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  • Articles  (257)
  • Gravity, Geodesy and Tides  (98)
  • Synthetic Biology and Assembly Cloning  (70)
  • Genomics  (47)
  • Natural Disasters  (42)
  • Oxford University Press  (257)
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  • Articles  (257)
Years
  • 1
    Publication Date: 2017-01-05
    Description: The system of prior appropriation in the Western Unites States prioritizes property rights for water based on the establishment of beneficial use, creating a hierarchy where rights initiated first are more secure. I estimate the demand for security in water rights through their capitalization in agricultural property markets in the Yakima River Basin, a major watershed in Washington State. All water rights are satisfied in an average year, so the relative value of secure property rights is a function of water supply volatility and the costs of droughts are predominantly born by those with weak rights. In aggregate, security in water rights does not capitalize into property values at the irrigation district level; however, there is heterogeneity in the premium for secure water rights. The lack of a premium for district-level water security is robust to a variety of econometric methods to account for correlated district unobservables, and the null result produces an economically significant upper bound on the value to water security for the district. The ability for farmers to adapt to water supply volatility, as well as expectations about water markets and government infrastructure investment, are leading explanations for the lack of an aggregate premium. These explanations are supported by the pattern of heterogeneity in the water security premium.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q21 - Demand and Supply, Q24 - Land, Q25 - Water, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 2
    Publication Date: 2017-01-07
    Description: By introducing two types of zenith troposphere delay (ZTD) products in precise point positioning (PPP), we developed the ZTD-corrected PPP and the ZTD-constrained PPP, both of them reduced the PPP convergence time. Both enhanced PPP methods are examined by global empirical ZTD models and regional ZTD corrections. For global ZTD models, we verified that ZTD-corrected PPP will deviate the positioning results, while ZTD-constrained PPP could produce unbiased estimations. Therefore, the latter is utilized to study the performance of global ZTD models (ITG, GPT2w, GZTD and UNB3m). After numerous experiments, we found that the performance of ZTD models was positively related to the real ZTD accuracy, and we proposed a universal tropospheric stochastic model 2SQR(9rms) which denotes double the square of nine times ZTD rms, to constrain ZTD in PPP. The proposed model subsequently was validated by real-time static and kinematic ZTD-constrained PPP on the premise that the ZTD rms on every station was known. Compared with traditional PPP, in static PPP, the number of improved stations is increased by 15.5 per cent (ITG), 14.4 per cent (GPT2w), 11.1 per cent (GZTD) and 8.3 per cent (UNB3m). For kinematic PPP, PPP constrained by ITG model still had the best performance, the number of improved stations is increased by 14.4 per cent, after 30 min of initialization time, 13.4 cm east, 13.4 cm north and 11.7 cm up positioning accuracy was obtained, compared with 15.3 cm east, 15.3 cm north and 14.3 cm up accuracy by traditional PPP. In addition, experiments using regional ZTD corrections to enhance real-time PPP showed that both ZTD-corrected PPP and ZTD-constrained PPP can notably reduce the convergence time on the vertical component (within 15 cm).
    Keywords: Gravity, Geodesy and Tides
    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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  • 3
    Publication Date: 2017-01-01
    Description: We study fluctuations in the degree-2 zonal spherical harmonic coefficient of the Earth's gravity potential, C 20 , over the period 2003–2015. This coefficient is related to the Earth's oblateness and studying its temporal variations, C 20 , can be used to monitor large-scale mass movements between high and low latitude regions. We examine C 20 inferred from six different sources, including satellite laser ranging (SLR), GRACE and global geophysical fluids models. We further include estimates that we derive from measured variations in the length-of-day (LOD), from the inversion of global crustal displacements as measured by GPS, as well as from the combination of GRACE and the output of an ocean model as described by Sun et al. We apply a sequence of trend and seasonal moving average filters to the different time-series in order to decompose them into an interannual, a seasonal and an intraseasonal component. We then perform a comparison analysis for each component, and we further estimate the noise level contained in the different series using an extended version of the three-cornered-hat method. For the seasonal component, we generally obtain a very good agreement between the different sources, and except for the LOD-derived series, we find that over 90 per cent of the variance in the seasonal components can be explained by the sum of an annual and semiannual oscillation of constant amplitudes and phases, indicating that the seasonal pattern is stable over the considered time period. High consistency between the different estimates is also observed for the intraseasonal component, except for the solution from GRACE, which is known to be affected by a strong tide-like alias with a period of about 161 d. Estimated interannual components from the different sources are generally in agreement with each other, although estimates from GRACE and LOD present some discrepancies. Slight deviations are further observed for the estimate from the geophysical models, likely to be related to the omission of polar ice and groundwater changes in the model combination we use. On the other hand, these processes do not seem to play an important role at seasonal and shorter timescales, as the sum of modelled atmospheric, oceanic and hydrological effects effectively explains the observed C 20 variations at those scales. We generally obtain very good results for the solution from SLR, and we confirm that this well-established technique accurately tracks changes in C 20 . Good agreement is further observed for the estimate from the GPS inversion, showing that this indirect method is successful in capturing fluctuations in C 20 on scales ranging from intra- to interannual. Obtaining accurate estimates from LOD, however, remains a challenging task and more reliable models of atmospheric wind fields are needed in order to obtain high-quality C 20 , in particular at the seasonal scale. The combination of GRACE data and the output of an ocean model appears to be a promising approach, particularly since corresponding C 20 is not affected by tide-like aliases, and generally gives better results than the solution from GRACE, which still seems to be of rather poor quality.
    Keywords: Gravity, Geodesy and Tides
    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
    Publication Date: 2017-01-10
    Description: Despite the extensive use of  Saccharomyces cerevisiae  as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editing methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2016-07-28
    Description: Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.
    Keywords: Synthetic Biology and Assembly Cloning
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    Topics: Biology
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  • 6
    Publication Date: 2016-07-08
    Description: The geocentre motion is the motion of the centre of mass of the entire Earth, considered an isolated system, in a terrestrial system of reference. We first derive a formula relating the harmonic degree-1 Lagrangian variation of the gravity at a station to both the harmonic degree-1 vertical displacement of the station and the displacement of the whole Earth's centre of mass. The relationship is independent of the nature of the Earth deformation and is valid for any source of deformation. We impose no constraint on the system of reference, except that its origin must initially coincide with the centre of mass of the spherically symmetric Earth model. Next, we consider the geocentre motion caused by surface loading. In a system of reference whose origin is the centre of mass of the solid Earth, we obtain a specific relationship between the gravity variation at the surface, the geocentre displacement and the load Love number $h^{\prime }_1$ , which demands the Earth's structure and rheological behaviour be known. For various networks of real or fictitious stations, we invert synthetic signals of surface gravity variations caused by atmospheric loading to retrieve the degree-1 variation of gravity. We then select six well-distributed stations of the Global Geodynamics Project, which is a world network of superconducting gravimeters, to invert actual gravity data for the degree-1 variations and determine the geocentre displacement between the end of 2004 and the beginning of 2012, assuming it to be due to surface loading. We find annual and semi-annual displacements with amplitude 0.5–2.3 mm.
    Keywords: Gravity, Geodesy and Tides
    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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  • 7
    Publication Date: 2016-07-09
    Description: Large rural-urban wage gaps observed in many developing countries are suggestive of barriers to migration that keep potential migrants in rural areas. Using long panel data spanning nearly two decades, I study the extent to which migration rates are constrained by liquidity constraints in rural Tanzania. The analysis begins by quantifying the impact of weather variation on household welfare. The results show how household consumption co-moves with temperature, rendering households vulnerable to local weather events. These temperature-induced income shocks are then found to inhibit long-term migration among men, thus preventing them from tapping into the opportunities brought about by geographical mobility.
    Keywords: O12 - Microeconomic Analyses of Economic Development, O15 - Human Resources ; Human Development ; Income Distribution ; Migration, Q54 - Climate ; Natural Disasters ; Global Warming, R23 - Regional Migration ; Regional Labor Markets ; Population
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 8
    Publication Date: 2016-05-05
    Description: We review the theory of the Earth's elastic and gravitational response to a surface disk load. The solutions for displacement of the surface and the geoid are developed using expansions of Legendre polynomials, their derivatives and the load Love numbers. We provide a matlab  function called diskload that computes the solutions for both uncompensated and compensated disk loads. In order to numerically implement the Legendre expansions, it is necessary to choose a harmonic degree, n max , at which to truncate the series used to construct the solutions. We present a rule of thumb (ROT) for choosing an appropriate value of n max , describe the consequences of truncating the expansions prematurely and provide a means to judiciously violate the ROT when that becomes a practical necessity.
    Keywords: Gravity, Geodesy and Tides
    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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  • 9
    Publication Date: 2016-05-06
    Description: Two types of signals are clearly visible in continuous GPS (cGPS) time-series in Iceland, in particular in the vertical component. The first one is a yearly seasonal cycle, usually sinusoid-like with a minimum in the spring and a maximum in the fall. The second one is a trend of uplift, with higher values the closer the cGPS stations are to the centre of Iceland and ice caps. Here, we study the seasonal cycle signal by deriving its average at 71 GPS sites in Iceland. We estimate the annual and semi-annual components of the cycle in their horizontal and vertical components using a least-squares adjustment. The peak-to-peak amplitude of the cycle of the vertical component at the studied sites ranges from 4 mm near the coastline up to 27 mm at the centre of the Vatnajökull, the largest ice cap in Iceland. The minimum of the seasonal cycle occurs earlier in low lying areas than in the central part of Iceland, consistent with snow load having a large influence on seasonal deformation. Modelling shows that the seasonal cycle is well explained by accounting for elastically induced surface displacements due to snow, atmosphere, reservoir lake and ocean variations. Model displacement fields are derived considering surface loads on a multilayered isotropic spherical Earth. Through forward and inverse modelling, we were able to reproduce a priori information on the average seasonal cycle of known loads (atmosphere, snow in non-glaciated areas and lake reservoir) and get an estimation of other loads (glacier mass balance and ocean). The seasonal glacier mass balance cycle in glaciated areas and snow load in non-glaciated areas are the main contributions to the seasonal deformation. For these loads, induced seasonal vertical displacements range from a few millimetres far from the loads in Iceland, to more than 20 mm at their centres. Lake reservoir load also has to be taken into account on local scale as it can generate up to 20 mm of vertical deformation. Atmosphere load and ocean load are observable and generate vertical displacements in the order of a few millimetres. Inversion results also shows that the Iceland crust is less rigid than the world average. Interannual deviation from the GPS seasonal cycle can occur and are caused by unusual weather conditions over extended period of time.
    Keywords: Gravity, Geodesy and Tides
    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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  • 10
    Publication Date: 2016-07-09
    Description: Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.
    Keywords: Genomics
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    Topics: Biology
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  • 11
    Publication Date: 2016-07-28
    Description: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.
    Keywords: Genomics
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    Topics: Biology
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  • 12
    Publication Date: 2016-04-03
    Description: Seismic waves produced by fault ruptures give rise to gravity perturbations. So far, these perturbations have either been modelled as permanent coseismic gravity change in a half-space or spherical Earth model, or as full time-domain model in infinite space. In this paper, we present the explicit solution of gravity perturbations in time domain produced by a double-couple buried in a homogeneous half-space. This result is especially suited to study gravity perturbations up to a few hundreds of kilometres from the epicentre. It facilitates detailed parametric studies of gravity perturbations from fault rupture, and predicts gravity perturbations of real earthquakes with greatly improved accuracy. The results may serve to develop first designs of gravity-assisted earthquake early-warning systems, made possible by a new generation of ultrasensitive gravity gradiometers, which is currently under development.
