Radiative transfer in moving media II. Solution of the radiative transfer equation in axial symmetry

A new method for the formal solution of the 2D radiative transfer equation in axial symmetry in the presence of arbitrary velocity fields is presented. The combination of long and short characteristics methods is used to solve the radiative transfer equation. We include the velocity field in detail using the Local Lorentz Transformation. This allows us to obtain a significantly better description of the photospheric region, where the gradient of the global velocity is too small for the Sobolev approximation to be valid. Sample test calculations for the case of a stellar wind and a rotating atmosphere are presented.Comment: 11 pages, 19 figures. accepted by Astronomy and Astrophysic

A 3D radiative transfer framework: I. non-local operator splitting and continuum scattering problems

We describe a highly flexible framework to solve 3D radiation transfer problems in scattering dominated environments based on a long characteristics piece-wise parabolic formal solution and an operator splitting method. We find that the linear systems are efficiently solved with iterative solvers such as Gauss-Seidel and Jordan techniques. We use a sphere-in-a-box test model to compare the 3D results to 1D solutions in order to assess the accuracy of the method. We have implemented the method for static media, however, it can be used to solve problems in the Eulerian-frame for media with low velocity fields.Comment: A&A, in press. 14 pages, 19 figures. Full resolution figures available at ftp://phoenix.hs.uni-hamburg.de/preprints/3DRT_paper1.pdf HTML version (low res figures) at http://hobbes.hs.uni-hamburg.de/~yeti/PAPERS/3drt_paper1/index.htm

Structure-Based Design of Non-Natural Amino Acid Inhibitors of Amyloid Fibrillation

Many globular and natively disordered proteins can convert into amyloid fibers. These fibers are associated with numerous pathologies1 as well as with normal cellular functions2,3, and frequently form during protein denaturation4,5. Inhibitors of pathological amyloid fibers could serve as leads for therapeutics, provided the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibers as templates, we have designed and characterized an all D-amino acid inhibitor of fibrillation of the tau protein found in Alzheimer’s disease, and a non-natural L-amino acid inhibitor of an amyloid fiber that enhances sexual transmission of HIV. Our results indicate that peptides from structure-based designs can disrupt the fibrillation of full-length proteins, including those like tau that lack fully ordered native structures.We thank M.I. Ivanova, J. Corn, T. Kortemme, D. Anderson, M.R. Sawaya, M. Phillips, S. Sambashivan, J. Park, M. Landau, Q. Zhang, R. Clubb, F. Guo, T. Yeates, J. Nowick, J. Zheng, and M.J. Thompson for discussions, HHMI, NIH, NSF, the GATES foundation, and the Joint Center for Translational Medicine for support, R. Peterson for help with NMR experiments, E. Mandelkow for providing tau constructs, R. Riek for providing amyloid beta, J. Stroud for amyloid beta preparation. Support for JK was from the Damon Runyon Cancer Research Foundation, for HWC by the Ruth L. Kirschstein National Research Service Award, for JM from the programme for junior-professors by the ministry of science, Baden-Württemberg, and for SAS by a UCLA-IGERT bioinformatics traineeship

a comparison of two test methods

Die Inzidenz von postoperativen kognitiven Dysfunktionen (POCD) ist abhängig von der verwendeten Testbatterie und der angewendeten Berechnungsmethode. Die Messungen können mit einer Papier- und Bleistift-Testbatterie oder mit einer computerisierten Testbatterie durchgeführt werden. Ziel der Studie war es, die Inzidenzen und die Übereinstimmung von POCD, gemessen mit einer computerisierten Testbatterie und einer Papier- und Bleistift-Testbatterie, in demselben Patientenkollektiv zu bestimmen. Insgesamt wurden 74 Patienten eingeschlossen: 30 Patienten unterzogen sich einem operativen Eingriff unter Allgemeinanästhesie, 37 nicht chirurgische Patienten wurden als Kontrollgruppe eingeschlossen, 6 Patienten und ein Proband der Kontrollgruppe mussten ausgeschlossen werden. Die Patienten wurden im Abstand von 7 Tagen mit einer computerisierten Testbatterie und einer Papier- und Bleistift-Testbatterie getestet. Beide Testbatterien deckten dieselben kognitiven Domänen ab: Visuelles Lernen, Gedächtnis, Verarbeitungsgeschwindigkeit, visuelle Aufmerksamkeit. Die computerisierte Testbatterie detektierte 10% [95%-CI: 3,5% - 25,6%] POCD wohingegen die Papier- und Bleistift-Testbatterie 30% [95%-CI: 16,7% - 47,9%] POCD detektierte (p=0,03). Die Interrater Reliabilität zwischen den beiden Testbatterien zeigte eine angemessene (moderate) Übereinstimmung (Cohens Kappa = 0,41). Alle Patienten, die durch die computerisierte Testbatterie erkannt wurden, wurden ebenfalls durch die Papier- und Bleistift- Testbatterie erkannt. In der vorliegenden Studie konnte gezeigt werden, dass die POCD-Inzidenzen gemessen mit einer computerisierten Testbatterie und einer Papier- und Bleistift-Testbatterie, eine angemessene Übereinstimmung zeigen. Die Verwendung zweier neuropsychologischer Testbatterien, die theoretisch dieselben kognitiven Domänen abdecken, führt aber nicht automatisch zu denselben Klassifikationen.The test battery and the computation method used for the detection of postoperative cognitive dysfunction (POCD) do have a major impact on the measured incidence. Two types of test batteries (TB), computerized (CTB) and conventional paper and pencil (PPTB), can be employed for the detection of POCD. This study investigated the incidences of POCD measured with a CTB and PPTB. Furthermore, the accordance of the classifications given by the two test batteries was defined. 36 surgical patients scheduled for non-cardiac surgery were recruited. From these 36 patients 6 patients had to be excluded. 38 non- surgical patients were recruited as control group. From this group one patient had to be excluded. The patients were tested at the day of inclusion and seven days thereafter. The cognitive domains tested by the two test batteries were the same. The CTB detected in 10% [95%-CI: 3.5% - 25.6%] POCD, the PPTB in 30% [95%-CI: 16.7% - 47.9%] (p=0.03). The Cohens Kappa as measure of the inter- rater agreement was 0.41 i.e. moderate accordance. The patients who showed POCD in the CTB were also detected by the PPTB. The inter-rater reliability for the two test batteries was moderate. The usage of two neuropsychological test batteries covering the same cognitive domains, does not necessarily result in the same classification of POCD

Nef Enhances Human Immunodeficiency Virus Type 1 Infectivity and Replication Independently of Viral Coreceptor Tropism

We investigated the infectivities and replicative capacities of a large panel of variants of the molecular human immunodeficiency virus type 1 (HIV-1) NL4-3 clone that differ exclusively in the V3 region of the viral envelope glycoprotein and the nef gene. Our results demonstrate that Nef enhances virion infectivity and HIV-1 replication independently of the viral coreceptor tropism