Serendipity Shape Function for Hybrid Fluid/Kinetic-PIC Simulations

The Sun in our solar system and stars are capable of generating enormous amounts of energy. The process by which these gaseous, celestial bodies are able to produce such large amounts of energy is called thermonuclear fusion. Fusion happens when particles collide with one another at energy levels high enough to overcome the Coulomb force and then release vast amounts of energy. Plasma, the fourth state of matter, is the natural state of stars. Plasma is an ionized gas that consists of negatively and positively charged particles. Stars, which have immense mass, can confine the plasma through their gravity to sustain the fusion process. Laboratory plasma cannot be confined by gravity. Magnetic fields can be used instead. For the past 70 years, scientists and engineers have been working on harnessing energy from magnetized thermonuclear fusion. Current research contributes to creating a device capable of supporting fusion reactions and producing a clean sustainable energy source. Sustaining a burning or ignited plasma through fusion reactions is not an easy task. These complex systems can result in many instabilities that limit plasma temperatures and densities and prevent significant thermonuclear fusion from taking place. An important piece of the physics puzzle that either stabilizes or destabilizes the plasma is the interaction of energetic particles with the bulk plasma. This is called the wave-particle interaction or energetic particle interaction with magnetohydrodynamic (MHD) modes. Another example of this would be the solar wind from the sun (energetic particles) interacting with Earth’s magnetosphere (bulk plasma). This thesis focuses on an approach to more accurately and efficiently resolve the energetic particle motions using a computer code. This thesis will also compare two very different approaches to wave-plasma interaction problem by looking at the grow-rate of an instability that has been used to benchmark several computer codes used by the magnetic fusion energy community

Universal IMF vs dark halo response in early-type galaxies: breaking the degeneracy with the fundamental plane

We use the relations between aperture stellar velocity dispersion (\sigma_ap), stellar mass (M_sps), and galaxy size (R_e) for a sample of \sim 150,000 early-type galaxies from SDSS/DR7 to place constraints on the stellar initial mass function (IMF) and dark halo response to galaxy formation. We build LCDM based mass models that reproduce, by construction, the relations between galaxy size, light concentration and stellar mass, and use the spherical Jeans equations to predict \sigma_ap. Given our model assumptions (including those in the stellar population synthesis models), we find that reproducing the median \sigma_ap vs M_sps relation is not possible with {\it both} a universal IMF and a universal dark halo response. Significant departures from a universal IMF and/or dark halo response are required, but there is a degeneracy between these two solutions. We show that this degeneracy can be broken using the strength of the correlation between residuals of the velocity-mass (\Delta log \sigma_ap) and size-mass (\Delta log R_e) relations. The slope of this correlation, d_vr \equiv \Delta log \sigma_ap/\Delta log R_e, varies systematically with galaxy mass from d_vr \simeq -0.45 at M_sps \sim 10^{10}M_sun, to d_vr \simeq -0.15 at M_sps \sim 10^{11.6} M_sun. The virial fundamental plane (FP) has d_vr=-1/2, and thus we find the tilt of the observed FP is mass dependent. Reproducing this tilt requires {\it both} a non-universal IMF and a non-universal halo response. Our best model has mass-follows-light at low masses (Msps < 10^{11.2}M_sun) and unmodified NFW haloes at M_sps \sim 10^{11.5} M_sun. The stellar masses imply a mass dependent IMF which is "lighter" than Salpeter at low masses and "heavier" than Salpeter at high masses.Comment: 19 pages, 16 figures, accepted to MNRAS. More extensive discussion, 4 new figures, conclusions unchange

Solution conformations of early intermediates in Mos1 transposition

DNA transposases facilitate genome rearrangements by moving DNA transposons around and between genomes by a cut-and-paste mechanism. DNA transposition proceeds in an ordered series of nucleoprotein complexes that coordinate pairing and cleavage of the transposon ends and integration of the cleaved ends at a new genomic site. Transposition is initiated by transposase recognition of the inverted repeat sequences marking each transposon end. Using a combination of solution scattering and biochemical techniques, we have determined the solution conformations and stoichiometries of DNA-free Mos1 transposase and of the transposase bound to a single transposon end. We show that Mos1 transposase is an elongated homodimer in the absence of DNA and that the N-terminal 55 residues, containing the first helix-turn-helix motif, are required for dimerization. This arrangement is remarkably different from the compact, crossed architecture of the dimer in the Mos1 paired-end complex (PEC). The transposase remains elongated when bound to a single-transposon end in a pre-cleavage complex, and the DNA is bound predominantly to one transposase monomer. We propose that a conformational change in the single-end complex, involving rotation of one half of the transposase along with binding of a second transposon end, could facilitate PEC assembly