    Keywords: Gravity, Geodesy and Tides
    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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  • 13
    Publication Date: 2016-04-07
    Description: Continuous gravimetric observations have been made with three successive generations of superconducting gravimeter over 20 yr at Syowa Station ( $39.6\deg$ E, $69.0\deg$ S), East Antarctica. The third-generation instrument, OSG#058, was installed in January 2010 and was calibrated by an absolute gravimeter during January and February, 2010. The estimated scale factor was –73.823 ± 0.053 μGal V –1 (1 μGal = 10 –8 m s –2 ). The first 5 yr of OSG#058 data from 2010 January 7 to 2015 January 10 were decomposed into tidal waves (M3 to Ssa) and other non-tidal components by applying the Bayesian tidal analysis program BAYTAP. Long-term non-tidal gravity residuals, which were obtained by subtracting annual and 18.6 year tidal waves and the predicted gravity response to the Earth's variable rotation, showed significant correlation with the accumulated snow depth measured at Syowa Station. The greatest correlation occurred when the gravity variations lagged the accumulated snow depth by 21 d. To estimate the gravitational effect of the accumulated snow mass, we inferred a conversion factor of 3.13 ± 0.08 μGal m –1 from this relation. The accumulated snow depth at Syowa Station was found to represent an extensive terrestrial water storage (the snow accumulation) around Syowa Station, which was estimated from the Gravity Recovery and Climate Experiment satellite gravity data. The snow accumulation around Syowa Station was detectable by the superconducting gravimeter.
    Keywords: Gravity, Geodesy and Tides
    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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  • 14
    Publication Date: 2016-04-07
    Description: The new release AIUB-RL02 of monthly gravity models from GRACE GPS and K-Band range-rate data is based on reprocessed satellite orbits referring to the reference frame IGb08. The release is consistent with the IERS2010 conventions. Improvements with respect to its predecessor AIUB-RL01 include the use of reprocessed (RL02) GRACE observations, new atmosphere and ocean dealiasing products (RL05), an upgraded ocean tide model (EOT11A), and the interpolation of shallow ocean tides (admittances). The stochastic parametrization of AIUB-RL02 was adapted to include daily accelerometer scale factors, which drastically reduces spurious signal at the 161 d period in C 20 and at other low degree and order gravity field coefficients. Moreover, the correlation between the noise in the monthly gravity models and solar activity is considerably reduced in the new release. The signal and the noise content of the new AIUB-RL02 monthly gravity fields are studied and calibrated errors are derived from their non-secular and non-seasonal variability. The short-period time-variable signal over the oceans, mostly representing noise, is reduced by 50 per cent with respect to AIUB-RL01. Compared to the official GFZ-RL05a and CSR-RL05 monthly models, the AIUB-RL02 stands out by its low noise at high degrees, a fact emerging from the estimation of seasonal variations for selected river basins and of mass trends in polar regions. Two versions of the monthly AIUB-RL02 gravity models, with spherical harmonics resolution of degree and order 60 and 90, respectively, are available for the time period from March 2003 to March 2014 at the International Center for Global Earth Models or from ftp://ftp.unibe.ch/aiub/GRAVITY/GRACE (last accessed 22 March 2016).
    Keywords: Gravity, Geodesy and Tides
    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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  • 15
    Publication Date: 2016-01-09
    Description: Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.
    Keywords: Genomics
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  • 16
    Publication Date: 2016-01-09
    Description: Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a ‘DNA pulley’ for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 17
    Publication Date: 2016-01-09
    Description: Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is not enough to predict the behavior of designed circuits and thus, a costly trial-error process is eventually required. In this work, we provide a new theoretical framework for the predictive treatment of the genetic load. We mathematically and experimentally demonstrate that dependences among genes follow a quantitatively predictable behavior. Our theory predicts the observed reduction of the expression of a given synthetic gene when an extra genetic load is introduced in the circuit. The theory also explains that such dependence qualitatively differs when the extra load is added either by transcriptional or translational modifications. We finally show that the limitation of the cellular resources for gene expression leads to a mathematical formulation that converges to an expression analogous to the Ohm's law for electric circuits. Similitudes and divergences with this law are outlined. Our work provides a suitable framework with predictive character for the design process of complex genetic devices in synthetic biology.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 18
    Publication Date: 2016-01-01
    Description: We document two kinds of traveling ionospheric disturbances, namely, CTIDs (Co-tsunami-Traveling-Ionospheric-disturbances) and ATIDs (Ahead-of-Tsunami-Traveling-Ionospheric-disturbances) related to the Tohoku-Oki tsunami of 2011 March 11. They are referred to the disturbances that remain behind and ahead of the principal tsunami wave front, respectively. We first note their presence in a numerical experiment performed using a simulation code coupling the tsunami, atmosphere and ionosphere. This code uses the tsunami wavefield as an input and simulates acoustic-gravity waves (AGWs) in the atmosphere and TIDs, in the form of total electron content (TEC) disturbance, in the ionosphere. The simulated TEC reveals the excitation of CTIDs (at about 2 TECU) and ATIDs (at about 1 TECU), representing up to 5 per cent disturbance over the ambient electron density, and they arise from the dissipation of AGWs in the thermosphere. A novel outcome is that during the tsunami passage between ~6° and 12° of epicentral distance, strong ATIDs arrive ~20–60 min ahead of the tsunami wave front covering ~3°–10° of distance from the tsunami location. Simulation results are compared with the far-field observations using GNSS satellites and confirm that ATIDs are the first detected TEC maximum, occurring 20–60 min ahead of the tsunami arrival. Our simulation also confirms the presence of largest TEC maximum representing CTIDs, 10–20 min after the first tsunami wave. ATIDs reported in this study have characteristics that can be potentially used for the early warning of the tsunami.
    Keywords: Gravity, Geodesy and Tides
    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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  • 19
    Publication Date: 2016-07-03
    Description: Apparent acceleration in Gravity Recovery and Climate Experiment (GRACE) Antarctic ice mass time-series may reflect both ice discharge and surface mass balance contributions. However, a recent study suggests there is also contamination from errors in atmospheric pressure de-aliasing fields [European Center for Medium-Range Weather Forecast (ECMWF) operational products] used during GRACE data processing. To further examine this question, we compare GRACE atmospheric pressure de-aliasing (GAA) fields with in situ surface pressure data from coastal and inland stations. Differences between the two are likely due to GAA errors, and provide a measure of error in GRACE solutions. Time-series of differences at individual weather stations are fit to four presumed error components: annual sinusoids, a linear trend, an acceleration term and jumps at times of known ECMWF model changes. Using data from inland stations, we estimate that atmospheric pressure error causes an acceleration error of about +7.0 Gt yr –2 , which is large relative to prior GRACE estimates of Antarctic ice mass acceleration in the range of –12 to –14 Gt yr –2 . We also estimate apparent acceleration rates from other barometric pressure (reanalysis) fields, including ERA-Interim, MERRA and NCEP/DOE. When integrated over East Antarctica, the four mass acceleration estimates (from GAA and the three reanalysis fields) vary considerably (by ~2–16 Gt yr –2 ). This shows the need for further effort to improve atmospheric mass estimates in this region of sparse in situ observations, in order to use GRACE observations to measure ice mass acceleration and related sea level change.
    Keywords: Gravity, Geodesy and Tides
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    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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  • 20
    Publication Date: 2016-08-20
    Description: Light-regulated modules offer unprecedented new ways to control cellular behavior in precise spatial and temporal resolution. The availability of such tools may dramatically accelerate the progression of synthetic biology applications. Nonetheless, current optogenetic toolbox of prokaryotes has potential issues such as lack of rapid and switchable control, less portable, low dynamic expression and limited parts. To address these shortcomings, we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222. We demonstrated that by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely. We show that both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light. In addition, the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model. We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal. Overall, our modular approach layers a transformative platform for next-generation light-controllable synthetic biology systems in prokaryotes.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 21
    Publication Date: 2016-08-27
    Description: The long-wavelength gravity field contains information about processes in the sublithospheric mantle. As satellite-derived gravity models now provide the long to medium-wavelength gravity field at unprecedented accuracy, techniques used to process gravity data need to be updated. We show that when determining these long-wavelengths, the treatment of topographic-isostatic effect (TIE) and isostatic effects (IE) is a likely source of error. We constructed a global isostatic model and calculated global TIE and IE. These calculations were done for ground stations as well as stations at satellite height. We considered both gravity and gravity gradients. Using these results, we determined how much of the gravity signal comes from distant sources. We find that a significant long-wavelength bias is introduced if far-field effects on the topographic effect are neglected. However, due to isostatic compensation far-field effects of the topographic effect are to a large degree compensated by the far-field IE. This means that far-field effects can be reduced effectively by always considering topographic masses together with their compensating isostatic masses. We show that to correctly represent the ultra-long wavelengths, a global background model should be used. This is demonstrated both globally and for a continental-scale case area in North America. In the case of regional modelling, where the ultra-long wavelengths are not of prime importance, gravity gradients can be used to help minimize correction errors caused by far-field effects.
    Keywords: Gravity, Geodesy and Tides
    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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  • 22
    Publication Date: 2016-08-12
    Description: Constraining laterally varying structures in planetary interiors is important for understanding both the composition and the internal dynamics of a planet. Recognizing that seismic imaging technique is currently only viable for studying the Earth's interior structures, methods that can be supported by advanced space geodetic techniques may become alternatives to ‘image’ the interiors of other planets. The method of tidal tomography is one possibility, and it relies on high precision measurement of the response of a planet to its body tide. However, it is essential to develop an efficient analytical tool that computes the dependence of tidal response to 3-D interior structures. In this paper, we present a complete formulation of such an analytical tool, which calculates to high accuracy the tidal response of a terrestrial planet with lateral heterogeneities in its elastic and density structures. We treat the lateral heterogeneities as small perturbations and derive the governing equations based on the perturbation theory. In a spherical harmonic representation, equations at each order of perturbation are reduced into multiple matrix equations at harmonics that are allowed by mode couplings, and the total response equals the sum of all those single-harmonic responses, which can be solved semi-analytically. We test our perturbation method by applying it to the Moon with a harmonic degree-1 mantle structure for which the perturbation solutions of the tidal response are compared with those from a fully numerical method. The remarkable agreement between results from these two methods validates the perturbation method. As an example, we then use the perturbation method to evaluate the impact of lunar crustal thickness variations on tidal response of the Moon. We find that lunar crust produces much smaller degree-3 tidal responses than a relatively weak degree-1 structure in the deep lunar mantle. Our calculations show that degree-3 tidal response measurements may hold key constraints on possible degree-1 mantle structure of the Moon, as suggested from previous modelling results.
    Keywords: Gravity, Geodesy and Tides
    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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  • 23
    Publication Date: 2016-08-14
    Description: Seismic data are primarily used in studies of the Earth's lithospheric structure including the Moho geometry. In regions, where seismic data are sparse or completely absent, gravimetric or combined gravimetric-seismic methods could be applied to determine the Moho depth. In this study, we derive and present generalized expressions for solving the Vening Meinesz–Moritz's (VMM) inverse problem of isostasy for a Moho depth determination from gravity and vertical gravity-gradient data. By solving the (non-linear) Fredholm's integral equation of the first kind, the linearized observation equations, which functionally relate the (given) gravity/gravity-gradient data to the (unknown) Moho depth, are derived in the spectral domain. The VMM gravimetric results are validated by using available seismic and gravimetric Moho models. Our results show that the VMM Moho solutions obtained by solving the VMM problem for gravity and gravity-gradient data are almost the same. This finding indicates that in global applications, using the global gravity/gravity-gradient data coverage, the spherical harmonic expressions for the gravimetric forward and inverse modelling yield (theoretically) the same results. Globally, these gravimetric solutions have also a relatively good agreement with the CRUST1.0 and GEMMA GOCE models in terms of their rms Moho differences (4.7 km and 4.1 km, respectively).
    Keywords: Gravity, Geodesy and Tides
    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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  • 24
    Publication Date: 2016-08-20
    Description: A multi-year drought has taken a severe toll on the agricultural economy of California’s Central Valley. Index insurance is an instrument with the potential to protect water users from economic losses due to periodic water shortages. An index insurance product based on the Sacramento Index and adapted to the Central Valley Project water supply is proposed. To address the potential for intertemporal adverse selection, three product designs are suggested: (1) "early bird" insurance; (2) variable premium insurance; and (3) variable deductible insurance. The performance of the designs are assessed using loss functions from the Westlands Water District in the San Joaquin Valley.
