintained by an...

  3. 29 CFR 2520.104-27 - Alternative method of compliance for certain unfunded dues financed pension plans maintained by...

    Science.gov (United States)

    2010-07-01

    ... financed pension plans maintained by employee organizations. 2520.104-27 Section 2520.104-27 Labor... Alternative method of compliance for certain unfunded dues financed pension plans maintained by employee organizations. (a) Scope. Under the authority of section 110 of the Act, a pension benefit plan that meets the...

  4. An Alternate Method for Fourier Transform Infrared (FTIR) Spectroscopic Determination of Soil Nitrate Using Derivative Analysis and Sample Treatments

    NARCIS (Netherlands)

    Choe, E.; Meer, van der F.; Rossiter, D.; Salm, van der C.; Kim, K.W.

    2010-01-01

    This study aimed at examining effective sample treatments and spectral processing for an alternate method of soil nitrate determination using the attenuated total reflectance (ATR) of Fourier transform infrared (FTIR) spectroscopy. Prior to FTIR measurements, soil samples were prepared as paste to e

  5. 49 CFR 375.511 - May I use an alternative method for shipments weighing 3,000 pounds or less?

    Science.gov (United States)

    2010-10-01

    ... weighing 3,000 pounds or less? 375.511 Section 375.511 Transportation Other Regulations Relating to... alternative method for shipments weighing 3,000 pounds or less? For shipments weighing 3,000 pounds or less (1,362 kilograms or less), you may weigh the shipment upon a platform or warehouse certified scale...

  6. SU-E-J-35: Using CBCT as the Alternative Method of Assessing ITV Volume

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Y; Turian, J; Templeton, A; Redler, G; Chu, J [Rush University Medical Center, Chicago, IL (United States)

    2015-06-15

    Purpose To study the accuracy of Internal Target Volumes (ITVs) created on cone beam CT (CBCT) by comparing the visible target volume on CBCT to volumes (GTV, ITV, and PTV) outlined on free breathing (FB) CT and 4DCT. Methods A Quasar Cylindrical Motion Phantom with a 3cm diameter ball (14.14 cc) embedded within a cork insert was set up to simulate respiratory motion with a period of 4 seconds and amplitude of 2cm superioinferiorly and 1cm anterioposteriorly. FBCT and 4DCT images were acquired. A PTV-4D was created on the 4DCT by applying a uniform margin of 5mm to the ITV-CT. PTV-FB was created by applying a margin of the motion range plus 5mm, i.e. total of 1.5cm laterally and 2.5cm superioinferiorly to the GTV outlined on the FBCT. A dynamic conformal arc was planned to treat the PTV-FB with 1mm margin. A CBCT was acquired before the treatment, on which the target was delineated. During the treatment, the position of the target was monitored using the EPID in cine mode. Results ITV-CBCT and ITV-CT were measured to be 56.6 and 62.7cc, respectively, with a Dice Coefficient (DC) of 0.94 and disagreement in center of mass (COM) of 0.59 mm. On the other hand, GTV-FB was 11.47cc, 19% less than the known volume of the ball. PTV-FB and PTV-4D were 149 and 116 cc, with a DC of 0.71. Part of the ITV-CT was not enclosed by the PTV-FB despite the large margin. The cine EPID images have confirmed geometrical misses of the target. Similar under-coverage was observed in one clinical case and captured by the CBCT, where the implanted fiducials moved outside PTV-FB. Conclusion ITV-CBCT is in good agreement with ITV-CT. When 4DCT was not available, CBCT can be an effective alternative in determining and verifying the PTV margin.

  7. Linearized Alternating Direction Method with Adaptive Penalty and Warm Starts for Fast Solving Transform Invariant Low-Rank Textures

    CERN Document Server

    Ren, Xiang

    2012-01-01

    Transform Invariant Low-rank Textures (TILT) is a novel and powerful tool that can effectively rectify a rich class of low-rank textures in 3D scenes from 2D images despite significant deformation and corruption. The existing algorithm for solving TILT is based on the alternating direction method (ADM). It suffers from high computational cost and is not theoretically guaranteed to converge to a correct solution. In this paper, we propose a novel algorithm to speed up solving TILT, with guaranteed convergence. Our method is based on the recently proposed linearized alternating direction method with adaptive penalty (LADMAP). To further reduce computation, warm starts are also introduced to initialize the variables better and cut the cost on singular value decomposition. Extensive experimental results on both synthetic and real data demonstrate that this new algorithm works much more efficiently and robustly than the existing algorithm. It could be at least five times faster than the previous method.

  8. Alternative methods for skin irritation testing: the current status : ECVAM skin irritation task force report 1

    NARCIS (Netherlands)

    Botham, P.A.; Earl, L.K.; Fentem, J.H.; Roguet, R.; Sandt, J.J.M.

    1998-01-01

    The ECVAM Skin Irritation Task Force was established in November 1996, primarily to prepare a report on the current status of the development and validation of alternative tests for skin irritation and corrosion and, in particular, to identify any appropriate non-animal tests for predicting human

  9. 77 FR 61610 - Interagency Coordinating Committee on the Validation of Alternative Methods Evaluation Report and...

    Science.gov (United States)

    2012-10-10

    ... European Union Reference Laboratory for Alternatives to Animal Testing and the Japanese Center for the... equivalent to that provided by current testing procedures, while using up to 50% to 83% fewer animals. ICCVAM... animals used for eye safety testing across U.S. regulatory agencies and international test guidelines. The...

  10. Enzyme-linked immunospot: an alternative method for the detection of interferon gamma in Johne's disease

    DEFF Research Database (Denmark)

    Begg, Douglas J.; de Silva, Kumudika; Bosward, Katrina;

    2009-01-01

    To date, the sensitivity of the interferon gamma (IFN-) enzyme-linked immunosorbent assay (ELISA) to detect Johne's disease (JD) has been poor, especially in the early stages of disease. To improve the sensitivity of IFN- detection in the early stages of infection, an alternate assay needs...

  11. The Correlation Function of Multiple Dependent Poisson Processes Generated by the Alternating Renewal Process Method

    CERN Document Server

    Johnson, Don H

    2008-01-01

    We derive conditions under which alternating renewal processes can be used to construct correlated Poisson processes. The pairwise correlation function is also derived, showing that the resulting correlations can be negative. The technique and the analysis can be extended to the generation of two or more dependent renewal processes.

  12. Alternative methods for skin irritation testing: the current status : ECVAM skin irritation task force report 1

    NARCIS (Netherlands)

    Botham, P.A.; Earl, L.K.; Fentem, J.H.; Roguet, R.; Sandt, J.J.M.

    1998-01-01

    The ECVAM Skin Irritation Task Force was established in November 1996, primarily to prepare a report on the current status of the development and validation of alternative tests for skin irritation and corrosion and, in particular, to identify any appropriate non-animal tests for predicting human sk

  13. Mechanical pipe couplings. The alternative jointing method for PE gas pipes up to 10 bar; Mechanische Rohrkupplungen. Die alternative Verbindung fuer PE-Gas-Rohre bis 10 bar

    Energy Technology Data Exchange (ETDEWEB)

    Kroeger, Axel; Johnson, Alexander [PSI Products GmbH, Moessingen (Germany)

    2010-11-15

    Increasing competition nowadays obliges natural gas suppliers to adopt continuous cost-optimization. Many utilities are therefore rethinking their existing methods for jointing of plastic pipes. Around the world, mechanical pipe couplings are becoming established in this field as a rational-cost, safe and easy-to-install alternative to conventional welding methods. For this project, PSI Products GmbH and Elster Perfection are pursuing new routes for the development of solutions to problems in plastic-pipe jointing technology. As a specialist in accessories for the field of pipeline engineering, PSI Products GmbH has now also unveiled, in the form of the Permasert {sup registered} and PermaLock {sup registered} pipe-coupling and jointing systems, a complete product range, with DVGW approval, for mechanical jointing of gas supply pipelines for the German natural gas market. This system has proven its capabilities since its market launch in the USA more than thirty years ago, and is now one of the world's most widely used mechanical PE-pipe jointing methods. Simple and fast installation is the basis of this success. More than 45 million Permasert {sup registered} couplings and PermaLock {sup registered} tapping valves are now in use under virtually all conceivable climatic and soil conditions, and not only in North America and Europe, but also in Asia, Australia, the Middle East, and Central and South America. (orig.)

