bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncovering the Pattern of Forced Sea Level Rise in the Satellite Altimeter Record
Authors: Hamlington Benjamin D. , Fasullo John T. , Nerem R. Steven , Kim Kwang‐Yul , Landerer F. W.
Published: April 2019

The continuous and near‐global coverage of satellite altimeters has provided an improved understanding of sea level rise on both global and regional scales. With its relatively short record, however, questions have persisted regarding how well satellite‐measured trends reflect the trends associated with forced or anthropogenic forcing. Masking the forced sea level rise in the altimeter record is the presence of unaccounted‐for, naturally occurring variability. Here, a combined approach using models and observations is used to attribute a portion of the satellite‐measured sea level record to natural variability. The agreement between the observations and models makes clear the quality of current models and their ability to realistically capture sea level variability. This paper shows a regional trend pattern where the influence of natural variability has been reduced, providing a clearer picture of how anthropogenic forcing may impact sea level arise around the globe.
SuperDARN Evidence for Convection‐Driven Lagrangian Coherent Structures in the Polar Ionosphere
Authors: Ramirez U. , Wang Ningchao , Chartier Alex T. , Datta‐Barua S.
Published: April 2019

Polar cap patches are large sporadic enhancements of plasma density on the scale of hundreds of kilometers, which can impact the performance of Global Navigation Satellite Systems. Lagrangian Coherent Structures (LCSs) are ridges that show areas of maximal separation in a time‐evolving flow. Previous work based on modeled ionospheric flow showed that LCSs exist in the ionosphere and are barriers governing patch formation. In this work, we identify the first data‐driven LCSs in the high‐latitude ionosphere using Super Dual Auroral Radar Network (SuperDARN) ion convection fields. The LCSs found using the Ionosphere‐Thermosphere Algorithm for LCSs are compared during geomagnetically quiet and active periods. The shape of the LCS is found to be dependent on the electric potential pattern. A consistent two‐cell pattern results in a W‐shaped LCS, but when the two‐cell pattern breaks down, the LCS loses this characteristic shape. The changes in the electric potential, and thus the LCS, are likely due to changes in the interplanetary magnetic field. A comparison between LCSs obtained from empirical models and data reveal that the data‐driven LCSs are poleward of and have a shorter longitudinal span than the model‐based LCSs. A comparison of the LCS location and the formation of a polar cap patch on 17 March 2015 showed that the center of the patch developed from plasma on the main LCS ridge, and this is confirmed with a separate polar cap patch event from 26 September 2011.
Heavy Ion Composition of Mercury's Magnetosphere
Authors: Wurz P. , Gamborino D. , Vorburger A. , Raines J. M.
Published: April 2019

We modeled the exospheric densities for sputtering and thermal desorption in detail for the time period of the first MESSENGER flyby of Mercury. From the exospheric densities we calculate ion production rates. These ions will be transported to the location of MESSENGER if they are produced on magnetic field lines connecting the cusp with the downwind side. From these ions we produce mass spectra that we compared with the Fast Imaging Plasma Spectrometer measurements performed during this flyby. We find good qualitative agreement between the modeled and the measured ion mass spectrum. We find that sputtering is a major process to contribute to the population of planetary ions in the magnetosphere because of the large scale height of the exospheric particles and the resulting long flight times. In addition, thermal desorption of Na contributes significant amounts to the magnetospheric ion population. From the volatile species we can identify He, OH, H2O, and Ne in the measured mass spectrum. However, for most of the volatile species the reported upper limits must be reduced by 2–3 orders of magnitude to be compatible to the measured ion spectrum.
Evaporative Implications of Dry‐Air Outbreaks Over the Northern Red Sea
Authors: Menezes Viviane V. , Farrar J. Thomas , Bower Amy S.
Published: April 2019

We investigate the impacts of westward wind events on the Red Sea evaporation using the 35‐year second Modern‐Era Retrospective analysis for Research and Applications reanalysis and a 2‐year‐long record of in situ observations from a heavily instrumented air‐sea interaction mooring. These events are common during boreal winter, and their effects are similar to cold‐air outbreaks that occur in midpolar and subpolar latitudes. They cause extreme heat loss from the sea, which is dominated by latent heat fluxes. Different from cold‐air outbreaks, the intensified heat loss is due to the low relative humidity as we show through latent heat flux decomposition. Rainfall is negligible during these events, and we refer to them as dry‐air outbreaks. We also investigate the general atmospheric circulation pattern that favors their occurrence, which is associated with an intensified Arabian High at the north‐central portion of the Arabian Peninsula—a feature that seems to be an extension of the Siberian High. The analyses reveal that the westward winds over the northern Red Sea and the winter Shamal winds in the Persian Gulf are very likely to be part of the same subsynoptic‐scale feature. The second Modern‐Era Retrospective analysis for Research and Applications reanalysis indicates that the occurrence of westward wind events over the northern Red Sea has grown from 1980 to 2015, especially the frequency of large‐scale events, the cause of which is to be investigated. We hypothesize that dry‐air outbreaks may induce surface water mass transformation in the surface Red Sea Eastern Boundary Current and could represent a significant process for the oceanic thermohaline‐driven overturning circulation.
Wintertime Boundary Layer Evolution and Air Pollution Potential Over the Kathmandu Valley, Nepal
Authors: Regmi Ram P. , Kitada Toshihiro , Maharjan Sangeeta , Shrestha Sajan , Shrestha Saraswati , Regmi Greema
Published: April 2019

