Shear-Wave Velocity Characterization of the USGS Hawaiian Strong-Motion Network on the Island of Hawaii and Development of an NEHRP Site-Class Map

To assess the level and nature of ground shaking in Hawaii for the purposes of earthquake hazard mitigation and seismic design, empirical ground-motion prediction models are desired. To develop such empirical relationships, knowledge of the subsurface site conditions beneath strong-motion stations is critical. Thus, as a first step to develop ground-motion prediction models for Hawaii, wspectral-analysis-of-surface-waves (SASW) profiling was performed at the 22 free-field U.S. Geological Survey (USGS) strong-motion sites on the Big Island to obtain shear-wave velocity (V(S)) data. Nineteen of these stations recorded the 2006 Kiholo Bay moment magnitude (M) 6.7 earthquake, and 17 stations recorded the triggered M 6.0 Mahukona earthquake. V(S) profiling was performed to reach depths of more than 100 ft. Most of the USGS stations are situated on sites underlain by basalt, based on surficial geologic maps. However, the sites have varying degrees of weathering and soil development. The remaining strong-motion stations are located on alluvium or volcanic ash. V(S30) (average V(S) in the top 30 m) values for the stations on basalt ranged from 906 to 1908 ft/s [National Earthquake Hazards Reduction Program (NEHRP) site classes C and D], because most sites were covered with soil of variable thickness. Based on these data, an NEHRP site-class map was developed for the Big Island. These new V(S) data will be a significant input into an update of the USGS statewide hazard maps and to the operation of ShakeMap on the island of Hawaii.George E. Brown, Jr. Network for Earthquake Engineering Simulation (NEES) under NSF CMS-0086605FEMA HSFEHQ-06-D-0162, HSFEHQ-04-D-0733U.S. Geological Survey, Department of the Interior 08HQGR0036Geotechnical Engineering Cente

Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase.

Bacterial ClpB and yeast Hsp104 are homologous Hsp100 protein disaggregases that serve critical functions in proteostasis by solubilizing protein aggregates. Two AAA+ nucleotide binding domains (NBDs) power polypeptide translocation through a central channel comprised of a hexameric spiral of protomers that contact substrate via conserved pore-loop interactions. Here we report cryo-EM structures of a hyperactive ClpB variant bound to the model substrate, casein in the presence of slowly hydrolysable ATPγS, which reveal the translocation mechanism. Distinct substrate-gripping interactions are identified for NBD1 and NBD2 pore loops. A trimer of N-terminal domains define a channel entrance that binds the polypeptide substrate adjacent to the topmost NBD1 contact. NBD conformations at the seam interface reveal how ATP hydrolysis-driven substrate disengagement and re-binding are precisely tuned to drive a directional, stepwise translocation cycle

Enhanced dark hydrogen fermentation of Enterobacter aerogenes/HoxEFUYH with carbon cloth

Long-range extracellular electron transfer through microbial nanowires is critical for efficient bacterial behaviors. The application of carbon cloth on the dark hydrogen fermentation using transgenic Enterobacter aerogenes (E. aerogenes/HoxEFUYH) was first proposed to enhance hydrogen production from glucose. Scanning electron microscopy images showed that the microbial nanowires between E. aerogenes/HoxEFUYH cells almost vanished due to the presence of carbon cloth. Approximately 59.1% of microorganisms concentrated in biofilms on the surface of carbon cloth, which probably promoted the intercellular electron transfer. The results from Fourier transform infrared spectra and Excitation Emission Matrix spectra indicated that carbon cloth biofilms primarily included polysaccharide and protein. Moreover, the fluorophore of biofilms (88.1%) was much higher than that of supernatant (11.9%). The analysis of soluble metabolic degradation byproducts revealed that carbon cloth selectively enhanced the acetate pathway (C6H12O6+2H2O→2CH3COOH+2CO2+4H2), but weakened the ethanol pathway (C6H12O6→2C2H5OH+2CO2). With 1.0 g/L carbon cloth, the hydrogen yield increased by 26.6% to 242 mL/g, and the corresponding peak hydrogen production rate increased by 60.3%

Boosting biomethane yield and production rate with graphene: the potential of direct interspecies electron transfer in anaerobic digestion

