Outlier mining in high throughput screening experiments.

A data mining procedure for the rapid scoring of high-throughput screening (HTS) compounds is presented. The method is particularly useful for monitoring the quality of HTS data and tracking outliers in automated pharmaceutical or agrochemical screening, thus providing more complete and thorough structure-activity relationship (SAR) information. The method is based on the utilization of the assumed relationship between the structure of the screened compounds and the biological activity on a given screen expressed on a binary scale. By means of a data mining method, a SAR description of the data is developed that assigns probabilities of being a hit to each compound of the screen. Then, an inconsistency score expressing the degree of deviation between the adequacy of the SAR description and the actual biological activity is computed. The inconsistency score enables the identification of potential outliers that can be primed for validation experiments. The approach is particularly useful for detecting false-negative outliers and for identifying SAR-compliant hit/nonhit borderline compounds, both of which are classes of compounds that can contribute substantially to the development and understanding of robust SARs. In a first implementation of the method, one- and two-dimensional descriptors are used for encoding molecular structure information and logistic regression for calculating hits/nonhits probability scores. The approach was validated on three data sets, the first one from a publicly available screening data set and the second and third from in-house HTS screening campaigns. Because of its simplicity, robustness, and accuracy, the procedure is suitable for automation.

Expression of retinoid-regulated genes in lamellar ichthyosis vs. healthy control epidermis: changes after oral treatment with liarozole.

Lamellar ichthyosis is a keratinization disorder caused by TGM1, Ichthyin and several other gene mutations. A new treatment option is liarozole, which blocks the cytochrome P450 (CYP26)-mediated catabolism of endogenous all-trans retinoic acid. This study focuses on the expression of retinoid-related genes in ichthyotic epidermis before and after treatment with oral liarozole. We first compared the mRNA expression of cellular retinoic acid binding protein II (CRABPII), keratin (KRT) 2 and 4, CYP26A1 and B1, and two markers of inflammation (interleukin-1alpha and tumours necrosis factor (TNF)-alpha) in shave biopsies from 11 genetically defined, untreated patients and 12 age- and sex-matched healthy controls, finding no overt differences between the groups, besides elevated CRABPII expression. We then studied the biomarkers before and after 4 weeks of treatment with liarozole (75 or 150 mg/day), which produced a better therapeutic response in patients with Ichthyin (n=3) than in those with TGM1 (n=6) mutations. A significant decrease in the mRNA expression of KRT2 and TNF-alpha, and trends toward increased expression of KRT4 and CYP26A1 were observed in liarozole-treated patients, consistent with an increased retinoid stimulation of epidermis. However, there were no dose-related responses and the results of the immunostaining did not always parallel the mRNA findings. The results suggest that liarozole exerts a therapeutic effect in lamellar ichthyosis by mildly affecting the expression of retinoid- regulated genes in epidermis.

Efficacy of a single oral dose of 200 mg pramiconazole in vulvovaginal yeast infections: an exploratory phase IIa trial.

Pramiconazole (R126638) is a novel azole with potent antifungal activity against yeasts, dermatophytes and many other fungal species. The aim of this study was to evaluate the efficacy and tolerance of a single oral dose of 200 mg pramiconazole in acute and recurrent vulvovaginal yeast infections. Thirty-two patients (15 acute and 17 recurrent cases) were KOH microscopy- and culture-positive at inclusion. Clinical cure was 53% at one week and 66% at one month. Mycological eradication was obtained in 88% at one week, whereas at one month 75% of the patients were still culture-negative. Effects in both acute and recurrent cases appeared to be similar for mycological cure. The composite sign and symptom score (sum of scores for oedema, erythema, excoriation pruritus, burning and irritation) had a median value of 7.5 (range 2-17) at inclusion. At one week this value was reduced to 1.0 (range 0-8) and at one month a further reduction to 0 (range 0-11) was seen. p-values compared with baseline at both follow-up visits were <0.001. The drug was well tolerated and the reported adverse events were rare and minimal. In conclusion, the results of this trial indicate that pramiconazole possesses properties that warrant further clinical studies in a larger number of patients with acute and recurrent vulvo notvaginal yeast infection to confirm its efficacy and tolerability.

