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Processing Software (processing + software)
Kinds of Processing Software Selected AbstractsTime-based analysis of silver-stained proteins in acrylamide gelsELECTROPHORESIS, Issue 10 2006Bertram Becher Dr. Abstract Silver staining of proteins after PAGE often remains the method of choice in many laboratories. Nevertheless, it is known that quantification of protein levels is keenly restricted to a small range of protein concentrations leading to an over- or underestimation of protein amounts. To overcome this, a time-based analysis method was developed to avoid the saturation effect of the silver-staining reaction, thus resulting in an improved dynamic range of the gel image produced and therefore better quantification of proteins. Instead of the well-known end-point image analysis, gray intensities of time series images of a developing gel are determined and times until a threshold gray value is reached are calculated. These times are used to calculate a new grayscale image which can be analyzed using commercial image processing software. [source] Diagnostic accuracy of digital photography and image analysis for the measurement of foot conformation in the horseEQUINE VETERINARY JOURNAL, Issue 7 2008J. M. WHITE Summary Reasons for performing study: Rigorous evaluation of practicable methods for the objective assessment of foot conformation has not been performed. Objectives: To assess the practicability, precision and accuracy of the process of obtaining measurements of horses' feet using photography and image processing software. Methods: Precision study: Lateral photographs of horses' feet were obtained twice by 2 veterinary surgeons (image acquisition - IAc). Photographs were analysed by 2 masked veterinary surgeons on 2 occasions (image analysis - IAn). Measurements were compared within and between operators for self and non-self acquired photographs. Agreement indices (AIs) and 95% limits of agreement (LOA) were calculated for the IAn process alone and for the combined IAc + IAn processes. Accuracy study: Measurements obtained from lateral photographs were compared with those obtained from lateromedial radiographs. AIs and 95% LOA were calculated for each measurement. Results: Precision study: Mean intra- and interoperator AIs for the IAn process alone were ,0.90 while those for the combined IAc + IAn processes were ,0.89 for all measurements. Similar mean AIs and 95% LOA were calculated regardless of image origin. The 95% LOA for hoof angle, heel height/toe height% and coronary band angle for all comparisons were within target values. Accuracy study: Mean AIs were ,0.89 for all measurements. The 95% LOA for heel height/toe height% and coronary band angle were within target values. Conclusions: Excellent precision was identified within and between operators regardless of image origin. High levels of accuracy were also identified, especially for heel height/toe height% and coronary band angle, indicating that photography and radiography may be used interchangeably. Potential relevance: Acquisition and analysis of photographic images is an appropriate method for the objective measurement of foot conformation, both in clinical and research settings. [source] Regional variation of intracortical porosity in the midshaft of the human femur: age and sex differencesJOURNAL OF ANATOMY, Issue 2 2005C. David L. Thomas Abstract This study investigated age and sex differences in patterns of porosity distribution in the midshaft of the human femur. Cross-sections were obtained from 168 individuals from a modern Australian population. The sample comprised 73 females and 95 males, aged between 20 and 97 years. Microradiographs were made of 100-µm sections and pore and bone areas were determined using image processing software. Initially the sample was divided by age: young (20,44 years), middle (45,64 years) and old (65+ years), but it was found that analysis on the basis of the ratio of medullary area to total subperiosteal area gave clearer results. The cortex was divided into three rings radially and into octants circumferentially and the porosity of each segment was calculated. Results showed that a pattern with raised porosity in the posterior and anterolateral regions, and with greater porosity in the inner parts of the cortex, becomes more pronounced with age. In males this pattern develops steadily; in females there are much greater differences between the middle and older groups than earlier in life. The patterns observed are consistent with progressive bone loss occurring along a neutral axis of the cortex where bending stress is lowest and the mechanical advantage of the bone is least. [source] Searching for anthropogenic contaminants in human breast adipose tissues using gas chromatography-time-of-flight mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2009Félix Hernández Abstract The potential of gas chromatography-time-of-flight mass spectrometry (GC-TOF MS) for screening anthropogenic organic contaminants in human breast adipose tissues has been investigated. Initially a target screening was performed for a list of 125 compounds which included persistent halogen pollutants [organochlorine (OC) pesticides, polychlorinated biphenylss (PCBs), polybrominated diphenyl ethers (PBDEs)], polyaromatic hydrocarbons (PAHs), alkylphenols, and a notable number of pesticides from the different fungicide, herbicide and insecticide families. Searching for target pollutants was done by evaluating the presence of up to five representative ions for every analyte, all measured at accurate mass (20-mDa mass window). The experimental ion abundance ratios were then compared to those of reference standards for confirmation. Sample treatment consisted of an extraction with hexane and subsequent normal-phase (NP) High performance