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PubMed2000

Accounting for variability in the use of permutation testing to detect quantitative trait loci.

Locating quantitative trait loci (QTL), or genomic regions associated with known molecular markers, is of increasing interest in a wide variety of applications ranging from human genetics to agricultural genetics. The hope of locating QTL (or genes) affecting a quantitative trait is that it will lead to characterization and possible manipulations of these genes. However, the complexity of both statistical and genetic issues surrounding the location of these regions calls into question the asymptotic statistical results supplying the distribution of the test statistics employed. Coupled with the power of current-day computing, permutation theory was reintroduced for the purpose of estimating the distribution of any test statistic used to test for the location of QTL. Permutation techniques have offered an attractive alternative to significance measures based on asymptotic theory. The ideas of permutation testing are extended in this application to include confidence intervals for the thresholds and p-values estimated in permutation testing procedures. The confidence intervals developed account for the Monte Carlo error associated with practical applications of permutation testing and lead to an effective method of determining an efficient permutation sample size.

Biometry↗
PubMed2005

Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites.

Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain rejection probabilities. Here we develop a "haplotype configuration test" of neutrality (HCT) based on the full haplotype frequency distribution. To enable exact computation of rejection probabilities for small samples, we derive a recursion under the standard coalescent model for the joint distribution of the haplotype frequencies and the number of segregating sites. For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster.

Chromosome Segregation↗
PubMed2002

CYP1A1 gene polymorphism and risk of epithelial ovarian neoplasm.

OBJECTIVE: Gene-environment interactions have been the focus of a number of recent studies of the occurrence of human cancers, and an association between the risk and the CYP1A1*3 polymorphism has been noticed for several cancers. Previous studies suggest that estrogens are involved in the etiology of ovarian cancer. The cytochrome P450 1A1 (CYP1A1) gene polymorphism may play role in the development of epithelial ovarian neoplasm by detoxification of polycyclic hydrocarbons and other compounds and the concentration of estrogens and their metabolites. Therefore, we assessed the association of CYP1A1 gene polymorphism in patients with epithelial ovarian neoplasm in the Turkish populations through a case-control study. METHODS: Using an allele-specific polymerase chain reaction (PCR)-based method, CYP1A1*3 polymorphism, in exon 7 of the gene, was analyzed in 117 epithelial ovarian neoplasm patients and 202 control subjects. RESULTS: The CYP1A1 Ile/Val genotype significantly increased the risk for patients with epithelial ovarian neoplasm (OR 5.7, 95% CI 3.34-9.76). Furthermore, there were statistical differences in the distribution of CYP1A1 Val/Val genotype among all patients (OR 5.85, 95% CI 2.40-14.25). In other words, the presence of the Val allele significantly increased the risk of epithelial ovarian neoplasm. Among benign tumors, the frequency of Ile/Val and Val/Val genotypes was found to be statistically significant with an ORs of 6.01 and 4.38 (95% CI 2.61-13.84 and 1.04-18.38, respectively). In the benign serous ovarian tumors, patients with Ile/Val and Val/Val revealed a 7.2- and 10.5-fold higher risk of having ovarian carcinoma (95% CI 2.22-23.40 and 2.16-51.19), respectively. In the benign mucinous ovarian carcinoma patients, the frequency of Ile/Val was found to be statistically significant with an OR of 5.15 (95% CI 1.75-15.16). However, no patient with Val/Val genotype was observed in this group and no statistical distribution was performed. Among borderline tumors, CYP1A1 Ile/Val genotype significantly increased the risk for patients (OR 5.15, 95% CI 1.75-15.16). However, only one patient was observed with the Val/Val allele and the frequency of this genotype was not found to be statistically different with an OR of 2.50 (95% CI 0.27-22.64). Among ovarian cancer patients, there were statistically differences in the distribution of CYP1A1 Ile/Val and Val/Val genotypes (OR 5.73, 95% CI 3.04-10.76; and OR 7.42, 95% CI 2.80-19.66), suggesting that patients carrying these genotypes were at increased risk for ovarian carcinoma. In serous carcinoma, patients with CYP1A1 Ile/Val and Val/Val revealed a 6.5- and 10-fold higher risk of having ovarian cancer (OR 7.09, 95% CI 3.30-15.22; and OR 8.77, 95% CI 2.83-27.14). In mucinous carcinoma, patients with CYP1A1 Ile/Val and Val/Val also revealed a 5.4 and 10.5 times higher risk of having ovarian cancer. There were no statistical significance in the distribution of Val allele among endometroid-type cancer patients. CONCLUSIONS: Our data, although based on a small number of subjects, suggest that variant alleles of CYP1A1 gene in ovarian epithelial cells, directly or through other components, may contribute to initiation of ovarian carcinogenesis.