Meteorological effects on wintertime air pollution in the Kathmandu Valley were investigated using SOnic Detection and Ranging soundings, Automatic Weather Station measurements, numerical simulation using Weather Research and Forecasting data, and Chemical Transport Modeling during February 2013. A surrogate for black carbon was used for transport simulation in order to better understand the effects of local meteorological factors on air pollution. In the simulation, the emission strength of the black carbon surrogate was assumed temporally constant and spatially uniform over the Kathmandu Valley floor. The Weather Research and Forecasting simulation results were well correlated with observed meteorological measurements and demonstrated diurnal periodicity such as intrusion of westerly‐northwesterly wind into the Kathmandu Valley and modification of the boundary layer activity due to afternoon wind. The transport simulation suggested long‐lasting weak wind, thermally stable stratification, and associated small turbulence during the night and morning caused potentially severe air pollution. We propose a method using wind velocity and turbulent kinetic energy in the surface layer to characterize pollution level in the Kathmandu Valley.
Multiobjective Calibration of a Global Biogeochemical Ocean Model Against Nutrients, Oxygen, and Oxygen Minimum Zones
Authors: Sauerland Volkmar , Kriest Iris , Oschlies Andreas , Srivastav Anand
Published: April 2019

Global biogeochemical ocean models rely on many parameters, which govern the interaction between individual components, and their response to the physical environment. They are often assessed/calibrated against quasi‐synoptic data sets of dissolved inorganic tracers. However, a good fit to one observation might not necessarily imply a good match to another. We investigate whether two different metrics—the root‐mean‐square error to nutrients and oxygen and a metric measuring the overlap between simulated and observed oxygen minimum zones (OMZs)—help to constrain a global biogeochemical model in different aspects of performance. Three global model optimizations are carried out. Two single‐objective optimizations target the root‐mean‐square metric and a sum of both metrics, respectively. We then present and explore multiobjective optimization, which results in a set of compromise solutions. Our results suggest that optimal parameters for denitrification and nitrogen fixation differ when applying different metrics. Optimization against observed OMZs leads to parameters that enhance fixed nitrogen cycling; this causes too low nitrate concentrations and a too high global pelagic denitrification rate. Optimization against nutrient and oxygen concentrations leads to different parameters and a lower global fixed nitrogen turnover; this results in a worse fit to OMZs. Multiobjective optimization resolves this antagonistic effect and provides an ensemble of parameter sets, which help to address different research questions. We finally discuss how systematic model calibration can help to improve models used for projecting climate change and its effect on fisheries and climate gas emissions.
Generalized Additive Modeling Combined With Multiple Collinear for ICME Velocity Forecasting
Authors: Lu J. Y. , Jin C. Q. , Wang M. , Ji H. S. , Iluore K. , Guan H. Y. , Li J. F. , Li J. Y.
Published: April 2019

One of the main issues of space weather is the timely prediction of disturbed solar wind parameters at L1, especially caused by Coronal Mass Ejection (CME). Using the data from 170 front halo, flare‐associated CMEs, and in‐site solar wind data, an analysis of the Interplanetary Coronal Mass Ejection (ICME) peak velocity at L1 related to associated coronal parameters is performed. The statistical methods including the Generalized Additive Modeling (GAM) and Multiple Collinear (MC) have been applied to explain the underlying physical reasons and set up a new prediction model. Our results indicate that (1) X‐flare integral flux, CME linear velocity, and Acceleration observed on corona play key roles in ICME velocity, while other coronal parameters only present a weak correlation, such as the CME Mass and Angular Width, (2) the relationship between ICME velocity and CME Acceleration, as well as CME linear velocity, is nonstationary, and the ICME velocity will increase with the increasing CME Acceleration or linear velocity until saturation, and (3) MC is an effective method to improve the forecast model performance. Compared with 0.52 for only GAM, the correlation coefficient using GAM + MC reaches to 0.71. To further testify the prediction ability, the GAM + MC model results are compared with the Back‐Propagation network model and a typically empirical statistic relation proposed by Manoharan (2006, https://doi.org/10.1007/s11207-006-0100-y; their correlation coefficients and root mean squared errors are both roughly 0.6 and 100 km/s, respectively). It is found that the MC + GAM can upgrade the forecast at least over 10%.
An Approach to Tracking Meteorological Drought Migration
Authors: Zhou Han , Liu Yuanbo , Liu Yongwei
Published: April 2019

