Physics-Aware Convolutional Neural Networks for Computational Fluid Dynamics

Determining the behavior of fluids is of interest in many fields. In this work, we focus on incompressible, viscous, Newtonian fluids, which are well described by the incompressible Navier-Stokes equations. A common approach to solve them approximately is to perform Computational Fluid Dynamics (CFD) simulations. However, CFD simulations are very expensive and must be repeated if the geometry changes even slightly. We consider Convolutional Neural Networks (CNNs) as surrogate models for CFD simulations for various geometries. This can also be considered as operator learning. Typically, these models are trained on images of high-fidelity simulation results. The generation of this high-fidelity training data is expensive, and a fully data-driven approach usually requires a large data set. Therefore, we are interested in training a CNN in the absence of abundant training data. To this end, we leverage the underlying physics in the form of the governing equations to construct physical constraints that we then use to train a CNN. We present results for various model problems, including two- and three-dimensional flow in channels around obstacles of various sizes and in non-rectangular geometries, especially arteries and aneurysms. We compare our novel physics-aware approach to the state-of-the-art data-based approach and also to a combination of the two, a combined or hybrid approach. In addition, we present results for an extension of our approach to include variations in the boundary conditions

Exploring Influences on Theory of Mind Impairment in Opioid Dependent Patients

Theory of mind (ToM) is an aspect of social cognition impaired in different addictive disorders, including opioid addiction. This study aimed at replicating ToM deficits in opioid dependent patients undergoing opioid maintenance treatment (OMT) and exploring the influence of substance use related variables, executive functions and childhood maltreatment on ToM in opioid dependent patients. 66 opioid dependent patients were tested using the Movie for Assessment of Social Cognition (MASC) and compared with the data of healthy controls. Furthermore, the opioid dependent patients underwent testing for executive functions and filled in the Childhood Trauma Questionnaire (CTQ). Performance on the MASC was significantly poorer in the opioid dependence group than in the control group, even when recent additional drug use and psychiatric comorbidities were controlled for. No correlations were found between ToM and substance use related factors. Aspects of ToM performance in opioid dependent patients correlated significantly with different EF domains. ToM correlated significantly with the CTQ scales for physical maltreatment. The results confirm impaired ToM in opioid dependent patients and highlight executive functions and childhood maltreatment as influential factors. The lack of associations between ToM and substance use related variables and the association with childhood maltreatment suggest that ToM impairments might be a risk factor predating substance abuse.Peer Reviewe

A Reference Model for Common Understanding of Capabilities and Skills in Manufacturing

In manufacturing, many use cases of Industry 4.0 require vendor-neutral and machine-readable information models to describe, implement and execute resource functions. Such models have been researched under the terms capabilities and skills. Standardization of such models is required, but currently not available. This paper presents a reference model developed jointly by members of various organizations in a working group of the Plattform Industrie 4.0. This model covers definitions of most important aspects of capabilities and skills. It can be seen as a basis for further standardization efforts

Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing

MicroRNAs (miRNAs) are prevalent regulatory RNAs that mediate gene silencing and play key roles in diverse cellular processes. While synthetic RNA-based regulatory systems that integrate regulatory and sensing functions have been demonstrated, the lack of detail on miRNA structure–function relationships has limited the development of integrated control systems based on miRNA silencing. Using an elucidated relationship between Drosha processing and the single-stranded nature of the miRNA basal segments, we developed a strategy for designing ligand-responsive miRNAs. We demonstrate that ligand binding to an aptamer integrated into the miRNA basal segments inhibits Drosha processing, resulting in titratable control over gene silencing. The generality of this control strategy was shown for three aptamer–small molecule ligand pairs. The platform can be extended to the design of synthetic miRNAs clusters, cis-acting miRNAs and self-targeting miRNAs that act both in cis and trans, enabling fine-tuning of the regulatory strength and dynamics. The ability of our ligand-responsive miRNA platform to respond to user-defined inputs, undergo regulatory performance tuning and display scalable combinatorial control schemes will help advance applications in biological research and applied medicine

