An automated method for ATP analysis utilizing the luciferin-luciferase reaction

An automated method for the analysis of ATP has been described. This method uses the luciferin-luciferase reaction, with the firefly extract being delivered by means of an automatic pipetter interfaced with an automatic liquid scintillation spectrometer. A range of 10–300 pmoles is obtained with a standard deviation of 5·10%. An analysis rate of approximately 200 samples per hr can be attained. At least 1400 samples can be run from one standard curve when the firefly extract is stabilized with bovine serum albumin and mercaptoethanol.     

Continuing education for cytotechnologists: the Australian experience

The development of a continuing education scheme for cytotechonologists in Australia is described. The process involved the establishment of a working party with Terms of Reference to review current practice in Australia and existing schemes in other parts of the world. The scheme developed takes the form of a continuing education diary that provides guidelines on the various forms of continuing education activity and corresponding credit points. The diary also provides for a record of activity to be kept. The scheme requires bi-annual submission of personal activity which is logged into a national database. A peer profile is provided and successful achievement is marked by the issue of a certificate of participation. The programme has achieved a 57% compliance in its first year of operation.     

New technologies for automated cell counting based on optical image analysis `The Cellscreen'

A prototype of a newly developed apparatus for measuring cell growth characteristics of suspension cells in micro titre plates over a period of time was examined. Fully automated non-invasive cell counts in small volume cultivation vessels, e.g. 96 well plates, were performed with the Cellscreen system by Innovatis AG, Germany. The system automatically generates microscopic images of suspension cells which had sedimented on the base of the well plate. The total cell number and cell geometry was analysed without staining or sampling using the Cedex image recognition technology. Thus, time course studies of cell growth with the identical culture became possible. Basic parameters like the measurement range, the minimum number of images which were required for statistically reliable results, as well as the influence of the measurement itself and the effect of evaporation in 96 well plates on cell proliferation were determined. A comparison with standard methods including the influence of the cultured volume per well (25 l to 200 l) on cell growth was performed. Furthermore, the toxic substances ammonia, lactate and butyrate were used to show that the Cellscreen system is able to detect even the slightest changes in the specific growth rate.     

Issues for application of virtual microscopy to cytoscreening,perspectives based on questionnaire to Japanese cytotechnologists

To clarify the issues associated with the applications of virtual microscopy to the daily cytology slide screening, we conducted a survey at a slide conference of cytology. The survey was conducted specifically to the Japanese cytology technologists who use microscopes on a routine basis. Virtual slides (VS) were prepared from cytology slides using NanoZoomer (Hamamatsu Photonics, Japan), which is capable of adjusting focus on any part of the slide. A total of ten layers were scanned from the same slides, with 2 micrometer intervals. To simulate the cytology slide screening, no marker points were created. The total data volume of six slides was approximately 25 Giga Bytes. The slides were stored on the Windows 2003 Server, and were made accessible on the web to the cytology technologists. Most cytotechnologists answered "Satisfied" or "Acceptable" to the VS resolution and drawing speed, and "Dissatisfied" to the operation speed. To the ten layered focus, an answer "insufficient" was slightly more frequent than the answer "sufficient", while no one answered "fewer is acceptable" or "no need for depth". As for the use of cytology slide screening, answers "usable, but requires effort" and "not usable" were about equal in number. In a Japanese cytology meeting, a unique VS system has been used in slide conferences with markings to the discussion point for years. Therefore, Japanese cytotechnologists are relatively well accustomed to the use of VS, and the survey results showed that they regarded VS more positively than we expected. Currently, VS has the acceptable resolution and drawing speed even on the web. Most cytotechnologists regard the focusing capability crucial for cytology slide screening, but the consequential enlargement of data size, longer scanning time, and slower drawing speed are the issues that are yet to be resolved.     

Designing an automated clinical decision support system to match clinical practice guidelines for opioid therapy for chronic pain

Background

Opioid prescribing for chronic pain is common and controversial, but recommended clinical practices are followed inconsistently in many clinical settings. Strategies for increasing adherence to clinical practice guideline recommendations are needed to increase effectiveness and reduce negative consequences of opioid prescribing in chronic pain patients.

Methods

Here we describe the process and outcomes of a project to operationalize the 2003 VA/DOD Clinical Practice Guideline for Opioid Therapy for Chronic Non-Cancer Pain into a computerized decision support system (DSS) to encourage good opioid prescribing practices during primary care visits. We based the DSS on the existing ATHENA-DSS. We used an iterative process of design, testing, and revision of the DSS by a diverse team including guideline authors, medical informatics experts, clinical content experts, and end-users to convert the written clinical practice guideline into a computable algorithm to generate patient-specific recommendations for care based upon existing information in the electronic medical record (EMR), and a set of clinical tools.

