ALBERT

Description: Current earthquake early warning (EEW) systems lack the ability to appropriately handle multiple concurrent earthquakes, which led to many false alarms during the 2011 Tohoku earthquake sequence in Japan. This paper uses a Bayesian probabilistic approach to handle multiple concurrent events for EEW. We implement the theory using a two-step algorithm. First, an efficient approximate Bayesian model class selection scheme is used to estimate the number of concurrent events. Then, the Rao-Blackwellized Importance Sampling method with a sequential proposal probability density function is used to estimate the earthquake parameters, that is hypocentre location, origin time, magnitude and local seismic intensity. A real data example based on 2 months data (2011 March 9–April 30) around the time of the 2011 M 9 Tohoku earthquake is studied to verify the proposed algorithm. Our algorithm results in over 90 per cent reduction in the number of incorrect warnings compared to the existing EEW system operating in Japan.

Description: A Lagrangian advection scheme with shape matrix (LASM) for solving advection problems Geoscientific Model Development, 7, 2951-2968, 2014 Author(s): L. Dong, B. Wang, and L. Liu A new Lagrangian advection scheme with shape matrix (LASM) is proposed to take advantage of the extreme low numerical diffusion of the Lagrangian methods. The tracer is discretized into finite parcels, which move along the downstream trajectories. Different from other Lagrangian schemes, the parcel shape is simulated explicitly by a linear transformation matrix. By doing so, the aliasing error in the Lagrangian schemes is largely reduced without introducing substantial interparcel mixing in the pure advection stage, because the flow information will be respected when remapping tracer density onto the fixed model grids. An adaptive interparcel mixing algorithm is constructed to ensure the validity of the linear approximation of the parcel shape, where the mixing is only triggered when it is necessary and resembles the physical mixing. The total tracer mass on the parcels is conserved exactly. The new scheme is validated by using several test cases.

Description: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.

Description: Technical Note: Reducing the spin-up time of integrated surface water–groundwater models Hydrology and Earth System Sciences, 18, 5169-5179, 2014 Author(s): H. Ajami, J. P. Evans, M. F. McCabe, and S. Stisen One of the main challenges in the application of coupled or integrated hydrologic models is specifying a catchment's initial conditions in terms of soil moisture and depth-to-water table (DTWT) distributions. One approach to reducing uncertainty in model initialization is to run the model recursively using either a single year or multiple years of forcing data until the system equilibrates with respect to state and diagnostic variables. However, such "spin-up" approaches often require many years of simulations, making them computationally intensive. In this study, a new hybrid approach was developed to reduce the computational burden of the spin-up procedure by using a combination of model simulations and an empirical DTWT function. The methodology is examined across two distinct catchments located in a temperate region of Denmark and a semi-arid region of Australia. Our results illustrate that the hybrid approach reduced the spin-up period required for an integrated groundwater–surface water–land surface model (ParFlow.CLM) by up to 50%. To generalize results to different climate and catchment conditions, we outline a methodology that is applicable to other coupled or integrated modeling frameworks when initialization from an equilibrium state is required.

Description: Extending periodic eddy covariance latent heat fluxes through tree sapflow measurements to estimate long-term total evaporation in a peat swamp forest Hydrology and Earth System Sciences Discussions, 11, 13607-13661, 2014 Author(s): A. D. Clulow, C. S. Everson, M. G. Mengistu, J. S. Price, A. Nickless, and G. P. W. Jewitt A combination of measurement and modelling was used to find a pragmatic solution to estimate the annual total evaporation (ET) from the rare and indigenous Nkazana Peat Swamp Forest (PSF) on the east coast of Southern Africa to improve the water balance estimates within the area. Total evaporation was measured during three window periods (between seven and nine days each) using an eddy covariance (EC) system on a telescopic mast above the forest canopy. Sapflow of an understory and an emergent tree was measured using a low maintenance heat pulse velocity system for an entire hydrological year (October 2009 to September 2010). An empirical model was derived, describing the relationship between the observed ET of the Nkazana PSF measured during two of the window periods ( R 2 = 0.92 and 0.90) which, overlapped with sapflow measurements, thereby providing hourly estimates of predicted ET of the Nkazana PSF for a year, totalling 1125 mm (while rainfall was 650 mm). In building the empirical model, it was found that including the understory tree sapflow provided no benefit to the model performance. In addition, the observed emergent tree sapflow relationship with observed ET between the two field campaigns was consistent and could be represented by a single empirical model ( R 2 = 0.90; RMSE = 0.08 mm). During the window periods of EC measurement, no single meteorological variable was found to describe the Nkazana PSF ET satisfactorily. However, in terms of evaporation models, the hourly FAO56 Penman–Monteith equation best described the observed ET from EC during the August 2009 ( R 2 = 0.75), November 2009 ( R 2 = 0.85) and March 2010 ( R 2 = 0.76) field campaigns, compared to the Priestley–Taylor model ( R 2 = 0.54, 0.74 and 0.62 during the respective field campaigns). From the empirical model of ET and the FAO56 Penman–Monteith equation, a monthly crop factor ( K c ) was derived for the Nkazana PSF providing a method of estimating long-term swamp forest ET from meteorological data. The monthly crop factor indicated two distinct periods. From February to May, it was between 1.2 and 1.4 compared with June to January, when the crop factor was 0.8 to 1.0. The derived monthly K c values were verified as accurate (to one significant digit) using historical data measured at the same site, also using EC, from a~previous study. The measurements provided insights into the microclimate within a subtropical peat swamp forest and the contrasting sapflow of emergent and understory trees. They showed that expensive, high maintenance equipment can be used during manageable window periods in conjunction with low maintenance systems, dedicated to individual trees, to derive a model to estimate long-term ET over remote heterogeneous forests. In addition, the contrast in ET and rainfall emphasises the reliance of the Nkazana PSF on groundwater.

Description: We present a catalogue of 2D, point spread function-corrected de Vacouleurs, Sérsic, de Vacouleurs+Exponential, and Sérsic+Exponential fits of ~7 x 10 5 spectroscopically selected galaxies drawn from the Sloan Digital Sky Survey (SDSS) Data Release 7. Fits are performed for the SDSS r band utilizing the fitting routine galfit and analysis pipeline pymorph . We compare these fits to prior catalogues. Fits are analysed using a physically motivated flagging system. The flags suggest that more than 90 per cent of two-component fits can be used for analysis. We show that the fits follow the expected behaviour for early and late galaxy types. The catalogues provide a robust set of structural and photometric parameters for future galaxy studies. We show that some biases remain in the measurements, e.g. the presence of bars significantly affect the bulge measurements although the bulge ellipticity may be used to separate barred and non-barred galaxies, and about 15 per cent of bulges of two-component fits are also affected by resolution. The catalogues are available in electronic format. We also provide an interface for generating postage stamp images of the 2D model and residual as well as the 1D profile. These images can be generated for a user-uploaded list of galaxies on demand.

Description: Stratospheric ozone depletion from future nitrous oxide increases Atmospheric Chemistry and Physics, 14, 12967-12982, 2014 Author(s): W. Wang, W. Tian, S. Dhomse, F. Xie, J. Shu, and J. Austin We have investigated the impact of the assumed nitrous oxide (N 2 O) increases on stratospheric chemistry and dynamics using a series of idealized simulations with a coupled chemistry-climate model (CCM). In a future cooler stratosphere the net yield of NO y from N 2 O is shown to decrease in a reference run following the IPCC A1B scenario, but NO y can still be significantly increased by extra increases of N 2 O over 2001–2050. Over the last decade of simulations, 50% increases in N 2 O result in a maximal 6% reduction in ozone mixing ratios in the middle stratosphere at around 10 hPa and an average 2% decrease in the total ozone column (TCO) compared with the control run. This enhanced destruction could cause an ozone decline in the first half of this century in the middle stratosphere around 10 hPa, while global TCO still shows an increase at the same time. The results from a multiple linear regression analysis and sensitivity simulations with different forcings show that the chemical effect of N 2 O increases dominates the N 2 O-induced ozone depletion in the stratosphere, while the dynamical and radiative effects of N 2 O increases are overall insignificant. The analysis of the results reveals that the ozone depleting potential of N 2 O varies with the time period and is influenced by the environmental conditions. For example, carbon dioxide (CO 2 ) increases can strongly offset the ozone depletion effect of N 2 O.

Description: Corrigendum to "Air-sea exchange and gas-particle partitioning of polycyclic aromatic hydrocarbons in the Mediterranean" published in Atmos. Chem. Phys., 14, 8905–8915, 2014 Atmospheric Chemistry and Physics, 14, 12965-12965, 2014 Author(s): M. D. Mulder, A. Heil, P. Kukučka, J. Klánová, J. Kuta, R. Prokeš, F. Sprovieri, and G. Lammel No abstract available.

Description: Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide Atmospheric Chemistry and Physics, 14, 12951-12964, 2014 Author(s): A. W. Birdsall, C. R. Miner, L. E. Mael, and M. J. Elrod Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

Description: Megacity emission plume characteristics in summer and winter investigated by mobile aerosol and trace gas measurements: the Paris metropolitan area Atmospheric Chemistry and Physics, 14, 12931-12950, 2014 Author(s): S.-L. von der Weiden-Reinmüller, F. Drewnick, Q. J. Zhang, F. Freutel, M. Beekmann, and S. Borrmann For the investigation of megacity emission plume characteristics mobile aerosol and trace gas measurements were carried out in the greater Paris region in July 2009 and January–February 2010 within the EU FP7 MEGAPOLI project (Megacities: Emissions, urban, regional and Global Atmospheric POLlution and climate effects, and Integrated tools for assessment and mitigation). The deployed instruments measured physical and chemical properties of sub-micron aerosol particles, gas phase constituents of relevance for urban air pollution studies and meteorological parameters. The emission plume was identified based on fresh pollutant (e.g., particle-bound polycyclic aromatic hydrocarbons, black carbon, CO 2 and NO x ) concentration changes in combination with wind direction data. The classification into megacity influenced and background air masses allowed a characterization of the emission plume during summer and winter environmental conditions. On average, a clear increase of fresh pollutant concentrations in plume compared to background air masses was found for both seasons. For example, an average increase of 190% (+ 8.8 ng m −3 ) in summer and of 130% (+ 18.1 ng m −3 ) in winter was found for particle-bound polycyclic aromatic hydrocarbons in plume air masses. The aerosol particle size distribution in plume air masses was influenced by nucleation and growth due to coagulation and condensation in summer, while in winter only the latter process (i.e., particle growth) seemed to be initiated by urban pollution. The observed distribution of fresh pollutants in the emission plume – its cross sectional Gaussian-like profile and the exponential decrease of pollutant concentrations with increasing distance to the megacity – are in agreement with model results. Differences between model and measurements were found for plume center location, plume width and axial plume extent. In general, dilution was identified as the dominant process determining the axial variations within the Paris emission plume. For in-depth analysis of transformation processes occurring in the advected plume, simultaneous measurements at a suburban measurement site and a stationary site outside the metropolitan area using the mobile laboratory have proven to be most useful. Organic aerosol oxidation was observed in summer, while in winter transformation processes seemed to occur at a slower rate.

Description: A regional CO 2 observing system simulation experiment for the ASCENDS satellite mission Atmospheric Chemistry and Physics, 14, 12897-12914, 2014 Author(s): J. S. Wang, S. R. Kawa, J. Eluszkiewicz, D. F. Baker, M. Mountain, J. Henderson, T. Nehrkorn, and T. S. Zaccheo Top–down estimates of the spatiotemporal variations in emissions and uptake of CO 2 will benefit from the increasing measurement density brought by recent and future additions to the suite of in situ and remote CO 2 measurement platforms. In particular, the planned NASA Active Sensing of CO 2 Emissions over Nights, Days, and Seasons (ASCENDS) satellite mission will provide greater coverage in cloudy regions, at high latitudes, and at night than passive satellite systems, as well as high precision and accuracy. In a novel approach to quantifying the ability of satellite column measurements to constrain CO 2 fluxes, we use a portable library of footprints (surface influence functions) generated by the Stochastic Time-Inverted Lagrangian Transport (STILT) model in combination with the Weather Research and Forecasting (WRF) model in a regional Bayesian synthesis inversion. The regional Lagrangian particle dispersion model framework is well suited to make use of ASCENDS observations to constrain weekly fluxes in North America at a high resolution, in this case at 1° latitude × 1° longitude. We consider random measurement errors only, modeled as a function of the mission and instrument design specifications along with realistic atmospheric and surface conditions. We find that the ASCENDS observations could potentially reduce flux uncertainties substantially at biome and finer scales. At the grid scale and weekly resolution, the largest uncertainty reductions, on the order of 50%, occur where and when there is good coverage by observations with low measurement errors and the a priori uncertainties are large. Uncertainty reductions are smaller for a 1.57 μm candidate wavelength than for a 2.05 μm wavelength, and are smaller for the higher of the two measurement error levels that we consider (1.0 ppm vs. 0.5 ppm clear-sky error at Railroad Valley, Nevada). Uncertainty reductions at the annual biome scale range from ~40% to ~75% across our four instrument design cases and from ~65% to ~85% for the continent as a whole. Tests suggest that the quantitative results are moderately sensitive to assumptions regarding a priori uncertainties and boundary conditions. The a posteriori flux uncertainties we obtain, ranging from 0.01 to 0.06 Pg C yr −1 across the biomes, would meet requirements for improved understanding of long-term carbon sinks suggested by a previous study.

