bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Deep Neural Networks as Cost‐Effective Surrogate Models for Super‐Parameterized E3SM Radiative Transfer
Authors: Pal Anikesh , Mahajan Salil , Norman Matthew R. 
Published: May 2019

AbstractDeep neural networks (DNNs) are implemented in Super‐Parameterized Energy Exascale Earth System Model (SP‐E3SM) to imitate the shortwave and longwave radiative transfer calculations. These DNNs were able to emulate the radiation parameters with an accuracy of 90–95% at a cost of 8–10 times cheaper than the original radiation parameterization. A comparison of time‐averaged radiative fluxes and the prognostic variables manifested qualitative and quantitative similarity between the DNN emulation and the original parameterization. It has also been found that the differences between the DNN emulation and the original parameterization are comparable to the internal variability of the original parameterization. Although the DNNs developed in this investigation emulate the radiation parameters for a specific set of initial conditions, the results justify the need of further research to generalize the use of DNNs for the emulations of full model radiation and other parameterization for seasonal predictions and climate simulations.
Plasma Transport in Saturn's Low‐Latitude Ionosphere: Cassini Data
Authors: Cravens T. E. , Morooka M. , Renzaglia A. , Moore L. , Waite J. H. , Perryman R. , Perry M. , Wahlund J.‐E. , Persoon A. , Hadid L. 
Published: May 2019

AbstractIn 2017 the Cassini Orbiter made the first in situ measurements of the upper atmosphere and ionosphere of Saturn. The Ion and Neutral Mass Spectrometer in its ion mode measured densities of light ion species (H+, H2+, H3+, and He+), and the Radio and Plasma Wave Science instrument measured electron densities. During proximal orbit 287 (denoted P287), Cassini reached down to an altitude of about 3,000 km above the 1 bar atmospheric pressure level. The topside ionosphere plasma densities measured for P287 were consistent with ionospheric measurements during other proximal orbits. Spacecraft potentials were measured by the Radio and Plasma Wave Science Langmuir probe and are typically about negative 0.3 V. Also, for this one orbit, Ion and Neutral Mass Spectrometer was operated in an instrument mode allowing the energies of incident H+ ions to be measured. H+ is the major ion species in the topside ionosphere. Ion flow speeds relative to Saturn's atmosphere were determined. In the southern hemisphere, including near closest approach, the measured ion speeds were close to zero relative to Saturn's corotating atmosphere, but for northern latitudes, southward ion flow of about 3 km/s was observed. One possible interpretation is that the ring shadowing of the southern hemisphere sets up an interhemispheric plasma pressure gradient driving this flow.
Rates of Wintertime Atmospheric SO2 Oxidation based on Aircraft Observations during Clear‐Sky Conditions over the Eastern United States
Authors: Green Jaime R. , Fiddler Marc N. , Holloway John S. , Fibiger Dorothy L. , McDuffie Erin E. , Campuzano‐Jost Pedro , Schroder Jason C. , Jimenez Jose L. , Weinheimer Andrew J. , Aquino Janine , Montzka D. D. , Hall Samuel R. , Ullmann Kirk , Shah Viral , Jaeglé Lyatt , Thornton Joel A. , Bililign Solomon , Brown Steven S. 
Published: May 2019

AbstractSulfur dioxide (SO2) is emitted in large quantities from coal‐burning power plants and leads to various harmful health and environmental effects. In this study, we use plume intercepts from the Wintertime INvestigation of Transport, Emission and Reactivity (WINTER) campaign to estimate the oxidation rates of SO2 under wintertime conditions and the factors that determine SO2 removal. Observations suggest that OH governs the rate SO2 oxidation in the eastern United States during winter. The range of mean oxidation rates during the day from power plants were 0.22–0.71%/hr, producing SO2 lifetimes of 13–43 days, if SO2 consumption is assumed to occur during 10.5 hr of daylight in cloudless conditions. Though most nighttime rate measurements were zero within uncertainty, there is some evidence of nighttime removal, which suggests alternate oxidation mechanisms. The fastest nighttime observed SO2 oxidation rate was 0.25±0.07%/hr, producing a combined day/night SO2 lifetime of 8.5–21 days. The upper limit of the oxidation rate (the mean+1σ of the fastest day and night observations) is 16.5%/day, corresponding to a lifetime of 6.1 days. The analysis also quantifies the primary emission of sulfate from power plants. The median mole percentage of SO4‐2 from observed plumes was 1.7% and the mean percentage sulfate was 2.8% for intercepts within 1 hr of transit to power plants. The largest value observed from close intercepts was over 7% sulfate, and the largest extrapolated value was 18%, based on intercepts further from their source and fastest observed oxidation rate.
The Demographics of Water: A Review of Water Ages in the Critical Zone
Authors: Sprenger Matthias , Stumpp Christine , Weiler Markus , Aeschbach Werner , Allen Scott T. , Benettin Paolo , Dubbert Maren , Hartmann Andreas , Hrachowitz Markus , Kirchner James W. , McDonnell Jeffrey J. , Orlowski Natalie , Penna Daniele , Pfahl Stephan , Rinderer Michael , Rodriguez Nicolas , Schmidt Maximilian , Werner Christiane 
Published: May 2019

