NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

Development and validation of an ultra‐high‐performance liquid chromatography–tandem mass spectrometry method to determine the bioavailability of warfarin and its major metabolite 7‐hydroxy warfarin in rats dosed with oral formulations containing different polymorphic forms

A simple, sensitive and rapid ultra‐high‐performance liquid chromatography–electrospray ionization–tandem mass spectrometry method was developed and validated for the quantification of warfarin and 7‐hydroxy warfarin in Sprague Dawley (SD) rats. Animals were administered a single dose of warfarin sodium formulations (crystalline and amorphous) at 12 mg/kg via oral gavage and blood was drawn over a 96‐h time course. Sample process recoveries, matrix effect and analyte stability were determined. The linearity for warfarin and 7‐hydroxy warfarin was from 5 to 2000 ng/mL in blank SD rat plasma. Correlation coefficients (r²) for standard calibration curves were >.98 and analytes quantified within ±15% of target at all calibrator concentrations. The average percent accuracy and precision for intra‐ and inter‐day were 93.7%–113.8% and ≤12.1%, respectively, for warfarin and 7‐hydroxy warfarin, across the quality control standards (5, 10, 500, 1800 and 2000 ng/mL). Acceptable analytical recovery (>55%) was achieved with process efficiencies >41.5% and matrix effects <139.9% over the analytical range. Both analytes were stable in stock solution, autosampler, benchtop and three cycles of freeze–thaw with percent accuracy ≥90.2% and precision (percent relative standard deviation) ≤14%. The validated method was successfully applied to a pre‐clinical bioavailability study of crystalline and amorphous warfarin sodium formulations in SD rats.     

Polymer complexes. LXXVI. Synthesis,characterization, CT‐DNA binding,molecular docking and thermal studies of sulfoxine polymer complexes

Novel polymer complexes of 8‐hydroxyquinoline‐5‐sulfonic acid hydrate ( H ₂ L ) with Cu²⁺, Co²⁺ and Ni²⁺ chloride were prepared and characterized. Microanalysis, magnetic susceptibility, IR spectra, electron spin resonance, mass spectra, X‐ray, molar conductance, thermal, and UV–Vis spectra studies have been used to confirm the structure of the prepared polymer complexes. The molecular and electronic structures of the hydrogen bond conformers for ligand ( H ₂ L ) were optimized theoretically and the quantum chemical parameters were calculated. On the basis of elemental and IR data, the chemical structure of metal chelates commensurate that the tri‐dentate (H₂L) coordinate to metal chlorides through oxygen atom of phenolic OH and oxygen atom of SO₃‐H group by replacing H atoms and nitrogen of the quinoline ring. The magnetic studies suggested the octahedral geometrical structure for all produced polymer complexes with general formula {[ML (OH₂)₃] .xH₂O}_n (M = Cu²⁺, x = 1.; Co²⁺, x = 2 and Ni²⁺, x = 2) in molar ratio (1:1). Coats–Redfern and Horowitz–Metzger methods have been used for calculating the activation thermodynamic parameters of the thermal decomposition for H ₂ L and its polymer complexes. The interaction between H ₂ L and its transition metal complexes with the calf thymus DNA (CT‐DNA) was determined by UV–Vis spectra. Binding efficiency between H ₂ L with the receptors of the prostate cancer (PDB code 2Q7L Hormone) and the breast cancer (PDB code 1JNX Gene regulation) was studied by molecular docking. The inhibition behaviour of H ₂ L against the corrosion of carbon steel / HCl (2 M) solution was studied by weight loss, Tafel polarisation, electrochemical impedance spectroscopy (EIS) and electrochemical frequency modulation (EFM) techniques. The adsorption isotherm was found to be Friendlish isotherm. The morphology of inhibited carbon steel? s surface was studied using scanning electron microscope (SEM) and energy dispersive X‐ray spectroscopy (EDS).     

DNA interaction,cytotoxicity and molecular structure of cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide in the presence of secondary ligand pyridine

Novel cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide (sulfachloropyridazine) has been synthesized and characterized by elemental analysis, FT‐IR spectroscopy and magnetic susceptibility (VSM). Cobalt complex of Sulfachloropyridazine (Co‐SCP) crystallized in monoclinic space group P2₁/n with Z = 4. The structure is solved by direct method and refined to R = 0.099 for 4720 reflections with I ?4σ(I). The results of FT‐IR spectra suggest the binding of cobalt atom to the sulfonamide ligand which is in agreement with the crystal structure determination. In crystal structure, molecule is linked via, C‐H … π, C‐Cl … π and π … π intermolecular interactions. The computational studies like the optimization energy and root means square deviation compare with single crystal structure, frontier molecular orbital (Homo‐Lumo energy) and binding energy of the Co‐SCP has been carried out using DFT/B3LYP level of theory in gaseous phase. Hirshfeld surfaces and the 2D‐fingerprint analysis are performed to study the nature of interactions and their measurable contributions towards crystal packing. The interaction of the complex with DNA is investigated using viscosity measurement and absorption titration studies. The result shows the complex bind to DNA with intercalative mode with high DNA‐binding constant (K_b). Also, in vivo and in vitro cytotoxic studies are performed using S. pombe cells and brine shrimp lethality bioassay. DNA‐cleavage study shows better cleaving ability of the complex.     

