Heavy Quarkonia Production in p+p Collisions from the PHENIX Experiment

Quarkonia provide a sensitive probe of the properties of the hot dense medium created in high energy heavy ion collisions. Hard scattering processes result in the production of heavy quark pairs that interact with the collision medium during hadronization. These in-medium interactions convey information about the fundamental properties of the medium itself and can be used to examine the modification of the QCD confining potential in the collision environment. Baseline measurements from p+p and d+Au collision systems are used to distinguish cold nuclear matter effects while measurements from heavy ion collision systems are used to quantify in-medium effects. The PHENIX experiment has the capability of detecting heavy quarkonia at $1.2<|\eta|<2.2$ via the $\mu^+\mu^-$ decay channel and at $|\eta|<0.35$ via the $e^+e^-$ decay channel. Recent runs have resulted in the collection of high statistics p+p data sets that provide an essential baseline reference for heavy ion measurements and allow for further critical evaluation of heavy quarkonia production mechanisms. The latest PHENIX results for the production of the $J/\psi$ in p+p collisions are presented and future prospects for $\psi'$, $\chi_{c}$ and $\Upsilon$ measurements are discussed.Comment: 4 pages, 2 figures, Proceedings for Quark Matter 200

Molecular Mechanisms of White Spot Syndrome Virus Infection and Perspectives on Treatments.

Published onlineJournal ArticleReviewSince its emergence in the 1990s, White Spot Disease (WSD) has had major economic and societal impact in the crustacean aquaculture sector. Over the years shrimp farming alone has experienced billion dollar losses through WSD. The disease is caused by the White Spot Syndrome Virus (WSSV), a large dsDNA virus and the only member of the Nimaviridae family. Susceptibility to WSSV in a wide range of crustacean hosts makes it a major risk factor in the translocation of live animals and in commodity products. Currently there are no effective treatments for this disease. Understanding the molecular basis of disease processes has contributed significantly to the treatment of many human and animal pathogens, and with a similar aim considerable efforts have been directed towards understanding host-pathogen molecular interactions for WSD. Work on the molecular mechanisms of pathogenesis in aquatic crustaceans has been restricted by a lack of sequenced and annotated genomes for host species. Nevertheless, some of the key host-pathogen interactions have been established: between viral envelope proteins and host cell receptors at initiation of infection, involvement of various immune system pathways in response to WSSV, and the roles of various host and virus miRNAs in mitigation or progression of disease. Despite these advances, many fundamental knowledge gaps remain; for example, the roles of the majority of WSSV proteins are still unknown. In this review we assess current knowledge of how WSSV infects and replicates in its host, and critique strategies for WSD treatment.This work was funded by the Open Innovation Platform at the University of Exeter (Open Innovation Fund Initiative PHSW029) and by the Centre for Environment, Fisheries and Aquaculture Science (Cefas) (under seedcorn project DP318 to GDS) under the Strategic Alliance partnership between the University of Exeter and Cefas

De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways.

Journal ArticleCopyright © 2015 Verbruggen et al.BACKGROUND: The European shore crab, Carcinus maenas, is used widely in biomonitoring, ecotoxicology and for studies into host-pathogen interactions. It is also an important invasive species in numerous global locations. However, the genomic resources for this organism are still sparse, limiting research progress in these fields. To address this resource shortfall we produced a C. maenas transcriptome, enabled by the progress in next-generation sequencing technologies, and applied this to assemble information on the innate immune system in this species. RESULTS: We isolated and pooled RNA for twelve different tissues and organs from C. maenas individuals and sequenced the RNA using next generation sequencing on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome was generated encompassing 212,427 transcripts (153,699 loci). The transcripts were filtered, annotated and characterised using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including NCBI, Gene Ontology and KEGG). There were differential patterns of expression for between 1,223 and 2,741 transcripts across tissues and organs with over-represented Gene Ontology terms relating to their specific function. Based on sequence homology to immune system components in other organisms, we show both the presence of transcripts for a series of known pathogen recognition receptors and response proteins that form part of the innate immune system, and transcripts representing the RNAi, Toll-like receptor signalling, IMD and JAK/STAT pathways. CONCLUSIONS: We have produced an assembled transcriptome for C. maenas that provides a significant molecular resource for wide ranging studies in this species. Analysis of the transcriptome has revealed the presence of a series of known targets and functional pathways that form part of their innate immune system and illustrate tissue specific differences in their expression patterns.Cefas Seedcorn Contract #DP318University of Exeter’s Open Innovation PlatformWellcome Trust Institutional Strategic Support Awar

Bioavailability and kidney responses to Diclofenac in the fathead minnow (Pimephales promelas)