Results

The iterative revision process identified numerous and varied problems with the initially designed system despite diverse expert participation in the design process. The process of operationalizing the guideline identified areas in which the guideline was vague, left decisions to clinical judgment, or required clarification of detail to insure safe clinical implementation. The revisions led to workable solutions to problems, defined the limits of the DSS and its utility in clinical practice, improved integration into clinical workflow, and improved the clarity and accuracy of system recommendations and tools.

Conclusions

Use of this iterative process led to development of a multifunctional DSS that met the approval of the clinical practice guideline authors, content experts, and clinicians involved in testing. The process and experiences described provide a model for development of other DSSs that translate written guidelines into actionable, real-time clinical recommendations.

     

An automated, handheld biosensor for aflatoxin

A new immunoaffinity fluorometric biosensor has been developed for detecting and quantifying aflatoxins, a family of potent fungi-produced carcinogens that are commonly found in a variety of agriculture products. They have also been cited as a biological agent under weapons development. The handheld, self-contained biosensor is fully automatic, highly sensitive, quick, quantitative, and requires no special storage. Approximately 100 measurements can be made before refurbishment is required, and concentrations from 0.1 parts per billion (ppb) to 50 ppb can be determined in <2 min with a 1 ml sample volume. The device operates on the principles of immunoaffinity for specificity and fluorescence for a quantitative assay. The analytic procedure is flexible so that other chemical and biological analytes could be detected with minor modifications to the current device. Advances in electro-optical components, electronics, and miniaturized fluidics were combined to produce this reliable, small, and versatile instrument.     

Measuring driver impairments: sleepiness, distraction, and workload

Snow was falling heavily when Sarah was driving on a slippery road to her cousin's country cottage. It was dark outside, and the visibility was poor. She had planned to arrive before sunset, but the rental service had made a mistake, and it took hours before she got her rental car at the airport. It was past midnight now, and after a long day of traveling, Sarah was starting to get sleepy. Fortunately, there were only 15 km to go, but her eyelids were starting to feel heavy. To stay awake, she put her favorite CD on, turned up the volume, and started to sing along. This seemed to help a little-good-only 10 km to go. This was when Sarah's phone started ringing, and she awkwardly tried to find the mute button for the car stereo while answering the phone. As she looked up again, she barely caught a glimpse of the red brake lights of the car in front of her as she smashed into it.     

Liquid chromatography with multi-channel electrochemical detection for the determination of epigallocatechin gallate in rat plasma utilizing an automated blood sampling device

A liquid chromatography method with multi-channel electrochemical detection was developed for the determination of epigallocatechin gallate (EGCG) in rat plasma. After administration of EGCG, blood samples were periodically collected by Culex (an automated blood sampling robot). EGCG was extracted from 50 μl of diluted blood (blood and saline at a ratio of 1:1) with ethyl acetate. Chromatographic separation was achieved within 10 min using a C₈ (150×4.6 mm) 5 μm column with a mobile phase containing 20 mM sodium monochloroacetate, pH 2.8 and 12% acetonitrile at a flow-rate of 1.2 ml/min. A four-channel detector with glassy carbon electrodes was used with applied potentials of +700, 600, 500, 400 mV vs. Ag/AgCl. The limit of detection was 2 ng/ml at a signal-to-noise ratio of 3:1 and the limit of quantitation was 5 ng/ml. The calibration curve was linear over the range of 5–800 ng/ml. The intra- and inter-assay precisions were in the range of 1.3–4.5% and 2.2–4.4%, respectively. Using this method it was possible to determine plasma concentration following a single dose of EGCG to rats with good accuracy and precision. Thus the pharmacokinetic properties of EGCG in rats can be examined for intravenous, intraperitoneal and oral dosing.     

SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis

We have compared the accuracy, efficiency and robustness of three methods of genotyping single nucleotide polymorphisms on pooled DNAs. We conclude that (i) the frequencies of the two alleles in pools should be corrected with a factor for unequal allelic amplification, which should be estimated from the mean ratio of a set of heterozygotes (k); (ii) the repeatability of an assay is more important than pinpoint accuracy when estimating allele frequencies, and assays should therefore be optimised to increase the repeatability; and (iii) the size of a pool has a relatively small effect on the accuracy of allele frequency estimation. We therefore recommend that large pools are genotyped and replicated a minimum of four times. In addition, we describe statistical approaches to allow rigorous comparison of DNA pool results. Finally, we describe an extension to our ACeDB database that facilitates management and analysis of the data generated by association studies.     

