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PubMedDate not supplied

Growth variability in avian embryos as a source of experimental error.

To reduce variability in an embryonic population to be used in experiments with electromagnetic fields, 820 Japanese quail eggs (41 experiments, 20 eggs per experiment) were incubated to analyze different possible inputs of experimental variance. Eggs came from a randombred progenitor population obtained from a poultry farm and selectively maintained. The results show that growth variability is significantly higher in some progenies, which show bimodal distributions; this is evidence of the existence of a dichotomous population with different growth velocities within these populations. This phenomenon seems to be the result of growth factors inherited from the progenitors and not of environmental factors. A genetic selection of the progenitors used in the experimental lines dealing with growth variability in birds seems necessary to reduce any possible erroneous interpretation of the experimental results.

Animals↗
PubMed2006

Differences of vertebral area in serial bone density measurements: a common source of potential error in interpretation of BMD change.

Vertebral projected areas in serial BMD scans should not differ significantly to avoid measurement error due to apparent change in projected bone size. This criterion is rarely achieved in clinical practice. We analyzed 103 consecutive pairs of DXA reports to determine the frequency and magnitude of serial differences in vertebral area. Scans were performed at qualified community radiology sites and included if free from any technical errors, artifacts or rotation. We calculated the proportion of paired scans having at least 2 vertebrae differing in area by<2%,<3%,<4% or<5%. Using these differing sets of validity criteria, vertebrae not meeting the areal standard were removed form the analysis and the overall change in BMD recalculated. The new, recalculated BMD was compared to the original report to determine the frequency and magnitude by which the re-analysis would change the final report. Of the paired scans, 5%, 16%, 27% and 35% had all 4 vertebrae differ in area by less than 2%, 3%, 4% and 5% respectively. When only two vertebrae were required to meet acceptability criteria, 51%, 73%, 85% and 89% of scans met the 2%, 3%, 4% and 5% difference criteria. 11% of scans were non-comparable by even the least stringent criteria of two vertebra differing by<5% between scans. Re-analysis of BMD change in each group differed from the reported change by 0.012-0.015 g/cm(2). However, this amount was sufficient to change a clinical report from "significant change" to "non-significant change" in 26%, 27%, 21%, and 20% of scans in each of the four validity groups using a least significant change of 0.025 g/cm(2). Between 11%-17% of scans differed in the recalculated BMD change by an amount greater than the least significant change of 0.025 g/cm(2). Fewer serial BMD results were classified as non-acceptable when using the broader validity criteria of<5% area difference, but when corrected for areal differences, a similar and large proportion of scans would have a major change in the clinical interpretation of BMD change. These results do not change the interpretation of population BMD change in randomized trials but highlight the need for more caution in data analysis of serial densitometry results when used to make individual patient management decisions.

Absorptiometry, Photon↗
PubMed2003

mRNA 5' region sequence incompleteness: a potential source of systematic errors in translation initiation codon assignment in human mRNAs.

The amino acid sequence of gene products is routinely deduced from the nucleotide sequence of the relative cloned cDNA, according to the rules for recognition of start codon (first-AUG rule, optimal sequence context) and the genetic code. From this prediction stem most subsequent types of product analysis, although all standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. Revision by bioinformatics and cloning methods of 109 known genes located on human chromosome 21 (HC 21) shows that 60 mRNAs lack any in-frame stop upstream of the first-AUG, and that in five cases (DSCR1, KIAA0184, KIAA0539, SON, and TFF3) the coding region at the 5' end was incompletely characterized in the original descriptions. We describe the respective consequences for genomic annotation, domain and ortholog identification, and functional experiments design. We have also analyzed the sequences of 13,124 human mRNAs (RefSeq databank), discovering that in 6448 cases (49%), an in-frame stop codon is present upstream of the initiation codon, while in the other 6676 mRNAs (51%), identification of additional bases at the mRNA 5' region could well reveal some new upstream in-frame AUG codons in the optimal context. Proportionally to the HC 21 data, about 550 known human genes might thus be affected by this 5' end mRNA artifact.

5' Untranslated Regions↗
PubMed1996

Evaluating data acquisition and smoothing functions of currently available videokeratoscopes.

PURPOSE: To compare the accuracy of computerized videokeratography systems using identical, calibrated test objects. SETTING: Lions Eye Institute, Albany, New York. METHODS: We evaluated the accuracy and smoothing of raw data acquisition (axial solution) of seven commercially available videokeratoscopes: Alcon EyeMap, Computed Anatomy TMS, EyeSys CAS, Humphrey MasterVue, Topcon CM-1000, Optikon Keratron, and TechnoMed C-Scan. We used six calibrated test objects to simulate clinical settings: spherical, spherocylindrical, simulated myopic ablation, hyperopic ablation, and a simulated central island. RESULTS: None of the systems accurately imaged all objects. Although all systems imaged spherical objects with reasonable accuracy, errors greater than 4.0 diopters (D) frequently occurred in the central 6.0 mm optical zone (maximum error 10.0 D) Sources of error included excessive raw data smoothing, inability to read large transitions, loss of accuracy in the periphery, and poor central coverage. CONCLUSION: The clinician should be aware of the potential limitations of corneal topography when making clinical decisions.