AbstractThe time that water takes to travel through the terrestrial hydrological cycle and the critical zone is of great interest in Earth system sciences with broad implications for water quality and quantity. Most water age studies to date have focused on individual compartments (or subdisciplines) of the hydrological cycle such as the unsaturated or saturated zone, vegetation, atmosphere, or rivers. However, recent studies have shown that processes at the interfaces between the hydrological compartments (e.g., soil‐atmosphere or soil‐groundwater) govern the age distribution of the water fluxes between these compartments and thus can greatly affect water travel times. The broad variation from complete to nearly absent mixing of water at these interfaces affects the water ages in the compartments. This is especially the case for the highly heterogeneous critical zone between the top of the vegetation and the bottom of the groundwater storage. Here, we review a wide variety of studies about water ages in the critical zone and provide (1) an overview of new prospects and challenges in the use of hydrological tracers to study water ages, (2) a discussion of the limiting assumptions linked to our lack of process understanding and methodological transfer of water age estimations to individual disciplines or compartments, and (3) a vision for how to improve future interdisciplinary efforts to better understand the feedbacks between the atmosphere, vegetation, soil, groundwater, and surface water that control water ages in the critical zone.
Modeling Suspended Sediment Transport Under Influence of Turbulence Ejection and Sweep Events
Authors: Tsai Christina W. , Huang Shih‐Hsun 
Published: May 2019

AbstractIn conventional analysis of sedimentation in open channel flow, suspended sediment transport is regarded as an advection diffusion process. A series of theories based on Brownian motion are developed for describing the diffusion process of sediment particles attributed to turbulence. However, difficulties remain because these models cannot represent the time coherence of turbulence structures that affect instantaneous local sediment concentrations. Focusing on the impact of two flow structures in the near‐wall region on suspended sediment transport, ejection, and sweep events, this study proposes a new stochastic Lagrangian model to simulate sediment particle trajectory. While the occurrences of ejection/sweep events are confirmed to change the instantaneous sediment flux, their impact on the long‐term average sediment flux has yet to be confirmed. The simulation results identify the contributions of these structures to suspended sediment transport and show that the time coherence of flow velocity may be essential for flow to carry sediment particles in suspension. This study also points out that the duration of the flow events may be the key to interpret the diffusion coefficient in terms of turbulence intensity.
Salinity Yield Modeling of the Upper Colorado River Basin Using 30‐m Resolution Soil Maps and Random Forests
Authors: Nauman Travis W. , Ely Christopher P. , Miller Matthew P. , Duniway Michael C. 
Published: May 2019

AbstractSalinity loading in the Upper Colorado River Basin (UCRB) costs local economies upward of $300 million U.S. dollars annually. Salinity source models have generally included coarse spatial data to represent nonagriculture sources. We developed new predictive soil property and cover maps at 30‐m resolution to improve source representation in salinity modeling. Salinity loading erosion risk indices were also created based on soil properties, remotely sensed bare ground exposure, and topographic factors to examine potential surface soil erosion drivers. These new maps and data from previous SPARROW models were related to recently updated records of salinity at 309 stream gauges in the UCRB using random forest regressions. Resulting salinity yield predictions indicate more diffuse salinity sources, with slightly higher yields in more arid portions of the UCRB, and less overall load coming from irrigated agricultural sources. Model simulations still indicate irrigation to be the major human source of salinity (661,000 Mg or 12%) and also suggest that 75,000 Mg (1.4%) of annual salinity in the UCRB is coming from areas with excessive exposed bare ground in high‐elevation mountain areas. Model inputs allow for field‐scale screening of locations that could be targeted for salinity control projects. Results confirm recent studies indicating limited surface erosional influence on salinity loading in UCRB surface waters, but impacts of monsoonal runoff events are still not fully understood, particularly in drylands. The study highlights the utility of new predictive soil maps and machine learning for environmental modeling.
Mesoscale Soil Moisture Patterns Revealed Using a Sparse In Situ Network and Regression Kriging
Authors: Ochsner Tyson E. , Linde Evan , Haffner Matthew , Dong Jingnuo 
Published: May 2019

