A real-space grid implementation of the Projector Augmented Wave method

A grid-based real-space implementation of the Projector Augmented Wave (PAW) method of P. E. Blochl [Phys. Rev. B 50, 17953 (1994)] for Density Functional Theory (DFT) calculations is presented. The use of uniform 3D real-space grids for representing wave functions, densities and potentials allows for flexible boundary conditions, efficient multigrid algorithms for solving Poisson and Kohn-Sham equations, and efficient parallelization using simple real-space domain-decomposition. We use the PAW method to perform all-electron calculations in the frozen core approximation, with smooth valence wave functions that can be represented on relatively coarse grids. We demonstrate the accuracy of the method by calculating the atomization energies of twenty small molecules, and the bulk modulus and lattice constants of bulk aluminum. We show that the approach in terms of computational efficiency is comparable to standard plane-wave methods, but the memory requirements are higher.Comment: 13 pages, 3 figures, accepted for publication in Physical Review

Imaging low-energy positron beams in real-time with unprecedented resolution

Particle beams focused to micrometer-sized spots play a crucial role in forefront research using low-energy positrons. Their expedient and wide application, however, requires highly-resolved, fast beam diagnostics. We have developed two different methods to modify a commercial imaging sensor to make it sensitive to low-energy positrons. The first method consists in removing the micro-lens array and Bayer filter from the sensor surface and depositing a phosphor layer in their place. This procedure results in a detector capable of imaging positron beams with energies down to a few tens of eV, or an intensity as low as 35 particles/s/mm2 when the beam energy exceeds 10keV. The second approach omits the phosphor deposition; with the resulting device we succeeded in detecting single positrons with energies upwards of 6 keV and efficiency up to 93%. The achieved spatial resolution of 0.97 micrometers is unprecedented for real-time positron detectors.Comment: 18 pages, 6 figure

Serum concentration of HDL particles predicts mortality in acute heart failure patients

Clinical studies have shown that assessing circulating concentrations of high-density lipoprotein (HDL) particles by nuclear magnetic resonance (NMR) spectroscopy is superior to HDL-cholesterol in predicting cardiovascular risk. We tested the hypothesis that circulating concentrations of HDL particles predict 3-month mortality of patients with acute heart failure (AHF). Out of 152 included patients, 52% were female, additionally the mean patient age was 75.2 ± 10.3 years, and three-month mortality was 27%. Serum lipoprotein profile at admission was determined by NMR spectroscopy. Univariate logistic regression analyses revealed a significant inverse association of total (odds ratio (OR) 0.38 per 1-SD increase, 95% confidence interval (CI) 0.23-0.60, p < 0.001) and small HDL particle concentrations (OR 0.35 per 1-SD increase, 95% CI 0.19-0.60, p < 0.001) with 3-month mortality, whereas concentrations of large HDL particles (p = 0.353) or HDL-cholesterol (p = 0.107) showed no significant association. After adjustment for age, sex, mean arterial pressure, low-density lipoprotein cholesterol, glomerular filtration rate, urea, and N-terminal pro-brain natriuretic peptide, both the total and small HDL particle concentrations remained significantly associated with 3-month mortality. Based on our results, we conclude that total and small HDL particle concentrations strongly and independently predict 3-month mortality in AHF patients

Ausbildung in Evidenzbasierter Medizin am Universitätsklinikum Frankfurt am Main : meeting abstract