RFAC,a program for automated NMR R-factor estimation

A computer program (RFAC) has been developed, which allows the automated estimation of residual indices (R-factors) for protein NMR structures and gives a reliable measure for the quality of the structures. The R-factor calculation is based on the comparison of experimental and simulated ¹H NOESY NMR spectra. The approach comprises an automatic peak picking and a Bayesian analysis of the data, followed by an automated structure based assignment of the NOESY spectra and the calculation of the R-factor. The major difference to previously published R-factor definitions is that we take the non-assigned experimental peaks into account as well. The number and the intensities of the non-assigned signals are an important measure for the quality of an NMR structure. It turns out that for different problems optimally adapted R-factors should be used which are defined in the paper. The program allows to compute a global R-factor, different R-factors for the intra residual NOEs, the inter residual NOEs, sequential NOEs, medium range NOEs and long range NOEs. Furthermore, R-factors can be calculated for various user defined parts of the molecule or it is possible to obtain a residue-by-residue R-factor. Another possibility is to sort the R-factors according to their corresponding distances. The summary of all these different R-factors should allow the user to judge the structure in detail. The new program has been successfully tested on two medium sized proteins, the cold shock protein (TmCsp) from Termotoga maritima and the histidine containing protein (HPr) from Staphylococcus carnosus. A comparison with a previously published R-factor definition shows that our approach is more sensitive to errors in the calculated structure.     

Choosing the preventive workload in general practice: practical application of the Coronary Prevention Group guidelines and Dundee coronary risk-disk.

OBJECTIVE--To determine the workload implications for general practice of the Coronary Prevention Group and British Heart Foundation action plan for preventing heart disease. DESIGN--Computer simulation of plan, including calculation of Dundee risk scores, with data from OXCHECK trial. SUBJECTS--4759 patients aged 35-64 who had health checks during 1989-91. MAIN OUTCOME MEASURE--Effect of using different risk scores as thresholds on workload and coverage of patients at known risk. Thresholds of 6-20 were used for cholesterol screening (nearset) and 4-16 for special care (preset). RESULTS--On the basis of workload a nearset of 8 and preset of 12 would be reasonable. This implies cholesterol measurement in 1794 (37.7%) patients and special care in 1074 (22.6%). However, many patients with single risk factors were not allocated to special care at these thresholds: 11 (37.9%) patients with cholesterol concentrations > or = 10 mmol/l, 21 (33.9%) with systolic pressure > or = 180 mm Hg, and 213 (40.7%) heavy smokers (> 20 cigarettes/day) were missed. The distribution of scores was similar in those at established clinical risk, those with family history of heart disease, and others. CONCLUSION--The guidelines may help to make best use of resources within specific age-sex groups but sound protocols for unifactorial risk assessment and modification remain essential.     

MAK,a computational tool kit for automated MITE analysis

Miniature inverted repeat transposable elements (MITEs) are ubiquitous and numerous in higher eukaryotic genomes. Analysis of MITE families is laborious and time consuming, especially when multiple MITE families are involved in the study. Based on the structural characteristics of MITEs and genetic principles for transposable elements (TEs), we have developed a computational tool kit named MITE analysis kit (MAK) to automate the processes (http://perl.idmb.tamu.edu/mak.htm). In addition to its ability to routinely retrieve family member sequences and to report the positions of these elements relative to the closest neighboring genes, MAK is a powerful tool for revealing anchor elements that link MITE families to known transposable element families. Implementation of the MAK is described, as are genetic principles and algorithms used in its derivation. Test runs of the programs for several MITE families yielded anchor sequences that retain TIRs and coding regions reminiscent of transposases. These anchor sequences are consistent with previously reported putative autonomous elements for these MITE families. Furthermore, analysis of two MITE families with no known links to any transposon family revealed two novel transposon families, namely Math and Kid, belonging to the IS5/Harbinger/PIF superfamily.     

A quick,reliable, and automated method for fat cell sizing

Mean diameters of fat cells from abdominal tissues from 31 volunteers were determined by three methods based on fat cell isolation after collagenase digestion and methylene blue staining. The three methods were direct microscopy (Micro), manual measurement of diameters from digital images by using the public domain NIH Image program (Scion), and automated measurement of diameters from digital images using a customized program developed by Biomedical Imaging Resource at Mayo Clinic (AdCount). There was excellent agreement between the methods' measurement of mean abdominal fat cell diameter (concordance correlation coefficient >0.84). The Scion method gave slightly but systematically lower mean abdominal fat cell diameters than did either AdCount or Micro. The AdCount approach produced results that are comparable to those from Micro. Comparison of AdCount and Micro in measuring diameters of fat cells from thigh confirmed the good comparability between the two methods independent of fat depot. AdCount is very reliable, and the quickest and most objective of the three methods in measuring fat cell diameters from various depots.