bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Significance of Long‐Period Ground Motion at Regional to Teleseismic Distances From the 610‐km Deep Mw 8.3 Sea of Okhotsk Earthquake of 24 May 2013
Authors: Furumura T. , Kennett B. L. N. 
Published: August 2019

AbstractThe 24 May 2013 earthquake beneath the Sea of Okhotsk (610 km, Mw 8.3) produced significant ground motion across the whole span of the Japanese islands, from 1,300‐ to 4,200‐km epicentral distance. The largest shaking was concentrated along the back‐arc side of the subduction zone, which is the opposite of the normal pattern for deep earthquakes in the Pacific slab. Observations from the dense Hi‐net and F‐net arrays across Japan show that the largest shaking in northern Japan (near 2,000‐km epicentral distance) was caused by near‐caustic S waves, with triplication of upgoing and downgoing waves from the deep source and reflected waves from the 660‐km discontinuity. Three‐dimensional finite difference method simulations confirm that the antiwaveguide effect of the high‐wave speed slab is to push the zone of larger intensity 300 km farther to south than might be expected. The S wavefront distorted by the slab has near‐critical incidence at the free surface producing large sP and generating shear‐coupled PL (s‐PL) waves with period >3 s. With increasing epicentral distance the S incident angle exceeds critical, then total sS reflection creates large ground motion at large distance (>3,000 km) and even farther (>6,000 km) with sSS. The propagation of sS, sSS linking to sS‐PL, and sSS‐PL wave trains is very efficient in continental structures with thicker crust. The felt reports at large (4,000–8000 km) distances from the 2013 Sea of Okhotsk earthquake can be explained by lengthy, long‐period ground motion in the continental environment with amplification in sedimentary basins and in tall buildings.
The Relationship Between U.S. East Coast Sea Level and the Atlantic Meridional Overturning Circulation: A Review
Authors: Little Christopher M. , Hu Aixue , Hughes Chris W. , McCarthy Gerard D. , Piecuch Christopher G. , Ponte Rui M. , Thomas Matthew D. 
Published: August 2019

AbstractScientific and societal interest in the relationship between the Atlantic Meridional Overturning Circulation (AMOC) and U.S. East Coast sea level has intensified over the past decade, largely due to (1) projected, and potentially ongoing, enhancement of sea level rise associated with AMOC weakening and (2) the potential for observations of U.S. East Coast sea level to inform reconstructions of North Atlantic circulation and climate. These implications have inspired a wealth of model‐ and observation‐based analyses. Here, we review this research, finding consistent support in numerical models for an antiphase relationship between AMOC strength and dynamic sea level. However, simulations exhibit substantial along‐coast and intermodel differences in the amplitude of AMOC‐associated dynamic sea level variability. Observational analyses focusing on shorter (generally less than decadal) timescales show robust relationships between some components of the North Atlantic large‐scale circulation and coastal sea level variability, but the causal relationships between different observational metrics, AMOC, and sea level are often unclear. We highlight the importance of existing and future research seeking to understand relationships between AMOC and its component currents, the role of ageostrophic processes near the coast, and the interplay of local and remote forcing. Such research will help reconcile the results of different numerical simulations with each other and with observations, inform the physical origins of covariability, and reveal the sensitivity of scaling relationships to forcing, timescale, and model representation. This information will, in turn, provide a more complete characterization of uncertainty in relevant relationships, leading to more robust reconstructions and projections.
Does ERA‐5 Outperform Other Reanalysis Products for Hydrologic Applications in India?
Authors: Mahto Shanti Shwarup , Mishra Vimal 
Published: August 2019

