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PubMed1985

Curtailed binomial sampling procedures for clinical trials with paired data.

The use of curtailed sampling procedures in designing clinical trials with a dichotomous response and paired data is reviewed. Tables of expected sample size savings and a simple to evaluate asymptotic formula for the expected sample size savings are presented where the sample size savings is calculated relative to the fixed sample size test. Comparisons are made among fixed sample size, curtailed, and repeated significance hypothesis testing procedures. In view of the substantial savings in sample size available under certain conditions and the accuracy of the approximating formula, it is recommended that curtailed procedures be given serious consideration in the design of clinical trials.

Clinical Trials as Topic↗
PubMed1995

A few considerations in the design and analysis of experiments in neurotoxicology.

To help minimize errors and confusion in the scientific literature, a few principles can be followed. The original intent and hypothesis of each study should be made clear, and deviations from the initial purpose should be stated. The hypothesis-testing portions of the research need to be clearly differentiated from the hypothesis generating sections. If data were selected and reanalyzed in unintended ways, the analyses should be clearly identified as hypothesis generating, and no conclusions should be drawn from such data. The data should be unassailable. The control group should be adequate. The data analysis should be consistent with the experimental design. Given that the larger the number of P-values, the greater the rate of false declarations, the total number of derived P-values should be reasonable and should be reported. The publication should unveil all details necessary to understand and replicate the research project, including the data analysis. Alternate etiologies should be seriously considered in light of potential confounding factors. It is important to be critical of the results of a study, especially when data confirm a preconceived hypothesis.

Animals↗
PubMed2002

Emergency medical service rescue times in Riyadh.

The emergency medical service (EMS) in Saudi Arabia is managed by each hospital through the Saudi Red Crescent Society (SRCS). There are approximately 165 ambulance stations in the country, each with two ambulances. The SRCS collects data on EMS requests and ambulance arrival times at the accident scene. Each emergency incident has its own implications (accident, fire, injury, etc.) and must be dealt with individually. The aims of this study are to evaluate ambulance rescue time, which includes response time, in the city of Riyadh, the capital of Saudi Arabia; to analyze this time for road traffic accidents; and to compare the response time in Riyadh with corresponding times in other countries. A sample of 874 emergency calls was collected during 1999. Ambulance rescue time consists of three components: response time, time at the scene and travel time to the hospital. Data analysis showed that rescue time is, on average, 35.84 min (S.D. = 6.43 min). Within this time, the average response time is 10.23 min (S.D. = 5.66 min). Other service components (e.g. ambulance time at the accident scene and travel time to the hospital) are analyzed and detailed statistics are given. Ambulance speed to the accident averages approximately 55.05 km/h (S.D. = 27.42 km/h). One primary finding is that there is room for improvement in the rescue time in Riyadh, which would save more lives, through an increase in the efficiency of ambulance team performance. A test statistic is developed in this study to carry out a simple hypothesis testing for percentiles. This test statistic, which is generic and can be used for other applications, is used to compare EMS response time in Riyadh with that in other parts of the world.

Accidents, Traffic↗
PubMed1995

Sex-role orientation and satisfaction with life.

The hypothesis that androgynous people are more satisfied with life than others was tested by administering the Personal Attributes Questionnaire and the Satisfaction with Life Scale to 245 undergraduates (111 men and 134 women). Results strongly supported the tested hypothesis for men but not for women.

Adult↗
PubMed1995

Basic statistics for clinicians: 2. Interpreting study results: confidence intervals.

In the second of four articles, the authors discuss the "estimation" approach to interpreting study results. Whereas, in hypothesis testing, study results lead the reader to reject or accept a null hypothesis, in estimation the reader can assess whether a result is strong or weak, definitive or not. A confidence interval, based on the observed result and the size of the sample, is calculated. It provides a range of probabilities within which the true probability would lie 95% or 90% of the time, depending on the precision desired. It also provides a way of determining whether the sample is large enough to make the trial definitive. If the lower boundary of a confidence interval is above the threshold considered clinically significant, then the trial is positive and definitive, if the lower boundary is somewhat below the threshold, the trial is positive, but studies with larger samples are needed. Similarly, if the upper boundary of a confidence interval is below the threshold considered significant, the trial is negative and definitive. However, a negative result with a confidence interval that crosses the threshold means that trials with larger samples are needed to make a definitive determination of clinical importance.

Clinical Trials as Topic↗
PubMed1996

Potential of the back propagation neural network in the morphologic examination of thyroid lesions.