AbstractSoil moisture spatial patterns with length scales of 1‐100 km influence hydrological, ecological, and agricultural processes, but the footprint or support volume of existing monitoring systems, for example, satellite‐based radiometers and sparse in situ monitoring networks, is often either too large or too small to effectively observe these mesoscale patterns. This measurement scale gap hinders our understanding of soil water processes and complicates calibration and validation of hydrologic models and soil moisture satellites. One possible solution is to utilize geostatistical techniques that have proven effective for mapping static patterns in soil properties. The objective of this study was to determine how effectively dynamic, mesoscale soil moisture patterns can be mapped by applying regression kriging to the data from a sparse, large‐scale in situ network. The fully automated system developed here uses several data sets: daily soil moisture measurements from the Oklahoma Mesonet, sand content estimates from the Natural Resource Conservation Service Soil Survey Geographic Database, and an antecedent precipitation index computed from National Weather Service multisensor precipitation estimates. A multiple linear regression model is fitted daily to the observed data, and the residuals of that model are used in a semivariogram estimation and kriging routine to produce daily statewide maps of soil moisture at 5‐, 25‐, and 60‐cm depths at 800‐m resolution. During over 3 years of operation, this mapping system has revealed complex, dynamic, and depth‐specific mesoscale patterns, reflecting the shifting influences of both soil texture and precipitation, with a mean absolute error of ≤0.0576 cm3/cm3 across all three depths.
Tropical Teleconnections to Antarctic Sea Ice During Austral Spring 2016 in Coupled Pacemaker Experiments
Authors: Purich Ariaan , England Matthew H. 
Published: May 2019

AbstractFollowing a multidecade increase, Antarctic sea ice declined drastically during austral spring 2016. Suggested causes of the sea ice decline include lingering effects of the 2015/2016 extreme El Niño and a tropical Indian Ocean teleconnection to high‐latitude atmospheric circulation. Here, we conduct pacemaker experiments using a full coupled climate model forced with observed tropical sea surface temperature to examine the impact of the Indian and Pacific Oceans on southern high latitudes during spring 2016. Our experiments suggest that a Rossby wave teleconnection from the tropical Indian Ocean contributed to the sea ice decline during spring 2016, with less influence from the Pacific Ocean. However, we find considerable spread in the magnitude of sea ice anomalies across ensemble members, suggesting that while an Indian Ocean teleconnection likely played a role, intrinsic atmospheric variability and high‐latitude ocean conditions may also have been important in driving the observed 2016 spring sea ice decline.
Understand the Direct Effect of CO2 Increase on Tropical Circulation and TC Activity: Land Surface Warming Versus Direct Radiative Forcing
Authors: Zhou Wenyu , Zhao Ming , Yang Da 
Published: May 2019

AbstractThe direct effect of increased CO2 involves contributions from both land warming and direct radiative forcing. Here, their relative impacts on tropical circulation and tropical cyclones (TCs) are quantified by increasing CO2 over land and ocean separately in a high‐resolution atmosphere‐only model. It is found that land warming induces substantial vertical velocity changes over nearby oceans and such local changes are compensated by opposite motions within tropical ascending regions. The cloud mask effect leads to smaller CO2‐induced radiative heating over ascending regions. Such inhomogeneity in radiative forcing dominates compensated changes in surface fluxes and gross moist stability, leading to the slowdown of the tropical overturning circulation. TC activity is tightly linked with the large‐scale ascent because of the influence on the atmospheric humidity. Regional circulation changes caused by land warming strongly suppresses TC activity over the northwest Pacific, while weakened ascent from direct radiative forcing causes an overall TC reduction.
Statistical Analysis of Transverse Size of Lower Band Chorus Waves Using Simultaneous Multisatellite Observations
Authors: Shen Xiao‐Chen , Li Wen , Ma Qianli , Agapitov Oleksiy , Nishimura Yukitoshi 
Published: May 2019

