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  • 1
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    Long-lived shield volcanism within a monogenetic basaltic field: The conundrum of Rangitoto volcano, New Zealand (2016)
    Geological Society of America (GSA)
    Details
    Publication Date: 2016-06-24
    Description: Drilling through the edifice of Rangitoto, the youngest and largest volcano in the "monogenetic" Auckland volcanic field, reveals the multistage eruptive and magmatic history of a small basalt shield volcano. Activity commenced calendar year (cal.) 6000 cal. yr B.P., involving minor effusive and pyroclastic volcanism until 650 cal. yr B.P. This period either represents an early, less productive phase of a single polygenetic volcano, or, alternatively, Rangitoto is better described as a volcanic complex that includes one or more buried edifices concealed by the main structure. A voluminous shield-building phase occurred 650–550 cal. yr B.P., erupting isotopically uniform subalkalic basalts (Mg# 60–64). Four batches of magma distinguished by trace-element chemistry were erupted sequentially, but they lack genetic connection via fractional crystallization or assimilation. Two of the magma batches display linear trends of decreasing incompatible trace-element abundance and increasing ratios of moderately incompatible to highly incompatible elements with decreasing age. This is consistent with cycles of progressive partial melting at the source. The final phase of activity (ca. 550–500 cal. yr B.P.) was explosive and less voluminous, producing scoria cones at the summit. This phase involved more diversity in magma compositions, including more mafic subalkalic basalt, and alkali basalt, pointing to sourcing of magmas simultaneously from different depths in the mantle. Rangitoto volcano contributes to a growing body of evidence showing that major periods of volcanism in "monogenetic" basalt fields occur at centers that have experienced multiple eruption episodes. Changes in magma composition accompany changes in eruption style, but a lack of an obvious shared pattern in magmatic evolution at various volcanoes points to the localized mantle heterogeneity and conduit systems. Hazard scenarios for regions traditionally classified as "monogenetic" need to encompass the possibility of prolonged episodes of activity and reawakening of volcanoes, a significant implication where infrastructure is built on such regions.
    Print ISSN: 0016-7606
    Electronic ISSN: 1943-2674
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 2
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    Mutations in Dnaaf1 and Lrrc48 Cause Hydrocephalus, Laterality Defects, and Sinusitis in Mice (2016)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2016-08-10
    Description: We have previously described a forward genetic screen in mice for abnormalities of brain development. Characterization of two hydrocephalus mutants by whole-exome sequencing after whole-genome SNP mapping revealed novel recessive mutations in Dnaaf1 and Lrrc48 . Mouse mutants of these two genes have not been previously reported. The Dnaaf1 mutant carries a mutation at the splice donor site of exon 4, which results in abnormal transcripts. The Lrrc48 mutation is a missense mutation at a highly conserved leucine residue, which is also associated with a decrease in Lrrc48 transcription. Both Dnaaf1 and Lrrc48 belong to a leucine-rich repeat-containing protein family and are components of the ciliary axoneme. Their Chlamydomonas orthologs are known to be required for normal ciliary beat frequency or flagellar waveform, respectively. Some Dnaaf1 or Lrrc48 homozygote mutants displayed laterality defects, suggesting a motile cilia defect in the embryonic node. Mucus accumulation and neutrophil infiltration in the maxillary sinuses suggested sinusitis. Dnaaf1 mutants showed postnatal lethality, and none survived to weaning age. Lrrc48 mutants survive to adulthood, but had male infertility. ARL13B immunostaining showed the presence of motile cilia in the mutants, and the distal distribution of DNAH9 in the axoneme of upper airway motile cilia appeared normal. The phenotypic abnormalities suggest that mutations in Dnaaf1 and Lrrc48 cause defects in motile cilia function.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 3
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    Reconstruction of the slip distributions in historical earthquakes on the Sunda megathrust, W. Sumatra (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-04
    Description: Spatially heterogeneous inversions for the slip in major earthquakes are typically only available for modern, instrumentally recorded events. Stress reconstructions on active faults, which are potentially vital elements of earthquake hazard assessment, are usually based on one or two instrumental inversions and some semi-quantitative information concerning historical seismic activity. Here we develop a new Bayesian Monte Carlo inversion method for sparse, large uncertainty data, such as is available for many historical earthquakes. We use it to reconstruct the slip in two great historical earthquakes on the Sunda megathrust, from 200 yr of paleogeodetic data recorded in the stratigraphy of coral microatolls on the forearc islands. The technique is based on the stochastic forward modelling of many slip distributions, which are constrained by the observed fractal scaling in the slip field. A set of static elastic Green's functions is