Spatiotemporal behaviors of meteorological droughts are basic for understanding the development and driving forces of droughts. Currently, there are a limited number of approaches mainly used to analyze the spatiotemporal evolution of large‐scale soil moisture/hydrological drought events at global or continental scales. These behavior description approaches on the spatiotemporal dynamics of drought are not perfect and should be improved further. To this end, a new approach was proposed to investigate the migration of meteorological droughts based on topological spatial relations. It was used to identify drought clusters, migration trajectories, and migration directions of meteorological droughts. In the Poyang Lake basin (24°29′ to 30°04′N, 113°34′ to 118°28′E), China, monthly precipitation data were available from 1960 to 2007. The one‐month standardized precipitation index was used to characterize meteorological droughts. The proposed approach identified a total of 77 drought events and 454 drought clusters during the study period. Their drought centroids were tracked and analyzed. The migration distances of drought events exhibited a significant linear relationship with the drought duration (R2 > 0.8, slope of 165 km per month). More than 70% of drought events had a migrating displacement greater than 1° (approximately 100 km). These results indicated that the meteorological drought events traveled actively and occurred on a widespread basis in the basin. Moreover, two main patterns of drought cluster migration (northward and southward) were identified. The approach and findings can provide some important implications to investigate the migration of meteorological droughts in other regions.
Fast Bayesian Regression Kriging Method for Real‐Time Merging of Radar, Rain Gauge, and Crowdsourced Rainfall Data
Authors: Yang Pan , Ng Tze Ling
Published: April 2019

Crowdsourcing of rainfall measurements incorporating common citizens as a rich source of data is an emerging concept with huge potential to provide valuable high spatiotemporal resolution rainfall observations. Here we investigate the merging of crowdsourced rainfall data with traditional radar and rain gauge data to maximize their utility. For this purpose, we develop a tailored fast Bayesian regression kriging (FBRK) method combining regression kriging and Laplace approximation in a Bayesian framework. A strength of the FBRK method lies in its ability to capture the differences between rain gauge and crowdsourced measurement errors. Another lies in its fast yet reasonably accurate approximation of the Bayesian posterior, making it suitable to use in real time. We conduct synthetic computer simulations to evaluate the FBRK method alongside three other merging methods. In the simulations, we compare the accuracies of their resulting rainfall estimates, as well as the skill of those estimates as input to a storm water flow forecasting model. In both aspects, we observe the FBRK method to lead to more accurate results and truer representations of the associated uncertainties. However, we also observe the performance of the FBRK method to be sensitive to the choice of the Bayesian prior under certain conditions. Finally, from the synthetic simulations, we find merging crowdsourced data with traditional data to lead to more accurate estimation of the ground truth rainfall field and, subsequently, more accurate flow forecasts (though only when an adequate merging method, e.g., the FBRK method, is used), and the results to be fairly robust to bias in the input crowdsourced data.
Mapped Hydroclimatology of Evapotranspiration and Drainage Runoff Using SMAP Brightness Temperature Observations and Precipitation Information
Authors: Akbar Ruzbeh , Short Gianotti Daniel J. , Salvucci Guido D. , Entekhabi Dara
Published: April 2019

The partitioning of incident precipitation into evapotranspiration, runoff, drainage, storage change, and hydrologic fluxes depends on the soil moisture state. With the availability of global remotely sensed soil moisture fields, the functional dependence of each flux on soil moisture may be identifiable. In this study we develop an observation‐driven approach to map key hydroclimatology fields using remotely sensed soil moisture and gauge‐based precipitation data only. National Aeronautics and Space Administration's Soil Moisture Active Passive (SMAP) low‐frequency microwave brightness temperature observations and precipitation fields, from the National Centers for Environmental Prediction, are the sole inputs into an adjoint‐state variational estimation framework. Furthermore, the proposed methodology does not rely on micrometeorological information, or land surface models. The approach is flexible by design so that almost any partitioning pattern can result from estimation and corresponding evapotranspiration and drainage fields can be quantified. Three‐year averaged summer season evapotranspiration estimates are compared with available vapor flux at in situ AmeriFlux eddy‐covariance sites. Basin‐averaged drainage over major U.S. hydrologic units is also compared with U.S. Geological Survey streamgages measurements. The remote sensing‐based estimated hydroclimate fields explain about 70% of the variance in the in situ measurements. This exploratory study adds to the body of evidence emerging in literature that a significant amount of hydrologic information is encoded in the dynamic fields of remotely sensed soil moisture. Observation‐driven hydroclimate data fields that are independent of land surface models can provide valuable insights into the state of the water cycle and guide future development of land surface models.
Late Eocene Southern Ocean Cooling and Invigoration of Circulation Preconditioned Antarctica for Full‐Scale Glaciation
Authors: Houben Alexander J. P. , Bijl Peter K. , Sluijs Appy , Schouten Stefan , Brinkhuis Henk
Published: April 2019

