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  • Articles  (34)
  • Oxford University Press  (26)
  • Wiley  (4)
  • Wiley-Blackwell  (4)
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  • Articles  (34)
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  • 1
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    Automatic detection of low-frequency earthquakes (LFEs) based on a beamformed network response (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-16
    Description: Low-frequency earthquakes (LFEs), which frequently originate from multiplet-generating sources that are closely linked with tectonic tremor in subduction zones around the world, are difficult to observe and characterize due to their low signal-to-noise ratios. This obstacle can be sidestepped by detecting and then stacking all of the multiplets of a master LFE event, or template, using a matched-filter search; the difficulty however lies in finding an LFE event to use as a template. We implement here an automated beamforming algorithm to detect LFEs within the Mexican subduction zone that can then be used as templates in a matched-filter search. Seismograms recorded on a network of seismic stations are aligned to match the moveout of a potential source at depth and their energies are then summed; any spikes in the summed energy indicate an event originating from that potential source. We apply this method to a 1-d test case and we are able to detect 381 unique, potential LFE templates. We then compare our method to a previously introduced LFE detection scheme based on multiplet correlations for three test cases and find that the two methods are complementary.
    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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  • 2
    Electronic Resource
    Electronic Resource
    Histogenesis of Swiss white mouse secondary palate from nine and one-half days to fifteen and one-half days In utero. I. Epithelial-mesenchymal relationships - light and electron microscopyThis work was supported by Research grant DE 03002 from the National Institute of Dental Research, NIH. (1970)
    New York, NY : Wiley-Blackwell
    Journal of Morphology 130 (1970), S. 435-449 
    Details
    ISSN: 0362-2525
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Development of the secondary palate in Swiss white mouse embroyos was studied from age nine-and-one-half days in utero to the stage of mesenchymal coalescence in the secondary palate (approximately fifteen-and-one-half days). The greatest changes observed occur in the mesenchyme. At early stages, mesenchymal cells underlying oral ectoderm of the head are few and only occasionally contact the ectoderm. Electron micrographs show large intercellular spaces between the ectodermal cells. As embryogenesis continues, the mesenchymal cells become more numerous, closer to each other and closer to the epithelium. Just prior to horizontal transposition of shelves, the mesenchymal cells spread farther from each other and from the palatal epithelium and epithelium of the palatal tip becomes stretched. Ultrastructurally the intercellular spaces between epithelial cells of the palate tip have become much smaller. Some mitochondria in some epithelial cells are swollen and have clear matrices and distorted cristae. The shelves become horizontal and meet in the midpalate. Cells with degeneration bodies are seen in the epithelial seam. The seam undergoes autolysis and is replaced by mesenchyme. The morphological changes described, particularly in the mesenchyme, may play an important role in determining the effect of various teratogens at different stages of palatal development. The changes in both mesenchyme and epithelial cells in the later stages may constitute part of the process of preparing shelves for fusion as postulated by Pourtois ('66).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmor.1051300404
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  • 3
    Electronic Resource
    Electronic Resource
    Lanthanide-induced shifts in proton NMR spectra - IV:Part III, B. L. Shapiro and M. D. Johnston Jr, J. Am. Chem. Soc. in press. Praseodymium-induced shifts to lower applied fields and obscured chemical shifts from lanthanide-induced shift (LIS) data (1972)
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 4 (1972), S. 825-829 
    Details
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Praseodymium(III) tris(dipivalomethanato) [Pr(DPM)3] reduces the complex overlapping aromatic absorptions in the proton NMR spectrum of a monosubstituted naphthalene, cis-3-(1-naphthyl)-1,3,5,5-tetramethlcyclohexan-1-ol(1) to a virtually first-order pattern, whereas Eu(DPM)3 at the same and higher molar concentrations does not completely resolve the aromatic proton signals. Plots of the Pr(DPM)3-induced shifts measured in carbon tetrachloride solution versus molar equivalents of Pr(DPM)3 added may be extrapolated to provide accurate chemical shifts in the absence of added lanthanide shift reagent (LSR). The qualitative conformational conclusions from the Pr(DPM)3 shifts agree with those from the Eu(DPM)3-induced shifts, but there are detailed differences in the relative lanthanide-induced shifts (LIS) for different proton types in the molecule.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/mrc.1270040606
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  • 4
    Electronic Resource
    Electronic Resource
    Concerning some unusual trimethylsilyl proton chemical shiftsTaken, in part, from the PhD Dissertation of Thomas W. Proulx, Texas A & M University, 1975. (1976)
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 8 (1976), S. 40-44 
