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  • American Geophysical Union  (326)
  • Oxford University Press  (181)
  • 2015-2019  (361)
  • 1990-1994  (146)
  • 1
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    Gravity changes and deformation at Kīlauea Volcano, Hawaii, associated with summit eruptive activity, 2009–2012 (2015)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Analysis of microgravity and surface displacement data collected at the summit of Kīlauea Volcano, Hawaii (USA), between December 2009 and November 2012 suggests a net mass accumulation at ~1.5 km depth beneath the northeast margin of Halema‘uma‘u Crater, within Kīlauea Caldera. Although residual gravity increases and decreases are accompanied by periods of uplift and subsidence of the surface, respectively, the volume change inferred from the modeling of interferometric synthetic aperture radar deformation data can account for only a small portion (as low as 8%) of the mass addition responsible for the gravity increase. We propose that since the opening of a new eruptive vent at the summit of Kīlauea in 2008, magma rising to the surface of the lava lake outgasses, becomes denser, and sinks to deeper levels, replacing less dense gas-rich magma stored in the Halema‘uma‘u magma reservoir. In fact, a relatively small density increase (〈200 kgm_3) of a portion of the reservoir can produce the positive residual gravity change measured during the period with the largest mass increase, between March 2011 and November 2012. Other mechanisms may also play a role in the gravity increase without producing significant uplift of the surface, including compressibility of magma, formation of olivine cumulates, and filling of void space by magma. The rate of gravity increase, higher than during previous decades, varies through time and seems to be directly correlated with the volcanic activity occurring at both the summit and the east rift zone of the volcano.
    Description: Published
    Description: 7288–7305
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Mass accumulation ; Magma outgassing ; Gravity changes ; Ground deformation ; 04. Solid Earth::04.03. Geodesy::04.03.05. Gravity variations
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
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    Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci (2015)
    Coetzee, S. G., Shen, H. C., Hazelett, D. J., Lawrenson, K., Kuchenbaecker, K., Tyrer, J., Rhie, S. K., Levanon, K., Karst, A., Drapkin, R., Ramus, S. J., The Ovarian Cancer Association Consortium, The Consortium of Investigators of Modifiers of BRCA1/2, Couch, F. J., Offit, K., Chenevix-Trench, G., Monteiro, A. N. A., Antoniou, A., Freedman, M., Coetzee, G. A., Pharoah, P. D. P., Noushmehr, H., Gayther, S. A., The Ovarian Cancer Association Consortium, The Consortium of Investigators of Modifiers of BRCA1/2, Tyrer, Anton-Culver, Antonenkova, Baker, Bandera, Bean, Beckmann, Berchuck, Bisogna, Bjorge, Bogdanova, Brinton, Brooks-Wilson, Bruinsma, Butzow, Campbell, Carty, Chang-Claude, Chen, Chen, Cook, Cramer, Cunningham, Cybulski, Dansonka-Mieszkowska, Dennis, Dicks, Doherty, Dork, Bois, Durst, Eccles, Easton, Edwards, Eilber, Ekici, Fasching, Fridley, Gao, Gentry-Maharaj, Giles, Glasspool, Goode, Goodman, Grownwald, Harrington, Harter, Hasmad, Hein, Heitz, Hildebrandt, Hillemanns, Hogdall, Hogdall, Hosono, Iversen, Jakubowska, James, Jensen, Ji, Karlan, Kjaer, Kelemen, Kellar, Kelley, Kiemeney, Krakstad, Kupryjanczyk, Lambrechts, Lambrechts, Le, Lele, Leminen, Lester, Levine, Liang, Lissowska, Lu, Lubinski, Lundvall, Massuger, Matsuo, McGuire, McLaughlin, McNeish, Menon, Modugno, Moysich, Narod, Nedergaard, Ness, Azmi, Odunsi, Olson, Orlow, Orsulic, Weber, Pearce, Pejovic, Pelttari, Permuth-Wey, Phelan, Pike, Poole, Risch, Rosen, Rossing, Rothstein, Rudolph, Runnebaum, Rzepecka, Salvesen, Schildkraut, Schwaab, Sellers, Shu, Shvetsov, Siddiqui, Sieh, Song, Southey, Sucheston, Tangen, Teo, Terry, Thompson, Timorek, Tsai, Tworoger, Tyrer, van Altena, Van Nieuwenhuysen, Vergote, Vierkant, Wang-Gohrke, Walsh, Wentzensen, Whittemore, Wicklund, Wilkens, Woo, Wu, Wu, Yang, Zheng, Ziogas
    Oxford University Press
    Details
    Publication Date: 2015-06-09
    Description: Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs ( P = 3.8 x 10 –30 ), OSECs ( P = 2.4 x 10 –23 ) and HMECs ( P = 6.7 x 10 –15 ) but not for EECs ( P = 0.45) or LNCaP cells ( P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    In-depth N-glycome profiling of paired colorectal cancer and non-tumorigenic tissues reveals cancer-, stage- and EGFR-specific protein N-glycosylation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-28
    Description: Glycomics may assist in uncovering the structure–function relationships of protein glycosylation and identify glycoprotein markers in colorectal cancer (CRC) research. Herein, we performed label-free quantitative glycomics on a carbon-liquid chromatography–tandem mass spectrometry-based analytical platform to accurately profile the N-glycosylation changes associated with CRC malignancy. N -Glycome profiling was performed on isolated membrane proteomes of paired tumorigenic and adjacent non-tumorigenic colon tissues from a cohort of five males (62.6 ± 13.1 y.o.) suffering from colorectal adenocarcinoma. The CRC tissues were typed according to their epidermal growth factor receptor (EGFR) status by western blotting and immunohistochemistry. Detailed N -glycan characterization and relative quantitation identified an extensive structural heterogeneity with a total of 91 N -glycans. CRC-specific N-glycosylation phenotypes were observed including an overrepresentation of high mannose, hybrid and paucimannosidic type N -glycans and an under-representation of complex N -glycans ( P 〈 0.05). Sialylation, in particular α2,6-sialylation, was significantly higher in CRC tumors relative to non-tumorigenic tissues, whereas α2,3-sialylation was down-regulated ( P 〈 0.05). CRC stage-specific N-glycosylation was detected by high α2,3-sialylation and low bisecting β1,4-GlcNAcylation and Lewis-type fucosylation in mid-late relative to early stage CRC. Interestingly, a novel link between the EGFR status and the N-glycosylation was identified using hierarchical clustering of the N -glycome profiles. EGFR-specific N -glycan signatures included high bisecting β1,4-GlcNAcylation and low α2,3-sialylation (both P 〈 0.05) relative to EGFR-negative CRC tissues. This is the first study to correlate CRC stage and EGFR status with specific N -glycan features, thus advancing our understanding of the mechanisms causing the biomolecular deregulation associated with CRC.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
