Implementing and comparing sink particles in AMR and SPH

We implemented sink particles in the Adaptive Mesh Refinement (AMR) code FLASH to model the gravitational collapse and accretion in turbulent molecular clouds and cores. Sink particles are frequently used to measure properties of star formation in numerical simulations, such as the star formation rate and efficiency, and the mass distribution of stars. We show that only using a density threshold for sink particle creation is insufficient in case of supersonic flows, because the density can exceed the threshold in strong shocks that do not necessarily lead to local collapse. Additional physical collapse indicators have to be considered. We apply our AMR sink particle module to the formation of a star cluster, and compare it to a Smoothed Particle Hydrodynamics (SPH) code with sink particles. Our comparison shows encouraging agreement of gas and sink particle properties between the AMR and SPH code.Comment: 6 pages, 4 figures, conference proceedings of IAU Symposium 270 (eds. Alves, Elmegreen, Girart, Trimble) simulation movies available at http://www.ita.uni-heidelberg.de/~chfeder/pubs/sinks/sinks.shtml?lang=e

Anomalous Perceptions and Beliefs Are Associated With Shifts Toward Different Types of Prior Knowledge in Perceptual Inference.

Psychotic phenomena manifest in healthy and clinical populations as complex patterns of aberrant perceptions (hallucinations) and tenacious, irrational beliefs ( delusions). According to predictive processing accounts, hallucinations and delusions arise from atypicalities in the integration of prior knowledge with incoming sensory information. However, the computational details of these atypicalities and their specific phenomenological manifestations are not well characterized. We tested the hypothesis that hallucination-proneness arises from increased reliance on overly general application of prior knowledge in perceptual inference, generating percepts that readily capture the gist of the environment but inaccurately render its details. We separately probed the use of prior knowledge to perceive the gist vs the details of ambiguous images in a healthy population with varying degrees of hallucination- and delusion-proneness. We found that the use of prior knowledge varied with psychotic phenomena and their composition in terms of aberrant percepts vs aberrant beliefs. Consistent with previous findings, hallucination-proneness conferred an advantage using prior knowledge to perceive image gist but, contrary to predictions, did not confer disadvantage perceiving image details. Predominant hallucination-proneness actually conferred advantages perceiving both image gist and details, consistent with reliance on highly detailed perceptual knowledge. Delusion-proneness, and especially predominance of delusion-proneness over hallucination-proneness, conferred disadvantage perceiving image details but not image gist, though evidence of specific impairment of detail perception was preliminary. We suggest this is consistent with reliance on abstract, belief-like knowledge. We posit that phenomenological variability in psychotic experiences may be driven by variability in the type of knowledge observers rely upon to resolve perceptual ambiguity

Mk-801 Treatment Affects Glycolysis In Oligodendrocytes More Than In Astrocytes And Neuronal Cells: Insights For Schizophrenia