  14. State of the art on alternative methods to animal testing from an industrial point of view: ready for regulation?

    Science.gov (United States)

    Ashton, Rachel; De Wever, Bart; Fuchs, Horst W; Gaca, Marianna; Hill, Erin; Krul, Cyrille; Poth, Albrecht; Roggen, Erwin L

    2014-01-01

    Despite changing attitudes towards animal testing and current legislation to protect experimental animals, the rate of animal experiments seems to have changed little in recent years. On May 15-16, 2013, the In Vitro Testing Industrial Platform (IVTIP) held an open meeting to discuss the state of the art in alternative methods, how companies have, can, and will need to adapt and what drives and hinders regulatory acceptance and use. Several key messages arose from the meeting. First, industry and regulatory bodies should not wait for complete suites of alternative tests to become available, but should begin working with methods available right now (e.g., mining of existing animal data to direct future studies, implementation of alternative tests wherever scientifically valid rather than continuing to rely on animal tests) in non-animal and animal integrated strategies to reduce the numbers of animals tested. Sharing of information (communication), harmonization and standardization (coordination), commitment and collaboration are all required to improve the quality and speed of validation, acceptance, and implementation of tests. Finally, we consider how alternative methods can be used in research and development before formal implementation in regulations. Here we present the conclusions on what can be done already and suggest some solutions and strategies for the future.

  15. A family-based likelihood ratio test for general pedigree structures that allows for genotyping error and missing data.

    Science.gov (United States)

    Yang, Yang; Wise, Carol A; Gordon, Derek; Finch, Stephen J

    2008-01-01

    The purpose of this work is the development of a family-based association test that allows for random genotyping errors and missing data and makes use of information on affected and unaffected pedigree members. We derive the conditional likelihood functions of the general nuclear family for the following scenarios: complete parental genotype data and no genotyping errors; only one genotyped parent and no genotyping errors; no parental genotype data and no genotyping errors; and no parental genotype data with genotyping errors. We find maximum likelihood estimates of the marker locus parameters, including the penetrances and population genotype frequencies under the null hypothesis that all penetrance values are equal and under the alternative hypothesis. We then compute the likelihood ratio test. We perform simulations to assess the adequacy of the central chi-square distribution approximation when the null hypothesis is true. We also perform simulations to compare the power of the TDT and this likelihood-based method. Finally, we apply our method to 23 SNPs genotyped in nuclear families from a recently published study of idiopathic scoliosis (IS). Our simulations suggest that this likelihood ratio test statistic follows a central chi-square distribution with 1 degree of freedom under the null hypothesis, even in the presence of missing data and genotyping errors. The power comparison shows that this likelihood ratio test is more powerful than the original TDT for the simulations considered. For the IS data, the marker rs7843033 shows the most significant evidence for our method (p = 0.0003), which is consistent with a previous report, which found rs7843033 to be the 2nd most significant TDTae p value among a set of 23 SNPs.

  16. [Alternative methods to animal experiments. What can they afford in the safety testing of chemical substances under REACH?].

    Science.gov (United States)

    Lilienblum, Werner

    2008-12-01

    Alternative methods to safety studies using laboratory animals have been accepted by the OECD in areas such as local toxicity and mutagenicity. In more complex important fields, such as systemic single and repeated dose toxicity, toxicokinetics, sensitisation, reproductive toxicity and carcinogenicity, it is expected that the development and validation of computerised methods, testing batteries (in vitro and in silico) and tiered testing systems will need many years and have to overcome many scientific and regulatory obstacles, which makes it extremely difficult to predict the outcome and the time needed. Therefore, the validated alternative methods available will only have a limited impact on reducing the numbers of animals required under REACH. In the midterm, the strategy should be more directed towards the refinement or reduction of in vivo testing because the replacement concerning complex toxicological endpoints is at present not in sight.

  17. Brazilian Center for the Validation of Alternative Methods (BraCVAM) and the process of validation in Brazil.

    Science.gov (United States)

    Presgrave, Octavio; Moura, Wlamir; Caldeira, Cristiane; Pereira, Elisabete; Bôas, Maria H Villas; Eskes, Chantra

    2016-03-01

    The need for the creation of a Brazilian centre for the validation of alternative methods was recognised in 2008, and members of academia, industry and existing international validation centres immediately engaged with the idea. In 2012, co-operation between the Oswaldo Cruz Foundation (FIOCRUZ) and the Brazilian Health Surveillance Agency (ANVISA) instigated the establishment of the Brazilian Center for the Validation of Alternative Methods (BraCVAM), which was officially launched in 2013. The Brazilian validation process follows OECD Guidance Document No. 34, where BraCVAM functions as the focal point to identify and/or receive requests from parties interested in submitting tests for validation. BraCVAM then informs the Brazilian National Network on Alternative Methods (RENaMA) of promising assays, which helps with prioritisation and contributes to the validation studies of selected assays. A Validation Management Group supervises the validation study, and the results obtained are peer-reviewed by an ad hoc Scientific Review Committee, organised under the auspices of BraCVAM. Based on the peer-review outcome, BraCVAM will prepare recommendations on the validated test method, which will be sent to the National Council for the Control of Animal Experimentation (CONCEA). CONCEA is in charge of the regulatory adoption of all validated test methods in Brazil, following an open public consultation. 2016 FRAME.

  18. Lyme Disease Diagnosed by Alternative Methods: A Phenotype Similar to That of Chronic Fatigue Syndrome.

    Science.gov (United States)

    Patrick, David M; Miller, Ruth R; Gardy, Jennifer L; Parker, Shoshana M; Morshed, Muhammad G; Steiner, Theodore S; Singer, Joel; Shojania, Kam; Tang, Patrick

    2015-10-01

    A subset of patients reporting a diagnosis of Lyme disease can be described as having alternatively diagnosed chronic Lyme syndrome (ADCLS), in which diagnosis is based on laboratory results from a nonreference Lyme specialty laboratory using in-house criteria. Patients with ADCLS report symptoms similar to those reported by patients with chronic fatigue syndrome (CFS). We performed a case-control study comparing patients with ADCLS and CFS to each other and to both healthy controls and controls with systemic lupus erythematosus (SLE). Subjects completed a history, physical exam, screening laboratory tests, 7 functional scales, reference serology for Lyme disease using Centers for Disease Control and Prevention criteria, reference serology for other tick-associated pathogens, and cytokine expression studies. The study enrolled 13 patients with ADCLS (12 of whom were diagnosed by 1 alternative US laboratory), 25 patients with CFS, 25 matched healthy controls, and 11 SLE controls. Baseline clinical data and functional scales indicate significant disability among ADCLS and CFS patients and many important differences between these groups and controls, but no significant differences between each other. No ADCLS patient was confirmed as having positive Lyme serology by reference laboratory testing, and there was no difference in distribution of positive serology for other tick-transmitted pathogens or cytokine expression across the groups. In British Columbia, a setting with low Lyme disease incidence, ADCLS patients have a similar phenotype to that of CFS patients. Disagreement between alternative and reference laboratory Lyme testing results in this setting is most likely explained by false-positive results from the alternative laboratory. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Detection of the Klebsiella pneumoniae carbapenemase (KPC) in K. pneumoniae Isolated from the Clinical Samples by the Phenotypic and Genotypic Methods

