Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

S7N079-D536 c DEEP LEVEL DEFECT STUDIES IN MOCVD-GROWN [email protected] LATTICE-MATCHED TO GaAs

ABSTRACT Deep level defects in MOCVD-grown, unintentionally doped p-type InGaAsN films lattice matched to GaAs were investigated using deep level transient spectroscopy (DLTS) measurements. As-grown p-InGaAsN showed broad DLTS spectra suggesting that there exists a broad distribution of defect states within the band-gap. Moreover, the trap densities exceeded 10'5cm-3. Cross sectional transmission electron microscopy (TEM) measurements showed no evidence for threading dislocations within the TEM resolution limit of 107cm-z. A set of samples was annealed after growth for 1800 seconds at 650 'C to investigate the thermal stability of the traps. The DLTS spectra of the annealed samples simplified considerably, revealing three distinct hole trap levels with energy levels of 0.10 eV, 0.23 eV, and 0.48 eV above the valence band edge with trap concentrations of 3.5x10'4 cm-3,3.8x10'4 cm-3, and 8.2x10'4 cm-3, respectively. Comparison of as-grown and annealed DLTS spectra showed thatpost-growth annealing effectively reduced the total trap concentration by an order of magnitude across the bandgap. However, the concentration of a trap with an energy level of 0.48 eV was not affected by annealing indicating a higher thermal stability for this trap as compared with the overall distribution of shallow and deep traps

Singular charge fluctuations at a magnetic quantum critical point

Strange metal behavior is ubiquitous in correlated materials, ranging from cuprate superconductors to bilayer graphene, and may arise from physics beyond the quantum fluctuations of a Landau order parameter. In quantum-critical heavy-fermion antiferromagnets, such physics may be realized as critical Kondo entanglement of spin and charge and probed with optical conductivity. We present terahertz time-domain transmission spectroscopy on molecular beam epitaxy–grown thin films of YbRh₂Si₂, a model strange-metal compound. We observed frequency over temperature scaling of the optical conductivity as a hallmark of beyond-Landau quantum criticality. Our discovery suggests that critical charge fluctuations play a central role in the strange metal behavior, elucidating one of the long-standing mysteries of correlated quantum matter

Singular charge fluctuations at a magnetic quantum critical point

Strange metal behavior is ubiquitous in correlated materials, ranging from cuprate superconductors to bilayer graphene, and may arise from physics beyond the quantum fluctuations of a Landau order parameter. In quantum-critical heavy-fermion antiferromagnets, such physics may be realized as critical Kondo entanglement of spin and charge and probed with optical conductivity. We present terahertz time-domain transmission spectroscopy on molecular beam epitaxy–grown thin films of YbRh2Si2, a model strange-metal compound. We observed frequency over temperature scaling of the optical conductivity as a hallmark of beyond-Landau quantum criticality. Our discovery suggests that critical charge fluctuations play a central role in the strange metal behavior, elucidating one of the long-standing mysteries of correlated quantum matter

A new heat flux model for the Antarctic Peninsula incorporating spatially variable upper crustal radiogenic heat production

A new method for modelling heat flux shows the upper crust contributes up to 70% of the Antarctic Peninsula's subglacial heat flux, and that heat flux values are more variable at smaller spatial resolutions than geophysical methods can resolve. Results indicate a higher heat flux on the east and south of the Peninsula (mean 81 mWm-2) where silicic rocks predominate, than on the west and north (mean 67 mWm-2) where volcanic arc and quartzose sediments are dominant. Whilst the data supports the contribution of HPE-enriched granitic rocks to high heat flux values, sedimentary rocks can be of comparative importance dependent on their provenance and petrography. Models of subglacial heat flux must utilize a heterogeneous upper crust with variable radioactive heat production if they are to accurately predict basal conditions of the ice sheet. Our new methodology and dataset facilitate improved numerical model simulations of ice sheet dynamics

Early changes in biochemical markers of bone formation during teriparatide therapy correlate with improvements in vertebral strength in men with glucocorticoid-induced osteoporosis

Summary: Changes of the bone formation marker PINP correlated positively with improvements in vertebral strength in men with glucocorticoid-induced osteoporosis (GIO) who received 18-month treatment with teriparatide, but not with risedronate. These results support the use of PINP as a surrogate marker of bone strength in GIO patients treated with teriparatide. Introduction: To investigate the correlations between biochemical markers of bone turnover and vertebral strength estimated by finite element analysis (FEA) in men with GIO. Methods: A total of 92 men with GIO were included in an 18-month, randomized, open-label trial of teriparatide (20 μg/day, n = 45) and risedronate (35 mg/week, n = 47). High-resolution quantitative computed tomography images of the 12th thoracic vertebra obtained at baseline, 6 and 18 months were converted into digital nonlinear FE models and subjected to anterior bending, axial compression and torsion. Stiffness and strength were computed for each model and loading mode. Serum biochemical markers of bone formation (amino-terminal-propeptide of type I collagen [PINP]) and bone resorption (type I collagen cross-linked C-telopeptide degradation fragments [CTx]) were measured at baseline, 3 months, 6 months and 18 months. A mixed-model of repeated measures analysed changes from baseline and between-group differences. Spearman correlations assessed the relationship between changes from baseline of bone markers with FEA variables. Results: PINP and CTx levels increased in the teriparatide group and decreased in the risedronate group. FEA-derived parameters increased in both groups, but were significantly higher at 18 months in the teriparatide group. Significant positive correlations were found between changes from baseline of PINP at 3, 6 and 18 months with changes in FE strength in the teriparatide-treated group, but not in the risedronate group. Conclusions: Positive correlations between changes in a biochemical marker of bone formation and improvement of biomechanical properties support the use of PINP as a surrogate marker of bone strength in teriparatide-treated GIO patients

Pancreas transplantation: differences in activity between Europe and the United States

Background. Although pancreas transplantation (PT) is the treatment of choice in selected diabetic patients, the International Pancreas Transplant Registry (IPTR) has reported important differences in activity between USA and Europe. Of all cases reported, 75% are from USA and only 23% from Europe. Therefore, an analysis of PT activity in selected European countries (SEC) and USA was performed