During the Eocene‐Oligocene Transition (EOT; 34–33.5 Ma), Antarctic ice sheets relatively rapidly expanded, leading to the first continent‐scale glaciation of the Cenozoic. Declining atmospheric CO2 concentrations and associated feedbacks have been invoked as underlying mechanisms, but the role of the quasi‐coeval opening of Southern Ocean gateways (Tasman Gateway and Drake Passage) and resulting changes in ocean circulation is as yet poorly understood. Definitive field evidence from EOT sedimentary successions from the Antarctic margin and the Southern Ocean is lacking, also because the few available sequences are often incomplete and poorly dated, hampering detailed paleoceanographic and paleoclimatic analysis. Here we use organic dinoflagellate cysts (dinocysts) to date and correlate critical Southern Ocean EOT successions. We demonstrate that widespread winnowed glauconite‐rich lithological units were deposited ubiquitously and simultaneously in relatively shallow‐marine environments at various Southern Ocean localities, starting in the late Eocene (~35.7 Ma). Based on organic biomarker paleothermometry and quantitative dinocyst distribution patterns, we analyze Southern Ocean paleoceanographic change across the EOT. We obtain strong indications for invigorated surface and bottom water circulation at sites affected by polar westward‐flowing wind‐driven currents, including a westward‐flowing Antarctic Countercurrent, starting at about 35.7 Ma. The mechanism for this oceanographic invigoration remains poorly understood. The circum‐Antarctic expression of the phenomenon suggests that, rather than triggered by tectonic deepening of the Tasman Gateway, progressive pre‐EOT atmospheric cooling played an important role. At localities affected by the Antarctic Countercurrent, sea surface productivity increased and simultaneously circum‐Antarctic surface waters cooled. We surmise that combined, these processes contributed to preconditioning the Antarctic continent for glaciation.
Informing Future Risks of Record‐Level Rainfall in the United States
Authors: Sanderson Benjamin M. , Wobus Cameron , Mills Dave , Zarakas Claire , Crimmins Allison , Sarofim Marcus C. , Weaver Chris
Published: April 2019

The changing risk of extreme precipitation is difficult to project. Events are rare by definition, and return periods of heavy precipitation events are often calculated assuming a stationary climate. Furthermore, ensembles of climate model projections are not large enough to fully categorize the tails of the distribution. To address this, we cluster the contiguous United States into self‐similar hydroclimates to estimate changes in the expected frequency of extremely rare events under scenarios of global mean temperature change. We find that, although there is some regional variation, record events are projected in general to become more intense, with 500‐year events intensifying by 10–50% under 2 °C of warming and by 40–100% under 4 °C of warming. This analysis could provide information to inform regional prioritization of resources to improve the resilience of U.S. infrastructure.
Electron Inertial Effects on Linearly Polarized Electromagnetic Ion Cyclotron Waves at Earth's Magnetosphere
Authors: Kim Eun‐Hwa , Johnson Jay R. , Lee Dong‐Hun
Published: April 2019

We discuss a role of the electron inertial effect on linearly polarized electromagnetic ion cyclotron (EMIC) waves at Earth. The linearly polarized EMIC waves have been previously suggested to be generated via mode conversion from the fast compressional wave at the ion‐ion hybrid (IIH) resonance. When the electron inertial effects are neglected, the wave normal angle of the mode‐converted IIH waves is 90° because the wave vector perpendicular to the magnetic field becomes infinite at the IIH resonance. When the electron inertial effect is considered, the mode‐converted IIH waves can propagate across the magnetic field lines, and the wavelength perpendicular to the magnetic field approaches the electron inertial length scale near the Buchsbaum resonance. These waves are referred to as electron inertial waves. Due to the electron inertial effect, the perpendicular wave number to the ambient magnetic field near the IIH resonance remains finite, and the wave normal angle is less than 90°. The wave normal angle where the maximum absorption occurs in a dipole magnetic field is 30–80°, which is consistent with the observed values near the magnetic equator. Therefore, the numerical results suggest that the linearly polarized EMIC wave generated via mode conversion near the IIH resonance can be detected in between the Buchsbaum and the IIH resonance frequencies, and these waves can have normal angle less than 90°.
Paleoproductivity in the SW Pacific Ocean During the Early Holocene Climatic Optimum
Authors: Bostock H. C. , Prebble J. G. , Cortese G. , Hayward B. , Calvo E. , Quirós‐Collazos L. , Kienast M. , Kim K.
Published: April 2019

The oceans are warming, but it is unclear how marine productivity will be affected under future climate change. In this study we examined a wide range of paleoproductivity proxies along a latitudinal transect (36–58°S) in the SW Pacific during the early Holocene climatic optimum, to explore regional patterns of productivity in a slightly warmer‐than‐present world. During the early Holocene there is a small increase in productivity in the subtropical waters, no change at the subtropical frontal zone, and conflicting evidence in records immediately south of the subtropical front, where an increase is inferred from one core site, but not at the other. Evidence for an increase in productivity in Antarctic Surface Waters, south of the polar front, is also equivocal. We infer a small increase in productivity in subtropical waters, and the ocean just south of the subtropical front was associated with changes in the ocean circulation of the SW Pacific, driven by changes in the Southern Hemisphere Westerly Winds split‐jet structure in this region. The relatively modest warming during the early Holocene climatic optimum in the SW Pacific indicates that this time period may provide an analog for future productivity for the midcentury (2055) under Intergovernmental Panel on Climate Change Representative Concentration Pathway 8.5 or for the end of the century (2100) under Representative Concentration Pathway 4.5. However, higher‐resolution, downscaled models, with realistic Southern Hemisphere Westerly Winds, will be necessary to forecast future productivity for this oceanographically complex region.
Actigraphy Technology: Informing Assessment and Intervention for Sleep Disturbances in Young Children
Authors: Eaton Cyd K. , Henning Ellen , Lam Janet , Paasch Valerie
Published: April 2019