Interspecies electron transfer between bacteria and archaea plays a vital role in enhancing energy efficiency of anaerobic digestion (AD). Conductive carbon materials (i.e. graphene nanomaterial and activated charcoal) were assessed to enhance AD of ethanol (a key intermediate product after acidogenesis of algae). The addition of graphene (1.0 g/L) resulted in the highest biomethane yield (695.0 ± 9.1 mL/g) and production rate (95.7 ± 7.6 mL/g/d), corresponding to an enhancement of 25.0% in biomethane yield and 19.5% in production rate. The ethanol degradation constant was accordingly improved by 29.1% in the presence of graphene. Microbial analyses revealed that electrogenic bacteria of Geobacter and Pseudomonas along with archaea Methanobacterium and Methanospirillum might participate in direct interspecies electron transfer (DIET). Theoretical calculations provided evidence that graphene-based DIET can sustained a much higher electron transfer flux than conventional hydrogen transfer

Mining Disaggregase Sequence Space to Safely Counter TDP-43, FUS, and α-Synuclein Proteotoxicity.

Hsp104 is an AAA+ protein disaggregase, which can be potentiated via diverse mutations in its autoregulatory middle domain (MD) to mitigate toxic misfolding of TDP-43, FUS, and α-synuclein implicated in fatal neurodegenerative disorders. Problematically, potentiated MD variants can exhibit off-target toxicity. Here, we mine disaggregase sequence space to safely enhance Hsp104 activity via single mutations in nucleotide-binding domain 1 (NBD1) or NBD2. Like MD variants, NBD variants counter TDP-43, FUS, and α-synuclein toxicity and exhibit elevated ATPase and disaggregase activity. Unlike MD variants, non-toxic NBD1 and NBD2 variants emerge that rescue TDP-43, FUS, and α-synuclein toxicity. Potentiating substitutions alter NBD1 residues that contact ATP, ATP-binding residues, or the MD. Mutating the NBD2 protomer interface can also safely ameliorate Hsp104. Thus, we disambiguate allosteric regulation of Hsp104 by several tunable structural contacts, which can be engineered to spawn enhanced therapeutic disaggregases with minimal off-target toxicity

Bond-Selective Intensity Diffraction Tomography

Recovering molecular information remains a grand challenge in the widely used holographic and computational imaging technologies. To address this challenge, we developed a computational mid-infrared photothermal microscope, termed Bond-selective Intensity Diffraction Tomography (BS-IDT). Based on a low-cost brightfield microscope with an add-on pulsed light source, BS-IDT recovers both infrared spectra and bond-selective 3D refractive index maps from intensity-only measurements. High-fidelity infrared fingerprint spectra extraction is validated. Volumetric chemical imaging of biological cells is demonstrated at a speed of ~20 seconds per volume, with a lateral and axial resolution of ~350 nm and ~1.1 micron, respectively. BS-IDT's application potential is investigated by chemically quantifying lipids stored in cancer cells and volumetric chemical imaging on Caenorhabditis elegans with a large field of view (~100 micron X 100 micron)

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Numerical Simulation of Aerodynamic Performance of Off-grid Small Vertical Axis Wind Turbine

In this paper, a 2D off-grid small compact model of vertical axis wind turbine was established. The sliding grid technology, the RNG turbulence model and the Coupld algorithm was applied to simulate the unsteady value of the model's aerodynamic performance. Through the analysis on the flow field at difference moments, the rules about velocity fields, vortices distributions and the wind turbine's total torque were obtained. The results show that: the speed around wind turbine blades have obvious gradient, and the velocity distribution at different times show large differences in the computional domain. In the rotating domain vorticity is large. With away from the rotation domain, vorticity reduced quickly. In the process of rotating for vertical axis wind turbine, the wind turbine's total torque showed alternating positive and negative changes

Numerical Simulation of Aerodynamic Performance of Off-grid Small Vertical Axis Wind Turbine

In this paper, a 2D off-grid small compact model of vertical axis wind turbine was established. The sliding grid technology, the RNG turbulence model and the Coupld algorithm was applied to simulate the unsteady value of the model's aerodynamic performance. Through the analysis on the flow field at difference moments, the rules about velocity fields, vortices distributions and the wind turbine's total torque were obtained. The results show that: the speed around wind turbine blades have obvious gradient, and the velocity distribution at different times show large differences in the computional domain. In the rotating domain vorticity is large. With away from the rotation domain, vorticity reduced quickly. In the process of rotating for vertical axis wind turbine, the wind turbine's total torque showed alternating positive and negative changes