High-Energy Aspects of Solar Flares: Overview of the Volume

In this introductory chapter, we provide a brief summary of the successes and remaining challenges in understanding the solar flare phenomenon and its attendant implications for particle acceleration mechanisms in astrophysical plasmas. We also provide a brief overview of the contents of the other chapters in this volume, with particular reference to the well-observed flare of 2002 July 23Comment: This is the introductory article for a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

The computational fluid dynamics modelling of the autorotation of square, flat plates

This paper examines the use of a coupled Computational Fluid Dynamics (CFD) – Rigid Body Dynamics (RBD) model to study the fixed-axis autorotation of a square flat plate. The calibration of the model against existing wind tunnel data is described. During the calibration, the CFD models were able to identify complex period autoration rates, which were attributable to a mass eccentricity in the experimental plate. The predicted flow fields around the autorotating plates are found to be consistent with existing observations. In addition, the pressure coefficients from the wind tunnel and computational work were found to be in good agreement. By comparing these pressure distributions and the vortex shedding patterns at various stages through an autorotation cycle, it was possible to gain important insights into the flow structures that evolve around the plate. The CFD model is also compared against existing correlation functions that relate the mean tip speed ratio of the plate to the aspect ratio, thickness ratio and mass moment of inertia of the plate. Agreement is found to be good for aspect ratios of 1, but poor away from this value. However, other aspects of the numerical modelling are consistent with the correlations

Imaging Spectroscopy of a White-Light Solar Flare

We report observations of a white-light solar flare (SOL2010-06-12T00:57, M2.0) observed by the Helioseismic Magnetic Imager (HMI) on the Solar Dynamics Observatory (SDO) and the Reuven Ramaty High-Energy Solar Spectroscopic Imager (RHESSI). The HMI data give us the first space-based high-resolution imaging spectroscopy of a white-light flare, including continuum, Doppler, and magnetic signatures for the photospheric FeI line at 6173.34{\AA} and its neighboring continuum. In the impulsive phase of the flare, a bright white-light kernel appears in each of the two magnetic footpoints. When the flare occurred, the spectral coverage of the HMI filtergrams (six equidistant samples spanning \pm172m{\AA} around nominal line center) encompassed the line core and the blue continuum sufficiently far from the core to eliminate significant Doppler crosstalk in the latter, which is otherwise a possibility for the extreme conditions in a white-light flare. RHESSI obtained complete hard X-ray and \Upsilon-ray spectra (this was the first \Upsilon-ray flare of Cycle 24). The FeI line appears to be shifted to the blue during the flare but does not go into emission; the contrast is nearly constant across the line profile. We did not detect a seismic wave from this event. The HMI data suggest stepwise changes of the line-of-sight magnetic field in the white-light footpoints.Comment: 14 pages, 7 figures, Accepted by Solar Physic

Phase fluctuations, dissipation and superfluid stiffness in d-wave superconductors

We study the effect of dissipation on quantum phase fluctuations in d-wave superconductors. Dissipation, arising from a nonzero low frequency optical conductivity which has been measured in experiments below $T_c$, has two effects: (1) a reduction of zero point phase fluctuations, and (2) a reduction of the temperature at which one crosses over to classical thermal fluctuations. For parameter values relevant to the cuprates, we show that the crossover temperature is still too large for classical phase fluctuations to play a significant role at low temperature. Quasiparticles are thus crucial in determining the linear temperature dependence of the in-plane superfluid stiffness. Thermal phase fluctuations become important at higher temperatures and play a role near $T_c$.Comment: Presentation improved, new references added (10 latex pages, 3 eps figures). submitted to PR

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Integrated genomic characterization of pancreatic ductal adenocarcinoma

We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations. Protein profiling identified a favorable prognosis subset with low epithelial-mesenchymal transition and high MTOR pathway scores. Associations of non-coding RNAs with tumor-specific mRNA subtypes were also identified. Our integrated multi-platform analysis reveals a complex molecular landscape of PDAC and provides a roadmap for precision medicine

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Influences of non-singular stresses on plane-stress near-tip fields for pressure-sensitive materials and applications to transformation toughened ceramics

In this paper, we investigate the effects of the non-singular stress ( T stress) on the mode I near-tip fields for elastic perfectly plastic pressure-sensitive materials under plane-stress and small-scale yielding conditions. The T stress is the normal stress parallel to the crack faces. The yield criterion for pressure-sensitive materials is described by a linear combination of the effective stress and the hydrostatic stress. Plastic dilatancy is introduced by the normality flow rule. The results of our finite element computations based on a two-parameter boundary layer formulation show that the total angular span of the plastic sectors of the near-tip fields increases with increasing T stress for materials with moderately large pressure sensitivity. The T stress also has significant effects on the sizes and shapes of the plastic zones. The height of the plastic zone increases substantially as the T stress increases, especially for materials with large pressure sensitivity. When the plastic strains are considered to be finite as for transformation toughened ceramics, the results of our finite element computations indicate that the phase transformation zones for strong transformation ceramics with large pressure sensitivity can be approximated by those for elastic-plastic materials with no limit on plastic strains. When the T stress and the stress intensity factor K are prescribed in the two-parameter boundary layer formulation to simulate the crack-tip constraint condition for a single-edge notch bend specimen of zirconia ceramics, our finite element computation shows a spear shape of the phase transformation zone which agrees well with the corresponding experimental observation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42782/1/10704_2004_Article_BF00018779.pd