Could we use a million cores to solve an integer program?

Given the steady increase in cores per CPU, it is only a matter of time before supercomputers will have a million or more cores. In this article, we investigate the opportunities and challenges that will arise when trying to utilize this vast computing power to solve a single integer linear optimization problem. We also raise the question of whether best practices in sequential solution of ILPs will be effective in massively parallel environments.     

ToF-SIMS measurements with topographic information in combined images

In 2D and 3D time-of-flight secondary ion mass spectrometric (ToF-SIMS) analysis, accentuated structures on the sample surface induce distorted element distributions in the measurement. The origin of this effect is the 45° incidence angle of the analysis beam, recording planar images with distortion of the sample surface. For the generation of correct element distributions, these artifacts associated with the sample surface need to be eliminated by measuring the sample surface topography and applying suitable algorithms. For this purpose, the next generation of ToF-SIMS instruments will feature a scanning probe microscope directly implemented in the sample chamber which allows the performance of topography measurements in situ. This work presents the combination of 2D and 3D ToF-SIMS analysis with topographic measurements by ex situ techniques such as atomic force microscopy (AFM), confocal microscopy (CM), and digital holographic microscopy (DHM). The concept of the combination of topographic and ToF-SIMS measurements in a single representation was applied to organic and inorganic samples featuring surface structures in the nanometer and micrometer ranges. The correct representation of planar and distorted ToF-SIMS images was achieved by the combination of topographic data with images of 2D as well as 3D ToF-SIMS measurements, using either AFM, CM, or DHM for the recording of topographic data.     

A Maltol-Containing Ruthenium Polypyridyl Complex as a Potential Anticancer Agent

Cancer is one of the main causes of death worldwide. Chemotherapy, despite its severe side effects, is to date one of the leading strategies against cancer. Metal-based drugs present several potential advantages when compared to organic compounds and they have gained trust from the scientific community after the approval on the market of the drug cisplatin. Recently, we reported the ruthenium complex ([Ru(DIP)₂(sq)](PF₆) (where DIP is 4,7-diphenyl-1,10-phenantroline and sq is semiquinonate) with a remarkable potential as chemotherapeutic agent against cancer, both in vitro and in vivo. In this work, we analyse a structurally similar compound, namely [Ru(DIP)₂(mal)](PF₆), carrying the flavour-enhancing agent approved by the FDA, maltol (mal). To possess an FDA approved ligand is crucial for a complex, whose mechanism of action might include ligand exchange. Herein, we describe the synthesis and characterisation of [Ru(DIP)₂(mal)](PF₆), its stability in solutions and under conditions that resemble the physiological ones, and its in-depth biological investigation. Cytotoxicity tests on different cell lines in 2D model and on HeLa MultiCellular Tumour Spheroids (MCTS) demonstrated that our compound has higher activity than cisplatin, inspiring further tests. [Ru(DIP)₂(mal)](PF₆) was efficiently internalised by HeLa cells through a passive transport mechanism and severely affected the mitochondrial metabolism.     

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.     

The impact of blood on liver metabolite profiling – a combined metabolomic and proteomic approach

Metabolomics has entered the well‐established omic sciences as it is an indispensable information resource to achieve a global picture of biological systems. The aim of the present study was to estimate the influence of blood removal from mice liver as part of sample preparation for metabolomic and proteomic studies. For this purpose, perfused mice liver tissue (i.e. with blood removed) and unperfused mice liver tissue (i.e. containing blood) were compared by two‐dimensional gas chromatography time of flight mass spectrometry (GC × GC‐TOFMS) for the metabolomic part, and by liquid chromatography tandem mass spectrometry (LC‐MS/MS) for the proteomic part. Our data showed significant differences between the unperfused and perfused liver tissue samples. Furthermore, we also observed an overlap of blood and tissue metabolite profiles in our data, suggesting that the perfusion of liver tissue prior to analysis is beneficial for an accurate metabolic profile of this organ. Copyright © 2013 John Wiley & Sons, Ltd.     

19F-detected dual-optimized inverted 1JCC 1,n-ADEQUATE

Modification of the recently reported ¹⁹F-detected 1,1-ADEQUATE experiment that incorporates dual-optimization to selectively invert a wide range of ¹J_CC correlations in a 1,n-ADEQUATE experiment is reported. Parameters for the dual-optimization segment of the pulse sequence were modified to accommodate the increased size of ¹J_CC homonuclear coupling constants of poly- and perfluorinated molecules relative to protonated molecules to allow broadband inversion of the ¹J_CC correlations. The observation and utility of isotope shifts are reported for the first time for 1,1- and 1,n-ADEQUATE correlations.     

Switching the Switch: Ligand Induced Disulfide Formation in HDAC8

Human histone deacetylase 8 is a well-recognized target for T-cell lymphoma and particularly childhood neuroblastoma. PD-404,182 was shown to be a selective covalent inhibitor of HDAC8 that forms mixed disulfides with several cysteine residues and is also able to transform thiol groups to thiocyanates. Moreover, HDAC8 was shown to be regulated by a redox switch based on the reversible formation of a disulfide bond between cysteines Cys₁₀₂ and Cys₁₅₃. This study on the distinct effects of PD-404,182 on HDAC8 reveals that this compound induces the dose-dependent formation of intramolecular disulfide bridges. Therefore, the inhibition mechanism of HDAC8 by PD-404,182 involves both, covalent modification of thiols as well as ligand mediated disulfide formation. Moreover, this study provides a deep molecular insight into the regulation mechanism of HDAC8 involving several cysteines with graduated capability to form reversible disulfide bridges.     

Orbispaces as differentiable stratified spaces

We present some features of the smooth structure and of the canonical stratification on the orbit space of a proper Lie groupoid. One of the main features is that of Morita invariance of these structures—it allows us to talk about the canonical structure of differentiable stratified space on the orbispace (an object analogous to a separated stack in algebraic geometry) presented by the proper Lie groupoid. The canonical smooth structure on an orbispace is studied mainly via Spallek’s framework of differentiable spaces, and two alternative frameworks are then presented. For the canonical stratification on an orbispace, we extend the similar theory coming from proper Lie group actions. We make no claim to originality. The goal of these notes is simply to give a complementary exposition to those available and to clarify some subtle points where the literature can sometimes be confusing, even in the classical case of proper Lie group actions.