| 1. |
- Akhtar, Malik N., et al.
(författare)
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Accurate Assignment of Significance to Neuropeptide Identifications Using Monte Carlo K-Permuted Decoy Databases
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:10, s. e111112-
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Tidskriftsartikel (refereegranskat)abstract
- In support of accurate neuropeptide identification in mass spectrometry experiments, novel Monte Carlo permutation testing was used to compute significance values. Testing was based on k-permuted decoy databases, where k denotes the number of permutations. These databases were integrated with a range of peptide identification indicators from three popular open-source database search software (OMSSA, Crux, and X! Tandem) to assess the statistical significance of neuropeptide spectra matches. Significance p-values were computed as the fraction of the sequences in the database with match indicator value better than or equal to the true target spectra. When applied to a test-bed of all known manually annotated mouse neuropeptides, permutation tests with k-permuted decoy databases identified up to 100% of the neuropeptides at p-value < 10(-5). The permutation test p-values using hyperscore (X! Tandem), E-value (OMSSA) and Sp score (Crux) match indicators outperformed all other match indicators. The robust performance to detect peptides of the intuitive indicator "number of matched ions between the experimental and theoretical spectra" highlights the importance of considering this indicator when the p-value was borderline significant. Our findings suggest permutation decoy databases of size 1x10(5) are adequate to accurately detect neuropeptides and this can be exploited to increase the speed of the search. The straightforward Monte Carlo permutation testing (comparable to a zero order Markov model) can be easily combined with existing peptide identification software to enable accurate and effective neuropeptide detection. The source code is available at http://stagbeetle.animal.uiuc.edu/pepshop/MSMSpermutationtesting.
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| 2. |
- Akhtar, Malik N., et al.
(författare)
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Evaluation of Database Search Programs for Accurate Detection of Neuropeptides in Tandem Mass Spectrometry Experiments
- 2012
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 11:12, s. 6044-6055
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Tidskriftsartikel (refereegranskat)abstract
- Neuropeptide identification in mass spectrometry experiments using database search programs developed for proteins is challenging. Unlike proteins, the detection of the complete sequence using a single spectrum is required to identify neuropeptides or prohormone peptides. This study compared the performance of three open-source programs used to identify proteins, OMSSA, X!Tandem and Crux, to identify prohormone peptides. From a target database of 7850 prohormone peptides, 23550 query spectra were simulated across different scenarios. Crux was the only program that correctly matched all peptides regardless of p-value and at p-value < 1 X 10(-2), 33%, 64%, and >75%, of the 5, 6, and >= 7 amino acid-peptides were detected. Crux also had the best performance in the identification of peptides from chimera spectra and in a variety of missing ion scenarios. OMSSA, X!Tandem and Crux correctly detected 98.9% (99.9%), 93.9% (97.4%) and 88.7% (98.3%) of the peptides at E- or p-value < 1 X 10(-6) (< 1 X 10(-2)), respectively. OMSSA and X! Tandem outperformed the other programs in significance level and computational speed, respectively. A consensus approach is not recommended because some prohormone peptides were only identified by one program.
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| 3. |
- Akhtar, Malik N., et al.
(författare)
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Identification of best indicators of peptide-spectrum match using a permutation resampling approach
- 2014
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Ingår i: Journal of Bioinformatics and Computational Biology. - 0219-7200 .- 1757-6334. ; 12:5, s. 1440001-
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Tidskriftsartikel (refereegranskat)abstract
- Various indicators of observed-theoretical spectrum matches were compared and the resulting statistical significance was characterized using permutation resampling. Novel decoy databases built by resampling the terminal positions of peptide sequences were evaluated to identify the conditions for accurate computation of peptide match significance levels. The methodology was tested on real and manually curated tandem mass spectra from peptides across a wide range of sizes. Spectra match indicators from complementary database search programs were pro filed and optimal indicators were identified. The combination of the optimal indicator and permuted decoy databases improved the calculation of the peptide match significance compared to the approaches currently implemented in the database search programs that rely on distributional assumptions. Permutation tests using p-values obtained from software-dependent matching scores and E-values outperformed permutation tests using all other indicators. The higher overlap in matches between the database search programs when using end permutation compared to existing approaches con firmed the superiority of the end permutation method to identify peptides. The combination of effective match indicators and the end permutation method is recommended for accurate detection of peptides.
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| 4. |
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| 5. |
- Beheshti, Reza, et al.
(författare)
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Black Dross : Processing Salt Removal from Black Dross by Thermal Treatment
- 2014
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Ingår i: JOM. - : Springer Science and Business Media LLC. - 1047-4838 .- 1543-1851. ; 66:11, s. 2243-2252
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Tidskriftsartikel (refereegranskat)abstract
- The salt removal from black dross by thermal treatment has experimentally been studied under different conditions in both a stationary resistance furnace and in a laboratory scale rotary furnace. The experiments were designed based on partial pressure calculations using the Thermo-Calc software (Thermo-Calc Software, Stockholm, Sweden). The salt removal efficiency was evaluated by scanning electron microscope (SEM) energy-dispersive x-ray spectroscopy and x-ray diffraction analyses, and the optimum conditions for treatment established, i.e., temperature, gas flow rate, holding time, rotation rate, and sample size. The overall degree of chloride removal was established to increase as a function of time and temperature, as well as by reduced pressure. Under atmospheric pressure, the highest degree of chloride removal from a 20 g sample was obtained after 10 h at 1523 K resulting in a 98% removal and a final chloride content of 0.3 wt.% in the residue. Under reduced pressure, the chloride concentrate was lowered to 0.2 wt.% after thermal treatment of a 20 g sample at 1473 K for 8 h. In the case of 200 g samples treated in a rotary furnace, the chloride concentrate was 2.5 wt.% after 14 h at 1523 K, representing a removal of 87%. Below 0.3 wt.% chloride content, the material is deemed a nonhazardous waste.