Description: Estimating regional fluxes of CO 2 and CH 4 using space-borne observations of XCH 4 : XCO 2 Atmospheric Chemistry and Physics, 14, 12883-12895, 2014 Author(s): A. Fraser, P. I. Palmer, L. Feng, H. Bösch, R. Parker, E. J. Dlugokencky, P. B. Krummel, and R. L. Langenfelds We use the GEOS-Chem global 3-D atmospheric chemistry transport model to interpret XCH 4 :XCO 2 column ratios retrieved from the Japanese Greenhouse Gases Observing Satellite (GOSAT). The advantage of these data over CO 2 and CH 4 columns retrieved independently using a full physics optimal estimation algorithm is that they are less prone to scattering-related regional biases. We show that the model is able to reproduce observed global and regional spatial (mean bias =0.7%) and temporal variations (global r 2 =0.92) of this ratio with a model bias 〈 2.5%. We also show that these variations are driven by emissions of CO 2 and CH 4 that are typically 6 months out of phase, which may reduce the sensitivity of the ratio to changes in either gas. To simultaneously estimate fluxes of CO 2 and CH 4 we use a maximum likelihood estimation approach. We use two approaches to resolve independent flux estimates of these two gases using GOSAT observations of XCH 4 :XCO 2 : (1) the a priori error covariance between CO 2 and CH 4 describing common source from biomass burning; and (2) also fitting independent surface atmospheric measurements of CH 4 and CO 2 mole fraction that provide additional constraints, improving the effectiveness of the observed GOSAT ratio to constrain flux estimates. We demonstrate the impact of these two approaches using numerical experiments. A posteriori flux estimates inferred using only the GOSAT ratios and taking advantage of the error covariance due to biomass burning are not consistent with the true fluxes in our experiments, as the inversion system cannot judge which species' fluxes to adjust. This reflects the weak dependence of XCH 4 :XCO 2 on biomass burning. We find that adding the surface data effectively provides an "anchor" to the inversion that dramatically improves the ability of the GOSAT ratios to infer both CH 4 and CO 2 fluxes. We show that the regional flux estimates inferred from GOSAT XCH 4 :XCO 2 ratios together with the surface mole fraction data during 2010 are typically consistent with or better than the corresponding values inferred from fitting XCH 4 or the full-physics XCO 2 data products, as judged by a posteriori uncertainties. We show that the fluxes inferred from the ratio measurements perform best over regions where there is a large seasonal cycle such as Tropical South America, for which we report a small but significant annual source of CO 2 compared to a small annual sink inferred from the XCO 2 data. We argue that given that the ratio measurements are less compromised by systematic error than the full physics data products, the resulting a~posteriori estimates and uncertainties provide a more faithful description of the truth. Based on our analysis we also argue that by using the ratios we may be reaching the current limits on the precision of these observed space-based data.

Description: Long-term variability of storm surge frequency in the Venice Lagoon: an update thanks to eighteenth century sea level observations Natural Hazards and Earth System Sciences Discussions, 2, 7465-7486, 2014 Author(s): F. Raicich Sea level observations made in the Venice Lagoon between 1751 and 1792 have been recovered, consisting of two time series of daily data on high and low waters at Venice and Chioggia. From comparisons with modern observations the quality of the 18th century data appears to be good enough to allow a useful analysis. A composite time series of daily mean sea level is obtained by merging the 18th century data and 1872–2004 observations at Venice Punta della Salute. The absence of reliable information on vertical references prevents the connection of the two 18th century time series with each other and with modern observations. However, daily sea level anomalies relative to the mean sea level enable to recognize storm surge events, that appear to occur more frequently in the second half of the 18th century than in the late 19th and 20th centuries, particularly during the 1751–1769 period. The record-breaking storm surge of 4 November 1966 turns out to be a remarkable event also in comparison with the events extracted from the 18th century time series. Further work is required to fill the gap between the old and modern observations.

Description: Ground-penetrating radar observations for estimating the vertical displacement of rotational landslides Natural Hazards and Earth System Sciences Discussions, 2, 7487-7506, 2014 Author(s): C. Lissak, O. Maquaire, J.-P. Malet, F. Lavigne, C. Virmoux, C. Gomez, and R. Davidson The objective of this paper is to demonstrate the applicability of Ground Penetrating Radar (GPR) for monitoring the displacement of slow-moving landslides. GPR data is used to estimate the vertical movement of rotational slides in combination with other surveying techniques. The experimental site is located along the Normandy coast (North East France) here several rotational landslides are continuously affected by a seasonal kinematic pattern (low displacement rates of 0.01 to 0.10 m yr −1 ) and periodically by major acceleration events (high displacement of 1.0 to 7.0 m per event).

Description: We present new narrow-band (Hα and [O  iii ]) images and optical spectrophotometry of H  ii regions for a gas-rich low-surface-brightness irregular galaxy, KKR 17. The central surface brightness of the galaxy is μ 0 ( B ) = 24.15 ± 0.03 mag s –2 . The galaxy was detected by the Arecibo Legacy Fast ALFA survey (ALFALFA). Its mass is dominated by neutral hydrogen (H  i ) gas. In contrast, both the stellar masses of the bright H  ii and diffuse stellar regions are small. In addition, the fit to the spectral energy distribution to each region shows the stellar populations of H  ii and diffuse regions are different. The bright H  ii region contains a large fraction of O-type stars, revealing recent strong star formation, whereas the diffuse region is dominated by median age stars with a typical age of ~600 Myr. Using McGaugh's abundance model, we found that the average metallicity of KKR 17 is 12 + (O/H) = 8.0 ± 0.1. The star-formation rate of KKR 17 is 0.21 ± 0.04 M  yr –1 , which is ~1/5 of our Milky Way's. Based on the analysis results for young stellar clusters in the H  ii region, the bright H  ii region has two sub-components with different velocities and metallicities. This may be caused by the outflow of massive stars or merging events. However, the mechanism triggering star formation in the H  ii region is still uncertain.

Description: We review the results of the 1988 multiwavelength campaign on the late-type eclipsing binary YY Geminorum. Observations include: broad-band optical and near-infrared photometry, simultaneous optical and ultraviolet ( IUE ) spectroscopy, X-ray ( Ginga ) and radio (VLA) data. From models fitted to the optical light curves, fundamental physical parameters have been determined together with evidence for transient maculations (spots) located near quadrature longitudes and intermediate latitudes. Eclipses were observed at optical, ultraviolet and radio wavelengths. Significant drops in 6 cm radio emission near the phases of both primary and secondary eclipse indicate relatively compact radio emitting volumes that may lie between the binary components. IUE observations during secondary eclipse are indicative of a uniform chromosphere saturated with Mg  ii emission and an extended volume of Lyα emission. Profile fitting of high-dispersion Hα spectra confirms the chromospheric saturation and indicates significant Hα opacity to heights of a few per cent of the photospheric radius. There is evidence for an enhanced Hα emission region visible near phase 0.25–0.35 which may be associated with a large spot on the primary and with two small optical flares which were also observed at other wavelengths: one in microwave radiation and the other in X-rays. For both flares, L X / L opt is consistent with energy release in closed magnetic structures.

Description: Global representation of tropical cyclone-induced ocean thermal changes using Argo data – Part 2: Estimating air–sea heat fluxes and ocean heat content changes Ocean Science Discussions, 11, 2907-2937, 2014 Author(s): L. Cheng, J. Zhu, and R. L. Sriver We use Argo temperature data to examine changes in ocean heat content (OHC) and air–sea heat fluxes induced by tropical cyclones (TC)s on a global scale. A footprint technique that analyzes the vertical structure of cross-track thermal responses along all storm tracks during the period 2004–2012 is utilized (see part I). We find that TCs are responsible for 1.87 PW (11.05 W m −2 when averaging over the global ocean basin) of heat transfer annually from the global ocean to the atmosphere during storm passage (0–3 days) on a global scale. Of this total, 1.05 ± 0.20 PW (4.80 ± 0.85 W m −2 ) is caused by Tropical storms/Tropical depressions (TS/TD) and 0.82 ± 0.21 PW (6.25 ± 1.5 W m −2 ) is caused by hurricanes. Our findings indicate that ocean heat loss by TCs may be a substantial missing piece of the global ocean heat budget. Net changes in OHC after storm passage is estimated by analyzing the temperature anomalies during wake recovery following storm events (4–20 days after storm passage) relative to pre-storm conditions. Results indicate the global ocean experiences a 0.75 ± 0.25 PW (5.98 ± 2.1W m −2 ) net heat gain annually for hurricanes. In contrast, under TS/TD conditions, ocean experiences 0.41 ± 0.21 PW (1.90 ± 0.96 W m −2 ) net ocean heat loss, suggesting the overall oceanic thermal response is particularly sensitive to the intensity of the event. The net ocean heat uptake caused by all storms is 0.34 PW.

Description: Development and field testing of a rapid and ultra-stable atmospheric carbon dioxide spectrometer Atmospheric Measurement Techniques, 7, 4445-4453, 2014 Author(s): B. Xiang, D. D. Nelson, J. B. McManus, M. S. Zahniser, R. A. Wehr, and S. C. Wofsy We present field test results for a new spectroscopic instrument to measure atmospheric carbon dioxide (CO 2 ) with high precision (0.02 μmol mol −1 , or ppm at 1 Hz) and demonstrate high stability (within 0.1 ppm over more than 8 months), without the need for hourly, daily, or even monthly calibration against high-pressure gas cylinders. The technical novelty of this instrument (ABsolute Carbon dioxide, ABC) is the spectral null method using an internal quartz reference cell with known CO 2 column density. Compared to a previously described prototype, the field instrument has better stability and benefits from more precise thermal control of the optics and more accurate pressure measurements in the sample cell (at the mTorr level). The instrument has been deployed at a long-term ecological research site (the Harvard Forest, USA), where it has measured for 8 months without on-site calibration and with minimal maintenance, showing drift bounds of less than 0.1 ppm. Field measurements agree well with those of a commercially available cavity ring-down CO 2 instrument (Picarro G2301) run with a standard calibration protocol. This field test demonstrates that ABC is capable of performing high-accuracy, unattended, continuous field measurements with minimal use of reference gas cylinders.

Description: Meteorological factors controlling low-level continental pollutant outflow across a coast Atmospheric Chemistry and Physics, 14, 13295-13312, 2014 Author(s): D. L. Peake, H. F. Dacre, J. Methven, and O. Coceal Coastal outflow describes the horizontal advection of pollutants from the continental boundary layer (BL) across a coastline. The outflow can ventilate polluted continental BLs and thus regulate air quality in highly populated coastal regions. This paper investigates the factors controlling coastal outflow and quantifies their importance as a ventilation mechanism. Tracers in the Met Office Unified Model (MetUM) are used to examine the magnitude and variability of coastal outflow over the eastern United States during summer 2004. Over the 4 week period examined, ventilation of tracer from the continental BL via coastal outflow occurs with the same magnitude as vertical ventilation via convection and advection. The relative importance of tracer decay rate, cross-coastal advection rate, and a parameter based on the relative continental and marine BL heights on coastal outflow is assessed by reducing the problem to a time-dependent box model. The ratio of the advection rate and decay rate is a dimensionless parameter which determines whether tracers are long-lived or short-lived. Long- and short-lived tracers exhibit different behaviours with respect to coastal outflow. Short-lived tracers exhibit large diurnal variability in coastal outflow but long-lived tracers do not. For short-lived tracers, increasing the advection rate increases the diurnally averaged magnitude of coastal outflow, but this has the opposite effect for very long-lived tracers. By using the box-model solutions to interpret the MetUM simulations, a land width is determined which represents the distance inland over which emissions contribute significantly to coastal outflow. A land width of between 100 and 400 km is found to be representative for a tracer with a lifetime of 24 h.

Description: To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive. Stamatellos and collaborators introduced a scheme for smoothed particle hydrodynamics (SPH) simulations based on the notion of polytropic pseudo-clouds that uses only local quantities to estimate cooling rates. The computational approach is extremely efficient and works well in cases close to spherical symmetry, such as in star formation problems. Unfortunately, the method, which takes the local gravitational potential as an input, can be inaccurate when applied to non-spherical configurations, limiting its usefulness when studying discs or stellar collisions, among other situations of interest. Here, we introduce the ‘pressure scale height method,’ which incorporates the fluid pressure scaleheight into the determination of column densities and cooling rates, and show that it produces more accurate results across a wide range of physical scenarios while retaining the computational efficiency of the original method. The tested models include spherical polytropes as well as discs with specified density and temperature profiles. We focus on applying our techniques within an SPH code, although our method can be implemented within any particle-based Lagrangian or grid-based Eulerian hydrodynamic scheme. Our new method may be applied in a broad range of situations, including within the realm of stellar interactions, collisions, and mergers.

Description: Continental Portuguese Territory Flood Susceptibility Index – contribution for a vulnerability index Natural Hazards and Earth System Sciences Discussions, 2, 7521-7552, 2014 Author(s): R. Jacinto, N. Grosso, E. Reis, L. Dias, F. D. Santos, and P. Garrett This work defines a national flood susceptibility index for the Portuguese continental territory, by proposing the aggregation of different variables which represent natural conditions for permeability, runoff and accumulation. This index is part of the national vulnerability index developed in the scope of Flood Maps in Climate Change Scenarios (CIRAC) project, supported by the Portuguese Association of Insurers (APS). This approach expands on previous works by trying to bridge the gap between different floods mechanisms (e.g. progressive and flash floods) occurring at different spatial scales in the Portuguese territory through: (a) selecting homogeneously processed datasets, (b) aggregating their values to better translate the spatially continuous and cumulative influence in floods at multiple spatial scales. Results show a good ability to capture, in the higher susceptibility classes, different flood types: progressive floods and flash floods. Lower values are usually related to: mountainous areas, low water accumulation potential and more permeable soils. Validation with independent flood datasets confirmed these index characteristics, although some overestimation can be seen in the southern region of Alentejo where, due to a dense hydrographic network and an overall low slope, floods are not as frequent as a result of lower precipitation mean values. Future work will focus on: (i) including extreme precipitation datasets to represent the triggering factor, (ii) improving representation of smaller and stepper basins, (iii) optimizing variable weight definition process, (iii) developing more robust independent flood validation datasets.

Description: Simple, affordable and sustainable borehole observatories for complex monitoring objectives Geoscientific Instrumentation, Methods and Data Systems Discussions, 4, 653-681, 2014 Author(s): A. Kopf, T. Freudenthal, V. Ratmeyer, M. Bergenthal, M. Lange, T. Fleischmann, S. Hammerschmidt, C. Seiter, and G. Wefer Seafloor drill rigs are remotely operated systems that provide a cost effective means to recover sedimentary records of the upper sub-seafloor deposits. Recent increases in their payload included downhole logging tools or autoclave coring systems. We here report on another milestone in using seafloor rigs: the development and installation of shallow borehole observatories. Three different systems have been developed for the MARUM-MeBo seafloor drill, which is operated by MARUM, University of Bremen, Germany. A simple design, the MeBoPLUG, separates the inner borehole from the overlying ocean by using o-ring seals at the conical threads of the drill pipe. The systems are self-contained and include data loggers, batteries, thermistors and a differential pressure sensor. A second design, the so-called MeBoCORK, is more sophisticated and also hosts an acoustic modem for data transfer and, if desired, fluid sampling capability using osmotic pumps. Of these MeBoCORKs, two systems have to be distinguished: the CORK-A (A = autonomous) can be installed by the MeBo alone and monitors pressure and temperature inside and above the borehole (the latter for reference). The CORK-B (B = bottom) has a higher payload and can additionally be equipped with geochemical, biological or other physical components. Owing to its larger size, it is installed by ROV and utilises a hotstab connection in the upper portion of the drill string. Either design relies on a hotstab connection from beneath which coiled tubing with a conical drop weight is lowered to couple to the formation. These tubes are fluid-saturated and either serve to transmit pore pressure signals or collect pore water in the osmo-sampler. The third design, the MeBoPUPPI ( P op- U p P ore P ressure I nstrument), is similar to the MeBoCORK-A and monitors pore pressure and temperature in a self-contained manner. Instead of transferring data upon command using an acoustic modem, the MeBoPUPPI contains a pop-up telemetry with Iridium link. After a predefined period, the data unit with satellite link is released, ascends to the sea surface, and remains there for up to two weeks while sending the long-term data sets to shore. In summer 2012, two MeBoPLUGs, one MeBoCORK-A and one MeBoCORK-B were installed with MeBo on German RV Sonne in the Nankai Trough area, Japan. We have successfully downloaded data from the CORKs, attesting that coupling to the formation worked and pressure records were elevated relative to the seafloor reference. In the near future, we will further deploy the first two MeBoPUPPIs. Recovery of all monitoring systems by ROV is planned for 2016.

Description: Dye tracing for investigating flow and transport properties of hydrocarbon-polluted Rabots glaciär, Kebnekaise, Sweden Hydrology and Earth System Sciences Discussions, 11, 13711-13744, 2014 Author(s): C. C. Clason, C. Coch, J. Jarsjö, K. Brugger, P. Jansson, and G. Rosqvist Over 11 000 L of hydrocarbon pollution was deposited on the surface of Rabots glaciär on the Kebnekaise Massif, northern Sweden, following the crash of a Royal Norwegian Air Force aircraft in March 2012. An environmental monitoring programme was subsequently commissioned, including water, snow and ice sampling. The scientific programme further included a series of dye tracing experiments during the 2013 melt season, conducted to investigate flow pathways for pollutants through the glacier hydrological system, and to gain new insight to the internal hydrological system of Rabots glaciär. Results of dye tracing reveal a degree of homogeneity in the topology of the drainage system throughout July and August, with an increase in efficiency as the season progresses, as reflected by decreasing temporary storage and dispersivity. Early onset of melting likely led to formation of an efficient, discrete drainage system early in the melt season, subject to decreasing sinuosity and braiding as the season progressed. Analysis of turbidity-discharge hysteresis further supports the formation of discrete, efficient drainage, with clockwise diurnal hysteresis suggesting easy mobilisation of readily-available sediments in channels. Dye injection immediately downstream of the pollution source zone revealed prolonged storage of dye followed by fast, efficient release. Twinned with a low dye recovery, and supported by sporadic detection of hydrocarbons in the proglacial river, we suggest that meltwater, and thus pollutants in solution, may be released periodically from this zone of the glacier hydrological system. The here identified dynamics of dye storage, dispersion and breakthrough indicate that the ultimate fate and permanence of pollutants in the glacier system is likely to be governed by storage of pollutants in the firn layer and ice mass, or within the internal hydrological system, where it may refreeze. This shows that future studies on the fate of hydrocarbons in pristine, glaciated mountain environments should address the extent to which pollutants in solution act like water molecules or whether they are more susceptible to, for example, refreezing into the surrounding ice, becoming stuck in micro-fractures and pore spaces, or sorption onto subglacial sediments.

Description: Surface nuclear magnetic resonance (surface-NMR) is a promising technique for exploring shallow subsurface aquifer structures. Surface-NMR can be applied in environments that are characterized as a 1-D layered Earth. The technique utilizes a single loop and is referred to as magnetic resonance sounding. The technique referred to as magnetic resonance tomography (MRT) allows complex 2-D aquifer structures to be explored. Currently, MRT requires multiple loops and a roll along measurement scheme, which causes long survey time. We propose a loop layout using an elongated transmitter and an in-loop receiver arrays (ETRA) to conduct a 2-D survey with just one measurement. We present a comprehensive comparison between the new layout and the common approaches based on sensitivity and resolution analyses and show synthetic and field data. The results show that ETRA generates subsurface images at sufficient resolution with significantly lower survey times than other loop layouts.

Description: Measurements of ground deformation can be used to identify and interpret geophysical processes occurring at volcanoes. Most studies rely on a single geodetic technique, or fit a geophysical model to the results of multiple geodetic techniques. Here we present a methodology that combines GPS, Total Station measurements and InSAR into a single reference frame to produce an integrated 3-D geodetic velocity surface without any prior geophysical assumptions. The methodology consists of five steps: design of the network, acquisition and processing of the data, spatial integration of the measurements, time series computation and finally the integration of spatial and temporal measurements. The most significant improvements of this method are (1) the reduction of the required field time, (2) the unambiguous detection of outliers, (3) an increased measurement accuracy and (4) the construction of a 3-D geodetic velocity field. We apply this methodology to ongoing motion on Arenal's western flank. Integration of multiple measurement techniques at Arenal volcano revealed a deformation field that is more complex than that described by individual geodetic techniques, yet remains consistent with previous studies. This approach can be applied to volcano monitoring worldwide and has the potential to be extended to incorporate other geodetic techniques and to study transient deformation.

Description: Air temperature variability over three glaciers in the Ortles-Cevedale (Italian Alps): effects of glacier disintegration, intercomparison of calculation methods, and impacts on mass balance modeling The Cryosphere Discussions, 8, 6147-6192, 2014 Author(s): L. Carturan, F. Cazorzi, F. De Blasi, and G. Dalla Fontana Glacier mass balance models rely on accurate spatial calculation of input data, in particular air temperature. Lower temperatures (the so-called glacier cooling effect), and lower temperature variability (the so-called glacier damping effect) generally occur over glaciers, compared to ambient conditions. These effects, which depend on the geometric characteristics of glaciers and display a high spatial and temporal variability, have been mostly investigated on medium- to large-size glaciers so far, while observations on smaller ice bodies are scarce. Using a dataset from 8 on-glacier and 4 off-glacier weather stations, collected in summer 2010 and 2011, we analyzed the air temperature variability and wind regime over three different glaciers in the Ortles-Cevedale. The magnitude of the cooling effect and the occurrence of katabatic boundary layer (KBL) processes showed remarkable differences among the three ice bodies, suggesting the likely existence of important reinforcing mechanisms during glacier decay and disintegration. None of the methods proposed in the literature for calculating on-glacier temperature from off-glacier data fully reproduced our observations. Among them, the more physically-based procedure of Greuell and Böhm (1998) provided the best overall results where the KBL prevail, but it was not effective elsewhere (i.e. on smaller ice bodies and close to the glacier margins). The accuracy of air temperature estimations strongly impacted the results from a mass balance model which was applied to the three investigated glaciers. Most importantly, even small temperature deviations caused distortions in parameter calibration, thus compromising the model generalizability.

Description: We measure and quantify properties of galactic outflows and diffuse gas at z ≥ 1 in cosmological hydrodynamical simulations. Our novel subresolution model, Multi-Phase Particle Integrator (MUPPI), implements supernova feedback using fully local gas properties, where the wind velocity and mass loading are not given as input. We find the following trends at z  = 2 by analysing central galaxies having a stellar mass higher than 10 9 M . The outflow velocity and mass outflow rate ( $\dot{M}_{\rm out}$ ) exhibit positive correlations with galaxy mass and with the star formation rate (SFR). However, most of the relations present a large scatter. The outflow mass loading factor () is between 0.2 and 10. The comparison effective model generates a constant outflow velocity, and a negative correlation of with halo mass. The number fraction of galaxies where outflow is detected decreases at lower redshifts, but remains more than 80 per cent over z  = 1–5. The outflow velocity correlation with SFR becomes flatter at z  = 1, and displays a negative correlation with halo mass in massive galaxies. Our study demonstrates that both the MUPPI and effective models produce significant outflows at ~1/10 of the virial radius; at the same time shows that the properties of outflows generated can be different from the input speed and mass loading in the effective model. Our MUPPI model, using local properties of gas in the subresolution recipe, is able to develop galactic outflows whose properties correlate with global galaxy properties , and consistent with observations.

Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.

Description: The efficacy and the mutation spectrum of genome editing methods can vary substantially depending on the targeted sequence. A simple, quick assay to accurately characterize and quantify the induced mutations is therefore needed. Here we present TIDE, a method for this purpose that requires only a pair of PCR reactions and two standard capillary sequencing runs. The sequence traces are then analyzed by a specially developed decomposition algorithm that identifies the major induced mutations in the projected editing site and accurately determines their frequency in a cell population. This method is cost-effective and quick, and it provides much more detailed information than current enzyme-based assays. An interactive web tool for automated decomposition of the sequence traces is available. TIDE greatly facilitates the testing and rational design of genome editing strategies.

Description: NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients ( r 2 ) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.

Description: Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity ( T m ), nuclease stability, activity in vitro and in vivo , RNase H activation and cleavage patterns (both human and E. coli ) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro , while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo , the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.

Description: In an isogenic cell population, phenotypic heterogeneity among individual cells is common and critical for survival of the population under different environment conditions. DNA modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The single molecule real-time (SMRT) sequencing technology provides a unique platform for detecting a wide range of DNA modifications, including N6-methyladenine (6-mA), N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic haploid cells, in which the same loci of the genome are differentially modified. We tested the reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556. qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal population of ST556. Subsequent biochemical analyses revealed that the recognition sequences of two type I restriction–modification (R-M) systems are responsible for the intercellular heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA modification.

Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.

Description: In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies.

