Developments in radiation hodoscope technology for arms control treaty verification

New hodoscope radiation detection technology developments offer a wide range of unique capabilities for arms control treaty verification (ACTV). Originally developed for civilian nuclear power research by Argonne National Laboratory, this concept uses a radiation detector array to detect objects inside opaque containments. To avoid unnecessary intrusiveness in treaty verification, spatial resolution must be limited and confirmed. Material density data and identification by radiation means may be either required or prohibited. ACTV instruments also should be inherently resistant to false indications--either accidental, or from attempt at deception. Hodoscope technology can meet these needs. ACTV hodoscopes do not require the heavy collimators of reactor hodoscopes, and relatively weak sources are sufficient. Gamma-ray transmission hodoscopes can be used to inspect canisters, railcars, etc. or to monitor objects such as rocket motors. This technique is deception-resistant: absorbers hidden to mask objects will be detected; and sources hidden to mask absorption will be substracted out as background. Nuclear warheads are detectable by strong gamma-ray absorption. In some cases, intrinsic gamma-ray radiation from warheads also could be used in a passive mode. Neutron hodoscopes can utilize neutron transmission, intrinsic neutron emission, or neutron reactions (either prompt or delayed) stimulated by a neutron source. Warheads can be counted by tomography, or by simple analysis of count rate curve patterns, depending on application. Hodoscope technology is a powerful tool for potential treaty verification uses; This paper considers that technology. 21 refs., 8 figs., 1 tab

Engineering higher order Van Hove singularities in two dimensions: the example of the surface layer of Sr2_2RuO4_4

The properties of correlated electron materials are often intricately linked to Van Hove singularities (VHs) in the vicinity of the Fermi energy. The class of these VHs is of great importance, with higher order ones -- with power-law divergence in the density of states -- leaving frequently distinct signatures in physical properties. We use a new theoretical method to detect and analyse higher order Van Hove singularities (HOVHs) in two-dimensional materials and apply it to the electronic structure of the surface layer of Sr$_2$RuO$_4$. We then constrain a low energy model of the VHs of the surface layer of Sr$_2$RuO$_4$ against angle-resolved photoemission spectroscopy and quasiparticle interference data to analyse the VHs near the Fermi level. We show how these VHs can be engineered into HOVHs.Comment: 8 pages including Supplemental Material, 5 figure

Aluminum Abundance on the Surface of Mercury: Application of a New Background-Reduction Technique for the Analysis of Gamma-Ray Spectroscopy Data

A new technique has been developed for characterizing gamma-ray emission from a planetary surface in the presence of large background signals generated in a spacecraft. This technique is applied to the analysis of Al gamma rays measured by the MESSENGER Gamma-Ray Spectrometer to determine the abundance of Al on the surface of Mercury. The result (Al/Si = 0.29-0.13+0.05) is consistent with Al/Si ratios derived from the MESSENGER X-Ray Spectrometer and confirms the finding of low Al abundances. The measured abundance rules out a global, lunar-like feldspar-rich crust and is consistent with previously suggested analogs for surface material on Mercury, including terrestrial komatiites, low-iron basalts, partial melts of CB chondrites, and partial melts of enstatite chondrites. Additional applications of this technique include the measurement of other elements on Mercury's surface as well as the analysis of data from other planetary gamma-ray spectrometer experiments

MESSENGER Detection of Electron-Induced X-Ray Fluorescence from Mercury's surface

The X-Ray Spectrometer (XRS) on the MESSENGER spacecraft measures elemental abundances on the surface of Mercury by detecting fluorescent X-ray emissions induced on the planet's surface by the incident solar X-ray flux. The XRS began orbital observations on 23 March 2011 and has observed X-ray fluorescence (XRF) from the surface of the planet whenever a sunlit portion of Mercury has been within the XRS field of view. Solar flares are generally required to provide sufficient signal to detect elements that fluoresce at energies above ∼2 keV, but XRF up to the calcium line (3.69 keV) has been detected from Mercury's surface at times when the XRS field of view included only unlit portions of the planet. Many such events have been detected and are identified as electron-induced X-ray emission produced by the interaction of ∼1-10 keV electrons with Mercury's surface. Electrons in this energy range were detected by the XRS during the three Mercury flybys and have also been observed regularly in orbit about Mercury. Knowledge of the energy spectrum of the electrons precipitating at the planet's surface makes it possible to infer surface composition from the measured fluorescent spectra, providing additional measurement opportunities for the XRS. Abundance results for Mg, Al, and Si are in good agreement with those derived from solar-induced XRF data, providing independent validation of the analysis methodologies. Derived S and Ca abundances are somewhat higher than derived from the solar-induced fluorescence data, possibly reflecting incomplete knowledge of the energy spectra of electrons impacting the planet