Adenocarcinoma, Mucinous↗
PubMed1982

Migration between core and peripheral regions: a description and tentative explanation of the patterns in 22 countries.

"In the developed world at least, the century-long migration towards the high density core regions is over. To establish this thesis, internal migration statistics for 22 countries are examined, covering the period 1950-1979. Of these 22 countries, five categories are distinguished: (1) the countries of north-western Europe...; (2) the countries of North America...; (3) countries on the periphery of western Europe...[and] Japan and New Zealand; (4) the countries of eastern Europe...; and (5) two advanced developing countries in eastern Asia...." Migration trends among countries in the five categories are described, and a tentative explanation of these patterns is offered. "[An] appendix contains the data from which the figures in the text have been constructed, the exact sources from which the data have been taken, and the constituent administrative subdivisions of the regions chosen for study."

Demography↗
PubMed2006

Patient doses from noncardiac diagnostic and therapeutic interventional procedures.

PURPOSE: To determine the patient doses during noncardiac diagnostic and therapeutic interventional procedures carried out in a dedicated angiographic unit. MATERIALS AND METHODS: For 1,214 interventional procedures, the technique type, dose-area product (DAP), cumulative dose (CD), and fluoroscopy time were recorded. These procedures were classified into 23 categories (10 diagnostic and 13 therapeutic) that included nine to 259 patients each. For each category, descriptive statistical analysis was used to determine the characteristics of DAP, CD, and fluoroscopy time distributions. The statistical significance of the differences observed between categories in terms of DAP was assessed. RESULTS: For the 23 categories studied, the median DAP values ranged from 0.2 to 176.8 Gycm(2). In comparison with the literature, the mean and median DAP values in this study were within reported ranges for eight categories, greater for three, and less for six, whereas for the remaining six categories no relevant data were found in the literature. CONCLUSIONS: Overall, the results of this survey indicate that the techniques used by the interventionalists, the operation skills of radiation technologists, and the performance of the x-ray unit present no obvious deficiencies in terms of patient radiation protection. However, for those procedures in which lower DAP values were found in the literature, it should be further investigated whether patient doses could be reduced without degradation of the diagnostic and therapeutic outcomes.

Analysis of Variance↗
PubMed1994

Health practices and indices of a poor urban population in Indonesia. Part II: Immunization, nutrition, and incidence of diarrhea.

This second section in a two-part study of health indices and practices among a poor urban population in Indonesia focuses on problems related to immunization, nutrition, and incidence of diarrhea. Through a survey of 690 mothers and 593 children in two slum communities in Jakarta, we found that 1) 65% of the children were mildly to severely malnourished according to Gomez criteria, with malnutrition most prevalent among the poorest; 2) 75% of the mothers reported exclusive breastfeeding of their infants during the first four months after birth, but breastfeeding decreased sharply with increasing socioeconomic status; 3) of the 19% of one- to three-year-old children who were incompletely immunized, most were likely to be missing their measles and DPT3 immunizations; and 4) 28% of the mothers reported that at least one of their under-three-year-old children had diarrhea in the last month, with frequency of reporting highest among poor mothers and those using water from vendors. We concluded that selective interventions should be accompanied by development of a comprehensive health infrastructure that permits uninterrupted service delivery and follow up of those identified as high risk. Such a comprehensive primary health care system should be part of a multisectoral development strategy.

Breast Feeding↗
PubMed1998

Magnetic resonance imaging and knee stability following ACL reconstruction.

