Observable consequences of event-by-event fluctuations of HBT radii

We explore the effects of event-by-event fluctuations of Hanbury Brown-Twiss (HBT) radii and show how they can be observed experimentally. The relation of measured HBT radii extracted from ensemble-averaged correlation functions to the mean of their event-by-event probability distribution is clarified. We propose a method to experimentally determine the mean and variance of this distribution and test it on an ensemble of fluctuating events generated with the viscous hydrodynamic code VISH2+1. Using the same code, the sensitivity of the mean and variance of the HBT radii to the specific QGP shear viscosity $\eta/s$ is studied. We report sensitivity of the mean pion HBT radii and their variances to the temperature dependence of $\eta/s$ near the quark-hadron transition at a level similar (10-20%) to that which was previously observed for elliptic and quadrangular flow of charged hadrons [1].Comment: Proceedings for Quark Matter 2015 in Kobe, Japa

A deep Chandra observation of Abell 4059: a new face to radio-mode AGN feedback?

A deep Chandra observation of the cooling core cluster Abell 4059 (A4059) is presented. Previous studies have found two X-ray cavities in the central regions of A4059 together with a ridge of X-ray emission 20kpc south-west of the cluster center. These features are clearly related to the radio galaxy PKS2354-35 which resides in the cD galaxy. Our new data confirm these previous findings and strengthen previous suggestions that the south-western ridge is colder and denser than, but in approximate pressure equilibrium with, the surrounding ICM atmosphere. In addition, we find evidence for a weak shock that wraps around the north and east sides of the cavity structure. Our data allow us to map the 2-dimensional distribution of metals in the ICM of A4059 for the first time. We find that the SW ridge possesses an anomalously high (super-solar) metalicity. The unusual morphology, temperature structure and metal distribution all point to significant asymmetry in the ICM atmosphere prior to the onset of radio-galaxy activity. Motivated by the very high metalicity of the SW ridge, we hypothesize that the ICM asymmetry was caused by the extremely rapid stripping of metal enriched gas from a starburst galaxy that plunged through the core of A4059. Furthermore, we suggest that the onset of powerful radio-galaxy activity in the cD galaxy may have been initiated by this starburst/stripping event, either via the tidal-shocking of cold gas native to the cD galaxy, or the accretion of cold gas that had been stripped from the starburst galaxy.Comment: Accepted for publication in the Astrophysical Journal. 12 pages, 11 figures. A version of this paper including full resolution figures can be found at http://www.astro.umd.edu/~chris/publications/papers/a4059_2008.pd

Improving the economic performance of anaerobic digestion by integrating lactic acid recovery into two-stage food waste digestion