AbstractGlobal reanalysis products are extensively used for hydrologic applications in sparse data regions. European Centre for Medium‐Range Weather Forecasts Re‐Analysis version 5 (ERA‐5), among the new‐era reanalysis products, has been significantly improved for horizontal and vertical resolutions and data assimilation. However, the new‐era reanalysis products (ERA‐5, Climate Forecast System Reanalysis, ERA‐Interim, Modern Era Retrospective Analysis for Research and Applications version 2, and Japanese 55‐year Reanalysis Project) have not been evaluated for the hydrologic applications in India specially to understand if ERA‐5 outperforms the other reanalysis products or not. Here we use the five new‐era reanalysis products for the monsoon (June–September) season precipitation, maximum (Tmax) and minimum (Tmin) temperatures, total runoff, evapotranspiration, and soil moisture against the observations from India Meteorological Department in India for 1980–2018. We use a well‐calibrated and evaluated hydrological model (the Variable Infiltration Capacity model) to simulate hydrologic variables using the forcing from India Meteorological Department and reanalysis products. In addition, we evaluated the reanalysis products for streamflow and annual water budget for the two basins located in the diverse climatic settings in India. Our results show that ERA‐5 outperforms the other reanalysis products for the monsoon season precipitation, Tmax, evapotranspiration, and soil moisture. However, Climate Forecast System Reanalysis performs better than ERA‐5 for the monsoon season total runoff in India. Performance for streamflow and annual water budget for ERA‐5 is either better or comparable to the other reanalysis products in the two river basins. Overall, we find that ERA‐5 performs better than the other reanalysis products and can be used for the hydrologic assessments in India.
The Uplift of the Troodos Massif, Cyprus
Authors: Ring Uwe , Pantazides Hermes 
Published: August 2019

AbstractWe constrain the fault pattern and the kinematics of faulting that facilitated the uplift of the Troodos Massif in Cyprus in the eastern Mediterranean. The fault pattern consists of E‐W striking reverse faults, N‐S striking normal faults, and NW striking dextral and NE striking sinistral strike/oblique‐slip faults. Fault‐slip analysis reveals that this overall pattern resulted from subhorizontal NNW directed shortening and coeval, subhorizontal ENE directed extension. Dated sediments affected by faulting reveal that the N‐S striking normal faults are, at least in part, younger than 2.14 Ma. This suggests that the entire fault pattern, or at least a large part of it, resulted or was reworked during post‐2.14‐Ma deformation. Published work further shows that the uplift of the Troodos Massif was controlled by underthrusting of the Eratosthenes Seamount, which entered the Cyprus subduction zone by about 2 Ma. The alleged E‐W extent of the underthrust segment of the seamount approximately matches the size of the high‐topography area of the Troodos Mountains. We interpret this geometry to have caused spatially limited crustal thickening underneath the high‐topography area by subhorizontal N‐S shortening in front of and above the underthrusting seamount and coeval, subhorizontal E‐W extension at its flanks, and that the uplift of the high‐topography area occurred in the footwall of the N‐S striking normal faults. This model is broadly in line with seismicity and may also explain why serpentinized mantle rocks and dense gabbro are now exposed on top of the Troodos Massif.
The prion-like protein kinase Sky1 is required for efficient stress granule disassembly
Authors: Shattuck Jenifer E. , Paul Kacy R. , Cascarina Sean M. , Ross Eric D. 
Published: August 2019

AbstractStress granules are membraneless protein- and mRNA-rich organelles that form in response to perturbations in environmental conditions. Stress granule formation is reversible, and persistent stress granules have been implicated in a variety of neurodegenerative disorders, including amyotrophic lateral sclerosis. However, characterization of the factors involved in dissolving stress granules is incomplete. Many stress granule proteins contain prion-like domains (PrLDs), some of which have been linked to stress granule formation. Here, we demonstrate that the PrLD-containing yeast protein kinase Sky1 is a stress granule component. Sky1 is recruited to stress granules in part via its PrLD, and Sky1’s kinase activity regulates timely stress granule disassembly during stress recovery. This effect is mediated by phosphorylation of the stress granule component Npl3. Sky1 can compensate for defects in chaperone-mediated stress granule disassembly and vice-versa, demonstrating that cells have multiple overlapping mechanisms for re-solubilizing stress granule components.
A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites
Authors: Koirala Deepak , Shao Yaming , Koldobskaya Yelena , Fuller James R. , Watkins Andrew M. , Shelke Sandip A. , Pilipenko Evgeny V. , Das Rhiju , Rice Phoebe A. , Piccirilli Joseph A. 
Published: August 2019

AbstractPicornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crystal structure of hepatitis A virus IRES domain V (dV) in complex with a synthetic antibody fragment—a crystallization chaperone. The RNA adopts a three-way junction structure, topologically organized by an adenine-rich stem-loop motif. Despite no obvious sequence homology, the dV architecture shows a striking similarity to a circularly permuted form of encephalomyocarditis virus J-K domain, suggesting a conserved strategy for organizing the domain architecture. Recurrence of the motif led us to use homology modeling tools to compute a 3-dimensional structure of the corresponding domain of foot-and-mouth disease virus, revealing an analogous domain organizing motif. The topological conservation observed among these IRESs and other viral domains implicates a structured three-way junction as an architectural scaffold to pre-organize helical domains for recruiting the translation initiation machinery.
Virus lasers for biological detection
Authors: Hales John E. , Matmon Guy , Dalby Paul A. , Ward John M. , Aeppli Gabriel 
Published: August 2019

AbstractThe selective amplification of DNA in the polymerase chain reaction is used to exponentially increase the signal in molecular diagnostics for nucleic acids, but there are no analogous techniques for signal enhancement in clinical tests for proteins or cells. Instead, the signal from affinity-based measurements of these biomolecules depends linearly on the probe concentration. Substituting antibody-based probes tagged for fluorescent quantification with lasing detection probes would create a new platform for biomarker quantification based on optical rather than enzymatic amplification. Here, we construct a virus laser which bridges synthetic biology and laser physics, and demonstrate virus-lasing probes for biosensing. Our virus-lasing probes display an unprecedented > 10,000 times increase in signal from only a 50% increase in probe concentration, using fluorimeter-compatible optics, and can detect biomolecules at sub-100 fmol mL−1 concentrations.
Porous single-crystalline titanium dioxide at 2 cm scale delivering enhanced photoelectrochemical performance
Authors: Cheng Fangyuan , Lin Guoming , Hu Xiuli , Xi Shaobo , Xie Kui 
Published: August 2019

AbstractPorous single-crystalline (P-SC) titanium dioxide in large size would significantly enhance their photoelectrochemical functionalities owing to the structural coherence and large surface area. Here we show the growth of P-SC anatase titanium dioxide on an 2 cm scale through a conceptually different lattice reconstruction strategy by direct removal of K/P from KTiOPO4 lattice leaving the open Ti-O skeleton simultaneously recrystallizing into titanium dioxide. The (101) facet dominates the growth of titanium dioxide while the relative titanium densities on different parent crystal facets control the microstructures. Crystal growth in reducing atmospheres produces P-SC TinO2n-1 (n = 7~38) in magneli phases with enhanced visible-infrared light absorption and conductivity. The P-SC TinO2n-1 shows enhanced exciton lifetime and charge mobility. The P-SC TinO2n-1 boosts photoelectrochemical oxidation of benzene to phenol with P-SC Ti9O17 showing 60.1% benzene conversion and 99.6% phenol selectivity at room temperature which is the highest so far to the best of our knowledge.
Computer-aided discovery of connected metal-organic frameworks
Authors: Kwon Ohmin , Kim Jin Yeong , Park Sungbin , Lee Jae Hwa , Ha Junsu , Park Hyunsoo , Moon Hoi Ri , Kim Jihan 
Published: August 2019

AbstractComposite metal-organic frameworks (MOFs) tend to possess complex interfaces that prevent facile and rational design. Here we present a joint computational/experimental workflow that screens thousands of MOFs and identifies the optimal MOF pairs that can seamlessly connect to one another by taking advantage of the fact that the metal nodes of one MOF can form coordination bonds with the linkers of the second MOF. Six MOF pairs (HKUST-1@MOF-5, HKUST-1@IRMOF-18, UiO-67@HKUST-1, PCN-68@MOF-5, UiO-66@MIL-88B(Fe) and UiO-67@MIL-88C(Fe)) yielded from our theoretical predictions were successfully synthesized, leading to clean single crystalline MOF@MOF, demonstrating the power of our joint workflow. Our work can serve as a starting point to accelerate the discovery of novel MOF composites that can potentially be used for many different applications.
Protegrin-1 cytotoxicity towards mammalian cells positively correlates with the magnitude of conformational changes of the unfolded form upon cell interaction
Authors: Soundrarajan Nagasundarapandian , Park Suhyun , Le Van Chanh Quy , Cho Hye-sun , Raghunathan Govindan , Ahn Byeongyong , Song Hyuk , Kim Jin-Hoi , Park Chankyu 
Published: August 2019

