Investigating the influence of data splitting on the predictive ability of QSAR/QSPR models

The study was aimed at investigating how the method of splitting data into a training set and a test set influences the external predictivity of quantitative structure-activity and/or structure-property relationships (QSAR/QSPR) models. Six models of good quality were collected from the literature and then redeveloped and validated on the basis of five alternative splitting algorithms, namely: (i) a commonly used algorithm ('Z:1'), in which every zth (e.g. third) from the compounds sorted ascending (according to the response values, y) is selected into the test set; (ii-iv) three variations of the Kennard-Stone algorithm; and (v) the duplex algorithm. The external validation statistics reported for each model served as a basis for the final comparison. We demonstrated that the splitting techniques utilizing the values of molecular descriptors alone (X) or in combination with the model response (y) always lead to the development of the models yielding better external predictivity in comparison with the models designed with methodologies based on the y-values only. Moreover, we showed that the external validation coefficient (Q2EXT) is more sensitive to the splitting technique than the root mean square error of prediction (RMSEP). This difference becomes especially important when the test set is relatively small (between 5-10 compounds). In the case of the models trained/validated with a small number of compounds, it is strongly recommended that both statistics (Q2EXT and RMSEP) are taken into account for the external predictivity evaluation.JRC.I.6-Systems toxicolog

Addressing a bottle neck for regulation of nanomaterials: quantitative read-across (Nano-QRA) algorithm for cases when only limited data is available

The number and variety of engineered nanoparticles have been growing exponentially. Since the experimental evaluation of nanoparticles causing public health concerns is expensive and time consuming, efficient computational tools are amongst the most suitable approaches to identifying potential negative impacts, to the human health and the environment, of new nanomaterials before their production. However, developing computational models complimentary to experiments is impossible without incorporating consistent and high quality experimental data. Although there are limited available data in the literature, one may apply read-across techniques that seem to be an attractive and pragmatic alternative way of predicting missing physico-chemical or toxicological data. Unfortunately, the existing methods of read-across are strongly dependent on the expert's knowledge. In consequence, the results of estimations may vary dependently on personal experience of expert conducting the study and as such cannot guarantee the reproducibility of their results. Therefore, it is essential to develop novel read-across algorithm(s) that will provide reliable predictions of the missing data without the need to for additional experiments. We proposed a novel quantitative read-across approach for nanomaterials (Nano-QRA) that addresses and overcomes a basic limitation of existing methods. It is based on: one-point-slope, two-point formula, or the equation of a plane passing through three points. The proposed Nano-QRA approach is a simple and effective algorithm for filling data gaps in quantitative manner providing reliable predictions of the missing data. © The Royal Society of Chemistry

Novel approach for efficient predictions properties of large pool of nanomaterials based on limited set of species: nano-read-across

Creating suitable chemical categories and developing read-across methods, supported by quantum mechanical calculations, can be an effective solution to solving key problems related to current scarcity of data on the toxicity of various nanoparticles. This study has demonstrated that by applying a nano-read-across, the cytotoxicity of nano-sized metal oxides could be estimated with a similar level of accuracy as provided by quantitative structure-activity relationship for nanomaterials (nano-QSAR model(s)). The method presented is a suitable computational tool for the preliminary hazard assessment of nanomaterials. It also could be used for the identification of nanomaterials that may pose potential negative impact to human health and the environment. Such approaches are especially necessary when there is paucity of relevant and reliable data points to develop and validate nano-QSAR model

Scanning electron microscopy image representativeness: morphological data on nanoparticles.

A sample of a nanomaterial contains a distribution of nanoparticles of various shapes and/or sizes. A scanning electron microscopy image of such a sample often captures only a fragment of the morphological variety present in the sample. In order to quantitatively analyse the sample using scanning electron microscope digital images, and, in particular, to derive numerical representations of the sample morphology, image content has to be assessed. In this work, we present a framework for extracting morphological information contained in scanning electron microscopy images using computer vision algorithms, and for converting them into numerical particle descriptors. We explore the concept of image representativeness and provide a set of protocols for selecting optimal scanning electron microscopy images as well as determining the smallest representative image set for each of the morphological features. We demonstrate the practical aspects of our methodology by investigating tricalcium phosphate, Ca3 (PO4 )2 , and calcium hydroxyphosphate, Ca5 (PO4 )3 (OH), both naturally occurring minerals with a wide range of biomedical applications

Spektroskopia rezonansu magnetycznego w wewnątrzczaszkowych nowotworach pochodzenia glejowego