OBJECTIVE: To investigate the potential of back propagation (BP) neural networks (NNs) in the discrimination of benign from malignant thyroid lesions. STUDY DESIGN: The study was performed on May-Grünwald-Giemsa-stained smears obtained by fine needle aspiration (FNA). Using a custom image analysis system, 26 features that describe the size, shape and texture of the nucleus were measured from each cell. The cases were distributed according to categories, as follows: 25 cases of goiter and follicular adenomas, 1 case of follicular carcinoma, 12 cases of papillary carcinoma, 6 cases of oncocytic adenoma, 3 cases of oncocytic carcinoma and 4 cases of Hashimoto thyroiditis. From each case about 100 nuclei were measured; they formed a pool of 13,850 feature vectors. Out of this pool, 2,770 vectors were randomly selected to form the training set, and the remaining 11,080 vectors formed the test set. RESULTS: The application of a BP NN on the nuclear measurements permitted correct classification of 90.61% nuclei. Classification at the patient level was performed using a hypothesis test for proportion and two different hypothesis values, one equal to the overall accuracy of the NN and one equal to 50%. The second method permitted correct classification of 98% of patients. CONCLUSION: These results indicate that the use of NNs combined with image morphometry and statistical techniques may offer useful information on the potential malignancy of thyroid cells and may improve the diagnostic accuracy of FNA of the thyroid gland, especially in cases classified as suspicious for malignancy.

Humans↗
PubMed1999

Graphical simulation of early development of the cerebral cortex.

Much experimental data exists concerning the development of the cerebral cortex. There is a need for a common vehicle to integrate this data and to allow the testing of hypotheses concerning development. Computer simulation and visualization are powerful mechanisms for hypothesis testing. Our long-term goal is to create a robust, extensible, portable tool for simulation and visualization of cortical development to serve both research and educational purposes. This paper describes a simulation program, SimCortex, which models the early stages of development of the cerebral cortex of the mouse. Version 1.0 of SimCortex models the proliferation of progenitor cells in the pseudostratified ventricular epithelium (PVE), the generation of young neurons and their migration into the cortical plate, which is the forerunner of cell layers II through VI of the adult cortex. We present an overview of the design and implementation of SimCortex, sample output of the system and a comparison of our results with experimental data. We conclude with a brief overview of proposed future enhancements of the system.

Animals↗
PubMed1997

Reproducibility of the HERITAGE Family Study intervention protocol: drift over time.

PURPOSE: The primary goal of the HERITAGE Family Study was to document the role of the genotype in the response to aerobic exercise training. Toward this end, nuclear families were enrolled in a 20-week exercise training program, with a large variety of tests performed before and after the training. Since study drift has the potential to adversely affect the results, reproducibility and potential bias over six consecutive 4-month periods were examined for selected test. METHODS: Intraclass correlations (ICC), technical errors (TE), coefficients of variation within subject (CV), and means were calculated with use of the pretraining test results for each of the six time periods. To check for homogeneity, hypothesis tests were performed on the intraclass correlations and means. If homogeneity was not found across all six periods, further tests were performed to assess differences between pairs of time periods. RESULTS: There was little evidence for real drifts in reproducibility, with most tests having ICCs of 0.8 or better. Only a few tests showed any change over time, and in no case was there evidence of a systematic drift in mean values. CONCLUSIONS: Overall, the reproducibility of the HERITAGE Family Study tests and assays considered in this paper was found to be very good, with no evidence of any systematic drift over time.

Adolescent↗
PubMed2002

An approximately unbiased test of phylogenetic tree selection.

An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances.

Animals↗
PubMed2001

A bootstrapped commingling analysis of platelet monoamine oxidase activity levels corrected for cigarette smoking.

Monoamine oxidase (MAO) activity levels have been suggested as a possible biological marker for alcohol dependence and abuse, as well as for schizophrenia and other psychiatric conditions. Using platelet MAO activities in the Collaborative Study on the Genetics of Alcoholism data set, we applied bootstrapping methods as a novel way to test for admixture in families. This bootstrapping involved resampling in family units and hypothesis testing of the resampled datasets for commingling in the distribution of MAO activity levels. Prior to commingling analysis, we used linear models to find covariates of greatest effect on MAO activity levels. While an alcoholism diagnosis was significant in men (n = 1151, P < 0.0001) and women (n = 1254, P = 0.0003), the effect lost significance after controlling for cigarette smoking, indicating alcoholism and smoking behavior to be highly confounded. When smoking histories were compared, former smokers had levels (mean = 7.1) closer to those who never smoked (mean = 7.0) than to current smokers (mean = 5.4). Furthermore, current daily smoking and time since smoking cessation were significantly related to MAO levels, indicating smoking probably has a direct effect on MAO levels, rather than the reverse. These results suggest that studies using MAO levels as a biological marker should consider smoking as an important covariate. Finally, admixture was found in MAO levels controlled for smoking and sex, possibly indicating a major genetic locus; this confirms previous evidence for admixture.

