sj-docx-1-pom-10.1177_03057356241238004 – Supplemental material for Charity begins with prosocial music: Musical differences in intertemporal prosocial discounting and generosity

Supplemental material, sj-docx-1-pom-10.1177_03057356241238004 for Charity begins with prosocial music: Musical differences in intertemporal prosocial discounting and generosity by Mei Hong, Dapeng Liang and Teng Lu in Psychology of Music</p

The evolutionary rates and tMRCAs estimated for the 1a and 1b datasets in nine genomic regions and over ORF by root-to-tip regression.

¶<p>In the calendar year. <b>*</b> The evolutionary rate is negative and tMRCA locates in the future.</p

The median evolutionary rates and the tMRCAs estimated in the nine genomic regions and over the entire ORF of the subtype 1a and 1b datasets.

<p>Panels A, B, and C show the median evolutionary rates. Panels D, E, and F show the median tMRCAs. The blue columns represent the estimates for 1a. The red columns represent the estimates for 1b. The dash lines indicate the estimates for the entire ORF.</p

The violin plots of the posterior evolutionary rate estimated using the uniform (0, 0.01) rate prior in the nine genomic regions and over the entire ORF of the subtype 1a (A panel) and 1b (B panel) datasets.

<p>Combined with the GTR+I+Γ substitution model and Bayesian skyline coalesent model, the MCMC procedures were run under three clock models, exoponetial, lognormal, and strict, respectively, using BEAST. The vertical axis measures the substitution rate multiplied by 10⁻³ (substitution/site/year). The horizontal axis indicates the nine genomic regions and the entire ORF. The left three panels show the results for the 1a dataset. The right three panels show the results for the 1b dataset. In each panel, two violins are separated in a small case on the right, which indicate the rates estimated for the routinely amplified partial Core-E1 (P-C/E1) and partial NS5B (P-NS5B) regions.</p

The Evolutionary Rates of HCV Estimated with Subtype 1a and 1b Sequences over the ORF Length and in Different Genomic Regions

<div><p>Background</p><p>Considerable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance.</p><p>Methods/Results</p><p>176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10⁻³ substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure.</p><p>Conclusion</p><p>Among the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.</p></div

Root-to-tip regression to estimate the tMRCAs and clock rates.

<p>A simple linear regression of the root-to-tip genentic distances against the sampling dates was performed using the Path-o-gen software. The root was determined by maximizing the coefficent of determinant R². The vertical axis measures the genetic distances between the samples and the root while the horizontal axis scales the sampling dates (year). For subtype 1a (A), the mean evolutionary rate (the slope of regression line) is 9.05E-4 substitution/site/year and the tMRCA (the X-intercept) is located at 1941. For subtype 1b (B), the mean evolutionary rate is 4.82E-4 and the tMRCA is located at 1808.</p

Nanorods with Different Surface Properties in Directing the Compatibilization Behavior and the Morphological Transition of Immiscible Polymer Blends in Both Shear and Shear-Free Conditions

To explore the mechanism of how the nanorod surface properties regulate the compatibilization behavior and the morphology transition in demixing polymer blends, we perform dissipative particle dynamics simulations and study the impact of three typical nanorods on the phase separation kinetics and structure as well as their location and arrangement under both shear-free and shear conditions with the variation of nanorod–polymer affinity parameters. Depending on the dispersion and location of nanorods, blends in the quiescent case either undergo full phase separation and generate bulky two-phase morphology, or experience microphase separation and form BμE-like structure, or proceed viscoelastic phase separation and take the kinetically trapped cocontinuous network morphology, whereas shear flow can either accelerate domain coarsening or strongly impact the phase behavior through shear-induced bulk phase separation or shear-induced ordering transition. Particularly, the shear-induced lamellar phase in Janus nanorod-filled blends chooses parallel orientation and displays the lateral ordering within layers

Effects of Surface Tethering on the Thermodynamics and Kinetics of Frustrated Protein Folding

The interaction between the protein and surface plays an important role in biology and biotechnology. To understand how surface tethering influences the folding behavior of frustrated proteins, in this work, we systematically study the thermodynamics and folding kinetics of the bacterial immunity protein Im7 and Fyn SH3 domain tethered to a surface using Langevin dynamics simulations. Upon surface tethering, the stabilization often results from the entropic effect, whereas the destabilization is usually caused by either an energetic or entropic effect. For the Fyn SH3 domain with a two-state folding manner, the influence of nonnative interactions on thermodynamic stability is not significant, while nonnative interactions can weaken the effect of surface tethering on the change in the folding rate. By contrast, for the frustrated protein Im7, depending on where the protein is tethered, the surface tethering can promote or suppress misfolding by modulating specific nonnative contacts, thereby altering the folding rate and folding mechanism. Because surface tethering can change the intrachain diffusivity of unfolding, the kinetic stability cannot be well captured by the thermodynamic stability at some tether points. This study should be helpful in general to understand how surface tethering affects the folding energy landscape of frustrated proteins