    Details
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and 13C NMR data are presented for six different compounds containing the fragment C6H5—C—CH2SiMe3. In a number of instances it was observed that, in the 1H NMR spectrum, the SiMe3 groups had a chemical shift significantly upfield from internal tetramethylsilane (δ = -0·14 to -0·36). These unexpected upfield chemical shifts of the SiMe3 groups are suggested to result from the predominance, on a time averaged basis, of conformations which place the methyl groups attached to silicon in the face of an aromatic ring. The preference for such conformations is, in turn, the result of rotational preferences exhibited by the ‘flat’ aromatic ring. These results suggest that conformational analysis of systems containing a phenyl ring should take more explicit account of the fact that the preferred orientation of this phenyl ring can have a profound influence on the conformation adopted by the remainder of the molecule. In addition, the preferred conformation of the phenyl ring can have a significant effect upon the observed 1H NMR chemical shifts, while the 13C chemical shifts are relatively insensitive to conformational factors and can be explained by well-known substituent effects previously delineated for all-carbon systems.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/mrc.1270080110
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  • 5
    Electronic Resource
    Electronic Resource
    Lanthanide-induced shifts in proton NMR spectra of cyclohexanonesSee ref 1. (1973)
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 5 (1973), S. 21-27 
    Details
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The lanthanide-induced shifts (LIS) of the lanthanide shift reagent (LSR) Eu(FOD)3 are reported for a large number of cyclohexanones, especially those which are highly substituted. The following compounds were synthesized and characterized: 3-(aryl)-3,5,5-trimethylcyclohexanones, in which aryl = 1-naphthyl, phenyl, o-anisyl, m-anisyl, p-anisyl and p-chlorophenyl. Some analogous compounds were also studied: 3,5,5-trimethylcyclohexanone, 4-tert-butyl-cyclohexanone, 3,3,5,5-tetramethylcyclohexanone 3-(1-naphthyl)5,5-dimethylcyclohexanone and para-tert-butyl-anisole. A method for the regression analysis of the concentration dependence of the LIS of these substrates is developed and reported, and used to derive the limiting incremental LIS (Δ2) for the LS2 complex and to evaluate the proton chemical shifts (δ0) in the absence of LSR. An ‘incremental dilution’ technique was found to be most appropriate to insure constant substrate concentrations, needed to extract both Δ2 and δ0. The conformations of the 3-(aryl)-type systems and analogous compounds were studied via LIS and found to conform to: - (i) an axially disposed aryl substituent in the 3,3,5,5-tetra-substituted cyclohexanones and (ii) a flattened chair form of the cyclohexanone ring with distortions in this chair form being an increase in the syn-diaxial (C-3, C-5) substituent distance (C-3 and C-5 substituents still eclipsed). The LIS were fully compatible with these structural assumptions.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/mrc.1270050107
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  • 6
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    Genomic Data from Extinct North American Camelops Revise Camel Evolutionary History (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-20
    Description: Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicuñas). These results contradict previous morphology-based phylogenetic models for Camelops , which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages (2013)
    Oxford University Press
    Details
    Publication Date: 2013-01-19
    Description: In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci (2013)
    Oxford University Press
    Details
    Publication Date: 2013-02-06
    Description: Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Pycellerator: an arrow-based reaction-like modelling language for biological simulations (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-06
    Description: Motivation: We introduce Pycellerator, a Python library for reading Cellerator arrow notation from standard text files, conversion to differential equations, generating stand-alone Python solvers, and optionally running and plotting the solutions. All of the original Cellerator arrows, which represent reactions ranging from mass action, Michales–Menten–Henri (MMH) and Gene-Regulation (GRN) to Monod–Wyman–Changeaux (MWC), user defined reactions and enzymatic expansions (KMech), were previously represented with the Mathematica extended character set. These are now typed as reaction-like commands in ASCII text files that are read by Pycellerator, which includes a Python command line interface (CLI), a Python application programming interface (API) and an iPython notebook interface. Results: Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica. Availability and implementation: All software is available (GPL) from the github repository at https://github.com/biomathman/pycellerator/releases . Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information . Contact: bruce.e.shapiro@csun.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-31
    Description: Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recent western European neandertals (〈48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison with both eastern and older (〉48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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