Hybrid Large-Eddy/Reynolds-Averaged Simulation of a Supersonic Cavity Using VULCAN

Simulations of a supersonic recessed-cavity flow are performed using a hybrid large-eddy/Reynolds-averaged simulation approach utilizing an inflow turbulence recycling procedure and hybridized inviscid flux scheme. Calorically perfect air enters a three-dimensional domain at a free stream Mach number of 2.92. Simulations are performed to assess grid sensitivity of the solution, efficacy of the turbulence recycling, and the effect of the shock sensor used with the hybridized inviscid flux scheme. Analysis of the turbulent boundary layer upstream of the rearward-facing step for each case indicates excellent agreement with theoretical predictions. Mean velocity and pressure results are compared to Reynolds-averaged simulations and experimental data for each case and indicate good agreement on the finest grid. Simulations are repeated on a coarsened grid, and results indicate strong grid density sensitivity. Simulations are performed with and without inflow turbulence recycling on the coarse grid to isolate the effect of the recycling procedure, which is demonstrably critical to capturing the relevant shear layer dynamics. Shock sensor formulations of Ducros and Larsson are found to predict mean flow statistics equally well

An investigation into the role of protein-ligand interactions on obligate and transient protein-protein interactions

Protein-ligand and protein-protein interactions are critical to cellular function. Most cellular metabolic and signal tranduction pathways are influenced by these interactions, consequently molecular level understanding of these associations is an important area of biochemical research. We have examined the thermodynamics of several protein-protein associations and the protein-ligand interactions that mediate them. Using Fluorescence Correlation Spectroscopy, we have examined the putative interaction between pig heart malate dehydrogenase (MDH) and citrate synthase (CTS). We demonstrate a specific, low-affinity interaction between these enzymes. The association is highly polyethylene glycol (PEG)-dependent, and at high concentrations of NaCl or PEG, non-specific aggregates are formed. We demonstrate that oxaloacetate, the intermediate common to both CTS and MDH, induces the association at concentrations below the Km of CTS, suggesting that the open conformation of CTS is involved in the association. Using several biophysical techniques, we have examined the subunit associations of B. stearothermophilus phosphofructokinase (PFK). We demonstrate that the inhibitor bound conformation of the enzyme has reduced subunit affinity. The kinetics and thermodynamics of the phosphoenolpyrvuate (PEP)-induced dissociation of PFK have been quantified. Binding substrate, fructose-6-phosphate (F6P), stabilizes the enzyme to inhibitor-induced dissociation by 132-fold. These data suggest that subunit associations may play a role in the allosteric inhibition of PFK by PEP. The thermodynamics of the protein-ligand associations and allosteric inhibition of E. coli phosphofructokinase have been examined using intrinsic fluorescence and hydrostatic pressure. Both ligand-binding affinity and PEP inhibition are diminished by pressure, whereas substrate-binding affinity for inhibitor-bound enzyme is pressure-insensitive. Larger entropic than enthalpic changes with pressure lead to the overall reduction in free energies. Using a fluorescence-based assay, we have developed a series of baroresistant buffer mixtures. By combining a buffer with acid dissociation of negative volume with a buffer of positive volume, a pressure-resistant mixture is produced. Alteration of the molar ratio of the two component buffers yields mixtures that are pressure-insensitive at pH values around neutrality

Robust Machine Learning Applied to Astronomical Datasets I: Star-Galaxy Classification of the SDSS DR3 Using Decision Trees

We provide classifications for all 143 million non-repeat photometric objects in the Third Data Release of the Sloan Digital Sky Survey (SDSS) using decision trees trained on 477,068 objects with SDSS spectroscopic data. We demonstrate that these star/galaxy classifications are expected to be reliable for approximately 22 million objects with r < ~20. The general machine learning environment Data-to-Knowledge and supercomputing resources enabled extensive investigation of the decision tree parameter space. This work presents the first public release of objects classified in this way for an entire SDSS data release. The objects are classified as either galaxy, star or nsng (neither star nor galaxy), with an associated probability for each class. To demonstrate how to effectively make use of these classifications, we perform several important tests. First, we detail selection criteria within the probability space defined by the three classes to extract samples of stars and galaxies to a given completeness and efficiency. Second, we investigate the efficacy of the classifications and the effect of extrapolating from the spectroscopic regime by performing blind tests on objects in the SDSS, 2dF Galaxy Redshift and 2dF QSO Redshift (2QZ) surveys. Given the photometric limits of our spectroscopic training data, we effectively begin to extrapolate past our star-galaxy training set at r ~ 18. By comparing the number counts of our training sample with the classified sources, however, we find that our efficiencies appear to remain robust to r ~ 20. As a result, we expect our classifications to be accurate for 900,000 galaxies and 6.7 million stars, and remain robust via extrapolation for a total of 8.0 million galaxies and 13.9 million stars. [Abridged]Comment: 27 pages, 12 figures, to be published in ApJ, uses emulateapj.cl