OMIP contribution to CMIP6: experimental and diagnostic protocol for the physical component of the Ocean Model Intercomparison Project

The Ocean Model Intercomparison Project (OMIP) is an endorsed project in the Coupled Model Intercomparison Project Phase 6 (CMIP6). OMIP addresses CMIP6 science questions, investigating the origins and consequences of systematic model biases. It does so by providing a framework for evaluating (including assessment of systematic biases), understanding, and improving ocean, sea-ice, tracer, and biogeochemical components of climate and earth system models contributing to CMIP6. Among the WCRP Grand Challenges in climate science (GCs), OMIP primarily contributes to the regional sea level change and near-term (climate/decadal) prediction GCs. OMIP provides (a) an experimental protocol for global ocean/sea-ice models run with a prescribed atmospheric forcing; and (b) a protocol for ocean diagnostics to be saved as part of CMIP6. We focus here on the physical component of OMIP, with a companion paper (Orr et al., 2016) detailing methods for the inert chemistry and interactive biogeochemistry. The physical portion of the OMIP experimental protocol follows the interannual Coordinated Ocean-ice Reference Experiments (CORE-II). Since 2009, CORE-I (Normal Year Forcing) and CORE-II (Interannual Forcing) have become the standard methods to evaluate global ocean/sea-ice simulations and to examine mechanisms for forced ocean climate variability. The OMIP diagnostic protocol is relevant for any ocean model component of CMIP6, including the DECK (Diagnostic, Evaluation and Characterization of Klima experiments), historical simulations, FAFMIP (Flux Anomaly Forced MIP), C4MIP (Coupled Carbon Cycle Climate MIP), DAMIP (Detection and Attribution MIP), DCPP (Decadal Climate Prediction Project), ScenarioMIP, HighResMIP (High Resolution MIP), as well as the ocean/sea-ice OMIP simulations

A Transcription Factor Map as Revealed by a Genome-Wide Gene Expression Analysis of Whole-Blood mRNA Transcriptome in Multiple Sclerosis

Background: Several lines of evidence suggest that transcription factors are involved in the pathogenesis of Multiple Sclerosis (MS) but complete mapping of the whole network has been elusive. One of the reasons is that there are several clinical subtypes of MS and transcription factors that may be involved in one subtype may not be in others. We investigate the possibility that this network could be mapped using microarray technologies and contemporary bioinformatics methods on a dataset derived from whole blood in 99 untreated MS patients (36 Relapse Remitting MS, 43 Primary Progressive MS, and 20 Secondary Progressive MS) and 45 age-matched healthy controls. Methodology/Principal Findings: We have used two different analytical methodologies: a non-standard differential expression analysis and a differential co-expression analysis, which have converged on a significant number of regulatory motifs that are statistically overrepresented in genes that are either differentially expressed (or differentially co-expressed) in cases and controls (e.g., V$KROX_Q6, p-value ,3.31E-6; V$CREBP1_Q2, p-value ,9.93E-6, V$YY1_02, p-value ,1.65E-5). Conclusions/Significance: Our analysis uncovered a network of transcription factors that potentially dysregulate several genes in MS or one or more of its disease subtypes. The most significant transcription factor motifs were for the Early Growth Response EGR/KROX family, ATF2, YY1 (Yin and Yang 1), E2F-1/DP-1 and E2F-4/DP-2 heterodimers, SOX5, and CREB and ATF families. These transcription factors are involved in early T-lymphocyte specification and commitment as well as in oligodendrocyte dedifferentiation and development, both pathways that have significant biological plausibility in MS causation

Multiple Sclerosis Susceptibility-Associated SNPs Do Not Influence Disease Severity Measures in a Cohort of Australian MS Patients

