Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data.

Despite the central role of quantitative PCR (qPCR) in the quantification of mRNA transcripts, most analyses of qPCR data are still delegated to the software that comes with the qPCR apparatus. This is especially true for the handling of the fluorescence baseline. This article shows that baseline estimation errors are directly reflected in the observed PCR efficiency values and are thus propagated exponentially in the estimated starting concentrations as well as 'fold-difference' results. Because of the unknown origin and kinetics of the baseline fluorescence, the fluorescence values monitored in the initial cycles of the PCR reaction cannot be used to estimate a useful baseline value. An algorithm that estimates the baseline by reconstructing the log-linear phase downward from the early plateau phase of the PCR reaction was developed and shown to lead to very reproducible PCR efficiency values. PCR efficiency values were determined per sample by fitting a regression line to a subset of data points in the log-linear phase. The variability, as well as the bias, in qPCR results was significantly reduced when the mean of these PCR efficiencies per amplicon was used in the calculation of an estimate of the starting concentration per sample.

The effect of patient, provider and financing regulations on the intensity of ambulatory physical therapy episodes : a multilevel analysis based on routinely available data

Background: Many studies have found considerable variations in the resource intensity of physical therapy episodes. Although they have identified several patient-and provider-related factors, few studies have examined their relative explanatory power. We sought to quantify the contribution of patients and providers to these differences and examine how effective Swiss regulations are (nine-session ceiling per prescription and bonus for first treatments). Methods: Our sample consisted of 87,866 first physical therapy episodes performed by 3,365 physiotherapists based on referrals by 6,131 physicians. We modeled the number of visits per episode using a multilevel log linear regression with crossed random effects for physiotherapists and physicians and with fixed effects for cantons. The three-level explanatory variables were patient, physiotherapist and physician characteristics. Results: The median number of sessions was nine (interquartile range 6-13). Physical therapy use increased with age, women, higher health care costs, lower deductibles, surgery and specific conditions. Use rose with the share of nine-session episodes among physiotherapists or physicians, but fell with the share of new treatments. Geographical area had no influence. Most of the variance was explained at the patient level, but the available factors explained only 4% thereof. Physiotherapists and physicians explained only 6% and 5% respectively of the variance, although the available factors explained most of this variance. Regulations were the most powerful factors. Conclusion: Against the backdrop of abundant physical therapy supply, Swiss financial regulations did not restrict utilization. Given that patient-related factors explained most of the variance, this group should be subject to closer scrutiny. Moreover, further research is needed on the determinants of patient demand.

Latitude gradients in melanoma incidence and mortality in the non-Maori population of New Zealand

The variation with latitude of incidence and mortality for cutaneous malignant melanoma (CMM) in the non-Maori population of New Zealand was assessed. For those aged 20 to 74 years, the effects of age, time period, birth-cohort, gender, and region (latitude), and some interactions between them were evaluated by log-linear regression methods. Increasing age-standardized incidence and mortality rates with increasing proximity to the equator were found for men and women. These latitude gradients were greater for males than females. The relative risk of melanoma in the most southern part of New Zealand (latitude 44 degrees S) compared with the most northern region (latitude 36 degrees S) was 0.63 (95 percent confidence interval [CI] = 0.60-0.67) for incidence and 0.76 (CI = 0.68-0.86) for mortality, both genders combined. The mean percentage change in CMM rates per degree of latitude for males was greater than those reported in other published studies. Differences between men and women in melanoma risk with latitude suggest that regional sun-behavior patterns or other risk factors may contribute to the latitude gradient observed.