Objective: To demonstrate the clinical feasibility and utility of referring young children (ages 2 to 5 years old) presenting to an interdisciplinary pediatric sleep clinic for objective sleep assessment using actigraphy. Method: A retrospective chart review was conducted to identify young children referred for actigraphy from the sleep clinic. Each referred child wore an actigraph for approximately 1 week; caregivers completed daily sleep diaries to report on children’s estimated bedtime and wake time. Treatment recommendations provided after actigraphy and treatment responses were abstracted via chart review. Results: Of the 88 young children presenting to the sleep clinic during the study period, 11 were referred for and completed actigraphy monitoring. All referred children, including those with neurodevelopmental disabilities, tolerated wearing the actigraph on their wrist. All children were shown to have sleep disturbances via actigraphy results. The most common disturbances were the frequency and duration of night wakings, which reduced total sleep time compared to published norms from a healthy, same-aged sample. All children received behavioral treatment recommendations and the majority were prescribed medication for sleep concerns. The majority of children were considered treatment responders (73%). Conclusions: Actigraphy may be a feasible and informative assessment tool for clinicians to integrate into regular practice with young children to obtain objective sleep data that may not have otherwise been available. Clinical recommendations and practical concerns (e.g., billing) of using actigraphy in an interdisciplinary pediatric setting are discussed.

Implications for Impact Statement

Pediatric psychologists may implement objective sleep assessments using actigraphy with young children during clinical practice and use the data generated to communicate details about problematic sleep patterns to caregivers, which may inform intervention recommendations.
Increased expression of NAF1 contributes to malignant phenotypes of glioma cells through promoting protein synthesis and associates with poor patient survival
Authors: Wei Jing , Yang Qi , Shi Jing , Shi Bingyin , Ji Meiju , Hou Peng
Published: April 2019

The H/ACA ribonucleoprotein (RNP) complex noncore subunit NAF1 is an indispensable factor during H/ACA RNP maturation, and one of the widely known functions of H/ACA RNP is modulating ribosome biosynthesis. However, the specific biological role and exact mechanism of NAF1 in human cancers including glioma remain largely unclear. In this study, we found that NAF1 was highly expressed in gliomas relative to normal brain tissues, and demonstrated that increased expression of NAF1 was strongly correlated with poor patient survival. Further studies revealed that NAF1 was transcriptionally regulated by c-Myc, NRF2, and telomerase reverse transcriptase (TERT), which are the key molecules associated with malignant progression of gliomas. Moreover, we demonstrated that NAF1 was a functional oncogene in glioma cells through promoting cell growth in vitro and in vivo, survival, migration, and invasion. Mechanistically, NAF1 acted as a rate-limiting controller of cell growth and invasiveness through enhancing 40S subunit assembly and protein synthesis including c-Myc, NRF2, TERT, POLR1A, and POLR2A. These molecules in turn enhanced the transcription and translation of NAF1, thereby forming positive feedback loops between them to promote malignant phenotypes of glioma cells. In addition, our data also showed that NAF1 depletion could trigger ribosome stress, not only impairing ribosomal biosynthesis but also reactivating p53 signaling via blocking MDM2. Taken together, we demonstrated that NAF1 promotes the tumorigenesis and progression of glioma through modulating ribosome assembly and protein synthesis, and predicted that NAF1 may be a potential therapeutic target and valuable prognostic biomarker in gliomas.
Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13
Authors: Liu Zhu , Dong Xu , Yi Hua-Wei , Yang Ju , Gong Zhou , Wang Yi , Liu Kan , Zhang Wei-Ping , Tang Chun
Published: April 2019

The interaction between K48-linked ubiquitin (Ub) chain and Rpn13 is important for proteasomal degradation of ubiquitinated substrate proteins. Only the complex structure between the N-terminal domain of Rpn13 (Rpn13NTD) and Ub monomer has been characterized, while it remains unclear how Rpn13 specifically recognizes K48-linked Ub chain. Using single-molecule FRET, here we show that K48-linked diubiquitin (K48-diUb) fluctuates among distinct conformational states, and a preexisting compact state is selectively enriched by Rpn13NTD. The same binding mode is observed for full-length Rpn13 and longer K48-linked Ub chain. Using solution NMR spectroscopy, we have determined the complex structure between Rpn13NTD and K48-diUb. In this structure, Rpn13NTD simultaneously interacts with proximal and distal Ub subunits of K48-diUb that remain associated in the complex, thus corroborating smFRET findings. The proximal Ub interacts with Rpn13NTD similarly as the Ub monomer in the known Rpn13NTD:Ub structure, while the distal Ub binds to a largely electrostatic surface of Rpn13NTD. Thus, a charge-reversal mutation in Rpn13NTD weakens the interaction between Rpn13 and K48-linked Ub chain, causing accumulation of ubiquitinated proteins. Moreover, physical blockage of the access of the distal Ub to Rpn13NTD with a proximity-attached Ub monomer can disrupt the interaction between Rpn13 and K48-diUb. Taken together, the bivalent interaction of K48-linked Ub chain with Rpn13 provides the structural basis for Rpn13 linkage selectivity, which opens a new window for modulating proteasomal function.
Lattice strain-enhanced exsolution of nanoparticles in thin films
Authors: Han Hyeon , Park Jucheol , Nam Sang Yeol , Kim Kun Joong , Choi Gyeong Man , Parkin Stuart S. P. , Jang Hyun Myung , Irvine John T. S.
Published: April 2019

