Crystal structures and mechanical properties of osmium diboride at high pressure.

We have investigated the crystal structures and mechanical properties of osmium diboride (OsB2) based on the density functional theory. The structures of OsB2 from 0 to 400 GPa were predicted using the particle swarm optimization algorithm structure prediction technique. The orthorhombic Pmmn structure of OsB2 (oP6-OsB2) was found to be the most stable phase under zero pressure and it will transfer to the hexagonal P63/mmc structure (hP6-OsB2) around 12.4 GPa. Meanwhile, we have discovered a new stable orthorhombic Immm structure (oI12-OsB2) above 379.6 GPa. After that, a thorough and comprehensive investigation on mechanical properties of different OsB2 phases is performed in this work. Further studies showed that the hardness of oP6-OsB2 and hP6-OsB2 at zero pressure is 15.6 and 20.1 GPa, while that for oI12-OsB2 under 400 GPa is 15.4 GPa, indicating that these three phases should be potentially hard materials rather than superhard materials. Finally, the pressure-temperature phase diagram of OsB2 is constructed for the first time by using the quasi-harmonic approximation method. Our results showed that the transition pressures of oP6-OsB2 → hP6-OsB2 and hP6-OsB2 → oI12-OsB2 all decreases appreciably with the increase of temperature.

Orbital localization error of density functional theory in shear properties of vanadium and niobium.

It is believed that the density functional theory (DFT) describes most elements with s, p, and d orbitals very well, except some materials that have strongly localized and correlated valence electrons. In this work, we find that the widely employed exchange-correlation (XC) functionals, including local-density approximation (LDA), generalized gradient approximation (GGA), and meta-GGA, underestimate the shear modulus and phase stability of V and Nb greatly. The advanced hybrid functional that is usually better for correlated systems, on the other hand, completely fails in these two simple metals. This striking failure is revealed due to the orbital localization error in GGA, which is further deteriorated by hybrid functionals. This observation is corroborated by a similar failure of DFT+U and van der Waals functionals when applied to V and Nb. To remedy this problem, a semiempirical approach of DFT+J is proposed, which can delocalize electrons by facilitating the on-site exchange. Furthermore, it is observed that including density derivatives slightly improves the performance of the semilocal functionals, with meta-GGA outperforms GGA, and the latter is better than LDA. This discovery indicates the possibility and necessity to include higher-order density derivatives beyond the Laplacian level for the purpose of removing the orbital localization error (mainly from d orbitals) and delocalization error (mainly from s and p orbitals) completely in V and Nb so that a better description of their electronic structures is achieved. The same strategy can be applied to the other d electron system and f electron system.

Ab initio study of elastic anisotropies and thermal conductivities of rhenium diborides in different crystal structures.

The phase stabilities, elastic anisotropies, and thermal conductivities of ReB2 diborides under ambient conditions have been investigated by using density functional theory calculations. It was found that P63/mmc (hP6-ReB2), Pmmn (oP6-ReB2), R3̄m (hR3-ReB2), R3̄m (hR6-ReB2), and C2/m (mC12-ReB2) of ReB2 are both mechanically and dynamically stable, and the order of phase stability is hP6 > oP6 > hR3 > hR6 > mC12. Moreover, the calculated Vickers hardness showed that hP6-ReB2, oP6-ReB2, hR3-ReB2, and mC12-ReB2 were potential hard materials, while hR6-ReB2 could not be used as a candidate hard material. In addition, the elastic-dependent anisotropy properties of ReB2 in different crystal structures were also investigated. The results show that the anisotropic order of the Young's modulus and shear modulus of ReB2 is hR6 > mC12 > oP6 > hP6 > hR3, while that of the bulk modulus is mC12 > hR3 > hP6 > oP6 > hR6. Finally, by means of Clarke's and Cahill's models, the minimum thermal conductivities of ReB2 in different crystal structures were further evaluated, and the order of them is hR3 > hP6 > mC12 > oP6 > hR6. Moreover, the results show that all these ReB2 diborides exhibit relatively low thermal conductivities and are suitable for thermal insulation materials.

Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts.