Low-Dissipation Advection Schemes Designed for Large Eddy Simulations of Hypersonic Propulsion Systems

The 2nd-order upwind inviscid flux scheme implemented in the multi-block, structured grid, cell centered, finite volume, high-speed reacting flow code VULCAN has been modified to reduce numerical dissipation. This modification was motivated by the desire to improve the codes ability to perform large eddy simulations. The reduction in dissipation was accomplished through a hybridization of non-dissipative and dissipative discontinuity-capturing advection schemes that reduces numerical dissipation while maintaining the ability to capture shocks. A methodology for constructing hybrid-advection schemes that blends nondissipative fluxes consisting of linear combinations of divergence and product rule forms discretized using 4th-order symmetric operators, with dissipative, 3rd or 4th-order reconstruction based upwind flux schemes was developed and implemented. A series of benchmark problems with increasing spatial and fluid dynamical complexity were utilized to examine the ability of the candidate schemes to resolve and propagate structures typical of turbulent flow, their discontinuity capturing capability and their robustness. A realistic geometry typical of a high-speed propulsion system flowpath was computed using the most promising of the examined schemes and was compared with available experimental data to demonstrate simulation fidelity

Efficacy of Intraoperative Recurrent Laryngeal Nerve Monitoring: A Single-Institutions’ Experience

Objective: To evaluate the efficacy of intraoperative nerve monitoring (IONM) during thyroidectomy in preventing recurrent laryngeal nerve (RLN) injury. Design: Retrospective cohort study. Setting: Academic institution. Patients: Consecutive sample of subjects undergoing thyroidectomy by experienced endocrine surgeons between 2006 and 2008 at a single institution. Intervention: Intraoperative RLN monitoring. Main outcome measure: RLN injury. Results: Between 2006 and 2008, 296 subjects underwent thyroid lobectomy or total thyroidectomy by the authors. One patient was excluded because of preoperative documentation of RLN injury. IONM was used in 253 (88%) cases, with a total of 403 nerves at risk of injury. Loss of RLN signal following surgical dissection occurred in 13 cases, prompting a change in surgical plan in one case. Post-operative laryngoscopy was performed in eight patients with hoarseness, documenting vocal cord paralysis in one patient who had clear intraoperative anatomic evidence of RLN injury. In no case did loss of RLN signal after dissection lead to nerve injury in the absence of anatomical evidence of injury as detected by the surgeon. Conclusions: IONM added cost and resulted in surgeon angst in cases of malfunction without a clear benefit in RLN identification and protection. Anatomic identification of the RLN should remain the gold standard in preventing RLN injury during thyroidectomy

Honey bee foraged pollen reveals temporal changes in pollen protein content and changes in forager choice for abundant versus high protein flowers

Protein derived from pollen is an essential component of healthy bee diets. Protein content in honey bee foraged pollen varies temporally and spatially, but the drivers underlying this variation remain poorly characterized. We assessed the temporal and spatial variation in honey bee collected pollen in 12 Michigan apiaries over 3 summers (2015–2017). We simultaneously monitored forage in flowering habitats (uncultivated floristically-rich areas and conservation program land) near these apiaries throughout the growing season. We used these data, along with data from the literature on plant pollen protein content, to determine if honey bees collected a greater proportion of pollen from plant species growing in higher abundance or from plant species that have higher protein content. Protein content in honey bee collected pollen decreased from July to September every year, and there were among-year differences in pollen protein, highlighting the temporal variation in protein collected by these insects. Pollen protein was spatially consistent and broad-scale land use categories were not correlated with pollen protein content. Rather, our findings suggest flowering habitats found across land use categories can support honey bee foraging, which may confound broader land use effects. In early July and in early September, colonies collected a greater proportion of pollen from plants that grew in greater abundance in flowering habitats, but from late July through August, a greater proportion of pollen was collected from high-protein taxa, regardless of abundance. This suggests different factors may influence pollen forager decision-making throughout the season as colony needs and/or available forage communities change. Insights into the role of plant abundance and protein content on foraging could deepen our understanding of honey bee foraging behavior and help to inform habitat restoration programs for improved honey bee nutrition outcomes. Supplemental files in zip file attached belo