    Science.gov (United States)

    Bina, Masoume; Pournajaf, Abazar; Mirkalantari, Shiva; Talebi, Malihe; Irajian, Gholamreza

    2015-01-01

    Background and Objective: The production of carbapenemases especially Klebsiella pneumoniae carbapenemase (KPC) is the most important mechanism of enzymatic resistance in isolated Enterobacteriaceae such as K. pneumoniae . The purpose of this study was detected of the carbapenemase producer K. pneumoniae strains with phenotypic and genotypic methods. Method: Out of 800 strains, 270 K. pneumoniae strains (33.7%), were obtained. Antibiotic susceptibility test was performed by disk diffusion method in accordance with CLSI guidelines. Carbapenem resistant strains were identified by the Modified Hodge Test based on CLSI instruction and PCR for surveying the presence of bla -KPC gene. Results: A total 270 K. pneumoniae strains were collected. Antibiotic susceptibility test results showed the highest and lowest resistance was related to piperacillin (60.6%) and carbapenems (14.6%) respectively. 80.5% (33 of 41) isolates were positive by MHT, but all of them (100%) were negative for amplification of the bla -KPC gene in the PCR method. Conclusion: The MHT was an appropriate method for approving carbapenemase production. Moreover, a laboratory could accept the carbapenemase production with PCR method for the bla-KPC gene, which has the additional profit of validating which KPC is present. PMID:26351485

  20. Percutaneous methods of left atrial appendage exclusion: an alternative to the internist.

    Science.gov (United States)

    Le, Duong L; Khodjaev, Soidjon D; Morelli, Remo L

    2014-01-01

    Thromboembolic stroke from the left atrial appendage (LAA) is the most feared complication in patients with atrial fibrillation (AF). The cornerstone for the management of chronic non-valvular AF is stroke reduction with oral anticoagulation (OAC). However, poor compliance, maintaining a narrow therapeutic window, and major side effects such as bleeding have severely limited their use, which creates a therapeutic dilemma. As much as 20% of AF patients are not receiving OAC due to contraindications and less than half of AF patients are not on OAC due to reluctance of the prescribing physician and/or patient non-compliance. Fortunately, over the past decade, there have been great interests in providing an alternative strategy unbeknownst to the practicing internist. The introduction of percutaneous approaches for LAA occlusion has added a different dimension to the management of chronic AF in patients with OAC intolerance. Occlusion devices such as the Amplatzer Cardiac Plug and WATCHMAN device are currently being investigated for stroke prophylaxis. More recently, the LARIAT device may provide an alternative means for potential stroke prophylaxis without the need for short-term post-procedural OAC. We aim to review the current literature and bring attention to an alternative strategy for high-risk AF patients intolerant to OAC.

  1. A comparison of six methods for genomic DNA extraction suitable for PCR-based genotyping applications using ovine milk samples.

    Science.gov (United States)

    Psifidi, Androniki; Dovas, Chrysostomos I; Banos, Georgios

    2010-04-01

    Isolation of amplifiable genomic DNA is a prerequisite for the genetic assessment of diseases and disease susceptibility in farm animals. Milk somatic cells are a practical, animal friendly and cost-effective source of genomic DNA in milking ruminants. In this study, six different DNA extraction methods were optimized, evaluated and compared for the isolation of DNA from ovine milk samples. Methods 1 and 2 were direct applications of two commercial kits, Nucleospin((R)) Blood and Nucleospin((R)) Tissue, respectively. Methods 3 and 4 were based on modified protocols of methods 1 and 2, respectively, aiming at increasing DNA recovery and integrity, and eliminating PCR inhibitors. Method 5 was a standard Phenol-Chloroform protocol application and method 6 was based on an in-house developed protocol using silica as the affinity matrix. Spectrophotometer, gel electrophoresis and real-time PCR measurements were used as criteria for evaluating quantity and quality of the extracted DNA. Processing time, intensity of labor and cost for each method were also evaluated. Results suggested that methods 1-4 were considered suitable for molecular downstream applications and performed better than methods 5 and 6. Modifications of protocols 3 and 4 increased the quantity and quality of the extracted DNA from ovine milk samples. Method 3 was proved to be highly efficient and robust for large scale use as demonstrated by its successful application to 1000 individual ovine milk and 50 bulk milk samples.

  2. Evaluation of phenotypic and genotypic methods for epidemiological typing of Staphylococcus aureus isolates from bovine mastitis in Denmark

    DEFF Research Database (Denmark)

    Aarestrup, Frank Møller; Wegener, H. C.; Rosdahl, V. T.

    1995-01-01

    The value of five different typing methods (antibiogram typing, biotyping, phage typing, plasmid profiling and restriction fragment length polymorphism of the gene encoding 16S and 23S ribosomal RNA (ribotyping)), in discriminating 105 Staphylococcus aureus strains from bovine milk samples obtained....... The combination of phage, bio- or ribotyping or all three methods in combination are considered to be an efficient combination of typing methods for epidemiological investigation of S. aureus mastitis....

  3. Application of a high-throughput genotyping method for loci exclusion in non-consanguineous Australian pedigrees with autosomal recessive retinitis pigmentosa.

    Science.gov (United States)

    Paterson, Rachel L; De Roach, John N; McLaren, Terri L; Hewitt, Alex W; Hoffmann, Ling; Lamey, Tina M

    2012-01-01

    Retinitis pigmentosa (RP) is the most common form of inherited blindness, caused by progressive degeneration of photoreceptor cells in the retina, and affects approximately 1 in 3,000 people. Over the past decade, significant progress has been made in gene therapy for RP and related diseases, making genetic characterization increasingly important. Recently, high-throughput technologies have provided an option for reasonably fast, cost-effective genetic characterization of autosomal recessive RP (arRP). The current study used a single nucleotide polymorphism (SNP) genotyping method to exclude up to 28 possible disease-causing genes in 31 non-consanguineous Australian families affected by arRP. DNA samples were collected from 59 individuals affected with arRP and 74 unaffected family members from 31 Australian families. Five to six SNPs were genotyped for 28 genes known to cause arRP or the related disease Leber congenital amaurosis (LCA). Cosegregation analyses were used to exclude possible causative genes from each of the 31 families. Bidirectional sequencing was used to identify disease-causing mutations in prioritized genes that were not excluded with cosegregation analyses. Two families were excluded from analysis due to identification of false paternity. An average of 28.9% of genes were excluded per family when only one affected individual was available, in contrast to an average of 71.4% or 89.8% of genes when either two, or three or more affected individuals were analyzed, respectively. A statistically significant relationship between the proportion of genes excluded and the number of affected individuals analyzed was identified using a multivariate regression model (pgene as CRB1 in one family (c.2548 G>A) and USH2A in two families (c.2276 G>T). This study has shown that SNP genotyping cosegregation analysis can be successfully used to refine and expedite the genetic characterization of arRP in a non-consanguineous population; however, this method is

  4. A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

    Directory of Open Access Journals (Sweden)

    Tetreau Guillaume

    2008-10-01

    Full Text Available Abstract Background For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT. One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito Aedes aegypti as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs in the genome of this species. Results Ae. aegypti genomic representations were produced following a two-step procedure: (1 restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2 amplification of restriction fragments containing a particular MITE element called Pony using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the Pony element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished. Conclusion The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in Ae. egypti. Overall, our results testify of the flexibility of the DArT genotyping technique and open new

  5. A novel SVM-ID3 hybrid feature selection method to build a disease model for melanoma using integrated genotyping and phenotype data from dbGaP.

