Simplified Data Analysis Research Articles

Identification of a Small Molecule That Induces Mitotic Arrest Using a Simplified High-Content Screening Assay and Data Analysis Method

High-content screening has emerged as a new and powerful technique for identifying small-molecule modulators of mammalian cell biology. The authors describe the development and execution of a high-content screen to identify small molecules that induce mitotic arrest in mammalian cancer cells. Many widely used chemotherapeutics, such as Taxol and vinblastine, induce mitotic arrest, and the creation of new drugs that also induce mitotic arrest may have tremendous therapeutic value. In their screen, the authors employed a simple DNA stain (DAPI) and a sensitive nonparametric statistical test to identify compounds from an internal collection of approximately 13,000 high-quality lead-like small molecules. Subsequent analysis of 1 active compound indicated that it induces mitotic arrest, assessed using a high-content phosphohistone H3 detection assay, and caused cell proliferation defects in multiple cancer cell lines. The active compound, a quinazolinone originating from a natural product-like subset of the screened compounds, is active in cells at approximately 500 nM and appears to act by inhibiting the polymerization of tubulin.

Identification of Phytophthora Isolates to Species Level Using Restriction Fragment Length Polymorphism Analysis of a Polymerase Chain Reaction-Amplified Region of Mitochondrial DNA

ABSTRACT Polymerase chain reaction primers spanning the mitochondrially encoded coxI and II genes have been identified that were capable of amplifying target DNA from all 152 isolates of 31 species in the genus Phytophthora that were tested. Digestion of the amplicons with restriction enzymes generated species-specific restriction fragment length polymorphism banding profiles that were effective for isolate classification to a species level. Of the 24 species in which multiple isolates were examined, intraspecific polymorphisms were not observed for 16 species, while 5 species exhibited limited intraspecific polymorphism that could be explained by the addition/loss of a single restriction site. Intraspecific polymorphisms were observed for P. megakarya, P. megasperma, and P. syringae; however, these differences may be a reflection of the variation that exists in these species as reported in the literature. Although digestion with AluI alone could differentiate most species tested, single digests with a total of four restriction enzymes were used in this investigation to enhance the accuracy of the technique and minimize the effect of intraspecific variability on correct isolate identification. The use of the computer program BioNumerics simplified data analysis and identification of isolates. Successful template amplification was obtained with DNA recovered from hyphae using a boiling miniprep procedure, thereby reducing the time and materials needed for conducting this analysis.

196 poster Simplified data analysis with a relational database dedicated to prostate brachytherapy

196 poster Simplified data analysis with a relational database dedicated to prostate brachytherapy

Degradation mechanism of electrodeposited coatings in alkaline solution

Electrodeposited organic coatings are used as primers or as a single-layer coating for corrosion protection of domestic appliances. In this application, it is important to avoid any possible coating degradation that could be caused by detergent solution which may accidentally come in contact with the coating. These kinds of coatings are often tested by immersion of the coated metal sheet with a cross scribe in a detergent solution (pH 11, temperature 74 °C) for about 10 days, measuring the extent of delamination away from the scribe at the end of the test. In these tests, a high dispersion of data is noted: specimens that have been prepared to be equivalent show a range of delamination from almost zero to very high levels, unacceptable for the application. The aim of this work is to define the reasons for the anomalous and premature failure of some specimens. The experimental work was carried out using mainly electrochemical techniques and surface analysis. A mechanism of delaminative degradation has been proposed, based on the chemical conversion layer (zinc phosphate) of the steel substrate, the porosity of the organic coating (dependent on the deposition conditions) and the particular environment (high temperature and pH). The final results reveal the cause of the problem and allow a definition of a testing approach, based on electrochemical impedance measurements, capable of checking the coating quality during production. This test is conducted in well controlled conditions and with a simplified data analysis procedure.

In situ single‐particle characterization at Cape Grim

This paper describes operation of the particle analysis by laser mass spectrometry (PALMS) instrument at Cape Grim. Several changes to the instrument improved the uniformity of ionization, simplified data analysis, and reduced the minimum analyzable particle size to 0.16 μm. Almost all of the particles analyzed by PALMS at Cape Grim during clean marine conditions contained some sea salt. Almost all of the sulfate found during clean marine conditions was mixed with sea salt rather than in separate ammonium sulfate or sulfuric acid aerosols. Metals such as Cr, Fe, and Sn were detected in a few particles even in clean marine air masses. An NO+ peak in the mass spectra was associated with Mg, Ca, and Sr. This association could be caused either by the water retention of various salts or by different reactivities. It provides a reminder that other components of sea salt besides NaCl need to be considered for heterogeneous chemistry.