Inverse Electron-Demand [4 + 2]-Cycloadditions of Ynamides: Access to Novel Pyridine Scaffolds

Functionalized polycyclic aminopyridines are central to the chemical sciences, but their syntheses are still hampered by a number of shortcomings. These nitrogenated heterocycles can be efficiently prepared by an intramolecular inverse electron demand hetero Diels–Alder ( ih DA) cycloaddition of ynamides to pyrimidines. This ihDA/rDA sequence is general in scope and affords expedient access to novel types of aminopyridinyl scaffolds that hold great promise in terms of exit vector patterns

Adult Recipients of Matched Related Donor Blood Cell Transplants Given Myeloablative Regimens Including Pretransplant Antithymocyte Globulin Have Lower Mortality Related to Graft-versus-Host Disease: A Matched Pair Analysis

AbstractBecause pretransplantation anti-thymocyte globulin (ATG) seems to reduce graft-versus-host-disease (GVHD) and treatment-related mortality (TRM) after unrelated donor bone marrow transplantation (BMT), we investigated this agent in matched related donor (MRD) blood cell transplantation (BCT). Fifty-four adults receiving rabbit ATG, cyclosporine A, and methotrexate with myeloablative conditioning and undergoing first MRD BCT were matched for disease and stage with 54 patients not given ATG. Most ATG-treated patients had fludarabine with oral (7) or i.v. busulfan (46) with total body irradiation (TBI) in 10. Control patients largely received TBI with VP16 (28) or oral busulfan with cyclophosphamide (15) or fludarabine (7). The ATG was given at a total dose of 4.5 mg/kg over 3 d, finishing on day 0. Rates of acute GVHD (aGVHD) grade II-IV, aGVHD grade III-IV, and chronic GVHD (cGVHD) were 19 ± 5% versus 32 ± 6% (P = .1), 6 ± 3% versus 13 ± 5% (P = NS), and 55 ± 8% versus 96 ± 3% (P = .002) in the ATG and control groups, respectively. Patients given ATG had fewer sites involved by cGVHD compared with the control group (mean 2.1 ± 0.2 versus 2.8 ± 0.2, P = .04). Non-relapse mortality (NRM) with and without ATG, respectively, was 4 ± 3% versus 17 ± 5% at 100 d and 9 ± 4% versus 34 ± 7% at 4 yr (P = .002). Deaths were GVHD related in 3 ATG-treated patients versus 14 controls (P = .007). Despite a trend to more relapse with ATG (43 ± 7% versus 22 ± 7% at 4 yr, P = 0.05), survival was 66 ± 7% in the patients given ATG versus 50 ± 7% in the controls (P = 0.046). This study indicates that myeloablative regimens incorporating fludarabine and oral or i.v. busulfan with pretransplantation ATG given to recipients undergoing MRD BCT may result in less cGVHD, lower TRM, and probably improved quality of life in survivors compared with previous protocols

Convenient Synthesis of Copper (I) Thiolates and Related Compounds

Copper (I) salts of various anions including thiolates, diethyl dithiocarbamate, diethyl dithiophosphate, trithiocyanurate, 1-cyano-3-methylisothiourea, 2-aminothiazole, and tetrakis(1-imidazolyl)borate are conveniently synthesized by reducing copper (II) sulfate in aqueous ammonia. The addition of phosphine ligands to several of the products is demonstrated, and the crystal structure of [Cu2(MBT)2(DPPE)3] · Et2O (MBT = 2-mercaptobenzothiazolate, DPPE = 1,2-bis(diphenylphosphino)ethane) is reported