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Kim, Donghoon; Duffy, Thomas S.; Smith, Raymond F.; Ocampo, Ian K.; Coppari, Federica; Marshall, Michelle C.; Ginnane, Mary Kate; Wicks, June; Tracy, Sally J.; Millot, Marius; Lazicki, Amy; Rygg, Jame R.; Eggert, Jon H.
Chronic hepatitis B (CHB), caused by hepatitis B virus (HBV), remains a major medical problem. HBV has a high propensity for progressing to chronicity and can result in severe liver disease, including fibrosis, cirrhosis and hepatocellular carcinoma. CHB patients frequently present with viral coinfection, including HIV and hepatitis delta virus. About 10% of chronic HIV carriers are also persistently infected with HBV which can result in more exacerbated liver disease. Mechanistic studies of HBV-induced immune responses and pathogenesis, which could be significantly influenced by HIV infection, have been hampered by the scarcity of immunocompetent animal models. Here, we demonstrate that humanized mice dually engrafted with components of a human immune system and a human liver supported HBV infection, which was partially controlled by human immune cells, as evidenced by lower levels of serum viremia and HBV replication intermediates in the liver. HBV infection resulted in priming and expansion of human HLA-restricted CD8+ T cells, which acquired an activated phenotype. Notably, our dually humanized mice support persistent coinfections with HBV and HIV which opens opportunities for analyzing immune dysregulation during HBV and HIV coinfection and preclinical testing of novel immunotherapeutics.
This dataset contains input and output files to reproduce the results of the manuscript "Homogeneous ice nucleation in an ab initio machine learning model" by Pablo M. Piaggi, Jack Weis, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, and Roberto Car (arXiv preprint https://arxiv.org/abs/2203.01376). In this work, we studied the homogeneous nucleation of ice from supercooled liquid water using a machine learning model trained on ab initio energies and forces. Since nucleation takes place over times much longer than the simulation times that can be afforded using molecular dynamics simulations, we make use of the seeding technique that is based on simulating an ice cluster embedded in liquid water. The key quantity provided by the seeding technique is the size of the critical cluster (i.e., a size such that the cluster has equal probabilities of growing or shrinking at the given supersaturation). Using data from the seeding simulations and the equations of classical nucleation theory we compute nucleation rates that can be compared with experiments.
This dataset contains all data relevant to a forthcoming publication in which we used molecular simulation methods to study the phase behavior of supercooled water. The dataset contains simulation input and output files, processed data files, and image files used to create all plots in the manuscript. Python analysis scripts are also included, including instructions for how to re-generate all plots in the manuscript.