Biomarkers↗
PubMed1994

Certainty and uncertainty in science: the subjectivistic concept of probability in physiology and medicine.

Most physiological scientists have restricted understanding of probability as relative frequency in a large collection (for example, of atoms). Most appropriate for the relatively circumscribed problems of the physical sciences, this understanding of probability as a physical property has conveyed the widespread impression that the "proper" statistical "method" can eliminate uncertainty by determining the "correct" frequency or frequency distribution. However, many relatively recent developments in the theory of probability and decision making deny such exalted statistical ability. Proponents of Bayes's subjectivist theory, for example, assert that probability is "degree of belief," a more tentative idea than relative frequency or physical probability, even though degree of belief assessment may utilize frequency information. In the subjectivist view, probability and statistics are means of expressing a consistent opinion (a probability) to handle uncertainty but never means to eliminate it. In the physiological sciences the contrast between the two views is critical, because problems dealt with are generally more complex than those of physics, requiring judgments and decisions. We illustrate this in testing the efficacy of penicillin by showing how the physical probability method of "hypothesis testing" may contribute to the erroneous idea that science consists of "verified truths" or "conclusive evidence" and how this impression is avoided in subjectivist probability analysis.

Bayes Theorem↗
PubMed1996

Lay understanding of genetics: a test of a hypothesis.

There have been growing calls for more education in genetics for the public and in schools. However, studies of the public, school children, and those who have received genetic counselling show that understanding of scientific genetics is very limited. A hypothesis to explain this limited understanding is proposed and tested. It is argued that there is a widespread lay knowledge of inheritance which conflicts in a number of aspects with scientific explanations and which impedes the assimilation of the latter. It is suggested that this lay knowledge is derived from concepts of the social relationships of kinship. Concepts of kinship ties are sustained by everyday social activities and relationships which may make them resistant to change. A prediction which follows from the hypothesis that the lay understanding of genetics is derived from concepts of family and kinship relationships is that closeness in genetic terms will be determined by the closeness of the family ties of social relationship and social obligation. While the proportion of genes shared with parents, children, and sibs is, on average, the same, kin relationships and obligations are much stronger between parents and children than between sibs. The hypothesis was tested in a questionnaire study of two samples of adult women (n = 64 and n = 113) and one of social science students (n = 73). In all three groups a higher proportion of subjects gave the correct response for the proportion of shared genes with a father and child than with a sister, uncle, or grandmother. In the cases of sisters and uncle (and grandmother), there was a consistent tendency to underestimate the degree of genetic connection as predicted by the hypothesis. Answers to other questions are consistent with the hypothesis. The fundamental implications of the hypothesis for genetic education in the clinic and classroom are outlined.

Adult↗
PubMed1997

Using the POBF as an index of interocular blood flow effects during unilateral vascular stress.

Kergoat and Lovasik [(1994). Ophthalmic and Physiological Optics, 14, pp. 401-407] reported that a transient decrease in ocular perfusion pressure (OPP) decreased the neural function in the test eye but increased the responsivity in the contralateral untouched (control) eye. Here the hypothesis tested was that a transient unilateral vascular stress would induce an increase in the Pulsatile Ocular Blood Flow (POBF) in the opposite eye. The POBF was measured in 20 healthy volunteers with normal intraocular pressure (IOP) and brachial blood pressure (BP). The OPP was decreased in the test (right) eye by scleral suction, and a Langham OBF system was used to make four readings of the POBF for each eye for baseline conditions, and when the OPP was decreased in the test eye alone by 20 and 40% for a 2 min period. Each individual, as well as the group averaged data showed a progressive decrease in the POBF in the test eye during a stepwise reduction in the OPP. No change was found for the POBF for the control eyes. Within the limitations of the systems and testing procedures employed, it is concluded that unilateral alterations in the OPP do not cause a change in the POBF in the contralateral eye.

Adult↗
PubMed1998

Testing for differences in multiple quality of life dimensions: generating hypotheses from the experience of hospital staff.

In clinical trials with a quality of life (QoL) component, it is usual to monitor several QoL dimensions at several points in time. Multiple significance tests without formal hypotheses are problematic. It is not always feasible to specify a priori hypotheses for all variables. Can such studies be used to generate hypotheses for testing in later research only? We developed a method which can allow for formal hypothesis testing on a data set collected without a priori hypotheses in the protocol. We surveyed experienced physicians and nurses treating patients, to obtain independent expectations about differences in QoL dimensions. These 'staff expectations' will be used in the analysis of QoL data collected from breast cancer patients taking part in three randomized trials of adjuvant therapy. We propose frameworks for the informal and formal use of the experience of the staff in testing for group differences in patients' QoL scores. The method described here is anticipated to be useful for QoL studies in general, even when a priori hypotheses were specified before the studies were initiated.

