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PubMed2005

A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry.

There is an increasing interest in the quantitative proteomic measurement of the protein contents of substantially similar biological samples, e.g. for the analysis of cellular response to perturbations over time or for the discovery of protein biomarkers from clinical samples. Technical limitations of current proteomic platforms such as limited reproducibility and low throughput make this a challenging task. A new LC-MS-based platform is able to generate complex peptide patterns from the analysis of proteolyzed protein samples at high throughput and represents a promising approach for quantitative proteomics. A crucial component of the LC-MS approach is the accurate evaluation of the abundance of detected peptides over many samples and the identification of peptide features that can stratify samples with respect to their genetic, physiological, or environmental origins. We present here a new software suite, SpecArray, that generates a peptide versus sample array from a set of LC-MS data. A peptide array stores the relative abundance of thousands of peptide features in many samples and is in a format identical to that of a gene expression microarray. A peptide array can be subjected to an unsupervised clustering analysis to stratify samples or to a discriminant analysis to identify discriminatory peptide features. We applied the SpecArray to analyze two sets of LC-MS data: one was from four repeat LC-MS analyses of the same glycopeptide sample, and another was from LC-MS analysis of serum samples of five male and five female mice. We demonstrate through these two study cases that the SpecArray software suite can serve as an effective software platform in the LC-MS approach for quantitative proteomics.

Amino Acid Sequence↗
PubMed2005

Retrospective analysis of double-strand break rejoining data collected using warm-lysis PFGE protocols.

Sample preparation procedures for the pulsed-field gel electrophoresis (PFGE) assay usually involve a lysis step at temperatures as high as 50 degrees C. During this warm-lysis procedure, multiply damaged sites containing heat-labile sites (HLS) can be converted into double-strand breaks (DSB). Once formed, these DSB cannot be distinguished from the DSB formed directly by ionizing radiation. This paper develops a method to correct DSB estimates for the effects of HLS in warm-lysis protocols. A first-order repair model is used to predict the number of HLS available for conversion into DSB as a function of the time available for repair before initiating warm-lysis. A mathematical expression is derived to separate prompt DSB from those formed through the artefactual conversion of HLS into DSB. The proposed formalism only requires the specification of two adjustable parameters, both of which can be estimated from measured data. Estimates of prompt DSB yields obtained by correcting warm-lysis data are in good agreement with estimates obtained using cold-lysis protocols, which do not include the effect of HLS. The retrospective analyses of two published datasets suggest that corrections for HLS have a substantial impact on DSB yields within the first 20-30 min after irradiation. Bi-exponential fits to the DSB data for Chinese hamster ovary cells suggest that corrections for HLS reduce the half-time for fast DSB rejoining by about 15%, whereas the half-time for the slow DSB rejoining only decreases by 4%. The total DSB yield and the fraction of fast-rejoining DSB decrease by 24 and 38%, respectively, when the correction is applied. The proposed formalism can be used to characterize trends and uncertainties in DSB rejoining kinetics associated with the artefactual conversion of HLS into DSB. The retrospective application of the methodology to warm-lysis data enhances their relevance and usefulness for studies of DSB rejoining kinetics.

DNA Damage↗
PubMed1999

The finer things in X-ray diffraction data collection.

X-ray diffraction images from two-dimensional position-sensitive detectors can be characterized as thick or thin, depending on whether the rotation-angle increment per image is greater than or less than the crystal mosaicity, respectively. The expectations and consequences of the processing of thick and thin images in terms of spatial overlap, saturated pixels, X-ray background and I/sigma(I) are discussed. The d*TREK software suite for processing diffraction images is briefly introduced, and results from d*TREK are compared with those from another popular package.

Electronic Data Processing↗
PubMed1989

The Leukaemia Research Fund Data Collection Study: descriptive epidemiology of acute lymphoblastic leukemia.

