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George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
Representatives from several next-generation sequencer manufacturers take part in a panel discussion at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
The February 2014 eruption of Kelud volcano (Indonesia) destroyed most of the instruments near it. We use remote seismic and infrasound sensors to reconstruct the eruptive sequence. The first explosions were relatively weak seismic and infrasound events. A major stratospheric ash injection occurred a few minutes later and produced long-lasting atmospheric and ground-coupled acoustic waves that were detected as far as 11,000 km by infrasound sensors and up to 2300 km away on seismometers. A seismic event followed ~12 minutes later and was recorded 7000 km away by seismometers. We estimate a volcanic intensity around 10.9, placing the 2014 Kelud eruption between the 1980 Mount St. Helens and 1991 Pinatubo eruptions intensities. As a result, we demonstrate how remote infrasound and seismic sensors are critical for the early detection of volcanic explosions, and how they can help to constrain and understand eruptive sequences.
Abstract We develop a new methodology for determining earthquake stress drop and apparent stress values via spectral ratio asymptotic levels. With sufficient bandwidth, the stress ratio for a pair of events can be directly related to these low‐ and high‐frequency levels. This avoids the need to assume a particular spectral model and derive stress drop from cubed corner frequency measures. The method can be applied to spectral ratios for any pair of closely related earthquakes and is particularly well suited for coda envelope methods that provide good azimuthally averaged, point‐source measures. We apply the new method to the 2011 Prague and 2016 Pawnee earthquake sequences in Oklahoma. The sequences show stress scaling with size and depth, with the largest events having apparent stress levels near 1 MPa and smaller and/or shallower events having systematically lower stress values.
It is well established that subsurface injection of fluids increases pore fluid pressures that may lead to shear failure along a preexisting fault surface. Concern among oil and gas, geothermal, and carbon storage operators has risen dramatically over the past decade due to the increase in the number and magnitude of induced earthquakes. Efforts to mitigate the risk associated with injection-induced earthquakes include modeling of the interaction between fluids and earthquake faults. Here we investigate this relationship with simulations that couple a geomechanical reservoir model and RSQSim, a physics-based earthquake simulator. RSQSim employs rate- and state-dependent friction (RSF) that enables the investigation of the time-dependent nature of earthquake sequences. We explore the effect of two RSF parameters and normal stress on the spatiotemporal characteristics of injection-induced seismicity. We perform >200 simulations to systematically investigate the effect of these model components on the evolution of induced seismicity sequences and compare the spatiotemporal characteristics of our synthetic catalogs to observations of induced earthquakes. We find that the RSF parameters control the ability of seismicity to migrate away from the injection well, the total number and maximum magnitude of induced events. Additionally, the RSF parameters control the occurrence/absence of premonitory events. Finally, we find that earthquake stress drops can be modulated by the normal stress and/or the RSF parameters. Insight gained from this study can aid in further development of models that address best practice protocols for injection operations, site-specific models of injection-induced earthquakes, and probabilistic hazard and risk assessments.
Let us call a simple graph on $n$ ≥ 2 vertices a prime gap graph if its vertex degrees are 1 and the first $n$ - 1 prime gaps. We show that such a graph exists for every large n, and in fact for every $n$ ≥ 2 if we assume the Riemann hypothesis. Moreover, an infinite sequence of prime gap graphs can be generated by the so-called degree preserving growth process. This is the first time a naturally occurring infinite sequence of positive integers is identified as graphic. That is, we show the existence of an interesting, and so far unique, infinite combinatorial object.
