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  1. This study identifies hydrogeologic characteristics of complex aquifers based on constructing stratigraphic structure with large, non-uniform well log data. The approach was validated through a modeling study of the irrigation-intensive Chicot aquifer system, which is an important Pleistocene-Holocene aquifer of the Coastal Lowlands aquifer system in the southwestern Louisiana. Various well log types were unified into the same data structure, prioritized based on data sources, and interpolated to generate a detailed stratigraphic structure. More than 29,000 well logs were integrated to construct a stratigraphy model of 56 model layers for the Chicot aquifer system. The stratigraphy model revealed interconnections ofmore »various sands in the system, where 90% of the model domain is covered by fine-grained sediments. Although the groundwater model estimated a slight groundwater storage gain during 2005–2014 for the entire region, groundwater storage in the agricultural area was depleted. Nevertheless, the quick groundwater storage recovery during the non-irrigation seasons suggests that the Chicot aquifer system is a prolific aquifer system. The groundwater modeling result shows that the gulfward groundwater flow direction prior to pumping has been reversed toward inland pumping areas. The large upward vertical flow from the deeper sands indicates potential saltwater migration from the base of the Chicot aquifer system.« less
  2. Abstract Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expandsmore »these capabilities to cover additional types of models, model languages, parameter estimations, simulations and analyses of models, and analyses and visualizations of simulation results. To facilitate consistent practices across the community, Level 1 Version 4 also more clearly describes the use of SED-ML constructs, and includes numerous concrete validation rules. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including eight languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, over 20 simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/ .« less
  3. Abstract

    Chaperonins are molecular chaperones that play critical physiological roles, but they can be pathogenic. Malfunctional chaperonins cause chaperonopathies of great interest within various medical specialties. Although the clinical-genetic aspects of many chaperonopathies are known, the molecular mechanisms causing chaperonin failure and tissue lesions are poorly understood. Progress is necessary to improve treatment, and experimental models that mimic the human situation provide a promising solution. We present two models: one prokaryotic (the archaeonPyrococcus furiosus) with eukaryotic-like chaperonins and one eukaryotic (Chaetomium thermophilum), both convenient for isolation-study of chaperonins, and report illustrative results pertaining to a pathogenic mutation of CCT5.