Performance Comparison Of Methods Research Articles

Matrix-Specific Method Validation of an Automated Most-Probable-Number System for Use in Measuring Bacteriological Quality of Grade “A” Milk Products

The U.S. Food and Drug Administration (FDA) oversees a long-standing cooperative federal and state milk sanitation program that uses the grade "A" Pasteurized Milk Ordinance standards to maintain the safety of grade "A" milk sold in the United States. The Pasteurized Milk Ordinance requires that grade "A" milk samples be tested using validated total aerobic bacterial and coliform count methods. The objective of this project was to conduct an interlaboratory method validation study to compare performance of a film plate method with an automated most-probable-number method for total aerobic bacterial and coliform counts, using statistical approaches from international data standards. The matrix-specific validation study was administered concurrently with the FDA's annual milk proficiency test to compare method performance in five milk types. Eighteen analysts from nine laboratories analyzed test portions from 12 samples in triplicate. Statistics, including mean bias and matrix standard deviation, were calculated. Sample-specific bias of the alternative method for total aerobic count suggests that there are no large deviations within the population of samples considered. Based on analysis of 648 data points, mean bias of the alternative method across milk samples for total aerobic count was 0.013 log CFU/ml and the confidence interval for mean deviation was -0.066 to 0.009 log CFU/ml. These results indicate that the mean difference between the selected methods is small and not statistically significant. Matrix standard deviation was 0.077 log CFU/ml, showing that there is a low risk for large sample-specific bias based on milk matrix. Mean bias of the alternative method was -0.160 log CFU/ml for coliform count data. The 95% confidence interval was -0.210 to -0.100 log CFU/ml, indicating that mean deviation is significantly different from zero. The standard deviation of the sample-specific bias for coliform data was 0.033 log CFU/ml, indicating no significant effect of milk type.

Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods

Deep‐sea tubeworms (Annelida, Siboglinidae) represent dominant species in deep‐sea chemosynthetic communities (e.g. hydrothermal vents and cold methane seeps) and occur in muddy sediments and organic falls. Siboglinids lack a functional digestive tract as adults, and they rely on endosymbiotic bacteria for energy, making them of evolutionary and physiological interest. Despite their importance, inferred evolutionary history of this group has been inconsistent among studies based on different molecular markers. In particular, placement of bone‐eating Osedax worms has been unclear in part because of their distinctive biology, including harbouring heterotrophic bacteria as endosymbionts, displaying extreme sexual dimorphism and exhibiting a distinct body plan. Here, we reconstructed siboglinid evolutionary history using 12 newly sequenced transcriptomes. We parsed data into three data sets that accommodated varying levels of missing data, and we evaluate effects of missing data on phylogenomic inference. Additionally, several multispecies‐coalescent approaches and Bayesian concordance analysis (BCA) were employed to allow for a comparison of results to a supermatrix approach. Every analysis conducted herein strongly supported Osedax being most closely related to the Vestimentifera and Sclerolinum clade, rather than Frenulata, as previously reported. Importantly, unlike previous studies, the alternative hypothesis that frenulates and Osedax are sister groups to one another was explicitly rejected by an approximately unbiased (AU) test. Furthermore, although different methods showed largely congruent results, we found that a supermatrix method using data partitioning with site‐homogenous models potentially outperformed a supermatrix method using the CAT‐GTR model and multispecies‐coalescent approaches when the amount of missing data varies in a data set and when taxa susceptible to LBA are included in the analyses.

Comparative performance of transcriptome assembly methods for non-model organisms.