Description: In mammals, RNA interference is primarily a post-transcriptional mechanism. Evidence has accumulated for additional role in transcriptional gene silencing (TGS) but the question for a good paradigm for small interfering antigene RNA (agRNA)-induced chromatin modification remains unanswered. Here, we show that SETDB1, a histone H3-lysine 9 (H3K9)-specific methyltransferase, cooperates with Argonaute-2 (AGO2) and plays an essential role in agRNA-induced TGS. The androgen receptor ( AR ) gene was transcriptionally silenced by agRNA targeted to its promoter, and we show that this repression was mitigated by knockdown of SETDB1 or AGO2 . Chromatin immunoprecipitation demonstrated that agRNA-driven AGO2 was first targeted to the AR promoter, followed by SETDB1. SIN3A and HDAC1/2, the components of the SIN3-HDAC complex, immunoprecipitated with SETDB1, and localized at the agRNA-targeted promoter. Agreeing with the presence of SETDB1, trimethyl-H3K9 was enriched in the AR promoter. Both EZH2 and trimethyl-H3K27 were also present in the targeted locus; accordingly, EZH2 immunoprecipitated with SETDB1. DNA methylation level was not significantly changed, suggesting the absence of de novo methylating activity in agRNA-induced AR promoter. Our results demonstrate that SETDB1, together with AGO2, plays an essential role in TGS through recruiting chromatin remodeler and/or other modifiers, consequently creating a repressive chromatin milieu at the targeted promoter.

Description: LEF/TCFs direct the final step in Wnt/β-catenin signalling by recruiting β-catenin to genes for activation of transcription. Ancient, non-vertebrate TCFs contain two DNA binding domains, a High Mobility Group box for recognition of the Wnt Response Element (WRE; 5'-CTTTGWWS-3') and the C-clamp domain for recognition of the GC-rich Helper motif (5'-RCCGCC-3'). Two vertebrate TCFs (TCF-1/TCF7 and TCF-4/TCF7L2) use the C-clamp as an alternatively spliced domain to regulate cell-cycle progression, but how the C-clamp influences TCF binding and activity genome-wide is not known. Here, we used a doxycycline inducible system with ChIP-seq to assess how the C-clamp influences human TCF1 binding genome-wide. Metabolic pulse-labeling of nascent RNA with 4'Thiouridine was used with RNA-seq to connect binding to the Wnt transcriptome. We find that the C-clamp enables targeting to a greater number of gene loci for stronger occupancy and transcription regulation. The C-clamp uses Helper sites concurrently with WREs for gene targeting, but it also targets TCF1 to sites that do not have readily identifiable canonical WREs. The coupled ChIP-seq/4'Thiouridine-seq analysis identified new Wnt target genes, including additional regulators of cell proliferation. Thus, C-clamp containing isoforms of TCFs are potent transcriptional regulators with an expanded transcriptome directed by C-clamp-Helper site interactions.

Description: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.

Description: As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html .

Description: Mesoscale modeling study of the interactions between aerosols and PBL meteorology during a haze episode in China Jing–Jin–Ji and its near surrounding region – Part 1: Aerosol distributions and meteorological features Atmospheric Chemistry and Physics Discussions, 14, 31675-31717, 2014 Author(s): H. Wang, M. Xue, X. Y. Zhang, H. L. Liu, C. H. Zhou, S. C. Tan, H. Z. Che, B. Chen, and T. Li The urbanized region of Beijing–Tianjin–Hebei – often shortened to Jing–Jin–Ji and referred to as the 3JNS region in this paper – and its near surrounding region is becoming China's most polluted area by haze, exceeding even the Yangtze and Pearl river deltas. Aside from pollutant emission, the meteorology of the planetary boundary layer (PBL) is the most important factor affecting haze pollution. Focusing on July 2008, the aerosol optical properties and PBL meteorology features closely related with haze formation were simulated in 3JNS region using an online atmospheric chemical transport model. The relationship between regional PBL meteorology, PM 2.5 , and haze is discussed. Model results accurately simulated the aerosol optical depth (AOD), single scattering albedo (SSA) and asymmetry parameter (ASY), validate by comparison with observations from the MODerate Resolution Imaging Spectroradiometer (MODIS), the China Aerosol Remote Sensing NETwork (CARSNET) and the Aerosol Robotic NETwork (AERONET). Modeled PBL wind speeds showed reasonable agreement with those from the National Centers for Environmental Prediction (NCEP) Reanalysis 2. A monthly mean AOD value as high as 1.2 was found from both model and observations, with a daily mean larger than 2.0 during haze episodes in the 3JNS Region. Modeled and observed SSA values of 0.9–0.96 and ASY values of 0.72–0.74 demonstrated the high scattering characteristic of summer aerosols in this region. PBL wind speeds from modeled and NCEP data both showed a reversing trend of PM 2.5 variation, illustrating the importance of the "PBL window shadow" on haze formation. Turbulence diffusion and PBL height showed had opposite phases to surface PM 2.5 , indicating that lower PBL height and weaker PBL turbulence diffusion are essential to haze formation. It is noted that homogeneous air pressure does not occur at the surface but at an 85–950 hPa height during the haze episode. The momentum transmitting downward of the cold air from above the PBL to the low PBL and surface lead to an increase in surface wind speeds and haze dispersal.

Description: Impact of seawater Ca 2+ on the calcification and calcite Mg/Ca of Amphistegina lessonii Biogeosciences Discussions, 11, 17463-17489, 2014 Author(s): A. Mewes, G. Langer, S. Thoms, G. Nehrke, G.-J. Reichart, L. J. de Nooijer, and J. Bijma Mg/Ca ratios in foraminiferal tests are routinely used as paleo temperature proxy, but on long timescales, also hold the potential to reconstruct past seawater Mg/Ca. Impact of both temperature and seawater Mg/Ca on Mg incorporation in foraminifera have been quantified by a number of studies. The underlying mechanism responsible for Mg incorporation in foraminiferal calcite and its sensitivity to environmental conditions, however, is not fully identified. A recently published biomineralization model (Nehrke et al., 2013) proposes a combination of transmembrane transport and seawater leakage or vacuolization to link calcite Mg/Ca to seawater Mg/Ca and explains inter-species variability in Mg/Ca ratios. To test the assumptions of this model, we conducted a culture study in which seawater Mg/Ca was manipulated by varying [Ca 2+ ] and keeping [Mg 2+ ] constant. Foraminiferal growth rates, test thickness and calcite Mg/Ca of newly formed chambers were analyzed. Results showed optimum growth rates and test thickness at Mg/Ca closest to that of ambient seawater. Calcite Mg/Ca is positively correlated to seawater Mg/Ca, indicating that not absolute seawater [Ca 2+ ] and [Mg 2+ ], but the telative ratio controls Mg/Ca in tests. These results demonstrate that the calcification process cannot be based only on seawater vacuolization, supporting the mixing model proposed by Nehrke et al. (2013). Here we, however, suggest a transmembrane transport fractionation that is not as strong as suggested by Nehrke et al. (2013).

Description: The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R 2 N 2 stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and extensive ATP hydrolysis (~170 ATP/s/monomer) are required for site-specific DNA cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed positions (6–7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'. Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII enzymes may employ a unique catalytic mechanism for DNA cleavage.

Description: Emerging evidence points to roles for tRNA modifications and tRNA abundance in cellular stress responses. While isolated instances of stress-induced tRNA degradation have been reported, we sought to assess the effects of stress on tRNA levels at a systems level. To this end, we developed a next-generation sequencing method that exploits the paucity of ribonucleoside modifications at the 3'-end of tRNAs to quantify changes in all cellular tRNA molecules. Application of this tRNA-seq method to Saccharomyces cerevisiae identified all 76 expressed unique tRNA species out of 295 coded in the yeast genome, including all isoacceptor variants, with highly precise relative (fold-change) quantification of tRNAs. In studies of stress-induced changes in tRNA levels, we found that oxidation (H 2 O 2 ) and alkylation (methylmethane sulfonate, MMS) stresses induced nearly identical patterns of up- and down-regulation for 58 tRNAs. However, 18 tRNAs showed opposing changes for the stresses, which parallels our observation of signature reprogramming of tRNA modifications caused by H 2 O 2 and MMS. Further, stress-induced degradation was limited to only a small proportion of a few tRNA species. With tRNA-seq applicable to any organism, these results suggest that translational control of stress response involves a contribution from tRNA abundance.

Description: During meiosis programmed DNA double-strand breaks (DSBs) are repaired by homologous recombination using the sister chromatid or the homologous chromosome (homolog) as a template. This repair results in crossover (CO) and non-crossover (NCO) recombinants. Only CO formation between homologs provides the physical linkages guiding correct chromosome segregation, which are essential to produce healthy gametes. The factors that determine the CO/NCO decision are still poorly understood. Using Schizosaccharomyces pombe as a model we show that the Rad51/Dmc1-paralog complexes Rad55-Rad57 and Rdl1-Rlp1-Sws1 together with Swi5-Sfr1 play a major role in antagonizing both the FANCM-family DNA helicase/translocase Fml1 and the RecQ-type DNA helicase Rqh1 to limit hybrid DNA formation and promote Mus81-Eme1-dependent COs. A common attribute of these protein complexes is an ability to stabilize the Rad51/Dmc1 nucleoprotein filament, and we propose that it is this property that imposes constraints on which enzymes gain access to the recombination intermediate, thereby controlling the manner in which it is processed and resolved.

Description: To study target sequence specificity, selectivity, and reaction kinetics of Streptococcus pyogenes Cas9 activity, we challenged libraries of random variant targets with purified Cas9::guide RNA complexes in vitro . Cleavage kinetics were nonlinear, with a burst of initial activity followed by slower sustained cleavage. Consistent with other recent analyses of Cas9 sequence specificity, we observe considerable (albeit incomplete) impairment of cleavage for targets mutated in the PAM sequence or in ‘seed’ sequences matching the proximal 8 bp of the guide. A second target region requiring close homology was located at the other end of the guide::target duplex (positions 13–18 relative to the PAM). Sequences flanking the guide+PAM region had measurable (albeit modest) effects on cleavage. In addition, the first-base Guanine constraint commonly imposed by gRNA expression systems has little effect on overall cleavage efficiency. Taken together, these studies provide an in vitro understanding of the complexities of Cas9–gRNA interaction and cleavage beyond the general paradigm of site determination based on the ‘seed’ sequence and PAM.

Description: Transcripts possessing a 5'-triphosphate are a hallmark of viral transcription and can trigger the host antiviral response. 5'-triphosphates are also found on common host transcripts transcribed by RNA polymerase III (RNAP III), yet how these transcripts remain non-immunostimulatory is incompletely understood. Most microRNAs (miRNAs) are 5'-monophosphorylated as a result of sequential endonucleolytic processing by Drosha and Dicer from longer RNA polymerase II (RNAP II)-transcribed primary transcripts. In contrast, bovine leukemia virus (BLV) expresses subgenomic RNAP III transcripts that give rise to miRNAs independent of Drosha processing. Here, we demonstrate that each BLV pre-miRNA is directly transcribed by RNAP III from individual, compact RNAP III type II genes. Thus, similar to manmade RNAP III-generated short hairpin RNAs (shRNAs), the BLV pre-miRNAs are initially 5'-triphosphorylated. Nonetheless, the derivative 5p miRNAs and shRNA-generated 5p small RNAs (sRNAs) possess a 5'-monophosphate. Our enzymatic characterization and small RNA sequencing data demonstrate that BLV 5p miRNAs are co-terminal with 5'-triphosphorylated miRNA precursors (pre-miRNAs). Thus, these results identify a 5'-tri-phosphatase activity that is involved in the biogenesis of BLV miRNAs and shRNA-generated sRNAs. This work advances our understanding of retroviral miRNA and shRNA biogenesis and may have implications regarding the immunostimulatory capacity of RNAP III transcripts.

Description: Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses—the so-called transfer function—and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.

Description: The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al. , 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.

Description: Distinct translational initiation mechanisms between prokaryotes and eukaryotes limit the exploitation of prokaryotic riboswitch repertoire for regulatory RNA circuit construction in mammalian application. Here, we explored programmed ribosomal frameshifting (PRF) as the regulatory gene expression platform for engineered ligand-responsive RNA devices in higher eukaryotes. Regulation was enabled by designed ligand-dependent conformational rearrangements of the two cis-acting RNA motifs of opposite activity in -1 PRF. Particularly, RNA elements responsive to trans-acting ligands can be tailored to modify co-translational RNA refolding dynamics of a hairpin upstream of frameshifting site to achieve reversible and adjustable -1 PRF attenuating activity. Combined with a ligand-responsive stimulator, synthetic RNA devices for synergetic translational-elongation control of gene expression can be constructed. Due to the similarity between co-transcriptional RNA hairpin folding and co-translational RNA hairpin refolding, the RNA-responsive ligand repertoire provided in prokaryotic systems thus becomes accessible to gene-regulatory circuit construction for synthetic biology application in mammalian cells.