    Science.gov (United States)

    Son, Yeşim Aydın; Yücebaş, Sait Can

    2014-01-01

    The relations between Single Nucleotide Polymorphism (SNP) and complex diseases are likely to be non-linear and require analysis of the high dimensional data. Previous studies in the field mostly focus on genotyping and effects of various phenotypes are not considered. To fill this gap a hybrid feature selection model of support vector machine and decision tree has been designed. The designed method is tested on melanoma. We were able to select phenotypic features such as moles and dysplastic nevi, and SNPs those maps to specific genes such as CAMK1D. The performance results of the proposed hybrid model, on melanoma dataset are 79.07% of sensitivity and 0.81 of area under ROC curve.

  6. Hepatitis C Virus Genotypes

    Directory of Open Access Journals (Sweden)

    Kayhan Azadmanesh

    2005-09-01

    , based on its phenotype according to its disease pattern or cytopathology, and serotype based on a panel of cross-neutralization antibodies, impossible(21. Phylogenetic analysis may aid in the separation of sequences into distinct types(22. So far six majorgenotypes (HCV-1 to HCV-6 have been described, each containing multiple subtypes (e.g., 1a, 1b, etc.. More than 50 subtypes have been reported todate and are normally identified on the bases of partial gene sequences from E1 and NS5B. The isolates formerly published as genotypes 7 to 11 are now considered subtypes within genotypes 3 (subtype 10 and 6 (subtypes 7, 8, 9, and 11(22.In general, sequence characteristics of a particular subtype are found throughout the HCV genome. Thus, the HCV genotype has been determined primarily based on analysis of partial genome sequences. The most extensive database exists for the 5'-UTR, core, E1, and NS5B (23-28. Whereas the 5'-UTR is highly conserved and therefore preferred for diagnosis, the core, the envelope, and the NS5B regions are less conserved and therefore highly discriminative and preferred for subtyping. Although the 5'-UTR contains characteristic sequence motifs of some genotypes, analysis of this region may not accurately predict all genotypes or subtypes. HCV Genotyping MethodsMolecular Genotyping Because differences in geographical distribution, disease outcome, and response to therapy among HCV genotypes have been suggested, reliable 1 573 1149 2187 3078 4971 5916 9033C E1 E2 P7 NS2 NS3 NS4A NS4B NS5A NS5B Figure 1. The HCV genome contains a single open reading frame (ORF. The genes for structural proteins (C, E1, E2, P7 are situated towards the N-terminus of the ORF. Genes coding for proteins necessary for viral replication are found towards the C-terminus of the ORF. methods for determining the HCV genotype may become an important clinical test. The HCV genotype can be determined by nucleotide sequencing of a specific PCR-amplified portion of the HCV genome

  7. An alternative method of OBT measurement for the limited quantity of environmental samples using a combustion bomb.

    Science.gov (United States)

    Kim, Sang Bog; Stuart, Marilyne

    2013-12-01

    The measurement of organically bound tritium (OBT) in environmental samples is much more difficult than the measurement of tritiated water (HTO). This study describes an alternative method for OBT determination in plant materials in which tritium-free polyethylene beads are added to the plant sample prior to combustion in a combustion bomb. It is not always possible to collect large enough amounts of some plants (e.g. algae, plankton, grass) within a specific area or specific period. Excellent water recovery is achieved when dry plant materials are combusted with polyethylene beads. When Ultima Gold AB is used as the scintillation cocktail, it is possible to measure the combustion water directly without distillation. Correction factors were derived for the plants used in the study to account for the dilution of the combustion water due to addition of the polyethylene beads. The alternative method has a number of advantages, including an increased yield of combustion water for liquid scintillation counting, less color quenching, reduced sample size and decreased analysis time. Finally, accuracy tests comparing results of the conventional method with those of the alternative method were carried out using environmental samples.

  8. State university preparatory class EFL instructors' attitudes towards assessment methods used at their institutions and portfolios as a method of alternative assessment

    OpenAIRE

    Oğuz, Şebnem

    2003-01-01

    Cataloged from PDF version of article. The purpose of this study was to investigate preparatory class instructors’ attitudes towards the methods of assessment they are currently using at their institutions, and their knowledge about and attitudes towards portfolios as an alternative method of assessment. The study was conducted with 386 English instructors from the preparatory class programs of 14 Turkish state universities. Data were collected through a fourpart questio...

  9. An alternative method to record rising temperatures during dental implant site preparation: a preliminary study using bovine bone

    Directory of Open Access Journals (Sweden)

    Domenica Laurito

    2010-12-01

    Full Text Available Overheating is constantly mentioned as a risk factor for bone necrosis that could compromise the dental implant primary stability. Uncontrolled thermal injury can result in a fibrous tissue, interpositioned at the implant-bone interface, compromising the long-term prognosis. The methods used to record temperature rise include either direct recording by thermocouple instruments or indirect estimating by infrared thermography. This preliminary study was carried out using bovine bone and a different method of temperatures rising estimation is presented. Two different types of drills were tested using fluoroptic thermometer and the effectiveness of this alternative temperature recording method was evaluated.

  10. THE MURINE LOCAL LYMPH NODE ASSAY: AN ALTERNATIVE TEST METHOD FOR THE EVALUATION OF THE POTENTIAL FOR CHEMICALS TO ELICIT ALLERGIC CONTACT DERMATITIS

    Science.gov (United States)

    ABSTRACTThe process that a new toxicology test method must undergo to attain acceptance and regulatory implementation may seem daunting. As the first test method to undergo Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) review, the local...

  11. An alternative sensor fusion method for object orientation using low-cost MEMS inertial sensors

    Science.gov (United States)

    Bouffard, Joshua L.

    This thesis develops an alternative sensor fusion approach for object orientation using low-cost MEMS inertial sensors. The alternative approach focuses on the unique challenges of small UAVs. Such challenges include the vibrational induced noise onto the accelerometer and bias offset errors of the rate gyroscope. To overcome these challenges, a sensor fusion algorithm combines the measured data from the accelerometer and rate gyroscope to achieve a single output free from vibrational noise and bias offset errors. One of the most prevalent sensor fusion algorithms used for orientation estimation is the Extended Kalman filter (EKF). The EKF filter performs the fusion process by first creating the process model using the nonlinear equations of motion and then establishing a measurement model. With the process and measurement models established, the filter operates by propagating the mean and covariance of the states through time. The success of EKF relies on the ability to establish a representative process and measurement model of the system. In most applications, the EKF measurement model utilizes the accelerometer and GPS-derived accelerations to determine an estimate of the orientation. However, if the GPS-derived accelerations are not available then the measurement model becomes less reliable when subjected to harsh vibrational environments. This situation led to the alternative approach, which focuses on the correlation between the rate gyroscope and accelerometer-derived angle. The correlation between the two sensors then determines how much the algorithm will use one sensor over the other. The result is a measurement that does not suffer from the vibrational noise or from bias offset errors.

  12. Perpendicular distance sampling: an alternative method for sampling downed coarse woody debris

    Science.gov (United States)

    Michael S. Williams; Jeffrey H. Gove

    2003-01-01

    Coarse woody debris (CWD) plays an important role in many forest ecosystem processes. In recent years, a number of new methods have been proposed to sample CWD. These methods select individual logs into the sample using some form of unequal probability sampling. One concern with most of these methods is the difficulty in estimating the volume of each log. A new method...