AbstractChorus waves are known to accelerate or scatter energetic electrons via quasi‐linear or nonlinear wave‐particle interactions in the Earth's magnetosphere. In this letter, by taking advantage of simultaneous observations of chorus waveforms from at least a pair of probes among Van Allen Probes and/or Time History of Events and Macroscale Interactions during Substorms (THEMIS) missions, we statistically calculate the transverse size of lower band chorus wave elements. The average size of lower band chorus wave element is found to be ~315±32 km over L shells of ~5–6. Furthermore, our results suggest that the scale size of lower band chorus tends to be (1) larger at higher L shells; (2) larger at higher magnetic latitudes, especially on the dayside; and (3) larger in the azimuthal direction than in the radial direction. Our findings are crucial to quantify wave‐particle interaction process, particularly the nonlinear interactions between chorus and energetic electrons.
Flow Velocity and Field‐Aligned Current Associated With Field Line Resonance: SuperDARN Measurements
Authors: Fenrich Frances R. , Gillies D. Megan , Donovan Eric , Knudsen David 
Published: May 2019

AbstractThis study presents observations of the two‐dimensional velocities and field‐aligned currents of magnetospheric field line resonances. Knowledge of the two‐dimensional plasma flows is essential for determining the field‐aligned current structure of the field line resonance and for understanding the role that field line resonances play in the generation of some auroral arc forms. In this work the full velocity vectors are determined from a high‐resolution fit to the Super Dual Auroral Radar Network (SuperDARN) line‐of‐sight data. Two discrete field line resonance events are presented, one at 4.0 mHz (4‐ to 5‐min period) and the other at 0.6 mHz (30‐min period). Band‐pass filtering the north‐south and east‐west components of the total convection velocity vectors reveals the two‐dimensional velocity field specific to an individual field line resonance. The field line resonance velocities exhibit periodic vorticity, which correspond to periodic poleward moving bands of enhanced field‐aligned current. Assuming a constant ionospheric Pedersen conductance of 10 S, peak field‐aligned current values are estimated to be 2–4 μA/m2. The field‐aligned currents alternate between upward and downward directed and peak in magnitude ~0.5–1° poleward and/or equatorward of the peak in field line resonance flow velocity. A Swarm satellite overpass occurs directly over the 0.6‐mHz field line resonance. The SuperDARN field‐aligned current profile along the Swarm trajectory is found to be similar in magnitude and structure to that determined from Swarm‐A and Swarm‐C in situ measurements.
e‐POP and Red Line Optical Observations of Alfvénic Auroras
Authors: Liang Jun , Shen Y. , Knudsen D. , Spanswick E. , Burchill J. , Donovan E. 
Published: May 2019

AbstractSuprathermal electron bursts (STEBs), characterized by a board energy spectrum and a field‐aligned pitch angle distribution, have been well recognized to be associated with electron acceleration by inertial Alfvén waves and are thus conventionally termed as “Alfvénic aurora.” In this study, we report joint Enhanced‐Polar‐Outflow‐Probe (e‐POP) and ground‐based optical observations of Alfvénic auroras. In particular, we highlight the prominence of 630‐nm red line emissions under low‐energy Alfvénic auroral precipitation. During the event interval, e‐POP traverses two arcs. One bright arc dominated by green line emissions is clearly seen by all optical instruments; it is embedded in upward field‐aligned currents (FACs) yet leaves little imprint on the e‐POP suprathermal electron imager (SEI), likely due to that the precipitation is well above the upper energy limit of SEI. On the other hand, there is a red line arc that is pronounced only in 630‐nm images. Such a red‐line‐only arc is located in a transition from large‐scale upward FACs to downward FACs and is associated with a prominent STEB structure detected by e‐POP SEI. The STEB features an inverse energy time dispersion, namely, that lower‐energy electrons are seen earlier while higher‐energy electrons appear later. The red‐line‐only arc and its separation from the green line arc evolve in a repeatable fashion, each stemming from a poleward auroral intensification (PAI) propagated from higher latitudes. Following each poleward auroral intensification the green line arc progressively moved southward, while the red‐line‐only arc is quasi‐stationary and stayed relatively stable in latitude. We propose tentative interpretations of the above features based upon stationary inertial Alfvén waves.
An ATAC-seq atlas of chromatin accessibility in mouse tissues
Authors: Liu Chuanyu , Wang Mingyue , Wei Xiaoyu , Wu Liang , Xu Jiangshan , Dai Xi , Xia Jun , Cheng Mengnan , Yuan Yue , Zhang Pengfan , Li Jiguang , Feng Taiqing , Chen Ao , Zhang Wenwei , Chen Fang , Shang Zhouchun , Zhang Xiuqing , Peters Brock A. , Liu Longqi 
Published: May 2019