Purpose: To compare 2D gradient-recalled echo (GRE) and 2D spin-echo (SE) echo-planar imaging (EPI) MR elastography (MRE) for measurement of hepatic stiffness in adult patients with known or suspected liver disease at 3 Tesla. Materials and methods: Three hundred and eighty-seven consecutive patients underwent MRE of the liver at 3 Tesla with 2D-GRE and 2D-SE-EPI sequences. ‘Mean liver stiffness (LS)’ calculated by averaging 3 ROIs in the right lobe, ‘Maximum LS’ calculated by an ROI in the right lobe; and ‘Freehand LS’ calculated by an ROI in the entire liver were measured by two independent readers. Inter-observer and inter-class variability in stiffness measurements were assessed. Stiffness values were correlated with degree of liver fibrosis (METAVIR scores) in 97 patients who underwent biopsy. The diagnostic performance was compared by a receiver-operating characteristic analysis. Results: The technical failure rate was 2.8% for 2D-SE-EPI (11/387) and 4.1% for 2D-GRE (16/387, 9 had R{sub 2}* > 80 s{sup −1} indicating iron overload). There is high reproducibility for both GRE and SE-EPI variants (ICC = 0.84–0.94 for both GRE and SE-EPI MRE). The highest sensitivity, specificity, and accuracy of differentiating mild fibrosis (F0–F2) from advanced fibrosis (F3–F4) are 0.84 (GRE Freehand measurement), 0.92 (GRE Maximum stiffness measurement), and 0.88 (GRE Freehand measurement), respectively. Conclusions: High intra-class correlation and intra-reader correlation are seen on measured hepatic stiffness for both 2D-GRE and 2D-SE-EPI MRE. 2D-SE-EPI has lower failure rate. Diagnostic performance of both sequences is equivalent, with highest sensitivity for 2D-GRE Freehand stiffness measurement, and highest specificity 2D-GRE Maximum stiffness measurement.
Purpose: Robotically assisted sonic therapy (RAST) is a nonthermal, noninvasive ablation method based on histotripsy. Prior animal studies have demonstrated the ability to create hepatic ablation zones at the focal point of an ultrasound therapy transducer; however, these treatments resulted in thermal damage to the body wall within the path of ultrasound energy delivery. The purpose of this study was to evaluate the efficacy and safety of a pulse sequence intended to mitigate prefocal body wall injury. Materials and Methods: Healthy swine (n = 6) underwent hepatic RAST (VortxRx software version 1.0.1.3, HistoSonics, Ann Arbor MI) in the right hepatic lobe. A 3.0 cm spherical ablation zone was prescribed for each. Following treatment, animals underwent MRI which was utilized for ablation zone measurement, evaluation of prefocal injury, and assessment of complications. Each animal was euthanized, underwent necropsy, and the tissue was processed for histopathologic analysis of the ablation zone and any other sites concerning for injury. Results: No prefocal injury was identified by MRI or necropsy in the body wall or tissues overlying the liver. Ablation zones demonstrated uniform cell destruction, were nearly spherical (sphericity index = 0.988), and corresponded closely to the prescribed size (3.0 × 3.1 × 3.4 cm, p = 0.70, 0.36, and 0.01, respectively). Ablation zones were associated with portal vein (n = 3, one occlusive) and hepatic vein thrombosis (n = 4, one occlusive); however, bile ducts remained patent within ablation zones (n = 2). Conclusions: Hepatic RAST performed with a modified ultrasound pulse sequence in a porcine model can mitigate prefocal body wall injuries while maintaining treatment efficacy. Further study of hepatic RAST appears warranted, particularly in tumor models.
We generalize earlier results on the interpolation property for triples of cones (Q{sub 0}, Q{sub 1}, Q) (where Q{sub 0}, Q{sub 1}, and Q are cones in weighted spaces of numerical sequences) with respect to some triple of weighted spaces of numerical sequences.
Here, given a nonlinear, univariate, bounded, and differentiable function f(x), this article develops a sequence of Mixed Integer Linear Programming (MILP) and Linear Programming (LP) relaxations that converge to the graph of f(x) and its convex hull, respectively. Theoretical convergence of the sequence of relaxations to the graph of the function and its convex hull is established. For nonlinear non-convex optimization problems, the relaxations presented in this article can be used to construct tight MILP and LP relaxations. These MILP and the LP relaxations can also be used with MILP-based and spatial branch-and-bound based global optimization algorithms, respectively.