    Keywords: Q14 - Agricultural Finance, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 25
    Publication Date: 2016-08-20
    Description: Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated ‘CasHRA ( Cas 9-facilitated H omologous R ecombination A ssembly)’ that directly uses large circular DNAs in a one-step in vivo assembly process. The large circular DNAs are co-introduced into Saccharomyces cerevisiae by protoplast fusion, and they are cleaved by RNA-guided Cas9 nuclease to release the linear DNA segments for subsequent assembly by the endogenous homologous recombination system. The CasHRA method allows efficient assembly of multiple large DNA segments in vivo ; thus, this approach should be useful in the last stage of genome construction. As a proof of concept, we combined CasHRA with an upstream assembly method (Gibson procedure of genome assembly) and successfully constructed a 1.03 Mb MGE-syn1.0 ( M inimal G enome of Escherichia coli ) that contained 449 essential genes and 267 important growth genes. We expect that CasHRA will be widely used in megabase-sized genome constructions.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 26
    Publication Date: 2016-08-20
    Description: Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an i ntegrative and d iscriminative e pigenome a nnotation s ystem, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 27
    Publication Date: 2016-08-27
    Description: Geophysical techniques are widely used to monitor volcanic unrest. A number of studies have also demonstrated that hydrological processes can produce or trigger geophysical signals. Hydrologically induced gravity signals have previously been recorded by specifically designed gravity surveys as well as, inadvertently, by volcano monitoring studies. Water table corrections of microgravity surveys are commonplace. However, the fluctuations of the water table beneath survey locations are often poorly known, and such a correction fails to account for changes in water-mass storage in the unsaturated zone. Here, we combine 2-D axis-symmetrical numerical fluid-flow models with an axis-symmetric, distributed-mass, gravity calculation to model gravity changes in response to fluctuating hydrological recharge. Flow simulations are based on tropical volcanic settings where high surface permeabilities promote thick unsaturated zones. Our study highlights that mass storage (saturation) changes within the unsaturated zone beneath a survey point can generate recordable gravity changes. We show that for a tropical climate, recharge variations can generate gravity variations of over 150 μGal; although, we demonstrate that for the scenarios investigated here, the probability of recording such large signals is low. Our modelling results indicate that microgravity survey corrections based on water table elevation may result in errors of up to 100 μGal. The effect of inter-annual recharge fluctuations dominate over seasonal cycles which makes prediction and correction of the hydrological contribution more difficult. Spatial hydrogeological heterogeneity can also impact on the accuracy of relative gravity surveys, and can even result in the introduction of additional survey errors. The loading fluctuations associated with saturation variations in the unsaturated zone may also have implications for other geophysical monitoring techniques, such as geodetic monitoring of ground deformation.
    Keywords: Gravity, Geodesy and Tides
    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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  • 28
    Publication Date: 2016-06-19
    Description: Several attempts have been made to obtain a radiographic image inside volcanoes using cosmic-ray muons (muography). Muography is expected to resolve highly heterogeneous density profiles near the surface of volcanoes. However, several prior works have failed to make clear observations due to contamination by background noise. The background contamination leads to an overestimation of the muon flux and consequently a significant underestimation of the density in the target mountains. To investigate the origin of the background noise, we performed a Monte Carlo simulation. The main components of the background noise in muography are found to be low-energy protons, electrons and muons in case of detectors without particle identification and with energy thresholds below 1 GeV. This result was confirmed by comparisons with actual observations of nuclear emulsions. This result will be useful for detector design in future works, and in addition some previous works of muography should be reviewed from the view point of background contamination.
    Keywords: Gravity, Geodesy and Tides
    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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  • 29
    Publication Date: 2016-06-09
    Description: Essential to understanding sea level change and its causes during the last interglacial (LIG) is the quantification of uncertainties. In order to estimate the uncertainties, we develop a statistical framework for the comparison of palaeoclimatic sea level index points and GIA model predictions. For the investigation of uncertainties, as well as to generate better model predictions, we implement a massive ensemble approach by applying a data assimilation scheme based on particle filter methods. The different runs are distinguished through varying ice sheet reconstructions based on oxygen-isotope curves and different parameter selections within the GIA model. This framework has several advantages over earlier work, such as the ability to examine either the contribution of individual observations to the results or the probability of specific input parameters. This exploration of input parameters and data leads to a larger range of estimates than previously published work. We illustrate how the assumptions that enter into the statistical analysis, such as the existence of outliers in the observational database or the initial ice volume history, can introduce large variations to the estimate of the maximum highstand. Thus, caution is required to avoid overinterpreting results. We conclude that there are reasonable doubts whether the data sets previously used in statistical analyses are able to tightly constrain the value of maximum highstand during the LIG.
    Keywords: Gravity, Geodesy and Tides
    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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  • 30
    Publication Date: 2016-06-01
    Description: A 3-D density model of the crust and upper mantle beneath the Karoo basin is presented here. The model is constrained using potential field, borehole and seismic data. Uplift of the basin by the end of the Cretaceous has resulted in an unusually high plateau (〉1000 m) covering a large portion of South Africa. Isostatic studies show the topography is largely compensated by changes in Moho depths (~35 km on-craton and 〉45 km off-craton) and changes in lithospheric mantle densities between the Kaapvaal Craton and surrounding regions (~50 kg m –3 increase from on- to off-craton). This density contrast is determined by inverted satellite gravity and gravity gradient data. The highest topography along the edge of the plateau (〉1200 m) and a strong Bouguer gravity low over Lesotho, however, can only be explained by a buoyant asthenosphere with a density decrease of around 40 kg m –3 .
    Keywords: Gravity, Geodesy and Tides
    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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  • 31
    Publication Date: 2016-06-03
    Description: We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong 70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 32
    Publication Date: 2016-06-19
    Description: A method to estimate the rotation change in the orientation of the centre-of-figure (CF) frame caused by earthquakes is proposed for the first time. This method involves using the point dislocation theory based on a spherical, non-rotating, perfectly elastic and isotropic (SNREI) Earth. The rotation change in the orientation is related solely to the toroidal displacements of degree one induced by the vertical dip slip dislocation, and the spheroidal displacements induced by an earthquake have no contribution. The effects of two recent large earthquakes, the 2004 Sumatra and the 2011 Tohoku-Oki, are studied. Results showed that the Sumatra and Tohoku-Oki earthquakes both caused the CF frame to rotate by at least tens of μas (micro-arc-second). Although the visible co-seismic displacements are identified and removed from the coordinate time-series, the rotation change due to the unidentified ones and errors in removal is non-negligible. Therefore, the rotation change in the orientation of the CF frame due to seismic deformation should be taken into account in the future in reference frame and geodesy applications.
    Keywords: Gravity, Geodesy and Tides
    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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  • 33
    Publication Date: 2016-09-03
    Description: A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 x 10 –4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 x 10 –5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS 1 , IS 2 , IS 5 and IS 186 . Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS 186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
    Keywords: Genomics
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  • 34
    Publication Date: 2016-06-25
    Description: In this study, we propose an approach for determining the geopotential difference using high-frequency-stability microwave links between satellite and ground station based on Doppler cancellation system. Suppose a satellite and a ground station are equipped with precise optical-atomic clocks (OACs) and oscillators. The ground oscillator emits a signal with frequency f a towards the satellite and the satellite receiver (connected with the satellite oscillator) receives this signal with frequency f b which contains the gravitational frequency shift effect and other signals and noises. After receiving this signal, the satellite oscillator transmits and emits, respectively, two signals with frequencies f b and f c towards the ground station. Via Doppler cancellation technique, the geopotential difference between the satellite and the ground station can be determined based on gravitational frequency shift equation by a combination of these three frequencies. For arbitrary two stations on ground, based on similar procedures as described above, we may determine the geopotential difference between these two stations via a satellite. Our analysis shows that the accuracy can reach 1 m 2 s – 2 based on the clocks’ inaccuracy of about 10 –17 (s s –1 ) level. Since OACs with instability around 10 –18 in several hours and inaccuracy around 10 –18 level have been generated in laboratory, the proposed approach may have prospective applications in geoscience, and especially, based on this approach a unified world height system could be realized with one-centimetre level accuracy in the near future.
    Keywords: Gravity, Geodesy and Tides
    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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  • 35
    Publication Date: 2016-07-09
    Description: Climate change affects agriculture by altering not only output quantity, but also crop quality. We quantify the economic impacts of climate change on agriculture through changes in both quantity and quality, where quality is measured by crop grades. Our model controls for methodological issues regarding sample selection, aggregation, phenology, and nonlinearity. The empirical application to Japanese rice production indicates that temperature effects are asymmetric: quantity is especially vulnerable to cold, whereas quality is vulnerable to extremely high temperature. Using these results, we simulate the effect of global warming, and we find that warming (a 3 °C increase) increases farm revenues by improving yield but decreases revenues as a result of deteriorating quality. The net effect is negative, suggesting that quality matters more than quantity. The negative effect, however, can be mitigated by shifting cultivation periods and/or regions. Overall, our results suggest that the estimated impacts of climate change and adaptation strategies could be severely misleading unless quality is considered.
    Keywords: L15 - Information and Product Quality ; Standardization and Compatibility, Q10 - General, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 36
    Publication Date: 2016-02-03
    Description: The availability of practical mechanisms for comparing domestic efforts aimed at mitigating global climate change is important for the stability, equity, and efficiency of international climate agreements. We examine a variety of metrics that could be used to compare countries’ climate change mitigation efforts and illustrate their potential application to large developed and developing countries. Because there is no single, comprehensive, measurable metric that could be applied to all countries, we suggest using a set of indicators to characterize and compare mitigation effort, akin to using a set of economic statistics to indicate the health of the macroeconomy. Given the iterative pledge-and-review approach that is emerging in the current climate change negotiations, participation, commitment, and compliance could be enhanced if this set of indicators is able to show that all parties are doing their "fair share," both prospectively and retrospectively. The latter, in particular, highlights the need for a well-functioning policy surveillance regime. ( JEL : Q54, Q58, F55)
    Keywords: Q54 - Climate ; Natural Disasters ; Global Warming, Q58 - Government Policy, F55 - International Institutional Arrangements
    Print ISSN: 1750-6816
    Electronic ISSN: 1750-6824
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Political Science , Economics
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  • 37
    Publication Date: 2016-02-03
    Description: In this article, we provide an overview of the extensive literature on the impact of weather and climate on grapes and wine, with the goal of identifying how climate change is likely to affect their production. We first discuss the physical impact of weather on vine phenology (i.e., the timing of biological events such as bud break or flowering), berry composition, and yields. Then we examine the economic literature that measures the effects of temperature on wine quality, prices, costs, and profits and, based on this review, infer how climate change will affect these variables. We also describe what has been learned thus far about possible adaptation strategies for grape growers that would allow them to mitigate the economic effects of climate change. We conclude that climate change is likely to produce both winners and losers, with the winners being those located closer to the North and South Poles. There are also likely to be some substantial short-run costs as growers adapt to climate change. Nevertheless, wine making has survived through thousands of years of recorded history, a history that has included significant climate changes. ( JEL : Q13, Q18, Q54)
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 1750-6816
    Electronic ISSN: 1750-6824
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Political Science , Economics
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  • 38
    Publication Date: 2016-02-03
    Description: This article reviews the recent literature on ex post evaluation of the impacts of the European Union (EU) Emissions Trading Scheme (ETS) on regulated firms in the industrial and power sectors. We summarize the findings from original research papers concerning three broadly defined impacts: carbon dioxide emissions, economic performance and competitiveness, and innovation. We conclude by highlighting gaps in the current literature and suggesting priorities for future research on this landmark policy. ( JEL : Q52, Q54, Q58)
    Keywords: Q52 - Pollution Control Costs ; Distributional Effects ; Employment Effects, Q54 - Climate ; Natural Disasters ; Global Warming, Q58 - Government Policy
    Print ISSN: 1750-6816
    Electronic ISSN: 1750-6824
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Political Science , Economics
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  • 39
    Publication Date: 2016-02-03
    Description: This article provides an introduction to the European Union (EU) Emissions Trading System (ETS). First we describe the legislative development of the EU ETS, its evolution from free allocation to auctioning and centralized allocation rules, its relationship to the Kyoto Protocol and other trading systems, and its relationship to other EU climate and energy policies. This is followed by an assessment of the performance of the EU ETS, which focuses in particular on emissions, allowance prices, and the use of offsets. We conclude with a discussion of the current debate about the future of the EU ETS and proposals for changes to both the EU ETS and the climate policy environment in which it operates. ( JEL : Q54, Q58)
    Keywords: Q54 - Climate ; Natural Disasters ; Global Warming, Q58 - Government Policy
    Print ISSN: 1750-6816
    Electronic ISSN: 1750-6824
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Political Science , Economics
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  • 40
    Publication Date: 2016-02-03
    Description: The December 2015 Conference of the Parties (COP) to the United Nations Framework Convention on Climate Change meetings in Paris are likely to yield a global agreement that will slow the world’s growth of greenhouse gas emissions, but this agreement is unlikely to guarantee a decline in global emissions in the near future. Given this reality, climate change adaptation is an increasingly important topic for discussion and study. Although much research has focused on the macroeconomic relationship between economic growth and temperature at the national and/or annual level, microeconomic analysis also offers valuable insights. This Reflections discusses recent work on household and firm responses to three climate change challenges: increased summer heat, higher food prices, and increased natural disaster risk. ( JEL : Q54)
    Keywords: Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 1750-6816
    Electronic ISSN: 1750-6824
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Political Science , Economics
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  • 41
    Publication Date: 2016-02-26
    Description: A sequence of large earthquakes occurred along the North Anatolian fault in the 20th century. These earthquakes, including the 1999 Izmit/Düzce earthquakes, generally propagated westward towards the Marmara Sea, defining the Main Marmara fault as a potential seismic gap. It is important to conduct a detailed assessment of the seismic hazards along the main Marmara fault because the megacity Istanbul lies only approximately 10 km north of the eastern segment of the Main Marmara fault, which is referred to as the Princes’ Islands Fault segment (PIF). Here, we study the locking status of this fault segment to evaluate the seismic hazard potential. For the first time, combined ascending and descending Interferometric Synthetic Aperture Radar and Global Positioning System observations were used to investigate the crustal deformation associated with the PIF. After careful corrections of the estimated ground velocity, a deformation pattern relating to fault locking near the Princes’ Islands was identified. The modeling results revealed that the slip rate and locking depth of the fault segment show a clear trade-off, which were estimated as 18.9 ± 7.2 mm yr –1 and 12.1 ± 7.0 km, respectively. With a moment accumulation rate of 1.7 ± 0.4  x  10 17 Nm yr –1 (proportional to the product of slip rate and locking depth), our results imply a build-up of a geodetic moment on the PIF and therefore a potential for earthquake hazards in the vicinity of the Istanbul megacity.