  13. Evaluation of alternative age-based methods for estimating relative abundance from survey data in relation to assessment models

    DEFF Research Database (Denmark)

    Berg, Casper Willestofte; Nielsen, Anders; Kristensen, Kasper

    2014-01-01

    Indices of abundance from fishery-independent trawl surveys constitute an important source of information for many fish stock assessments. Indices are often calculated using area stratified sample means on age-disaggregated data, and finally treated in stock assessment models as independent...... observations. We evaluate a series of alternative methods for calculating indices of abundance from trawl survey data (delta-lognormal, delta-gamma, and Tweedie using Generalized Additive Models) as well as different error structures for these indices when used as input in an age-based stock assessment model...... the different indices produced. The stratified mean method is found much more imprecise than the alternatives based on GAMs, which are found to be similar. Having time-varying index variances is found to be of minor importance, whereas the independence assumption is not only violated but has significant impact...

  14. A comparison of six methods for genomic DNA extraction suitable for PCR-based genotyping applications using ovine milk samples

    OpenAIRE

    Psifidi, Androniki; Dovas, Chrysostomos I.; Banos, Georgios

    2010-01-01

    Isolation of amplifiable genomic DNA is a prerequisite for the genetic assessment of diseases and disease susceptibility in farm animals. Milk somatic cells are a practical, animal friendly and cost-effective source of genomic DNA in milking ruminants. In this study, six different DNA extraction methods were optimized, evaluated and compared for the isolation of DNA from ovine milk samples. Methods I and 2 were direct applications of two commercial kits, Nucleospin (R) Blood and Nucleospin (R...

  15. State of the art on alternative methods to animal testing from an industrial point of view: ready for regulation?

    OpenAIRE

    KRUL Cyrille; Ashton, Rachel; Roggen, Erwin; Fuchs, Horst; Gaca, Marianna; Hill, Erin; Poth, Albrecht; Wever, De, Bart

    2014-01-01

    Despite changing attitudes towards animal testing and current legislation to protect experimental animals, the rate of animal experiments seems to have changed little in recent years. On May 15–16, 2013, the In Vitro Testing Industrial Platform (IVTIP) held an open meeting to discuss the state of the art in alternative methods, how companies have, can, and will need to adapt and what drives and hinders regulatory acceptance and use. Several key messages arose from the meeting. First, industry...

  16. Mechanical Color Reading of Wood-Staining Fungal Pigment Textile Dyes: An Alternative Method for Determining Colorfastness

    OpenAIRE

    Eric M. Hinsch; Robinson, Sara C

    2016-01-01

    Colorfastness to washing and crocking (color loss due to rubbing) are essential qualities for any dye/fabric combination that will be used for garments or upholstery. In this study, colorfastness to washing and crocking of fabrics dyed with wood-staining fungal pigments was compared to colorfastness of commercial dyes using an alternative mechanical testing method. Overall, wood-staining fungal pigments out performed commercial dyes for colorfastness to washing and wet and dry crocking. Xylin...

  17. Alternative applications of the method of moments: from electromagnetic waves to source synthesis, deconvolution, and data processing in navigation systems

    Science.gov (United States)

    Tamas, Razvan; Dumitrascu, Ana; Caruntu, George

    2015-02-01

    The method of moments is mostly used in electromagnetism to solve linear operator equations. In this paper, we present three different, alternative applications of this numerical technique: resolution of the integral equation of convolution i.e., deconvolution, synthesis of electromagnetic radiators optimized to yield a given time-domain or frequency-domain response, and processing of data provided by an inertial navigation system, with the aim to decompose a complex displacement into elementary movements.

  18. Patient-controlled analgesia with remifentanil versus alternative parenteral methods for pain management in labour

    DEFF Research Database (Denmark)

    Weibel, Stephanie; Jelting, Yvonne; Afshari, Arash

    2017-01-01

    BACKGROUND: Multiple analgesic strategies for pain relief during labour are available. Recently remifentanil, a short-acting opioid, has recently been used as an alternative analgesic due to its unique pharmacological properties. OBJECTIVES: To systematically assess the effectiveness of remifenta......BACKGROUND: Multiple analgesic strategies for pain relief during labour are available. Recently remifentanil, a short-acting opioid, has recently been used as an alternative analgesic due to its unique pharmacological properties. OBJECTIVES: To systematically assess the effectiveness...... review authors independently assessed trials for inclusion, extracted data, and appraised study quality.We contacted study authors for additional information other than incomplete outcome data. We performed random-effects meta-analysis.To reduce the risk of random error in meta-analysis we performed...... relevant and non-relevant treatment effects is compatible with this result. AUTHORS' CONCLUSIONS: Based on the current systematic review, there is mostly low-quality evidence to inform practice and future research may significantly alter the current situation. The quality of evidence is mainly limited...

  19. Don't spin the pen: two alternative methods for second-stage sampling in urban cluster surveys

    Directory of Open Access Journals (Sweden)

    Rose Angela MC

    2007-06-01

    Full Text Available Abstract In two-stage cluster surveys, the traditional method used in second-stage sampling (in which the first household in a cluster is selected is time-consuming and may result in biased estimates of the indicator of interest. Firstly, a random direction from the center of the cluster is selected, usually by spinning a pen. The houses along that direction are then counted out to the boundary of the cluster, and one is then selected at random to be the first household surveyed. This process favors households towards the center of the cluster, but it could easily be improved. During a recent meningitis vaccination coverage survey in Maradi, Niger, we compared this method of first household selection to two alternatives in urban zones: 1 using a superimposed grid on the map of the cluster area and randomly selecting an intersection; and 2 drawing the perimeter of the cluster area using a Global Positioning System (GPS and randomly selecting one point within the perimeter. Although we only compared a limited number of clusters using each method, we found the sampling grid method to be the fastest and easiest for field survey teams, although it does require a map of the area. Selecting a random GPS point was also found to be a good method, once adequate training can be provided. Spinning the pen and counting households to the boundary was the most complicated and time-consuming. The two methods tested here represent simpler, quicker and potentially more robust alternatives to spinning the pen for cluster surveys in urban areas. However, in rural areas, these alternatives would favor initial household selection from lower density (or even potentially empty areas. Bearing in mind these limitations, as well as available resources and feasibility, investigators should choose the most appropriate method for their particular survey context.

  20. Determination of Molecular Genotyping of Ureaplasma SPP in Women with Genital Infections by 16S–23S rDNA PCR-RFLP Method

    Directory of Open Access Journals (Sweden)

    R. Mirnejad

    2011-04-01

    Full Text Available Introduction & Objective: So far, despite the wide range of methods such as analytic methods used for differentiation of Mycoplasma, the diagnosis of Mycoplasma species is still difficult. Generally the low-level discriminatory power of serological methods because of the rapid changes in size and phase of the dominant antigens in the immune cell surface of Mycoplasmas greatly limits their applicability to the typing of Mycoplasmas. On the contrary,molecular methods do not suffer from these drawbacks and can be used for typing of Mycoplasmas. The aim of this investigation was molecular identification and genotyping of ureaplasma SPP in women with genital infections by 16S–23S rDNA PCR-RFLP.Materials & Methods: Genital swabs were taken from 210 patients who referred to gynecology clinic of Rasool hospital in Tehran, Iran during December 2007 until June 2008. The swabs suspended in PBS, were immediately transferred to laboratory .Following DNA extraction, PCR assay was performed using a genus specific primer pair. These primer sets amplified a 559 bp fragment for Ureaplasma Spp. Samples containing bands of the expected size for Ureaplasma strains were subjected to digestion with different restriction endonuclease enzymes (AluI, Taq I, CacI8, BbsI, EcoRI. Results: Of the 210 samples, Ureaplasma Spp was isolated from 93 patients (44.3% by PCR and 69 samples by culture. In the present study only Biovar 1 (Ureaplasma parvum was isolated from clinical specimens and the results were confirmed using a cutting enzyme TaqI (enzyme specific species of ureaplasma SPP. The results of this analysis using PCR-RFLP and sequencing showed that all had the same genotype and shared identical sequence with the genome sequence of serovar 3 Ureaplasma parvum.Conclusion: Ureaplasma parvum is generally isolated from the genital samples. In this study all isolates were identical and no difference was found among the enzyme patterns of the bacteria after PCR-RFLP .So