This paper analyzes Bit Error Rate (BER) of Optical Code Division Multiple Access (OCDMA) networks for different class of services which are data, voice, and video; whereas Multi-Length Weighted Modified Prime Code (ML-WMPC) sequences are utilized as a spreading code in with respect to previously used ML-Optical Orthogonal codes. Due to variations in bit rates between the mentioned services, each of them assigns a different WMPC sequence length. In addition, the shot noise, thermal noise, and the Multiple Access Interference (MAI) are included and considered as sources of noise in the BER performance analysis. Furthermore, Pulse Position Modulation, Manchester encoding and MAI cancellation (MAIC) technique are utilized to improve the network performance at a higher number of active users. For analysis, the BER performance calculations are investigated for three types of OCDMA receivers such as simple receiver, receiver with MAIC technique, and receiver with MAIC and Manchester encoding. Moreover, the BER mathematical models have been introduced for different bit rates according to the type of service in the presence of the ML-WMPC and the last of three mentioned OCDMA receivers. Finally, these models and their results are compared with the other existing models, where the results show an improvement in BER performance in the proposed approach.
The feature size effect is significant research interest in the field of microforming. It is assumed that the size effect is influenced by the material preparation process. To verify this, the feature size effects associated with the tensile yield strength of Cu sheets with thicknesses ranging from 100 to 200 μm, produced using different sequences involving annealing, rolling, and grinding, were studied. Differing feature size effects were observed in the Cu specimens, and it was confirmed that the size effect was indeed influenced by the specimen preparation sequence. The tensile yield strengths of the annealed–ground–rolled and annealed–rolled specimens increased as the specimen thicknesses decreased. However, an opposing size effect was observed in the case of the annealed–rolled–annealed, annealed–ground, and annealed–rolled–ground specimens. The reduction ratio did not alter the trend associated with the size effect, but influenced the intensity of the size effect. It is believed that the reinforcement and erosion of the surface-hardened layer introduced during rolling resulted in the contradictory results.
To identify switchgrass homologs of rice genes, known/predicted to control biomass and stress response-related traits, we screened 96,000 clones from two switchgrass bacterial artificial chromosome (BAC) libraries. Full-length sequencing of 311 BAC clones revealed sequence for ~3.2 % (51.7 Mb) of the switchgrass genome, coding for 3948 genes. A comparison with Arabidopsis and five grass genomes revealed that switchgrass genes share the highest number of homologs with rice (95.5 %) followed by foxtail millet (91.7 %) and Sorghum (91.5 %). One hundred eighteen of the annotated genes are unique to switchgrass. Gene annotation and ontology analysis revealed 695 genes belonging to gene families targeted in the screening. These include 350 kinase, 203 glycosyltransferase (GT), 109 glycoside hydrolase (GH), and 33 ethylene responsive transcription factor (ERF) family genes. Rice homologs of 65 genes, identified here, have demonstrated roles in bioenergy-relevant traits. These include 14 GT2 family genes involved in the synthesis of cellulose and hemicelluloses. Finally, comparative expression analysis in six switchgrass organs revealed a conserved expression pattern for three cellulose synthase (CesA1, CesA2, and CesA9) and five cellulose-synthase-like genes (CslA2, CslA11, CslC1, CslD4, and CslE6). CslF genes that encode mixed linkage glucans are expressed in wider range of tissues in switchgrass compared with rice.
The Rayleigh–Ritz variation method using a multiconfiguration interaction wavefunction is carried out on the high-lying core-excited states {sup 6}S{sup e,o}(n) and {sup 6}P{sup e,o}(n) (n=1–5) for the boron isoelectronic sequence (Z=6–10), including mass polarization and relativistic corrections. Energy levels, fine structure, transition rates, and transition wavelengths for this system are calculated. Some energy levels of the high-n states are reported for the first time. Wavelengths of the electric-dipole transitions from these core-excited sextet states with quantum electro-dynamical effects and higher-order relativistic corrections are included. The lifetimes of the 1s2s2p{sup 2}3p{sup 6}S{sup o},1s2p{sup 3}3s{sup 6}S{sup o},1s2s2p{sup 2}3s{sup 6}P, 1s2s2p{sup 2}3d{sup 6}P, and 1s2p{sup 3}3p{sup 6}P states for the boron isoelectronic sequence are also reported. Our calculated results agree well in most cases with available theoretical and experimental data in the literature. -- Highlights: •The core-excited states {sup 6}S{sup e,o}(n) and {sup 6}P{sup e,o}(n) of B-like ions are studied. •Some energy levels for the high-n sextet series are reported for the first time. •Configuration structures of these states are checked by fine structure splittings. •Transition rates, wavelengths for these core-excited sextet states are reported.