    Keywords: Gravity, Geodesy and Tides
    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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  • 42
    Publication Date: 2016-03-01
    Description: Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development.
    Keywords: Synthetic Biology and Assembly Cloning
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    Topics: Biology
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  • 43
    Publication Date: 2016-03-01
    Description: Recent developments in synthetic biology have positioned lactic acid bacteria (LAB) as a major class of cellular chassis for applications. To achieve the full potential of LAB, one fundamental prerequisite is the capacity for rapid engineering of complex gene networks, such as natural biosynthetic pathways and multicomponent synthetic circuits, into which cellular functions are encoded. Here, we present a synthetic biology platform for rapid construction and optimization of large-scale gene networks in LAB. The platform involves a copy-controlled shuttle for hosting target networks and two associated strategies that enable efficient genetic editing and phenotypic validation. By using a nisin biosynthesis pathway and its variants as examples, we demonstrated multiplex, continuous editing of small DNA parts, such as ribosome-binding sites, as well as efficient manipulation of large building blocks such as genes and operons. To showcase the platform, we applied it to expand the phenotypic diversity of the nisin pathway by quickly generating a library of 63 pathway variants. We further demonstrated its utility by altering the regulatory topology of the nisin pathway for constitutive bacteriocin biosynthesis. This work demonstrates the feasibility of rapid and advanced engineering of gene networks in LAB, fostering their applications in biomedicine and other areas.
    Keywords: Synthetic Biology and Assembly Cloning
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    Topics: Biology
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  • 44
    Publication Date: 2016-02-20
    Description: Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
    Keywords: Genomics
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  • 45
    Publication Date: 2016-02-20
    Description: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts ( trans -spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (〉98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans -spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans -spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
    Keywords: Genomics
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  • 46
    Publication Date: 2016-02-20
    Description: We present a distributed slip model for the 1999 M w 6.3 Chamoli earthquake of north India using interferometric synthetic aperture radar (InSAR) data from both ascending and descending orbits and Bayesian estimation of confidence levels and trade-offs of the model geometry parameters. The results of fault-slip inversion in an elastic half-space show that the earthquake ruptured a $9 _{ - 2.2}^{\circ + 3.4}$ northeast-dipping plane with a maximum slip of ~1 m. The fault plane is located at a depth of ~ $15.9_{ - 3.0}^{ + 1.1}$ km and is ~120 km north of the Main Frontal Thrust, implying that the rupture plane was on the northernmost detachment near the mid-crustal ramp of the Main Himalayan Thrust. The InSAR-determined moment is 3.35 x 10 18 Nm with a shear modulus of 30 GPa, equivalent to M w 6.3, which is smaller than the seismic moment estimates of M w 6.4–6.6. Possible reasons for this discrepancy include the trade-off between moment and depth, uncertainties in seismic moment tensor components for shallow dip-slip earthquakes and the role of earth structure models in the inversions. The released seismic energy from recent earthquakes in the Garhwal region is far less than the accumulated strain energy since the 1803 M s 7.5 earthquake, implying substantial hazard of future great earthquakes.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 47
    Publication Date: 2016-03-02
    Description: We use a Bayesian formalism combined with a grid node discretization for the linear inversion of gravimetric data in terms of 3-D density distribution. The forward modelling and the inversion method are derived from seismological inversion techniques in order to facilitate joint inversion or interpretation of density and seismic velocity models. The Bayesian formulation introduces covariance matrices on model parameters to regularize the ill-posed problem and reduce the non-uniqueness of the solution. This formalism favours smooth solutions and allows us to specify a spatial correlation length and to perform inversions at multiple scales. We also extract resolution parameters from the resolution matrix to discuss how well our density models are resolved. This method is applied to the inversion of data from the volcanic island of Basse-Terre in Guadeloupe, Lesser Antilles. A series of synthetic tests are performed to investigate advantages and limitations of the methodology in this context. This study results in the first 3-D density models of the island of Basse-Terre for which we identify: (i) a southward decrease of densities parallel to the migration of volcanic activity within the island, (ii) three dense anomalies beneath Petite Plaine Valley, Beaugendre Valley and the Grande-Découverte-Carmichaël-Soufrière Complex that may reflect the trace of former major volcanic feeding systems, (iii) shallow low-density anomalies in the southern part of Basse-Terre, especially around La Soufrière active volcano, Piton de Bouillante edifice and along the western coast, reflecting the presence of hydrothermal systems and fractured and altered rocks.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 48
    Publication Date: 2016-02-20
    Description: In the estimation of Ricardian models the endogeneity of adaptation measures is typically ignored. In this article we propose a new estimation strategy that explicitly recognises the endogeneity of the farm type and irrigation to climate. Based on the latest census data on over 270,000 farms in Germany, we estimate a cross-sectional, spatial-IV model that decomposes the effects of climate on farm profitability into direct (unmediated) and indirect (mediated by the variables that reflect adaptation). Our results show that neglecting the endogenous nature of adaptation measures may substantially bias the magnitude of the total effect of climate on farm profitability.
    Keywords: C21 - Cross-Sectional Models ; Spatial Models ; Treatment Effect Models, C25 - Discrete Regression and Qualitative Choice Models, C36- Instrumental Variables (IV) Estimation, Q18 - Agricultural Policy ; Food Policy, Q51 - Valuation of Environmental Effects, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 49
    Publication Date: 2016-02-20
    Description: We compute the gravimetric factor at the Chandler wobble (CW) frequency using time-series from superconducting gravimeters (SG) longer than a decade. We first individually process the polar motion and data at each individual gravity station to estimate the gravimetric factor amplitude and phase, then we make a global analysis by applying a stacking method to different subsets of up to seven SG stations. The stacking is an efficient way of getting rid of local effects and improving the signal-to-noise ratio of the combined data sets. Using the stacking method, we find a gravimetric factor amplitude and phase of 1.118 ± 0.016 and –0.45 ± 0.66 deg, respectively, which is smaller in amplitude than expected. The sources of error are then carefully considered. For both local and global analyses, the uncertainties on our results are reliably constrained by computing the standard deviation of the estimates of the gravimetric factor amplitude and phase for increasing length of the time-series. Constraints on the CW anelastic dissipation can be set since any departure of the gravimetric factor from its elastic value may provide some insights into the dissipative processes that occur at the CW period. In particular, assuming given rheological models for the Earth's mantle enables us to make the link between the gravimetric factor phase and the CW quality factor.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 50
    Publication Date: 2016-02-21
    Description: Analysing independent 1-yr data sets of 10 European superconducting gravimeters (SG) reveals statistically significant temporal variations of M2 tidal parameters. Both common short-term (〈2 yr) and long-term (〉2 yr) features are identified in all SG time-series but one. The averaged variations of the amplitude factor are about 0.2. The path of load vector variations equivalent to the temporal changes of tidal parameters suggests the presence of an 8.85 yr modulation (lunar perigee). The tidal waves having the potential to modulate M2 with this period belong to the 3rd degree constituents. Their amplitude factors turn out to be much closer to body tide model predictions than that of the main 2nd degree M2, which indicates ocean loading for 3rd degree waves to be less prominent than for 2nd degree waves within the M2 group. These two different responses to the loading suggest that the observed modulation is more due to insufficient frequency resolution of limited time-series rather than to time variable loading. Presently, SG gravity time-series are still too short to prove if time variable loading processes are involved too as in case of the annual M2 modulation known to appear for analysis intervals of less than 1 yr. Whatever the variations are caused by, they provide the upper accuracy limit for earth model validation and permit estimating the temporal stability of SG scale factors and assessing the quality of gravity time-series.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 51
    Publication Date: 2016-02-27
    Description: A sequence of large earthquakes occurred along the North Anatolian fault in the 20th century. These earthquakes, including the 1999 Izmit/Düzce earthquakes, generally propagated westward towards the Marmara Sea, defining the Main Marmara fault as a potential seismic gap. It is important to conduct a detailed assessment of the seismic hazards along the main Marmara fault because the megacity Istanbul lies only approximately 10 km north of the eastern segment of the Main Marmara fault, which is referred to as the Princes’ Islands Fault segment (PIF). Here, we study the locking status of this fault segment to evaluate the seismic hazard potential. For the first time, combined ascending and descending Interferometric Synthetic Aperture Radar and Global Positioning System observations were used to investigate the crustal deformation associated with the PIF. After careful corrections of the estimated ground velocity, a deformation pattern relating to fault locking near the Princes’ Islands was identified. The modeling results revealed that the slip rate and locking depth of the fault segment show a clear trade-off, which were estimated as 18.9 ± 7.2 mm yr –1 and 12.1 ± 7.0 km, respectively. With a moment accumulation rate of 1.7 ± 0.4  x  10 17 Nm yr –1 (proportional to the product of slip rate and locking depth), our results imply a build-up of a geodetic moment on the PIF and therefore a potential for earthquake hazards in the vicinity of the Istanbul megacity.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 52
    Publication Date: 2016-02-06
    Description: Deformation analysis in general and strain analysis in particular using permanent GPS networks require proper analysis of time-series in which all functional effects are taken into consideration and all stochastic effects are captured using an appropriate noise model. This contribution addresses both issues when considering the strain parameters of a GPS network. Estimates of spatial correlation, time correlated noise, and multivariate power spectrum for daily position time-series of the Southern California Integrated GPS Network (SCIGN) stations collected between 1996 and 2011 are obtained. Significant signals with periods of 13.63 d and those related to the GPS draconitic year are identified in these time-series. We aim to assess the effect of a realistic noise model of the series on the uncertainties of the strain parameters including displacements, normal and shear strains, and rotations. For the SCIGN network considered, the following results are highlighted. Contrary to the common belief, the uncertainties of the displacements parameters become smaller when taking a realistic noise model into account. This however was not the case when assessing the noise characteristics of the normal and shear strain, and rotation parameters. The uncertainties increase nearly by a factor of two, in agreement to what is expected. Some of the significant deformation parameters of the white noise model become less significant in case of the realistic noise model.