  1. Development of an alternative method for testing the immunogenicity of diphtheria vaccines.

    Science.gov (United States)

    Manghi, M A; Pasetti, M F; Brero, M L; Deluchi, S; di Paola, G; Mathet, V; Eriksson, P V

    1995-04-01

    The immunogenicity of the diphtheria component of 73 commercial vaccines from five different manufacturers was tested by the toxin neutralization test (TNT) and the enzyme-linked immunosorbent assay (ELISA) developed in our laboratory. A comparison of the antibody levels measured by both assays showed a very good correlation (r = 0.95, p antibody levels as low as 5.5 x 10(-5) IU ml-1. To evaluate the possibility of accelerating the active immunization during the activity test of vaccines, an alternative schedule using one single human dose was assayed. A very good correlation was observed between the IgG antibody response obtained with this schedule and with the traditional programme. Therefore, the cost and the time required to perform the activity test may be considerably reduced when both the rapid immunization schedule and the ELISA are used.

  2. Variance component estimation with longitudinal data: a simulation study with alternative methods

    Directory of Open Access Journals (Sweden)

    Simone Inoe Araujo

    2009-01-01

    Full Text Available A pedigree structure distributed in three different places was generated. For each offspring, phenotypicinformation was generated for five different ages (12, 30, 48, 66 and 84 months. The data file was simulated allowing someinformation to be lost (10, 20, 30 and 40% by a random process and by selecting the ones with lower phenotypic values,representing the selection effect. Three alternative analysis were used, the repeatability model, random regression model andmultiple-trait model. Random regression showed to be more adequate to continually describe the covariance structure ofgrowth over time than single-trait and repeatability models, when the assumption of a correlation between successivemeasurements in the same individual was different from one another. Without selection, random regression and multiple-traitmodels were very similar.

  3. The use of alternative preference elicitation methods in complex discrete choice experiments.

    Science.gov (United States)

    Yoo, Hong Il; Doiron, Denise

    2013-12-01

    We analyse stated preference data over nursing jobs collected from two different discrete choice experiments: a multi-profile case best-worst scaling experiment (BWS) prompting selection of the best and worst among alternative jobs, and a profile case BWS wherein the respondents choose the best and worst job attributes. The latter allows identification of additional utility parameters and is believed to be cognitively easier. Results suggest that respondents place greater value on pecuniary over non-pecuniary gains in the multi-profile case. There is little evidence that this discrepancy is induced by the extra cognitive burden of processing several profiles at once in the multi-profile case. We offer thoughts on other likely mechanisms.

  4. An integrated method for assessing climate-related risks and adaptation alternatives in urban areas

    Directory of Open Access Journals (Sweden)

    Yvonne Andersson-Sköld

    2015-01-01

    Full Text Available The urban environment is a complex structure with interlinked social, ecological and technical structures. Global warming is expected to have a broad variety of impacts, which will add to the complexity. Climate changes will force adaptation, to reduce climate-related risks. Adaptation measures can address one aspect at the time, or aim for a holistic approach to avoid maladaptation. This paper presents a systematic, integrated approach for assessing alternatives for reducing the risks of heat waves, flooding and air pollution in urban settings, with the aim of reducing the risk of maladaptation. The study includes strategies covering different spatial scales, and both the current climate situation and the climate predicted under climate change scenarios. The adaptation strategies investigated included increasing vegetation; selecting density, height and colour of buildings; and retreat or resist (defend against sea-level rise. Their effectiveness was assessed with regard to not only flooding, heat stress and air quality but also with regard to resource use, emissions to air (incl. GHG, soil and water, and people’s perceptions and vulnerability. The effectiveness of the strategies were ranked on a common scale (from −3 to 3 in an integrated assessment. Integrated assessments are recommended, as they help identify the most sustainable solutions, but to reduce the risk of maladaptation they require experts from a variety of disciplines. The most generally applicable recommendation, derived from the integrated assessment here, taking into account both expertise from different municipal departments, literature surveys, life cycle assessments and publics perceptions, is to increase the urban greenery, as it contributes to several positive aspects such as heat stress mitigation, air quality improvement, effective storm-water and flood-risk management, and it has several positive social impacts. The most favourable alternative was compact, mid

  5. Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle

    DEFF Research Database (Denmark)

    Ma, Peipei; Brøndum, Rasmus Froberg; Qin, Zahng

    2013-01-01

    This study investigated the imputation accuracy of different methods, considering both the minor allele frequency and relatedness between individuals in the reference and test data sets. Two data sets from the combined population of Swedish and Finnish Red Cattle were used to test the influence...... of these factors on the accuracy of imputation. Data set 1 consisted of 2,931 reference bulls and 971 test bulls, and was used for validation of imputation from 3,000 markers (3K) to 54,000 markers (54K). Data set 2 contained 341 bulls in the reference set and 117 in the test set, and was used for validation...... of imputation from 54K to high density [777,000 markers (777K)]. Both test sets were divided into 4 groups according to their relationship to the reference population. Five imputation methods (Beagle, IMPUTE2, findhap, AlphaImpute, and FImpute) were used in this study. Imputation accuracy was measured...

  6. The genetic origin of honey bee colonies used in the COLOSS Genotype-Environment Interactions Experiment: a comparison of methods

    DEFF Research Database (Denmark)

    Francis, Roy M; Kryger, Per; Meixner, Marina;

    2014-01-01

    to describe the genetic background and population allocation of the bees used in this experiment. Two wing morphometric and two genetic methods were employed to discriminate bee populations. Classical morphometry of 11 angles on the wings were carried out on 350 bees. Geometric morphometry on 19 wing...... landmarks was carried out on 381 individuals. DNA microsatellite analysis was carried out on 315 individuals using 24 loci. Allozyme analysis was performed on 90 individuals using six enzyme systems. DNA microsatellite markers produced the best discrimination between the subspecies (Apis mellifera carnica......, A. m. ligustica, A. m. macedonica, A. m. mellifera and A. m. siciliana) used in the experiment. Morphometric methods generally showed an intermediate level of discrimination, usually best separating A. m. siciliana and A. m. ligustica from the remaining populations. Allozyme markers lack power...

  7. Usefulness of phenotypic and genotypic methods for metallo-beta-lactamases detection in carbapenem-resistant Acinetobacter baumannii strains

    OpenAIRE

    2013-01-01

    Background Acinetobacter baumannii is an opportunistic microorganism with an increasing role in nosocomial outbreaks. For the last 2 decades, a growing number of carbapenem-resistant A. baumannii strains have been identified, including the metallo-beta-lactamases (MBLs) producers. The study aimed to investigate the genetic relatedness of, and MBLs production among, a collection of A. baumannii isolates from Poland. Material/Methods This study involved 78 clinical isolates of carbapenem-resist...

  8. Fast method for the simultaneous quantification of toxic polyphenols applied to the selection of genotypes of yam bean (Pachyrhizus sp.) seeds.