liquid chromatography (HPLC) or SPE cleanup. The fat-free LC fractions were then investigated by GC-TOF MS. Full-spectral acquisition and accurate mass data generated by GC-TOF MS also allowed the investigation of nontarget compounds using appropriate processing software to manage MS data. Identification was initially based on library fit using commercial nominal mass libraries. This was followed by comparing the experimental accurate masses of the most relevant ions with the theoretical exact masses with calculations made using the elemental composition calculator included in the software. The application of both target and nontarget approaches to around 40 real samples allowed the detection and confirmation of several target pollutants including p,p,-DDE, hexachlorobenzene (HCB), and some polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Several nontarget compounds that could be considered anthropogenic pollutants were also detected. These included 3,5-di- tert -butyl-4-hydroxy-toluene (BHT) and its metabolite 3,5-di- tert -butyl-4-hydroxybenzaldehyde (BHT-CHO), dibenzylamine, N -butyl benzenesulfonamide (N -BBSA), some naphthalene-related compounds and several PCBs isomers not included in the target list. As some of the compounds detected are xenoestrogens, the methodology developed in this paper could be useful in human breast cancer research. Copyright © 2008 John Wiley & Sons, Ltd. [source] Morphometric and spatial analysis of thaw lakes and drained thaw lake basins in the western Arctic Coastal Plain, AlaskaPERMAFROST AND PERIGLACIAL PROCESSES, Issue 4 2005K. M. Hinkel Abstract Landsat-7 ETM,+ scenes were acquired for the western Arctic Coastal Plain of Alaska extending from 152° to 162° W longitude. A segmentation algorithm was used to classify lakes and drained thaw lake basins (DTLBs) exceeding 1,ha in size. A total of 13,214 lakes and 6539 DTLBs were identified. Several indices were obtained from the image processing software and used for a comparative analysis of lakes and basins including object size, goodness of elliptic fit, shape complexity, shape asymmetry, and orientation of the major axis. Nonparametric statistical analyses indicate that lakes and basins share similar orientation only. Three subregions of the western Arctic Coastal Plain were identified based on landscape age, as demarcated by ancient shorelines. The surfaces become progressively older inland and include the Younger Outer Coastal Plain, the Outer Coastal Plain, and the oldest Inner Coastal Plain. Lakes and basins in all subregions have statistically similar orientation, indicating that summer wind direction has not changed appreciably over the past several thousand years. Basin orientation is less clustered than lake orientation. Lakes are highly elliptical, while basins have more complex shapes. Lake coverage (%) is fairly constant across the three subregions, while DTLB coverage decreases on older surfaces. Lake and basin size decreases on progressively older surfaces, but the number of features per unit area increases. It is uncertain if surface age is responsible for differences in regional metrics as an analysis of the Inner Coastal Plain demonstrates significant internal variation. Distance from the coast, ground ice content, surficial sediments, and local relief may also influence lake morphometry. Copyright © 2005 John Wiley & Sons, Ltd. [source] Isobaric metabolite interferences and the requirement for close examination of raw data in addition to stringent chromatographic separations in liquid chromatography/tandem mass spectrometric analysis of drugs in biological matrixRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2008Zhengyin Yan In addition to matrix effects, common interferences observed in liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses can be caused by the response of drug-related metabolites to the multiple reaction monitoring (MRM) channel of a given drug, as a result of in-source reactions or decomposition of either phase I or II metabolites. However, it has been largely ignored that, for some drugs, metabolism can lead to the formation of isobaric or isomeric metabolites that exhibit the same MRM transitions as parent drugs. The present study describes two examples demonstrating that interference caused by isobaric or isomeric metabolites is a practical issue in analyzing biological samples by LC/MS/MS. In the first case, two sequential metabolic reactions, demethylation followed by oxidation of a primary alcohol moiety to a carboxylic acid, produced an isobaric metabolite that exhibits a MRM transition identical to the parent drug. Because the drug compound was rapidly metabolized in rats and completely disappeared in plasma samples, the isobaric metabolite appeared as a single peak in the total ion current (TIC) trace and could easily be quantified as the drug since it was eluted at a retention time very close to that of the drug in a 12-min LC run. In the second example, metabolism via the ring-opening of a substituted isoxazole moiety led to the formation of an isomeric product that showed an almost identical collision-induced dissociation (CID) MS spectrum as the original drug. Because two components were co-eluted, the isomeric product could be mistakenly quantified and reported by data processing software as the parent drug if the TIC trace was not carefully inspected. Nowadays, all LC/MS data are processed by computer software in a highly automated fashion, and some analysts may spend much less time to visually examine raw TIC traces than they used to do. Two examples described in this article remind us that quality data require both adequate chromatographic separations and close examination of raw data in LC/MS/MS analyses of drugs in biological matrix. Copyright © 2008 John Wiley & Sons, Ltd. [source] | |||||||||||||