Regularized Harmonic Surface Deformation

Harmonic surface deformation is a well-known geometric modeling method that creates plausible deformations in an interactive manner. However, this method is susceptible to artifacts, in particular close to the deformation handles. These artifacts often correlate with strong gradients of the deformation energy.In this work, we propose a novel formulation of harmonic surface deformation, which incorporates a regularization of the deformation energy. To do so, we build on and extend a recently introduced generic linear regularization approach. It can be expressed as a change of norm for the linear optimization problem, i.e., the regularization is baked into the optimization. This minimizes the implementation complexity and has only a small impact on runtime. Our results show that a moderate use of regularization suppresses many deformation artifacts common to the well-known harmonic surface deformation method, without introducing new artifacts

Pairbreaking Without Magnetic Impurities in Disordered Superconductors

We study analytically the effects of inhomogeneous pairing interactions in short coherence length superconductors, using a spatially varying Bogoliubov-deGennes model. Within the Born approximation, it reproduces all of the standard Abrikosov-Gor'kov pairbreaking and gaplessness effects, even in the absence of actual magnetic impurities. For pairing disorder on a single site, the T-matrix gives rise to bound states within the BCS gap. Our results are compared with recent scanning tunneling microscopy measurements on Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ with Zn or Ni impurities.Comment: 4 pages, 2 figures, submitted to PR

In situ visualization of large-scale turbulence simulations in Nek5000 with ParaView Catalyst

In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time. We develop an in situ adaptor for Paraview Catalyst and Nek5000, a massively parallel Fortran and C code for computational fluid dynamics. We perform a strong scalability test up to 2048 cores on KTH’s Beskow Cray XC40 supercomputer and assess in situ visualization’s impact on the Nek5000 performance. In our study case, a high-fidelity simulation of turbulent flow, we observe that in situ operations significantly limit the strong scalability of the code, reducing the relative parallel efficiency to only ≈ 21 % on 2048 cores (the relative efficiency of Nek5000 without in situ operations is ≈ 99 %). Through profiling with Arm MAP, we identified a bottleneck in the image composition step (that uses the Radix-kr algorithm) where a majority of the time is spent on MPI communication. We also identified an imbalance of in situ processing time between rank 0 and all other ranks. In our case, better scaling and load-balancing in the parallel image composition would considerably improve the performance of Nek5000 with in situ capabilities. In general, the result of this study highlights the technical challenges posed by the integration of high-performance simulation codes and data-analysis libraries and their practical use in complex cases, even when efficient algorithms already exist for a certain application scenario

Hard-boiled Ecologies: Ross Macdonald’s Environmental Crime Fiction

Although Ross Macdonald’s position in the annals of great American hardboiled crime writers is unquestioned, what often been overlooked in the study of his works are the underlying environmental preoccupations that frequently serve as the background to, or context for, crime. This context of ecological violence is forcefully manifested in two of Macdonald’s later Archer novels The Underground Man (1971) and Sleeping Beauty (1973). This essay scrutinizes the environmental imperatives of Macdonald’s work, arguing that the damage and destruction inflicted upon the environment in these two texts becomes symbiotically connected to the broader, morally fraught social milieu of the city

Consistent Approximation of Local Flow Behavior for 2D Vector Fields Using Edge Maps

