Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets

The curated CSAR-NRC benchmark sets provide valuable opportunity for testing or comparing the performance of both existing and novel scoring functions. We apply two different scoring functions, both independently and in combination, to predict binding affinity of ligands in the CSAR-NRC datasets. One, reported here for the first time, employs multiple chemical-geometrical descriptors of the protein-ligand interface to develop Quantitative Structure – Binding Affinity Relationships (QSBAR) models; these models are then used to predict binding affinity of ligands in the external dataset. Second is a physical force field-based scoring function, MedusaScore. We show that both individual scoring functions achieve statistically significant prediction accuracies with the squared correlation coefficient (R2) between actual and predicted binding affinity of 0.44/0.53 (Set1/Set2) with QSBAR models and 0.34/0.47 (Set1/Set2) with MedusaScore. Importantly, we find that the combination of QSBAR models and MedusaScore into consensus scoring function affords higher prediction accuracy than any of the contributing methods achieving R2 of 0.45/0.58 (Set1/Set2). Furthermore, we identify several chemical features and non-covalent interactions that may be responsible for the inaccurate prediction of binding affinity for several ligands by the scoring functions employed in this study

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce. To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. Our approach combined genome-wide association studies (GWAS) and scans for signatures of selection applied to a cattle population (Hereford and Kazakh Whiteheaded beef breeds) bred in Siberia. We utilized the GGP HD150K DNA chip containing 139,376 single nucleotide polymorphism markers

Patterned Drug-Eluting Coatings for Tracheal Stents Based on PLA, PLGA, and PCL for the Granulation Formation Reduction: In Vivo Studies

Expandable metallic stent placement is often the only way to treat airway obstructions. Such treatment with an uncoated stent causes granulation proliferation and subsequent restenosis, resulting in the procedure’s adverse complications. Systemic administration of steroids drugs in high dosages slows down granulation tissue overgrowth but leads to long-term side effects. Drug-eluting coatings have been used widely in cardiology for many years to suppress local granulation and reduce the organism’s systemic load. Still, so far, there are no available analogs for the trachea. Here, we demonstrate that PLA-, PCL- and PLGA-based films with arrays of microchambers to accommodate therapeutic substances can be used as a drug-eluting coating through securely fixing on the surface of an expandable nitinol stent. PCL and PLA were most resistant to mechanical damage associated with packing in delivery devices and making it possible to keep high-molecular-weight cargo. Low-molecular-weight methylprednisolone sodium succinate is poorly retained in PCL- and PLGA-based microchambers after immersion in deionized water (only 9.5% and 15.7% are left, respectively). In comparison, PLA-based microchambers retain 96.3% after the same procedure. In vivo studies on rabbits have shown that effective granulation tissue suppression is achieved when PLA and PLGA are used for coatings. PLGA-based microchamber coating almost completely degrades in 10 days in the trachea, while PLA-based microchamber films partially preserve their structure. The PCL-based film coating is most stable over time, which probably causes blocking the outflow of fluid from the tracheal mucosa and the aggravation of the inflammatory process against the background of low drug concentration. Combination and variability of polymers in the fabrication of films with microchambers to retain therapeutic compounds are suggested as a novel type of drug-eluting coating

Exploration of the crystal structure and thermal and spectroscopic properties of monoclinic praseodymium sulfate Pr2(SO4)3

Praseodymium sulfate was obtained by the precipitation method and the crystal structure was determined by Rietveld analysis. Pr2(SO4)3 is crystallized in the monoclinic structure, space group C2/c, with cell parameters a = 21.6052 (4), b = 6.7237 (1) and c = 6.9777 (1) Å, β = 107.9148 (7)°, Z = 4, V = 964.48 (3) Å3 (T = 150 °C). The thermal expansion of Pr2(SO4)3 is strongly anisotropic. As was obtained by XRD measurements, all cell parameters are increased on heating. However, due to a strong increase of the monoclinic angle β, there is a direction of negative thermal expansion. In the argon atmosphere, Pr2(SO4)3 is stable in the temperature range of T = 30–870 °C. The kinetics of the thermal decomposition process of praseodymium sulfate octahydrate Pr2(SO4)3·8H2O was studied as well. The vibrational properties of Pr2(SO4)3 were examined by Raman and Fourier-transform infrared absorption spectroscopy methods. The band gap structure of Pr2(SO4)3 was evaluated by ab initio calculations, and it was found that the valence band top is dominated by the p electrons of oxygen ions, while the conduction band bottom is formed by the d electrons of Pr3+ ions. The exact position of ZPL is determined via PL and PLE spectra at 77 K to be at 481 nm, and that enabled a correct assignment of luminescent bands. The maximum luminescent band in Pr2(SO4)3 belongs to the 3P0 → 3F2 transition at 640 nm

The ALICE Transition Radiation Detector: construction, operation, and performance

The Transition Radiation Detector (TRD) was designed and built to enhance the capabilities of the ALICE detector at the Large Hadron Collider (LHC). While aimed at providing electron identification and triggering, the TRD also contributes significantly to the track reconstruction and calibration in the central barrel of ALICE. In this paper the design, construction, operation, and performance of this detector are discussed. A pion rejection factor of up to 410 is achieved at a momentum of 1 GeV/ c in p–Pb collisions and the resolution at high transverse momentum improves by about 40% when including the TRD information in track reconstruction. The triggering capability is demonstrated both for jet, light nuclei, and electron selection