ALBERT

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 9 (2017): 659-676, doi:10.1093/gbe/evx023.

Description: Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.

Description: This work was primarily supported by a grant from the National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398 to J.K.C., D.L.C., M.E.H., S.I.K., M.F.O., J.R.S., W.W., and A.W.). Further support was provided by the National Institute of Environmental Health Sciences (1R01ES021934-01 to A.W., P42ES7373 to T.H.H., P42ES007381 to M.E.H., and R01ES019324 to J.R.S.), the National Institute of General Medical Sciences (P20GM103423 and P20GM104318 to B.L.K.), and the National Science Foundation (DBI-0640462 and XSEDE-MCB100147 to D.G.).

Description: Elastic reverse time migration (RTM) can yield accurate subsurface information (e.g. PP and PS reflectivity) by imaging the multicomponent seismic data. However, the existing RTM methods are still insufficient to provide satisfactory results because of the finite recording aperture, limited bandwidth and imperfect illumination. Besides, the P - and S -wave separation and the polarity reversal correction are indispensable in conventional elastic RTM. Here, we propose an iterative elastic least-squares RTM (LSRTM) method, in which the imaging accuracy is improved gradually with iteration. We first use the Born approximation to formulate the elastic de-migration operator, and employ the Lagrange multiplier method to derive the adjoint equations and gradients with respect to reflectivity. Then, an efficient inversion workflow (only four forward computations needed in each iteration) is introduced to update the reflectivity. Synthetic and field data examples reveal that the proposed LSRTM method can obtain higher-quality images than the conventional elastic RTM. We also analyse the influence of model parametrizations and misfit functions in elastic LSRTM. We observe that Lamé parameters, velocity and impedance parametrizations have similar and plausible migration results when the structures of different models are correlated. For an uncorrelated subsurface model, velocity and impedance parametrizations produce fewer artefacts caused by parameter crosstalk than the Lamé coefficient parametrization. Correlation- and convolution-type misfit functions are effective when amplitude errors are involved and the source wavelet is unknown, respectively. Finally, we discuss the dependence of elastic LSRTM on migration velocities and its antinoise ability. Imaging results determine that the new elastic LSRTM method performs well as long as the low-frequency components of migration velocities are correct. The quality of images of elastic LSRTM degrades with increasing noise.

Description: Seismic noise measurements (ambient vibrations) have been increasingly used in rock slope stability assessment for both investigation and monitoring purposes. Recent studies made on gravitational hazard revealed significant spectral amplification at given frequencies and polarization of the wave-field in the direction of maximum rock slope displacement. Different properties (resonance frequencies, polarization and spectral ratio amplitudes) can be derived from the spectral analysis of the seismic noise to characterize unstable rock masses. The objective here is to identify the dynamic parameters that could be used to gain information on prone-to-fall rock columns’ geometry. To do so, the dynamic response of prone-to-fall columns to seismic noise has been studied on two different sites exhibiting cliff-like geometry. Dynamic parameters (main resonance frequency and spectral ratio amplitudes) that could characterize the column decoupling were extracted from seismic noise and their variations were studied taking into account the external environmental parameter fluctuations. Based on this analysis, a two-dimensional numerical model has been set up to assess the influence of the rear vertical fractures identified on both sites on the rock column motion response. Although a simple relation was found between spectral ratio amplitudes and the rock column slenderness, it turned out that the resonance frequency is more stable than the spectral ratio amplitudes to characterize this column decoupling, provided that the elastic properties of the column can be estimated. The study also revealed the effect of additional remote fractures on the dynamic parameters, which in turn could be used for detecting the presence of such discontinuities.