Variations in the Abundances of Potassium and Thorium on the Surface of Mercury: Results from the MESSENGER Gamma-Ray Spectrometer

A technique for converting gamma-ray count rates measured by the Gamma-Ray Spectrometer on the MESSENGER spacecraft to spatially resolved maps of the gamma-ray emission from the surface of Mercury is utilized to map the surface distributions of the elements Si, O, and K over the planet's northern hemisphere. Conversion of the K gamma-ray count rates to elemental abundances on the surface reveals variations from 300 to 2400 ppm. A comparison of these abundances with models for the maximum surface temperature suggests the possibility that a temperature-related process is controlling the K abundances on the surface as well as providing K to the exosphere. The abundances of K and Th have been determined for several geologically distinct regions, including Mercury's northern smooth plains and the plains interior to the Caloris basin. The lack of a significant variation in the measured Th abundances suggests that there may be considerable variability in the K/Th abundance ratio over the mapped regions

Major-Element Abundances on the Surface of Mercury: Results from the MESSENGER Gamma-Ray Spectrometer

Orbital gamma-ray measurements obtained by the MESSENGER spacecraft have been analyzed to determine the abundances of the major elements Al, Ca, S, Fe, and Na on the surface of Mercury. The Si abundance was determined and used to normalize those of the other reported elements. The Na analysis provides the first abundance estimate of 2.9 plus or minus 0.1 wt% for this element on Mercury's surface. The other elemental results (S/Si = 0.092 plus or minus 0.015, Ca/Si = 0.24 plus or minus 0.05, and Fe/Si = 0.077 plus or minus 0.013) are consistent with those previously obtained by the MESSENGER X-Ray Spectrometer, including the high sulfur and low iron abundances. Because of different sampling depths for the two techniques, this agreement indicates that Mercury's regolith is, on average, homogenous to a depth of tens of centimeters. The elemental results from gamma-ray and X-ray spectrometry are most consistent with petrologic models suggesting that Mercury's surface is dominated by Mg-rich silicates. We also compare the results with those obtained during the MESSENGER flybys and with ground-based observations of Mercury's surface and exosphere

Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures

Comparing independent high-throughput gene-expression experiments can generate hypotheses about which gene-expression programs are shared between particular biological processes. Current techniques to compare expression profiles typically involve choosing a fixed differential expression threshold to summarize results, potentially reducing sensitivity to small but concordant changes. We present a threshold-free algorithm called Rank–rank Hypergeometric Overlap (RRHO). This algorithm steps through two gene lists ranked by the degree of differential expression observed in two profiling experiments, successively measuring the statistical significance of the number of overlapping genes. The output is a graphical map that shows the strength, pattern and bounds of correlation between two expression profiles. To demonstrate RRHO sensitivity and dynamic range, we identified shared expression networks in cancer microarray profiles driving tumor progression, stem cell properties and response to targeted kinase inhibition. We demonstrate how RRHO can be used to determine which model system or drug treatment best reflects a particular biological or disease response. The threshold-free and graphical aspects of RRHO complement other rank-based approaches such as Gene Set Enrichment Analysis (GSEA), for which RRHO is a 2D analog. Rank–rank overlap analysis is a sensitive, robust and web-accessible method for detecting and visualizing overlap trends between two complete, continuous gene-expression profiles. A web-based implementation of RRHO can be accessed at http://systems.crump.ucla.edu/rankrank/

Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses

G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NF\u3baB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5'-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data

Cancer is known to have abundant copy number alterations (CNAs) that greatly contribute to its pathogenesis and progression. Investigation of CNA regions could potentially help identify oncogenes and tumor suppressor genes and infer cancer mechanisms. Although single-nucleotide polymorphism (SNP) arrays have strengthened our ability to identify CNAs with unprecedented resolution, a comprehensive collection of CNA information from SNP array data is still lacking. We developed a web-based CaSNP (http://cistrome.dfci.harvard.edu/CaSNP/) database for storing and interrogating quantitative CNA data, which curated ∼11 500 SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization. Finally, we used CaSNP to study the CNA of protein-coding genes as well as LincRNA genes across all cancer SNP arrays, and found putative regions harboring novel oncogenes and tumor suppressors. In summary, CaSNP is a useful tool for cancer CNA association studies, with the potential to facilitate both basic science and translational research on cancer