used to estimate the vertical displacement at the coral locations resulting from each trial slip distribution. The posterior expected value of the slip and its variance are obtained from the average of the trial slips, weighted by their ability to reproduce the coral displacements. We successfully test the method on a synthetic slip distribution, before applying it to reconstruct the slip in a recent, instrumentally recorded event. We then invert for the great 1797 and 1833 megathrust events under the Mentawai Islands west of Sumatra. When compared with the slip distributions in recent earthquakes, our results unambiguously indicate that the sequence is not consistent with the classic characteristic earthquake model; earthquakes tend to incrementally tessellate the active fault plane rather than repeatedly breaking a segment of it. The results indicate that homogeneous loading of a fault with heterogeneous initial stress is enough to explain the observations on the Mentawai segment of the Sunda megathrust; no time dependence of material properties, for example, is necessary. Furthermore, we speculate that even small amounts of nonlinearity in the rupture process would ensure that any tessellating sequence will not be repeated, even over very long times. This method could be adapted to incorporate other historical information, such as records of tsunami run up and Mercalli Intensity estimates. Finally, we suggest that reconstruction of stress based on long-term slip histories may prove useful in identifying the possible locations of future earthquakes.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
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    Research thrives on integration of natural and social sciences (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fisher, Erik -- Biggs, Simon -- Lindsay, Stuart -- Zhao, Jie -- England -- Nature. 2010 Feb 25;463(7284):1018. doi: 10.1038/4631018a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20182491" target="_blank"〉PubMed〈/a〉
    Keywords: Creativity ; Natural Science Disciplines/*methods ; *Research Design ; Research Personnel ; Social Sciences/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Human CHN1 mutations hyperactivate alpha2-chimaerin and cause Duane's retraction syndrome (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-26
    Description: Duane's retraction syndrome (DRS) is a complex congenital eye movement disorder caused by aberrant innervation of the extraocular muscles by axons of brainstem motor neurons. Studying families with a variant form of the disorder (DURS2-DRS), we have identified causative heterozygous missense mutations in CHN1, a gene on chromosome 2q31 that encodes alpha2-chimaerin, a Rac guanosine triphosphatase-activating protein (RacGAP) signaling protein previously implicated in the pathfinding of corticospinal axons in mice. We found that these are gain-of-function mutations that increase alpha2-chimaerin RacGAP activity in vitro. Several of the mutations appeared to enhance alpha2-chimaerin translocation to the cell membrane or enhance its ability to self-associate. Expression of mutant alpha2-chimaerin constructs in chick embryos resulted in failure of oculomotor axons to innervate their target extraocular muscles. We conclude that alpha2-chimaerin has a critical developmental function in ocular motor axon pathfinding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593867/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593867/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miyake, Noriko -- Chilton, John -- Psatha, Maria -- Cheng, Long -- Andrews, Caroline -- Chan, Wai-Man -- Law, Krystal -- Crosier, Moira -- Lindsay, Susan -- Cheung, Michelle -- Allen, James -- Gutowski, Nick J -- Ellard, Sian -- Young, Elizabeth -- Iannaccone, Alessandro -- Appukuttan, Binoy -- Stout, J Timothy -- Christiansen, Stephen -- Ciccarelli, Maria Laura -- Baldi, Alfonso -- Campioni, Mara -- Zenteno, Juan C -- Davenport, Dominic -- Mariani, Laura E -- Sahin, Mustafa -- Guthrie, Sarah -- Engle, Elizabeth C -- G9900837/Medical Research Council/United Kingdom -- G9900989/Medical Research Council/United Kingdom -- R01 EY015298/EY/NEI NIH HHS/ -- R01 EY015298-01/EY/NEI NIH HHS/ -- R01 EY015298-02/EY/NEI NIH HHS/ -- R01 EY015298-03/EY/NEI NIH HHS/ -- R01 EY015298-04/EY/NEI NIH HHS/ -- R01 EY015298-05/EY/NEI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):839-43. doi: 10.1126/science.1156121. Epub 2008 Jul 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine (Genetics), Children's Hospital Boston, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653847" target="_blank"〉PubMed〈/a〉
    Keywords: Abducens Nerve/abnormalities ; Amino Acid Sequence ; Animals ; Axons/physiology ; Cell Line ; Cell Membrane/metabolism ; Chick Embryo ; Chimerin 1/chemistry/*genetics/*metabolism ; Duane Retraction Syndrome/*genetics ; Female ; Gene Expression Profiling ; Heterozygote ; Humans ; Male ; Molecular Sequence Data ; *Mutation, Missense ; Oculomotor Muscles/embryology/innervation/metabolism ; Oculomotor Nerve/abnormalities/embryology ; Pedigree
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Translocation of single-stranded DNA through single-walled carbon nanotubes (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-02
