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1. Functional consequences of convergently evolved microscopic skin features on snake locomotion

   https://doi.org/10.1073/pnas.2018264118  

   Rieser, Jennifer M. ; Li, Tai-De ; Tingle, Jessica L. ; Goldman, Daniel I. ; Mendelson, Joseph R. ( February 2021 , Proceedings of the National Academy of Sciences)

   The small structures that decorate biological surfaces can significantly affect behavior, yet the diversity of animal–environment interactions essential for survival makes ascribing functions to structures challenging. Microscopic skin textures may be particularly important for snakes and other limbless locomotors, where substrate interactions are mediated solely through body contact. While previous studies have characterized ventral surface features of some snake species, the functional consequences of these textures are not fully understood. Here, we perform a comparative study, combining atomic force microscopy measurements with mathematical modeling to generate predictions that link microscopic textures to locomotor performance. We discover an evolutionary convergence inmore »the ventral skin structures of a few sidewinding specialist vipers that inhabit sandy deserts—an isotropic texture that is distinct from the head-to-tail-oriented, micrometer-sized spikes observed on a phylogenetically broad sampling of nonsidewinding vipers and other snakes from diverse habitats and wide geographic range. A mathematical model that relates structural directionality to frictional anisotropy reveals that isotropy enhances movement during sidewinding, whereas anisotropy improves movement during slithering via lateral undulation of the body. Our results highlight how an integrated approach can provide quantitative predictions for structure–function relationships and insights into behavioral and evolutionary adaptations in biological systems.« less
2. A single mode of population covariation associates brain networks structure and behavior and predicts individual subjects’ age

   https://doi.org/10.1038/s42003-021-02451-0  

   McPherson, Brent C. ; Pestilli, Franco ( August 2021 , Communications Biology)

   Multiple human behaviors improve early in life, peaking in young adulthood, and declining thereafter. Several properties of brain structure and function progress similarly across the lifespan. Cognitive and neuroscience research has approached aging primarily using associations between a few behaviors, brain functions, and structures. Because of this, the multivariate, global factors relating brain and behavior across the lifespan are not well understood. We investigated the global patterns of associations between 334 behavioral and clinical measures and 376 brain structural connections in 594 individuals across the lifespan. A single-axis associated changes in multiple behavioral domains and brain structural connections (r = 0.5808).more »Individual variability within the single association axis well predicted the age of the subject (r = 0.6275). Representational similarity analysis evidenced global patterns of interactions across multiple brain network systems and behavioral domains. Results show that global processes of human aging can be well captured by a multivariate data fusion approach.

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3. Shear-wave Velocity Structure of the Crust and Upper Mantle beneath East Antarctica from Full-Waveform Ambient Noise Tomography

   Kumar, Ashish ; Emry, Erica ; Hansen, Samantha ( July 2020 , Scientific Committee on Antarctic Research)

   The origin and tectonic evolution of various features in East Antarctica, such as the Wilkes Subglacial Basin (WSB), Aurora Subglacial Basin (ASB), Transantarctic Mountains (TAMs), and Gamburtsev Subglacial Mountains (GSM), are unconstrained due to thick ice coverage and a lack of direct geologic samples. We are modeling the crustal and upper mantle structure beneath these areas using a full-waveform tomography method to further our understanding the tectonic evolution of the continent as well as the behavior of the overlying ice sheet. A frequency-time normalization approach is employed to extract empirical Green’s functions (EGFs) from ambient seismic noise, between periods ofmore »15-340 seconds. EGF ray path coverage is dense throughout East Antarctica, indicating that our study will provide new, high resolution imaging of this area. Synthetic waveforms are simulated through a three-dimensional heterogeneous Earth model using a finite-difference wave propagation method with a grid spacing of 0.025º, which accurately reproduces Rayleigh waves at 15+ seconds. Following this, phase delays are measured between the synthetics and the data, sensitivity kernels are constructed using the scattering integral approach, and we invert using a sparse, least-squares method. Preliminary results show that slow velocities are present beneath both the WSB and ASB, possibly indicating old rift systems or other inherited tectonic structures. The transition from slow to fast velocities beneath the Northern Victoria Land section of the TAMs is consistent with thermal loading beneath the mountain range. The presence of slow velocities near the GSM may be associated with rifting along the Lambert Rift System.« less
4. Shear-wave Velocity Structure of the Crust and Upper Mantle beneath East Antarctica from Full-Waveform Ambient Noise Tomography

