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On Emerging Use Cases and Techniques in Large Networked Data in Biomedical and Social Media Domain
Published in Yulei Wu, Fei Hu, Geyong Min, Albert Y. Zomaya, Big Data and Computational Intelligence in Networking, 2017
Vishrawas Gopalakrishnan, Aidong Zhang
Guilt by association (GBA) is a common approach used in social network analyses, where new associations with a node in the graph are determined based on its existing associations and the associations of candidate nodes. This principle has been widely adopted in the biological domain. For example, goh2007human constructed a gene network based on association with the same genes and tian2008combining combined protein interactions, genetic interactions, and gene expression correlation. At the same time, walk-based approaches have also gained popular support in determining relationships or link prediction [32]. Refs. [4, 33] attempt to train a classifier to determine the validity of a new link between two concepts. Such link prediction tasks are formulated as PU learning tasks (positive unlabelled learning). Under such learning, one has limited access to a set of positive samples and treats randomly obtained unlabeled samples as negative. It then trains a biased SVM where it penalizes false negatives more heavily than false positives. The underlying principle is that since the positive samples are known to be true and the negative ones are created from the unlabeled set, getting the positive ones incorrect is more serious and cannot be condoned. Such PU-based learning has also been extensively used in social network settings. Furthermore, analogous to collaborative filtering where nodes/entities similar to the query node/entity are identified for profile enrichment of the latter and determining and recommending friends [34] or movies [35], works like [4, 5, 36] extend that principle to gather evidence from diverse, but related species and create a heterogeneous network for analyses. For instance, the human neural crest related developmentaldisorder Waardenburg syndrome shares gene modules with gravitropism (the ability to detect up and down) in plants, and mammalian angiogenesis has been found to involve the same pathways as lovastatin sensitivity in yeast. In this way, graph modeling of a data set enables us to leverage existing approaches and practices from one domain to other new and relatively less investigated areas.
Embryotoxic effects of Rovral® for early chicken (Gallus gallus) development
Published in Journal of Toxicology and Environmental Health, Part A, 2021
Beatriz Mitidiero Stachissini Arcain, Maria Cláudia Gross, Danúbia Frasson Furtado, Carla Vermeulen Carvalho Grade
Defects in the cranial region of the embryos treated with Rovral® were predominantly incomplete formation of the head/brain, absence of the beak and microphthalmia. The formation of the head depends upon the coordination of several complex processes, which include neurulation and correct closure of the neural tube (Schoenwolf 2018), as well as cephalic folding of the embryo’s body (Gilbert and Barresi 2016). Further, neural crest cells released from neural ridges migrate to the rostral region, filling the pharyngeal arches and contributing to the formation of the skeleton, melanocytes, connective tissue, smooth muscle, fascia and parts of the peripheral nervous system of the face and neck (Creuzet, Couly, and Le Douarin 2005). Defects in neurulation and incorrect cephalic formation lead to anencephaly or encephalocele (Wolujewicz and Ross 2019). Poor neural crest migration in the rostral region might affect structures of the face and neck, and, in humans, results in conditions such as the Waardenburg syndrome (Dourmishev et al. 1999) and CATCH 22 syndrome (Boyarchuk, Volyanska, and Dmytrash 2017).