Description: Surface-related multiples have been utilized in the reverse-time migration (RTM) procedures, and additional illumination for subsurface can be provided. Meanwhile, many cross-talks are generated from undesired interactions between forward- and backward-propagated seismic waves. In this paper, subsequent to analysing and categorizing these cross-talks, we propose RTM of first-order multiples to avoid most undesired interactions in RTM of all-order multiples, where only primaries are forward-propagated and crosscorrelated with the backward-propagated first-order multiples. With primaries and multiples separated during regular seismic data processing as the input data, first-order multiples can be obtained by a two-step scheme: (1) the dual-prediction of higher-order multiples; and (2) the adaptive subtraction of predicted higher-order multiples from all-order multiples within local offset-time windows. In numerical experiments, two synthetic and a marine field data sets are used, where different cross-talks generated by RTM of all-order multiples can be identified and the proposed RTM of first-order multiples can provide a very interpretable image with a few cross-talks.

Description: By introducing two types of zenith troposphere delay (ZTD) products in precise point positioning (PPP), we developed the ZTD-corrected PPP and the ZTD-constrained PPP, both of them reduced the PPP convergence time. Both enhanced PPP methods are examined by global empirical ZTD models and regional ZTD corrections. For global ZTD models, we verified that ZTD-corrected PPP will deviate the positioning results, while ZTD-constrained PPP could produce unbiased estimations. Therefore, the latter is utilized to study the performance of global ZTD models (ITG, GPT2w, GZTD and UNB3m). After numerous experiments, we found that the performance of ZTD models was positively related to the real ZTD accuracy, and we proposed a universal tropospheric stochastic model 2SQR(9rms) which denotes double the square of nine times ZTD rms, to constrain ZTD in PPP. The proposed model subsequently was validated by real-time static and kinematic ZTD-constrained PPP on the premise that the ZTD rms on every station was known. Compared with traditional PPP, in static PPP, the number of improved stations is increased by 15.5 per cent (ITG), 14.4 per cent (GPT2w), 11.1 per cent (GZTD) and 8.3 per cent (UNB3m). For kinematic PPP, PPP constrained by ITG model still had the best performance, the number of improved stations is increased by 14.4 per cent, after 30 min of initialization time, 13.4 cm east, 13.4 cm north and 11.7 cm up positioning accuracy was obtained, compared with 15.3 cm east, 15.3 cm north and 14.3 cm up accuracy by traditional PPP. In addition, experiments using regional ZTD corrections to enhance real-time PPP showed that both ZTD-corrected PPP and ZTD-constrained PPP can notably reduce the convergence time on the vertical component (within 15 cm).

Description: We investigated post-seismic velocity changes within the fault zone of the 2008 M 7.9 Wenchuan earthquake using coda wave data of repeating small earthquakes. We employed template matching and grid search methods to identify well-defined repeating earthquakes in order to minimize artefacts induced by variations in source location. We identified a total of 12 isolated patches in the fault zone that ruptured more than twice in a 1 yr period after the M 7.9 earthquake. We applied the coda wave interferometry technique to the waveform data of the 34 identified repeating earthquakes to estimate velocity changes between the first and subsequent events in each cluster. We found that major post-seismic velocity changes occurred in the southwestern part of the rupture area, where the main rupture was initiated and characterized by thrust motion, while the Beichuan area in the northeastern part of the rupture zone appears to experience very little post-seismic velocity changes.

Description: In this study, we demonstrate the feasibility of imaging broad-band (10–150 s) Rayleigh wave phase velocity maps on a continental scale using ambient noise tomography (ANT). We obtain broad-band Rayleigh waves from cross-correlations of ambient noise data between all station pairs of USArray and measure the dispersion curves from these cross-correlations at a period band of 10–150 s. The large-scale dense USArray enables us to obtain over 500 000 surface wave paths which cover the contiguous United States densely. Using these paths, we generate Rayleigh wave phase velocity maps at 10–150 s periods. Our phase velocity maps are similar to other reported phase velocity maps based on ambient noise data at short periods (〈50 s) and based on earthquake data at intermediate/long periods (50–90 s). This study extends ANT from short/intermediate periods (〈50 s) to long periods up to 150 s in a continental scale of the USA. These broad-band phase velocity maps from ANT can be used to construct 3-D lithospheric and asthenospheric velocity structures.