Description: Cutaneous photosensitization is a common side effect of drug treatment and can be associated with an increased skin cancer risk. The immunosuppressant azathioprine, the fluoroquinolone antibiotics and vemurafenib—a BRAF inhibitor used to treat metastatic melanoma—are all recognized clinical photosensitizers. We have compared the effects of UVA radiation on cultured human cells treated with 6-thioguanine (6-TG, a DNA-embedded azathioprine surrogate), the fluoroquinolones ciprofloxacin and ofloxacin and vemurafenib. Despite widely different structures and modes of action, each of these drugs potentiated UVA cytotoxicity. UVA photoactivation of 6-TG, ciprofloxacin and ofloxacin was associated with the generation of singlet oxygen that caused extensive protein oxidation. In particular, these treatments were associated with damage to DNA repair proteins that reduced the efficiency of nucleotide excision repair. Although vemurafenib was also highly phototoxic to cultured cells, its effects were less dependent on singlet oxygen. Highly toxic combinations of vemurafenib and UVA caused little protein carbonylation but were nevertheless inhibitory to nucleotide excision repair. Thus, for three different classes of drugs, photosensitization by at least two distinct mechanisms is associated with reduced protection against potentially mutagenic and carcinogenic DNA damage.

Description: The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g. after DNA replication, remains poorly understood. It is known that random sequential adsorption of impenetrable particles on a line reaches high density extremely slowly, due to a jamming phenomenon. The nucleosome-shifting action of remodeling enzymes has been proposed as a mechanism to resolve such jams. Here, we suggest two biophysical mechanisms which assist rapid filling of DNA with nucleosomes, and we quantitatively characterize these mechanisms within mathematical models. First, we show that the ‘softness’ of nucleosomes, due to nucleosome breathing and stepwise nucleosome assembly, significantly alters the filling behavior, speeding up the process relative to ‘hard’ particles with fixed, mutually exclusive DNA footprints. Second, we explore model scenarios in which the progression of the replication fork could eliminate nucleosome jamming, either by rapid filling in its wake or via memory of the parental nucleosome positions. Taken together, our results suggest that biophysical effects promote rapid nucleosome filling, making the reassembly of densely packed nucleosomes after DNA replication a simpler task for cells than was previously thought.

Description: Abasic (AP) lesions are the most frequent type of damages occurring in cellular DNA. Here we describe the conformational effects of AP sites substituted for 2'-deoxyadenosine in the first ( ap7 ), second ( ap13 ) or third ( ap19 ) loop of the quadruplex formed in K + by the human telomere DNA 5'-d[AG 3 (TTAG 3 ) 3 ]. CD spectra and electrophoresis reveal that the presence of AP sites does not hinder the formation of intramolecular quadruplexes. NMR spectra show that the structural heterogeneity is substantially reduced in ap7 and ap19 as compared to that in the wild-type. These two ( ap7 and ap19 ) sequences are shown to adopt the hybrid-1 and hybrid-2 quadruplex topology, respectively, with AP site located in a propeller-like loop. All three studied sequences transform easily into parallel quadruplex in dehydrating ethanol solution. Thus, the AP site in any loop region facilitates the formation of the propeller loop. Substitution of all adenines by AP sites stabilizes the parallel quadruplex even in the absence of ethanol. Whereas guanines are the major determinants of quadruplex stability, the presence or absence of loop adenines substantially influences quadruplex folding. The naturally occurring adenine-lacking sites in the human telomere DNA can change the quadruplex topology in vivo with potentially vital biological consequences.

Description: The DNA sequence preferences of nearly all sequence specific DNA binding proteins are influenced by the identities of bases that are not directly contacted by protein. Discrimination between non-contacted base sequences is commonly based on the differential abilities of DNA sequences to allow narrowing of the DNA minor groove. However, the factors that govern the propensity of minor groove narrowing are not completely understood. Here we show that the differential abilities of various DNA sequences to support formation of a highly ordered and stable minor groove solvation network are a key determinant of non-contacted base recognition by a sequence-specific binding protein. In addition, disrupting the solvent network in the non-contacted region of the binding site alters the protein's ability to recognize contacted base sequences at positions 5–6 bases away. This observation suggests that DNA solvent interactions link contacted and non-contacted base recognition by the protein.

Description: We give a bordism-theoretic characterization of those closed almost contact $(2q{+ }1)$ -manifolds (with $q\geq 2$ ) that admit a Stein fillable contact structure. Our method is to apply Eliashberg's $h$ -principle for Stein manifolds in the setting of Kreck's modified surgery. As an application, we show that any simply connected almost contact 7-manifold with torsion-free second homotopy group is Stein fillable. We also discuss the Stein fillability of exotic spheres and examine subcritical Stein fillability.

Description: Casson-type invariants emerging from Donaldson theory over certain negative-definite four-manifolds were recently suggested by Teleman. These are defined by an algebraic count of points in a zero-dimensional moduli space of flat instantons. Motivated by the cobordism programme of proving Witten's conjecture, we use a moduli space of ${\rm PU}(2)$ Seiberg–Witten monopoles to exhibit an oriented one-dimensional cobordism of the instanton moduli space to the empty space. The Casson-type invariant must therefore vanish.

Description: The dynamical and stationary behaviors of a fourth-order equation in the unit ball with clamped boundary conditions and a singular reaction term are investigated. The equation arises in the modeling of microelectromechanical systems and includes a positive voltage parameter $\lambda$ . It is shown that there is a threshold value $\lambda _* 〉 0$ of the voltage parameter such that no radially symmetric stationary solution exists for $\lambda 〉 \lambda _* $ , while at least two such solutions exist for $\lambda \in (0,\lambda _* )$ . Local and global well-posedness results are obtained for the corresponding hyperbolic and parabolic evolution problems as well as the occurrence of finite time singularities when $\lambda 〉 \lambda _* $ .

Description: Laminated sediments in the Bering Sea reveal atmospheric teleconnections to Greenland climate on millennial to decadal timescales during the last deglaciation Climate of the Past, 10, 2215-2236, 2014 Author(s): H. Kuehn, L. Lembke-Jene, R. Gersonde, O. Esper, F. Lamy, H. Arz, G. Kuhn, and R. Tiedemann During the last glacial termination, the upper North Pacific Ocean underwent dramatic and rapid changes in oxygenation that lead to the transient intensification of oxygen minimum zones (OMZs), recorded by the widespread occurrence of laminated sediments on circum-Pacific continental margins. We present a new laminated sediment record from the mid-depth (1100 m) northern Bering Sea margin that provides insight into these deglacial OMZ maxima with exceptional, decadal-scale detail. Combined ultrahigh-resolution micro-X-ray-fluorescence (micro-XRF) data and sediment facies analysis of laminae reveal an alternation between predominantly terrigenous and diatom-dominated opal sedimentation. The diatomaceous laminae are interpreted to represent spring/summer productivity events related to the retreating sea ice margin. We identified five laminated sections in the deglacial part of our site. Lamina counts were carried out on these sections and correlated with the Bølling–Allerød and Preboreal phases in the North Greenland Ice Core (NGRIP) oxygen isotope record, indicating an annual deposition of individual lamina couplets (varves). The observed rapid decadal intensifications of anoxia, in particular within the Bølling–Allerød, are tightly coupled to short-term warm events through increases in regional export production. This dependence of laminae formation on warmer temperatures is underlined by a correlation with published Bering Sea sea surface temperature records and δ 18 O data of planktic foraminifera from the Gulf of Alaska. The rapidity of the observed changes strongly implies a close atmospheric teleconnection between North Pacific and North Atlantic regions. We suggest that concomitant increases in export production and subsequent remineralization of organic matter in the Bering Sea, in combination with oxygen-poor waters entering the Being Sea, drove down oxygen concentrations to values below 0.1 mL L −1 and caused laminae preservation. Calculated benthic–planktic ventilation ages show no significant variations throughout the last deglaciation, indicating that changes in formation rates or differing sources of North Pacific mid-depth waters are not prime candidates for strengthening the OMZ at our site. The age models established by our correlation procedure allow for the determination of calendar age control points for the Bølling–Allerød and the Preboreal that are independent of the initial radiocarbon-based chronology. Resulting surface reservoir ages range within 730–990 yr during the Bølling–Allerød, 800–1100 yr in the Younger Dryas, and 765–775 yr for the Preboreal.

Description: Implication of methodological uncertainties for mid-Holocene sea surface temperature reconstructions Climate of the Past, 10, 2237-2252, 2014 Author(s): I. Hessler, S. P. Harrison, M. Kucera, C. Waelbroeck, M.-T. Chen, C. Anderson, A. de Vernal, B. Fréchette, A. Cloke-Hayes, G. Leduc, and L. Londeix We present and examine a multi-sensor global compilation of mid-Holocene (MH) sea surface temperatures (SST), based on Mg/Ca and alkenone palaeothermometry and reconstructions obtained using planktonic foraminifera and organic-walled dinoflagellate cyst census counts. We assess the uncertainties originating from using different methodologies and evaluate the potential of MH SST reconstructions as a benchmark for climate-model simulations. The comparison between different analytical approaches (time frame, baseline climate) shows the choice of time window for the MH has a negligible effect on the reconstructed SST pattern, but the choice of baseline climate affects both the magnitude and spatial pattern of the reconstructed SSTs. Comparison of the SST reconstructions made using different sensors shows significant discrepancies at a regional scale, with uncertainties often exceeding the reconstructed SST anomaly. Apparent patterns in SST may largely be a reflection of the use of different sensors in different regions. Overall, the uncertainties associated with the SST reconstructions are generally larger than the MH anomalies. Thus, the SST data currently available cannot serve as a target for benchmarking model simulations. Further evaluations of potential subsurface and/or seasonal artifacts that may contribute to obscure the MH SST reconstructions are urgently needed to provide reliable benchmarks for model evaluations.

Description: Stored-heat assessments: a review in the light of field experience Geothermal Energy Science, 2, 49-54, 2014 Author(s): M. A. Grant Stored-heat or volumetric assessments of geothermal resources are appealingly simple: the resource being exploited is heat. A stored-heat calculation simply computes the amount of heat in the resource, similarly to computing the amount of ore in an ore body. The method has theoretical support in numerical simulations of resource production. While there are significant unknowns in any resource, some of these can be covered by probabilistic approaches, notably a Monte Carlo method. The Australian Geothermal Reporting Code represents one specification of such stored-heat assessments. However the experience of recent decades, with the development of significant numbers of geothermal resources, has shown that the method is highly unreliable and usually biased high. The tendency to overestimates, in particular, has led to the reduced credibility of the method. An example is quoted where simple application of the apparently simple rules gives a ridiculous result. Much of the problem lies in the "recovery factor", the proportion of the resource that can actually be exploited, where comparison with actual performance shows past values have been in all cases too high, as is the current version of the Australian code. There are further problems, usually overlooked, in the way that the reservoir volume and "cutoff temperature" are defined. Differing approaches mean that results between different reports are not comparable. The different approaches also imply unrecognised assumptions about the physical processes controlling reservoir depletion. The failure of Monte Carlo methods is similarly due to unrecognised violation of logical consistency in the use of probabilities. The net effect of these problems is that the method is not a simple means to generate a rough resource estimate, and it often generates faulty results. Usually, such results are overestimates. Monte Carlo methods do not provide a protection against these errors. The Australian Geothermal Reporting Code should be used for hydrothermal systems with an average recovery factor of 10%. With this average, results are subject to an error of ±70%. For enhanced geothermal systems (EGS), the recovery factor should be a few percent.

Description: Sensitivity of the Mediterranean sea level to atmospheric pressure and free surface elevation numerical formulation in NEMO Geoscientific Model Development, 7, 3001-3015, 2014 Author(s): P. Oddo, A. Bonaduce, N. Pinardi, and A. Guarnieri The sensitivity of the dynamics of the Mediterranean Sea to atmospheric pressure and free surface elevation formulation using NEMO (Nucleus for European Modelling of the Ocean) was evaluated. Four different experiments were carried out in the Mediterranean Sea using filtered or explicit free surface numerical schemes and accounting for the effect of atmospheric pressure in addition to wind and buoyancy fluxes. Model results were evaluated by coherency and power spectrum analysis with tide gauge data. We found that atmospheric pressure plays an important role for periods shorter than 100 days. The free surface formulation is important to obtain the correct ocean response for periods shorter than 30 days. At frequencies higher than 15 days −1 the Mediterranean basin's response to atmospheric pressure was not coherent and the performance of the model strongly depended on the specific area considered. A large-amplitude seasonal oscillation observed in the experiments using a filtered free surface was not evident in the corresponding explicit free surface formulation case, which was due to a phase shift between mass fluxes in the Gibraltar Strait and at the surface. The configuration with time splitting and atmospheric pressure always performed best; the differences were enhanced at very high frequencies.