Recent association studies in multiple sclerosis (MS) have identified and replicated several single nucleotide polymorphism (SNP) susceptibility loci including CLEC16A, IL2RA, IL7R, RPL5, CD58, CD40 and chromosome 12q13–14 in addition to the well established allele HLA-DR15. There is potential that these genetic susceptibility factors could also modulate MS disease severity, as demonstrated previously for the MS risk allele HLA-DR15. We investigated this hypothesis in a cohort of 1006 well characterised MS patients from South-Eastern Australia. We tested the MS-associated SNPs for association with five measures of disease severity incorporating disability, age of onset, cognition and brain atrophy. We observed trends towards association between the RPL5 risk SNP and time between first demyelinating event and relapse, and between the CD40 risk SNP and symbol digit test score. No associations were significant after correction for multiple testing. We found no evidence for the hypothesis that these new MS disease risk-associated SNPs influence disease severity

Medulloblastoma Exome Sequencing Uncovers Subtype-Specific Somatic Mutations

Medulloblastomas are the most common malignant brain tumors in children1. Identifying and understanding the genetic events that drive these tumors is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma based on transcriptional and copy number profiles2–5. Here, we utilized whole exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas exhibit low mutation rates consistent with other pediatric tumors, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR, and LDB1, novel findings in medulloblastoma. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant but not wild type beta-catenin. Together, our study reveals the alteration of Wnt, Hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic beta-catenin signaling in medulloblastoma

Emerging IT risks: insights from German banking

How do German banks manage the emerging risks stemming from IT innovations such as cyber risk? With a focus on process, roles and responsibilities, field data from ten banks participating in the 2014 ECB stress test were collected by interviewing IT managers, risk managers and external experts. Current procedures for handling emerging risks in German banks were identified from the interviews and analysed, guided by the extant literature. A clear gap was found between enterprise risk management (ERM) as a general approach to risks threatening firms’ objectives and ERM’s neglect of emerging risks, such as those associated with IT innovations. The findings suggest that ERM should be extended towards the collection and sharing of knowledge to allow for an initial understanding and description of emerging risks, as opposed to the traditional ERM approach involving estimates of impact and probability. For example, as cyber risks emerge from an IT innovation, the focus may need to switch towards reducing uncertainty through knowledge acquisition. Since individual managers seldom possess all relevant knowledge of an IT innovation, various stakeholders may need to be involved to exploit their expertise

Onset symptoms, tobacco smoking, and progressive-onset phenotype are associated with a delayed onset of multiple sclerosis, and marijuana use with an earlier onset

Background: Age at symptom onset (ASO) is a prognostic factor that could affect the accrual of disability in multiple sclerosis (MS) patients. Some factors are known to influence the risk of multiple sclerosis (MS), but their influence on the ASO is less well-investigated. Objective: Examine the associations between known or emerging MS risk factors and ASO. Methods: This was a multicenter study, incident cases (n = 279) with first clinical diagnosis of demyelinating event aged 18–59 years recruited at four Australian centres (latitudes 27°-43°S), from 1 November 2003 to 31 December 2006. Environmental/behavioral variables and initial symptoms were recorded at baseline interview. Linear regression was used to assess the association between risk factors and ASO. Results: Five factors were significantly associated with ASO: a history of tobacco smoking was associated with 3.05-years later ASO (p = 0.002); a history of marijuana use was associated with 6.03-years earlier ASO (p < 0.001); progressive-onset cases had 5.61-years later ASO (p = 0.001); an initial presentation of bowel & bladder and cerebral dysfunctional were associated with 3.39 (p = 0.017) and 4.37-years (p = 0.006) later ASO, respectively. Other factors, including sex, offspring number, latitude of study site, history of infectious mononucleosis, HLA-DR15 & HLA-A2 genotype, 25(OH)D levels, and ultraviolet radiation exposure were not associated with ASO. Including all five significant variables into one model explained 12% of the total variance in ASO. Conclusion: We found a novel association between a history of tobacco smoking and later onset, whereas marijuana use was associated with earlier onset. Behavioral factors seem important drivers of MS onset timing although much of the variance remains unexplained.Chunrong Tao, Steve Simpson Jr., Bruce V. Taylor, Leigh Blizzard, Robyn M. Lucas, Anne-Louise Ponsonby, Simon Broadley, Keith Dear, AusLong, Ausimmune Investigators Group and Ingrid van der Me