Processing PSE and DFD pork

1 online resource (PDF, 4 pages)This archival publication may not reflect current scientific knowledge or recommendations. Current information available from the University of Minnesota Extension: https://www.extension.umn.edu

Thermodynamically Important Contacts in Folding of Model Proteins

We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.Comment: 5 pages, 5 figures; to be published in PR

Corrigendum to “Effects of therapeutic hypothermia on the gut microbiota and metabolome of infants suffering hypoxic-ischemic encephalopathy at birth” [Int. J. Biochem. Cell Biol. 93 (December) (2017), 110-118]

peer-reviewedCorrigendum Refers to: Watkins, C., Murphy, K., Yen, S., Carafa, I., Dempsey, E., O’Shea, C., Vercoe, E., Ross, R., Stanton, C. and Ryan, C. (2017). Effects of therapeutic hypothermia on the gut microbiota and metabolome of infants suffering hypoxic-ischemic encephalopathy at birth. The International Journal of Biochemistry & Cell Biology, [online] 93, pp.110-118. Available at: https://doi.org/10.1016/j.biocel.2017.08.01

Optimality of mutation and selection in germinal centers

The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved. However, the existing models encountered some conflicts with experiments. To resolve these conflicts, we present a coarse-grained model to calculate the B cell population development in affinity maturation, which allows a comprehensive analysis of its parameter space to look for optimal values of mutation rate, selection strength, and initial antibody-antigen binding level that maximize the affinity improvement. With these optimized parameters, the model is compatible with the experimental observations such as the ~100-fold affinity improvements, the number of mutations, the hypermutation rate, and the "all or none" phenomenon. Moreover, we study the reasons behind the optimal parameters. The optimal mutation rate, in agreement with the hypermutation rate in vivo, results from a tradeoff between accumulating enough beneficial mutations and avoiding too many deleterious or lethal mutations. The optimal selection strength evolves as a balance between the need for affinity improvement and the requirement to pass the population bottleneck. These findings point to the conclusion that germinal centers have been optimized by evolution to generate strong affinity antibodies effectively and rapidly. In addition, we study the enhancement of affinity improvement due to B cell migration between germinal centers. These results could enhance our understandings to the functions of germinal centers.Comment: 5 figures in main text, and 4 figures in Supplementary Informatio

Dispersity-Driven Melting Transition in Two Dimensional Solids

We perform extensive simulations of $10^4$ Lennard-Jones particles to study the effect of particle size dispersity on the thermodynamic stability of two-dimensional solids. We find a novel phase diagram in the dispersity-density parameter space. We observe that for large values of the density there is a threshold value of the size dispersity above which the solid melts to a liquid along a line of first order phase transitions. For smaller values of density, our results are consistent with the presence of an intermediate hexatic phase. Further, these findings support the possibility of a multicritical point in the dispersity-density parameter space.Comment: In revtex format, 4 pages, 6 postscript figures. Submitted to PR

Liquid State Anomalies for the Stell-Hemmer Core-Softened Potential

We study the Stell-Hemmer potential using both analytic (exact $1d$ and approximate $2d$) solutions and numerical $2d$ simulations. We observe in the liquid phase an anomalous decrease in specific volume and isothermal compressibility upon heating, and an anomalous increase in the diffusion coefficient with pressure. We relate the anomalies to the existence of two different local structures in the liquid phase. Our results are consistent with the possibility of a low temperature/high pressure liquid-liquid phase transition.Comment: 4 pages in one gzipped ps file including 11 figures; One RevTex and 11 gzipped eps figure

A life in progress: motion and emotion in the autobiography of Robert M. La Follette

This article is a study of a La Follette’s Autobiography, the autobiography of the leading Wisconsin progressive Robert M. La Follette, which was published serially in 1911 and, in book form, in 1913. Rather than focusing, as have other historians, on which parts of La Follette’s account are accurate and can therefore be trusted, it explains instead why and how this major autobiography was conceived and written. The article shows that the autobiography was the product of a sustained, complex, and often fraught series of collaborations among La Follette’s family, friends, and political allies, and in the process illuminates the importance of affective ties as well as political ambition and commitment in bringing the project to fruition. In the world of progressive reform, it argues, personal and political experiences were inseparable

Prospecting in ultracool dwarfs : Measuring the metallicities of mid- and late-m dwarfs

© 2014. The American Astronomical Society. All rights reserved.Metallicity is a fundamental parameter that contributes to the physical characteristics of a star. The low temperatures and complex molecules present in M dwarf atmospheres make it difficult to measure their metallicities using techniques that have been commonly used for Sun-like stars. Although there has been significant progress in developing empirical methods to measure M dwarf metallicities over the last few years, these techniques have been developed primarily for early- to mid-M dwarfs. We present a method to measure the metallicity of mid- to late-M dwarfs from moderate resolution (R ∼ 2000) K-band (≃ 2.2 μm) spectra. We calibrate our formula using 44 wide binaries containing an F, G, K, or early-M primary of known metallicity and a mid- to late-M dwarf companion. We show that similar features and techniques used for early-M dwarfs are still effective for late-M dwarfs. Our revised calibration is accurate to ∼0.07 dex for M4.5-M9.5 dwarfs with -0.58 <[Fe/H] <+0.56 and shows no systematic trends with spectral type, metallicity, or the method used to determine the primary star metallicity. We show that our method gives consistent metallicities for the components of M+M wide binaries. We verify that our new formula works for unresolved binaries by combining spectra of single stars. Lastly, we show that our calibration gives consistent metallicities with the Mann et al. study for overlapping (M4-M5) stars, establishing that the two calibrations can be used in combination to determine metallicities across the entire M dwarf sequence.Peer reviewe