Identifying robust biomarkers of drug response constitutes a key challenge in precision medicine. Patient-derived tumor xenografts (PDX) have emerged as reliable preclinical models that more accurately recapitulate tumor response to chemo- and targeted therapies. However, the lack of computational tools makes it difficult to analyze high-throughput molecular and pharmacologic profiles of PDX. We have developed Xenograft Visualization & Analysis (Xeva), an open-source software package for in vivo pharmacogenomic datasets that allows for quantification of variability in gene expression and pathway activity across PDX passages. We found that only a few genes and pathways exhibited passage-specific alterations and were therefore not suitable for biomarker discovery. Using the largest PDX pharmacogenomic dataset to date, we identified 87 pathways that are significantly associated with response to 51 drugs (FDR < 0.05). We found novel biomarkers based on gene expressions, copy number aberrations, and mutations predictive of drug response (concordance index > 0.60; FDR < 0.05). Our study demonstrates that Xeva provides a flexible platform for integrative analysis of preclinical in vivo pharmacogenomics data to identify biomarkers predictive of drug response, representing a major step forward in precision oncology. SIGNIFICANCE: A computational platform for PDX data analysis reveals consistent gene and pathway activity across passages and confirms drug response prediction biomarkers in PDX.See related commentary by Meehan, p. 4324.

RNA sequencing identified specific circulating miRNA biomarkers for early detection of diabetes retinopathy.

Diabetic retinopathy (DR) is the leading cause of blindness in patients with diabetes. However, biomarkers for early detection of DR are still lacking. MicroRNAs (miRNAs) regulate multiple biological functions and are often deregulated in DR. We aimed to investigate whether circulating miRNAs can be used as biomarkers of early-stage DR. We used RNA-seq and qRT-PCR to identify differential serum miRNAs in patients with type 2 diabetes mellitus with DR (T2DM-DR), T2DM without DR (T2DM-no-DR), and healthy controls. We validated differential circulating miRNAs in two phases using qRT-PCR assays. RNA-seq analysis identified 7 differential circulating miRNAs between T2DM-DR and T2DM-no-DR and 47 differential miRNAs between T2DM-DR and healthy subjects. Two-stage analysis verified that a profile of five serum miRNAs (hsa-let-7a-5p, hsa-miR-novel-chr5_15976, hsa-miR-28-3p, has-miR-151a-5p, has-miR-148a-3p) was significantly associated with T2DM-DR. Receiver-operator-characteristic analyses showed that a panel of three miRNAs (hsa-let-7a-5p, hsa-miR-novel-chr5_15976, and hsa-miR-28-3p) presented 0.92 sensitivity and 0.94 specificity for distinguishing T2DM-DR from T2DM-no-DR, and 0.93 sensitivity and 0.86 specificity for differentiating early-stage T2DM-DR (NPDR) from late-stage DR (PDR). Lentivirus-mediated overexpression of hsa-let-7a-5p in human retinal microvascular endothelial cells (HRMECs) significantly promoted proliferation rates of HRMECs. In conclusion, the three-miRNA signature from serum may serve as a noninvasive diagnostic biomarker for DR. Furthermore, we showed that DR-associated miRNAs may be involved in the pathogenesis of DR, at least in part, through modifying proliferation of HRMECs.

Stability of rhombohedral phases in vanadium at high-pressure and high-temperature: first-principles investigations.

The pressure-induced transition of vanadium from BCC to rhombohedral structures is unique and intriguing among transition metals. In this work, the stability of these phases is revisited by using density functional theory. At finite temperatures, a novel transition of rhombohedral phases back to BCC phase induced by thermal electrons is discovered. This reentrant transition is found not driven by phonons, instead it is the electronic entropy that stabilizes the latter phase, which is totally out of expectation. Parallel to this transition, we find a peculiar and strong increase of the shear modulus C44 with increasing temperature. It is counter-intuitive in the sense that it suggests an unusual harding mechanism of vanadium by temperature. With these stability analyses, the high-pressure and finite-temperature phase diagram of vanadium is proposed. Furthermore, the dependence of the stability of RH phases on the Fermi energy and chemical environment is investigated. The results demonstrate that the position of the Fermi level has a significant impact on the phase stability, and follows the band-filling argument. Besides the Fermi surface nesting, we find that the localization/delocalization of the d orbitals also contributes to the instability of rhombohedral distortions in vanadium.