In this project we will build a structured database of properties of food ingredients, focusing in particular on the taste and texture properties. By large-scale collection and text mining on a large number of textual resources, a comprehensive data set on ingredient properties will be created, along with knowledge on the relationships between these ingredients. This database will then be used for to find new potential applications for healthy and taste enhancing ingredient combinations by network-based discovery methods and artificial intelligence algorithms will be used. A concrete focus will be on application questions formulated by the industrial partners. The resulting hypothesis will be validated in a real life setting at the premises of the industrial partners.
The deliverables of this project will be:
• A reusable open-access ingredient database that is accessible via a user-friendly web portal
• A set of state-of-the-art mining algorithms that can address a wide variety of industry driven use cases
• Novel product formulations that can be further developed for the consumer and business2business market
The search for existing non-animal alternative methods for use in experiments is currently challenging because of the lack of both comprehensive structured databases and balanced keyword-based search strategies to mine unstructured textual databases. In this paper we describe 3Ranker, which is a fast, keyword-independent algorithm for finding non-animal alternative methods for use in biomedical research. The 3Ranker algorithm was created by using a machine learning approach, consisting of a Random Forest model built on a dataset of 35 million abstracts and constructed with weak supervision, followed by iterative model improvement with expert curated data. We found a satisfactory trade-off between sensitivity and specificity, with Area Under the Curve (AUC) values ranging from 0.85-0.95. Trials showed that the AI-based classifier was able to identify articles that describe potential alternatives to animal use, among the thousands of articles returned by generic PubMed queries on dermatitis and Parkinson's disease. Application of the classification models on time series data showed the earlier implementation and acceptance of Three Rs principles in the area of cosmetics and skin research, as compared to the area of neurodegenerative disease research. The 3Ranker algorithm is freely available at www.open3r.org; the future goal is to expand this framework to cover multiple research domains and to enable its broad use by researchers, policymakers, funders and ethical review boards, in order to promote the replacement of animal use in research wherever possible.
Objectives: Pulmonary hypertension is one of the leading causes of death in systemic sclerosis. Early detection and treatment of pulmonary hypertension in systemic sclerosis is crucial. Nailfold capillaroscopy microscopy, vascular autoantibodies AT1R and ETAR, and several candidate-biomarkers have the potential to serve as noninvasive tools to identify systemic sclerosis patients at risk for developing pulmonary hypertension. Here, we explore the classifying potential of nailfold capillaroscopy microscopy characteristics and serum levels of selected candidate-biomarkers in a sample of systemic sclerosis patients with and without different forms of pulmonary hypertension.Methods: A total of 81 consecutive systemic sclerosis patients were included, 40 with systemic sclerosis pulmonary hypertension and 41 with no pulmonary hypertension. In each group, quantitative and qualitative nailfold capillaroscopy microscopy characteristics, vascular autoantibodies AT1R and ETAR, and serum levels of 24 soluble serum factors were determined. For evaluation of the nailfold capillaroscopy microscopy characteristics, linear regression analysis accounting for age, sex, and diffusing capacity of the lungs for carbon monoxide percentage predicted was used. Autoantibodies and soluble serum factor levels were compared using two-sample t test with equal variances.Results: No statistically significant differences were observed in quantitative or qualitative nailfold capillaroscopy microscopy characteristics, or vascular autoantibody ETAR and AT1R titer between systemic sclerosis-pulmonary hypertension and systemic sclerosis-no pulmonary hypertension. In contrast, several serum levels of soluble factors differed between groups: Endostatin, sVCAM, and VEGFD were increased, and CXCL4, sVEGFR2, and PDGF-AB/BB were decreased in systemic sclerosis-pulmonary hypertension. Random forest classification identified Endostatin and CXCL4 as the most predictive classifiers to distinguish systemic sclerosispulmonary hypertension from systemic sclerosis-no pulmonary hypertension.Conclusion: This study shows the potential for several soluble serum factors to distinguish systemic sclerosis-pulmonary hypertension from systemic sclerosis-no pulmonary hypertension. We found no classifying potential for qualitative or quantitative nailfold capillaroscopy microscopy characteristics, or vascular autoantibodies.
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