Nanoparticles formed on oxide surfaces are of key importance in many fields such as catalysis and renewable energy. Here, we control B-site exsolution via lattice strain to achieve a high degree of exsolution of nanoparticles in perovskite thin films: more than 1100 particles μm−2 with a particle size as small as ~5 nm can be achieved via strain control. Compressive-strained films show a larger number of exsolved particles as compared with tensile-strained films. Moreover, the strain-enhanced in situ growth of nanoparticles offers high thermal stability and coking resistance, a low reduction temperature (550 °C), rapid release of particles, and wide tunability. The mechanism of lattice strain-enhanced exsolution is illuminated by thermodynamic and kinetic aspects, emphasizing the unique role of the misfit-strain relaxation energy. This study provides critical insights not only into the design of new forms of nanostructures but also to applications ranging from catalysis, energy conversion/storage, nano-composites, nano-magnetism, to nano-optics.
USP8 maintains embryonic stem cell stemness via deubiquitination of EPG5
Authors: Gu Haifeng , Shi Xingxing , Liu Chao , Wang Chaoqun , Sui Ning , Zhao Yu , Gong Jiaqi , Wang Fuping , Zhang Hong , Li Wei , Zhao Tongbiao
Published: April 2019

Embryonic stem cells (ESCs) can propagate in an undifferentiated state indefinitely in culture and retain the potential to differentiate into any somatic lineage as well as germ cells. The catabolic process autophagy has been reported to be involved in ESC identity regulation, but the underlying mechanism is still largely unknown. Here we show that EPG5, a eukaryotic-specific autophagy regulator which mediates autophagosome/lysosome fusion, is highly expressed in ESCs and contributes to ESC identity maintenance. We identify that the deubiquitinating enzyme USP8 binds to the Coiled-coil domain of EPG5. Mechanistically, USP8 directly removes non-classical K63-linked ubiquitin chains from EPG5 at Lysine 252, leading to enhanced interaction between EPG5 and LC3. We propose that deubiquitination of EPG5 by USP8 guards the autophagic flux in ESCs to maintain their stemness. This work uncovers a novel crosstalk pathway between ubiquitination and autophagy through USP8-EPG5 interaction to regulate the stemness of ESCs.
Multiple low-temperature skyrmionic states in a bulk chiral magnet
Authors: Bannenberg Lars J. , Wilhelm Heribert , Cubitt Robert , Labh Ankit , Schmidt Marcus P. , Lelièvre-Berna Eddy , Pappas Catherine , Mostovoy Maxim , Leonov Andrey O.
Published: April 2019

Magnetic skyrmions are topologically protected nanoscale spin textures with particle-like properties. In bulk cubic helimagnets, they appear under applied magnetic fields and condense spontaneously into a lattice in a narrow region of the phase diagram just below the magnetic ordering temperature, the so-called A-phase. Theory, however, predicts skyrmions to be locally stable in a wide range of magnetic fields and temperatures. Our neutron diffraction measurements reveal the formation of skyrmion states in large areas of the magnetic phase diagram, from the lowest temperatures up to the A-phase. We show that nascent and disappearing spiral states near critical lines catalyze topological charge changing processes, leading to the formation and destruction of skyrmionic states at low temperatures, which are thermodynamically stable or metastable depending on the orientation and strength of the magnetic field. Skyrmions are surprisingly resilient to high magnetic fields: the memory of skyrmion lattice states persists in the field polarized state, even when the skyrmion lattice signal has disappeared. These findings highlight the paramount role of magnetic anisotropies in stabilizing skyrmionic states and open up new routes for manipulating these quasi-particles towards energy-efficient spintronics applications.
The survey and reference assisted assembly of the Octopus vulgaris genome
Authors: Zarrella Ilaria , Herten Koen , Maes Gregory E. , Tai Shuaishuai , Yang Ming , Seuntjens Eve , Ritschard Elena A. , Zach Michael , Styfhals Ruth , Sanges Remo , Simakov Oleg , Ponte Giovanna , Fiorito Graziano
Published: April 2019

The common octopus, Octopus vulgaris, is an active marine predator known for the richness and plasticity of its behavioral repertoire, and remarkable learning and memory capabilities. Octopus and other coleoid cephalopods, cuttlefish and squid, possess the largest nervous system among invertebrates, both for cell counts and body to brain size. O. vulgaris has been at the center of a long-tradition of research into diverse aspects of its biology. To leverage research in this iconic species, we generated 270 Gb of genomic sequencing data, complementing those available for the only other sequenced congeneric octopus, Octopus bimaculoides. We show that both genomes are similar in size, but display different levels of heterozygosity and repeats. Our data give a first quantitative glimpse into the rate of coding and non-coding regions and support the view that hundreds of novel genes may have arisen independently despite the close phylogenetic distance. We furthermore describe a reference-guided assembly and an open genomic resource (CephRes-gdatabase), opening new avenues in the study of genomic novelties in cephalopods and their biology.
Cyclone avoidance behaviour by foraging seabirds
Authors: Weimerskirch Henri , Prudor Aurélien
Published: April 2019