BackgroundThe technological revolution in next-generation sequencing has brought unprecedented opportunities to study any organism of interest at the genomic or transcriptomic level. Transcriptome assembly is a crucial first step for studying the molecular basis of phenotypes of interest using RNA-Sequencing (RNA-Seq). However, the optimal strategy for assembling vast amounts of short RNA-Seq reads remains unresolved, especially for organisms without a sequenced genome. This study compared four transcriptome assembly methods, including a widely used de novo assembler (Trinity), two transcriptome re-assembly strategies utilizing proteomic and genomic resources from closely related species (reference-based re-assembly and TransPS) and a genome-guided assembler (Cufflinks).ResultsThese four assembly strategies were compared using a comprehensive transcriptomic database of Aedes albopictus, for which a genome sequence has recently been completed. The quality of the various assemblies was assessed by the number of contigs generated, contig length distribution, percent paired-end read mapping, and gene model representation via BLASTX. Our results reveal that de novo assembly generates a similar number of gene models relative to genome-guided assembly with a fragmented reference, but produces the highest level of redundancy and requires the most computational power. Using a closely related reference genome to guide transcriptome assembly can generate biased contig sequences. Increasing the number of reads used in the transcriptome assembly tends to increase the redundancy within the assembly and decrease both median contig length and percent identity between contigs and reference protein sequences.ConclusionsThis study provides general guidance for transcriptome assembly of RNA-Seq data from organisms with or without a sequenced genome. The optimal transcriptome assembly strategy will depend upon the subsequent downstream analyses. However, our results emphasize the efficacy of de novo assembly, which can be as effective as genome-guided assembly when the reference genome assembly is fragmented. If a genome assembly and sufficient computational resources are available, it can be beneficial to combine de novo and genome-guided assemblies. Caution should be taken when using a closely related reference genome to guide transcriptome assembly. The quantity of read pairs used in the transcriptome assembly does not necessarily correlate with the quality of the assembly.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2923-8) contains supplementary material, which is available to authorized users.

Comparative performance of isolation methods using Preston broth, Bolton broth and their modifications for the detection of Campylobacter spp. from naturally contaminated fresh and frozen raw poultry meat

The performance of different isolation methods was evaluated for the detection of Campylobacter from naturally contaminated raw poultry meat. Therefore, fresh and frozen poultry meat samples were analysed using the standard procedure (ISO 10272-1:2006), enrichment in Preston broth, and enrichment in modified Bolton broth (supplemented with (i) potassium clavulanate (C-BB), (ii) triclosan (T-BB), (iii) polymyxin B (P-BB)). The enrichment cultures were streaked onto both modified charcoal cefoperazone deoxycholate agar (mCCDA) and RAPID'Campylobacter agar (RCA). Moreover, direct plating on mCCDA and RCA was performed to quantify Campylobacter. In total, 33 out of 59 fresh retail meat samples (55.9%) were Campylobacter positive. For both fresh and frozen poultry meat samples, enrichment in Bolton broth (ISO 10272-1:2006) resulted in a higher number of positive samples than enrichment in Preston broth. Supplementation of Bolton broth with potassium clavulanate (C-BB) and triclosan (T-BB) enhanced the Campylobacter recovery from fresh poultry meat compared to non-supplemented Bolton broth, although the use of C-BB was less applicable than T-BB for Campylobacter recovery from frozen samples. Additionally, the use of RCA resulted in a higher isolation rate compared to mCCDA. The present study demonstrates the impact of culture medium on the recovery of Campylobacter from fresh and frozen naturally contaminated poultry meat samples and can support laboratories in choosing the most appropriate culturing method to detect Campylobacter.

Evaluation of static and dynamic perfusion cardiac computed tomography for quantitation and classification tasks.

Cardiac computed tomography (CT) acquisitions for perfusion assessment can be performed in a dynamic or static mode. Either method may be used for a variety of clinical tasks, including (1)stratifying patients into categories of ischemia and (2)using a quantitative myocardial blood flow (MBF) estimate to evaluate disease severity. In this simulation study, we compare method performance on these classification and quantification tasks for matched radiation dose levels and for different flow states, patient sizes, and injected contrast levels. Under conditions simulated, the dynamic method has low bias in MBF estimates (0 to [Formula: see text]) compared to linearly interpreted static assessment (0.45 to [Formula: see text]), making it more suitable for quantitative estimation. At matched radiation dose levels, receiver operating characteristic analysis demonstrated that the static method, with its high bias but generally lower variance, had superior performance ([Formula: see text]) in stratifying patients, especially for larger patients and lower contrast doses [area under the curve [Formula: see text] to 96 versus 0.86]. We also demonstrate that static assessment with a correctly tuned exponential relationship between the apparent CT number and MBF has superior quantification performance to static assessment with a linear relationship and to dynamic assessment. However, tuning the exponential relationship to the patient and scan characteristics will likely prove challenging. This study demonstrates that the selection and optimization of static or dynamic acquisition modes should depend on the specific clinical task.