    Science.gov (United States)

    Lautié, E; Rozet, E; Hubert, P; Vandelaer, N; Billard, F; Felde, T Zum; Grüneberg, W J; Quetin-Leclercq, J

    2013-12-15

    The purpose of the research was to develop and validate a rapid quantification method able to screen many samples of yam bean seeds to determine the content of two toxic polyphenols, namely pachyrrhizine and rotenone. The analytical procedure described is based on the use of an internal standard (dihydrorotenone) and is divided in three steps: microwave assisted extraction, purification by solid phase extraction and assay by ultra high performance liquid chromatography (UHPLC). Each step was included in the validation protocol and the accuracy profiles methodology was used to fully validate the method. The method was fully validated between 0.25 mg and 5 mg pachyrrhizin per gram of seeds and between 0.58 mg/g and 4 mg/g for rotenone. More than one hundred samples from different accessions, locations of growth and harvest dates were screened. Pachyrrhizine concentrations ranged from 3.29 mg/g to lower than 0.25 mg/g while rotenone concentrations ranged from 3.53 mg/g to lower than 0.58 mg/g. This screening along with principal component analysis (PCA) and discriminant analysis (DA) analyses allowed the selection of the more interesting genotypes in terms of low concentrations of these two toxic polyphenols.

  9. Development and application of a multilocus sequence analysis method for the identification of genotypes within genus Bradyrhizobium and for establishing nodule occupancy of soybean (Glycine max L. Merr).

    Science.gov (United States)

    van Berkum, Peter; Elia, Patrick; Song, Qijian; Eardly, Bertrand D

    2012-03-01

    A multilocus sequence typing (MLST) method based on allelic variation of seven chromosomal loci was developed for characterizing genotypes (GT) within the genus Bradyrhizobium. With the method, 29 distinct multilocus GT were identified among 190 culture collection soybean strains. The occupancy of 347 nodules taken from uninoculated field-grown soybean plants also was determined. The bacteroid GT were either the same as or were closely related to GT identified among strains in the culture collection. Double-nodule occupancy estimates of 2.9% were much lower than values published based on serology. Of the 347 nodules examined, 337 and 10 were occupied by Bradyrhizobium japonicum and B. elkanii, respectively. The collection strains within the species B. japonicum and B. elkaniialso were compared with Bradyrhizobium cultures from other legumes. In many cases, the observed GT varied more according to their geographic origin than by their trap hosts of isolation. In other cases, there were no apparent relationships with either the legume or geographic source. The MLST method that was developed should be a useful tool in determining the influence of geographic location, temperature, season, soil type, and host plant cultivar on the distribution of GT of Bradyrhizobium spp.

  10. Searching for Methods on Evaluation Alternatives and Studying Decision Making System Regarding Enhancing Publicity of Nuclear Spent Fuel

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Seongkyung [Myongji Univ., Seoul (Korea, Republic of); Choi, Seungho; Kim, Hyerim; Song, Jiyeon [DOMO Communication Consulting, Seoul (Korea, Republic of); Lee, Yoonsup; Sohn, Seohyun [Fleishman-Hillard Korea, Seoul (Korea, Republic of)

    2013-05-15

    This study was done in order to anticipate the aspect of publicity enhancement on nuclear spent fuel so that it can find the evaluation methods of alternative ways of management which could applied actually and make the decision making system of Publicity Enhancement Committee in advance. In Korea, the nuclear spent fuel is temporarily stored inside of the nuclear facility field, and it is expected that Gori nuclear facility is going to be saturated since 2016 but the solutions are still incomplete. The problem of management of nuclear spent fuel is an important issue in terms of not only the nuclear power policy but also of safe management of the already made nuclear spent fuel. This study has its meaning to draw the evaluation criteria of the management alternatives on nuclear spent fuel which can be applied in Korean case, and to find the necessity of verifying the evaluation of management alternatives through Publicity Enhancement because of different stands according to the interests. As a result, rather than technological engineering safety evaluation, qualitative analysis in terms of social costs, quantitative evaluation in terms of economic costs, this study advises the methods of public hearings and citizen juries which are effective, which makes it meaningful.

  11. EU sales ban on new cosmetics tested on animals: impact on alternative methods, WTO implications and animal welfare aspects.

    Science.gov (United States)

    Ruhdel, Irmela W

    2004-06-01

    In 1993, the European Union (EU) adopted Directive 93/35/EEC, calling for a sales ban on new cosmetic products containing ingredients tested on animals after 1 January, 1998, provided that alternative methods had been developed by then. In May 2000, for the second time, the European Commission postponed that ban. The Commission justified the repeated postponement of the sales ban by saying that no animal-free methods were available, although three in vitro methods were scientifically approved in 1997. With three years delay, these methods have been published and therefore "made available" in the EU. OECD acceptance is still awaited. Another reason for the postponement was the fear of possible World Trade Organisation (WTO) conflicts. However, according to WTO rules, the protection of public morality or animal health could justify a restriction of the free trade principle. From the animal welfare point of view, an unqualified EU sales ban, combined with an animal testing ban, would provide the incentive to further promote the development and acceptance of alternative methods and to prove that ethical standards are legitimate concerns under WTO rules.

  12. Alternatives to the gravimetric method for quantification of diesel particulate matter near the lower level of detection.

    Science.gov (United States)

    Swanson, Jacob; Kittelson, David; Pui, David; Watts, Winthrop

    2010-10-01

    This paper is part of the Journal of the Air & Waste Management Association's 2010 special issue on combustion aerosol measurements. The issue is a combination of papers that synthesize and evaluate ideas and perspectives that were presented by experts at a series of workshops sponsored by the Coordinating Research Council that aimed to evaluate the current and future status of diesel particulate matter (DPM) measurement. Measurement of DPM is a complex issue with many stakeholders, including air quality management and enforcement agencies, engine manufacturers, health experts, and climatologists. Adoption of the U.S. Environmental Protection Agency 2007 heavy-duty engine DPM standards posed a unique challenge to engine manufacturers. The new standards reduced DPM emissions to the point that improvements to the gravimetric method were required to increase the accuracy and the sensitivity of the measurement. Despite these improvements, the method still has shortcomings. The objectives of this paper are to review the physical and chemical properties of DPM that make gravimetric measurement difficult at very low concentrations and to review alternative metrics and methods that are potentially more accurate, sensitive, and specific. Particle volatility, size, surface area, and number metrics are considered, as well as methods to quantify them. Although the authors believe that an alternative method is required to meet the needs of engine manufacturers, the methods reviewed in the paper are applicable to other areas where the gravimetric method detection limit is approached and greater accuracy and sensitivity are required. The paper concludes by suggesting a method to measure active surface area, combined with a method to separate semi-volatile and solid fractions to further increase the specificity of the measurement, has potential for reducing the lower detection limit of DPM and enabling engine manufacturers to reduce DPM emissions in the future.

  13. Development and validation of an alternative to conventional pretreatment methods for residue analysis of butachlor in water, soil, and rice.

    Science.gov (United States)

    Xue, Jiaying; Jiang, Wenqing; Liu, Fengmao; Zhao, Huiyu; Wang, Suli; Peng, Wei

    2014-01-01

    A rapid and effective alternative analytical method for residues of butachlor in water, soil, and rice was established. The operating variables affecting performance of this method, including different extraction conditions and cleanup adsorbents, were evaluated. The determination of butachlor residues in soil, straw, rice hull, and husked rice was performed using GC/MS after extraction with n-hexane and cleanup with graphite carbon black. The average recoveries ranged from 81.5 to 102.7%, with RSDs of 0.6-7.7% for all of the matrixes investigated. The limits of quantitation were 0.05 mg/kg in water and rice plant, and 0.01 mg/kg in soil, straw, rice hull, and husked rice. A comparison among this proposed method, the conventional liquid-liquid extraction, the Quick, Easy, Cheap, Effective, Rugged, and Safe method, and Soxhlet extraction indicated that this method was more suitable for analyzing butachlor in rice samples. The further validation of the proposed method was carried out by Soxhlet extraction for the determination of butachlor residues in the husked rice samples, and the residue results showed there was no obvious difference obtained from these two methods. Samples from a rice field were found to contain butachlor residues below the maximum residue limits set by China (0.5 mg/kg) and Japan (0.1 mg/kg). The proposed method has a strong potential for application in routine screening and processing of large numbers of samples. This study developed a more effective alternative to the conventional analytical methods for analyzing butachlor residues in various matrixes.