In the context of climate change, how extreme climatic events, such as cyclones, will affect the foraging abilities of marine vertebrates is still poorly known. During the course of a study on the foraging behaviour of two tropical seabirds, red-footed boobies and great frigatebirds, several cyclones have affected their breeding grounds and foraging zones, allowing us to study their response to extreme wind conditions. We examined whether adults and young naïve birds were able to predict the arrival of a cyclone and behave accordingly to reduce mortality risks and optimise foraging. We show that when a cyclone approached, juveniles and adults of the two species differed in their decisions to leave the colony for the sea. When the winds reached gale force, the juveniles of both species and adult frigatebirds remained at the colony, whereas adult boobies continued their foraging routine. The mortality of the individuals remaining on land remained limited. When encountering at-sea gale conditions, adult birds were able to avoid the centre of the low pressure systems and moved westward to bypass the route of the cyclones and circumvent the moving cyclone. Frigatebirds climb to high altitudes when close to the eye of the cyclone to bypass it at high speeds. These movements likely reduce the mortality risk at sea but can temporarily cause birds to move outside their normal range at sea or over land masses. We discuss the potential consequences of an increase in cyclonic conditions on seabird populations.
A decade of sustained selection pressure on two surface sites of the VP1 protein of Enterovirus A71 suggests that immune evasion may be an indirect driver for virulence
Authors: Roberts Ryan , Yee Pinn Tsin Isabel , Mujawar Shama , Lahiri Chandrajit , Poh Chit Laa , Gatherer Derek
Published: April 2019

Enterovirus A71 (EV-A71) is an emerging pathogen in the Enterovirus A species group. EV-A71 causes hand, foot and mouth disease (HFMD), with virulent variants exhibiting polio-like acute flaccid paralysis and other central nervous system manifestations. We analysed all enterovirus A71 complete genomes with collection dates from 2008 to mid-2018. All sub-genotypes exhibit a strong molecular clock with omega (dN/dS) suggesting strong purifying selection. In sub-genotypes B5 and C4, positive selection can be detected at two surface sites on the VP1 protein, also detected in positive selection studies performed prior to 2008. Toggling of a limited repertoire of amino acids at these positively selected residues over the last decade suggests that EV-A71 may be undergoing a sustained frequency-dependent selection process for immune evasion, raising issues for vaccine development. These same sites have also been previously implicated in virus-host binding and strain-associated severity of HFMD, suggesting that immune evasion may be an indirect driver for virulence (154 words).
Effect of cell culture density on dental pulp-derived mesenchymal stem cells with reference to osteogenic differentiation
Authors: Noda Sonoko , Kawashima Nobuyuki , Yamamoto Mioko , Hashimoto Kentaro , Nara Keisuke , Sekiya Ichiro , Okiji Takashi
Published: April 2019

Dental pulp stem cells (DPSCs) are a good source for tissue regeneration, however, the number of DPSCs in the pulp tissue is limited. Cell propagation is essential for tissue engineering using DPSCs and the cell culture conditions may affect the properties of DPSCs. The purpose of this study was to analyze the effect of cell culture condition, especially dense culture condition, on the property and differentiation pathway of DPSCs. We cultured DPSCs under sparse (sDPSCs; 5 × 103 cells/cm2) or dense (dDPSCs; 1 × 105 cells/cm2) conditions for 4 days and compared their properties. The populations of CD73+ and CD105+ cells were significantly decreased in dDPSCs. Both groups showed multi-differentiation potential, but mineralized nodule formation was enhanced in dDPSCs. The phosphorylation of focal adhesion kinase (FAK) and phosphoinositide 3-kinase (PI3K) proteins was promoted in dDPSCs, and alkaline phosphatase (ALP) mRNA expression in dDPSCs was abolished in the presence of pan-PI3K and FAK inhibitors. dDPSCs implanted into mouse bone cavities induced more mineralized tissue formation than sDPSCs and control. These findings indicate that dense culture conditions modified the properties of DPSCs and gave rise to osteogenic-lineage commitment via integrin signaling and suggest that dense culture conditions favor the propagation of DPSCs to be used for mineralized tissue regeneration.
Modeling the Effects of Morphine-Altered Virus Specific Antibody Responses on HIV/SIV Dynamics
Authors: Mutua Jones M. , Perelson Alan S. , Kumar Anil , Vaidya Naveen K.
Published: April 2019

Drugs of abuse, such as opiates, have been widely associated with enhancing HIV replication, accelerating disease progression and diminishing host-immune responses, thereby making it harder to effectively manage HIV infection. It is thus important to study the effects of drugs of abuse on HIV-infection and immune responses. Here, we develop mathematical models that incorporate the effects of morphine-altered antibody responses on HIV/SIV dynamics. Based on fitting the model to experimental data from simian immunodeficiency virus (SIV) infections in control and morphine-addicted macaques, we found that two of the most significant effects of virus specific antibodies are neutralizing viral particles and enhancing viral clearance. Using our model, we quantified how morphine alters virus-specific antibody responses, and how this alteration affects the key components of virus dynamics such as infection rate, virus clearance, viral load, CD4+T cell count, and CD4+T cell loss in SIV-infected macaques under conditioning with morphine. We found that in a subpopulation of SIV-infected morphine addicted macaques, the presence of drugs of abuse may cause significantly diminished antibody responses, resulting in more severe infection with increased SIV infectivity, a decreased viral clearance rate, increased viral load, and higher CD4+T cell loss.
Theory for spin torque in Weyl semimetal with magnetic texture
Authors: Kurebayashi Daichi , Nomura Kentaro
Published: April 2019