    Keywords: Gravity, Geodesy and Tides
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  • 53
    Publication Date: 2016-02-03
    Description: We have extended backwards from 2001 to 1979 the current release 05 (RL05) of the Gravity Recovery and Climate Experiment (GRACE) Atmospheric and Oceanic De-aliasing Level-1B (AOD1B) product and studied the impact of this and a previous release 04 (RL04) of the AOD1B product on precise orbits of five altimetry satellites (ERS-1, ERS-2, TOPEX/Poseidon, Envisat and Jason-1) for the time span 1991–2012, as compared to the case when no AOD1B product is used. We have found that using AOD1B RL05 product reduces root mean square (RMS) fits of satellite laser ranging (SLR) observations by about 1.0–6.4 per cent, 2-d arc overlaps in radial, cross-track and along-track directions by about 1.3–12.0, 0.3–10.0 and 2.0–10.0 per cent, respectively, for various satellites tested, as compared to the case without AOD1B product. Using AOD1B RL05 product instead of RL04 one reduces SLR RMS fits by 0.1–0.7 per cent, 2-d arc overlaps in radial, cross-track and along-track directions by 0.1–0.6, 0.1–1.3 and 0.2–1.2 per cent, respectively, for the satellite orbits tested. The multi-mission crossover analysis shows that the application of an AOD1B product reduces the scatter of radial errors by 0.4–2.8 per cent for the satellite missions studied. At the regions with the most pronounced changes the use of the AOD1B products improves the consistency between the sea level as measured by the TOPEX and ERS-2 missions and by the Jason-1 and Envisat missions by 5 to 10 per cent (globally by about 2 per cent). The results of our study show that extended AOD1B RL05 product performs better than the AOD1B RL04 and improves orbits of altimetry satellites and consistency of sea level products.
    Keywords: Gravity, Geodesy and Tides
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  • 54
    Publication Date: 2016-05-14
    Description: A new analytical method for the computation of a truncated series of solid spherical harmonic coefficients (HCs) from data on a spheroid (i.e. an oblate ellipsoid of revolution) is derived, using a transformation between surface and solid spherical HCs. A two-step procedure is derived to extend this transformation beyond degree and order (d/o) 520. The method is compared to the Hotine–Jekeli transformation in a numerical study based on the EGM2008 global gravity model. Both methods are shown to achieve submicrometre precision in terms of height anomalies for a model to d/o 2239. However, both methods result in spherical harmonic models that are different by up to 7.6 mm in height anomalies and 2.5 mGal in gravity disturbances due to the different coordinate system used. While the Hotine–Jekeli transformation requires the use of an ellipsoidal coordinate system, the new method uses only spherical polar coordinates. The Hotine–Jekeli transformation is numerically more efficient, but the new method can more easily be extended to cases where (a linear combination of) normal derivatives of the function under consideration are given on the surface of the spheroid. It therefore provides a solution to many types of ellipsoidal boundary-value problems in the spectral domain.
    Keywords: Gravity, Geodesy and Tides
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  • 55
    Publication Date: 2016-05-20
    Description: Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling of chromosomal loci can realize this goal. However, the current methods are constrained mainly by insufficient labeling throughput, efficiency, flexibility as well as photostability. Here we have developed a new approach to realize dual-color chromosomal loci imaging based on a modified single-guide RNA (sgRNA) of the CRISPR/Cas9 system. The modification of sgRNA was optimized by structure-guided engineering of the original sgRNA, consisting of RNA aptamer insertions that bind fluorescent protein-tagged effectors. By labeling and tracking telomeres, centromeres and genomic loci, we demonstrate that the new approach is easy to implement and enables robust dual-color imaging of genomic elements. Importantly, our data also indicate that the fast exchange rate of RNA aptamer binding effectors makes our sgRNA-based labeling method much more tolerant to photobleaching than the Cas9-based labeling method. This is crucial for continuous, long-term tracking of chromosomal dynamics. Lastly, as our method is complementary to other live-cell genomic labeling systems, it is therefore possible to combine them into a plentiful palette for the study of native chromatin organization and genome ultrastructure dynamics in living cells.
    Keywords: Genomics
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  • 56
    Publication Date: 2016-04-29
    Description: We explore Earth's elastic deformation response to ocean tidal loading (OTL) using kinematic Global Positioning System (GPS) observations and forward-modelled predictions across South America. Harmonic coefficients are extracted from up to 14 yr of GPS-inferred receiver locations, which we estimate at 5 min intervals using precise point positioning. We compare the observed OTL-induced surface displacements against predictions derived from spherically symmetric, non-rotating, elastic and isotropic (SNREI) Earth models. We also compare sets of modelled predictions directly for various ocean-tide and Earth-model combinations. The vector differences between predicted displacements computed using separate ocean-tide models reveal uniform-displacement components common to all stations in the South America network. Removal of the network-mean OTL-induced displacements from each site substantially reduces the vector differences between observed and predicted displacements. We focus on the dominant astronomical tidal harmonics from three distinct frequency bands: semidiurnal (M 2 ), diurnal (O 1 ) and fortnightly (M f ). In each band, the observed OTL-induced surface displacements strongly resemble the modelled displacement-response patterns, and the residuals agree to about 0.3 mm or better. Even with the submillimetre correspondence between observations and predictions, we detect regional-scale spatial coherency in the final set of residuals, most notably for the M 2 harmonic. The spatial coherency appears relatively insensitive to the specific choice of ocean-tide or SNREI-Earth model. Varying the load model or 1-D elastic structure yields predicted OTL-induced displacement differences of order 0.1 mm or less for the network. Furthermore, estimates of the observational uncertainty place the noise level below the magnitude of the residual displacements for most stations, supporting our interpretation that random errors cannot account for the entire misfit. Therefore, the spatially coherent residuals may reveal deficiencies in the a priori SNREI Earth models. In particular, the residuals may indicate sensitivity to regional deviations from standard globally averaged Earth structure due to the presence of the South American craton.
    Keywords: Gravity, Geodesy and Tides
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  • 57
    Publication Date: 2016-03-20
    Description: Planar faults are widely adopted during inversions to determine slip distributions and fault geometries using geodetic observations; however, little research has been conducted with respect to curved faults. We attribute this to the lack of an appropriate parameterized modelling method. In this paper, we present a curved-fault modelling method (CFMM) that describes a curved fault according to specific parameters, and we also develop a corresponding hybrid iterative inversion algorithm (HIIA) to perform inversions for parametric curved-fault geometries and slips. The results of the strike-component and dip-component synthetic tests show that a complex S-shaped fault surface and a circular slip distribution are successfully recovered, indicating the strong performance of the CFMM and HIIA methods. In addition, we describe and verify a scenario for determining the number of necessary geometrical parameters for the HIIA and examine the case study of the Wenchuan earthquake, which occurred on a complex listric fault surface. During the iteration process of the HIIA, both the fault geometry and slip distribution of the Beichuan and Pengguan faults converge to optimal values, indicating a Beichuan fault (BCF) model with a continuous listric shape and gradual steepening from the southwest to the northeast, which is highly consistent with geological survey results. Both the synthetic and real-world case studies show that the HIIA and the CMFF are superior to the conventional fault modelling method based on rectangular planes and that these models have the potential for use in more integrated research involving inversion studies, such as joint slip/curved-fault-geometry inversions that take into account data resolving power.
    Keywords: Gravity, Geodesy and Tides
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  • 58
    Publication Date: 2016-03-19
    Description: While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192–252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131–250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput ‘Dial-Out PCR’ protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 59
    Publication Date: 2016-05-22
    Description: Globally gridded estimates of monthly-mean anomalies of terrestrial water storage (TWS) are estimated from the most recent GRACE release 05a of GFZ Potsdam in order to provide non-geodetic users a convenient access to state-of-the-art GRACE monitoring data. We use an ensemble of five global land model simulations with different physics and different atmospheric forcing to obtain reliable gridded scaling factors required to correct for spatial leakage introduced during data processing. To allow for the application of this data-set for large-scale monitoring tasks, model validation efforts, and subsequently also data assimilation experiments, globally gridded estimates of TWS uncertainties that include (i) measurement, (ii) leakage and (iii) re-scaling errors are provided as well. The results are generally consistent with the gridded data provided by Tellus, but deviate in some basins which are largely affected by the uncertainties of the model information required for re-scaling, where the approach based on the median of a small ensemble of global land models introduced in this paper leads to more robust results.
    Keywords: Gravity, Geodesy and Tides
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  • 60
    Publication Date: 2016-04-24
    Description: We construct a stochastic dynamic dual model to investigate the structural adjustment of two aggregate output and three aggregate input categories in US agriculture under stochastic climatic change. More than a century of national annual data (1910–2011) is used in the empirical analysis. No constraints on asset fixity are imposed. Results indicate that, with rational expectations, both output categories as well as all input categories exhibit quasi-fixity in response to market change and stochastic climate change. Crops adjust more than twice as fast as livestock—49% versus 20% of the way toward their long-run equilibrium in one year. Fertilizer adjusts most rapidly toward equilibrium levels (88% in one year), and capital adjusts most slowly (5% in one year). Labor oscillates rather than converging smoothly toward equilibrium; its distance from equilibrium is the same as if it adjusted 59% of the way toward its optimal level in one year. Failing to anticipate climate change dramatically slows the estimated rate of adjustment for two netputs and modestly speeds the rate for two others, thus likely increasing overall adjustment costs. Failing to account for uncertainty in anticipated climate change has little impact on adjustment rates.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 61
    Publication Date: 2016-02-10
    Description: This study quantifies how leakage behavior from afforesting agricultural land affects the intensification of agricultural production. In particular, we examine the leakage percentage from carbon offset allowance at specific southern regions in the United States as a part of a carbon market. We use the Forest and Agriculture Sector Optimization Model-Greenhouse Gases model to examine responses between sectors as part of the regional afforestation policy analysis. Regional characteristics and a policy's time frame are found to play important roles in achieving net gains, in terms of greenhouse gases stored, from such regional policies. In some cases, however, leakage greater than 100% is evident.
    Keywords: Q23 - Forestry, Q54 - Climate ; Natural Disasters ; Global Warming, R14 - Land Use Patterns
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 62
    Publication Date: 2016-02-10
    Description: Regional recovery of the disturbing gravitational potential in the area of Central Europe from satellite gravitational gradients data is discussed in this contribution. The disturbing gravitational potential is obtained by inverting surface integral formulas which transform the disturbing gravitational potential onto disturbing gravitational gradients in the spherical local north-oriented frame. Two numerical approaches that solve the inverse problem are considered. In the first approach, the integral formulas are rigorously decomposed into two parts, that is, the effects of the gradient data within near and distant zones. While the effect of the near zone data is sought as an inverse problem, the effect of the distant zone data is synthesized from the global gravitational model GGM05S using spectral weights given by truncation error coefficients up to the degree 150. In the second approach, a reference gravitational field up to the degree 180 is applied to reduce and smooth measured gravitational gradients. In both cases we recovered the disturbing gravitational potential from each of the four well-measured gravitational gradients of the GOCE satellite separately as well as from their combination. Obtained results are compared with the EGM2008, DIR-r2, TIM-r2 and SPW-r2 global gravitational models. The best fit was achieved for EGM2008 and the second approach combining all four well-measured gravitational gradients with rms of 1.231 m 2  s –2 .
    Keywords: Gravity, Geodesy and Tides
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  • 63
    Publication Date: 2016-02-12
    Description: We present efficient Fourier-domain algorithms for modelling gravity effects due to topographic masses. The well-known Parker's formula originally based on the standard fast Fourier transform (FFT) algorithm is modified by applying the Gauss–FFT method instead. Numerical precision of the forward and inverse Fourier transforms embedded in Parker's formula and its extended forms are significantly improved by the Gauss–FFT method. The topographic model is composed of two major aspects, the geometry and the density. Versatile geometric representations, including the mass line model, the mass prism model, the polyhedron model and smoother topographic models interpolated from discrete data sets using high-order splines or pre-defined by analytical functions, in combination with density distributions that vary both laterally and vertically in rather arbitrary ways following exponential or general polynomial functions, now can be treated in a consistent framework by applying the Gauss–FFT method. The method presented has been numerically checked by space-domain analytical and hybrid analytical/numerical solutions already established in the literature. Synthetic and real model tests show that both the Gauss–FFT method and the standard FFT method run much faster than space-domain solutions, with the Gauss–FFT method being superior in numerical accuracy. When truncation errors are negligible, the Gauss–FFT method can provide forward results almost identical to space-domain analytical or semi-numerical solutions in much less time.