Einführung: Obwohl international die Integration der Evidenzbasierten Medizin (EbM) in die klinische Medizin und in die Ausbildung voranschreitet, ist die Verbreitung im deutschen Klinikalltag eine fortbestehende Herausforderung. Vor allem ist die Vernetzung der theoretischen Lerninhalte mit den klinisch-praktischen Fertigkeiten eine weit verbreitete Schwierigkeit. Die neue Ärzteapprobationsordnung bietet Möglichkeiten für innovative Konzepte im medizinischen Curriculum. Sowohl die systematische Informationssuche als auch die kritische Bewertung und Anwendung medizinischer Informationen sind wichtige Kernkompetenzen der ärztlichen Tätigkeit. Zum Wintersemester 03/04 wurde in Frankfurt das erste curriculare Seminar EbM als Teilfach des Querschnittsbereiches I (Epidemiologie, Med. Biometrie und Med. Informatik) auf der Basis des peer-teaching eingeführt und wissenschaftlich begleitet. Methoden: Für alle Studierenden des 2. klinischen Semesters wird in Kleingruppenseminaren an 4 Terminen ein Basiskurs EbM nach den Kriterien des Deutschen Netzwerkes für Evidenzbasierte Medizin e.V. durchgeführt. Dabei werden die Module Vierteilige Frage, Internetrecherche, Diagnose und Therapie erarbeitet. Ein individuelles Fallbeispiel (klinische Fragestellung) wird von jedem Studierenden selbständig mit allen Schritten der EbM bearbeitet. Jede Seminararbeit wird im Rahmen eines journal clubs von dem Studierenden vorgestellt und in der Kleingruppe diskutiert. Während des ersten unterrichteten Semesters erhielt jeder Seminarteilnehmer zu Seminarbeginn und zum Seminarende einen Testfragebogen mit 20 Fragen, sowie zum Ende einen anonymisierten Fragebogen mit der Bitte um Einschätzung. Die anonymisierten Fragebogen werden seitdem weiter in jedem Semester eingesetzt. Ergebnisse: Es wurden im Durchschnitt nach dem Seminar 7,48 (99% KI 6.61-8.36) Fragen mehr als vor dem Seminar richtig beantwortet. Der Kurs wurde im Median mit der Note gut eingeschätzt (Weberschock et al 2005, im Druck). Die Auswertungen der Einschätzungen der nachfolgenden Semester zeigten noch bessere Ergebnisse. Schlussfolgerung: EbM ist in der medizinischen Ausbildung sehr gut durchführbar und wird mit den richtigen didaktischen Konzepten auch voll akzeptiert. Vor allem die Fähigkeit, medizinische Informationen korrekt zu bewerten und sie klinisch fachgerecht anzuwenden ist eine essentielle Kompetenz für die ärztliche Tätigkeit und bedarf den sichern Umgang mit den Methoden und Medien. Ausblick: Die Vernetzung der theoretischen Aspekte bei der medizinischen Informationsverarbeitung mit der klinischen Anwendung der gewonnenen Erkenntnisse ist für die Ausbildung in EbM ein essentieller Bestandteil. Um die Lehrenden auf diese Aufgabe adäquat vorbereiten zu können, werden in naher Zukunft in Zusammenarbeit mit dem Deutschen Netzwerk Evidenzbasierte Medizin (DNEbM), der Arbeitsgemeinschaft der wissenschaftlich medizinischen Fachgesellschaften (AWMF) und der Gesellschaft für medizinische Ausbildung (GMA) Train-the Teacher-Seminare veranstaltet. Diese Seminare sollen einerseits die didaktischen Methoden und Fertigkeiten der EbM-Lehrenden weiter ausbauen und andererseits eine Brücke zwischen theoretischen Lerninhalten und klinischen Bezügen schlagen

Sample size considerations using mathematical models: an example with Chlamydia trachomatis infection and its sequelae pelvic inflammatory disease.

BACKGROUND The success of an intervention to prevent the complications of an infection is influenced by the natural history of the infection. Assumptions about the temporal relationship between infection and the development of sequelae can affect the predicted effect size of an intervention and the sample size calculation. This study investigates how a mathematical model can be used to inform sample size calculations for a randomised controlled trial (RCT) using the example of Chlamydia trachomatis infection and pelvic inflammatory disease (PID). METHODS We used a compartmental model to imitate the structure of a published RCT. We considered three different processes for the timing of PID development, in relation to the initial C. trachomatis infection: immediate, constant throughout, or at the end of the infectious period. For each process we assumed that, of all women infected, the same fraction would develop PID in the absence of an intervention. We examined two sets of assumptions used to calculate the sample size in a published RCT that investigated the effect of chlamydia screening on PID incidence. We also investigated the influence of the natural history parameters of chlamydia on the required sample size. RESULTS The assumed event rates and effect sizes used for the sample size calculation implicitly determined the temporal relationship between chlamydia infection and PID in the model. Even small changes in the assumed PID incidence and relative risk (RR) led to considerable differences in the hypothesised mechanism of PID development. The RR and the sample size needed per group also depend on the natural history parameters of chlamydia. CONCLUSIONS Mathematical modelling helps to understand the temporal relationship between an infection and its sequelae and can show how uncertainties about natural history parameters affect sample size calculations when planning a RCT

Chlorophyll Catabolites – Chemical and Structural Footprints of a Fascinating Biological Phenomenon

Twenty years ago, the molecular basis for the seasonal disappearance of chlorophyll was still enigmatic. In the meantime, our knowledge on chlorophyll breakdown has grown considerably. As outlined here, it has been possible to decipher the basic transformations involved in natural chlorophyll breakdown by identification of chlorophyll catabolites in higher plants, and with the help of the synthesis of (putative) catabolic intermediates. In vascular plants, chlorophyll breakdown typically converts the green plant pigments efficiently into colorless and non-fluorescent tetrapyrroles. It involves colored intermediates only fleetingly and in an (elusive) enzyme-bound form. The non-fluorescent chlorophyll catabolites accumulate in the vacuoles of degreened leaves and are considered the products, primarily, of a detoxification process. However, they are effective antioxidants, and may thus also have physiologically beneficial chemical properties.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009