Analysis of angular side berthing against a rubber Cone Fender

This paper analyzes fender selection process in berth design and focuses on the case of a rigid berth with rubber cone fenders. Fender types and performance comparison methods are studied along with current numerical models. Berth design methods are analyzed with a focus on berthing energy calculation and fender selection. A new approach to determine the required fender capacity is suggested. A finite elements rubber cone model is tested and used in simulations of angular side berthing. Results show that the energy absorbed by the fender can be much higher than what can be calculated with the current berth design method. A new form for the expression of the energy that must be absorbed by the fender during angular berthing impact is suggested.

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

Genome-scale metabolic models have proven highly valuable in investigating cell physiology. Recent advances include the development of methods to extract context-specific models capable of describing metabolism under more specific scenarios (e.g., cell types). Yet, none of the existing computational approaches allows for a fully automated model extraction and determination of a flux distribution independent of user-defined parameters. Here we present RegrEx, a fully automated approach that relies solely on context-specific data and ℓ1-norm regularization to extract a context-specific model and to provide a flux distribution that maximizes its correlation to data. Moreover, the publically available implementation of RegrEx was used to extract 11 context-specific human models using publicly available RNAseq expression profiles, Recon1 and also Recon2, the most recent human metabolic model. The comparison of the performance of RegrEx and its contending alternatives demonstrates that the proposed method extracts models for which both the structure, i.e., reactions included, and the flux distributions are in concordance with the employed data. These findings are supported by validation and comparison of method performance on additional data not used in context-specific model extraction. Therefore, our study sets the ground for applications of other regularization techniques in large-scale metabolic modeling.

Soft Set Theory Oriented Forecast Combination Method for Business Failure Prediction

This paper presents a new combined forecasting method that is guided by the soft set theory (CFBSS) to predict business failures with different sample sizes. The proposed method combines both qualitative analysis and quantitative analysis to improve forecasting performance. We considered an expert system (ES), logistic regression (LR), and support vector machine (SVM) as forecasting components whose weights are determined by the receiver operating characteristic (ROC) curve. The proposed procedure was applied to real data sets from Chinese listed firms. For performance comparison, single ES, LR, and SVM methods, the combined forecasting method based on equal weights (CFBEWs), the combined forecasting method based on neural networks (CFBNNs), and the combined forecasting method based on rough sets and the D-S theory (CFBRSDS) were also included in the empirical experiment. CFBSS obtains the highest forecasting accuracy and the second-best forecasting stability. The empirical results demonstrate the superior forecasting performance of our method in terms of accuracy and stability.

A study on JPEG steganalytic features: Co-occurrence matrix vs. Markov transition probability matrix

Statistical feature selection is a key issue affecting the performance of steganalytic methods. In this paper, a performance comparison method for different types of image steganalytic features was proposed firstly based on the changing rates. Then, for two types of typical steganalytic features – co-occurrence matrix and Markov transition probability matrix, the performances of them were discussed and theoretically compared for detecting two types of well-known JPEG steganography that preserve DCT coefficients histogram and lead the histogram to shrink respectively. At last, a conclusion on the sensitivity comparison between components of these two types of features was derived: for the steganography that preserve the histogram, their sensitivities are comparable to each other; whereas for the other one (such as the steganography that subtract 1 from absolute value of the coefficient), different feature components have different sensitivities, on the basis of that, a new steganalytic feature could be obtained by fusing better components. Experimental results based on detection of three typical JPEG steganography (F5, Outguess and MB1) verified the theoretical comparison results, and showed that the detection accuracy of the fused new feature outperforms that of existing typical features.

