Bifurcation theory provides a powerful framework to analyze the dynamics of differential systems as a function of specific parameters. Abou-Jaoudé et al. (2009) introduced the concept of logical bifurcation diagrams, an analog of bifurcation diagrams for the logical modeling framework. In this work, we propose a formal definition of this concept. Since logical models are inherently discrete, we use the piecewise differential (PWLD) framework to introduce the underlying bifurcation parameters. Given a regulatory graph, a set of PWLD models is mapped to a set of logical models consistent with this graph, thereby linking continuous changes of bifurcation parameters to sequences of valuations of logical parameters. A logical bifurcation diagram corresponds then to a sequence of valuations of the logical parameters (with their associated set of attractors) consistent with at least one bifurcation diagram of the set of PWLD models. Necessary conditions on logical bifurcation diagrams in the general case, as well as a characterization of these diagrams in the Boolean case, exploiting a partial order between the logical parameters, are provided. We also propose a procedure to determine a logical bifurcation diagram of maximum length, starting from an initial valuation of the logical parameters, in the Boolean case. Finally, we apply our methodology to the analysis of a biological model of the p53-Mdm2 network.
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http://dx.doi.org/10.1016/j.jtbi.2019.01.008 | DOI Listing |
Health Hum Rights
December 2024
Associate professor of women, gender, and sexuality studies in the Frederik Meijer Honors College at Grand Valley State University, Allendale, Michigan, United States.
Reproductive rights and reproductive justice paradigms have long been viewed as incompatible, largely because of their divergent orientations to the notion of choice. According to this oppositional framing, reproductive rights approaches have centered the right of (white, middle-class, heterosexual) women to choose not to have children while reproductive justice organizing has focused on gendered, racialized, and classed obstacles to control over whether and how to have and raise children. Amid increasing examination of assisted reproductive technologies (ARTs) vis-à-vis human rights principles, I see an opportunity to narrow the perceived gap between the politics of rights and justice.
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China.
The vast neuronal diversity in the human neocortex is vital for high-order brain functions, necessitating elucidation of the regulatory mechanisms underlying such unparalleled diversity. However, recent studies have yet to comprehensively reveal the diversity of neurons and the molecular logic of neocortical origin in humans at single-cell resolution through profiling transcriptomic or epigenomic landscapes, owing to the application of unimodal data alone to depict exceedingly heterogeneous populations of neurons. In this study, we generated a comprehensive compendium of the developing human neocortex by simultaneously profiling gene expression and open chromatin from the same cell.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
May 2024
Université Paris-Saclay, Département de Biologie, Faculté des Sciences d'Orsay, Signalisation Radiobiology and Cancer, CNRS UMR 3347, INSERM U1021, Orsay F-91405, France.
Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of early molecular choices orchestrating the emergence of neural crest heterogeneity from the embryonic ectoderm remains elusive. Gene-regulatory-networks (GRN) govern early development and cell specification toward definitive neural crest.
View Article and Find Full Text PDFComput Methods Biomech Biomed Engin
December 2024
Department of Applied Mechanics and Biomedical Engineering, IIT Madras, Chennai, India.
An aneurysm is a disease condition, which is due to the pathological weakening of an arterial wall. These aneurysms are often found in various branch points and bifurcations of an artery in the cerebral circulation. Most aneurysms come to medical attention, either due to brain hemorrhages caused by rupture or found unruptured.
View Article and Find Full Text PDFIntroduction: Carotid bifurcation stenosis may co-exist simultaneously with more proximal common carotid artery (CCA) atherosclerotic plaquing, primarily at the vessel origin in the aortic arch. This scenario is relatively infrequent and its' management does not have quality randomized data to support medical vs surgical treatment. It is logical to treat any high grade common carotid lesions proximal to a carotid bifurcation endarterectomy (CEA) site both to prevent perioperative emboli or thrombosis as well as future embolization.
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