The global production of food waste (FW) is of significant economic and environmental concern, having been estimated to produce 8% of globally produced anthropogenic greenhouse gas emissions and result in the loss of nearly USD1 trillion each year. Consequently, the correct disposal and recovery of value from FWs is a global challenge and responsibility. Anaerobic digestion (AD) is a capable technology which can recycle FW to produce renewable energy and recover nutrients. However high capital, operational, and management costs and low value of biogas and digestate lead to questionable economic benefit. As a result, the AD technology heavily relies on subsidies and policy incentives for feasibility. Integration of lactic acid (LA) production technologies into AD could convert the low-value process into a high-value LA-AD biorefinery, reducing reliance on government support. This study aims to address the above by exploring the integration of LA production to AD within the FW context. This involved detailed investigations into the production of LA from FWs, including within the commercial FW context, and integration of FW fermentation for LA into existing AD facilities. Accordingly, following optimisation of LA fermentation, and exploring the feasibility of recovering LA along with its impact on downstream AD, multiple integration scenarios were proposed detailing the potential economic benefits from integrating LA production into FW AD. The assessment of LA production within the FW context was first explored. For this, LA production within a pre-fermenter at a commercial two-stage FW AD facility was monitored, exploring the impact of environmental conditions, feedstock composition, and operational procedures on LA production performance and stability. Results showed standard operation of the pre-fermenter, favoured the formation of LA leading to LA being the dominant organic acid produced from fermentation. Furthermore, standard operation of the AD facility led to the selective dominance of Lactobacillus, a bacterium commonly associated with LA production. While LA production fluctuated over the monitoring period, the LA concentration was surprisingly stable, especially considering the variation in process variables (pH, temperature, retention time, feed rate, and feed composition). Even so, it was outlined that there would be significant opportunity to improve LA production performance, and consequently, economic performance by targeted process optimisation and control. Optimisation of LA fermentation showed the commercially adapted inoculum was capable of high LA yields and selectivities. In addition, the results showed optimal conditions promoted the growth of Lactobacillus, while alternative flanking microorganisms were inhibited. Moreover, optimisation effectively eliminated the conversion of LA to butyrate, allowing the sustained accumulation of LA. Further study of the commercial inoculum showed LA production could be effectively enhanced by supplementing FW with a simple carbohydrate (sucrose) and implementing partial digestate recirculation. While digestate enhanced LA production, it also increased microbial diversity which promoted the production of alternate organic acids. However, the effects of digestate could be effectively controlled through sucrose addition, which promoted the growth of Lactobacillus and inhibited the growth of the flanking community. Following optimisation of fermentation, the feasibility of recovering LA from complex fermentation media and its impact on downstream AD performance was explored. While real commercial broth reduced LA uptake, compared to pure LA solutions, LA was effectively recovered from highly complex fermentation media. Moreover, LA recovery only led to a minor reduction in methane production following the AD of the solid and liquid extraction residues. In this respect, LA production could outweigh the loss in methane production in terms of relative value, indicating the LA-AD biorefinery concept could be commercially attractive. A technoeconomic assessment indeed showed the benefit of integrating LA production into two-stage FW AD, yielding a highly profitable scenario. Furthermore, while integration scenarios were most profitable, Greenfield LA-AD biorefinery scenarios showed significantly higher profitability estimates compared to sole FW AD. Finally, the insight achieved into different aspects of the LA-AD biorefinery led to a series of recommendations for future research in the context of the FW biorefinery concept

Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization.

Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using genome-wide global run-on sequencing (GRO-Seq). We demonstrate that half of VEGF-A-regulated gene promoters are characterized by a transcriptionally competent paused RNA polymerase II (Pol II). We show that transition into productive elongation is a major mechanism of gene activation of virtually all VEGF-regulated genes, whereas only ∼40% of the genes are induced at the level of initiation. In addition, we report a comprehensive chromatin interaction map generated in HUVECs using tethered conformation capture (TCC) and characterize chromatin interactions in relation to transcriptional activity. We demonstrate that sites of active transcription are more likely to engage in chromatin looping and cell type-specific transcriptional activity reflects the boundaries of chromatin interactions. Furthermore, we identify large chromatin compartments with a tendency to be coordinately transcribed upon VEGF-A stimulation. We provide evidence that these compartments are enriched for clusters of regulatory regions such as super-enhancers and for disease-associated single nucleotide polymorphisms (SNPs). Collectively, these findings provide new insights into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells

Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages.

Genome-wide investigations of host-pathogen interactions are often limited by analyses of mixed populations of infected and uninfected cells, which lower sensitivity and accuracy. To overcome these obstacles and identify key mechanisms by which Zika virus (ZIKV) manipulates host responses, we developed a system that enables simultaneous characterization of genome-wide transcriptional and epigenetic changes in ZIKV-infected and neighboring uninfected primary human macrophages. We demonstrate that transcriptional responses in ZIKV-infected macrophages differed radically from those in uninfected neighbors and that studying the cell population as a whole produces misleading results. Notably, the uninfected population of macrophages exhibits the most rapid and extensive changes in gene expression, related to type I IFN signaling. In contrast, infected macrophages exhibit a delayed and attenuated transcriptional response distinguished by preferential expression of IFNB1 at late time points. Biochemical and genomic studies of infected macrophages indicate that ZIKV infection causes both a targeted defect in the type I IFN response due to degradation of STAT2 and reduces RNA polymerase II protein levels and DNA occupancy, particularly at genes required for macrophage identity. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected macrophages thereby reveals the coincident evolution of dominant proviral or antiviral mechanisms, respectively, that determine the outcome of ZIKV exposure