A proposal for regularly updated review/survey articles: "Perpetual Reviews"

We advocate the publication of review/survey articles that will be updated regularly, both in traditional journals and novel venues. We call these "perpetual reviews." This idea naturally builds on the dissemination and archival capabilities present in the modern internet, and indeed perpetual reviews exist already in some forms. Perpetual review articles allow authors to maintain over time the relevance of non-research scholarship that requires a significant investment of effort. Further, such reviews published in a purely electronic format without space constraints can also permit more pedagogical scholarship and clearer treatment of technical issues that remain obscure in a brief treatment.Comment: This is a draft white paper and we seek comments from the communit

The effect of temperature, initial moisture content, and level of inoculum of aflatoxin and ochratoxin production in corn

Mycotoxin contamination of grains can occur as a result of invasion by field fungi or by growth of storage fungi in improperly stored crops. Environmental factors and competing mycoflora can affect fungal growth and mycotoxin production. Since mycotoxins pose a potential health hazard to both man and animals, this study was con-ducted to evaluate combinations of temperature, initial moisture content (MC), and level of inoculum during storage of corn to determine optimal and limiting conditions for aflatoxin and ochratoxin production during fungal competition and growth in pure culture. Two fungi.were used in this study, Aspergillus parasiticus NRRL 3145 and A. sulphureus NRRL 4077. Fungal spores were added to sterilized corn at levels of 101, 103, 105, and 107 per 50g corn at 16%, 20%, 24%, and 28% MC. Samples were incubated at 20, 24, 28, and 32C for 3 weeks. Aflatoxins and ochratoxin A were then extracted from corn samples and analyzed by HPLC and TLC. More toxin was produced during fungal competition than when each fungus was grown alone. Maximum production of aflatoxin B1, ochratoxin A, and total toxin was at a lower temperature (24C) in mixed culture than in pure culture. Maximum production of aflatoxin G1 occurred at 24C in both pure and mixed culture. For aflatoxin B1, G1, ochratoxin A, and total toxin in mixed culture, 24C resulted in significantly more toxin production (P\u3c0.05) than 20, 28, and 32C. In pure culture, 20C resulted in significantly less aflatoxin B1, G22, ochratoxin A, and total toxin production (P\u3c0.05) than 24, 28, and 32C. Competition affected the temperature dependent relationship of aflatoxin B1 and G1. In both pure and mixed culture, 16% was the minimum MC for toxin production. For pure cultures, 16% MC resulted in significantly less aflatoxin Bi1, aflatoxin G1, ochratoxin A, and total toxin pro duction (P\u3c0.05) than 20, 24, and 28% MC. Optimum conditions for toxin production were more limited during fungal competition. Inoculum was not a significant source of variation. Only for aflatoxin G1 and ochratoxin A in pure culture did the 101 inoculum level result in significantly less toxin production (P\u3c0.05) than the other three inoculum levels. No significant differences between inoculum levels were found in mixed culture. In summary, the presence of A. parasiticus enhanced ochratoxin A production by A. sulphureus and the presence of A. sulphureus enhanced aflatoxin production by A. parasiticus. Toxin production increased probably as a means of survival. Based on the results of this experiment, recommendations for corn storage to reduce or prevent toxin formation by A. parasiticus and A. sulphureus are: a moisture content \u3c 16%; a temperature \u3c 20%; and an inoculum level \u3c 101 spores/50g since in some cases, 10 spores per 50 grams of corn resulted in toxin production

Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a new method for quantifying this uncertainty in implicit solvation calculations of small molecules using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many more types of atomic charges; therefore, construction of surrogate models for the charge parameter space requires compressed sensing combined with an iterative rotation method to enhance problem sparsity. We demonstrate the application of the method by presenting results for the uncertainties in small molecule solvation energies based on these approaches. The method presented in this paper is a promising approach for efficiently quantifying uncertainty in a wide range of force field parameterization problems, including those beyond continuum solvation calculations.The intent of this study is to provide a way for developers of implicit solvent model parameter sets to understand the sensitivity of their target properties (solvation energy) on underlying choices for solute radius and charge parameters

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

We review insights from computational studies of affinities of ligands binding to proteins. The power of structural biology is in translating knowledge of protein structures into insights about their forces, binding, and mechanisms. However, the complementary power of computer modeling is in showing “the rest of the story” (i.e., how motions and ensembles and alternative conformers and the entropies and forces that cannot be seen in single molecular structures also contribute to binding affinities). Upon binding to a protein, a ligand can bind in multiple orientations; the protein or ligand can be deformed by the binding event; waters, ions, or cofactors can have unexpected involvement; and conformational or solvation entropies can sometimes play large and otherwise unpredictable roles. Computer modeling is helping to elucidate these factors

Scattering error corrections for in situ absorption and attenuation measurements

Monte Carlo simulations are used to establish a weighting function that describes the collection of angular scattering for the WETLabs AC-9 reflecting tube absorption meter. The equivalent weighting function for the AC-9 attenuation sensor is found to be well approximated by a binary step function with photons scattered between zero and the collection half-width angle contributing to the scattering error and photons scattered at larger angles making zero contribution. A new scattering error correction procedure is developed that accounts for scattering collection artifacts in both absorption and attenuation measurements. The new correction method does not assume zero absorption in the near infrared (NIR), does not assume a wavelength independent scattering phase function, but does require simultaneous measurements of spectrally matched particulate backscattering. The new method is based on an iterative approach that assumes that the scattering phase function can be adequately modeled from estimates of particulate backscattering ratio and Fournier-Forand phase functions. It is applied to sets of in situ data representative of clear ocean water, moderately turbid coastal water and highly turbid coastal water. Initial results suggest significantly higher levels of attenuation and absorption than those obtained using previously published scattering error correction procedures. Scattering signals from each correction procedure have similar magnitudes but significant differences in spectral distribution are observed

Mame

https://thekeep.eiu.edu/mame_1970/1020/thumbnail.jp

Generation

https://thekeep.eiu.edu/generation_1968/1026/thumbnail.jp

Generation

https://thekeep.eiu.edu/generation_1968/1013/thumbnail.jp

Mame

https://thekeep.eiu.edu/mame_1970/1023/thumbnail.jp