Background and purpose To determine in vivo magnetic resonance spectroscopy (MRS) characteristics of intracranial glial tumours and to assess MRS reliability in glioma grading and discrimination between different histopathological types of tumours. Material and methods Analysis of spectra of 26 patients with glioblastomas, 6 with fibrillary astrocytomas, 4 with anaplastic astrocytomas, 2 with pilocytic astrocytoma, 3 with oligodendrogliomas, 3 with anaplastic oligodendrogliomas and 17 control spectra taken from healthy hemispheres. Results All tumours’ metabolite ratios, except for Cho/Cr in fibrillary astrocytomas (p = 0.06), were statistically signiflcantly different from the control. The tumours showed decreased Naa and Cr contents and a high Cho signal. The Lac-Lip signal was high in grade III astrocytomas and glioblastomas. Reports that Cho/Cr ratio increases with glioma's grade whereas Naa/Cr decreases were not confirmed. Anaplastic astrocytomas compared to grade II astrocytomas had a statistically significantly greater ml/Cr ratio (p = 0.02). In pilocytic astrocytomas the Naa/Cr value (2.58 ± 0.39) was greater, whilst the Cho/Naa ratio was lower (2.14 ± 0.64) than in the other astrocytomas. The specific feature of oligodendrogliomas was the presence of glutamate/glutamine peak Glx. However, this peak was absent in two out of three anaplastic oligodendrogliomas. Characteristically, the latter tumours had a high Lac-Lip signal. Conclusions MRS in vivo cannot be used as a reliable method for glioma grading. The method is useful in discrimination between WHO grade I and WHO grade II astrocytomas as well as oligodendrogliomas from other gliomas.Wstęp i cel pracy Ustalenie charakterystyki spektroskopii magnetycznego rezonansu jądrowego (magnetic resonance spectroscopy – MRS) u chorych z nowotworami wewnątrzczaszkowymi pochodzenia glejowego oraz ocena przydatności tego badania w diagnostyce różnicowej typów histologicznych glejaków. Materiał i metody Przeprowadzono analizę widm MRS nowotworów u 26 chorych z glejakami wielopostaciowymi, 6 z gwiaździakami włókienkowymi, 4 z gwiaździakami anaplastycznymi, 2 z włosowatokomórkowymi, 3 ze skąpodrzewiakami, 3 ze skąpodrzewiakami anaplastycznymi oraz 17 widm kontrolnych pochodzących ze zdrowych półkul mózgu. Wyniki Wszystkie wskaźniki metaboliczne w przypadkach nowotworów, z wyjątkiem Cho/Cr w gwiaździakach włókienkowych (p = 0,06), różniły się znamiennie od tych w grupie kontrolnej. Nowotwory wykazywały zmniejszoną zawartość Naa i Cr oraz wysoki sygnał Cho. Sygnał Lac-Lip był wysoki w gwiaździakach III stopnia wg WHO i glejakach wielopostaciowych. Nie udało się potwierdzić doniesień, że wskaźnik Cho/Cr rośnie, a wskaźnik Naa/Cr maleje wraz ze wzrostem stopnia złośliwości glejaka. Gwiaździaki anaplastyczne wykazywały znamiennie wyższy wskaźnik ml/Cr (p = 0,02) w porównaniu z gwiaździakami II stopnia wg WHO. W gwiaździakach włosowatokomórkowych wartość Naa/Cr (2,58 ± 0,39) była większa, a Cho/Naa mniejsza (2,14 ± 0,64) niż w innych gwiaździakach. Skąpodrzewiaki charakteryzowała obecność szczytu glutaminianu/glutaminy (Glx), którego jednak nie obserwowano w 2 spośród 3 przypadków skąpodrzewiaków anaplastycznych. Dla tych ostatnich symptomatyczna była obecność silnego sygnału Lac-Lip. Wnioski Badanie MRS in vivo nie jest niezawodną metodą różnicującą glejaki wewnątrzczaszkowe. Wydaje się użyteczne w diagnostyce różnicowej gwiaździaków I i II stopnia wg WHO oraz w odróżnianiu skąpodrzewiaków od pozostałych glejaków

Comparing the CORAL and random forest approaches for modelling the in vitro cytotoxicity of silica nanomaterials

Nanotechnology is one of the most important technological developments of the twenty-first century. In silico methods such as quantitative structure-activity relationships (QSARs) to predict toxicity promote the safe-by-design approach for the development of new materials, including nanomaterials. In this study, a set of cytotoxicity experimental data corresponding to 19 data points for silica nanomaterials was investigated to compare the widely employed CORAL and Random Forest approaches in terms of their usefulness for developing so-called “nano-QSAR” models. “External” leave-one-out cross-validation (LOO) analysis was performed to validate the two different approaches. An analysis of variable importance measures and signed feature contributions for both algorithms was undertaken in order to interpret the models developed. CORAL showed a more pronounced difference between the average coefficient of determination (R2) between training and LOO (0.83 and 0.65 for training and LOO respectively) compared to Random Forest (0.87 and 0.78 without bootstrap sampling, 0.90 and 0.78 with bootstrap sampling), which may be due to overfitting. The aspect ratio and zeta potential from amongst the nanomaterials’ physico-chemical properties were found to be the two most important variables for the Random Forest and the average feature contributions calculated for the corresponding descriptors were consistent with the clear trends observed in the dataset: less negative zeta potential values and lower aspect ratio values were associated with higher cytotoxicity. In contrast, CORAL failed to capture these trends

Comparing the CORAL and Random Forest approaches for modelling the in vitro cytotoxicity of silica nanomaterials.

Nanotechnology is one of the most important technological developments of the 21st century. In silico methods to predict toxicity, such as quantitative structure-activity relationships (QSARs), promote the safe-by-design approach for the development of new materials, including nanomaterials. In this study, a set of cytotoxicity experimental data corresponding to 19 data points for silica nanomaterials were investigated, to compare the widely employed CORAL and Random Forest approaches in terms of their usefulness for developing so-called 'nano-QSAR' models. 'External' leave-one-out cross-validation (LOO) analysis was performed, to validate the two different approaches. An analysis of variable importance measures and signed feature contributions for both algorithms was undertaken, in order to interpret the models developed. CORAL showed a more pronounced difference between the average coefficient of determination (R²) for training and for LOO (0.83 and 0.65 for training and LOO, respectively), compared to Random Forest (0.87 and 0.78 without bootstrap sampling, 0.90 and 0.78 with bootstrap sampling), which may be due to overfitting. With regard to the physicochemical properties of the nanomaterials, the aspect ratio and zeta potential were found to be the two most important variables for Random Forest, and the average feature contributions calculated for the corresponding descriptors were consistent with the clear trends observed in the data set: less negative zeta potential values and lower aspect ratio values were associated with higher cytotoxicity. In contrast, CORAL failed to capture these trends

Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations

Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth