ALBERT

Description: Taranaki (Mt. Egmont) in the western North Island of New Zealand is a high-K andesite volcano with an eruptive history extending over more than 200 kyr. In general, petrological research has concentrated on the post-10 ka record of the modern edifice. This study focuses on the earlier history, which is recorded in 11 major pre-7 ka debris avalanche deposits. Each of these formed as a result of a catastrophic collapse of the edifice of the time. The clast assemblages of these deposits provide insights into the chemical compositions of magmas erupted during the earlier stages of activity of the volcano and form the basis for a new chemo-stratigraphic analysis of the pre-10 ka volcanic succession. Sample suites from the studied debris avalanche deposits show a progressive enrichment in K 2 O and large ion lithophile elements (LILE), reflecting a gradual evolution to high-K andesite. The early magmatic system (pre-100 ka) produced a wide range of compositions including relatively primitive basalts and basaltic andesites. These rocks contain phenocryst assemblages that indicate crystallization within the lower crust or mantle, including a broad range of clinopyroxene compositions, high-Al 2 O 3 hornblende, olivine and phlogopite. A higher proportion of high-silica compositions in the younger sample suites and the appearance of late-stage, low-pressure mineral phases, such as high-TiO 2 hornblende, biotite and Fe-rich orthopyroxene, reflect a gradual shift to more evolved magmas with time. These new data are interpreted to reflect a multi-stage origin for Taranaki andesites. Parental magmas were generated within a lower crustal ‘hot zone’, which formed as a result of repeated intrusions of primitive melts into the lower crust. The geochemical and mineralogical evidence indicates that prior to 100 ka this zone was relatively thin and cold, so that primitive magmas were able to rise rapidly through the crust without significant interaction and modification. As the hot zone evolved, larger proportions of intruded and underplated mafic material were partially remelted, and interaction of these melts with fractionating mantle-derived magmas generated progressively more K- and LILE-enriched compositions. A complex and dispersed magma assembly and storage system developed in the upper crust where the hot-zone melts were further modified by fractional crystallization and magma mixing and mingling.

Description: : Aptamers are ‘synthetic antibodies’ that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro , rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a M eta-motif-based statistical framework and pipeline to P redict the Bind ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis. Availability and implementation : MPBind software and documents are available at http://www.morgridge.net/MPBind.html . The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge.net/Aptamer/ . Contact : RStewart@morgridge.org Supplementary information : Supplementary data are available at Bioinformatics online.

Description: To understand their influence on elastic wave propagation, anisotropic cracked media have been widely investigated in many theoretical and experimental studies. In this work, we report on laboratory ultrasound measurements carried out to investigate the effect of source frequency on the elastic parameters (wave velocities and the Thomsen parameter ) and shear wave attenuation) of fractured anisotropic media. Under controlled conditions, we prepared anisotropic model samples containing penny-shaped rubber inclusions in a solid epoxy resin matrix with crack densities ranging from 0 to 6.2 per cent. Two of the three cracked samples have 10 layers and one has 17 layers. The number of uniform rubber inclusions per layer ranges from 0 to 100. S -wave splitting measurements have shown that scattering effects are more prominent in samples where the seismic wavelength to crack aperture ratio ranges from 1.6 to 1.64 than in others where the ratio varied from 2.72 to 2.85. The sample with the largest cracks showed a magnitude of scattering attenuation three times higher compared with another sample that had small inclusions. Our S -wave ultrasound results demonstrate that elastic scattering, scattering and anelastic attenuation, velocity dispersion and crack size interfere directly in shear wave splitting in a source-frequency dependent manner, resulting in an increase of scattering attenuation and a reduction of shear wave anisotropy with increasing frequency.

Description: The autosomal recessive disorder ataxia-telangiectasia (A-T) is characterized by genome instability, cancer predisposition and neurodegeneration. Although the role of ataxia-telangiectasia mutated (ATM) protein, the protein defective in this syndrome, is well described in the response to DNA damage, its role in protecting the nervous system is less clear. We describe the establishment and characterization of patient-specific stem cells that have the potential to address this shortcoming. Olfactory neurosphere (ONS)-derived cells were generated from A-T patients, which expressed stem cell markers and exhibited A-T molecular and cellular characteristics that included hypersensitivity to radiation, defective radiation-induced signaling and cell cycle checkpoint defects. Introduction of full-length ATM cDNA into these cells corrected defects in the A-T cellular phenotype. Gene expression profiling and pathway analysis revealed defects in multiple cell signaling pathways associated with ATM function, with cell cycle, cell death and DNA damage response pathways being the most significantly dysregulated. A-T ONS cells were also capable of differentiating into neural progenitors, but they were defective in neurite formation, number of neurites and length of these neurites. Thus, ONS cells are a patient-derived neural stem cell model that recapitulate the phenotype of A-T, do not require genetic reprogramming, have the capacity to differentiate into neurons and have potential to delineate the neurological defect in these patients.

Description: Ultrasonic velocities were measured on a stack of synthetic materials (Plexiglass plates), at low (90/120 kHz, long wavelength range: 12–23 mm) and high (431/480 kHz, short wavelength range: 1–6 mm) frequencies. The Plexiglass plates were pressed together with uniaxial normal stress. The ultrasonic measurements were repeated under different uniaxial stresses with and without circular rubber inclusions between the plates. The stress dependence of measured P -wave velocities is more pronounced (about 200 m s –1 difference) at low frequency compared to the high frequency measurements. S -wave velocity measurements in the vertical direction (perpendicular to plates) and horizontal direction with polarization perpendicular to the plates show that, without rubber inclusions, the model can be approximated as a vertical transverse isotropy (VTI) medium (difference of about 20 m s –1 between the two S -wave velocities for stresses higher than 6 MPa), whereas, for the case with inclusions, there is a significant difference (about 350 m s –1 for stresses higher than 6 MPa). The difference in vertically propagating and horizontally propagating vertically polarized S -wave velocities indicates that the medium is inhomogeneous at these wavelengths. Ultrasonic velocity measurements were used to calculate fracture compliances and VTI anisotropy parameters. For both experiments (with and without rubber disc inclusion), fracture compliances and also absolute values of VTI anisotropy parameters, decrease with increasing stress and frequency. For our experiments, Thomsen's anisotropy parameter is highly correlated to and (with average correlation coefficients of about 95 per cent). For all measurements, the medium showed positive anellipticity (i.e. – 〉 0). In all cases, the tangential compliance was greater than the normal compliance. For experiments without inclusions, the normal to tangential compliance ratios show an increasing trend with increasing normal stress. For experiments with inclusions, these ratios show a decreasing trend, especially at higher frequency ranges.

Description: Ruapehu, New Zealand’s largest active andesite volcano, is located at the southern tip of the Taupo Volcanic Zone (TVZ), the main locus of subduction-related volcanism in the North Island. Geophysical data indicate that crustal thickness increases from 〈25 km within the TVZ to 40 km beneath Ruapehu. The volcano is built on a basement of Mesozoic meta-greywacke, and geophysical evidence together with xenoliths contained in lavas indicates that this is underlain by oceanic, meta-igneous lower crust. The present-day Ruapehu edifice has been constructed by a series of eruptive events that produced a succession of lava flow-dominated stratigraphic units. In order from oldest to youngest, these are the Te Herenga (250–180 ka), Wahianoa (160–115 ka), Mangawhero (55–45 ka and 20–30 ka), and Whakapapa (15–2 ka) Formations. The dominant rock types are plagioclase- and pyroxene-phyric basaltic andesite and andesite. Dacite also occurs but only one basalt flow has been identified. There have been progressive changes in the minor and trace element chemistry and isotopic composition of Ruapehu eruptive rocks over time. In comparison with rocks from younger formations, Te Herenga eruptive rocks have lower K 2 O abundances and a relatively restricted range in major and trace element and Nd–Sr isotopic composition. Post-Te Herenga andesites and dacites define a Sr–Nd isotopic array that overlaps with the field for TVZ rhyolites and basalts, but Te Herenga Formation lavas and the Ruapehu basalt have higher 143 Nd/ 144 Nd ratios. The isotopic, and major and trace element composition of Te Herenga andesite can be replicated by models involving mixing of an intra-oceanic andesite with a crustal component derived from a meta-igneous composition. Post-Te Herenga andesites show considerable variation in major and trace element and Sr and Nd isotopic compositions ( 87 Sr/ 86 Sr ranges from 0·7049 to 0·7060 and 143 Nd/ 144 Nd from 0·51264 to 0·51282). The range of compositions can be modeled by assimilation–fractional crystallization (AFC) involving meta-greywacke as the assimilant, closed-system fractionation, or by mixing of intra-oceanic andesite or basalt and a meta-greywacke crustal composition. Plagioclase and pyroxene compositions vary over wide ranges within single rocks and few of these have compositions consistent with equilibration with a melt having the composition of either the host-rock or groundmass. The 87 Sr/ 86 Sr compositions of plagioclase also vary significantly within single whole-rock samples. Glass inclusions and groundmasses of andesitic rocks all have dacitic or rhyolitic major and trace element compositions. The application of various mineral geothermometers and geobarometers indicates pre-eruption temperatures between 950 and 1190°C and pressures ranging from 1 to 0·2 GPa. These pressure estimates are consistent with those obtained from xenolith mineral assemblages and geophysical information. Plagioclase hygrometry and the paucity of amphibole are indications that melts were relatively dry (〈 4 wt % H 2 O). Magmas represented by Ruapehu andesites were dacitic or rhyolitic melts carrying complex crystal and lithic cargoes derived from the mantle and at least two crustal sources. They have evolved through a complex interplay between assimilation, crystal fractionation, crustal anatexis and magma mixing. Parental magmas were sourced in both the mantle and crust, but erupted compositions very strongly reflect modification by intracrustal processes. Geochemical variation in systematically sampled lava flow sequences is consistent with random tapping of a complex plumbing system in which magma has been stored on varying time scales within a plexus of dispersed reservoirs. Each magma batch is likely to have had a unique history with different sized magma storages evolving on varying time scales with a specific combination of AFC and mixing processes.

Description: Motivation: Messenger RNA expression is important in normal development and differentiation, as well as in manifestation of disease. RNA-seq experiments allow for the identification of differentially expressed (DE) genes and their corresponding isoforms on a genome-wide scale. However, statistical methods are required to ensure that accurate identifications are made. A number of methods exist for identifying DE genes, but far fewer are available for identifying DE isoforms. When isoform DE is of interest, investigators often apply gene-level (count-based) methods directly to estimates of isoform counts. Doing so is not recommended. In short, estimating isoform expression is relatively straightforward for some groups of isoforms, but more challenging for others. This results in estimation uncertainty that varies across isoform groups. Count-based methods were not designed to accommodate this varying uncertainty, and consequently, application of them for isoform inference results in reduced power for some classes of isoforms and increased false discoveries for others. Results: Taking advantage of the merits of empirical Bayesian methods, we have developed EBSeq for identifying DE isoforms in an RNA-seq experiment comparing two or more biological conditions. Results demonstrate substantially improved power and performance of EBSeq for identifying DE isoforms. EBSeq also proves to be a robust approach for identifying DE genes. Availability and implementation: An R package containing examples and sample datasets is available at http://www.biostat.wisc.edu/~kendzior/EBSEQ/ . Contact: kendzior@biostat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.