   Kumar, Ashish ; Emry, Erica L ; Hansen, Samantha E ( June 2020 , Scientific Committee on Antarctic Research, Summer 2020 Meeting)

   The origin and tectonic evolution of various features in East Antarctica, such as the Wilkes Subglacial Basin (WSB), Aurora Subglacial Basin (ASB), Transantarctic Mountains (TAMs), and Gamburtsev Subglacial Mountains (GSM), are unconstrained due to thick ice coverage and a lack of direct geologic samples. We are modeling the crustal and upper mantle structure beneath these areas using a full-waveform tomography method to further our understanding the tectonic evolution of the continent as well as the behavior of the overlying ice sheet. A frequency-time normalization approach is employed to extract empirical Green’s functions (EGFs) from ambient seismic noise, between periods ofmore »15-340 seconds. EGF ray path coverage is dense throughout East Antarctica, indicating that our study will provide new, high resolution imaging of this area. Synthetic waveforms are simulated through a three-dimensional heterogeneous Earth model using a finite-difference wave propagation method with a grid spacing of 0.025º, which accurately reproduces Rayleigh waves at 15+ seconds. Following this, phase delays are measured between the synthetics and the data, sensitivity kernels are constructed using the scattering integral approach, and we invert using a sparse, least-squares method. Preliminary results show that slow velocities are present beneath both the WSB and ASB, possibly indicating old rift systems or other inherited tectonic structures. The transition from slow to fast velocities beneath the Northern Victoria Land section of the TAMs is consistent with thermal loading beneath the mountain range. The presence of slow velocities near the GSM may be associated with rifting along the Lambert Rift System.« less
5. Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities

   https://doi.org/10.1186/s13321-021-00493-4  

   Ji, Beihong ; He, Xibing ; Zhang, Yuzhao ; Zhai, Jingchen ; Man, Viet Hoang ; Liu, Shuhan ; Wang, Junmei ( December 2021 , Journal of Cheminformatics)

   Abstract In this study, we developed a novel algorithm to improve the screening performance of an arbitrary docking scoring function by recalibrating the docking score of a query compound based on its structure similarity with a set of training compounds, while the extra computational cost is neglectable. Two popular docking methods, Glide and AutoDock Vina were adopted as the original scoring functions to be processed with our new algorithm and similar improvement performance was achieved. Predicted binding affinities were compared against experimental data from ChEMBL and DUD-E databases. 11 representative drug receptors from diverse drug target categories were applied tomore »evaluate the hybrid scoring function. The effects of four different fingerprints (FP2, FP3, FP4, and MACCS) and the four different compound similarity effect (CSE) functions were explored. Encouragingly, the screening performance was significantly improved for all 11 drug targets especially when CSE = S 4 (S is the Tanimoto structural similarity) and FP2 fingerprint were applied. The average predictive index (PI) values increased from 0.34 to 0.66 and 0.39 to 0.71 for the Glide and AutoDock vina scoring functions, respectively. To evaluate the performance of the calibration algorithm in drug lead identification, we also imposed an upper limit on the structural similarity to mimic the real scenario of screening diverse libraries for which query ligands are general-purpose screening compounds and they are not necessarily structurally similar to reference ligands. Encouragingly, we found our hybrid scoring function still outperformed the original docking scoring function. The hybrid scoring function was further evaluated using external datasets for two systems and we found the PI values increased from 0.24 to 0.46 and 0.14 to 0.42 for A2AR and CFX systems, respectively. In a conclusion, our calibration algorithm can significantly improve the virtual screening performance in both drug lead optimization and identification phases with neglectable computational cost.« less