Comparisons of ambient spray ionization imaging methods

Ambient ionization methods allow for the examination of surfaces in their native conditions at atmospheric pressure with minimal or no preparation. Spray-based ambient ionization methods such as desorption electrospray ionization (DESI) and easy ambient sonic-spray ionization (EASI) have been successfully applied to imaging mass spectrometry. In 2012, a comparative study between DESI and EASI on spatial resolution and sensitivity was published by Janfelt and Nørgaard (J. Am. Soc. Mass Spectrom., 23 (2012) 1670–1678). We expand on that work by comparing DESI and EASI techniques for the assessment of the limit of detection (LOD) of several drugs on a PTFE surface and for the determination of the spray spot size varying flow rate and solvent composition for imaging purposes. MS/MS imaging was also done with both methods for performance comparison. The results showed that good ion images can be obtained by both techniques in the MS or MS/MS mode. No significant difference was observed in the spray spot size produced by DESI and EASI. DESI was found to have similar or higher sensitivity than EASI depending on the analyte interrogated.

A new class of split exponential propagation iterative methods of Runge–Kutta type (sEPIRK) for semilinear systems of ODEs

In this paper the framework of the exponential propagation iterative methods of Runge–Kutta type (EPIRK) is extended to construct split EPIRK (sEPIRK) integrators for semilinear systems of ODEs. The structure of the sEPIRK methods possesses the flexibility and generality that allows construction of very efficient schemes. We demonstrate how bicolored trees-based B-series can be used to derive the order conditions for the new integrators. An algorithm is developed to solve the order conditions up to order three and several new schemes with desirable properties are proposed. The numerical results illustrate the advantages offered by the new class of integrators. The experiments also address the comparative performance of split vs. non-split EPIRK methods and the question of improving efficiency by optimizing coefficients of the sEPIRK schemes. It is shown that specific schemes can be custom-built to improve computational efficiency for a particular problem.

On comparative performance of multiple imputation methods for moderate to large proportions of missing data in clinical trials: a simulation study

Abstract Background: Longitudinal clinical trial has measurements at successive occasions, and unavailability of patient at a scheduled visit causes missingness in expected full sequence of the measurements. Missing

Research On Wtg Power Performance Monitoring Methods Of Regional Wind Power Group

Abstract With growth of the wind power scale and the increasing of urgent requirement on operating life extension of units followed with which, how to monitor regional wind power group automatically and find recession performance of WTG power so as to take measures timely to restore the health condition and reduce power losses has become an important problem to be solved by wind farm operators. Horizontal and longitudinal performance comparison methods of the power characteristics for the same area and model units are proposed in this paper. Different real-time monitoring and analysis methods are used. The core technology of which is using wind speed partitioning technology and Wavelet analysis. Longitudinal power performance monitoring comparison method of single-unit is used as a further preferred aspect scheme of information fusion. Research results are verified by Matlab simulation platform. The study results integrated with the developed centralized monitoring system software, can improve the efficiency of wind farm operation and monitoring in large degree, further ensure the profitability production for wind farm plants.

Structural Bionic Design for Digging Shovel of Cassava Harvester Considering Soil Mechanics

In order to improve the working performance of cassava harvester, structural bionic design for its digging shovel was conducted. Taking the oriental mole cricket's paws as bionic prototype, a new structural bionic design method for digging shovel was established, which considers the morphology-configuration-function coupling bionic. A comprehensive performance comparison method was proposed, which is used to select the bionic design schemes. The proposed bionic design method was used to improve digging shovel structure of a digging-pulling style cassava harvester, and nine bionic-type digging shovels were obtained with considering the impact of soil mechanics. After conducting mechanical properties comparative analysis for bionic-type digging shovels, the bionic design rules were summed up, and the optimal design scheme of digging shovel was obtained through combining the proposed comprehensive performance comparison method with Analytic Hierarchy Process (AHP). Studies have shown that bionic design method not only can improve the overall mechanical properties of digging shovel, but also can help to improve the harvesting effect of cassava harvester, which provides a new idea for crops harvesting machinery's structural optimization design.