This study was undertaken to determine whether there is a correlation between magnetic resonance imaging (MRI) and clinical success after reconstruction of the anterior cruciate ligament (ACL). In a prospective study, 28 patients underwent clinical and MRI examination 3 to 5 years after ACL reconstruction with either the semitendinosus tendon (n = 15) or patellar ligament (n = 13). Knee stability was assessed both clinically and by KT-1000 arthrometer testing. Magnetic resonance imaging was performed with a 0.2-T dedicated system (Artoscan, Esaote, Italy) including sagittal and oblique coronal T1 and T2-weighted images. Magnetic resonance images were evaluated by two readers with regard to signal intensity and continuity of the ACL reconstruction and presence or absence of posterior cruciate ligament buckling. Knee stability and MRI evaluation were each summarized in a 6-point score. Statistical correlation was checked with the Spearman ranked correlation for testing non-normal distributed samples. Statistical testing of all patients' results together showed a significant correlation with a prediction value of 12%, indicating no significant correlation between clinical results and MRI evaluation. Separate statistical testing of the patellar ligament and semitendinosus patients' results showed no significant correlation in either group at all. Thus, no correlation between clinical stability and MRI could be established. Magnetic resonance images after ACL reconstruction using the techniques mentioned above should be interpreted with caution, as they may not relate to the clinical function of the ligament.

Adolescent↗
PubMed2006

Statistical analysis of CDR3 length distributions for the assessment of T and B cell repertoire biases.

Complementarity-determining region 3 (CDR3) length distribution analysis explores the diversity of the T cell receptor (TCR) and immunoglobulin (Ig) repertoire at the transcriptome level. Studies of the CDR3, the most hypervariable part of these molecules, have been frequently used to identify recruitment of T and B cell clones involved in immunological responses. CDR3 length distribution analysis gives a clear perception of repertoire variations between individuals and over time. However, the complexity of CDR3 length distribution patterns and the high number of possible repertoire alterations per individual called for the development of robust data analysis methods. The goal of these methods is to identify, quantify and statistically assess differences between repertoires so as to offer a better diagnostic or predictive tool for pathologies involving the immune system. In this review we will explain the benefit of analyzing CDR3 length distribution for the study of immune cell diversity. We will start by describing this technology and its associated data processing, and will subsequently focus on the statistical methods used to compare CDR3 length distribution patterns. Finally, we will address the various methods for assessing CDR3 length distribution gene signatures in pathological states.

Animals↗
PubMed1999

Comparing two methods for calculating phantom scatter.

Two methods are compared for calculating the field-size dependence of the phantom scatter component of dose for x-ray beams. One model sums three Gaussian distributions; the other model is a two-parameter function. With a measurement of the beam quality as input to determine parameters, both models accurately reproduce the relative phantom scatter. However, there are important differences between the models. For all beam energies, the two-parameter model characterizes the absolute phantom scatter as a function of depth and field size, while, also for all beam energies, the six-parameter Gaussian model characterizes the relative phantom scatter at a single depth of 10 cm. For small field sizes, the phantom scatter calculated from the two-parameter model agrees with Monte Carlo calculations better than the Gaussian model. In the Gaussian model, the parameters can be obtained for beam energies between 60Co and 25 MV by linear interpolation based on the measured beam quality. In the two-parameter model, and for energies above 4 MV, the parameters can be obtained using linear functions of the dose-weighted average linear attenuation coefficient, which is related to beam quality.

Calibration↗
PubMed1988

Who consults and where? Sociocultural differentiation in access to health care in urban Africa.

Sociocultural differentiation in health behaviour was studied among 500 mothers randomly chosen in the suburban area of Dakar, Senegal. Variables were age, marital status, educational level, socioeconomic conditions, urban experience, town integration, village attachment, social insurance, ethnic group and disease categories. Access to health care was considered for the last illness of the mother and her youngest child under five. Town integration and disease category (and social insurance for children) were the only variables correlated with the number of consultations. Socioeconomic level and social insurance (and educational level for mothers) were associated with preference for private rather than public health systems.

Adult↗
PubMed1985

Distribution of gamma exposure rates in a reactor effluent stream flood plain system.

Ground-level gamma dosimetry surveys were conducted along the length of a radiocesium-contaminated reactor effluent stream flood plain system to determine the extent and patterns of isotope distribution over a decade after reactor releases were stopped. The maximum mean exposure rates were found at upstream locations near the source of the contamination and in a downstream sedimentary delta. Gamma exposure rates were not uniformly distributed and high exposure rates were generally restricted to small areas of the flood plain. There was little similarity in either the spatial distribution or magnitudes of maximum gamma exposure rates across flood plains along the stream. Frequency the measured exposure rates tended to be highly skewed and most closely approximated the log-normal distribution in most areas along the stream. However, the complex and changing patterns of dose distributions strongly affected the ability to predict the probability of encountering unusually high exposure rates. Complex statistical and distributional models are required to provide precise descriptions of the dosimetry environment in such complex ecosystems and different models could be required on a site-by-site basis.

Cesium Radioisotopes↗