    Description: We report the fabrication of devices in which one single-walled carbon nanotube spans a barrier between two fluid reservoirs, enabling direct electrical measurement of ion transport through the tube. A fraction of the tubes pass anomalously high ionic currents. Electrophoretic transport of small single-stranded DNA oligomers through these tubes is marked by large transient increases in ion current and was confirmed by polymerase chain reaction analysis. Each current pulse contains about 10(7) charges, an enormous amplification of the translocated charge. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurements, and may open avenues for control of DNA translocation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801077/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801077/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Haitao -- He, Jin -- Tang, Jinyao -- Liu, Hao -- Pang, Pei -- Cao, Di -- Krstic, Predrag -- Joseph, Sony -- Lindsay, Stuart -- Nuckolls, Colin -- R21 HG004770/HG/NHGRI NIH HHS/ -- R21 HG004770-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 1;327(5961):64-7. doi: 10.1126/science.1181799.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044570" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA, Single-Stranded ; Electric Conductivity ; Electrochemistry ; Ion Transport ; Molecular Dynamics Simulation ; *Nanotubes, Carbon ; *Oligodeoxyribonucleotides ; Polymerase Chain Reaction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1 (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-25
    Description: Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related ( P 〈 10 –6 ) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.
    Keywords: Taxonomy & Systematics
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-12
    Description: The DNA origami method, in which long, single-stranded DNA segments are folded into shapes by short staple segments, was used to create nucleic acid probe tiles that are molecular analogs of macroscopic DNA chips. One hundred trillion probe tiles were fabricated in one step and bear pairs of 20-nucleotide-long single-stranded DNA segments that act as probe sequences. These tiles can hybridize to their targets in solution and, after adsorption onto mica surfaces, can be examined by atomic force microscopy in order to quantify binding events, because the probe segments greatly increase in stiffness upon hybridization. The nucleic acid probe tiles have been used to study position-dependent hybridization on the nanoscale and have also been used for label-free detection of RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ke, Yonggang -- Lindsay, Stuart -- Chang, Yung -- Liu, Yan -- Yan, Hao -- New York, N.Y. -- Science. 2008 Jan 11;319(5860):180-3. doi: 10.1126/science.1150082.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ 85287, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18187649" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/genetics ; Adsorption ; Aluminum Silicates ; Animals ; Cell Line ; DNA, Single-Stranded ; Gene Expression Profiling/*methods ; Genes, RAG-1 ; Genes, myc ; Mice ; Microscopy, Atomic Force ; *Molecular Probe Techniques ; *Nanostructures ; Nucleic Acid Hybridization/*methods ; *Oligonucleotide Probes ; RNA/*analysis/genetics ; Sensitivity and Specificity ; Solubility
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    T-cell restimulation at the autoimmune site [Immunology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-06-25
    Description: Defining the processes of autoimmune attack of tissues is important for inhibiting continued tissue destruction. In type 1 diabetes, it is not known how cytotoxic effector T cell responses evolve over time in the pancreatic islets targeted for destruction. We used two-photon microscopy of live, intact, individual islets to investigate...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Gravity inversion using wavelet-based compression on parallel hybrid CPU/GPU systems: application to southwest Ghana (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-04
    Description: We solve the 3-D gravity inverse problem using a massively parallel voxel (or finite element) implementation on a hybrid multi-CPU/multi-GPU (graphics processing units/GPUs) cluster. This allows us to obtain information on density distributions in heterogeneous media with an efficient computational time. In a new software package called TOMOFAST3D, the inversion is solved with an iterative least-square or a gradient technique, which minimizes a hybrid L 1 -/ L 2 -norm–based misfit function. It is drastically accelerated using either Haar or fourth-order Daubechies wavelet compression operators, which are applied to the sensitivity matrix kernels involved in the misfit minimization. The compression process behaves like a pre-conditioning of the huge linear system to be solved and a reduction of two or three orders of magnitude of the computational time can be obtained for a given number of CPU processor cores. The memory storage required is also significantly reduced by a similar factor. Finally, we show how this CPU parallel inversion code can be accelerated further by a factor between 3.5 and 10 using GPU computing. Performance levels are given for an application to Ghana, and physical information obtained after 3-D inversion using a sensitivity matrix with around 5.37 trillion elements is discussed. Using compression the whole inversion process can last from a few minutes to less than an hour for a given number of processor cores instead of tens of hours for a similar number of processor cores when compression is not used.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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