A pilot study on seborrheic dermatitis using pramiconazole as a potent oral anti-Malassezia agent.

BACKGROUND: Seborrheic dermatitis is considered to be a Malassezia-driven disease. Little objective information is available so far from biometrological quantitative assessments of this skin condition. Pramiconazole is a novel triazole with potent in vitro antifungal activity, especially against Malassezia spp. OBJECTIVE: To study the sequential effects of pramiconazole on Malassezia, inflammation and epidermal changes. METHOD: This study was performed in 2 groups of subjects suffering from seborrheic dermatitis. The first group (n = 17) remained untreated and was used as control. Clinical, mycological and biometrological assessments were performed at inclusion and during the following 2 weeks. The second group of subjects (n = 10) received a single 200-mg oral dose of pramiconazole at inclusion. Clinical, mycological and biometrological evaluations were performed before and during 1 month following the single antifungal intake. For both parts of the study, several parameters were assessed including yeast density, desquamation, erythema, itching and sebum excretion. RESULTS: In the control group, no significant changes were observed in any of the parameters during the observation period. The findings were markedly different in the pramiconazole-treated subjects. The yeast density was significantly improved on days 3, 7 and 28. Desquamation, erythema, itching, and the global clinical evaluation as assessed by the patients and investigators became significantly improved on days 7 and 28. A trend in decrease of scaliness was noted. No effect on sebum excretion was evidenced. In conclusion, a single 200-mg dose of pramiconazole exhibitsin vivo efficacy in controlling some important clinical aspects of seborrheic dermatitis. Following a reduction in the number of yeasts on day 3, a decrease in the severity of clinical signs and symptoms occurred from day 7 onwards. Sebum excretion appeared uninvolved in the clearing process of seborrheic dermatitis. CONCLUSION: A single 200-mg dose of pramiconazole appears to abate seborrheic dermatitis. The density in Malassezia present on lesional skin is first decreased, followed by clearing of the clinical signs.

A modeling approach to the analysis of nerve regenerative experiments.

Many experiments aiming at the investigation of nerve repair involve elaborate testing over a certain time period. Data arising from such experiments are often analyzed by time-point. Such a cross-sectional approach is often very inefficient. In this paper, we consider a case study in which repeated measurements of two response variables assumed to be Poisson distributed are obtained. We show how a repeated measures modeling approach, based on generalized linear models, can handle both responses in one model and improve the inference in the nerve repair experiments. The benefits of the model as well as problems that can occur are illustrated and discussed.

Teaching statistical thinking to life scientists a case-based approach.

We describe a workshop on statistical thinking for scientists involved in pharmaceutical discovery research. The objectives were 1) to improve the quality of research data by developing a structured approach to bias and variability and 2) to establish a collaborative and informed relationship between scientists and statisticians by broadening their common basis. The corner stone was the introduction of statistical thinking and the didactical route to achieve this goal.

Design and analysis of drug combination experiments.

In this paper we present and discuss a novel, simple and easy to implement parametric modeling approach to assess synergy. An extended three parameter log-logistic model is used to analyse the data and calculate confidence intervals of the interaction indices. In addition the model corrects for the bias due to plate-location effects. The analysis is performed with PROC NLMIXED and SAS-code is provided. The approach is illustrated using data coming from an oncology study in which the inhibition effect of a combination of two compounds is studied using 96-well plates and a fixed-ratio design.

Graphical exploration of gene expression data: a comparative study of three multivariate methods.

This article describes three multivariate projection methods and compares them for their ability to identify clusters of biological samples and genes using real-life data on gene expression levels of leukemia patients. It is shown that principal component analysis (PCA) has the disadvantage that the resulting principal factors are not very informative, while correspondence factor analysis (CFA) has difficulties interpreting distances between objects. Spectral map analysis (SMA) is introduced as an alternative approach to the analysis of microarray data. Weighted SMA outperforms PCA, and is at least as powerful as CFA, in finding clusters in the samples, as well as identifying genes related to these clusters. SMA addresses the problem of data analysis in microarray experiments in a more appropriate manner than CFA, and allows more flexible weighting to the genes and samples. Proper weighting is important, since it enables less reliable data to be down-weighted and more reliable information to be emphasized.