A Review of X-Ray Absorption Near-Edge Spectroscopic Studies of Pyrochlore-Type Oxides Proposed for Nuclear Materials Applications

Pyrochlore-type oxides (A2B2O7) have received considerable attention for nuclear waste sequestration applications. It is important to understand how the electronic structure of these materials changes depending on the composition and how the structure of these materials is affected by radiation. X-ray absorption near-edge spectroscopy (XANES) is a powerful technique that can be used to study the electronic structure of the materials as well as the effect of radiation-induced structural damage on these materials. The objective of this contribution is to demonstrate how XANES can be used to extract important information on pyrochlore-type oxides, including: oxidation state, coordination number (CN), antisite disorder, and the effect of radiation on the structure of the material.NSER

1 Construction of a 12 ” Cyclotron

Our chapter proposes to design and construct a 12 ” cyclotron. The design and construction process will be split over multiple semesters to offset costs and allow more students the opportunity to participate. The final product will be a fixture of our physics department for future undergraduate research, education, and outreach. 3 Statement of the Activity: Background and Relation to the Clemson SPS Chapter Objectives: The cyclotron was one of the major workhorses of atomic physics in the mid-twentieth century and is still used in medicine due to its high ion energy relative to its size. Because of the spherical path it accelerates ions along, a 9 ” cyclotron can obtain maximum ion energies of 184 keV or more and a 12 ” can reach 800 keV [1]. Furthermore, a very barebones 6 ” cyclotron was able to be built from scratch for under $1000 using hand-made or second-hand components [2], showing that such an undertaking is possible on a limited budget. The Clemson University physics department has a strong departmental background in atmospheric physics, astrophysics, and quantum physics but fewer opportunities in particle or accelerator physics. As such, the Clemson University chapter of the Society of Physics Student

Concert recording 2017-09-20

[Tracks 1-4]. String quartet in A major, op. 18, no. 5 [Tracks 5-8]. String quartet in C minor, op. 18, no. 6 / Ludwig van Beethoven

Spatial Clustering of Galaxies in Large Datasets

Datasets with tens of millions of galaxies present new challenges for the analysis of spatial clustering. We have built a framework that integrates a database of object catalogs, tools for creating masks of bad regions, and a fast (NlogN) correlation code. This system has enabled unprecedented efficiency in carrying out the analysis of galaxy clustering in the SDSS catalog. A similar approach is used to compute the three-dimensional spatial clustering of galaxies on very large scales. We describe our strategy to estimate the effect of photometric errors using a database. We discuss our efforts as an early example of data-intensive science. While it would have been possible to get these results without the framework we describe, it will be infeasible to perform these computations on the future huge datasets without using this framework.Comment: original documents at http://research.microsoft.com/scripts/pubs/view.asp?TR_ID=MSR-TR-2002-8

The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour

Neuronal synapses play fundamental roles in information processing, behaviour and disease. Neurotransmitter receptor complexes, such as the mammalian N-methyl-D-aspartate receptor complex (NRC/MASC) comprising 186 proteins, are major components of the synapse proteome. Here we investigate the organisation and function of NRC/MASC using a systems biology approach. Systematic annotation showed that the complex contained proteins implicated in a wide range of cognitive processes, synaptic plasticity and psychiatric diseases. Protein domains were evolutionarily conserved from yeast, but enriched with signalling domains associated with the emergence of multicellularity. Mapping of protein–protein interactions to create a network representation of the complex revealed that simple principles underlie the functional organisation of both proteins and their clusters, with modularity reflecting functional specialisation. The known functional roles of NRC/MASC proteins suggest the complex co-ordinates signalling to diverse effector pathways underlying neuronal plasticity. Importantly, using quantitative data from synaptic plasticity experiments, our model correctly predicts robustness to mutations and drug interference. These studies of synapse proteome organisation suggest that molecular networks with simple design principles underpin synaptic signalling properties with important roles in physiology, behaviour and disease

Mycobacterium tuberculosis PPD-induced immune biomarkers measurable in vitro following BCG vaccination of UK adolescents by multiplex bead array and intracellular cytokine staining

