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In Silico Prediction of Organ Level Toxicity
Mark T.D. Cronin,Steven J. Enoch,Claire L. Mellor,Katarzyna R. Przybylak,Andrea-Nicole Richarz,Judith C. Madden 한국독성학회 2017 Toxicological Research Vol.33 No.3
In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs) as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to consider organ level effects, as opposed to modelling the NO(A)EL itself. This review has focussed on the use of structural alerts to identify potential liver toxicants. In silico profilers, or groups of structural alerts, have been developed based on mechanisms of action and informed by current knowledge of Adverse Outcome Pathways. These profilers are robust and can be coded computationally to allow for prediction. However, they do not cover all mechanisms or modes of liver toxicity and recommendations for the improvement of these approaches are given.
In Silico Prediction of Organ Level Toxicity: Linking Chemistry to Adverse Effects
Cronin, Mark T.D.,Enoch, Steven J.,Mellor, Claire L.,Przybylak, Katarzyna R.,Richarz, Andrea-Nicole,Madden, Judith C. Korean Society of ToxicologyKorea Environmental Mu 2017 Toxicological Research Vol.33 No.3
In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs) as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to consider organ level effects, as opposed to modelling the NO(A)EL itself. This review has focussed on the use of structural alerts to identify potential liver toxicants. In silico profilers, or groups of structural alerts, have been developed based on mechanisms of action and informed by current knowledge of Adverse Outcome Pathways. These profilers are robust and can be coded computationally to allow for prediction. However, they do not cover all mechanisms or modes of liver toxicity and recommendations for the improvement of these approaches are given.
The virtual penetration laboratory: new developments for projectile penetration in concrete
Mark D. Adley,Andreas O. Frank,Kent T. Danielson,Stephen A. Akers,James L. O’Daniel 사단법인 한국계산역학회 2010 Computers and Concrete, An International Journal Vol.7 No.2
This paper discusses new capabilities developed for the Virtual Penetration Laboratory (VPL) software package to address the challenges of determining Penetration Resistance (PR) equations for concrete materials. Specifically, the paper introduces a three-invariant concrete constitutive model recently developed by the authors. The Advanced Fundamental Concrete (AFC) model was developed to provide a fast-running predictive model to simulate the behavior of concrete and other high-strength geologic materials. The Continuous Evolutionary Algorithms (CEA) automatic fitting algorithms used to fit the new model are discussed, and then examples are presented to demonstrate the effectiveness of the new AFC model. Finally, the AFC model in conjunction with the VPL software package is used to develop a PR equation for a concrete material.
Mark D. Adley,Andreas O. Frank,Kent T. Danielson 사단법인 한국계산역학회 2012 Computers and Concrete, An International Journal Vol.9 No.4
This paper discusses a new constitutive model called the high-rate brittle microplane (HRBM) model and also presents the details of a new software package called the Virtual Materials Laboratory (VML). The VML software package was developed to address the challenges of fitting complex material models such as the HRBM model to material property test data and to study the behavior of those models under a wide variety of stress- and strain-paths. VML employs Continuous Evolutionary Algorithms (CEA) in conjunction with gradient search methods to create automatic fitting algorithms to determine constitutive model parameters. The VML code is used to fit the new HRBM model to a well-characterized conventional strength concrete called WES5000. Finally, the ability of the new HRBM model to provide high-fidelity simulations of material property experiments is demonstrated by comparing HRBM simulations to laboratory material property data.
Numerical procedures for extreme impulsive loading on high strength concrete structures
Kent T. Danielson,Mark D. Adley,James L. O'Daniel 사단법인 한국계산역학회 2010 Computers and Concrete, An International Journal Vol.7 No.2
This paper demonstrates numerical techniques for complex large-scale modeling with microplane constitutive theories for reinforced high strength concrete, which for these applications, is defined to be around the 7000 psi (48 MPa) strength as frequently found in protective structural design. Applications involve highly impulsive loads, such as an explosive detonation or impact-penetration event. These capabilities were implemented into the authors’ finite element code, ParaAble and the PRONTO 3D code from Sandia National Laboratories. All materials are explicitly modeled with eight-noded hexahedral elements. The concrete is modeled with a microplane constitutive theory, the reinforcing steel is modeled with the Johnson-Cook model, and the high explosive material is modeled with a JWL equation of state and a programmed burn model. Damage evolution, which can be used for erosion of elements and/or for postanalysis examination of damage, is extracted from the microplane predictions and computed by a modified Holmquist-Johnson-Cook approach that relates damage to levels of inelastic strain increment and pressure. Computation is performed with MPI on parallel processors. Several practical analyses demonstrate that large-scale analyses of this type can be reasonably run on large parallel computing systems.