Abstract not provide

Expression signatures of TP53 mutations in serous ovarian cancers

<p>Abstract</p> <p>Background</p> <p>Mutations in the <it>TP53 </it>gene are extremely common and occur very early in the progression of serous ovarian cancers. Gene expression patterns that relate to mutational status may provide insight into the etiology and biology of the disease.</p> <p>Methods</p> <p>The <it>TP53 </it>coding region was sequenced in 89 frozen serous ovarian cancers, 40 early stage (I/II) and 49 advanced stage (III/IV). Affymetrix U133A expression data was used to define gene expression patterns by mutation, type of mutation, and cancer stage.</p> <p>Results</p> <p>Missense or chain terminating (null) mutations in <it>TP53 </it>were found in 59/89 (66%) ovarian cancers. Early stage cancers had a significantly higher rate of null mutations than late stage disease (38% vs. 8%, p < 0.03). In advanced stage cases, mutations were more prevalent in short term survivors than long term survivors (81% vs. 30%, p = 0.0004). Gene expression patterns had a robust ability to predict <it>TP53 </it>status within training data. By using early versus late stage disease for out of sample predictions, the signature derived from early stage cancers could accurately (86%) predict mutation status of late stage cancers.</p> <p>Conclusions</p> <p>This represents the first attempt to define a genomic signature of <it>TP53 </it>mutation in ovarian cancer. Patterns of gene expression characteristic of <it>TP53 </it>mutation could be discerned and included several genes that are known p53 targets or have been described in the context of expression signatures of <it>TP53 </it>mutation in breast cancer.</p

Multiscale modeling of magnetospheric reconnection

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95438/1/jgra18824.pd

Identification of S-nitrosated mitochondrial proteins by S-nitrosothiol difference in gel electrophoresis (SNO-DIGE): implications for the regulation of mitochondrial function by reversible S-nitrosation

The S-nitrosation of mitochondrial proteins as a consequence of NO metabolism is of physiological and pathological significance. We previously developed a MitoSNO (mitochondria-targeted S-nitrosothiol) that selectively S-nitrosates mitochondrial proteins. To identify these S-nitrosated proteins, here we have developed a selective proteomic methodology, SNO-DIGE (S-nitrosothiol difference in gel electrophoresis). Protein thiols in control and MitoSNO-treated samples were blocked, then incubated with copper(II) and ascorbate to selectively reduce S-nitrosothiols. The samples were then treated with thiol-reactive Cy3 (indocarbocyanine) or Cy5 (indodicarbocyanine) fluorescent tags, mixed together and individual protein spots were resolved by 2D (two-dimensional) gel electrophoresis. Fluorescent scanning of these gels revealed S-nitrosated proteins by an increase in Cy5 red fluorescence, allowing for their identification by MS. Parallel analysis by Redox-DIGE enabled us to distinguish S-nitrosated thiol proteins from those which became oxidized due to NO metabolism. We identified 13 S-nitrosated mitochondrial proteins, and a further four that were oxidized, probably due to evanescent S-nitrosation relaxing to a reversible thiol modification. We investigated the consequences of S-nitrosation for three of the enzymes identified using SNO-DIGE (aconitase, mitochondrial aldehyde dehydrogenase and α-ketoglutarate dehydrogenase) and found that their activity was selectively and reversibly inhibited by S-nitrosation. We conclude that the reversible regulation of enzyme activity by S-nitrosation modifies enzymes central to mitochondrial metabolism, whereas identification and functional characterization of these novel targets provides mechanistic insight into the potential physiological and pathological roles played by this modification. More generally, the development of SNO-DIGE facilitates robust investigation of protein S-nitrosation across the proteome

Serum proteome analysis for profiling protein markers associated with carcinogenesis and lymph node metastasis in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC), one of the most common cancers in population with Chinese or Asian progeny, poses a serious health problem for southern China. It is unfortunate that most NPC victims have had lymph node metastasis (LNM) when first diagnosed. We believe that the 2D based serum proteome analysis can be useful in discovering new biomarkers that may aid in the diagnosis and therapy of NPC patients. To filter the tumor specific antigen markers of NPC, sera from 42 healthy volunteers, 27 non-LNM NPC patients and 37 LNM NPC patients were selected for screening study using 2D combined with MS. Pretreatment strategy, including sonication, albumin and immunoglobulin G (IgG) depletion, was adopted for screening differentially expressed proteins of low abundance in serum. By 2D image analysis and MALDI-TOF-MS identification, twenty-three protein spots were differentially expressed. Three of them were further validated in the sera using enzyme-linked immunosorbent assay (ELISA). Our research demonstrates that HSP70, sICAM-1 and SAA, confirmed with ELISA at sera and immunohistochemistry, are potential NPC metastasis-specific serum biomarkers which may be of great underlying significance in clinical detection and management of NPC