Compositional analysis of bivariate discrete probabilities

A joint distribution of two discrete random variables with finite support can be displayed as a two way table of probabilities adding to one. Assume that this table hasn rows and m columns and all probabilities are non-null. This kind of table can beseen as an element in the simplex of n · m parts. In this context, the marginals areidentified as compositional amalgams, conditionals (rows or columns) as subcompositions. Also, simplicial perturbation appears as Bayes theorem. However, the Euclideanelements of the Aitchison geometry of the simplex can also be translated into the tableof probabilities: subspaces, orthogonal projections, distances.Two important questions are addressed: a) given a table of probabilities, which isthe nearest independent table to the initial one? b) which is the largest orthogonalprojection of a row onto a column? or, equivalently, which is the information in arow explained by a column, thus explaining the interaction? To answer these questionsthree orthogonal decompositions are presented: (1) by columns and a row-wise geometric marginal, (2) by rows and a columnwise geometric marginal, (3) by independenttwo-way tables and fully dependent tables representing row-column interaction. Animportant result is that the nearest independent table is the product of the two (rowand column)-wise geometric marginal tables. A corollary is that, in an independenttable, the geometric marginals conform with the traditional (arithmetic) marginals.These decompositions can be compared with standard log-linear models.Key words: balance, compositional data, simplex, Aitchison geometry, composition,orthonormal basis, arithmetic and geometric marginals, amalgam, dependence measure,contingency table

Trends in smoking and lung cancer mortality in Switzerland.

Patterns of cigarette smoking in Switzerland were analyzed on the basis of sales data (available since 1924) and national health surveys conducted in the last decade. There was a steady and substantial increase in cigarettes sales up to the early 1970s. Thereafter, the curve tended to level off around an average value of 3,000 cigarettes per adult per year. According to the 1981-1983 National Health Survey, 37% of Swiss men were current smokers, 25% were ex-smokers, and 39% were never smokers. Corresponding porportions in women were 22, 11, and 67%. Among men, smoking prevalence was higher in lower social classes, and some moderate decline was apparent from survey data over the period 1975-1981 mostly in later middle-age. Trends in lung cancer death certification rates over the period 1950-1984 were analyzed using standard cross-sectional methods and a log-linear Poisson model to isolate the effects of age, birth cohort, and year of death. Mortality from lung cancer increased substantially among Swiss men between the early 1950s and the late 1970s, and levelled off (around a value of 70/100,000 men) thereafter. Among women, there has been a steady upward trend which started in the mid-1960s, and continues to climb steadily, although lung cancer mortality is still considerably lower in absolute terms (around 8/100,000 women) than in several North European countries or in North America. Cohort analyses indicate that the peak rates in men were reached by the generation born around 1910 and mortality stabilized for subsequent generations up to the 1930 birth cohort. Among females, marked increases were observed in each subsequent birth cohort. This pattern of trends is consistent with available information on smoking prevalence in successive generations, showing a peak among men for the 1910 cohort, but steady upward trends among females. Over the period 1980-1984, about 90% of lung cancer deaths among Swiss men and about 40% of those among women could be attributed to smoking (overall proportion, 85%).

Sexual dysfunctions among young men: prevalence and associated factors.

PURPOSE: The purposes of this study are to measure the prevalence of premature ejaculation (PE) and erectile dysfunction (ED) among a population of Swiss young men and to assess which factors are associated with these sexual dysfunctions in this age-group. METHODS: For each condition (PE and ED), we performed separate analyses comparing young men suffering from the condition with those who were not. Groups were compared for substance use (tobacco, alcohol, cannabis, other illegal drugs, and medication without a prescription), self-reported body mass index, sexual orientation, physical activity, professional activity, sexual experience (sexual life length and age at first intercourse), depression status, mental health, and physical health in a bivariate analysis. We then used a log-linear analysis to consider all significant variables simultaneously. RESULTS: Prevalence rates for PE and ED were 11% and 30%, respectively. Poor mental health was the only variable to have a direct association with both conditions after controlling for potential confounders. In addition, PE was directly associated with tobacco, illegal drugs, professional activity, and physical activity, whereas ED was directly linked with medication without a prescription, length of sexual life, and physical health. CONCLUSIONS: In Switzerland, one-third of young men suffer from at least one sexual dysfunction. Multiple health-compromising factors are associated with these dysfunctions. These should act as red flags for health professionals to encourage them to take any opportunity to talk about sexuality with their young male patients.

How does the body-scale model affect back-calculated growth: the example of arctic charr Salvelinus alpinus (L.) of Lake Geneva (Switzerland)

When back-calculating fish length from scale measurements, the choice of the body-scale relationship is a fundamental step. Using data from the arctic charrSalvelinus alpinus (L.) of Lake Geneva (Switzerland) we show the need for a curvilinear model, on both statistical and biological grounds. From several 2-parameters models, the log-linear relationship appears to provide the best fit. A 3-parameters, Bertalanffy model did not improve the fit. We show moreover that using the proportional model would lead to important misinterpretations of the data.