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| 6. |
- Beheshti, Reza, et al.
(författare)
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Heat treatment of black dross for the production of a value added material - a preliminary study
- 2012
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Ingår i: EPD Congress 2012. - Hoboken, NJ, USA : John Wiley & Sons. - 9781118291405 ; , s. 353-360
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Konferensbidrag (refereegranskat)abstract
- The potential use of Black Dross (BD) as a raw material for the production of refractories, fluxing agents and glasses is the main motivation of the present study. Heat treatment experiments were carried out in Ar, and under reduced pressure (20 Pa), to evaluate the salt removal efficiency. The chemical composition of the BD after heat treatment was investigated by SEM-EDS and XRD analyses. Based on the present results, it is established that the salt starts to evaporate at ≈1273 K in Ar, and under reduced pressure. The salt removal efficiency in a 20 g sample was found to increase in both cases as a function of time and temperature. Moreover, in Ar the chlorine concentration was lowered to 0.3 wt% after heat treatment at 1523 K for 10 hours. Under reduced pressure, however, 0.2 wt% residual chlorine was obtained after 8 hours at 1473 K.
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| 7. |
- Kennedy, Mark W., et al.
(författare)
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Analytical and Experimental Validation of Electromagnetic Simulations Using COMSOL®, re Inductance, Induction Heating and Magnetic Fields
- 2011
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Konferensbidrag (refereegranskat)abstract
- This paper presents a snap shot of experimental work, which has been conducted at NTNU on billet heating with induction coils. A significant volume of experimental data have been collected for coils running with up to 0.2T: high accuracy Hall probe readings (+/-1%), metal conductivity (+/-0.5%), and heat generation (+/- 4%) have been collected.Results are analyzed using newly developed analytical models and COMSOL 2D axial symmetric models. Agreement is exceptionally good for both magnetic field strength/distribution and induced heating in the aluminium billets.
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| 8. |
- Kennedy, Mark W., et al.
(författare)
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Analytical and FEM modeling of aluminum billet induction heating with experimental verification
- 2012
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Ingår i: Light Metals 2012. - Hoboken, NJ, USA : John Wiley & Sons. ; , s. 269-275
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Konferensbidrag (refereegranskat)abstract
- Induction heating is commonly used in the re-heating of aluminum billets before forging or extrusion. Powerful finite element modeling (FEM) tools are available to assist in the design of such processes; however, such models should be validated by comparison with analytical solutions or experimental results to ensure accuracy. Induction heating experiments have been performed using a number of different coil designs and work piece dimensions at 50 Hz. Aluminum alloys with different electrical conductivities have been used, i.e. 6060 and A356. Process parameters such as: current, power, magnetic field, electrical conductivity, etc. have been measured with high precision instrumentation. Experimental data are presented and compared with equivalent 1D analytical and 2D axial symmetric FEM modeling results. The effect of frequency on the induction heating process is reviewed using the validated analytical and FEM models. Some recommendations are given with respect to appropriate modeling techniques, boundary conditions and numerical mesh sizes.
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| 9. |
- Kennedy, Mark William, et al.
(författare)
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Characterization of Ceramic Foam Filters Used for Liquid Metal Filtration
- 2013
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Ingår i: Metallurgical and materials transactions. B, process metallurgy and materials processing science. - : Springer Science and Business Media LLC. - 1073-5615 .- 1543-1916. ; 44:3, s. 671-690
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Tidskriftsartikel (refereegranskat)abstract
- In the current study, the morphology including tortuosity, and the permeability of 50-mm thick commercially available 30, 40, 50, and 80 pores per inch (PPI) alumina ceramic foam filters (CFFs) have been investigated. Measurements have been taken of cell (pore), window, and strut sizes, porosity, tortuosity, and liquid permeability. Water velocities from similar to 0.015 to 0.77 m/s have been used to derive both first-order (Darcy) and second-order (Non-Darcy) terms for being used with the Forchheimer equation. Measurements were made using 49-mm "straight through" and 101-mm diameter "expanding flow field" designs. Results from the two designs are compared with calculations made using COMSOL 4.2a(A (R)) 2D axial symmetric finite element modeling (FEM), as a function of velocity and filter PPI. Permeability results are correlated using directly measurable parameters and compared with the previously published results. Development of improved wall sealing (49 mm) and elimination of wall effects (101 mm) have led to a high level of agreement between experimental, analytic, and FEM methods (+/- 0 to 7 pct on predicted pressure drop) for both types of experiments. Tortuosity has been determined by two inductive methods, one using cold-solidified samples at 60 kHz and the other using liquid metal at 50 Hz, giving comparable results.
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| 10. |
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