Development of an impregnated reagent and automation of solid-phase analytical derivatization for carbonyls: proof of principle.
This study undertakes reduction of scale and automation of a solid-phase analytical derivatization of carbonyls with 2,4-dinitrophenylhyrazine on a styrene-divinylbenzene resin (XAD-2). Three processes are tested. In the batch process, an aqueous phase consisting of 50 microL of sample and 150 microL of reagent solution is contacted with 6 mg XAD-2 by shaking. An impregnated reagent consisting of 2,4-dinitrophenylhydrazine hydrochloride (DNPH) deposited on XAD-2 enables two additional processes. In-vial derivatization with an impregnated reagent requires shaking 50 microL of sample with 6 mg of the impregnated reagent and reduced the reaction time from 10 to 5 min. The third process involves packing impregnated reagent a mini-column and flowing 50 microL of sample through under positive pressure supplied by a Harvard Pump. This reduces sample preparation time to 1 min. Studies are conducted with worst-case model analytes: butanone, 2-pentanone, and malonyldialdehyde. The carbonyl of the two ketones is hindered, and, thus, these two compounds react very slowly with DNPH in aqueous solution. Malonyldialdehyde is highly water soluble, and it does not react in aqueous phase but also would not sorb onto XAD-2 for reaction. Nevertheless, derivatization/extraction of all model compounds any of the three procedures result in reproducible and high yields. (+info)
An automated method for rapid identification of putative gene family members in plants.
BACKGROUND: Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences following duplication (adaptive selection) appears to be a common mechanism of evolution in plants and can be accompanied by purifying selection on the coding region. Such negative selection can be detected by a bias toward synonymous over nonsynonymous substitutions. However, the process of identifying this bias requires many steps usually employing several different software programs. We have simplified the process and significantly shortened the time required by condensing many steps into a few scripts or programs to rapidly identify putative gene family members beginning with a single query sequence. RESULTS: In this report we 1) describe the software tools (SimESTs, PCAT, and SCAT) developed to automate the gene family identification, 2) demonstrate the validity of the method by correctly identifying 3 of 4 PAL gene family members from Arabidopsis using EST data alone, 3) identify 2 to 6 CAD gene family members from Glycine max (previously unidentified), and 4) identify 2 members of a putative Glycine max gene family previously unidentified in any plant species. CONCLUSION: Gene families in plants, particularly that subset where purifying selection has occurred in the coding region, can be identified quickly and easily by integrating our software tools and commonly available contig assembly and ORF identification programs. (+info)
Early experiences in evolving an enterprise-wide information model for laboratory and clinical observations.
As Electronic Healthcare Records become more prevalent, there is an increasing need to ensure unambiguous data capture, interpretation, and exchange within and across heterogeneous applications. To address this need, a common, uniform, and comprehensive approach for representing clinical information is essential. At Partners HealthCare System, we are investigating the development and implementation of enterprise-wide information models to specify the representation of clinical information to support semantic interoperability. This paper summarizes our early experiences in: (1) defining a process for information model development, (2) reviewing and comparing existing healthcare information models, (3) identifying requirements for representation of laboratory and clinical observations, and (4) exploring linkages to existing terminology and data standards. These initial findings provide insight to the various challenges ahead and guidance on next steps for adoption of information models at our organization. (+info)
Performance of automated slidemakers and stainers in a working laboratory environment - routine operation and quality control.
Comparison between automated and manual measurements of carotid intima-media thickness in clinical practice.
BACKGROUND AND AIM: The measurement of carotid intima-media thickness (cIMT) has been used as a marker of arterial wall disease. Manual measurements have been performed in most epidemiological studies, but, due to the introduction of new technologies, automated software has been increasingly used. This study aimed to compare manual versus automated cIMT measurements in common carotid (CC), bifurcation (BIF), and internal carotid (IC). METHODS: Automated and manual cIMT measurements were performed online in 43 middle-aged females. Carotid segment measurements were compared by Bland-Altman plot and the variation and repeatability coefficients between observers were also determined for comparison. RESULTS: The average timespan for manual measurements (57.30 s) were significantly higher than for automated measurements (2.52 s). There were no systematic errors between methods in any carotid segments. The variation coefficient was 5.54% to 6.34% for CC and BIF, 9.76% for IC, and absolute differences were 85% below 0.1 mm and 70% below 0.05 mm. Interobserver agreement showed no systematic error. The variation and the repeatability coefficients were better for the automated than manual measures. CONCLUSION: Although both methods are reliable for cIMT measurements, the automated technique allows faster evaluation with lesser variability for all carotid segments currently used in atherosclerosis research. (+info)
Three-dimensional imaging core laboratory of the endovascular aneurysm repair trials: validation of methodology.
Manual versus automatic sampling variations of a preliminary alcohol screening device.
Utilization of a manual sampling function as an alternative to the automatic sampling function in the Alco-Sensor IV Black Dot Model has been recognized by the manufacturer to potentially underestimate an individual's true breath alcohol content (BrAC). A controlled human subject study was conducted to analyze the possible breath-sampling differences between the standard automatic technique and three manual techniques. Subjects were dosed with vodka and orange juice and then tested during the descending limb of their BrAC curve. Differences between the automatic and the manual techniques were found to be statistically significant with the three manual techniques underestimating the BrAC. The average maximum difference between the automatic BrAC level, as compared to the lowest manual level in each data set, was 27.9% (median 27.7%) with underestimations from 20.8% to 40.0%. In no instance did any of the manual techniques produce higher BrACs than the automatic technique. (+info)