Stimulation of Microvascular Networks on Sulfonated Polyrotaxane Surfaces with Immobilized Vascular Endothelial Growth Factor

Modulation of material properties and growth factor application are critical in constructing suitable cell culture environments to induce desired cellular functions. Sulfonated polyrotaxane (PRX) surfaces with immobilized vascular endothelial growth factors (VEGFs) are prepared to improve network formation in vascular endothelial cells. Sulfonated PRXs, whereby sulfonated α‐cyclodextrins (α‐CDs) are threaded onto a linear poly(ethylene glycol) chain capped with bulky groups at both terminals, are coated onto surfaces. The molecular mobility of sulfonated PRX surfaces is modulated by tuning the number of threading α‐CDs. VEGF is immobilized onto surfaces with varying mobility. Low mobility and VEGF‐immobilization reinforce cell proliferation, yes‐associated protein activity, and rhoA, pdgf, ang‐1, and pecam‐1 gene expression. Highly mobile surfaces and soluble VEGF weakly affect these cell responses. Network formation is strongly stimulated in vascular endothelial cells only on low‐mobility VEGF‐immobilized surfaces, suggesting that molecular mobility and VEGF immobilization synergistically control cell function.     

A New Approach for the Synthesis of Miktoarm Star Polymers Through a Combination of Thiol–Epoxy “Click” Chemistry and ATRP/Ring‐Opening Polymerization Techniques

A new approach was developed for synthesis of certain A₃B₃‐type of double hydrophilic or amphiphilic miktoarm star polymers using a combination of “grafting onto” and “grafting from” methods. To achieve the synthesis of desired miktoarm star polymers, acetyl protected poly(ethylene glycol) (PEG) thiols (M_n = 550 and 2000 g mol^?1) were utilized to generate A₃‐type of homoarm star polymers through an in situ protective group removal and a subsequent thiol–epoxy “click” reaction with a tris‐epoxide core viz. 1,1,1‐tris(4‐hydroxyphenyl)ethane triglycidyl ether. The secondary hydroxyl groups generated adjacent to the core upon the thiol–epoxy reaction were esterified with α‐bromoisobutyryl bromide to install atom transfer radical polymerization (ATRP) initiating sites. ATRP of N‐isopropylacrylamide (NIPAM) using the three‐arm star PEG polymer fitted with ATRP initiating sites adjacent to the core afforded A₃B₃‐type of double hydrophilic (PEG)₃[poly(N‐isopropylacrylamide)] (PNIPAM)₃ miktoarm star polymers. Furthermore, the generated hydroxyl groups were directly used as initiator for ring‐opening polymerization of ε‐caprolactone to prepare A₃B₃‐type of amphiphilic (PEG)₃[poly(ε‐caprolactone)]₃ miktoarm star polymers. The double hydrophilic (PEG)₃(PNIPAM)₃ miktoarm star polymers showed lower critical solution temperature around 34 °C. The preliminary transmission electron microscopy analysis indicated formation of self‐assembly of (PEG)₃(PNIPAM)₃ miktoarm star polymer in aqueous solution. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 146–156     

A dynamic free-entry oligopoly with sluggish entry and exit adjustments

We study a dynamic free-entry oligopoly with sluggish entry and exit of firms under general demand and cost functions. We show that the number of firms in a steady-state open-loop solution for a dynamic free-entry oligopoly is smaller than that at static equilibrium and that the number of firms in a steady-state memoryless closed-loop solution is larger than that in an open-loop solution.     

Unconditionally Superclose Analysis of a New Mixed Finite Element Method for Nonlinear Parabolic Equation

This paper develops a framework to deal with the unconditional superclose analysis of nonlinear parabolic equation. Taking the finite element pair $Q_{11}/Q_{01} × Q_{10}$ as an example, a new mixed finite element method (FEM) is established and the $τ$ -independent superclose results of the original variable $u$ in $H^1$-norm and the flux variable $\mathop{q} \limits ^{\rightarrow}= −a(u)∇u$ in $L^2$-norm are deduced ($τ$ is the temporal partition parameter). A key to our analysis is an error splitting technique, with which the time-discrete and the spatial-discrete systems are constructed, respectively. For the first system, the boundedness of the temporal errors is obtained. For the second system, the spatial superclose results are presented unconditionally, while the previous literature always only obtain the convergent estimates or require certain time step conditions. Finally, some numerical results are provided to confirm the theoretical analysis, and show the efficiency of the proposed method.