Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on 10^3 pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype

Fibrinogen primes the microglial NLRP3 inflammasome and propagates pro-inflammatory signaling via extracellular vesicles: Implications for blood-brain barrier dysfunction

The brain's response to acute injury is characterized by increased permeability of the blood-brain barrier (BBB) and pro-inflammatory microglia signaling, both of which have been linked to poor cognitive outcomes and neurological disease. The damaged BBB has increased leakiness, allowing serum proteins like fibrinogen into the brain, which interacts with local cells in a deleterious manner. At the same time, in response to injury, microglia demonstrate increased NLRP3 inflammasome activity and heightened release of pro-inflammatory cytokines. The relationship between increased fibrinogen uptake and microglial inflammasome signaling in the injured brain has not been well described. In this work, we investigate fibrinogen mediated NLRP3 inflammasome priming of BV-2 cells and primary adult microglia and propose a role for extracellular vesicles (EVs) as propagators of this interaction. Following exposure to fibrinogen microglia significantly upregulate transcription of IL-1β, IL-6, NLRP3 and other pro-inflammatory cytokines which was sustained by repeated fibrinogen exposure. Inhibition of fibrinogen mediated NLRP3 signaling was achieved at the transcriptional and assembly level using cannabidiol (CBD) and the NLRP3 inhibitor MCC950, respectively. EVs released following NLRP3 priming carry IL-1β, IL-18 mRNA and fibrinogen, propagate inflammatory signaling and can be detected in the circulation following BBB disruption in a preclinical stroke model. In conclusion, the interplay between fibrinogen extravasation, microglial NLRP3 signaling, and EV release can perpetuate chronic pro-inflammatory signaling and represents a novel method of inflammatory propagation

Closing the loop Approaches to monitoring the state of the Arctic Mediterranean during the International Polar Year 20072008

During the 4th International Polar Year 2007–2009 (IPY), it has become increasingly obvious that we need to prepare for a new era in the Arctic. IPY occurred during the time of the largest retreat of Arctic sea ice since satellite observations started in 1979. This minimum in September sea ice coverage was accompanied by other signs of a changing Arctic, including the unexpectedly rapid transpolar drift of the Tara schooner, a general thinning of Arctic sea ice and a double-dip minimum of the Arctic Oscillation at the end of 2009. Thanks to the lucky timing of the IPY, those recent phenomena are well documented as they have been scrutinized by the international research community, taking advantage of the dedicated observing systems that were deployed during IPY. However, understanding changes in the Arctic System likely requires monitoring over decades, not years. Many IPY projects have contributed to the pilot phase of a future, sustained, observing system for the Arctic. We now know that many of the technical challenges can be overcome. The Norwegian projects iAOOS-Norway, POLEWARD and MEOP were significant ocean monitoring/research contributions during the IPY. A large variety of techniques were used in these programs, ranging from oceanographic cruises to animal-borne platforms, autonomous gliders, helicopter surveys, surface drifters and current meter arrays. Our research approach was interdisciplinary from the outset, merging ocean dynamics, hydrography, biology, sea ice studies, as well as forecasting. The datasets are tremendously rich, and they will surely yield numerous findings in the years to come. Here, we present a status report at the end of the official period for IPY. Highlights of the research include: a quantification of the Meridional Overturning Circulation in the Nordic Seas (“the loop”) in thermal space, based on a set of up to 15-year-long series of current measurements; a detailed map of the surface circulation as well as characterization of eddy dispersion based on drifter data; transport monitoring of Atlantic Water using gliders; a view of the water mass exchanges in the Norwegian Atlantic Current from both Eulerian and Lagrangian data; an integrated physical–biological view of the ice-influenced ecosystem in the East Greenland Current, showing for instance nutrient-limited primary production as a consequence of decreasing ice cover for larger regions of the Arctic Ocean. Our sea ice studies show that the albedo of snow on ice is lower when snow cover is thinner and suggest that reductions in sea ice thickness, without changes in sea ice extent, will have a significant impact on the arctic atmosphere. We present up-to-date freshwater transport numbers for the East Greenland Current in the Fram Strait, as well as the first map of the annual cycle of freshwater layer thickness in the East Greenland Current along the east coast of Greenland, from data obtained by CTDs mounted on seals that traveled back and forth across the Nordic Seas. We have taken advantage of the real-time transmission of some of these platforms and demonstrate the use of ice-tethered profilers in validating satellite products of sea ice motion, as well as the use of Seagliders in validating ocean forecasts, and we present a sea ice drift product – significantly improved both in space and time – for use in operational ice-forecasting applications. We consider real-time acquisition of data from the ocean interior to be a vital component of a sustained Arctic Ocean Observing System, and we conclude by presenting an outline for an observing system for the European sector of the Arctic Ocean

BIOPROCESS DEVELOPMENT FOR SERINE ALKALINE PROTEASE PRODUCTION: A REVIEW

This work is the result of the convergence of the research in biochemical reaction engineering and metabolic flux analysis for serine alkaline protease (SAP) production. The genus Bacillus includes a variety of industrially important species that are known to secrete a large number of extracellular proteases and are used among many species as producer of SAP enzyme. Therefore, in the first part of the present article an overview to serine alkaline protease and regulation of its synthesis and secretion in Bacillus is presented. In the second part, a detailed review of the published information on the bioprocess medium design and bioreactor operation parameters are discussed in relation to the concentrations of the byproducts, i.e. neutral protease, amylase, amino acids, organic acids and alcohols. In the third part, papers on metabolic flux analysis for SAP are reviewed with the emphasis on SAP overproduction potential of the Bacillus licheniformis, the effect of oxygen transfer on the bioreaction-network fluxes and the need for oxygen transfer strategies. The metabolic bottlenecks and strategies for increasing the yield and selectivity of SAP fermentation process are discussed