BACKGROUND: The vaccine efficacy reported following Mycobacterium bovis Bacillus Calmette Guerin (BCG) administration to UK adolescents is 77% and defining the cellular immune response in this group can inform us as to the nature of effective immunity against tuberculosis. The aim of this study was to identify which cytokines and lymphocyte populations characterise the peripheral blood cellular immune response following BCG vaccination. RESULTS: Diluted blood from before and after vaccination was stimulated with Mycobacterium tuberculosis purified protein derivative for 6 days, after which soluble biomarkers in supernatants were assayed by multiplex bead array. Ten out of twenty biomarkers measured were significantly increased (p < 0.0025) 1 month after BCG vaccination when compared to paired samples (n = 12) taken prior to vaccination (IFNgamma, TNFalpha, IL-1alpha, IL-2, IL-6, IL-10, IL-17, GM-CSF, MIP1alpha, IP-10). All of these remained detectable by multiplex bead array in samples taken 12 months after BCG vaccination of a partially overlapping adolescent group (n = 12). Intracellular cytokine staining after 24 hour Mycobacterium tuberculosis purified protein derivative stimulation of PBMC samples from the 12 month group revealed that IFNgamma expression was detectable in CD4 and CD8 T-cells and natural killer cells. Polyfunctional flow cytometry analysis demonstrated that cells expressing IFNgamma alone formed the majority in each subpopulation of cells. Only in CD4 T-cells and NK cells were there a notable proportion of responding cells of a different phenotype and these were single positive, TNFalpha producers. No significant expression of the cytokines IL-2, IL-17 or IL-10 was seen in any population of cells. CONCLUSIONS: The broad array of biomarker responses detected by multiplex bead array suggests that BCG vaccination is capable, in this setting, of inducing a complex immune phenotype. Although polyfunctional T-cells have been proposed to play a role in protective immunity, they were not present in vaccinated adolescents who, based on earlier epidemiological studies, should have developed protection against pulmonary tuberculosis. This may be due to the later sampling time point available for testing or on the kinetics of the assays used

Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2

Isocitrate dehydrogenase (IDH) genes 1 and 2 are frequently mutated in acute myeloid leukaemia (AML), low-grade glioma, cholangiocarcinoma (CC) and chondrosarcoma (CS). For AML, low-grade glioma and CC, mutant IDH status is associated with a DNA hypermethylation phenotype, implicating altered epigenome dynamics in the aetiology of these cancers. Here we show that the IDH variants in CS are also associated with a hypermethylation phenotype and display increased production of the oncometabolite 2-hydroxyglutarate, supporting the role of mutant IDH-produced 2-hydroxyglutarate as an inhibitor of TET-mediated DNA demethylation. Meta-analysis of the acute myeloid leukaemia, low-grade glioma, cholangiocarcinoma and CS methylation data identifies cancer-specific effectors within the retinoic acid receptor activation pathway among the hypermethylated targets. By analysing sequence motifs surrounding hypermethylated sites across the four cancer types, and using chromatin immunoprecipitation and western blotting, we identify the transcription factor EBF1 (early B-cell factor 1) as an interaction partner for TET2, suggesting a sequence-specific mechanism for regulating DNA methylation

Identification of pathogen genomic variants through an integrated pipeline

Background: Whole-genome sequencing represents a powerful experimental tool for pathogen research. We present methods for the analysis of small eukaryotic genomes, including a streamlined system (called Platypus) for finding single nucleotide and copy number variants as well as recombination events. Results: We have validated our pipeline using four sets of Plasmodium falciparum drug resistant data containing 26 clones from 3D7 and Dd2 background strains, identifying an average of 11 single nucleotide variants per clone. We also identify 8 copy number variants with contributions to resistance, and report for the first time that all analyzed amplification events are in tandem. Conclusions: The Platypus pipeline provides malaria researchers with a powerful tool to analyze short read sequencing data. It provides an accurate way to detect SNVs using known software packages, and a novel methodology for detection of CNVs, though it does not currently support detection of small indels. We have validated that the pipeline detects known SNVs in a variety of samples while filtering out spurious data. We bundle the methods into a freely available package