AbstractPorcine protegrin-1 (PG-1) is a broad-spectrum antimicrobial peptide (AMP) with potent antimicrobial activities. We produced recombinant PG-1 and evaluated its cytotoxicity toward various types of mammalian cell lines, including embryonic fibroblasts, retinal cells, embryonic kidney cells, neuroblastoma cells, alveolar macrophage cells, and neutrophils. The sensitivity of the different mammalian cells to cytotoxic damage induced by PG-1 differed significantly among the cell types, with retinal neuron cells and neutrophils being the most significantly affected. A circular dichroism analysis showed there was a precise correlation between conformational changes in PG-1 and the magnitude of cytotoxicity among the various cell type. Subsequently, a green fluorescent protein (GFP) penetration assay using positively charged GFPs indicated there was a close correlation between the degree of penetration of charged GFP into cells and the magnitude of PG-1 cytotoxicity. Furthermore, we also showed that inhibition of the synthesis of anionic sulphated proteoglycans on the cell surface decreases the cytotoxic damage induced by PG-1 treatment. Taken together, the observed cytotoxicity of PG-1 towards different membrane surfaces is highly driven by the membrane’s anionic properties. Our results reveal a possible mechanism underlying cell-type dependent differences in cytotoxicity of AMPs, such as PG-1, toward mammalian cells.
Biological learning curves outperform existing ones in artificial intelligence algorithms
Authors: Uzan Herut , Sardi Shira , Goldental Amir , Vardi Roni , Kanter Ido 
Published: August 2019

AbstractRecently, deep learning algorithms have outperformed human experts in various tasks across several domains; however, their characteristics are distant from current knowledge of neuroscience. The simulation results of biological learning algorithms presented herein outperform state-of-the-art optimal learning curves in supervised learning of feedforward networks. The biological learning algorithms comprise asynchronous input signals with decaying input summation, weights adaptation, and multiple outputs for an input signal. In particular, the generalization error for such biological perceptrons decreases rapidly with increasing number of examples, and it is independent of the size of the input. This is achieved using either synaptic learning, or solely through dendritic adaptation with a mechanism of swinging between reflecting boundaries, without learning steps. The proposed biological learning algorithms outperform the optimal scaling of the learning curve in a traditional perceptron. It also results in a considerable robustness to disparity between weights of two networks with very similar outputs in biological supervised learning scenarios. The simulation results indicate the potency of neurobiological mechanisms and open opportunities for developing a superior class of deep learning algorithms.
Towards A Microbead Occlusion Model of Glaucoma for a Non-Human Primate
Authors: Lambert Wendi S. , Carlson Brian J. , Ghose Purnima , Vest Victoria D. , Yao Vincent , Calkins David J. 
Published: August 2019

AbstractGlaucoma is a group of optic neuropathies associated with aging and sensitivity to intraocular pressure (IOP). The disease causes vision loss through the degeneration of retinal ganglion cell neurons and their axons in the optic nerve. Using an inducible model of glaucoma, we elevated IOP in the squirrel monkey (Saimiri boliviensis) using intracameral injection of 35 μm polystyrene microbeads and measured common pathogenic outcomes in the optic projection. A 42% elevation in IOP over 28 weeks reduced anterograde transport of fluorescently-labeled cholera toxin beta from retina to the lateral geniculate nucleus (60% decrease), and to the superior colliculus (49% decrease). Pressure also reduced survival of ganglion cellaxons in the optic nerve by 22%. The same elevation caused upregulation of proteins associated with glaucomatous neurodegeneration in the retina and optic nerve, including complement 1q, interleukin 6, and brain-derived neurotrophic factor. That axon degeneration in the nerve lagged deficits in anterograde transport is consistent with progression in rodent models, while the observed protein changes also occur in tissue from human glaucoma patients. Thus, microbead occlusion in a non-human primate with a visual system similar to our own represents an attractive model to investigate neurodegenerative mechanisms and therapeutic interventions for glaucoma.
Particulate matter-attributable mortality and relationships with carbon dioxide in 250 urban areas worldwide
Authors: Anenberg Susan C. , Achakulwisut Pattanun , Brauer Michael , Moran Daniel , Apte Joshua S. , Henze Daven K. 
Published: August 2019