Remediation of radioiodine using polyamine anion exchange resins
Daniel N.T. Barton,Thomas J. Robshaw,Oluwatobi Okusanya,김대근,Sarah E. Pepper,Clint A. Sharrad,이택승,Mark D. Ogden 한국공업화학회 2019 Journal of Industrial and Engineering Chemistry Vol.78 No.-
Two weak base anion exchange resins, Lewatit A365 and Purolite MTS9850, have been tested for theremoval of aqueous iodide from conditions simulating nuclear waste reprocessing streams. pH variationand relevant co-contaminant addition (nitrate, molybdate and iodine) allowed for assessment of iodideextraction behaviour of each resin. Isotherm experiments were performed and maximum uptakecapacities obtained exceed current industrial adsorbents, such as silver-impregnated zeolites. Maximumloading capacities, determined by Dubinin–Radushkevich isotherm, were 76114 mg g 1 for MTS9850and 589 15 mg g 1 for A365. Uptake for both resins was significantly suppressed by nitrate andmolybdate ions. The presence of dissolved iodine in the raffinate however, was found to increase iodideuptake. This was explained by characterisation of the spent resin surface by infrared and Ramanspectroscopy, which determined the presence of triiodide, indicating charge-transfer complex formationon the surface. Dynamic studies assessed the effect of co-contaminants on iodide uptake in a columnenvironment. Data wasfitted to three dynamic models, with the Dose-Response model providing the bestdescription of breakthrough. In all cases iodide breakthrough was accelerated, indicating suppression ofuptake, but capacity was still significant.
The Role of Inflammatory Mediators in the Pathogenesis of Otitis Media and Sequelae
Steven K. Juhn,정민교,Mark D. Hoffman,Brian R. Drew,Diego A. Preciado,Nicholas J. Sausen,Timothy T.K. Jung,Bo Hyung Kim,박상유,Jizhen Lin,Frank G. Ondrey,David R. Mains,Tina Huang 대한이비인후과학회 2008 Clinical and Experimental Otorhinolaryngology Vol.1 No.3
This review deals with the characteristics of various inflammatory mediators identified in the middle ear during otitis media and in cholesteatoma. The role of each inflammatory mediator in the pathogenesis of otitis media and cholesteatoma has been discussed. Further, the relation of each inflammatory mediator to the pathophysiology of the middle and inner ear along with its mechanisms of pathological change has been described. The mechanisms of hearing loss including sensorineural hearing loss (SNHL) as a sequela of otitis media are also discussed. The passage of inflammatory mediators through the round window membrane into the scala tympani is indicated. In an experimental animal model, an application of cytokines and lipopolysaccharide (LPS), a bacterial toxin, on the round window membrane induced sensorineural hearing loss as identified through auditory brainstem response threshold shifts. An increase in permeability of the blood-labyrinth barrier (BLB) was observed following application of these inflammatory mediators and LPS. The leakage of the blood components into the lateral wall of the cochlea through an increase in BLB permeability appears to be related to the sensorineural hearing loss by hindering K+ recycling through the lateral wall disrupting the ion homeostasis of the endolymph. Further studies on the roles of various inflammatory mediators and bacterial toxins in inducing the sensorineumral hearing loss in otitis media should be pursued.
Andreas O. Frank,Mark D. Adley,Kent T. Danielson,Henry S. McDevitt, Jr. 사단법인 한국계산역학회 2012 Computers and Concrete, An International Journal Vol.9 No.4
In this paper, we examine the behavior of the High-Rate Brittle Microplane (HRBM) concrete model based on a series of penetration experiments. These experiments were conducted with three different slab thicknesses (127, 216 and 254 mm) that provided a significant challenge for the numerical simulations. The 127 mm slab provided little resistance, the 216 mm slab provided nominal resistance and the 254 mm slab approached the perforation limit thickness of the projectile. These experiments provide a good baseline for evaluating material models since they have been shown to be extremely challenging; in fact, we have not encountered many material models that can provide quantitatively predictive results in terms of both projectile exit velocity and material damage. In a companion paper, we described the HRBM material model and its fit to various quasi-static material property data for WES-5000 concrete. In this paper, we show that, when adequately fit to these quasi-static data, the HRBM model does not have significant predictive capabilities, even though the quasi-static material fit may be exceptional. This was attributed to the rate-dependent response of the material. After various rate effects were introduced into the HRBM model, the quantitative predictive nature of the calculations dramatically increased. Unfortunately, not much rate-dependent material property data are in the literature; hence, accurate incorporation of rate effects into material models is difficult. Nonetheless, it seems that rate effects may be critical in obtaining an accurate response for concrete during projectile perforation events.
Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing
Kim, Jin S.,Nanfara, Michael T.,Chodavarapu, Sundari,Jin, Kyeong S.,Babu, Vignesh ,M. ,P.,Ghazy, Mohamed A.,Chung, Scisung,Kaguni, Jon M.,Sutton, Mark D.,Cho, Yunje Oxford University Press 2017 Nucleic acids research Vol.45 No.7
<P><B>Abstract</B></P><P>Regulatory inactivation of DnaA (RIDA) is one of the major regulatory mechanisms of prokaryotic replication licensing. In RIDA, the Hda–sliding clamp complex loaded onto DNA directly interacts with adenosine triphosphate (ATP)-bound DnaA and stimulates the hydrolysis of ATP to inactivate DnaA. A prediction is that the activity of Hda is tightly controlled to ensure that replication initiation occurs only once per cell cycle. Here, we determined the crystal structure of the Hda–β clamp complex. This complex contains two pairs of Hda dimers sandwiched between two β clamp rings to form an octamer that is stabilized by three discrete interfaces. Two separate surfaces of Hda make contact with the β clamp, which is essential for Hda function in RIDA. The third interface between Hda monomers occludes the active site arginine finger, blocking its access to DnaA. Taken together, our structural and mutational analyses of the Hda–β clamp complex indicate that the interaction of the β clamp with Hda controls the ability of Hda to interact with DnaA. In the octameric Hda–β clamp complex, the inability of Hda to interact with DnaA is a novel mechanism that may regulate Hda function.</P>