MOTIVATION: Understanding the mechanisms by which the zebrafish pectoral fin develops is expected to produce insights on how vertebrate limbs grow from a 2D cell layer to a 3D structure. Two mechanisms have been proposed to drive limb morphogenesis in tetrapods: a growth-based morphogenesis with a higher proliferation rate at the distal tip of the limb bud than at the proximal side, and directed cell behaviors that include elongation, division and migration in a non-random manner. Based on quantitative experimental biological data at the level of individual cells in the whole developing organ, we test the conditions for the dynamics of pectoral fin early morphogenesis. RESULTS: We found that during the development of the zebrafish pectoral fin, cells have a preferential elongation axis that gradually aligns along the proximodistal (PD) axis of the organ. Based on these quantitative observations, we build a center-based cell model enhanced with a polarity term and cell proliferation to simulate fin growth. Our simulations resulted in 3D fins similar in shape to the observed ones, suggesting that the existence of a preferential axis of cell polarization is essential to drive fin morphogenesis in zebrafish, as observed in the development of limbs in the mouse, but distal tip-based expansion is not. AVAILABILITYAND IMPLEMENTATION: Upon publication, biological data will be available at http://bioemergences.eu/modelingFin, and source code at https://github.com/guijoe/MaSoFin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Topic Modelling has been applied in many successful applications in data mining, text mining, machine learning and information filtering. The limitation is that the quality of topics generated from modelled corpus are not always good because many topics contain intrusive and ambiguous words. This negative drawback would affect the performance of text based application systems based on topic models. Hence, topic evaluation to assess and to rank the topics is really important for the good quality topics before applying those topics to text based applications. In this study, we proposed an ontology-based topic evaluation method for enhancing information filtering, named as STRbTCM. This new model assesses the quality of topics by matching topic models with headings in Library Congress Subject Heading (LCSH) ontology. To evaluate the effectiveness of our proposed model, we compare the model with two existing topic evaluation methods applied to information filtering system. In addition, we also compare our proposed model to term-based model BM25 and two other models based on topics: TNG and LDA_words. Through extensive experiments, we find that our proposed model performed better than other baseline models according to four main evaluating measures.