Structural Bionic Design for Digging Shovel of Cassava Harvester Considering Soil Mechanics

In order to improve the working performance of cassava harvester, structural bionic design for its digging shovel was conducted. Taking the oriental mole cricket's paws as bionic prototype, a new structural bionic design method for digging shovel was established, which considers the morphology-configuration-function coupling bionic. A comprehensive performance comparison method was proposed, which is used to select the bionic design schemes. The proposed bionic design method was used to improve digging shovel structure of a digging-pulling style cassava harvester, and nine bionic-type digging shovels were obtained with considering the impact of soil mechanics. After conducting mechanical properties comparative analysis for bionic-type digging shovels, the bionic design rules were summed up, and the optimal design scheme of digging shovel was obtained through combining the proposed comprehensive performance comparison method with Analytic Hierarchy Process (AHP). Studies have shown that bionic design method not only can improve the overall mechanical properties of digging shovel, but also can help to improve the harvesting effect of cassava harvester, which provides a new idea for crops harvesting machinery's structural optimization design.

Detection of faulted phase type in distribution systems based on one end voltage measurement

Distribution power systems exposed to various unexpected failures due to many random causes. These failures are mostly happened as a result of phase faults in power system and will affect negatively the availability and reliability of the power system. Accurate detection of these faults will help in restoration of power in a timely manner and not to cause any severe damage to the power system equipment. This paper investigates the problem of accurate detection of faulted phase types occurred in the distribution system. The features of the voltage waveforms recorded from one end measurement of the distribution system during the fault occurrence are used in the proposed technique. Clarke’s transformation criterion used to identify if the fault is line-to-ground (grounded fault) or phase-to-phase (ungrounded fault). Then the fault types are classified by the high performance comparison method of the voltage signals using phase angle shift prior and during the fault occurrence. Different types of faults namely, single-phase to ground, double-phase to ground, phase–phase and balanced three-phase faults that are occurred at different locations with different fault resistances and inception angles are tested and analyzed. Results from simulation of faults on a model of 33kV distribution system typical networks presented.

Comparative diagnostic and analytical performance of PCR and LAMP-based trypanosome detection methods estimated using pooled whole tsetse flies and midguts

Detection of trypanosomes that cause disease in human beings and livestock within their tsetse fly hosts is an essential component of vector and disease control programmes. Several molecular-based diagnostic tests have been developed for this purpose. Many of these tests, while sensitive, require analysis of trypanosome DNA extracted from single flies, or from pooled tsetse fly heads and amplified trypanosome DNA. In this study, we evaluated the relative analytical and diagnostic sensitivities of two PCR-based tests (ITS and TBR) and a Trypanozoon specific LAMP assay using pooled whole tsetse flies and midguts spiked with serially diluted procyclics of a laboratory strain of Trypanosoma brucei brucei (KETRI 3386). Test sensitivity was also evaluated using experimentally infected tsetse flies. The aim was to determine the most appropriate pooling strategy for whole tsetse and midguts. RIME-LAMP had the highest diagnostic sensitivity (100%) followed by TBR-PCR (95%) and ITS-PCR (50%) in detecting trypanosome DNA from pooled tsetse midguts. RIME-LAMP also had the best diagnostic specificity (75%) followed by ITS-PCR (68%) and TBR-PCR (50%). The relative detection limit determined by serial dilution of procyclics was below 10−6 (equivalent to 1parasite/ml). Using TBR-PCR, ITS-PCR and RIME-LAMP, it was possible to detect trypanosome DNA in single flies or in pools of 2, 3, 4, 5, 10, or 15 flies/midguts. The proportion of positive pools declined by up to 60% when testing pools of 15 whole flies as opposed to testing pools of 5–10 flies. Additionally, it was possible to detect DNA in a single infected tsetse fly in the background of 4, 9, or 14 uninfected tsetse flies. Averaged across pool sizes and tsetse species, RIME-LAMP detected the highest proportion of positive pools in spiked whole tsetse and midguts (86.6% and 87.2%) followed by TBR-PCR (78. 6% and 79.2%) and ITS-PCR (34.3% and 40.2%). There were no significant differences between the proportions of positive pools detected in whole flies and midguts. We conclude that pooling of whole tsetse/midguts is an effective strategy to reduce hands-on-time and hence has potential application in large scale xenomonitoring to generate epidemiological data for decision making. RIME-LAMP offers the best diagnostic sensitivity and specificity on pooled tsetse midguts, thus demonstrating its superior diagnostic performance when compared with TBR-PCR and ITS-PCR. Using pools of whole tsetse or midguts as source of DNA does not have any significant effect on test results and is more representative of the field conditions where the proportion of flies with infected midguts tends to be higher than flies with infected salivary glands. Therefore to save time and minimize costs, pooling of whole tsetse flies is recommended.