Description: In finite-difference (FD) method, numerical dispersion is the dominant factor influencing the accuracy of seismic modelling. Various optimized FD schemes for scalar wave modelling have been proposed to reduce grid dispersion, while the optimized time–space domain FD schemes for elastic wave modelling have not been fully investigated yet. In this paper, an optimized FD scheme with Equivalent Staggered Grid (ESG) for elastic modelling has been developed. We start from the constant P - and S -wave speed elastic wave equations and then deduce analytical plane wave solutions in the wavenumber domain with eigenvalue decomposition method. Based on the elastic plane wave solutions, three new time–space domain dispersion relations of ESG elastic modelling are obtained, which are represented by three equations corresponding to P -, S - and converted-wave terms in the elastic equations, respectively. By using these new relations, we can study the dispersion errors of different spatial FD terms independently. The dispersion analysis showed that different spatial FD terms have different errors. It is therefore suggested that different FD coefficients to be used to approximate the three spatial derivative terms. In addition, the relative dispersion error in L2-norm is minimized through optimizing FD coefficients using Newton's method. Synthetic examples have demonstrated that this new optimal FD schemes have superior accuracy for elastic wave modelling compared to Taylor-series expansion and optimized space domain FD schemes.

Description: Markov chain Monte-Carlo (McMC) sampling generates correlated random samples such that their distribution would converge to the true distribution only as the number of samples tends to infinity. In practice, McMC is found to be slow to converge, convergence is not guaranteed to be achieved in finite time, and detection of convergence requires the use of subjective criteria. Although McMC has been used for decades as the algorithm of choice for inference in complex probability distributions, there is a need to seek alternative approaches, particularly in high dimensional problems. Walker & Curtis ( 2014 ) developed a method for Bayesian inversion of 2-D spatial data using an exact sampling alternative to McMC which always draws independent samples of the target distribution. Their method thus obviates the need for convergence and removes the concomitant bias exhibited by finite sample sets. Their algorithm is nevertheless computationally intensive and requires large memory. We propose a more efficient method for Bayesian inversion of categorical variables, such as geological facies that requires no sampling at all. The method is based on a 2-D Hidden Markov Model (2D-HMM) over a grid of cells where observations represent localized data constraining each cell. The data in our example application are seismic attributes such as P - and S -wave impedances and rock density; our categorical variables are the hidden states and represent the geological rock types in each cell—facies of distinct subsets of lithology and fluid combinations such as shale, brine-sand and gas-sand. The observations at each location are assumed to be generated from a random function of the hidden state (facies) at that location, and to be distributed according to a certain probability distribution that is independent of hidden states at other locations – an assumption referred to as ‘localized likelihoods’. The hidden state (facies) at a location cannot be determined solely by the observation at that location as it also depends on prior information concerning the spatial distribution of other hidden states elsewhere. The prior information is included in the inversion in the form of a training image which represents a conceptual depiction of local geologies that might be expected, but other forms of prior information can be used in the method as desired. The method provides direct estimates of posterior marginal probability distributions over each variable, so these do not need to be estimated from samples such as in McMC. Nevertheless, in the case that samples are desired, these can be generated. On a 2-D test example the method is shown to outperform previous methods significantly, at a fraction of the computational cost. In many foreseeable applications there are therefore no serious impediments to extending the method to 3-D cases.

Description: A double-correlation method is introduced to locate tremor sources based on stacks of complex, doubly-correlated tremor records of multiple triplets of seismographs back projected to hypothetical source locations in a geographic grid. Peaks in the resulting stack of moduli are inferred source locations. The stack of the moduli is a robust measure of energy radiated from a point source or point sources even when the velocity information is imprecise. Application to real data shows how double correlation focuses the source mapping compared to the common single correlation approach. Synthetic tests demonstrate the robustness of the method and its resolution limitations which are controlled by the station geometry, the finite frequency of the signal, the quality of the used velocity information and noise level. Both random noise and signal or noise correlated at time shifts that are inconsistent with the assumed velocity structure can be effectively suppressed. Assuming a surface wave velocity, we can constrain the source location even if the surface wave component does not dominate. The method can also in principle be used with body waves in 3-D, although this requires more data and seismographs placed near the source for depth resolution.