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    Generation and Rejuvenation of a Supervolcanic Magmatic System: a Case Study from Mangakino Volcanic Centre, New Zealand (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-01
    Description: The Kidnappers [~1200 km 3 dense rock equivalent (DRE)] and Rocky Hill (~200 km 3 DRE) caldera-forming events in the Taupo Volcanic Zone, New Zealand, were erupted in close succession from the Mangakino volcanic centre. They have identical radiometric ages at ~1 Ma, yet erosion along the contact between the two deposits suggests that some years to decades separated the two eruptions. Field constraints and the similarities of crystal textures and compositions and glass chemistries of both eruption deposits demonstrate that they came from one overall magmatic system with a common crystal mush source. However, second-order variations in these parameters confirm that the Kidnappers and Rocky Hill deposits represent distinct events and are not the products of a single zoned magma chamber. The systematically zoned Kidnappers fall deposits provide evidence for the tapping of three discrete magma bodies, whereas the succeeding Kidnappers ignimbrite is compositionally more diverse. The transition from fall to flow deposition marks a change in the style of caldera collapse and the simultaneous evacuation of discrete but compositionally diverse melts, each of which underwent a distinct evolution and was held at slightly different P–T conditions prior to eruption. Contrasting plagioclase and orthopyroxene zonation patterns are present in pumices originating from three discrete magma bodies. Less evolved mafic melts interacted with the system, which mobilized portions of the final erupted melt through heating and volatile or chemical exchange in the mush. The two largest Kidnappers melt-dominant bodies were re-tapped in modified form, or re-established from their common mush source, prior to the Rocky Hill event. Rocky Hill pumices contain common, fluid-affected antecrystic crystal clots derived from chamber wall material. Amphibole compositions from each eruption reflect melt evolution processes and, in particular, the contemporaneous crystallization of biotite and breakdown of orthopyroxene. Plagioclase and orthopyroxene from Rocky Hill pumices share common zonation patterns with those from the two largest magma bodies in the Kidnappers. The rapid production of new melt-dominant bodies and the triggering of the Rocky Hill eruption reflect the ability of the magmatic system to rejuvenate on a geologically short timescale. The Mangakino centre did not follow a typical cycle of decreased activity after the supervolcanic Kidnappers event, instead producing a second caldera-forming eruption, within years to decades from the same system.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
    Published by Oxford University Press
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  • 5
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    Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-22
    Description: Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the p iwi- i nteracting-RNA pathway of gene silencing, for example, the female germline-restricted TE silencer, HP1D/Rhino . Host genomes can also innovate via gene duplication and divergence. However, the importance of gene family expansions, contractions, and gene turnover to host genome defense has been largely unexplored. Here, we functionally characterize Oxpecker , a young, tandem duplicate gene of HP1D/rhino . We demonstrate that Oxpecker supports female fertility in Drosophila melanogaster and silences several TE families that are incompletely silenced by HP1D/Rhino in the female germline. We further show that, like Oxpecker , at least ten additional, structurally diverse, HP1D/rhino -derived daughter and "granddaughter" genes emerged during a short 15-million year period of Drosophila evolution. These young paralogs are transcribed primarily in germline tissues, where the genetic conflict between host genomes and TEs plays out. Our findings suggest that gene family expansion is an underappreciated yet potent evolutionary mechanism of genome defense diversification.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    49 new T dwarfs identified using methane imaging (2015)
    Oxford University Press
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    Publication Date: 2015-05-08