Updated site compilation of the Latin American Pollen Database

Flantua, Suzette G A et al.The updated inventory of the Latin American Pollen Database (LAPD) offers a wide range of new insights. This paper presents a systematic compilation of palynological research in Latin America. A comprehensive inventory of publications in peer-reviewed and grey literature shows a major expansion of studies over the last decades. The inventory includes 1379 cores and sections with paleoecological data and more than 4800 modern samples from throughout the continent. Through the years, pollen datasets extend over increasing spans of time and show improved taxonomic and temporal resolution. Currently, these datasets are from 12 modern biomes and 30 countries, covering an altitudinal range of 0 to 6300. m asl. The most densely sampled regions are the Colombian Andes, the southeast coast of Brazil, and Patagonia. Underrepresented biomes are the warm temperate mixed forest (3%), dry forests (3%), and warm temperate rainforest (1%); whereas steppe, tropical rainforest, and cool grass shrublands, such as the páramos, are generally well represented (all >. 17%). There are 126 records that span the late Pleistocene to the Last Glacial Maximum transition (21,000. cal. yr BP), and >. 20% of the records cover the Younger Dryas interval and the Pleistocene/Holocene transition. Reanalysis of numerous sites using multiproxy tools emphasize the informative value of this approach in paleoenvironmental reconstruction. We make suggestions for several pollen sites and regions to be visited again; similarly we identify some key research questions that have yet to be answered. The updated LAPD now provides the platform to support an exciting new phase of global palynological research in which multi-site data are being integrated to address current cutting-edge research questions. The LAPD compilation of sites and the literature database will be available through the Neotoma Paleoecology Database website and a new LAPD website by the end of 2015We thank the Netherlands Organization for Scientific Research (NWO, grant 2012/13248/ALW) for financial support of this project.Peer reviewe

miR-19a-3p containing exosomes improve function of ischemic myocardium upon shock wave therapy

AIMS: As many current approaches for heart regeneration exert unfavorable side-effects, the induction of endogenous repair mechanisms in ischemic heart disease is of particular interest. Recently, exosomes carrying angiogenic miRNAs have been described to improve heart function. However, it remains challenging to stimulate specific release of reparative exosomes in ischemic myocardium. In the present study, we sought to test the hypothesis that the physical stimulus of shock wave therapy (SWT) causes the release of exosomes. We aimed to substantiate the pro-angiogenic impact of the released factors, to identify the nature of their cargo, and to test their efficacy in vivo supporting regeneration and recovery after myocardial ischemia. METHODS AND RESULTS: Mechanical stimulation of ischemic muscle via SWT caused extracellular vesicle (EV) release from endothelial cells both in vitro and in vivo. Characterization of EVs via electron microscopy, nanoparticle tracking analysis and flow cytometry revealed specific exosome morphology and size with presence of exosome markers CD 9, CD81 and CD63. Exosomes exhibited angiogenic properties activating protein kinase b (Akt) and extracellular-signal regulated kinase (ERK) resulting in enhanced endothelial tube formation and proliferation. A miRNA array and transcriptome analysis via next-generation sequencing were performed to specify exosome content. miR-19a-3p was identified as responsible cargo, antimir-19a-3p antagonized angiogenic exosome effects. Exosomes and target miRNA were injected intramyocardially in mice after left anterior descending artery (LAD) ligation. Exosomes resulted in improved vascularization, decreased myocardial fibrosis and increased left ventricular ejection fraction as shown by transthoracic echocardiography. CONCLUSIONS: The mechanical stimulus of SWT causes release of angiogenic exosomes. miR-19a-3p is the vesicular cargo responsible for the observed effects. Released exosomes induce angiogenesis, decrease myocardial fibrosis and improve left ventricular function after myocardial ischemia. Exosome release via SWT could develop an innovative approach for the regeneration of ischemic myocardium

Late Holocene vegetation, fire, climate and upper forest line dynamics in the Podocarpus National Park, southeastern Ecuador

Late Holocene vegetation, fire, climate and upper forest line dynamics were studied based on detailed pollen and charcoal analyses. Two sediment cores, from the Rabadilla de Vaca mire (RVM) and the Valle Pequeo bog (VP), with an age of about 2100 and 1630 cal yrs b.p., respectively, were taken at the modern upper forest line in the Parque Nacional Podocarpus (Podocarpus National Park) in southeastern Ecuador. The two pollen records reflect relatively stable vegetation with slight changes in floral composition during the recorded period. Changes of the proportion between subparamo and paramo vegetation are related to lower and higher frequency of fires. The RVM records show that the upper forest line moved to a higher elevation between 1630 and 880 cal yrs b.p., stabilising after 310 cal yrs b.p. Human impact is suggested by a high fire frequency, mainly between 1800-1600 and 880-310 cal yrs b.p. The VP records indicate no marked changes in the upper forest line. The charcoal records suggest an increased human impact from 230 cal yrs b.p. to the present. The results indicate that high fire frequency is an important factor in reducing the expansion of subparamo vegetation and upper montane rainforest and in favouring the distribution of grass paramo. Since there is a clear correlation between fire and vegetation dynamics, it is difficult to detect how far climate change also played a significant role in upper forest line changes during the late Holocene