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Schizophrenia is a debilitating mental disorder, affecting more than 30 million people worldwide. As a multifactorial disease, the underlying causes of schizophrenia require analysis by multiplex methods such as proteomics to allow identification of whole protein networks. Previous post-mortem proteomic studies on brain tissues from schizophrenia patients have demonstrated changes in activation of glycolytic and energy metabolism pathways. However, it is not known whether these changes occur in neurons or in glial cells. To address this question, we treated neuronal, astrocyte, and oligodendrocyte cell lines with the NMDA receptor antagonist MK-801 and measured the levels of six glycolytic enzymes by Western blot analysis. MK-801 acts on the glutamatergic system and has been proposed as a pharmacological means of modeling schizophrenia. Treatment with MK-801 resulted in significant changes in the levels of glycolytic enzymes in all cell types. Most of the differences were found in oligodendrocytes, which had altered levels of hexokinase 1 (HK1), enolase 2 (ENO2), phosphoglycerate kinase (PG, and phosphoglycerate mutase 1 after acute MK-801 treatment (8 h), and HK1, ENO2, PGK, and triosephosphate isomerase (TPI) following long term treatment (72 h). Addition of the antipsychotic clozapine to the cultures resulted in counter-regulatory effects to the MK-801 treatment by normalizing the levels of ENO2 and PGK in both the acute and long term cultures. In astrocytes, MK-801 affected only aldolase C (ALDOC) under both acute conditions and HK1 and ALDOC following long term treatment, and TPI was the only enzyme affected under long term conditions in the neuronal cells. In conclusion, MK-801 affects glycolysis in oligodendrocytes to a larger extent than neuronal cells and this may be modulated by antipsychotic treatment. Although cell culture studies do not necessarily reflect the in vivo pathophysiology and drug effects within the brain, these results suggest that neurons, astrocytes, and oligodendrocytes are affected differently in schizophrenia. Employing in vitro models using neurotransmitter agonists and antagonists may provide new insights about the pathophysiology of schizophrenia which could lead to a novel system for drug discovery.9Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAEPEX UNICAMP [519.292]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Oxidation of allylic and benzylic alcohols to aldehydes and carboxylic acids

An oxidation of allylic and benzylic alcohols to the corresponding carboxylic acids is effected by merging a Cu-catalyzed oxidation using O2 as a terminal oxidant with a subsequent chlorite oxidation (Lindgren oxidation). The protocol was optimized to obtain pure products without chromatography or crystallization. Interception at the aldehyde stage allowed for Z/E-isomerization, thus rendering the oxidation stereoconvergent with respect to the configuration of the starting material

Industrial biotechnology of Pseudomonas putida: advances and prospects

Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory

Effect Of Mk-801 And Clozapine On The Proteome Of Cultured Human Oligodendrocytes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Separate lines of evidence have demonstrated the involvement of N-methyl-D-aspartate (NMDA) receptor and oligodendrocyte dysfunctions in schizophrenia. Here, we have carried out shotgun mass spectrometry proteome analysis of oligodendrocytes treated with the NMDA receptor antagonist MK-801 to gain potential insights into these effects at the molecular level. The MK-801 treatment led to alterations in the levels of 68 proteins, which are associated with seven distinct biological processes. Most of these proteins are involved in energy metabolism and many have been found to be dysregulated in previous proteomic studies of post-mortem brain tissues from schizophrenia patients. Finally, addition of the antipsychotic clozapine to MK-801 treated oligodendrocyte cultures resulted in changes in the levels of 45 proteins and treatment with clozapine alone altered 122 proteins and many of these showed opposite changes to the MK-801 effects. Therefore, these proteins and the associated energy metabolism pathways should be explored as potential biomarkers of antipsychotic efficacy. In conclusion, MK-801 treatment of oligodendrocytes may provide a useful model for testing the efficacy of novel treatment approaches.10Sao Paulo Research Foundation (FAPESP) [13/08711-3, 14/21035-0, 14/14881-1, 14/10068-4]Brazilian National Council for Scientific and Technological Development (CNPq) [460289/2014-4]Research Fund (FAEPEX) from University of Campinas [0986/14]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

A Bivariate Measure of Redundant Information

We define a measure of redundant information based on projections in the space of probability distributions. Redundant information between random variables is information that is shared between those variables. But in contrast to mutual information, redundant information denotes information that is shared about the outcome of a third variable. Formalizing this concept, and being able to measure it, is required for the non-negative decomposition of mutual information into redundant and synergistic information. Previous attempts to formalize redundant or synergistic information struggle to capture some desired properties. We introduce a new formalism for redundant information and prove that it satisfies all the properties necessary outlined in earlier work, as well as an additional criterion that we propose to be necessary to capture redundancy. We also demonstrate the behaviour of this new measure for several examples, compare it to previous measures and apply it to the decomposition of transfer entropy.Comment: 16 pages, 15 figures, 1 table, added citation to Griffith et al 2012, Maurer et al 199