    Keywords: Gravity, Geodesy and Tides
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  • 64
    Publication Date: 2016-02-14
    Description: The gravity gradient tensor (GGT) has been increasingly used in practical applications, but the advantages and the disadvantages of the analysis of GGT components versus the analysis of the vertical component of the gravity field are still debated. We analyse the performance of joint inversion of GGT components versus separate inversion of the gravity field alone, or of one tensor component. We perform our analysis by inspection of the Picard Plot, a Singular Value Decomposition tool, and analyse both synthetic data and gradiometer measurements carried out at the Vredefort structure, South Africa. We show that the main factors controlling the reliability of the inversion are algebraic ambiguity (the difference between the number of unknowns and the number of available data points) and signal-to-noise ratio. Provided that algebraic ambiguity is kept low and the noise level is small enough so that a sufficient number of SVD components can be included in the regularized solution, we find that: (i) the choice of tensor components involved in the inversion is not crucial to the overall reliability of the reconstructions; (ii) GGT inversion can yield the same resolution as inversion with a denser distribution of gravity data points, but with the advantage of using fewer measurement stations.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 65
    Publication Date: 2016-09-03
    Description: This paper compares GRACE (Gravity Recovery and Climate Experiment) and ICESat (Ice, Cloud and land Elevation Satellite) observations to confirm whether the observed gravity increase in the Tibetan Plateau (TP) was primarily caused by lake storage gain, and comprehensively analyses the changing pattern of lake level over 2003–2009. An improved automated method was used to obtain lake-level changes and the underestimation of lake water storage was considered due to lake area expansion and lake density. The result demonstrates that GRACE recorded a mass gain (16.43 ± 1.65/11.79 ± 1.25 gt a –1 ) in the total/inner TP, of which lake storage increase accounts for (8.78 ± 0.75/7.53 ± 0.56 gt a –1 ) based on ICESat. The northwestern residual may be stored in new lakes and soil moisture as a result of net precipitation gain. According to the character of the lake-level changes, we divide the TP into four subregions. Generally, the changing pattern of lake level concurs with the distribution of precipitation, which is increasing in the inner TP and decreasing in the upstream area of the Indus and Brahmaputra Rivers. An excess of rainfall in the northeastern TP in the summer of 2005 and 2009 caused a simultaneous large increase in water level in many lakes. The correlation of lake changes with precipitation demonstrates that precipitation rather than glacial melt is the main cause of lake-level change in most places. Nonetheless, the meltwater is a considerable supplement for lakes near glaciers such as Selin Co and Nam Co, which partly explains why GRACE indicates a much weaker signal in this region.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 66
    Publication Date: 2016-09-03
    Description: Libraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli , such libraries are lacking for the Gram-positive model Bacillus subtilis , a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis . We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ~14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis .
    Keywords: Synthetic Biology and Assembly Cloning
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    Topics: Biology
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  • 67
    Publication Date: 2016-11-19
    Description: Traditional processing of Global Navigation Satellite System (GNSS) data using dedicated scientific software has provided the highest levels of positional accuracy, and has been used extensively in geophysical deformation studies. To achieve these accuracies a significant level of understanding and training is required, limiting their availability to the general scientific community. Various online GNSS processing services, now freely available, address some of these difficulties and allow users to easily process their own GNSS data and potentially obtain high quality results. Previous research into these services has focused on Continually Operating Reference Station (CORS) GNSS data. Less research exists on the results achievable with these services using large campaign GNSS data sets, which are inherently noisier than CORS data. Even less research exists on the quality of velocity fields derived from campaign GNSS data processed through online precise point positioning services. Particularly, whether they are suitable for geodynamic and deformation studies where precise and reliable velocities are needed. In this research, we process a very large campaign GPS data set (spanning 10 yr) with the online Jet Propulsion Laboratory Automated Precise Positioning Service. This data set is taken from a GNSS network specifically designed and surveyed to measure deformation through the central North Island of New Zealand. This includes regional CORS stations. We then use these coordinates to derive a horizontal and vertical velocity field. This is the first time that a large campaign GPS data set has been processed solely using an online service and the solutions used to determine a horizontal and vertical velocity field. We compared this velocity field to that of another well utilized GNSS scientific software package. The results show a good agreement between the CORS positions and campaign station velocities obtained from the two approaches. We discuss the implications of these results for how future GNSS campaign field surveys might be conducted and how their data might be processed.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 68
    Publication Date: 2016-12-04
    Description: We have developed a method to estimate the geometry, location and densities of anomalies coming from 2-D gravity data based on compact gravity inversion technique. Compact gravity inversion is simple, fast and user friendly but severely depends on the number of model parameters, that is, by increasing the model parameters, the anomalies tend to concentrate near the surface. To overcome this ambiguity new weighting functions based on density contrast, depth, and compactness models have been introduced. Variable compactness factors have been defined here to get either a sharp or a smooth model based on the depth of the source or existence of prior information. Depth weighting derived from one station of gravity data whereas the effect of gravity data is 2-D and 3-D. To compensate this limitation an innovating weighting function namely kernel function has been introduced which multiplies with weight and compactness matrixes to yield a general model weighting function. The method is tested using three different sets of synthetic examples: a body at various depths (20, 40, 80 and 140 m), two bodies at the same depth but various distances to estimate lateral resolution and three bodies with negative and positive density contrast in different depths. The method is also applied to three real gravity data of Woodlawn massive sulphide body, sulphides mineralization of British Colombia and iron ore body of Missouri. The method produces solutions consistent with the known geologic attributes of the gravity sources, illustrating its potential practicality.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 69
    Publication Date: 2016-10-26
    Description: This paper resurrects a version of Poisson's Partial Differential Equation (PDE) associated with the gravitational field at the Earth's surface and illustrates how the PDE possesses a capability to extract the mass density of Earth's topography from land-based gravity data. Herein, first we propound a theorem which mathematically introduces this version of Poisson's PDE adapted for the Earth's surface and then we use this PDE to develop a method of approximating the terrain mass density. Also, we carry out a real case study showing how the proposed approach is able to be applied to a set of land-based gravity data. In the case study, the method is summarized by an algorithm and applied to a set of gravity stations located along a part of the north coast of the Persian Gulf in the south of Iran. The results were numerically validated via rock-samplings as well as a geological map. Also, the method was compared with two conventional methods of mass density reduction. The numerical experiments indicate that the Poisson PDE at the Earth's surface has the capability to extract the mass density from land-based gravity data and is able to provide an alternative and somewhat more precise method of estimating the terrain mass density.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 70
    Publication Date: 2016-11-01
    Description: Presence of excess unaltered, wild-type (WT) DNA providing no information of biological or clinical value often masks rare alterations containing diagnostic or therapeutic clues in cancer, prenatal diagnosis, infectious diseases or organ transplantation. With the surge of high-throughput technologies there is a growing demand for removing unaltered DNA over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), a single-step approach with broad genome coverage that can remove WT-DNA from numerous sequences simultaneously, prior to genomic analysis. NaME-PrO employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating WT-DNA targets and guiding nuclease digestion to these sites. Mutation-containing DNA creates probe-DNA mismatches that inhibit digestion, thus subsequent DNA-amplification magnifies DNA-alterations at all selected targets. We demonstrate several-hundred-fold mutation enrichment in diverse human samples on multiple clinically relevant targets including tumor samples and circulating DNA in 50-plex reactions. Enrichment enables routine mutation detection at 0.01% abundance while by adjusting conditions it is possible to sequence mutations down to 0.00003% abundance, or to scan tumor-suppressor genes for rare mutations. NaME-PrO introduces a simple and highly parallel process to remove un-informative DNA sequences and unmask clinically and biologically useful alterations.
    Keywords: Genomics
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    Topics: Biology
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  • 71
    Publication Date: 2016-10-20
    Description: The Moho surface can be determined according to isostatic theories, and among them, the recent Vening Meinesz-Moritz (VMM) theory of isostasy has been successfully applied for this purpose. In this paper, this method is studied from a theoretical prospective and its connection to the Airy–Heiskanen (AH) and Vening Meinesz original theories are presented. Jeffrey's inverse solution to isostasy is developed according to the recent developments of the VMM method and both are compared in similar situations. It is shown that they are generalizations of the AH model in a global and continuous domain. In the VMM spherical harmonic solution for Moho depth, the mean Moho depth contributes only to the zero-degree term of the series, while in Jeffrey's solution it contributes to all frequencies. In addition, the VMM spherical harmonic series is improved further so that the mean Moho can contribute to all frequencies of the solution. This modification makes the VMM global solution superior to the Jeffrey one, but in a global scale, the difference between both solutions is less than 3 km. Both solutions are asymptotically convergent and we present two methods to obtain smooth solutions for Moho from them.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 72
    Publication Date: 2016-11-20
    Description: In a pioneering study, Wahr & Bergen developed the widely adopted, pseudo-normal mode framework for predicting the impact of anelastic effects on the Earth's body tides. Lau et al. have recently derived an extended normal mode treatment of the problem (as well as a minor variant of the theory known as the direct solution method) that makes full use of theoretical developments in free oscillation seismology spanning the last quarter century and that avoids a series of assumptions and approximations adopted in the traditional theory for predicting anelastic effects. There are two noteworthy differences between these two theories: (1) the traditional theory only considers perturbations to the eigenmodes of an elastic Earth, whereas the new theory augments this set of modes to include the relaxation modes that arise in anelastic behaviour; and (2) the traditional theory approximates the complex perturbation to the tidal Love number as a scaled version of the complex perturbation to the elastic moduli, whereas the new theory computes the full complex perturbation to each eigenmode. In this study, we highlight the above differences using a series of synthetic calculations, and demonstrate that the traditional theory can introduce significant error in predictions of the complex perturbation to the Love numbers due to anelasticity and the related predictions of tidal lag angles. For the simplified Earth models we adopt, the computed lag angles differ by ~20 per cent. The assumptions in the traditional theory have important implications for previous studies that use model predictions to correct observables for body tide signals or that analyse observations of body tide deformation to infer mantle anelastic structure. Finally, we also highlight the fundamental difference between apparent attenuation (i.e. attenuation inferred from observations or predicted using the above theories) and intrinsic attenuation (i.e. the material property investigated through experiments), where both are often expressed in terms of lag angles or Q –1 . In particular, we demonstrate the potentially significant (factor of two or more) bias introduced in estimates of Q –1 and its frequency dependence in studies that have treated Q –1 determined from tidal phase lags or measured experimentally as being equal. The observed or theoretically predicted lag angle (or apparent Q –1 ) differs from the intrinsic, material property due to inertia, self-gravity and effects associated with the energy budget. By accounting for these differences we derive, for a special case, an expression that accurately maps apparent attenuation predicted using the extended normal mode formalism of Lau et al. into intrinsic attenuation. The theory allows for more generalized mappings which may be used to robustly connect observations and predictions of tidal lag angles to results from laboratory experiments of mantle materials.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 73
    Publication Date: 2016-12-22
    Description: We consider a new approach to both the forward and inverse problems in post-seismic deformation. We present a method for forward modelling post-seismic deformation in a self-gravitating, heterogeneous and compressible earth with a variety of linear and nonlinear rheologies. We further demonstrate how the adjoint method can be applied to the inverse problem both to invert for rheological structure and to calculate the sensitivity of a given surface measurement to changes in rheology or time-dependence of the source. Both the forward and inverse aspects are illustrated with several numerical examples implemented in a spherically symmetric earth model.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 74
    Publication Date: 2016-10-27
    Description: The Seiland Igneous Province (SIP) is the largest complex of mafic and ultramafic intrusions in northern Fennoscandia intruded at ca . 580–560 Ma. The depth extent and the deep structure of the SIP are mainly unknown apart from three profiles modelled by gravity and refraction seismic data. Utilizing 3-D gravity modelling, a complex model of the deep subsurface structure of the SIP has been developed. The structure is presented in a multiprofile model ranging from the surface to the Moho. The mafic/ultramafic rocks of the SIP are modelled with densities of 3100 and 3300 kg m –3 , the surrounding rocks by densities of 2700 and 2900 kg m –3 for upper and lower crust, respectively. This density model explains the pronounced positive Bouguer gravity anomaly of up to 100 mGal above background. Its minimum volume is estimated from the subsurface model to 17 000 km 3 and as such we revise downwards the earlier estimations of 25 000 km 3 . The new subsurface model suggests that most of the SIP has a thickness between 2 and 4 km. An area with roots in an annular pattern is found and two deep-reaching roots have been identified located below the islands of Seiland and Sørøy. The depth of these roots is estimated to approximatively 9 km. The SIP is presently interpreted to be in the Caledonian Kalak Nappe Complex and the roots depth constrains its minimum thickness which is larger than earlier estimated. Furthermore, the rather undisturbed shape of the annular root pattern indicates that the SIP has not been subjected to strong tectonic reworking during the Caledonian orogeny.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 75
    Publication Date: 2016-11-12
    Description: Estimating the relief of the Moho from gravity data is a computationally intensive nonlinear inverse problem. What is more, the modelling must take the Earths curvature into account when the study area is of regional scale or greater. We present a regularized nonlinear gravity inversion method that has a low computational footprint and employs a spherical Earth approximation. To achieve this, we combine the highly efficient Bott's method with smoothness regularization and a discretization of the anomalous Moho into tesseroids (spherical prisms). The computational efficiency of our method is attained by harnessing the fact that all matrices involved are sparse. The inversion results are controlled by three hyperparameters: the regularization parameter, the anomalous Moho density-contrast, and the reference Moho depth. We estimate the regularization parameter using the method of hold-out cross-validation. Additionally, we estimate the density-contrast and the reference depth using knowledge of the Moho depth at certain points. We apply the proposed method to estimate the Moho depth for the South American continent using satellite gravity data and seismological data. The final Moho model is in accordance with previous gravity-derived models and seismological data. The misfit to the gravity and seismological data is worse in the Andes and best in oceanic areas, central Brazil and Patagonia, and along the Atlantic coast. Similarly to previous results, the model suggests a thinner crust of 30–35 km under the Andean foreland basins. Discrepancies with the seismological data are greatest in the Guyana Shield, the central Solimões and Amazonas Basins, the Paraná Basin, and the Borborema province. These differences suggest the existence of crustal or mantle density anomalies that were unaccounted for during gravity data processing.