Cornea↗
PubMed2002

Oxidation of 7,8-dihydro-8-oxoguanine affords lesions that are potent sources of replication errors in vivo.

Three single-stranded DNA genomes have been constructed that contain the 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) oxidation products oxaluric acid, oxazalone, and cyanuric acid. Oligonucleotides containing each lesion were synthesized by treating an oligonucleotide containing a single 8-oxodG with peroxynitrite, and the desired products were isolated by HPLC. The modified oligonucleotides were ligated into M13mp7L2 bacteriophage DNA in such a way that the lesion was situated at a known site in the lacZ gene fragment of the viral genome. The circular genomes were transfected into wild-type AB1157 Escherichia coli. The relative efficiency of lesion bypass by DNA polymerase was determined by counting the number of initial independent infections produced by each genome relative to that of an unmodified DNA control. Viral progeny were analyzed for mutation frequency and type by PCR amplification of the insert region followed by a recently developed post-labeling assay. All three secondary lesions were readily bypassed, causing G --> T transversions at frequencies at least an order of magnitude higher than 8-oxodG. These data establish a model whereby the modestly mutagenic primary lesion 8-oxodG is oxidized in vivo to much more highly mutagenic secondary lesions.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2003

The hydantoin lesions formed from oxidation of 7,8-dihydro-8-oxoguanine are potent sources of replication errors in vivo.

Single-stranded DNA genomes have been constructed that site-specifically contain the 7,8-dihydro-8-oxo-2'-deoxyguanine (8-oxoG) oxidation products guanidinohydantoin (Gh) and the two stable stereoisomers of spiroiminodihydantoin (Sp1 and Sp2). The circular viral genomes were transfected into wild-type AB1157 Escherichia coli, and the efficiency of lesion bypass by DNA polymerase(s) was assessed. Viral progeny were analyzed for mutation frequency and type using the recently developed restriction endonuclease and postlabeling (REAP) assay. Gh was bypassed nearly as efficiently as the parent 8-oxoG but was highly mutagenic, causing almost exclusive G --> C transversions. The stereoisomers Sp1 and Sp2 were, in comparison, much stronger blocks to DNA polymerase extension and caused a mixture of G --> T and G --> C transversions. The ratio of G --> T to G --> C mutations for each Sp lesion was dependent on the stereochemical configuration of the base. All observed mutation frequencies were at least an order of magnitude higher than those caused by 8-oxoG. Were these lesions to be formed in vivo, our data show that they are absolutely miscoding and may be refractory to repair after translesion synthesis.

DNA↗
PubMed2001

What happens to the student? The neglected variable in educational outcome research.

Disputes about the superiority of teaching methods often remain unresolved. The essential question we continuously want to answer is: Which teaching methods yield the best knowledge and skills in students? Abundant literature, in medical education and in education in general, on research with educational methods as independent variables and measures of outcome (e.g., test scores) as the dependent variable often point at "no significant difference" or only small differences between methods. Many factors do influence the educational outcome in students and large statistical power (such as meta analysis) should be helpful to eliminate many sources of error. However, one source we cannot tackle this way. That is, students will usually adapt quantity and quality of studying to meet testing requirements. In doing so, they may compensate for teaching quality. Some teaching may generate more effort in students than other teaching. Since test scores reflect primarily student activities, it is their efforts that may bring differences in teaching methods close to equality in test scores. Therefore, knowledge and skills should not be considered the primary outcome of teaching but the outcome of learning activities. If we want to discriminate between teaching methods, we must at least consider what happens to students.

Clinical Competence↗
PubMed2003

The potential synergy between cognitive models and modern psychometric models.

Analyses of cognitive aspects of survey methodology (CASM) and psychometric analysis are two methods that are able to complement each other. We use concrete examples to illustrate how psychometric analyses can test hypotheses from CASM. The psychometrics framework recognizes that survey responses are affected by other factors than the concept being assessed, for example by cognitive factors and processes. Such factors are subsumed under the concept of measurement error. Possible sources of measurement error can be tested, e.g. by randomized experiments. A standard way to reduce measurement error is to ask several questions about the same concept and combine the answers into a multi-item scale that is more precise than the individual items. Techniques like structural equation models use the item correlations to assess the magnitude of measurement error and to test the assumptions behind the multi-item scale, e.g. the effect of common response choices and item time frames. A central problem in modern psychometrics is how to model the mapping of the continuous latent variable onto the item response choice categories. This is achieved by threshold models (e.g. item response models and structural equation models for categorical data). These models can, for example, analyze the impact of mode of administration, test whether the items function in the same way for all people (measurement invariance/differential item functioning) and examine the consistency of responses from any single person. Such analyses provide new possibilities for combining psychometrics and cognitive methods.

Attitude to Health↗