Description: Are seasonal calving dynamics forced by buttressing from ice mélange or undercutting by melting? Outcomes from full-Stokes simulations of Store Glacier, West Greenland The Cryosphere, 8, 2353-2365, 2014 Author(s): J. Todd and P. Christoffersen We use a full-Stokes 2-D model (Elmer/Ice) to investigate the flow and calving dynamics of Store Glacier, a fast-flowing outlet glacier in West Greenland. Based on a new, subgrid-scale implementation of the crevasse depth calving criterion, we perform two sets of simulations: one to identify the primary forcing mechanisms and another to constrain future stability. We find that the mixture of icebergs and sea ice, known as ice mélange or sikussak, is principally responsible for the observed seasonal advance of the ice front. On the other hand, the effect of submarine melting on the calving rate of Store Glacier appears to be limited. Sensitivity analysis demonstrates that the glacier's calving dynamics are sensitive to seasonal perturbation, but are stable on interannual timescales due to the strong topographic control on the flow regime. Our results shed light on the dynamics of calving glaciers and may help explain why neighbouring glaciers do not necessarily respond synchronously to changes in atmospheric and oceanic forcing.

Description: Deglaciation of the Caucasus Mountains, Russia/Georgia, in the 21st century observed with ASTER satellite imagery and aerial photography The Cryosphere, 8, 2367-2379, 2014 Author(s): M. Shahgedanova, G. Nosenko, S. Kutuzov, O. Rototaeva, and T. Khromova Changes in the map area of 498 glaciers located on the Main Caucasus ridge (MCR) and on Mt. Elbrus in the Greater Caucasus Mountains (Russia and Georgia) were assessed using multispectral ASTER and panchromatic Landsat imagery with 15 m spatial resolution in 1999/2001 and 2010/2012. Changes in recession rates of glacier snouts between 1987–2001 and 2001–2010 were investigated using aerial photography and ASTER imagery for a sub-sample of 44 glaciers. In total, glacier area decreased by 4.7 ± 2.1% or 19.2 ± 8.7 km 2 from 407.3 ± 5.4 km 2 to 388.1 ± 5.2 km 2 . Glaciers located in the central and western MCR lost 13.4 ± 7.3 km 2 (4.7 ± 2.5%) in total or 8.5 km 2 (5.0 ± 2.4%) and 4.9 km 2 (4.1 ± 2.7%) respectively. Glaciers on Mt. Elbrus, although located at higher elevations, lost 5.8 ± 1.4 km 2 (4.9 ± 1.2%) of their total area. The recession rates of valley glacier termini increased between 1987–2000/01 and 2000/01–2010 (2000 for the western MCR and 2001 for the central MCR and Mt.~Elbrus) from 3.8 ± 0.8, 3.2 ± 0.9 and 8.3 ± 0.8 m yr −1 to 11.9 ± 1.1, 8.7 ± 1.1 and 14.1 ± 1.1 m yr −1 in the central and western MCR and on Mt. Elbrus respectively. The highest rate of increase in glacier termini retreat was registered on the southern slope of the central MCR where it has tripled. A positive trend in summer temperatures forced glacier recession, and strong positive temperature anomalies in 1998, 2006, and 2010 contributed to the enhanced loss of ice. An increase in accumulation season precipitation observed in the northern MCR since the mid-1980s has not compensated for the effects of summer warming while the negative precipitation anomalies, observed on the southern slope of the central MCR in the 1990s, resulted in stronger glacier wastage.

Description: Long-duration gamma-ray bursts (GRBs) are thought to come from the core collapse of Wolf–Rayet stars. Whereas their stellar masses M * have a rather narrow distribution, the population of GRBs is very diverse, with gamma-ray luminosities L spanning several orders of magnitude. This suggests the existence of a ‘hidden’ stellar variable whose burst-to-burst variation leads to a spread in L . Whatever this hidden variable is, its variation should not noticeably affect the shape of GRB light curves, which display a constant luminosity (in a time-average sense) followed by a sharp drop at the end of the burst seen with Swift /XRT. We argue that such a hidden variable is progenitor star's large-scale magnetic flux. Shortly after the core collapse, most of stellar magnetic flux accumulates near the black hole (BH) and remains there. The flux extracts BH rotational energy and powers jets of roughly a constant luminosity, L j . However, once BH mass accretion rate $\dot{M}$ falls below ~ L j / c 2 , the flux becomes dynamically important and diffuses outwards, with the jet luminosity set by the rapidly declining mass accretion rate, $L_{\rm j}\sim \dot{M}c^2$ . This provides a potential explanation for the sharp end of GRBs and the universal shape of their light curves. During the GRB, gas infall translates spatial variation of stellar magnetic flux into temporal variation of L j . We make use of the deviations from constancy in L j to perform stellar magnetic flux ‘tomography’. Using this method, we infer the presence of magnetized tori in the outer layers of progenitor stars for GRB 920513 and GRB 940210.

Description: We make use of a large set of fast simulations of an intensity mapping experiment with characteristics similar to those expected of the Square Kilometre Array in order to study the viability and limits of blind foreground subtraction techniques. In particular, we consider three different approaches: polynomial fitting, principal component analysis (PCA) and independent component analysis (ICA). We review the motivations and algorithms for the three methods, and show that they can all be described, using the same mathematical framework, as different approaches to the blind source separation problem. We study the efficiency of foreground subtraction both in the angular and radial (frequency) directions, as well as the dependence of this efficiency on different instrumental and modelling parameters. For well-behaved foregrounds and instrumental effects, we find that foreground subtraction can be successful to a reasonable level on most scales of interest. We also quantify the effect that the cleaning has on the recovered signal and power spectra. Interestingly, we find that the three methods yield quantitatively similar results, with PCA and ICA being almost equivalent.

Description: Observed galaxies with high stellar masses or in dense environments have low specific star formation rates, i.e. they are quenched. Based on cosmological hydrodynamic simulations that include a prescription where quenching occurs in regions dominated by hot (〉10 5.4  K) gas, we argue that this hot gas quenching in haloes 〉10 12 M drives both mass quenching (i.e. central quenching) and environment quenching (i.e. satellite quenching). These simulations reproduce a broad range of locally observed trends among quenching, halo mass, stellar mass, environment, and distance to halo centre. Mass quenching is independent of environment because ~10 12 –10 13 M ‘mass quenching haloes’ inhabit a large range of environments. On the other hand, environment quenching is independent of stellar mass because galaxies of all stellar masses may live in dense environments as satellites of groups and clusters. As in observations, the quenched fraction of satellites increases with halo mass and decreases with distance to the centre of the group or cluster. We investigate pre-processing in group haloes, ejected former satellites, and hot gas that extends beyond the virial radius. The agreement of our model with key observational trends suggests that hot gas in massive haloes plays a leading role in quenching low-redshift galaxies.

Description: We used Arecibo Observatory and the Green Bank Telescope to observe OH in 12 early-type galaxies with known reservoirs of dense gas. We present three new detections of OH in absorption in the 1667 MHz line. One objective of our survey was to find evidence of molecular outflows, but our sensitivity and the strength of the OH absorption were insufficient to detect outflows. The detected sources have infrared luminosities and dust temperatures among the lowest of any galaxy detected in OH absorption. The ratio L HCN / L CO , a measure of the dense gas fraction in galaxies, is a powerful selector of OH megamasers for galaxies with high infrared luminosity. In early-type galaxies, which have much lower infrared luminosities, L HCN / L CO is also a promising tool for discovering OH, but in absorption rather than in maser emission. In addition to dense molecular gas, a radio continuum source and a favourable line of sight to the observer are likely key factors in detecting OH absorbers.

Description: The initial mass function (IMF) of the Arches cluster, which was formed a few million years ago in the harsh environment of the Galactic Centre (GC), has long been a target of interest to those who study the GC and the theory of star formation. The distinct star-forming conditions in the GC might have caused the cluster to have a shallower slope or an elevated lower mass cutoff in its IMF. But its mass function (MF) has been revealed only down to 1–2 M (the lower limit of resolved stars), and the low-end MF of the Arches is still unknown. To estimate the unresolved part of the Arches MF, we have devised a novel photometric method that involves the histogram of pixel intensities in the observed image, which contains information on the unresolved, faint stars. By comparing the pixel intensity histograms (PIHs) of numerous artificial images constructed from model IMFs with the observed PIH, we find that the best-fitting model IMF for the Arches cluster has a cutoff mass less than or similar to 0.1 M and a shape very close to that of the Kroupa MF. Our findings imply that the IMF of the Arches cluster is similar to those found in the Galactic disc.

Description: Inversion method for initial tsunami waveform reconstruction Natural Hazards and Earth System Sciences Discussions, 2, 7735-7772, 2014 Author(s): V. V. Voronin, T. A. Voronina, and V. A. Tcheverda This paper deals with the application of r-solution method to recover the initial tsunami waveform in a tsunami source area by remote water-level measurements. Wave propagation is considered within the scope of a linear shallow-water theory. An ill-posed inverse problem is regularized by means of least square inversion using a truncated SVD approach. The properties of obtained solution are determined to a large extent by the properties of an inverse operator, which were numerically investigated. The method presented allows one to control instability of the numerical solution and to obtain an acceptable result in spite of ill-posedness of the problem. It is shown that the accuracy of tsunami source reconstruction strongly depends on the signal-to-noise ratio, the azimuthal coverage of recording stations with respect to the source area and bathymetric features along the wave path. The numerical experiments were carried out with synthetic data and various computational domains including a real bathymetry. The method proposed allows us to make a preliminary prediction of the efficiency of the inversion with a given set of the recording stations and to find out the most informative part of the existing observation system. This essential property of the method can prove to be useful in designing a monitoring system for tsunamis.

Description: Reevaluation of stratospheric ozone trends from SAGE II data using a simultaneous temporal and spatial analysis Atmospheric Chemistry and Physics, 14, 13455-13470, 2014 Author(s): R. P. Damadeo, J. M. Zawodny, and L. W. Thomason This paper details a new method of regression for sparsely sampled data sets for use with time-series analysis, in particular the Stratospheric Aerosol and Gas Experiment (SAGE) II ozone data set. Non-uniform spatial, temporal, and diurnal sampling present in the data set result in biased values for the long-term trend if not accounted for. This new method is performed close to the native resolution of measurements and is a simultaneous temporal and spatial analysis that accounts for potential diurnal ozone variation. Results show biases, introduced by the way data are prepared for use with traditional methods, can be as high as 10%. Derived long-term changes show declines in ozone similar to other studies but very different trends in the presumed recovery period, with differences up to 2% per decade. The regression model allows for a variable turnaround time and reveals a hemispheric asymmetry in derived trends in the middle to upper stratosphere. Similar methodology is also applied to SAGE II aerosol optical depth data to create a new volcanic proxy that covers the SAGE II mission period. Ultimately this technique may be extensible towards the inclusion of multiple data sets without the need for homogenization.

Description: Investigating uptake of N 2 O in agricultural soils using a high-precision dynamic chamber method Atmospheric Measurement Techniques, 7, 4455-4462, 2014 Author(s): N. J. Cowan, D. Famulari, P. E. Levy, M. Anderson, D. S. Reay, and U. M. Skiba Uptake (or negative flux) of nitrous oxide (N 2 O) in agricultural soils is a controversial issue which has proved difficult to investigate in the past due to constraints such as instrumental precision and methodological uncertainties. Using a recently developed high-precision quantum cascade laser gas analyser combined with a closed dynamic chamber, a well-defined detection limit of 4 μg N 2 O-N m −2 h −1 could be achieved for individual soil flux measurements. 1220 measurements of N 2 O flux were made from a variety of UK soils using this method, of which 115 indicated uptake by the soil (i.e. a negative flux in the micrometeorological sign convention). Only four of these apparently negative fluxes were greater than the detection limit of the method, which suggests that the vast majority of reported negative fluxes from such measurements are actually due to instrument noise. As such, we suggest that the bulk of negative N 2 O fluxes reported for agricultural fields are most likely due to limits in detection of a particular flux measurement methodology and not a result of microbiological activity consuming atmospheric N 2 O.

Description: Comparison of spatial association approaches for landscape mapping of soil organic carbon stocks SOIL Discussions, 1, 757-802, 2014 Author(s): B. A. Miller, S. Koszinski, M. Wehrhan, and M. Sommer The distribution of soil organic carbon (SOC) can be variable at small analysis scales, but consideration of its role in regional and global issues demands the mapping of large extents. There are many different strategies for mapping SOC, among which are to model the variables needed to calculate the SOC stock indirectly or to model the SOC stock directly. The purpose of this research is to compare direct and indirect approaches to mapping SOC stocks from rule-based, multiple linear regression models applied at the landscape scale via spatial association. The final products for both strategies are high-resolution maps of SOC stocks (kg m −2 ), covering an area of 122 km 2 , with accompanying maps of estimated error. For the direct modelling approach, the estimated error map was based on the internal error estimations from the model rules. For the indirect approach, the estimated error map was produced by spatially combining the error estimates of component models via standard error propagation equations. We compared these two strategies for mapping SOC stocks on the basis of the qualities of the resulting maps as well as the magnitude and distribution of the estimated error. The direct approach produced a map with less spatial variation than the map produced by the indirect approach. The increased spatial variation represented by the indirect approach improved R 2 values for the topsoil and subsoil stocks. Although the indirect approach had a lower mean estimated error for the topsoil stock, the mean estimated error for the total SOC stock (topsoil + subsoil) was lower for the direct approach. For these reasons, we recommend the direct approach to modelling SOC stocks be considered a more conservative estimate of the SOC stocks' spatial distribution.