    Keywords: Gravity, Geodesy and Tides
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  • 76
    Publication Date: 2016-11-14
    Description: Geophysical parameters of the deep Earth's interior can be evaluated through the resonance effects associated with the core and inner-core wobbles on the forced nutations of the Earth's figure axis, as observed by very long baseline interferometry (VLBI), or on the diurnal tidal waves, retrieved from the time-varying surface gravity recorded by superconducting gravimeters (SGs). In this paper, we inverse for the rotational mode parameters from both techniques to retrieve geophysical parameters of the deep Earth. We analyse surface gravity data from 15 SG stations and VLBI delays accumulated over the last 35 yr. We show existing correlations between several basic Earth parameters and then decide to inverse for the rotational modes parameters. We employ a Bayesian inversion based on the Metropolis–Hastings algorithm with a Markov-chain Monte Carlo method. We obtain estimates of the free core nutation resonant period and quality factor that are consistent for both techniques. We also attempt an inversion for the free inner-core nutation (FICN) resonant period from gravity data. The most probable solution gives a period close to the annual prograde term (or S 1 tide). However the 95 per cent confidence interval extends the possible values between roughly 28 and 725 d for gravity, and from 362 to 414 d from nutation data, depending on the prior bounds. The precisions of the estimated long-period nutation and respective small diurnal tidal constituents are hence not accurate enough for a correct determination of the FICN complex frequency.
    Keywords: Gravity, Geodesy and Tides
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    Topics: Geosciences
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  • 77
    Publication Date: 2016-11-10
    Description: We evaluate the benefit of different global geophysical loading products on the internal scatter of GPS position time-series from 240 globally distributed sites. We focus on the non-tidal atmospheric pressure loading predicted from NASA's Modern-Era Retrospective Analysis for Research and Applications (MERRA-NATML) and the European Center for Medium-Range Weather Forecasts operational model (ECMWF-NATML), non-tidal ocean loading predicted from the Ocean Model for Circulation and Tides model (OMCT-NTOL), and the continental water storage loading predicted from the MERRA model (MERRA-CWSL) and the GFZ's Land Surface Discharge Model (LSDM-CWSL), respectively. The result shows that the root mean square (RMS) discrepancy of different CWSL models is larger than that of NATML models in the vertical component due to the varying model parameters and input data choices. We discuss the performance of different loading models and their combination to reduce the weighted RMS of GPS up-coordinates. MERRA-NATML & OMCT-NTOL & MERRA-CWSL reduced the weighted RMS (WRMS) in 96 per cent (JPL solutions) and 86 per cent (SOPAC solutions) of the cases, and ECMWF-NATML & OMCT-NTOL & LSDM-CWSL reduced the WRMS in 95 per cent (JPL solutions) and 88 per cent (SOPAC solutions) of the cases. The result shows that local effects and technical uncertainties in GPS time-series hamper the meaningful comparison between GPS observations and mass loading models. Hence, simply using the RMS of the time-series as the assessment criteria may lead to biased comparison results. Nonetheless, we give a detailed comparison (differences in phase and amplitude at seasonal timescales) for eight representative stations located adjacent to great rivers, lakes and reservoirs. We find that LSDM can provide a complementary model to study the small-scale hydrological loading like loading extremes along river channels. However, such small-scale hydrological loading effects are still instable to be modelled in some regions with its current accuracy. Finally, we discuss the impacts of mass loading corrections on the velocity and noise estimates. The noise reductions have the consistent performance as WRMS reductions for most sites, whereas some sites have their noise increased even though GPS signal WRMS is decreased there, suggesting that our posterior correction is potentially feasible, but not sufficient.
    Keywords: Gravity, Geodesy and Tides
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  • 78
    Publication Date: 2016-11-10
    Description: Although an amount of hydrocarbon has been discovered in the West Korea Bay Basin (WKBB), located in the North Korean offshore area, geophysical investigations associated with these hydrocarbon reservoirs are not permitted because of the current geopolitical situation. Interpretation of satellite-derived potential field data can be alternatively used to image the 3-D density distribution in the sedimentary basin associated with hydrocarbon deposits. We interpreted the TRIDENT satellite-derived gravity field data to provide detailed insights into the spatial distribution of sedimentary density structures in the WKBB. We used 3-D forward density modelling for the interpretation that incorporated constraints from existing geological and geophysical information. The gravity data interpretation and the 3-D forward modelling showed that there are two modelled areas in the central subbasin that are characterized by very low density structures, with a maximum density of about 2000 kg m –3 , indicating some type of hydrocarbon reservoir. One of the anticipated hydrocarbon reservoirs is located in the southern part of the central subbasin with a volume of about 250 km 3 at a depth of about 3000 m in the Cretaceous/Jurassic layer. The other hydrocarbon reservoir should exist in the northern part of the central subbasin, with an average volume of about 300 km 3 at a depth of about 2500 m.
    Keywords: Gravity, Geodesy and Tides
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  • 79
    Publication Date: 2016-12-01
    Description: The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci. RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a plant homeodomain (PHD) finger. The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known. Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1. Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci. Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin: the first is driven by H3K4me3, promoter-focused and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused and dependent on ‘non-core’ portions of RAG1. Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome. RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity and reveals a novel role for the RAG1 non-core region in RAG1 targeting.
    Keywords: Genomics
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  • 80
    Publication Date: 2016-12-07
    Description: Much attention has been paid to the potential role that climate and food security has on conflict, especially in the Middle East. However, there has been little critical examination beyond the statistical correlation of events, which demonstrates whether a causal link exists and if it does, what can be done about it. This paper explores the conceptual linkages between food and conflict and attempts to draw attention to the opportunity cost of conflict as the nexus for decision-making in this context.
    Keywords: D74 - Conflict ; Conflict Resolution ; Alliances, Q18 - Agricultural Policy ; Food Policy, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 81
    Publication Date: 2016-12-07
    Description: What are second-generation (2G) biofuel technologies worth to global society? A dynamic, economic model is used to assess the impact that introducing 2G biofuels technology has on crops, livestock, biofuels, forestry, and environmental services, as well as greenhouse gas emissions. Under baseline conditions, this amounts to $64 billion and is $84 billion under the optimistic technology case, suggesting that investing in 2G technology could be appropriate. Under greenhouse gas regulation, global valuation more than doubles to $139 and $174 billion, respectively. A flat energy price scenario eliminates the value of 2G technology to society.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q42 - Alternative Energy Sources, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 2040-5790
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 82
    Publication Date: 2016-10-08
    Description: A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10 7 variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 83
    Publication Date: 2016-09-23
    Description: We develop a high-resolution regional gravity field model by a combination of spherical harmonics, band-limited spherical radial basis functions (SRBFs) and the residual terrain model (RTM) technique. As the main input data set, we employ a dense terrestrial gravity database (3–6 stations km –2 ), which enables gravity field modelling up to very short spatial scales. The approach is based on the remove–compute–restore methodology in which all the parts of the signal that can be modelled are removed prior to the least-squares adjustment in order to smooth the input gravity data. To this end, we utilize degree-2159 spherical harmonic models and the RTM technique using topographic models at 2 arcsec resolution. The residual short-scale gravity signal is modelled via the band-limited Shannon SRBF expanded up to degree 21 600, which corresponds to a spatial resolution of 30 arcsec. The combined model is validated against GNSS/levelling-based height anomalies, independent surface gravity data, deflections of the vertical and terrestrial vertical gravity gradients achieving an accuracy of 2.7 cm, 0.53 mGal, 0.39 arcsec and 279 E in terms of the RMS error, respectively. A key aspect of the combined approach, especially in mountainous areas, is the quality of the RTM. We therefore compare the performance of two RTM techniques within the innermost zone, the tesseroids and the polyhedron. It is shown that the polyhedron-based approach should be preferred in rugged terrain if a high-quality RTM is required. In addition, we deal with the RTM computations at points located below the reference surface of the residual terrain which is known to be a rather delicate issue.
    Keywords: Gravity, Geodesy and Tides
    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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  • 84
    Publication Date: 2016-10-08
    Description: Advances in synthetic biology and our understanding of the rules of promoter architecture have led to the development of diverse synthetic constitutive and inducible promoters in eukaryotes and prokaryotes. However, the design of promoters inducible by specific endogenous or environmental conditions is still rarely undertaken. In this study, we engineered and characterized a set of strong, synthetic promoters for budding yeast Saccharomyces cerevisiae that are inducible under acidic conditions (pH ≤ 3). Using available expression and transcription factor binding data, literature on transcriptional regulation, and known rules of promoter architecture we improved the low-pH performance of the YGP1 promoter by modifying transcription factor binding sites in its upstream activation sequence. The engineering strategy outlined for the YGP1 promoter was subsequently applied to create a response to low pH in the unrelated CCW14 promoter. We applied our best promoter variants to low-pH fermentations, enabling ten-fold increased production of lactic acid compared to titres obtained with the commonly used, native TEF1 promoter. Our findings outline and validate a general strategy to iteratively design and engineer synthetic yeast promoters inducible to environmental conditions or stresses of interest.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 85
    Publication Date: 2016-11-19
    Description: In this paper we present the potential of a new compact superconducting gravimeter (GWR iGrav) designed for groundwater monitoring. At first, 3 yr of continuous gravity data are evaluated and the performance of the instrument is investigated. With repeated absolute gravity measurements using a Micro-g Lacoste FG5, the calibration factor (–894.8 nm s –2 V –1 ) and the long-term drift of this instrument (45 nm s –2 yr –1 ) are estimated for the first time with a high precision and found to be respectively constant and linear for this particular iGrav. The low noise level performance is found similar to those of previous superconducting gravimeters and leads to gravity residuals coherent with local hydrology. The iGrav is located in a fully instrumented hydrogeophysical observatory on the Durzon karstic basin (Larzac plateau, south of France). Rain gauges and a flux tower (evapo-transpiration measurements) are used to evaluate the groundwater mass balance at the local scale. Water mass balance demonstrates that the karst is only capacitive: all the rainwater is temporarily stored in the matrix and fast transfers to the spring through fractures are insignificant in this area. Moreover, the upper part of the karst around the observatory appears to be representative of slow transfer of the whole catchment. Indeed, slow transfer estimated on the site fully supports the low-flow discharge at the only spring which represents all groundwater outflows from the catchment. In the last part of the paper, reservoir models are used to characterize the water transfer and storage processes. Particular highlights are done on the advantages of continuous gravity data (compared to repeated campaigns) and on the importance of local accurate meteorological data to limit misinterpretation of the gravity observations. The results are complementary with previous studies at the basin scale and show a clear potential for continuous gravity time-series assimilation in hydrological simulations, even on heterogeneous karstic systems.