The spin-transfer torque is a fundamental physical quantity to operate the spintronics devices such as racetrack memory. We theoretically study the spin-transfer torque and analyze the dynamics of the magnetic domain walls in magnetic Weyl semimetals. Owing to the strong spin-orbit coupling in Weyl semimetals, the spin-transfer torque can be significantly enhanced, because of which they can provide a more efficient means of controlling magnetic textures. We derive the analytical expression of the spin-transfer torque and find that the velocity of the domain wall is one order of magnitude greater than that of conventional ferromagnetic metals. Furthermore, due to the suppression of longitudinal conductivity in the thin domain-wall configuration, the dissipation due to Joule heating for the spin-transfer torque becomes much smaller than that in bulk metallic ferromagnets. Consequently, the fast-control of the domain wall can be achieved with smaller dissipation from Joule heating in the Weyl semimetals as required for application to low-energy-consumption spintronics devices.
Reproductive interference in live-bearing fish: the male guppy is a potential biological agent for eradicating invasive mosquitofish
Authors: Tsurui-Sato K. , Fujimoto S. , Deki O. , Suzuki T. , Tatsuta H. , Tsuji K.
Published: April 2019

The eradication of invasive exotic species is desirable but often infeasible. Here, we show that male guppies are a potential biological agent for eradicating invasive mosquitofish through the mechanism of reproductive interference, which is defined as any sexual behavior erratically directed at a different species that damages female and/or male fitness. Together with decades of data on species distribution, our field surveys suggest that mosquitofish initially became established on Okinawa Island before being replaced by the more recently introduced guppies. More importantly, our laboratory experiments suggest that reproductive interference was one of the mechanisms underlying this species exclusion, and that in this case, the negative effects were asymmetric, i.e., they only impacted mosquitofish. Reproductive interference may offer a safer and more convenient method of biological control than the traditional sterile male release method because radiation is not necessary.
Means and Long-Term Trends of Global Coastal Zone Precipitation
Authors: Curtis Scott
Published: April 2019

Precipitation in the coastal zone is important to the socio-economic and ecological well-being of the world. Meteorologically, precipitation is generated by unique mechanisms at the land-sea interface, which is why coastal zone precipitation is not well resolved by global climate models. Yet, to date, much more effort has been placed in analyzing global precipitation over the oceans and land. In this study, global coastal zone precipitation is quantified by selecting Global Precipitation Climatology Centre V2018 0.5° grid cells in 50 km zones from the shoreline into the interior. The transition from maritime to continental precipitation regimes is revealed in the long-term (1931–2010) average, as there is a pronounced coast-to-interior decline in rainfall from approximately 911.5 mm yr−1 within 50 km of the coast to 727.2 mm yr−1 from 100 to 150 km away from the coast. Globally, coastal zone precipitation peaks in boreal summer, extending into fall for precipitation at the coastline. Dividing the long-term record into early and late 40-year periods reveals an increasing trend in precipitation in the coastal zone, with the interior increasing faster than at the coastline. Averaging over 30-year climate normals from 1931–60 to 1981–2010 further confirms this result. A seasonal analysis reveals that the upward trends, and discrepancy between the coast and inland are maximized in the austral summer season. Interestingly, from May to September there is a declining trend in rainfall at the coastline, whereas the interior only shows minimal declines in August and September. Potential forcing mechanisms that could favor a wetter interior coastal zone include changes in the sea breeze circulation, urban heat island effect, or precipitation content associated with synoptic systems or monsoonal circulations.
A New Eye Dual-readout Method for MiRNA Detection based on Dissolution of Gold nanoparticles via LSPR by CdTe QDs Photoinduction
Authors: Borghei Yasaman-Sadat , Hosseini Morteza
Published: April 2019

Breast cancer (BC) is the most frequent cancer that affects one in eight women worldwide. Recent advances in early cancer diagnosis anticipates more efficient treatment and prolong patient survival. MicroRNAs expression profiling plays a key role in diagnosis of cancer such as BC in early stages. For the first time we describe direct injection of hot electrons from plasmonic gold nanoparticles (AuNPs) to adsorbed water molecules with photoinduction of CdTe quantum dots (QDs) with emission wavelength at ~560 nm. As a result of hot electrons exiting from AuNPs with red color, gold cations (holes) are gradually discharged (AuNPs dissolution) leading to a colorless solution. Our group applied this phenomenon to propose a spectral method for miRNA recognition based on different responsive disaggregation and aggregation of CdTe QDs interacted with single strand DNA probes and DNA/RNA heteroduplex respectively resulting in a detection limit of 4.4 pM. This method has been applied also for the determination of miR-155 in the human breast carcinoma MCF-7 cells and normal human embryonic kidney cell line (HEK 293).