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 .     

Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

A method of constructing 2-resolvable t-designs for $$t=3,4$$ t = 3 , 4

Designs, Codes and Cryptography - The paper introduces a method for constructing 2-resolvable t-designs for $$t=3,4$$ . The main idea is based on the assumption that there exists a partition of a...     

New fused pyrroles with rA1/A2A antagonistic activity as potential therapeutics for neurodegenerative disorders

Molecular Diversity - In a pilot study, eleven pyrrolopyridine and pyrrolopyrimidine derivatives (specifically, 7-azaindole and 7-deazapurine derivatives) were synthesised by Suzuki cross-coupling...     

Highly sensitive and rapid determination of tacrolimus in peripheral blood mononuclear cells by liquid chromatography–tandem mass spectrometry

After solid organ transplantation, tacrolimus is given to prevent rejection. Therapeutic drug monitoring is used to reach target concentrations of tacrolimus in whole blood. Because the site of action of tacrolimus is the lymphocyte, and tacrolimus binds ~80% to erythrocytes, the intracellular tacrolimus concentration in lymphocytes is possibly more relevant. For this purpose, we aimed to develop, improve and validate a UPLC–MS/MS method to measure tacrolimus concentrations in isolated peripheral blood mononuclear cells (PBMCs). PBMCs were isolated using a Ficoll separation technique, followed by a washing step using red blood cell lysis. A cell suspension of 50 μL containing 1 million PBMCs was used in combination with MagSiMUS‐TDM^PREP. To each sample we added 30 μL lysis buffer, 20 μL reconstitution buffer containing ¹³C²H₄‐tacrolimus as internal standard, 40 μL MagSiMUS‐TDM^PREP Type I Particle Mix and 175 μL Organic Precipitation Reagent VI for methanol‐based protein precipitation. A 10 μL aliquot of the supernatant was injected into the UPLC–MS/MS system. The method was validated, resulting in high sensitivity and specificity. The method was linear (r² = 0.997) over the range 5.0–1250 pg/1 × 10⁶ PBMCs. The inaccuracy was <5% and the imprecision was <15%. The washing steps following Ficoll isolation could be performed at either room temperature or on ice, with no effect of the temperature on the results. A method for the analysis of tacrolimus concentrations in PBMCs was developed and successfully validated. Further research will be performed to investigate the correlation between concentrations in PBMCs and clinical outcome.     

Synthesis of Highly Functionalized N,N-Diarylamides by an Anodic C,N-Coupling Reaction

We report an innovative, sustainable and straightforward protocol for the synthesis of N,N-diarylamides equipped with nonprotected hydroxyl groups by using electrosynthesis. The concept allows the application of various substrates furnishing diarylamides with yields up to 57 % within a single and direct electrolytic protocol. The method is thereby easy to conduct in an undivided cell with constant current conditions offering a versatile and short-cut alternative to conventional pathways.     

Synthesis,Crystal Structure,and Selected Properties of [Au(S2CNH2)2]SCN: A Precursor for Gold Macro-Needles Consisting of Gold Nanoparticles Glued by Graphitic Carbon Nitride

A new preparation route is developed for the synthesis of needle-like crystals of [Au(S₂CNH₂)₂]SCN, which avoids disproportionation of the Au^I salt used as a starting material. In the crystal structure, the two crystallographically independent Au^III centers are in a square-planar environment of two S₂CNH₂ ligands. The Hirshfeld surface analysis reveals the presence of noncovalent intermolecular S⋅⋅⋅S interactions, which are essential for the spatial arrangement of the molecules. Density functional theory (DFT) calculations including dispersion and damping corrections result in a unit cell volume very close to the value determined experimentally. Thermal decomposition in an inert atmosphere generates black needles with lengths of up to 500 μm. X-ray powder diffraction and pair distribution function analyses demonstrate that the needles are composed of nanosized crystals with a volume-weighted average domain size of 20(1) nm. According to results of X-ray photoemission experiments, the black needles are covered by a nitrogen-rich carbon nitride with composition near (CN)₂N. ¹³C solid-state NMR investigations indicate that two different carbon species are present, with signals corresponding well to heptazine units as in melon and triazine units as in poly(triazin imide) type compounds. Scanning transmission electron microscopy tomography evidences that the needles are composed of slightly elongated nanoparticles.     

Effective Power Series Computations

Foundations of Computational Mathematics - Let K be an effective field of characteristic zero. An effective tribe is a subset of $$K [[z_1, z_2, \ldots ]] = K \cup K {[}[z_1]] \cup K [[z_1, z_2]]...