This paper reports on cases of acute lymphoblastic leukemia (ALL) recorded by a specialist registry of hematopoietic malignancies. The cases have been diagnosed since January 1, 1984, and originate from certain parts of the United Kingdom. The information is analyzed by age, sex, and area of residence at diagnosis. The age distribution shows a childhood peak but fails to show an adult peak previously reported in literature from abroad. At a broad geographic level the county of Cumbria is shown to display the highest rates of ALL in all ages both in the 3 years of formal analyses (1984-1986) and in the 2 recent years. The administrative districts of Copeland, Sedgemoor, and North Devon also show excesses in all ages with Copeland having the highest SRR and level of statistical significance. This is a new observation for Copeland, the district containing the Sellafield nuclear reprocessing facility in that the high rates are for all ages of ALL. These new data were not considered in earlier official reports about that area. A regression analysis at electoral ward level shows no statistically significant association but excesses of cases, which are mirrored in a larger "all leukemias" data set, occur in wards near estuaries (a new observation) and in the upper socioeconomic groups.

Adolescent↗
PubMed1995

[Historical cohort study in the German rubber industry: goals, study design and data collection].

A historical cohort study is carried out to investigate occupational hazards in the German rubber industry since 1991. We present and discuss the study objectives and study design features such as cohort definition, assessment of occupational exposure and selection of the reference population. Cohort enumeration, assessment of vital status and cause of death ascertainment are described. With approximately 2,800 deaths throughout the observation period 1981 to 1991 it will be possible also to study the occupational etiology of rare diseases.

Cause of Death↗
PubMedDate not supplied

Impact of a computer-based patient record system on data collection, knowledge organization, and reasoning.

OBJECTIVE: To assess the effects of a computer-based patient record system on human cognition. Computer-based patient record systems can be considered "cognitive artifacts," which shape the way in which health care workers obtain, organize, and reason with knowledge. DESIGN: Study 1 compared physicians' organization of clinical information in paper-based and computer-based patient records in a diabetes clinic. Study 2 extended the first study to include analysis of doctor-patient-computer interactions, which were recorded on video in their entirety. In Study 3, physicians' interactions with computer-based records were followed through interviews and automatic logging of cases entered in the computer-based patient record. RESULTS: Results indicate that exposure to the computer-based patient record was associated with changes in physicians' information gathering and reasoning strategies. Differences were found in the content and organization of information, with paper records having a narrative structure, while the computer-based records were organized into discrete items of information. The differences in knowledge organization had an effect on data gathering strategies, where the nature of doctor-patient dialogue was influenced by the structure of the computer-based patient record system. CONCLUSION: Technology has a profound influence in shaping cognitive behavior, and the potential effects of cognition on technology design needs to be explored.

Cognition↗
PubMed1998

Medical baseline data collection on bone and muscle change with space flight.

It has been documented that astronauts suffer from a progressive and continuous negative calcium balance in space flight. The National Space Development Agency of Japan (NASDA) discussed the experimental protocols with the National Aeronautics and Space Agency's (NASA's) Johnson Space Center (JSC) and has started a medical baseline collection on bone and calcium metabolism, and muscle changes with space flight. The subjects were two astronauts, a 42-year-old female and a 32-year-old male, who experienced real space flights. Fractional excretion of calcium (FECa) increased in both subjects just after the space flight. There was a negative calcium balance with urinary calcium leak even after a short flight. We also noticed a decrease (-3.0%) of bone mineral density (BMD) of the lumbar spine (L2-4), a weight bearing bone. These bone changes may be due to a negative calcium balance. However, the BMD of the skull, a nonweight bearing bone, increased after the flight. This indicates that the effect of weightlessness on bone is different in respective bones, depending on the weight loading. Our data of the bone metabolic marker clearly indicate that bone resorption is stimulated, shown by an elevation of urinary pyridinolinks and plasma tartrate-resistant acid phosphate (TRACP) activity. Bone specific alkaline phosphatase, a bone formation marker, was elevated in both subjects, but not intact osteocalcin. Whether this pathophysiological phenomenon is due to an accelerated bone resorption or suppressed bone formation is still obscure. In addition, the physiological cross-sectional area (PCSA) of muscle in the legs greatly decreased (from - 10% to -15%) after the flight, and it took over a month to be recovered in both subjects. However, the muscle volume loss in the legs seemed to be reversible. To examine bone and muscle metabolism with space flight, further investigations and international standardization of experimental protocols are necessary.