Bayes Theorem↗
PubMed2001

Interpretation, design, and analysis of gene array expression experiments.

Experiments using arrays of cDNA targets to compare patterns of gene expression are beginning to play a prominent role in biogerontology, but drawing reliable conclusions from the resulting data sets requires careful application of statistical methods that discriminate chance events from those likely to reflect real differences among the samples under study. This essay discusses flaws in the logic of studies that base their conclusions on ratio calculations alone, reviews the multiple comparison traps inherent in high throughput systems that test a very large number of mRNAs simultaneously, and advocates a two-stage design in which significance testing applied to exploratory data is used to guide a second round of hypothesis-testing experiments conducted in a separate set of experimental samples.

Aging↗
PubMed2002

Inhibition of platelet-derived growth factor actions in the embryonic testis influences normal cord development and morphology.

Platelet-derived growth factors (PDGFs) are paracrine factors with roles in mesenchymal-epithelial interactions during normal and pathologic processes. Previously, PDGF and its receptor (PDGFR) have been shown to be present in perinatal, peripubertal, and adult rat testes. The role of PDGF in embryonic testicular cord formation is not known. The hypothesis tested is that PDGFs and PDGFRs are expressed during cord formation and that inhibition of their action influences normal cord formation during embryonic testis development. Embryonic Day (E) 13 gonadal organ cultures were used. Organs were cultured for 3 days and treated daily with vehicle or a PDGFR-specific tyrosine phosphorylation inhibitor (i.e., the tyrphostin AG1295 or AG1296). Vehicle-treated testes formed normal cords, whereas tyrphostin-treated testes formed "swollen cords," a phenomenon characterized by a significant decrease in the number of cords per testis area and increased cord diameter due to fusion of cords. Expression of PDGF and PDGFR in E13, E14, E16, Postnatal Day (P) 0, and P20 testes was examined. Messenger RNAs for PDGF-A and -B and PDGF alpha- and beta-receptors were expressed in isolated testes during all developmental periods examined. Immunoreactivity for PDGF was present throughout the testicular compartment at E14, restricted primarily to testicular cords at E16, and present in cells of the testicular cords with a stronger immunoreactivity in certain interstitial cell types of P0 testis. PDGFR beta-receptor immunoreactivity was primarily localized to the mesonephros of E14 organs and the testicular interstitium of E16 and P0 testes. Tyrphostins did not affect apoptotic cell number in the testis. PDGF had no effect on cell growth in P0 testis cultures. The results show that PDGFs and PDGFRs are expressed in embryonic testis during cord formation in a tissue-specific manner. Inhibition of PDGF actions does not inhibit cord formation but does alter normal cord development and morphology. The observations provide insight into the factors involved in male sex differentiation and embryonic testis development.

Animals↗
PubMed1997

The role of the apolipoprotein E polymorphism in the prediction of coronary artery disease age of onset.

We investigated the role of the apolipoprotein (Apo) E polymorphism in the prediction of CAD age of onset in a sample of unrelated living male (n = 65) and female (n = 54) Caucasian subjects diagnosed with CAD. Cumulative distributions of age at the first diagnosis of CAD were estimated for each Apo E genotype and tested for homogeneity using the log-rank test. The Apo epsilon 33 genotype was used as a reference group for all hypothesis tests. Analyses were performed separately in males and females. We found evidence suggesting that the presence of the Apo epsilon 32 genotype in males is associated with a significantly earlier CAD age of onset. These results suggest that the Apo E polymorphism may be a gender-specific predictor of CAD age of onset.

Adult↗
PubMed2004

Numerical deconvolution of cDNA microarray signal: simulation study.

A computational model for simulation of the cDNA microarray experiments has been created. The simulation allows one to foresee the statistical properties of replicated experiments without actually performing them. We introduce a new concept, the so-called bio-weight, which allows for reconciliation between conflicting meanings of biological and statistical significance in microarray experiments. It is shown that, for a small sample size, the bio-weight is a more powerful criterion of the presence of a signal in microarray data as compared to the standard approach based on t test. Joint simulation of microarray and quantitative PCR data shows that the genes recovered by using the bio-weight have better chances to be confirmed by PCR than those obtained by the t test technique. We also employ extreme value considerations to derive plausible cutoff levels for hypothesis testing.

Cell Line, Tumor↗