Description: The possibility of applying one explicit finite-difference (FD) scheme to all interior grid points (points not lying on a grid border) no matter what their positions are with respect to the material interface is one of the key factors of the computational efficiency of the FD modelling. Smooth or discontinuous heterogeneity of the medium is accounted for only by values of the effective grid moduli and densities. Accuracy of modelling thus very much depends on how these effective grid parameters are evaluated. We present an orthorhombic representation of a heterogeneous medium for the FD modelling. We numerically demonstrate its superior accuracy. Compared to the harmonic-averaging representation the orthorhombic representation is more accurate mainly in the case of strong surface waves that are especially important in local surface sedimentary basins. The orthorhombic representation is applicable to modelling seismic wave propagation and earthquake motion in isotropic models with material interfaces and smooth heterogeneities using velocity–stress, displacement–stress and displacement FD schemes on staggered, partly staggered, Lebedev and collocated grids.

Description: Infectious diseases are potential catalysts for exploring ‘engaged citizen’ or socioscientific themes given their interwoven economic, political, scientific and social dimensions. This article describes how an undergraduate course on the history of infectious diseases was modified to explore the impact of two ‘engaged citizen’ themes (poverty and technology), and to consider the ramifications of those themes on past, present and future infectious disease outbreaks. Four outbreaks were used as the foundation for the course: plague (1350s), puerperal fever (1840s), cholera (1850s) and syphilis (1930s). The first part of the article describes the general course structure and the role of university-wide ‘engaged citizen’ themes in its semester-specific construction. The second part of the article demonstrates how poverty and technology ‘threads’ were explored in each of the four historical contexts, and subsequently how they were considered in current and future contexts; appendices with lesson suggestions are provided. The third and final part of the article discusses how this specific model might be more broadly applied to other microbiology instructional contexts.

Description: We study fluctuations in the degree-2 zonal spherical harmonic coefficient of the Earth's gravity potential, C 20 , over the period 2003–2015. This coefficient is related to the Earth's oblateness and studying its temporal variations, C 20 , can be used to monitor large-scale mass movements between high and low latitude regions. We examine C 20 inferred from six different sources, including satellite laser ranging (SLR), GRACE and global geophysical fluids models. We further include estimates that we derive from measured variations in the length-of-day (LOD), from the inversion of global crustal displacements as measured by GPS, as well as from the combination of GRACE and the output of an ocean model as described by Sun et al. We apply a sequence of trend and seasonal moving average filters to the different time-series in order to decompose them into an interannual, a seasonal and an intraseasonal component. We then perform a comparison analysis for each component, and we further estimate the noise level contained in the different series using an extended version of the three-cornered-hat method. For the seasonal component, we generally obtain a very good agreement between the different sources, and except for the LOD-derived series, we find that over 90 per cent of the variance in the seasonal components can be explained by the sum of an annual and semiannual oscillation of constant amplitudes and phases, indicating that the seasonal pattern is stable over the considered time period. High consistency between the different estimates is also observed for the intraseasonal component, except for the solution from GRACE, which is known to be affected by a strong tide-like alias with a period of about 161 d. Estimated interannual components from the different sources are generally in agreement with each other, although estimates from GRACE and LOD present some discrepancies. Slight deviations are further observed for the estimate from the geophysical models, likely to be related to the omission of polar ice and groundwater changes in the model combination we use. On the other hand, these processes do not seem to play an important role at seasonal and shorter timescales, as the sum of modelled atmospheric, oceanic and hydrological effects effectively explains the observed C 20 variations at those scales. We generally obtain very good results for the solution from SLR, and we confirm that this well-established technique accurately tracks changes in C 20 . Good agreement is further observed for the estimate from the GPS inversion, showing that this indirect method is successful in capturing fluctuations in C 20 on scales ranging from intra- to interannual. Obtaining accurate estimates from LOD, however, remains a challenging task and more reliable models of atmospheric wind fields are needed in order to obtain high-quality C 20 , in particular at the seasonal scale. The combination of GRACE data and the output of an ocean model appears to be a promising approach, particularly since corresponding C 20 is not affected by tide-like aliases, and generally gives better results than the solution from GRACE, which still seems to be of rather poor quality.

