Validity and validation of expert (Q)SAR systems

At a recent workshop in Setubal (Portugal) principles were drafted to assess the suitability of (quantitative) structure-activity relationships ((Q)SARs) for assessing the hazards and risks of chemicals. In the present study we applied some of the Setubal principles to test the validity of three (Q)SAR expert systems and validate the results. These principles include a mechanistic basis, the availability of a training set and validation. ECOSAR, BIOWIN and DEREK for Windows have a mechanistic or empirical basis. ECOSAR has a training set for each QSAR. For half of the structural fragments the number of chemicals in the training set is >4. Based on structural fragments and log Kow, ECOSAR uses linear regression to predict ecotoxicity. Validating ECOSAR for three 'valid' classes results in predictivity of > or = 64%. BIOWIN uses (non-)linear regressions to predict the probability of biodegradability based on fragments and molecular weight. It has a large training set and predicts non-ready biodegradability well. DEREK for Windows predictions are supported by a mechanistic rationale and literature references. The structural alerts in this program have been developed with a training set of positive and negative toxicity data. However, to support the prediction only a limited number of chemicals in the training set is presented to the user. DEREK for Windows predicts effects by 'if-then' reasoning. The program predicts best for mutagenicity and carcinogenicity. Each structural fragment in ECOSAR and DEREK for Windows needs to be evaluated and validated separately.     

Fitting scattered data on spherelike surfaces using tensor products of trigonometric and polynomial splines

Summary A method is presented for fitting a function defined on a general smooth spherelike surfaceS, given measurements on the function at a set of scattered points lying onS. The approximating surface is constructed by mapping the surface onto a rectangle, and using a tensor-product of polynomial splines with periodic trigonometric splines. The use of trigonometric splines allows a convenient solution of the problem of assuring that the resulting surface is continuous and has continuous tangent planes at all points onS. Two alternative algorithms for computing the coefficients of the tensor fit are presented; one based on global least-squares, and the other on the use of local quasi-interpolators. The approximation order of the method is established, and the numerical performance of the two algorithms is compared.Supported in part by the National Science Foundation under Grant DMS-8902331 and by the Alexander von Humboldt Foundation     

Validity and validation of expert (Q)SAR systems

At a recent workshop in Setubal (Portugal) principles were drafted to assess the suitability of (quantitative) structure–activity relationships ((Q)SARs) for assessing the hazards and risks of chemicals. In the present study we applied some of the Setubal principles to test the validity of three (Q)SAR expert systems and validate the results. These principles include a mechanistic basis, the availability of a training set and validation. ECOSAR, BIOWIN and DEREK for Windows have a mechanistic or empirical basis. ECOSAR has a training set for each QSAR. For half of the structural fragments the number of chemicals in the training set is >4. Based on structural fragments and log Kow, ECOSAR uses linear regression to predict ecotoxicity. Validating ECOSAR for three ‘valid’ classes results in predictivity of ?≥?64%. BIOWIN uses (non-)linear regressions to predict the probability of biodegradability based on fragments and molecular weight. It has a large training set and predicts non-ready biodegradability well. DEREK for Windows predictions are supported by a mechanistic rationale and literature references. The structural alerts in this program have been developed with a training set of positive and negative toxicity data. However, to support the prediction only a limited number of chemicals in the training set is presented to the user. DEREK for Windows predicts effects by ‘if-then’ reasoning. The program predicts best for mutagenicity and carcinogenicity. Each structural fragment in ECOSAR and DEREK for Windows needs to be evaluated and validated separately.     

Anti-Inflammatory and Anti-Platelet Properties of Lipid Bioactives from Apple Cider By-Products

The valorization of food industry by-products as sources of bioactive compounds is at the forefront of research in functional foods and nutraceuticals. This study focuses on bioactives of apple cider by-products (ACBPs) with putative cardio-protective properties. Total lipids (TLs) were extracted from ACBPs of apple varieties that are low (ACBP1), medium (ACBP2), and high (ACBP3) in tannins and were further separated into polar lipids (PLs) and neutral lipids (NLs). The functionality of these lipid extracts and of their HPLC-derived lipid fractions/PL subclasses were assessed in vitro against human platelet aggregation induced by the thrombotic and inflammatory platelet agonists platelet-activating factor (PAF) and adenosine diphosphate (ADP). The fatty acid profile of PLs and their most bioactive lipid fractions were evaluated by GC–MS analysis. The PL extracts exhibited higher specificity against the PAF-induced platelet aggregation compared to their anti-ADP effects, while TL and NL showed lower bioactivities in all ACBPs. HPLC analysis unveiled that the most bioactive PL from all ACBPs were those in PL fraction 3 containing phosphatidylcholines (PCs). PLs from all ACBPs and their PC bioactives were rich in polyunsaturated fatty acids (PUFAs) and especially in the essential omega-6 (n-6) linoleic acid (LA) and omega-3 (n-3) alpha linolenic acid (ALA), with favorably low values of the n-6/n-3 PUFA ratio, thus providing a rationale for their higher anti-inflammatory bioactivities. Within this study, highly bioactive PL compounds with strong anti-inflammatory and anti-platelet properties were identified in ACBPs, which can be potentially utilized for producing cardio-protective functional foods and/or nutraceuticals.     

On computational aspects of simplicial splines

Some new results on multivariate simplex B-splines and their practical application are presented. New recurrence relations are derived based on [2] and [15]. Remarks on boundary conditions are given and an example of an application of bivariate quadratic simplex splines is presented. The application concerns the approximation of a surface which is constrained by a differential equation.Communicated by Charles Micchelli.     

External validation of EPIWIN biodegradation models

The BIOWIN biodegradation models were evaluated for their suitability for regulatory purposes. BIOWIN includes the linear and non-linear BIODEG and MITI models for estimating the probability of rapid aerobic biodegradation and an expert survey model for primary and ultimate biodegradation estimation. Experimental biodegradation data for 110 newly notified substances were compared with the estimations of the different models. The models were applied separately and in combinations to determine which model(s) showed the best performance. The results of this study were compared with the results of other validation studies and other biodegradation models. The BIOWIN models predict not-readily biodegradable substances with high accuracy in contrast to ready biodegradability. In view of the high environmental concern of persistent chemicals and in view of the large number of not-readily biodegradable chemicals compared to the readily ones, a model is preferred that gives a minimum of false positives without a corresponding high percentage false negatives. A combination of the BIOWIN models (BIOWIN2 or BIOWIN6) showed the highest predictive value for not-readily biodegradability. However, the highest score for overall predictivity with lowest percentage false predictions was achieved by applying BIOWIN3 (pass level 2.75) and BIOWIN6.