  14. 78 FR 11174 - Recent Postings of Broadly Applicable Alternative Test Methods

    Science.gov (United States)

    2013-02-15

    ... Oil- emitting EGU Fired Electric (LEE)testing Utility Steam for mercury Generating emissions. Units... Internal Analyzer and Combustion Method 18- Engines. Measurment of Gaseous Organic Compound Emissions by... Municipal Method 18- Solid Waste Measurment of Landfills. Gaseous Organic Compound Emissions by...

  15. Forest control and regulation ... a comparison of traditional methods and alternatives

    Science.gov (United States)

    LeRoy C. Hennes; Michael J. Irving; Daniel I. Navon

    1971-01-01

    Two traditional techniques of forest control and regulation-formulas and area-volume check-are compared to linear programing, as used in a new computerized planning system called Timber Resource Allocation Method ( Timber RAM). Inventory data from a National Forest in California illustrate how each technique is used. The traditional methods are simpler to apply and...

  16. 40 CFR Appendix D to Part 63 - Alternative Validation Procedure for EPA Waste and Wastewater Methods

    Science.gov (United States)

    2010-07-01

    ... EPA Waste and Wastewater Methods D Appendix D to Part 63 Protection of Environment ENVIRONMENTAL... Procedure for EPA Waste and Wastewater Methods 1. Applicability This procedure is to be applied exclusively.... For the purposes of this appendix, “waste” means waste and wastewater. 2. Procedure This...

  17. Isolation of S-locus F-box alleles in Prunus avium and their application in a novel method to determine self-incompatibility genotype.

    Science.gov (United States)

    Vaughan, S P; Russell, K; Sargent, D J; Tobutt, K R

    2006-03-01

    This study characterises a series of 12 S-locus haplotype-specific F-box protein genes (SFB) in cherry (Prunus avium) that are likely candidates for the pollen component of gametophytic self-incompatibility in this species. Primers were designed to amplify 12 SFB alleles,including the introns present in the 50 untranslated region;sequences representing the S-alleles S1, S2, S3, S4, S40, S5,S6, S7, S10, S12, S13 and S16 were cloned and characterized. [The nucleotide sequences reported in this paper have been submitted to the EMBL/GenBank database under the following accession numbers: PaSFB1(AY805048), PaSFB2 (AY805049), PaSFB3 (AY805057),PaSFB4 (AY649872), PaSFB40 (AY649873), PaSFB5(AY805050), PaSFB6 (AY805051), PaSFB7 (AY805052),PaSFB10 (AY805053), PaSFB12 (AY805054), PaSFB13(AY805055), PaSFB16 (AY805056).] Though the coding regions of six of these alleles have been reported previously,the intron sequence has previously been reported only for S6. Analysis of the introns revealed sequence and length polymorphisms. A novel, PCR-based method to genotype cultivars and wild accessions was developed which combines fluorescently labelled primers amplifying the intron of SFB with similar primers for the first intron of S-RNase alleles. Intron length polymorphisms were then ascertained using a semi-automated sequencer. The convenience and reliability of this method for the determination of the self-incompatibility (SI) genotype was demonstrated both in sweet cherry cultivars representing alleles S1 to S16 and in individuals from a wild population encompassing S-alleles S17 to S22. This method will greatly expedite SI characterisation in sweet cherry and also facilitate large-scale studies of self-incompatibility in wild cherry and other Prunus populations.

  18. Development of alternative methods for the determination of raloxifene hydrochloride in tablet dosage form

    Directory of Open Access Journals (Sweden)

    Fernanda Rodrigues Salazar

    2015-06-01

    Full Text Available Three methods are proposed for the quantitative determination of raloxifene hydrochloride in pharmaceutical dosage form: ultraviolet method (UV high performance liquid chromatography (HPLC and micellar capillary electrophoresis (MEKC. These methods were developed and validated and showed good linearity, precision and accuracy. Also they demonstrated to be specific and robust. The HPLC and MEKC methods were tested in regards to be stability indicating methods and they showed to have this attribute. The UV method used methanol as solvent and optimal wavelength at 284 nm, obeying Lambert-Beer law in these conditions. The chromatographic conditions for the HPLC method included: NST column C18 (250 x 4.6 mm x 5 µm, mobile phase water:acetonitrile:triethylamine (67:33:0,3 v/v, pH 3.5, flow rate 1.0 mL min-1, injection volume 20.0 µl, UV detection 287 nm and analysis temperature 30 °C. The MEKC method was performed on a fused-silica capillary (40 cm effective length x 50 µm i.d. using as background electrolyte 35.0 mmol L-1 borate buffer and 50.0 mmol L-1 anionic detergent sodium dodecyl sulfate (SDS at pH 8.8. The capillary temperature was 32°C, applied voltage 25 kV, UV detection at 280 nm and injection was perfomed at 45 mBar for 4 s, hydrodimanic mode. In this MEKC method, potassium diclofenac (200.0 µg mL-1 was used as internal standard. All these methods were statistically analyzed and demonstrated to be equivalent for quantitative analysis of RLX in tablets and were successfully applied for the determination of the drug.

  19. A rugged, precise and accurate new gravimetry method for the determination of gold: an alternative to fire assay method.

    Science.gov (United States)

    Singh, Nahar

    2012-01-01

    A new, rugged, precise, accurate and fast primary method of measurement has been proposed for the determination of gold in various gold articles. Precise and accurate measurement of gold is the primary requirement for hall marking and to trade gold internationally, as billions of dollars of gold are trading world wide for the various applications. At present Fire Assay ASTM E 1335-08 is the only Standard Test Method for the determination of Gold, which is accepted internationally. But the method is time consuming, cumbersome and required expertise to perform the test. In the present investigation, a method has been developed gravimetry based on direct determination of gold after reducing gold in zero-valent state by hydroxylamine hydrochloride. Gravimetry is the most reliable technique and having highest metrological qualities in comparison to titremetry and instrumental method and the results of gravimetry are directly traceable to SI unit. The results of gravimetric method are accepted without reference to a standard of the same quantity. Several experiments were carried out with and without impurities and it has been concluded that gold can be determined accurately and precisely in presence of several impurities. Five replicates of approximate 0.2 g gold samples were analyzed following method proposed and percentage purity were found to be 99.993 ± 0.0056 with 95% confidence level (k = 2). The combined uncertainty in gold measurement has also been evaluated using potential sources of the method according to the EURACHEM/GUM guidelines.

  20. Reconciling alternate methods for the determination of charge distributions: A probabilistic approach to high-dimensional least-squares approximations

    CERN Document Server

    Champagnat, Nicolas; Faou, Erwan

    2010-01-01

    We propose extensions and improvements of the statistical analysis of distributed multipoles (SADM) algorithm put forth by Chipot et al. in [6] for the derivation of distributed atomic multipoles from the quantum-mechanical electrostatic potential. The method is mathematically extended to general least-squares problems and provides an alternative approximation method in cases where the original least-squares problem is computationally not tractable, either because of its ill-posedness or its high-dimensionality. The solution is approximated employing a Monte Carlo method that takes the average of a random variable defined as the solutions of random small least-squares problems drawn as subsystems of the original problem. The conditions that ensure convergence and consistency of the method are discussed, along with an analysis of the computational cost in specific instances.