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Diclofenac is one of the most widely prescribed nonsteroidal anti-inflammatory drugs worldwide. It is frequently detected in surface waters; however, whether this pharmaceutical poses a risk to aquatic organisms is debated. Here we quantified the uptake of diclofenac by the fathead minnow (Pimephales promelas) following aqueous exposure (0.2-25.0 μg L(-1)) for 21 days, and evaluated the tissue and biomolecular responses in the kidney. Diclofenac accumulated in a concentration- and time-dependent manner in the plasma of exposed fish. The highest plasma concentration observed (for fish exposed to 25 μg L(-1) diclofenac) was within the therapeutic range for humans. There was a strong positive correlation between exposure concentration and the number of developing nephrons observed in the posterior kidney. Diclofenac was not found to modulate the expression of genes in the kidney associated with its primary mode of action in mammals (prostaglandin-endoperoxide synthases) but modulated genes associated with kidney repair and regeneration. There were no significant adverse effects following 21 days exposure to concentrations typical of surface waters. The combination of diclofenac's uptake potential, effects on kidney nephrons and relatively small safety margin for some surface waters may warrant a longer term chronic health effects analysis for diclofenac in fish.This work was funded by Knowledge Transfer Partnership (KTP): Use of ‘omic’ technologies in the environmental risk assessment of pharmaceuticals (KTP007650) and AstraZeneca’s Safety, Health and Environment (SHE) Research Programme. We thank Lina Gunnarsson, Matt Winter and James Cresswell (Exeter University), and former members of the Brixham Environmental Laboratory for their advice and assistance. Authors declare no competing financial interest

Experience with Community‐Based Amphotericin B Infusion Therapy

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90368/1/phco.25.5.690.63591.pd

The limitations (and potential) of non-parametric morphology statistics for post-merger identification

Non-parametric morphology statistics have been used for decades to classify galaxies into morphological types and identify mergers in an automated way. In this work, we assess how reliably we can identify galaxy post-mergers with non-parametric morphology statistics. Low-redshift (z<0.2), recent (t_post-merger 100 kpc) post-merger galaxies are drawn from the IllustrisTNG100-1 cosmological simulation. Synthetic r-band images of the mergers are generated with SKIRT9 and degraded to various image qualities, adding observational effects such as sky noise and atmospheric blurring. We find that even in perfect quality imaging, the individual non-parametric morphology statistics fail to recover more than 55% of the post-mergers, and that this number decreases precipitously with worsening image qualities. The realistic distributions of galaxy properties in IllustrisTNG allow us to show that merger samples assembled using individual morphology statistics are biased towards low mass, high gas fraction, and high mass ratio. However, combining all of the morphology statistics together using either a linear discriminant analysis or random forest algorithm increases the completeness and purity of the identified merger samples and mitigates bias with various galaxy properties. For example, we show that in imaging similar to that of the 10-year depth of the Legacy Survey of Space and Time (LSST), a random forest can identify 89% of mergers with a false positive rate of 17%. Finally, we conduct a detailed study of the effect of viewing angle on merger observability and find that there may be an upper limit to merger recovery due to the orientation of merger features with respect to the observer.Comment: 32 pages, 21 figures Accepted for publication by MNRA

Galaxy mergers can rapidly shut down star formation

Galaxy mergers trigger both star formation and accretion onto the central supermassive black hole. As a result of subsequent energetic feedback processes, it has long been proposed that star formation may be promptly extinguished in galaxy merger remnants. However, this prediction of widespread, rapid quenching in late stage mergers has been recently called into question with modern simulations and has never been tested observationally. Here we perform the first empirical assessment of the long-predicted end phase in the merger sequence. Based on a sample of ~500 post-mergers identified from the Ultraviolet Near Infrared Optical Northern Survey (UNIONS), we show that the frequency of post-merger galaxies that have rapidly shutdown their star formation following a previous starburst is 30-60 times higher than expected from a control sample of non-merging galaxies. No such excess is found in a sample of close galaxy pairs, demonstrating that mergers can indeed lead to a rapid halt to star formation, but that this process only manifests after coalescence.PostprintPeer reviewe

Transverse Spin at PHENIX: Results and Prospects

The Relativistic Heavy Ion Collider (RHIC), as the world's first and only polarized proton collider, offers a unique environment in which to study the spin structure of the proton. In order to study the proton's transverse spin structure, the PHENIX experiment at RHIC took data with transversely polarized beams in 2001-02 and 2005, and it has plans for further running with transverse polarization in 2006 and beyond. Results from early running as well as prospective measurements for the future will be discussed.Comment: 6 pages, 2 figures, presented at Transversity 2005, Como, Ital