The relativistic Multi-Reference Møller–Plesset (MR-MP) many-body perturbation theory was applied to calculate the energies of all excited states within the 3s3p, 3p{sup 2}, 3s3d, 3p3d and 3d{sup 2} configurations for every ion of the Mg isoelectronic sequence (Z=12−100). The results are compared with previous calculations and available experimental data. The MR-MP excitation energies agree with experiment typically within 100 ppm over a wide range of Z, particularly for mid- and high-range Z. Experimental data for highly charged ions in this isoelectronic sequence are limited and the complete and accurate dataset presented here is expected to ease the identification process upon measurements.
We investigated the effect of core–valence and core–core correlations on the energy levels and transition probabilities along the Mg isoelectronic sequence from Si{sup 2+} to U{sup 80+}. In order to attain a certain accuracy for the atomic structure we considered configurations obtained by electron promotions from the n=3 up to n=7 valence shells. Core–valence and core–core correlations are systematically included in the model by allowing single and double electron promotions from the n=2 core up to the n=6 and n=5 shells with l≤4 and l≤2, respectively. The present results contain the energy of the levels arising from the valence configurations along with oscillator strengths and radiative rates corresponding to E1, M1, E2, M2 transitions between states arising from 3l3l{sup ′} with l,l{sup ′}≤2 and 3snl{sup ′′} with n≤7 and l{sup ′′}≤4 configurations. We conclude the data accuracy trend along the magnesium isoelectronic sequence as a result of the detailed study of the correlation effects on the radiative properties. The core–valence correlations generally improve both energy and radiative rate values, while the core–core correlations mostly give better oscillator strengths but may slightly increase the energy deviations. The calculations have been performed by employing the fully relativistic model-potential Flexible Atomic Code.
Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several variants of concern emerged globally, including the UK variant (B.1.1.7), the South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California variants of interest (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. On the basis of our extensive genome sequencing program involving 20,453 coronavirus disease 2019 patient samples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital (Houston, TX) patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency (aggregate of 1.1%) in the population, they are geographically widespread. Houston is the first city in the United States in which active circulation of all six current variants of concern has been documented by genome sequencing. Finally, as vaccine deployment accelerates, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence, frequency, and medical impact of consequential variants and their patterns and trajectory of dissemination.
GLI1 is a key downstream transcription effector of the Hedgehog (Hh) signaling pathway that is involved in promoting cell growth, differentiation and tissue patterning in embryonic development. GLI1 over-activation and its nuclear localization has also been linked to the increased aggressiveness of a number of cancers. It has previously been demonstrated that DYRK1A (dual-specificity tyrosine-regulated kinase 1A) can phosphorylate GLI1 and promote GLI1 nuclear localization and its transcriptional activity. Utilizing recombinant human GLI1 and DYRK1A proteins and phospho-peptide mass spectrometry, we demonstrated that GLI1 is phosphorylated by DYRK1A at Ser408, a phospho-site that falls within the putative nuclear localization sequence (NLS) of GLI1, suggesting a possible mechanistic role in modulating its translocation. Further, we showed that the Ser408 site on GLI1 was not phosphorylated in the presence of the selective DYRK1A inhibitor harmine. The data described herein provide the first identification of a DYRK1A-mediated site of phosphorylation on GLI1 within its NLS and may serve as a valuable mechanism for further understanding Hh signaling modulation. - Highlights: • We describe a novel direct DYRK1A phosphorylation site on GLI1 at Ser408. • Harmine a selective DYRK1A inhibitor, blocks DYRK1A-mediated GLI1 phosphorylation. • The Ser408 phospho-site is within the GLI1 nuclear localization sequence (380–420). • This phosphorylation site provides a potential anti-Hh therapeutic target.