Description: Glacier-like forms on Mars The Cryosphere, 8, 2047-2061, 2014 Author(s): B. Hubbard, C. Souness, and S. Brough More than 1300 glacier-like forms (GLFs) are located in Mars' mid-latitudes. These GLFs are predominantly composed of ice–dust mixtures and are visually similar to terrestrial valley glaciers, showing signs of downhill viscous deformation and an expanded former extent. However, several fundamental aspects of their behavior are virtually unknown, including temporal and spatial variations in mass balance, ice motion, landscape erosion and deposition, and hydrology. Here, we investigate the physical glaciology of martian GLFs. We use satellite images of specific examples and case studies to build on existing knowledge relating to (i) GLF current and former extent, exemplified via a GLF located in Phlegra Montes; (ii) indicators of GLF motion, focusing on the presence of surface crevasses on several GLFs; (iii) processes of GLF debris transfer, focusing on mapping and interpreting boulder trains on one GLF located in Protonilus Mensae, the analysis of which suggests a best-estimate mean GLF flow speed of 7.5 mm a −1 ; and (iv) GLF hydrology, focusing on supra-GLF gulley networks. On the basis of this information, we summarize the current state of knowledge of the glaciology of martian GLFs and identify future research avenues.

Description: Strategy of valid 14 C dates choice in syngenetic permafrost The Cryosphere Discussions, 8, 5589-5621, 2014 Author(s): Y. K. Vasil'chuk and A. C. Vasil'chuk The main problem of radiocarbon dating within permafrost is the uncertain reliability of the 14 C dates. Syngenetic sediments contain allochthonous organic deposit that originated at a distance from its present position. Due to the very good preservation of organic materials in permafrost conditions and numerous re-burials of the fossils from ancient deposits into younger ones the dates could be both younger and older than the true age of dated material. The strategy for the most authentic radiocarbon date selection for dating of syncryogenic sediments is considered taking into account the fluvial origin of the syngenetic sediments. The re-deposition of organic material is discussed in terms of cyclic syncryogenic sedimentation and also the possible re-deposition of organic material in subaerial-subaqueous conditions. The advantages and the complications of dating organic micro-inclusions from ice wedges by the accelerator mass spectrometry (AMS) method are discussed applying to true age of dated material search. Radiocarbon dates of different organic materials from the same samples are compared. The younger age of the yedoma from cross-sections of Duvanny Yar in Kolyma River and Mamontova Khayata in the mouth of Lena River is substantiated due to the principle of the choice of the youngest 14 C date from the set.

Description: Modeling the elastic transmission of tidal stresses to great distances inland in channelized ice streams The Cryosphere, 8, 2007-2029, 2014 Author(s): J. Thompson, M. Simons, and V. C. Tsai Geodetic surveys suggest that ocean tides can modulate the motion of Antarctic ice streams, even at stations many tens of kilometers inland from the grounding line. These surveys suggest that ocean tidal stresses can perturb ice stream motion at distances about an order of magnitude farther inland than tidal flexure of the ice stream alone. Recent models exploring the role of tidal perturbations in basal shear stress are primarily one- or two-dimensional, with the impact of the ice stream margins either ignored or parameterized. Here, we use two- and three-dimensional finite-element modeling to investigate transmission of tidal stresses in ice streams and the impact of considering more realistic, three-dimensional ice stream geometries. Using Rutford Ice Stream as a real-world comparison, we demonstrate that the assumption that elastic tidal stresses in ice streams propagate large distances inland fails for channelized glaciers due to an intrinsic, exponential decay in the stress caused by resistance at the ice stream margins. This behavior is independent of basal conditions beneath the ice stream and cannot be fit to observations using either elastic or nonlinear viscoelastic rheologies without nearly complete decoupling of the ice stream from its lateral margins. Our results suggest that a mechanism external to the ice stream is necessary to explain the tidal modulation of stresses far upstream of the grounding line for narrow ice streams. We propose a hydrologic model based on time-dependent variability in till strength to explain transmission of tidal stresses inland of the grounding line. This conceptual model can reproduce observations from Rutford Ice Stream.

Description: Simulating the Antarctic ice sheet in the Late-Pliocene warm period: PLISMIP-ANT, an ice-sheet model intercomparison project The Cryosphere Discussions, 8, 5539-5588, 2014 Author(s): B. de Boer, A. M. Dolan, J. Bernales, E. Gasson, H. Goelzer, N. R. Golledge, J. Sutter, P. Huybrechts, G. Lohmann, I. Rogozhina, A. Abe-Ouchi, F. Saito, and R. S. W. van de Wal In the context of future climate change, understanding the nature and behaviour of ice sheets during warm intervals in Earth history is of fundamental importance. The Late-Pliocene warm period (also known as the PRISM interval: 3.264 to 3.025 million years before present) can serve as a potential analogue for projected future climates. Although Pliocene ice locations and extents are still poorly constrained, a significant contribution to sea-level rise should be expected from both the Greenland ice sheet and the West and East Antarctic ice sheets based on palaeo sea-level reconstructions. Here, we present results from simulations of the Antarctic ice sheet by means of an international Pliocene Ice Sheet Modeling Intercomparison Project (PLISMIP-ANT). For the experiments, ice-sheet models including the shallow ice and shelf approximations have been used to simulate the complete Antarctic domain (including grounded and floating ice). We compare the performance of six existing numerical ice-sheet models in simulating modern control and Pliocene ice sheets by a suite of four sensitivity experiments. Ice-sheet model forcing fields are taken from the HadCM3 atmosphere–ocean climate model runs for the pre-industrial and the Pliocene. We include an overview of the different ice-sheet models used and how specific model configurations influence the resulting Pliocene Antarctic ice sheet. The six ice-sheet models simulate a comparable present-day ice sheet, although the models are setup with their own parameter settings. For the Pliocene simulations using the Bedmap1 bedrock topography, some models show a small retreat of the East Antarctic ice sheet, which is thought to have happened during the Pliocene for the Wilkes and Aurora basins. This can be ascribed to either the surface mass balance, as the HadCM3 Pliocene climate shows a significant increase over the Wilkes and Aurora basin, or the initial bedrock topography. For the latter, our simulations with the recently published Bedmap2 bedrock topography indicate a significantly larger contribution to Pliocene sea-level rise from the East Antarctic ice sheet for all six models relative to the simulations with Bedmap1.

Description: Fluctuations of a Greenlandic tidewater glacier driven by changes in atmospheric forcing: observations and modelling of Kangiata Nunaata Sermia, 1859–present The Cryosphere, 8, 2031-2045, 2014 Author(s): J. M. Lea, D. W. F. Mair, F. M. Nick, B. R. Rea, D. van As, M. Morlighem, P. W. Nienow, and A. Weidick Many tidewater glaciers in Greenland are known to have undergone significant retreat during the last century following their Little Ice Age maxima. Where it is possible to reconstruct glacier change over this period, they provide excellent records for comparison to climate records, as well as calibration/validation for numerical models. These glacier change records therefore allow for tests of numerical models that seek to simulate tidewater glacier behaviour over multi-decadal to centennial timescales. Here we present a detailed record of behaviour from Kangiata Nunaata Sermia (KNS), SW Greenland, between 1859 and 2012, and compare it against available oceanographic and atmospheric temperature data between 1871 and 2012. We also use these records to evaluate the ability of a well-established one-dimensional flow-band model to replicate behaviour for the observation period. The record of terminus change demonstrates that KNS has advanced/retreated in phase with atmosphere and ocean climate anomalies averaged over multi-annual to decadal timescales. Results from an ensemble of model runs demonstrate that observed dynamics can be replicated. Model runs that provide a reasonable match to observations always require a significant atmospheric forcing component, but do not necessarily require an oceanic forcing component. Although the importance of oceanic forcing cannot be discounted, these results demonstrate that changes in atmospheric forcing are likely to be a primary driver of the terminus fluctuations of KNS from 1859 to 2012. We propose that the detail and length of the record presented makes KNS an ideal site for model validation exercises investigating links between climate, calving rates, and tidewater glacier dynamics.

Description: Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. Results: We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7–25 times faster than a standard iterative algorithm. Availability and implementation: Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html . BitPAl is implemented in C and runs on all major operating systems. Contact : jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu Supplementary information : Supplementary data are available at Bioinformatics online.

Description: : Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential. In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify 〉175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction. Availability and implementation: The source code can be downloaded at http://www.heiderlab.de Contact: d.heider@wz-straubing.de

Description: : We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: hengli@broadinstitute.org

Description: : AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub ( www.github.com/AliView ). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections. Result: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k -mer spectrum. With high-quality k -mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net . Contact: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of 〉97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock . Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online

Description: Rapid, optical measurement of the atmospheric pressure on a fast research aircraft using open-path TDLAS Atmospheric Measurement Techniques, 7, 3653-3666, 2014 Author(s): B. Buchholz, A. Afchine, and V. Ebert Because of the high travel speed, the complex flow dynamics around an aircraft, and the complex dependency of the fluid dynamics on numerous airborne parameters, it is quite difficult to obtain accurate pressure values at a specific instrument location of an aircraft's fuselage. Complex simulations using computational fluid dynamics (CFD) models can in theory computationally "transfer" pressure values from one location to another. However, for long flight patterns, this process is inconvenient and cumbersome. Furthermore, these CFD transfer models require a local experimental validation, which is rarely available. In this paper, we describe an integrated approach for a spectroscopic, calibration-free, in-flight pressure determination in an open-path White cell on an aircraft fuselage using ambient, atmospheric water vapour as the "sensor species". The presented measurements are realised with the HAI (Hygrometer for Atmospheric Investigations) instrument, built for multiphase water detection via calibration-free TDLAS (tunable diode laser absorption spectroscopy). The pressure determination is based on raw data used for H 2 O concentration measurement, but with a different post-flight evaluation method, and can therefore be conducted at deferred time intervals on any desired flight track. The spectroscopic pressure is compared in-flight with the static ambient pressure of the aircraft avionic system and a micro-mechanical pressure sensor, located next to the open-path cell, over a pressure range from 150 to 800 hPa, and a water vapour concentration range of more than 3 orders of magnitude. The correlation between the micro-mechanical pressure sensor measurements and the spectroscopic pressure measurements shows an average deviation from linearity of only 0.14% and a small offset of 9.5 hPa. For the spectroscopic pressure evaluation we derive measurement uncertainties under laboratory conditions of 3.2 and 5.1% during in-flight operation on the HALO airplane. Under certain flight conditions we quantified, for the first time, stalling-induced, dynamic pressure deviations of up to 30% (at 200 hPa) between the avionic sensor and the optical and mechanical pressure sensors integrated in HAI. Such severe local pressure deviations from the typically used avionic pressure are important to take into account for other airborne sensors employed on such fast flying platforms as the HALO aircraft.

Description: Long term measurements of optical properties and their hygroscopic enhancement Atmospheric Chemistry and Physics Discussions, 14, 27731-27767, 2014 Author(s): M. Hervo, K. Sellegri, J. M. Pichon, J. C. Roger, and P. Laj Optical properties of aerosols were measured from the GAW Puy de Dôme station (1465 m) over a seven year period (2006–2012). The impact of hygroscopicity on aerosol optical properties was calculated over a two year period (2010–2011). The analysis of the spatial and temporal variability of the optical properties showed that while no long term trend was found, a clear seasonal and diurnal variation was observed on the extensive parameters (scattering, absorption). Scattering and absorption coefficients were highest during the warm season and daytime, in concordance with the seasonality and diurnal variation of the PBL height reaching the site. Intensive parameters (single scattering albedo, asymmetry factor, refractive index) did not show such a strong diurnal variability, but still indicated different values depending on the season. Both extensive and intensive optical parameters were sensitive to the air mass origin. A strong impact of hygroscopicity on aerosol optical properties was calculated, mainly on aerosol scattering, with a dependence on the aerosol type. At 90% humidity, the scattering factor enhancement ( f σ sca ) was more than 4.4 for oceanic aerosol that have mixed with a pollution plume. Consequently, the aerosol radiative forcing was estimated to be 2.8 times higher at RH = 90% and 1.75 times higher at ambient RH when hygroscopic growth of the aerosol was considered. The hygroscopicity enhancement factor of the scattering coefficient was parameterized as a function of humidity and air mass type.