    Description: We present the discovery of 49 new photometrically classified T dwarfs from the combination of large infrared and optical surveys combined with follow-up Telescopio Nazionale Galileo photometry. We used multiband infrared and optical photometry from the United Kingdom Infrared Telescope and Sloan Digital Sky Surveys to identify possible brown dwarf candidates, which were then confirmed using methane filter photometry. We have defined a new photometric conversion between CH 4 s – CH 4 l colour and spectral type for T4–T8 brown dwarfs based on a part of the sample that has been followed up using methane photometry and spectroscopy. Using methane differential photometry as a proxy for spectral type for T dwarfs has proved to be a very efficient technique. Of a subset of 45 methane selected brown dwarfs that were observed spectroscopically, 100 per cent were confirmed as T dwarfs. Future deep imaging surveys will produce large samples of faint brown dwarf candidates, for which spectroscopy will not be feasible. When broad wavelength coverage is unavailable, methane imaging offers a means to efficiently classify candidates from such surveys using just a pair of near-infrared images.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae) (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-28
    Description: Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such as dosage compensation. Numerous studies in model organisms have found complex and, at times contradictory, relationships among these genomic attributes highlighting the need to examine these patterns in other systems characterized by abundant sexual selection. Therefore, we examined the association among novel gene creation, tissue-specific gene expression, and chromosomal gene content within stalk-eyed flies. Flies in this family are characterized by strong sexual selection and the presence of a newly evolved X chromosome. We generated RNA-seq transcriptome data from the testes for three species within the family and from seven additional tissues in the highly dimorphic species, Teleopsis dalmanni . Analysis of dipteran gene orthology reveals dramatic testes-specific gene creation in stalk-eyed flies, involving numerous gene families that are highly conserved in other insect groups. Identification of X-linked genes for the three species indicates that the X chromosome arose prior to the diversification of the family. The most striking feature of this X chromosome is that it is highly masculinized, containing nearly twice as many testes-specific genes as expected based on its size. All the major processes that may drive differential sex chromosome gene content—creation of genes with male-specific expression, development of male-specific expression from pre-existing genes, and movement of genes with male-specific expression—are elevated on the X chromosome of T. dalmanni . This masculinization occurs despite evidence that testes expressed genes do not achieve the same levels of gene expression on the X chromosome as they do on the autosomes.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    GeneWeaver: data driven alignment of cross-species genomics in biology and disease (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: The GeneWeaver data and analytics website ( www.geneweaver.org ) is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, environments, anatomical structures and diseases implicitly found through gene set intersections. Since the previous review in the 2012 Nucleic Acids Research Database issue, GeneWeaver's underlying analytics platform has been enhanced, its number and variety of publically available gene set data sources has been increased, and its advanced search mechanisms have been expanded. In addition, its interface has been redesigned to take advantage of flexible web services, programmatic data access, and a refined data model for handling gene network data in addition to its original emphasis on gene set data. By enumerating the common and distinct biological molecules associated with all subsets of curated or user submitted groups of gene sets and gene networks, GeneWeaver empowers users with the ability to construct data driven descriptions of shared and unique biological processes, diseases and traits within and across species.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    CpG methylation differences between neurons and glia are highly conserved from mouse to human (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: Understanding epigenetic differences that distinguish neurons and glia is of fundamental importance to the nascent field of neuroepigenetics. A recent study used genome-wide bisulfite sequencing to survey differences in DNA methylation between these two cell types, in both humans and mice. That study minimized the importance of cell type-specific differences in CpG methylation, claiming these are restricted to localized genomic regions, and instead emphasized that widespread and highly conserved differences in non-CpG methylation distinguish neurons and glia. We reanalyzed the data from that study and came to markedly different conclusions. In particular, we found widespread cell type-specific differences in CpG methylation, with a genome-wide tendency for neuronal CpG-hypermethylation punctuated by regions of glia-specific hypermethylation. Alarmingly, our analysis indicated that the majority of genes identified by the primary study as exhibiting cell type-specific CpG methylation differences were misclassified. To verify the accuracy of our analysis, we isolated neuronal and glial DNA from mouse cortex and performed quantitative bisulfite pyrosequencing at nine loci. The pyrosequencing results corroborated our analysis, without exception. Most interestingly, we found that gene-associated neuron vs. glia CpG methylation differences are highly conserved across human and mouse, and are very likely to be functional. In addition to underscoring the importance of independent verification to confirm the conclusions of genome-wide epigenetic analyses, our data indicate that CpG methylation plays a major role in neuroepigenetics, and that the mouse is likely an excellent model in which to study the role of DNA methylation in human neurodevelopment and disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    EMDataBank unified data resource for 3DEM (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata ( emdatabank.org ). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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