AbstractUrban air pollution is high on global health and sustainability agendas, but information is limited on associated city-level disease burdens. We estimated fine particulate matter (PM2.5) mortality in the 250 most populous cities worldwide using PM2.5 concentrations, population, disease rates, and concentration-response relationships from the Global Burden of Disease 2016 Study. Only 8% of these cities had population-weighted mean concentrations below the World Health Organization guideline for annual average PM2.5. City-level PM2.5-attributable mortality rates ranged from 13–125 deaths per 100,000 people. PM2.5 mortality rates and carbon dioxide (CO2) emission rates were weakly positively correlated, with regional influences apparent from clustering of cities within each region. Across 82 cities globally, PM2.5 concentrations and mortality rates were negatively associated with city gross domestic product (GDP) per capita, but we found no relationship between GDP per capita and CO2 emissions rates. While results provide only a cross-sectional snapshot of cities worldwide, they point to opportunities for cities to realize climate, air quality, and health co-benefits through low-carbon development. Future work should examine drivers of the relationships (e.g. development stage, fuel mix for electricity generation and transportation, sector-specific PM2.5 and CO2 emissions) uncovered here and explore uncertainties to test the robustness of our conclusions.
Diet-related selectivity of macroplastic ingestion in green turtles (Chelonia mydas) in the eastern Mediterranean
Authors: Duncan Emily M. , Arrowsmith Jessica A. , Bain Charlotte E. , Bowdery Hannah , Broderick Annette C. , Chalmers Tierney , Fuller Wayne J. , Galloway Tamara S. , Lee Jonathon H. , Lindeque Penelope K. , Omeyer Lucy C. M. , Snape Robin T. E. , Godley Brendan J. 
Published: August 2019

AbstractUnderstanding the drivers of key interactions between marine vertebrates and plastic pollution is now considered a research priority. Sea turtles are primarily visual predators, with the ability to discriminate according to colour and shape; therefore these factors play a role in feeding choices. Classification methodologies of ingested plastic currently do not record these variables, however here, refined protocols allow us to test the hypothesis that plastic is selectively ingested when it resembles the food items of green turtles (Chelonia mydas). Turtles in the eastern Mediterranean displayed strong diet-related selectivity towards certain types (sheet and threadlike), colours (black, clear and green) and shapes (linear items strongly preferred) of plastic when compared to the environmental baseline of plastic beach debris. There was a significant negative relationship between size of turtle (curved carapace length) and number/mass of plastic pieces ingested, which may be explained through naivety and/or ontogenetic shifts in diet. Further investigation in other species and sites are needed to more fully ascertain the role of selectivity in plastic ingestion in this marine vertebrate group.
Construction of a synthetic pathway for the production of 1,3-propanediol from glucose
Authors: Frazão Cláudio J. R. , Trichez Débora , Serrano-Bataille Hélène , Dagkesamanskaia Adilia , Topham Christopher M. , Walther Thomas , François Jean Marie 
Published: August 2019

AbstractIn this work, we describe the construction of a synthetic metabolic pathway enabling direct biosynthesis of 1,3-propanediol (PDO) from glucose via the Krebs cycle intermediate malate. This non-natural pathway extends a previously published synthetic pathway for the synthesis of (L)-2,4-dihydroxybutyrate (L-DHB) from malate by three additional reaction steps catalyzed respectively, by a DHB dehydrogenase, a 2-keto-4-hydroxybutyrate (OHB) dehydrogenase and a PDO oxidoreductase. Screening and structure-guided protein engineering provided a (L)-DHB dehydrogenase from the membrane-associated (L)-lactate dehydrogenase of E. coli and OHB decarboxylase variants derived from the branched-chain keto-acid decarboxylase encoded by kdcA from Lactococcus lactis or pyruvate decarboxylase from Zymomonas mobilis. The simultaneous overexpression of the genes encoding these enzymes together with the endogenous ydhD-encoded aldehyde reductase enabled PDO biosynthesis from (L)-DHB. While the simultaneous expression of the six enzymatic activities in a single engineered E. coli strain resulted in a low production of 0.1 mM PDO from 110 mM glucose, a 40-fold increased PDO titer was obtained by co-cultivation of an E. coli strain expressing the malate-DHB pathway with another strain harboring the DHB-to-PDO pathway.