Selective NMR Experiments on Macromolecules: Implementation and Analysis of QUIET-NOESY

The QUIET-NOESY experiment (Zwahlenet al., J. Am. Chem Soc.116, 362–368, 1994) is applied to measure the mobility of the flexible extensions in the large aggregate (800 kDa) of a small heat-shock protein. The proper choices of the experimental protocol and parameters are discussed in order to employ a simplified data analysis procedure. Further experimental verification of the proposed strategy is also presented using the cyclic peptide gramicidin S as a model compound. Under suitable conditions, the determinations based on the analysis of QUIET-NOESY data are affected to a negligible extent by the approximations that are introduced by the proposed approach.

Towards a device independent digital image processing software for photoelastic analysis

AbstractThe application of digital image processing (DIP) techniques to photoelasticity has greatly simplified data reduction and analysis. The softwares reported so far are hardware dependent and hence not portable. A simple PC based device independent software for collection of photoelastic data from digitised fringe patterns is presented. The software is validated by evaluating the near crack tip stress field parameters for a crack subjected to mode I and mode II loadings.

H*(10) Response of the REM-2 Recombination Chamber in Monoenergetic Neutron Fields

Measurements with the REM-2 recombination chamber were performed in the monoenergetic reference neutron fields at the PTB. The energy dependence of the H*(10) ambient dose equivalent response was investigated for 12 different neutron energies ranging from 75 keV to 19 MeV. A new simplified data analysis for the determination of H*(10) with the ICRP 60 quality factor was tested. The results indicate that the REM-2 recombination chamber is well suited for the direct determination of the ambient dose equivalent in mixed neutron/photon radiation fields.

Thermal anemometry, current state, and future directions

The variation in heat transfer between a fine wire and the surrounding fluid has traditionally been the most accepted method for measuring the detailed movements of a flow fluid. This paper reviews the present understanding of thermal techniques as used in research and recent advancements of the technique. While the basic research sensor is still a fine wire, modern electronics has greatly simplified data analysis as well as established constant temperature operation of the sensor as the control method of choice. Film sensors have extended the use of thermal sensors to new applications. Comparisons with laser Doppler velocimeters help to identify experiments where thermal sensors still represent the best choice. The ability of modern electronics to easily address the typical nonlinear response of thermal sensors has resulted in increased use for commercial applications. While in these applications fast response can be a factor (e.g., fuel flow control in engines), generally only average flows are needed. As a result, calibration shifts due to deposits on the sensor surface when exposed to contaminated fluids can generally be reduced to acceptable levels by using larger sensors.

Ultrasonic integrated backscatter: Simplified data analysis with a MacIntosh-based videodigitization system: Samuel A. Wickline, Mark R. Holland, Scott M. Handley, Julio E. Perez and James G. Miller, Washington University, St. Louis, MO 63130

Ultrasonic integrated backscatter: Simplified data analysis with a MacIntosh-based videodigitization system: Samuel A. Wickline, Mark R. Holland, Scott M. Handley, Julio E. Perez and James G. Miller, Washington University, St. Louis, MO 63130

Kinetic mechanism of the type II calmodulin-dependent protein kinase: studies of the forward and reverse reactions and observation of apparent rapid-equilibrium ordered binding