Serum concentrations of Citrate, Tyrosine, 2- and 3- Hydroxybutyrate are associated with increased 3-month mortality in acute heart failure patients

Considering the already established relationship between the extent of the metabolic dysfunction and the severity of heart failure (HF), it is conceivable that the metabolomic profile of the serum may have a prognostic capacity for 3-month mortality in acute heart failure (AHF). Out of 152 recruited patients, 130 serum samples were subjected to the metabolomic analyses. The 3-month mortality rate was 24.6% (32 patients). Metabolomic profiling by nuclear magnetic resonance spectroscopy found that the serum levels of 2-hydroxybutyrate (2-HB), 3-hydoxybutyrate (3-HB), lactate, citrate, and tyrosine, were higher in patients who died within 3 months compared to those who were alive 3 months after onset of AHF, which was confirmed by univariable logistic regression analyses (p = 0.009, p = 0.005, p = 0.008, p<0.001, and p<0.001, respectively). These associations still remained significant for all tested metabolites except for lactate after adjusting for established prognostic parameters in HF. In conclusion, serum levels of 2-HB, 3-HB, tyrosine, and citrate measured at admission are associated with an increased 3-month mortality rate in AHF patients and might thus be of prognostic value in AHF

Metabolic syndrome modulates association between endothelial lipase and lipid/lipoprotein plasma levels in acute heart failure patients

We hypothesised that the established association of endothelial lipase (EL) plasma levels with atherogenic lipid profile is altered in acute heart failure (AHF) and additionally affected by overlapping metabolic syndrome (MetS). We examined the association of EL plasma levels and lipid/lipoprotein plasma levels in AHF patients without and with overlapping MetS. The study was performed as a single-centre, observational study on 152 AHF patients, out of which 85 had overlapping MetS. In the no-MetS group, EL plasma levels were significantly positively correlated with plasma levels of atherogenic lipids/lipoproteins, including total cholesterol, low-density lipoprotein (LDL)-cholesterol, total LDL particles and triglycerides, but also with plasma levels of antiatherogenic high-density lipoprotein (HDL)-cholesterol, total HDL particles and small HDL particles. In the MetS group, EL plasma levels were positively correlated with triglyceride and small LDL-particle levels, and significantly negatively correlated with plasma levels of large HDL particles as well as with LDL- and HDL-particle size, respectively. EL- and lipid/lipoprotein- plasma levels were different in the no-MetS patients, compared to MetS patients. The association of EL with atherogenic lipid profile is altered in AHF and additionally modified by MetS, which strongly modulates EL- and lipid/lipoprotein-plasma levels in AHF

Serum concentrations of free fatty acids are associated with 3-month mortality in acute heart failure patients

Background: Plasma free fatty acids (FFA) are higher in heart failure (HF) patients compared to healthy controls. Considering that the extent of FFA elevation in HF might mirror the severity of HF, we hypothesized that the serum levels of FFA may be a useful prognostic indicator for 3-month mortality in acute heart failure (AHF). ----- Methods: We analyzed the serum samples of AHF patients obtained at admission to the emergency department. Serum levels of FFA were analyzed using an enzymatic reagent on an automatic analyzer. ----- Results: Out of 152 included AHF patients that were originally included, serum samples of 132 patients were available for the quantification of FFA. Of these, 35 (26.5%) died within 3 months of onset of AHF. These patients had significantly higher serum levels of FFA compared to AHF patients who were alive 3 months after onset of AHF. Univariable logistic regression analyses showed a significant positive association of FFA levels with 3-month mortality (odds ratio [OR] 2.76 [95% confidence interval 1.32-6.27], p = 0.010). Importantly, this association remained significant after adjusting for age and sex, as well as for further clinical and laboratory parameters that showed a significant association with 3-month mortality in the univariate analyses. ----- Conclusions: We conclude that the admission serum levels of FFA are associated with 3-month mortality in AHF patients. Therefore, measurements of circulating FFA levels may help identifying high-risk AHF patients

Molecular transport calculations with Wannier functions

We present a scheme for calculating coherent electron transport in atomic-scale contacts. The method combines a formally exact Green's function formalism with a mean-field description of the electronic structure based on the Kohn-Sham scheme of density functional theory. We use an accurate plane-wave electronic structure method to calculate the eigenstates which are subsequently transformed into a set of localized Wannier functions (WFs). The WFs provide a highly efficient basis set which at the same time is well suited for analysis due to the chemical information contained in the WFs. The method is applied to a hydrogen molecule in an infinite Pt wire and a benzene-dithiol (BDT) molecule between Au(111) surfaces. We show that the transmission function of BDT in a wide energy window around the Fermi level can be completely accounted for by only two molecular orbitals.Comment: 15 pages, 12 figures, submitted to Chemical Physic