Adult↗
PubMed2000

Electronic data collection by trainee anaesthetists using palm top computers.

The Royal College of Anaesthetist requires that trainees wishing to specialise in Anaesthesia register with the College and keep a logbook documenting their experience and training in clinical anaesthesia. There are a number of advantages if such logbooks are kept in an electronic format. For the first time in the United Kingdom, we have evaluated the usefulness in a district general hospital of introducing a computerized system of record keeping based on a portable palm top computer. This has enabled the careful analysis of the individual work load of each trainee in the department by means of a specific program designed to generate a comprehensive report after the information from each individual has been downloaded on to a standard desk top computer. We have found a number of interesting and unexpected results and have highlighted ways in which the system may be improved.

Anesthesiology↗
PubMed2002

Spreadsheets for automated data collection, analysis, and report generation for diagnostic medical physics: publicly available on the world wide web.

A library of spreadsheets has been developed to facilitate the practice of diagnostic physics quality assurance. Each spreadsheet follows a standard template and uses the highest ranking controlling authority (within the United States) for pass/fail criteria and testing procedures. Sheets are now available for CT (computed tomography), MR (magnetic resonance), US (ultrasound), screen-film mammography, stereotactic breast, radiographic, fluoroscopic, computed radiography, film digitizer, and display quality control. Use is made of spreadsheet "workbooks" so that each testing event is a single sheet in the workbook. Thus, results over the lifetime of the device are gathered in a single file, and historical control charts are gathered on the first sheet. The spreadsheets are available at http://radweb.mcis.washington.edu/~sglanger, and are released under the Gnu (a recursive acronym. Gnu's Not Unix) public license. It is expected that others will add improvements, and they are expected and requested to submit them back to the author to be shared with the diagnostic physicist community at large.

Diagnostic Imaging↗
PubMed2003

Prediction of experimental data for an independent variable using the experimental data collected for other independent variables in a study of skin cancer caused by exposure to UV radiation.

In this study, two algorithms (ONE and TWO) are introduced to determine the position of the t-distribution of variable V(i) (with 95% confidence) in the treated group in reference to the t-distribution of variable V(i) (with 95% confidence) in the control group of an experimental study involving UV radiation exposure of a group of rodents. The outcome of applying the two algorithms is two discretized files. A reduct of each file is generated using the rough sets methodology and then the measurements for one independent variable are predicted using the measurements of the other independent variables in the same reduct. The rough sets methodology and the fuzzy-rough classifier are used for this prediction. The results reveal that (1) algorithm TWO is the best, (2) the values for non-core variables are predicted with minimum accuracy of 87%, and (3) the prediction of values for core variables is not successful.

Algorithms↗
PubMed1988

Between-group differences in basal metabolic rates: an analysis of data collected in Scotland, the Gambia and Thailand.

Basal metabolic rate (BMR; using the Douglas bag method), body weight, and fat-free mass (FFM; using the skinfold method) were measured in 46 Scottish and 47 Gambian women in the non-pregnant non-lactating state and in 91 Scottish, 50 Gambian and 52 Thai women early in pregnancy. There were significant between-country differences in BMR (1) in absolute terms (MJ/d), (2) per kg body weight and (3) per kg FFM. However, these differences probably resulted from differences between the groups in average body weight and body composition. Differences per kg body weight were in part explained by differences in body fat content and the relatively low metabolic rate of adipose tissue. Differences in BMR/kg FFM were largely explained by between-group differences in the mass of the FFM, together with the finding that within each group, the BMR/kg FFM tended to decrease as weight increased. There were no significant differences in BMR between Scottish, Gambian and Thai women of similar FFM. There were, therefore, no apparent effects on BMR due to differences in race, climate, diet or nutritional status. Differences in the composition of the FFM could explain the 15 per cent lower BMR/kg FFM in the heaviest compared to the lightest subjects. This brings into question the widespread practice of using FFM as a metabolic reference standard. In contrast, BMR divided by the square root of FFM was similar in all three countries: for non-pregnant women, in MJ/kg0.5/d (mean and s.d.), Scotland 0.87 (0.07) and The Gambia 0.89 (0.07), and for pregnant women, Scotland 0.86 (0.07), The Gambia 0.87 (0.06) and Thailand 0.87 (0.08), and this may be a useful basis for comparing different groups in future. The accuracy of two equations for predicting BMR was assessed. The equation of FAO/WHO/UNU (1985) accurately predicted, from body weight, the average BMR of Scottish women, but under-estimated the average BMR of Gambian and Thai women by 5-10 per cent. The equation of Garby et al. (1988), which predicts BMR from FFM and fat mass, under-estimated the BMR of Scottish, Gambian and Thai women by 5, 10 and 14 per cent respectively, with the largest error within each group being for subjects with the smallest FFM.