Individual prediction of automobile bodily injury claims liabilities

[spa] La mayoría de siniestros con daños corporales se liquidan mediante negociación, llegando a juicio menos del 5% de los casos. Una estrategia de negociación bien definida es, por tanto, fundamental para las compañías aseguradoras. En este artículo asumimos que la compensación monetaria concedida en juicio es la máxima cuantía que debería ser ofrecida por el asegurador en el proceso de negociación. Usando una base de datos real, implementamos un modelo log-lineal para estimar la máxima oferta de negociación. Perturbaciones no-esféricas son detectadas. Correlación ocurre cuando más de una siniestro se liquida en la misma sentencia judicial. Heterocedasticidad por grupos se debe a la influencia de la valoración del forense en la indemnización final.

Individual prediction of automobile bodily injury claims liabilities

[spa] La mayoría de siniestros con daños corporales se liquidan mediante negociación, llegando a juicio menos del 5% de los casos. Una estrategia de negociación bien definida es, por tanto, fundamental para las compañías aseguradoras. En este artículo asumimos que la compensación monetaria concedida en juicio es la máxima cuantía que debería ser ofrecida por el asegurador en el proceso de negociación. Usando una base de datos real, implementamos un modelo log-lineal para estimar la máxima oferta de negociación. Perturbaciones no-esféricas son detectadas. Correlación ocurre cuando más de una siniestro se liquida en la misma sentencia judicial. Heterocedasticidad por grupos se debe a la influencia de la valoración del forense en la indemnización final.

Trends in mortality from coronary heart and cerebrovascular disease in Switzerland, 1969-87.

Trends in age-specific and age-standardized death certification rates from all ischaemic heart disease and cerebrovascular disease in Switzerland have been analysed for the period 1969-87, i.e. since the introduction of the Eighth Revision of the International Classification of Diseases for coding causes of death. For coronary heart disease, overall age-standardized rates of males in the mid-late 1980's were similar to those in the late 1960's, although some upward trend was evident up to the mid 1970's (with a peak rate of 120.4/100,000, World standard, in 1978) followed by steady declines in more recent years (103.8/100,000 in 1987). These falls were larger in truncated (35 to 64 years) rates. For females, overall age-standardized rates were stable around a value of 40/100,000, while truncated rates tended to decrease, particularly over most recent years, with an overall decline of over 25%. Examination of age-specific trends showed that in both sexes declines at younger ages were already evident in the earlier calendar period, while above age 50 some fall became evident only in most recent years. Thus, in a formal log-linear age/period/cohort model, both a period and a cohort component emerged. In relation to cerebrovascular diseases, the overall declines were around 40% in males (from 67.4 to 41.2/100,000, World standard) and 45% for females (from 56.6 to 31.7/100,000), and were proportionally comparable across subsequent age groups above age 45. The estimates for the age/period/cohort model were thus downwards both for the period and the cohort component although, in such a situation, it is difficult to disentangle the major underlying component.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of age, birth cohort and period of death on Swiss cancer mortality, 1951-1984.

Swiss death certification data over the period 1951-1984 for total cancer mortality and 30 major cancer sites in the population aged 25 to 74 years were analysed using a log-linear Poisson model with arbitrary constraints on the parameters to isolate the effects of birth cohort, calendar period of death and age. The overall pattern of total cancer mortality in males was stable for period values and showed some moderate decreases in cohort values restricted to the generations born after 1930. Cancer mortality trends were more favourable in females, with steady, though moderate, declines in both cohort and period values. According to the estimates from the model, the worst affected generation for male lung cancer was that born around 1910, and a flattening of trends or some moderate decline was observed for more recent cohorts, although this decline was considerably more limited than in other European countries. There were decreases in cohort and period values for stomach, intestine and oesophageal cancer in both sexes and (cervix) uteri in females. Increases were observed in both cohort and period trends for pancreas and liver in males and for several other neoplasms, including prostate, brain, leukaemias and lymphomas, restricted, however, for the latter sites, to the earlier cohorts and hence partly attributable to improved diagnosis and certification in the elderly. Although age values for lung cancer in females were around 10-times lower than in males, upward trends in female lung cancer cohort values were observed in subsequent cohorts and for period values from the late 1960's onwards. Therefore, future trends in female lung cancer mortality should continue to be monitored. The application of these age/period/cohort models thus provides a summary guide for the reading and interpretation of cancer mortality trends, although it cannot replace careful inspection of single age-specific rates.