The kinetic reaction mechanism of the type II calmodulin-dependent protein kinase was studied by using its constitutively active kinase domain. Lacking regulatory features, the catalytic domain simplified data collection, analysis, and interpretation. To further facilitate this study, a synthetic peptide was used as the kinase substrate. Initial velocity measurements of the forward reaction were consistent with a sequential mechanism. The patterns of product and dead-end inhibition studies best fit an ordered Bi Bi kinetic mechanism with ATP binding first to the enzyme, followed by binding of the peptide substrate. Initial-rate patterns of the reverse reaction of the kinase suggested a rapid-equilibrium mechanism with obligatory ordered binding of ADP prior to the phosphopeptide substrate; however, this apparent rapid-equilibrium ordered mechanism was contrary to the observed inhibition by the phosphopeptide which is not supposed to bind to the kinase in the absence of ADP. Inspection of product inhibition patterns of the phosphopeptide with both ATP and peptide revealed that an ordered Bi Bi mechanism can show initial-rate patterns of a rapid-equilibrium ordered system when a Michaelis constant for phosphopeptide, Kip, is large relative to the concentration of phosphopeptide used. Thus, the results of this study show an ordered Bi Bi mechanism with nucleotide binding first in both directions of the kinase reaction. All the kinetic constants in the forward and reverse directions and the Keq of the kinase reaction are reported herein. To provide theoretical bases and diagnostic aid for mechanisms that can give rise to typical rapid-equilibrium ordered kinetic patterns, a discussion on various sequential cases is presented in the Appendix.

A simplified competition data analysis for radioligand specific activity determination

Non-linear regression and two-step linear fit methods were developed to determine the actual specific activity of 125I-ovine prolactin by radioreceptor self-displacement analysis. The experimental results obtained by the different methods are superposable. The non-linear regression method is considered to be the most adequate procedure to calculate the specific activity, but if its software is not available, the other described methods are also suitable.

A rapid, multisample technique for detection of trace elements in trees by energy-dispersive X-ray fluorescence spectroscopy

A new method is presented for studying the distribution of trace elements in trees. A tree core is removed, sectioned into very thin slices (≤400 μm), and analyzed directly using X-ray fluorescence spectroscopy. The technique offers a number of advantages, including minimal sample preparation time, elimination of contamination or leaching, and rapid simplified data analysis. Analysis of 10 or more samples per annual ring is possible. Application of the technique in two studies (first, using trees as indicators of airborne pollutants and second, analyzing pesticide residues in trees) is described. In the first study there were significant correlations between seasonal airborne pollution levels and the levels of lead and zinc detected in the phloem tissue of red alder, Alnusrubra Bong. In the other study, the technique was used to analyze arsenic content in lodgepole pines, Pinuscontorta var. latifolia Englemann, treated with monosodium methanearsonate. Vertical arsenic profiles in treated trees indicated accumulations of arsenic near the site of injection at the base of the bole and in the foliage. Differential radial uptake was also apparent.

Ion beam analysis with a 6 MV van de Graaff

Rutherford backscattering and channeling techniques using 4He analysis beams with energies less than 2.5 MeV have proven to be powerful methods for determination of stoichiometry, structure, thickness and impurity concentrations in thin films. We discuss examples illustrating the advantages of routine use of analysis ion beams (from a single-ended 6 MV Van de Graaff) with energies greater than 2.5 MeV. We compare 170° 4He backscattering spectra obtained at higher energies (3.8 and 4.7 MeV) with similar spectra obtained at 1.9 MeV to show that use of the higher energies leads to simplified data analysis, greater probing depth and more accurate determination of film stoichiometry. We briefly report progress in attempts to 1) use backscattering of 12C analysis beams to obtain improved mass and depth resolution, 2) use 4He analysis beams to depth profile P in Si using (α, p) nuclear reactions at incident 4He energies of 3.655 and 4.343 MeV and 3) use 15N2+ analysis beams with energies ≥ 6.3 MeV to depth profile 1H in films using the (15N, αγ) nuclear reaction at 6.385 MeV.

Simplified data analysis for an inexpensive manual analogue penetrometer

A simple, rapid, semi-automated digitization method was developed for a microcomputer to aid in the collection and analysis of data obtained from an inexpensive, manual analogue recording penetrometer. Soil strength measurements were taken in a Norfolk loamy sand at Florence, SC using a hand-operated recording penetrometer with a 30°, 12.5 mm diameter cone tip. Three probings were taken at each position within each plot and recorded by pen tracings on an index card. Soil strength readings were taken at 0.1-m spacings across planted rows. Data were read from the cards for each 50-mm depth interval by placing them under the control of a microcomputer and the program “DIGIT”. Once initialized for the soil surface, the program automatically moved an eyepiece in the horizontal direction to the position on the card for a specific depth. The operator then moved the eyepiece vertically over the tracings and recorded the data via the digitization process using a flat-bed plotter and microcomputer. These data were averaged over replicates and plotted as isostrength contours using a locally written interpolation plotting routine.