Adipose Tissue↗
PubMed2000

Towards the Design of Open-Framework Cluster Materials: A Novel Layered Niobium Oxochloride with a Honeycomblike Structure The authors are grateful to Dr. Peter White from the University of North Carolina at Chapel Hill, USA, for crystal data collection, and Prof. Hanno zur Loye, University of South Carolina, USA, for magnetic susceptibility measurements. Wake Forest University supported this research through a grant from the Research and Creativity Fund.

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Journal Article↗
PubMed1986

A possible relationship between figure drawing data collected in medical school and later health status among physicians.

Figure drawings obtained while subjects were in medical school were scored using two different scales: (a) Sophistication-of-Body-Concept, a scoring system that measures the overall quality of the drawings; and (b) Conventionality/deviancy of the drawings, as determined by the relative frequency with which 42 different characteristics occurred in the total sample of drawings. Figure drawings were obtained from 1951 to 1964. As of 1984, subjects were classified into 1 of 11 health outcome (disease) categories plus a "healthy" category. Statistical analysis included one-way analyses of variance and multiple logistic regression in which age and cigarette consumption were controlled. Several statistically significant differences among groups were noted with respect to Conventionality/deviancy, but not with respect to Sophistication-of-Body-Concept.

Adult↗
PubMed2000

Human albumin solution for resuscitation and volume expansion in critically ill patients. The Albumin Reviewers.

BACKGROUND: Human albumin solutions are used in a range of medical and surgical problems. Licensed indications are the emergency treatment of shock and other conditions where restoration of blood volume is urgent, burns, and hypoproteinaemia. Human albumin solutions are more expensive than other colloids and crystalloids. OBJECTIVES: To quantify the effect on mortality of human albumin and plasma protein fraction (PPF) administration in the management of critically ill patients. SEARCH STRATEGY: We searched the Cochrane Injuries Group trials register, Cochrane Controlled Trials Register, Medline, Embase and BIDS Index to Scientific and Technical Proceedings. Reference lists of trials and review articles were checked, and authors of identified trials were contacted. The search was last updated in November 1999. SELECTION CRITERIA: Randomised controlled trials comparing albumin/PPF with no albumin/PPF, or with a crystalloid solution, in critically ill patients with hypovolaemia, burns or hypoalbuminaemia. DATA COLLECTION AND ANALYSIS: We collected data on the participants, albumin solution used, mortality at the end of follow up, and quality of allocation concealment. Analysis was stratified according to patient type. We assessed publication bias using the regression test for funnel plot asymmetry. MAIN RESULTS: We found 30 trials meeting the inclusion criteria and reporting death as an outcome. There were 156 deaths among 1419 trial participants. For each patient category the risk of death in the albumin treated group was higher than in the comparison group. For hypovolaemia the relative risk of death following albumin administration was 1.46 (95% confidence interval 0.97 to 2.22), for burns the relative risk was 2.40 (1.11 to 5.19), and for hypoalbuminaemia the relative risk was 1.69 (1.07 to 2.67). The pooled relative risk of death with albumin administration was 1.68 (1.26 to 2.23). Overall, the risk of death in patients receiving albumin was 14% compared to 8% in the control groups, an increase in the risk of death of 6% (3% to 9%). These data suggest that for every 17 critically ill patients treated with albumin there is one additional death. REVIEWER'S CONCLUSIONS: There is no evidence that albumin administration reduces the risk of death in critically ill patients with hypovolaemia, burns or hypoalbuminaemia, and a strong suggestion that it may increase the risk of death. These data suggest that the use of human albumin in critically ill patients should be urgently reviewed and that it should not be used outside the context of a rigorously conducted randomised controlled trial.