Description: With the alarming rise of antibiotic resistance, clinical professionals are called upon to manage antibiotic therapies using the most relevant and recent clinical and laboratory data. To this end, antimicrobial stewardship (AMS) programs aim to reduce unnecessary or suboptimal use of antibiotics while maximizing outcomes for the patient. For AMS programs to succeed, the active participation of clinical professionals at all levels of patient care is required. Although programs exist to train established clinicians in AMS, there is a paucity of literature on how and when to integrate AMS concepts and skills in pre-clinical and clinical coursework. Here, we discuss the crucial microbiology concepts and proficiencies that are necessary for building and supporting an AMS program. We provide recommendations for key points to include in clinical curricula in order to develop the necessary microbiology interpretation skills to participate in AMS. The influence of AMS programs on local organism susceptibility patterns is emphasized. The importance of antibiograms, rapid diagnostic testing and the practical interpretations of microbiology laboratory reporting are discussed in regard to prioritization in clinical curricula. We also review the current literature on instructional strategies for introducing AMS into clinical programs, and propose concepts that should be included in didactic coursework in order to provide a foundation for AMS education.

Description: We present two independent, automated methods for estimating the absolute horizontal misorientation of seismic sensors. We apply both methods to 44 free-fall ocean-bottom seismometers (OBSs) of the RHUM-RUM experiment ( http://www.rhum-rum.net/ ). The techniques measure the 3-D directions of particle motion of (1) P -waves and (2) Rayleigh waves of earthquake recordings. For P -waves, we used a principal component analysis to determine the directions of particle motions (polarizations) in multiple frequency passbands. We correct for polarization deviations due to seismic anisotropy and dipping discontinuities using a simple fit equation, which yields significantly more accurate OBS orientations. For Rayleigh waves, we evaluated the degree of elliptical polarization in the vertical plane in the time and frequency domain. The results obtained for the RHUM-RUM OBS stations differed, on average, by 3.1° and 3.7° between the methods, using circular mean and median statistics, which is within the methods’ estimate uncertainties. Using P -waves, we obtained orientation estimates for 31 ocean-bottom seismometers with an average uncertainty (95 per cent confidence interval) of 11° per station. For 7 of these OBS, data coverage was sufficient to correct polarization measurements for underlying seismic anisotropy and dipping discontinuities, improving their average orientation uncertainty from 11° to 6° per station. Using Rayleigh waves, we obtained misorientation estimates for 40 OBS, with an average uncertainty of 16° per station. The good agreement of results obtained using the two methods indicates that they should also be useful for detecting misorientations of terrestrial seismic stations.

Description: We investigate the elastic and anelastic structure of the lowermost mantle at the western edge of the Pacific large low shear velocity province (LLSVP) by inverting a collection of S and ScS waveforms. The transverse component data were obtained from F-net for 31 deep earthquakes beneath Tonga and Fiji, filtered between 12.5 and 200 s. We observe a regional variation of S and ScS arrival times and amplitude ratios, according to which we divide our region of interest into three subregions. For each of these subregions, we then perform 1-D (depth-dependent) waveform inversions simultaneously for radial profiles of shear wave velocity ( V S ) and seismic quality factor ( Q ). Models for all three subregions show low V S and low Q structures from 2000 km depth down to the core–mantle boundary. We further find that V S and Q in the central subregion, sampling the Caroline plume, are substantially lower than in the surrounding regions, whatever the depth. In the central subregion, V S -anomalies with respect to PREM (d V S ) and Q are about –2.5 per cent and 216 at a depth of 2850 km, and –0.6 per cent and 263 at a depth of 2000 km. By contrast, in the two other regions, d V S and Q are –2.2 per cent and 261 at a depth of 2850 km, and –0.3 per cent and 291 at a depth of 2000 km. At depths greater than ~2500 km, these differences may indicate lateral variations in temperature of ~100 K within the Pacific LLSVP. At shallower depths, they may be due to the temperature difference between the Caroline plume and its surroundings, and possibly to a small fraction of iron-rich material entrained by the plume.