Theoretical structure and vibrational spectra of ciprofloxacin: Density functional theory study

The molecular structure and vibrational spectra of ciprofloxacin(1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid) have been calculated using the different density functional theory (DFT) methods and various basis sets. This paper examines the comparative performance of different DFT methods at various basis sets in predicting molecular and vibrational spectra of ciprofloxacin. The calculation results show that SVWN/LANL2DZ level and SVWN/6-31G level offer the highest certainty to predict the structure and vibrational spectra of ciprofloxacin, respectively.

The Historical Simulation Method for Value-at-Risk: A Research Based Evaluation of the Industry Favorite

This paper surveys the literature relating to the historical simulation method of calculating VaR. The historical simulation method is the most popular method for VaR calculation in the banking industry. Thirty Eight papers are surveyed to understand the performance measures for VaR methods and the comparative performance of Historical Simulation VaR methods. The performance measures are broadly divided into unconditional coverage and conditional coverage measures. While regulatory requirements are limited to unconditional coverage measures, conditional coverage measures have been developed to spot the phenomenon of exception clustering. The performance of historical simulation - the basic and modified methods - in comparison with other methods is surveyed through available studies. The historical simulation approach is found to provide superior unconditional coverage among a wide variety of alternate methods ranging from the simple variance covariance approach to the sophisticated GARCH, explaining its popularity in the industry. This superiority translates into lesser likelihood of regulatory penalties since the regulatory back testing framework is based on unconditional coverage. The advantage of superior performance by historical simulation is lost when it is measured on conditional coverage measures (joint tests of unconditional coverage and independence). However, the sophisticated conditional volatility models like GARCH are not much better than the historical simulation in conditional coverage. A modification to the historical simulation method, the filtered historical simulation method emerges as the best performer using conditional coverage criteria. This study has an important contribution to make to available research. First it compiles the performance measures of VaR methods. Second it surveys the modifications to the historical simulation approach. Third and most important it presents a comparative picture of the most popular approach vis a vis other methods on a variety of performance parameters.

Characteristics and comparative performance of direct culture, direct PCR and enumeration methods for detection and quantification of Campylobacter spp. in broiler caeca

Detection and enumeration of Campylobacter spp. in broiler chicken flocks are key components of research and surveillance studies aimed at reducing Campylobacter infections in people. Direct culture of caecal contents onto selective agar is the typical method used to confirm flock colonisation. Modified charcoal cefoperazone deoxycholate agar (mCCDA) is commonly used for this method, although alternative selective media have been used. Additionally, PCR methods to detect Campylobacter DNA from caecal contents may provide a rapid alternative. However comparative performance data for these methods is limited and therefore required to ensure optimal detection methods for this sample type. In this study, 306 broiler caeca were tested for Campylobacter using direct culture on mCCDA, Skirrows and Preston agars and two real-time PCR methods, one specific for mapA/ceuE regions and another for the flaA gene region. Additionally, the suitability of spread plating and spiral plating methods for enumeration of Campylobacter and the impact of sample storage were assessed.This study confirmed modified CCDA as an optimal media for detection of Campylobacter in broiler caeca. It was significantly more sensitive than Skirrows or Preston agars. This study also demonstrated that the mapA/ceuE PCR had excellent agreement with culture on mCCDA and is a genuine alternative method. Spread plating and spiral plating methods were suitable for enumeration although spiral plating appeared more sensitive for stored samples (72h). A 1 log reduction in viable Campylobacters was observed in stored samples, therefore storage effects should be considered for quantitative studies with broiler caeca.