Blood Proteins↗
PubMed2000

Premedication for anxiety in adult day surgery.

BACKGROUND: Surgery is increasingly performed on a day-case basis. Many patients are anxious pre-operatively and might benefit from pharmacological anxiolysis. Drugs are sometimes not used, however, for fear of delaying discharge from hospital. OBJECTIVES: To asses the effect of anxiolytic premedication on time to discharge in adult patients undergoing day case surgery under general anaesthesia. SEARCH STRATEGY: Trials were identified by computerised searches of the Cochrane Controlled Trials Register, MEDLINE, EMBASE, by checking the reference lists of trials and review articles, by hand-searching three main anaesthesia journals and by contacting five researchers active in the field and the Product Information departments of the manufacturers of five commonly used premedicants. SELECTION CRITERIA: All randomised controlled trials comparing an anxiolytic drug(s) with placebo before general anaesthesia in adult day case surgical patients. DATA COLLECTION AND ANALYSIS: We collected data on anaesthetic drugs used, results of tests of psychomotor function where these were used to assess residual effect of premedication, and on times from end of anaesthesia to ability to walk unaided or readiness for discharge from hospital. Formal statistical synthesis of individual trials was not performed in view of the variety of drugs studied. MAIN RESULTS: Searching identified twenty-nine reports; fourteen studies, with data from a total of 1263 patients, were considered eligible for analysis. Only two studies specifically addressed the discharge question; both found no delay in premedicated patients. Three other studies used clinical criteria to assess fitness for discharge, though times were not given. Again, there was no difference from placebo. Four studies used both clinical measures and tests of psychomotor function as tests of recovery from anaesthesia. In none of these studies did the premedication appear to delay discharge, although performance on tests of psychomotor function was sometimes still impaired. Of the four studies which used tests of psychomotor function to assess recovery, three showed impaired recovery (after midazolam 7.5mg, midazolam 15mg or diazepam 15mg) which might possibly interfere with discharge from hospital. REVIEWER'S CONCLUSIONS: We have found no evidence of a difference in time to discharge from hospital in patients who received anxiolytic premedication. However, in view of the age and variety of anaesthetic techniques used, inferences for current day-case practice should be made with caution.

Adult↗
PubMed2000

A Dodecanuclear Copper(II) Cage Containing Phosphonate and Pyrazole Ligands This work was supported by a grant from the Department of Science and Technology (DST), New Delhi (V.C.). V.C. is also grateful to the Homi Bhabha Fellowship Council for a fellowship. We thank the DST for funding the National Facility for X-ray Crystallography at the Indian Institute of Technology, Kanpur. We thank Prof. Dr. P. K. Bharadwaj for his help in the data collection and X-ray analysis, and Prof. Dr. A. R. Chakravorthy, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India for the magnetic measurements on 1.

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Journal Article↗
PubMed1995

The suitability of a monofunctional reagent of an undecagold cluster for phasing data collected from the large ribosomal subunits from Bacillus stearothermophilus.

An electron density map of the large ribosomal subunit from Bacillus stearothermophilus was obtained at 26 A resolution by single isomorphous replacement (SIR) from a derivative formed by specific quantitative labeling with a dense undecagold cluster. For derivatization, a monofunctional reagent of this cluster was bound to a sulfhydryl group of a purified ribosomal protein, which was in turn reconstituted with core particles of a mutant lacking this protein. The native, mutated, and derivatized 50S ribosomal subunits crystallize under the same conditions in the same space group. Under favorable conditions, crystals of the derivatized subunit proved to be isomorphous with the native ones, whereas the crystals of the mutant may have somewhat different packing. After resolving the SIR phase ambiguity by solvent flattening, the electron density shows a packing that is consistent with the noncrystallographic symmetry found by Patterson searches as well as with the motif observed in electron micrographs of thin sections of the crystals. These studies established that phase information can be obtained from heavy metal clusters, even when the crystals under investigation are unstable and weakly diffracting. These results encouraged further effort at the construction of specifically derivatized crystals from other ribosomal particles that diffract to higher resolution.

Crystallography, X-Ray↗