Description: Fluxes of carbon and nutrients to the Iceland Sea surface layer and inferred primary productivity and stoichiometry Biogeosciences Discussions, 11, 15399-15433, 2014 Author(s): E. Jeansson, R. G. J. Bellerby, I. Skjelvan, H. Frigstad, S. R. Ólafsdóttir, and J. Ólafsson Fluxes of carbon and nutrients to the upper 100 m of the Iceland Sea are evaluated. The study utilises hydro-chemical data from the Iceland Sea time-series station (68.00° N, 12.67° W), for the years between 1993 and 2006. By comparing data of dissolved inorganic carbon (DIC) and nutrients in the surface layer (upper 100 m), and a sub-surface layer (100–200 m), we calculate monthly deficits in the surface, and use these to deduce the surface layer fluxes that affect the deficits: vertical mixing, horizontal advection, air–sea exchange, and biological activity. The deficits show a clear seasonality with a minimum in winter, when the mixed layer is at the deepest, and a maximum in early autumn, when biological uptake has removed much of the nutrients. The annual vertical fluxes of DIC and nitrate amounts to 1.7 ± 0.3 and 0.23 ± 0.07 mol m −2 yr −1 , respectively, and the annual air–sea uptake of atmospheric CO 2 is 4.4 ± 1.1 mol m −2 yr −1 . The biologically driven changes in DIC during the year relates to net community production (NCP), and the net annual NCP corresponds to export production, and is here calculated to 6.1 ± 0.9 mol C m −2 yr −1 . The typical, median C : N ratio during the period of net community uptake is 11, and thus clearly higher than Redfield, but is varying during the season.

Description: Motivation: The identification of active transcriptional regulatory elements is crucial to understand regulatory networks driving cellular processes such as cell development and the onset of diseases. It has recently been shown that chromatin structure information, such as DNase I hypersensitivity (DHS) or histone modifications, significantly improves cell-specific predictions of transcription factor binding sites. However, no method has so far successfully combined both DHS and histone modification data to perform active binding site prediction. Results: We propose here a method based on hidden Markov models to integrate DHS and histone modifications occupancy for the detection of open chromatin regions and active binding sites. We have created a framework that includes treatment of genomic signals, model training and genome-wide application. In a comparative analysis, our method obtained a good trade-off between sensitivity versus specificity and superior area under the curve statistics than competing methods. Moreover, our technique does not require further training or sequence information to generate binding location predictions. Therefore, the method can be easily applied on new cell types and allow flexible downstream analysis such as de novo motif finding. Availability and implementation: Our framework is available as part of the Regulatory Genomics Toolbox. The software information and all benchmarking data are available at http://costalab.org/wp/dh-hmm . Contact: ivan.costa@rwth-aachen.de or eduardo.gusmao@rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant ‘superbugs’, a rapid diagnostic target identification process is needed. Results: A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k -mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures. Availability and implementation: The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com . The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip Contact: yazhousun@synblex.com Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/ . Contact: sjh@cmp.uea.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Recent studies on human disease have revealed that aberrant interaction between proteins probably underlies a substantial number of human genetic diseases. This suggests a need to investigate disease inheritance mode using interaction, and based on which to refresh our conceptual understanding of a series of properties regarding inheritance mode of human disease. Results: We observed a strong correlation between the number of protein interactions and the likelihood of a gene causing any dominant diseases or multiple dominant diseases, whereas no correlation was observed between protein interaction and the likelihood of a gene causing recessive diseases. We found that dominant diseases are more likely to be associated with disruption of important interactions. These suggest inheritance mode should be understood using protein interaction. We therefore reviewed the previous studies and refined an interaction model of inheritance mode, and then confirmed that this model is largely reasonable using new evidences. With these findings, we found that the inheritance mode of human genetic diseases can be predicted using protein interaction. By integrating the systems biology perspectives with the classical disease genetics paradigm, our study provides some new insights into genotype–phenotype correlations. Contact: haodapeng@ems.hrbmu.edu.cn or biofomeng@hotmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. Availability and implementation: DCB is an open source Web-based tool that is freely available at: http://www.maayanlab.net/LINCS/DCB Contact: avi.maayan@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: As an important subtype of structural variations, chromosomal translocation is associated with various diseases, especially cancers, by disrupting gene structures and functions. Traditional methods for identifying translocations are time consuming and have limited resolutions. Recently, a few studies have employed next-generation sequencing (NGS) technology for characterizing chromosomal translocations on human genome, obtaining high-throughput results with high resolutions. However, these studies are mainly focused on mechanism-specific or site-specific translocation mapping. In this study, we conducted a comprehensive genome-wide analysis on the characterization of human chromosomal material exchange with regard to the chromosome translocations. Using NGS data of 1,481 subjects from the 1000 Genomes Project, we identified 15,349,092 translocated DNA fragment pairs, ranging from 65 to 1,886 bp and with an average size of approximately 102 bp. On average, each individual genome carried about 10,364 pairs, covering approximately 0.069% of the genome. We identified 16 translocation hot regions, among which two regions did not contain repetitive fragments. Results of our study overlapped with a majority of previous results, containing approximately 79% of approximately 2,340 translocations characterized in three available translocation databases. In addition, our study identified five novel potential recurrent chromosomal material exchange regions with greater than 20% detection rates. Our results will be helpful for an accurate characterization of translocations in human genomes, and contribute as a resource for future studies of the roles of translocations in human disease etiology and mechanisms.

Description: Fractured rocks are known to exhibit seismic anisotropy and shear wave splitting (SWS). SWS is commonly used for fractured rock characterization and has been shown to be sensitive to fluid type. The presence of partial liquid/gas saturation is also known to affect the elastic properties of rocks. The combined effect of both fractures and partial liquid/gas saturation is still unknown. Using synthetic, silica-cemented sandstones with aligned penny-shaped voids, we conducted laboratory ultrasonic experiments to investigate the effect fractures aligned at an oblique angle to wave propagation would have on SWS under partial liquid/gas saturation conditions. The result for the fractured rock shows a saturation dependence which can be explained by combining a fractured rock model and a partial saturation model. At high to full water saturation values, SWS decreases as a result of the fluid bulk modulus effect on the quasi-shear wave. This bulk modulus effect is frequency dependent as a result of wave-induced fluid flow mechanisms, which would in turn lead to frequency dependent SWS. This result suggests the possible use of SWS for discriminating between full liquid saturation and partial liquid/gas saturation.

Description: The effect of network density and geometric distribution on kinematic non-linear source inversion is investigated by inverting synthetic ground motions from a buried strike-slip fault ( M w 6.5), that have been generated by dynamic spontaneous rupture modelling. For the inversion, we use a physics-based regularized Yoffe function as slip velocity function. We test three different cases of station network geometry: (i) single station, varying azimuth and epicentral distance; (ii) multistation circular configurations, that is stations at similar distances from the fault, and regularly spaced around the fault; (iii) irregular multistation configurations using different numbers of stations. Our results show: (1) single station tests suggest that it may be possible to obtain a relatively good source model even using a single station. The best source model using a single station is obtained with stations at which amplitude ratios between three components are not large. We infer that both azimuthal angle and source-to-station distance play an important role in the design of optimal seismic network for source inversion. (2) Multistation tests show that the quality of the inverted source systematically correlates neither with the number of stations, nor with waveform misfit. (3) Waveform misfit has a direct correlation with the number of stations, resulting in overfitting the observed data without any systematic improvement of the source. It suggests that the best source model is not necessarily derived from the model with minimum waveform misfit. (4) A seismic network with a small number of well-spaced stations around the fault may be sufficient to obtain acceptable source inversion.

Description: Fermat's interferometric principle is used to compute interior transmission traveltimes pq from exterior transmission traveltimes sp and sq . Here, the exterior traveltimes are computed for sources s on a boundary B that encloses a volume V of interior points p and q . Once the exterior traveltimes are computed, no further ray tracing is needed to calculate the interior times pq . Therefore this interferometric approach can be more efficient than explicitly computing interior traveltimes pq by ray tracing. Moreover, the memory requirement of the traveltimes is reduced by one dimension, because the boundary B is of one fewer dimension than the volume V . An application of this approach is demonstrated with interbed multiple (IM) elimination. Here, the IMs in the observed data are predicted from the migration image and are subsequently removed by adaptive subtraction. This prediction is enabled by the knowledge of interior transmission traveltimes pq computed according to Fermat's interferometric principle. We denote this principle as the ‘traveltime holographic principle’, by analogy with the holographic principle in cosmology where information in a volume is encoded on the region's boundary.

Description: Earthquake hypocentre locations are crucial in many domains of application (academic and industrial) as seismic event location maps are commonly used to delineate faults or fractures. The interpretation of these maps depends on location accuracy and on the reliability of the associated uncertainties. The largest contribution to location and uncertainty errors is due to the fact that the velocity model errors are usually not correctly taken into account. We propose a new Bayesian formulation that integrates properly the knowledge on the velocity model into the formulation of the probabilistic earthquake location. In this work, the velocity model uncertainties are first estimated with a Bayesian tomography of active shot data. We implement a sampling Monte Carlo type algorithm to generate velocity models distributed according to the posterior distribution. In a second step, we propagate the velocity model uncertainties to the seismic event location in a probabilistic framework. This enables to obtain more reliable hypocentre locations as well as their associated uncertainties accounting for picking and velocity model uncertainties. We illustrate the tomography results and the gain in accuracy of earthquake location for two synthetic examples and one real data case study in the context of induced microseismicity.

Description: Clinical and neuropathological similarities between dementia with Lewy bodies (DLB), Parkinson's and Alzheimer's diseases (PD and AD, respectively) suggest that these disorders may share etiology. To test this hypothesis, we have performed an association study of 54 genomic regions, previously implicated in PD or AD, in a large cohort of DLB cases and controls. The cohort comprised 788 DLB cases and 2624 controls. To minimize the issue of potential misdiagnosis, we have also performed the analysis including only neuropathologically proven DLB cases (667 cases). The results show that the APOE is a strong genetic risk factor for DLB, confirming previous findings, and that the SNCA and SCARB2 loci are also associated after a study-wise Bonferroni correction, although these have a different association profile than the associations reported for the same loci in PD. We have previously shown that the p.N370S variant in GBA is associated with DLB, which, together with the findings at the SCARB2 locus, suggests a role for lysosomal dysfunction in this disease. These results indicate that DLB has a unique genetic risk profile when compared with the two most common neurodegenerative diseases and that the lysosome may play an important role in the etiology of this disorder. We make all these data available.

Description: Efficient performance of the Met Office Unified Model v8.2 on Intel Xeon partially used nodes Geoscientific Model Development Discussions, 7, 7395-7425, 2014 Author(s): I. Bermous The atmospheric Unified Model (UM) developed at the UK Met Office is used for weather and climate prediction by forecast teams at a number of international meteorological centres and research institutes on a wide variety of hardware and software environments. Over its 25 year history the UM sources have been optimised for a better application performance on a number of HPC systems including NEC SX vector architecture systems and recently the IBM Power6/Power7 platforms. Understanding the influence of the compiler flags, MPI libraries and run configurations is crucial to achieving the shortest elapsed times for a UM application on any particular HPC system. These aspects are very important for applications that must run within operational time frames. Driving the current study is the HPC industry trend since 1980 for processor arithmetic performance to increase at a faster rate than memory bandwidth. This gap has been growing especially fast for multicore processors in the past 10 years and it can have significant implication for the performance and performance scaling of memory bandwidth intensive applications, such as the UM. Analysis of partially used nodes on Intel Xeon clusters is provided in this paper for short and medium range weather forecasting systems using global and limited-area configurations. It is shown that on the Intel Xeon based clusters the fastest elapsed times and the most efficient system usage can be achieved using partially committed nodes.

Description: Mitochondrial DNA mutations at MT-ATP6 gene are relatively common in individuals suffering from striatal necrosis syndromes. These patients usually do not show apparent histochemical and/or biochemical signs of oxidative phosphorylation dysfunction. Because of this, MT-ATP6 is not typically analyzed in many other mitochondrial disorders that have not been previously associated to mutations in this gene. To correct this bias, we have performed a screening of the MT-ATP6 gene in a large collection of patients suspected of suffering different mitochondrial DNA (mtDNA) disorders. In three cases, biochemical, molecular-genetics and other analyses in patient tissues and cybrids were also carried out. We found three new pathologic mutations. Two of them in patients showing phenotypes that have not been commonly associated to mutations in the MT-ATP6 gene. These results remark the importance of sequencing the MT-ATP6 gene in patients with striatal necrosis syndromes, but also within other mitochondrial pathologies. This gene should be sequenced at least in all those patients suspected of suffering an mtDNA disorder disclosing normal results for histochemical and biochemical analyses of respiratory chain.