Density, climate and varying return points: an analysis of long-term population fluctuations in the threatened European tree frog.

Experimental research has identified many putative agents of amphibian decline, yet the population-level consequences of these agents remain unknown, owing to lack of information on compensatory density dependence in natural populations. Here, we investigate the relative importance of intrinsic (density-dependent) and extrinsic (climatic) factors impacting the dynamics of a tree frog (Hyla arborea) population over 22 years. A combination of log-linear density dependence and rainfall (with a 2-year time lag corresponding to development time) explain 75% of the variance in the rate of increase. Such fluctuations around a variable return point might be responsible for the seemingly erratic demography and disequilibrium dynamics of many amphibian populations.

Problematic Internet use is associated with substance use in young adolescents.

AIM: This study examined whether problematic Internet use was associated with substance use among young adolescents and assessed whether this association accounted for the use of tobacco, alcohol, cannabis and other drugs. METHODS: Using the Internet Addiction Test, we divided a representative sample of 3067 adolescents in Switzerland (mean age 14 years) into regular and problematic Internet users. We performed a bivariate analysis and two logistic regression models, to analyse substances separately and simultaneously, and developed a log-linear model to define the associations between significant variables. RESULTS: Problematic Internet users were more likely to be female, to use substances, to come from nonintact families, to report poor emotional well-being and to be below average students. The first model showed significant associations between problematic users and each substance, with adjusted odds ratios of 2.05 for tobacco, 1.72 for alcohol, 1.94 for cannabis and 2.73 for other drugs. Only smoking remained significant in the second model, with an adjusted odds ratio of 1.71. CONCLUSION: Problematic Internet use is associated with other risky behaviours and may be an important early predictor of adolescent substance use. Therefore, it should be included in the psychosocial screening of adolescents.

Parent-adolescent relationship in youths with a chronic condition.

BACKGROUND: Suffering from a chronic disease or disability (CDD) during adolescence can be a burden for both the adolescents and their parents. The aim of the present study is to assess how living with a CDD during adolescence, the quality of parent-adolescent relationship (PAR) and the adolescent's psychosocial development interact with each other. METHODS: Using the Swiss Multicenter Adolescent Survey on Health 2002 (SMASH02) database, we compared adolescents aged 16-20 years with a CDD (n = 760) with their healthy peers (n = 6493) on sociodemographics, adolescents' general and psychosocial health, interparental relationship and PAR. RESULTS: Bivariate analyses showed that adolescents with a CDD had a poorer psychosocial health and a more difficult relationship with their parents. The log-linear model indirectly linked CDD and poor PAR through four variables: two of the adolescents' psychosocial health variables (suicide attempt and sensation seeking), the need for help regarding difficulties with parents and a highly educated mother that acted as a protective factor, allowing for a better parent-adolescent with a CDD relationship. CONCLUSION: It is essential for health professionals taking care of adolescents with a CDD to distinguish between issues in relation with the CDD from other psychosocial difficulties, in order to help these adolescents and their parents deal with them appropriately and thus maintain a healthy PAR.

Tipping the scales: Evolution of the allometric slope independent of average trait size.

The scaling of body parts is central to the expression of morphology across body sizes and to the generation of morphological diversity within and among species. Although patterns of scaling-relationship evolution have been well documented for over one hundred years, little is known regarding how selection acts to generate these patterns. In part, this is because it is unclear the extent to which the elements of log-linear scaling relationships-the intercept or mean trait size and the slope-can evolve independently. Here, using the wing-body size scaling relationship in Drosophila melanogaster as an empirical model, we use artificial selection to demonstrate that the slope of a morphological scaling relationship between an organ (the wing) and body size can evolve independently of mean organ or body size. We discuss our findings in the context of how selection likely operates on morphological scaling relationships in nature, the developmental basis for evolved changes in scaling, and the general approach of using individual-based selection experiments to study the expression and evolution of morphological scaling.