    Keywords: Gravity, Geodesy and Tides
    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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  • 86
    Publication Date: 2016-11-19
    Description: A thorough understanding of time-dependent noise in Global Navigation Satellite System (GNSS) position time-series is necessary for computing uncertainties in any signals found in the data. However, estimation of time-correlated noise is a challenging task and is complicated by the difficulty in separating noise from signal, the features of greatest interest in the time-series. In this paper, we investigate how linear trends affect the estimation of noise in daily GNSS position time-series. We use synthetic time-series to study the relationship between linear trends and estimates of time-correlated noise for the six most commonly cited noise models. We find that the effects of added linear trends, or conversely de-trending, vary depending on the noise model. The commonly adopted model of random walk (RW), flicker noise (FN) and white noise (WN) is the most severely affected by de-trending, with estimates of low-amplitude RW most severely biased. FN plus WN is least affected by adding or removing trends. Non-integer power-law noise estimates are also less affected by de-trending, but are very sensitive to the addition of trend when the spectral index is less than one. We derive an analytical relationship between linear trends and the estimated RW variance for the special case of pure RW noise. Overall, we find that to ascertain the correct noise model for GNSS position time-series and to estimate the correct noise parameters, it is important to have independent constraints on the actual trends in the data.
    Keywords: Gravity, Geodesy and Tides
    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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  • 87
    Publication Date: 2016-12-01
    Description: Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function. We hence explored whether the homodimeric Rhodobacter sphaeroides light-oxygen-voltage (LOV) domain ( Rs LOV) that dissociates upon blue-light exposure can confer light sensitivity onto effector proteins, via a mechanism of light-induced functional site release. We chose the RNA-guided programmable DNA endonuclease Cas9 as proof-of-principle effector, and constructed a comprehensive library of Rs LOV inserted throughout the Cas9 protein. Screening with a high-throughput assay based on transcriptional repression in Escherichia coli yielded paRC9, a moderately light-activatable variant. As domain insertion can lead to protein destabilization, we also screened the library for temperature-sensitive variants and isolated tsRC9, a variant with robust activity at 29°C but negligible activity at 37°C. Biochemical assays confirmed temperature-dependent DNA cleavage and binding for tsRC9, but indicated that the light sensitivity of paRC9 is specific to the cellular setting. Using tsRC9, the first temperature-sensitive Cas9 variant, we demonstrate temperature-dependent transcriptional control over ectopic and endogenous genetic loci. Taken together, Rs LOV can confer light sensitivity onto an unrelated effector; unexpectedly, the same LOV domain can also impart strong temperature sensitivity.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 88
    Publication Date: 2015-08-11
    Description: Using a mathematical programming model of Norwegian agriculture, we explore interconnections between trade liberalization and reductions in greenhouse gas (GHG) emissions. We show that the Doha Round proposals for a new agreement on agriculture through the World Trade Organization would not generate significant reductions in emissions. Further trade liberalization would reduce emissions by cutting agricultural production but would not change production methods. Imposing a carbon tax would lead both to a reduction in output and the extensification of production. In contrast, if farmers are allowed to claim a credit for carbon sequestration the effect is to intensify agricultural production.
    Keywords: F18 - Trade and Environment, Q17 - Agriculture in International Trade, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 89
    Publication Date: 2015-09-19
    Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 90
    Publication Date: 2015-09-24
    Description: Previous formalisms for determining the static perturbation of spherically symmetric self-gravitating elastic Earth models due to displacement dislocations deal with each infinitesimal element of the fault system in its epicentral reference frame. In this work, we overcome this restriction and present novel and compact formulas for obtaining the perturbation due to the whole fault system in an arbitrary and common reference frame. Furthermore, we show that, even in an arbitrary reference frame, it is still possible to discriminate the contributions associated with the polar, bipolar and quadrupolar patterns of the seismic source response, as well as their relation with the along strike, along dip and tensile components of the displacement dislocation. These results allow a better understanding of the relation between the static perturbation and the whole fault system, and find direct applications in geodetic problems, like the modelling of long-wavelength geoid or gravity data from GRACE and GOCE space missions and of the perturbation of the deviatoric inertia tensor of the Earth.
    Keywords: Gravity, Geodesy and Tides
    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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  • 91
    Publication Date: 2015-09-26
    Description: Sensitive instruments like strainmeters and tiltmeters are necessary for measuring slowly varying low amplitude Earth deformations. Nonetheless, laser and fibre interferometers are particularly suitable for interrogating such instruments due to their extreme precision and accuracy. In this paper, a practical design of a simple pendulum borehole tiltmeter based on laser fibre interferometric displacement sensors is presented. A prototype instrument has been constructed using welded borosilicate with a pendulum length of 0.85 m resulting in a main resonance frequency of 0.6 Hz. By implementing three coplanar extrinsic fibre Fabry-Perot interferometric probes and appropriate signal filtering, our instrument provides tilt measurements that are insensitive to parasitic deformations caused by temperature and pressure variations. This prototype has been installed in an underground facility (Rustrel, France) where results show accurate measurements of Earth strains derived from Earth and ocean tides, local hydrologic effects, as well as local and remote earthquakes. The large dynamic range and the high sensitivity of this tiltmeter render it an invaluable tool for numerous geophysical applications such as transient fault motion, volcanic strain and reservoir monitoring.
    Keywords: Gravity, Geodesy and Tides
    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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  • 92
    Publication Date: 2015-08-29
    Description: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 93
    Publication Date: 2015-05-29
    Description: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 94
    Publication Date: 2015-05-03
    Description: Data from the Gravity Recovery and Climate Experiment (GRACE) satellite mission can be used to estimate the mass change rate for separate drainage systems (DSs) of the Greenland Ice Sheet (GrIS). One approach to do so is by inversion of the level-2 spherical harmonic data to surface mass changes in predefined regions, or mascons. However, the inversion can be numerically unstable for some individual DSs. This occurs mainly for DSs with a small mass change signal that are located in the interior region of Greenland. In this study, we present a modified mascon inversion approach with an improved implementation of the constraint equations to obtain better estimates for individual DSs. We use separate constraints for mass change variability in the coastal zone, where run-off takes place, and for the ice sheet interior above 2000 m, where mass changes are smaller. A multi-objective optimization approach is used to find optimal prior variances for these two areas based on a simulation model. Correlations between adjacent DSs are suppressed when our optimized prior variances are used, while the mass balance estimates for the combination of the DSs that make up the GrIS above 2000 m are not affected significantly. The resulting mass balance estimates for some DSs in the interior are significantly improved compared to an inversion with a single constraint, as determined by a comparison with mass balance estimates from surface mass balance modelling and discharge measurements. The rate of mass change of the GrIS for the period of January 2003 to December 2012 is found to be –266.1 ± 17.2 Gt yr –1 in the coastal zone and areas below 2000 m, and +8.2 ± 8.6 Gt yr –1 in the interior region.
    Keywords: Gravity, Geodesy and Tides
    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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  • 95
    Publication Date: 2015-05-03
    Description: Transformation-associated recombination (TAR) protocol allowing the selective isolation of full-length genes complete with their distal enhancer regions and entire genomic loci with sizes up to 250 kb from complex genomes in yeast S. cerevisiae has been developed more than a decade ago. However, its wide spread usage has been impeded by a low efficiency (0.5–2%) of chromosomal region capture during yeast transformants which in turn requires a time-consuming screen of hundreds of colonies. Here, we demonstrate that pre-treatment of genomic DNA with CRISPR-Cas9 nucleases to generate double-strand breaks near the targeted genomic region results in a dramatic increase in the fraction of gene-positive colonies (up to 32%). As only a dozen or less yeast transformants need to be screened to obtain a clone with the desired chromosomal region, extensive experience with yeast is no longer required. A TAR-CRISPR protocol may help to create a bank of human genes, each represented by a genomic copy containing its native regulatory elements, that would lead to a significant advance in functional, structural and comparative genomics, in diagnostics, gene replacement, generation of animal models for human diseases and has a potential for gene therapy.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 96
    Publication Date: 2015-04-02
    Description: With read lengths of currently up to 2 x 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.
    Keywords: Genomics
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  • 97
    Publication Date: 2015-04-02
    Description: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 98
    Publication Date: 2015-04-06
    Description: The static and transient deformations produced by earthquakes cause density perturbations which, in turn, generate immediate, long-range perturbations of the Earth's gravity field. Here, an analytical solution is derived for gravity perturbations produced by a point double-couple source in homogeneous, infinite, non-self-gravitating elastic media. The solution features transient gravity perturbations that occur at any distance from the source between the rupture onset time and the arrival time of seismic P waves, which are of potential interest for real-time earthquake source studies and early warning. An analytical solution for such prompt gravity perturbations is presented in compact form. We show that it approximates adequately the prompt gravity perturbations generated by strike-slip and dip-slip finite fault ruptures in a half-space obtained by numerical simulations based on the spectral element method. Based on the analytical solution, we estimate that the observability of prompt gravity perturbations within 10 s after rupture onset by current instruments is severely challenged by the background microseism noise but may be achieved by high-precision gravity strainmeters currently under development. Our analytical results facilitate parametric studies of the expected prompt gravity signals that could be recorded by gravity strainmeters.
    Keywords: Gravity, Geodesy and Tides
    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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  • 99
    Publication Date: 2015-04-14
    Description: Our article contributes to the emerging micro-level strand of the literature on the link between local variations in weather shocks and conflicts by focusing on a pixel-level analysis for North and South Sudan between 1997 and 2009. Temperature anomalies are found to strongly affect the risk of conflict, whereas the risk is expected to magnify in a range of 24–31% in the future under a median scenario. Our analysis also sheds light on the competition over natural resources, in particular water, as the main driver of such relationship in a region where pastoralism constitutes the dominant livelihood.
    Keywords: D74 - Conflict ; Conflict Resolution ; Alliances, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q54 - Climate ; Natural Disasters ; Global Warming, R11 - Regional Economic Activity: Growth, Development, and Changes
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
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  • 100
    Publication Date: 2015-04-18
    Description: Climate change will most likely confront agricultural producers with natural, economic, and political conditions that have not previously been observed and are largely uncertain. As a consequence, extrapolation from past data reaches its limits, and a process-based analysis of farmer adaptation is required. Simulation of changes in crop yields using crop growth models is a first step in that direction. However, changes in crop yields are only one pathway through which climate change affects agricultural production. A meaningful process-based analysis of farmer adaptation requires a whole-farm analysis at the farm level. We use a highly disaggregated mathematical programming model to analyze farm-level climate change adaptation for a mountainous area in southwest Germany. Regional-level results are obtained by simulating each full-time farm holding in the study area. We address parameter uncertainty and model underdetermination using a cautious calibration approach and a comprehensive uncertainty analysis. We deal with the resulting computational burden using efficient experimental designs and high-performance computing. We show that in our study area, shifted crop management time slots can have potentially significant effects on agricultural supply, incomes, and various policy objectives promoted under German and European environmental policy schemes. The simulated effects are robust against model uncertainty and underline the importance of a comprehensive assessment of climate change impacts beyond merely looking at crop yield changes. Our simulations demonstrate how farm-level models can contribute to a process-based analysis of climate change adaptation if they are embedded into a systematic framework for treating inherent model uncertainty.
    Keywords: C61 - Optimization Techniques ; Programming Models ; Dynamic Analysis, C63 - Computational Techniques, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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