Interface dipoles of organic molecules on Ag(111) in hybrid density-functional theory

We investigate the molecular acceptors 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA), 2,3,5,6-tetra uoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ), and 4,5,9,10-pyrenetetraone (PYTON) on Ag(111) using densityfunctional theory. For two groups of the HSE(\alpha, \omega) family of exchange-correlation functionals (\omega = 0 and \omega = 0.2\AA) we study the isolated components as well as the combined systems as a function of the amount of exact-exchange (\alpha). We find that hybrid functionals favour electron transfer to the adsorbate. Comparing to experimental work-function data, we report for (\alpha) ca. 0.25 a notable but small improvement over (semi)local functionals for the interface dipole. Although Kohn-Sham eigenvalues are only approximate representations of ionization energies, incidentally, at this value also the density of states agrees well with the photoelectron spectra. However, increasing (\alpha) to values for which the energy of the lowest unoccupied molecular orbital matches the experimental electron affinity in the gas phase worsens both the interface dipole and the density of states. Our results imply that semi-local DFT calculations may often be adequate for conjugated organic molecules on metal surfaces and that the much more computationally demanding hybrid functionals yield only small improvements.Comment: submitted to New Journal of Physics (2013). More information can be found at http://th.fhi-berlin.mpg.de/site/index.php?n=Publications.Publication

Acceleration of Python Applications on GPU

Konvenčne sa v oblasti high performance computing (HPC) používajú prekladané jazyky, ako napríklad C++. Skriptovacie jazyky ako Python sú však pohodlnejšie a vývoj aplikácií je v nich rýchlejší a jednoduchší. Táto práca porovnáva jazyky C++ a Python z hľadiska možnosti akcelerácie výpočtov na grafickej karte. Jej cieľom je ukázať, že skriptovacie jazyky sú taktiež použiteľné na implementáciu HPC aplikácií a poukázať na ich výhody a nevýhody oproti prekladaným jazykom. Za týmto účelom je implementovaných niekoľko programov. Tie pozostávajú z niekoľkých menších testovacích programov a jedného väčšieho programu, riešiaceho výpočtovo náročný problém. Implementácie týchto programov v jazykoch C++ a Python sú porovnané ako z hľadiska výkonu, tak z hľadiska náročnosti implementácie.Compiled languages, such as C++, are conventionally used in the field of high performance computing (HPC). However, scripting languages like Python are more convenient and application development is quicker and simpler in these languages. This work compares C++ and Python in terms of the possibilities of computation acceleration on graphics card. Its aim is to show that scripting languages are also suitable for the implementation of HPC applications, and point out their advantages and disadvantages compared to compiled languages. To this purpose, a number of programs have been implemented. Several smaller programs for testing purposes and a larger one, implementing a computationally intensive problem. The implementations of these programs in C++ and Python are compared in terms of performance, as well as difficulty of implementation.

Investigation of the link between fluid shift and airway collapsibility as a mechanism for obstructive sleep apnea in congestive heart failure

The increased prevalence of obstructive sleep apnea (OSA) in congestive heart failure (CHF) may be associated with rostral fluid shift. We investigated the effect of overnight rostral fluid shift on pharyngeal collapsibility (Pcrit), pharyngeal caliber (APmean), and apnea‐hypopnea index (AHI) in CHF patients. Twenty‐three optimally treated systolic CHF patients were studied. Neck circumference was measured immediately prior to sleep in the evening and immediately after waking in the morning as a marker of rostral fluid shift. Pcrit was measured during sleep, early and late in the night. APmean was measured using acoustic reflection at the same times as neck circumference measurements. 15/23 CHF patients experienced an overnight increase in neck circumference; overall neck circumference significantly increased overnight (mean±SD, evening: 41.7 ± 3.2 cm; morning: 42.3 ± 3.1 cm; P = 0.03). Pcrit increased significantly overnight (early‐night: −3.8 ± 3.3 cmH2O; late‐night: −2.6 ± 3.0 cmH2O; P = 0.03) and APmean decreased (evening: 4.2 ± 1.3 cm2; morning: 3.7 ± 1.3 cm2; P = 0.006). The total AHI correlated with neck circumference (r = 0.4; P = 0.04) and Pcrit (r = 0.5; P = 0.01). APmean correlated with neck circumference (r = −0.47; P = 0.02). There was no significant change in AHI between the first and second half of the night (first‐half: 12.9 ± 12.4/h; second‐half: 13.7 ± 13.3/h; P = 0.6). Overnight rostral fluid shift was associated with increased pharyngeal collapsibility and decreased pharyngeal caliber during sleep in CHF patients. Rostral fluid shift may be an important mechanism of OSA in this patient group

Structural Basis for Substrate Specificity in Human Monomeric Carbonyl Reductases

Carbonyl reduction constitutes a phase I reaction for many xenobiotics and is carried out in mammals mainly by members of two protein families, namely aldo-keto reductases and short-chain dehydrogenases/reductases. In addition to their capacity to reduce xenobiotics, several of the enzymes act on endogenous compounds such as steroids or eicosanoids. One of the major carbonyl reducing enzymes found in humans is carbonyl reductase 1 (CBR1) with a very broad substrate spectrum. A paralog, carbonyl reductase 3 (CBR3) has about 70% sequence identity and has not been sufficiently characterized to date. Screening of a focused xenobiotic compound library revealed that CBR3 has narrower substrate specificity and acts on several orthoquinones, as well as isatin or the anticancer drug oracin. To further investigate structure-activity relationships between these enzymes we crystallized CBR3, performed substrate docking, site-directed mutagenesis and compared its kinetic features to CBR1. Despite high sequence similarities, the active sites differ in shape and surface properties. The data reveal that the differences in substrate specificity are largely due to a short segment of a substrate binding loop comprising critical residues Trp229/Pro230, Ala235/Asp236 as well as part of the active site formed by Met141/Gln142 in CBR1 and CBR3, respectively. The data suggest a minor role in xenobiotic metabolism for CBR3. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region

Mangafodipir Protects against Hepatic Ischemia-Reperfusion Injury in Mice

Mangafodipir is a contrast agent used in magnetic resonance imaging that concentrates in the liver and displays pleiotropic antioxidant properties. Since reactive oxygen species are involved in ischemia-reperfusion damages, we hypothesized that the use of mangafodipir could prevent liver lesions in a mouse model of hepatic ischemia reperfusion injury. Mangafodipir (MnDPDP) was compared to ischemic preconditioning and intermittent inflow occlusion for the prevention of hepatic ischemia-reperfusion injury in the mouse.Mice were subjected to 70% hepatic ischemia (continuous ischemia) for 90 min. Thirty minutes before the ischemic period, either mangafodipir (10 mg/kg) or saline was injected intraperitoneally. Those experimental groups were compared with one group of mice preconditioned by 10 minutes' ischemia followed by 15 minutes' reperfusion, and one group with intermittent inflow occlusion. Hepatic ischemia-reperfusion injury was evaluated by measurement of serum levels of aspartate aminotransferase (ASAT) activity, histologic analysis of the livers, and determination of hepatocyte apoptosis (cytochrome c release, caspase 3 activity). The effect of mangafodipir on the survival rate of mice was studied in a model of total hepatic ischemia.<0.01), and by higher rates of survival in treated than in untreated animals (P<0.001). The level of protection by mangafodipir was similar to that observed following intermittent inflow occlusion and higher than after ischemic preconditioning.Mangafodipir is a potential new preventive treatment for hepatic ischemia-reperfusion injury