AbstractThe Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics in multiple species. A comprehensive reference of ATAC-seq datasets for mammalian tissues is important for the understanding of regulatory specificity and developmental abnormality caused by genetic or environmental alterations. Here, we report an adult mouse ATAC-seq atlas by producing a total of 66 ATAC-seq profiles from 20 primary tissues of both male and female mice. The ATAC-seq read enrichment, fragment size distribution, and reproducibility between replicates demonstrated the high quality of the full dataset. We identified a total of 296,574 accessible elements, of which 26,916 showed tissue-specific accessibility. Further, we identified key transcription factors specific to distinct tissues and found that the enrichment of each motif reflects the developmental similarities across tissues. In summary, our study provides an important resource on the mouse epigenome and will be of great importance to various scientific disciplines such as development, cell reprogramming, and genetic disease.
Protein phosphatase 2A interacts with Verthandi/Rad21 to regulate mitosis and organ development in Drosophila
Authors: Kim Lee-Hyang , Hong Sung-Tae , Choi Kwang-Wook 
Published: May 2019

AbstractRad21/Scc1 is a subunit of the cohesin complex implicated in gene regulation as well as sister chromatid cohesion. The level of Rad21/Scc1 must be controlled for proper mitosis and gene expression during development. Here, we identify the PP2A catalytic subunit encoded by microtubule star (mts) as a regulator of Drosophila Rad21/Verthandi (Vtd). Mutations in mts and vtd cause synergistic mitotic defects, including abnormal spindles and loss of nuclei during nuclear division in early embryo. Depletion of Mts and Vtd in developing wing synergistically reduces the Cut protein level, causing severe defects in wing growth. Mts and PP2A subunit Twins (Tws) interact with Vtd protein. Loss of Mts or Tws reduces Vtd protein level. Reduced proteasome function suppresses mitotic defects caused by mutations in mts and vtd. Taken together, this work provides evidence that PP2A is required for mitosis and wing growth by regulating the Vtd level through the proteasomal pathway.
Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy
Authors: Velez Gabriel , Yang Jing , Li Angela S. , Tsang Stephen H. , Bassuk Alexander G. , Mahajan Vinit B. 
Published: May 2019

AbstractCAPN5 Neovascular Inflammatory Vitreoretinopathy (CAPN5-NIV; OMIM 193235) is a poorly-understood rare, progressive inflammatory intraocular disease with limited therapeutic options. To profile disease effector proteins in CAPN5-NIV patient vitreous, liquid vitreous biopsies were collected from two groups: eyes from control subjects (n = 4) with idiopathic macular holes (IMH) and eyes from test subjects (n = 12) with different stages of CAPN5-NIV. Samples were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein expression changes were evaluated by principal component analysis, 1-way ANOVA (significant p-value < 0.05), hierarchical clustering, gene ontology, and pathway representation. There were 216 differentially-expressed proteins (between CAPN5-NIV and control vitreous), including those unique to and abundant in each clinical stage. Gene ontology analysis revealed decreased synaptic signaling proteins in CAPN5-NIV vitreous compared to controls. Pathway analysis revealed that inflammatory mediators of the acute phase response and the complement cascade were highly-represented. The CAPN5-NIV vitreous proteome displayed characteristic enrichment of proteins and pathways previously-associated with non-infectious posterior uveitis, rhegmatogenous retinal detachment (RRD), age-related macular degeneration (AMD), proliferative diabetic retinopathy (PDR), and proliferative vitreoretinopathy (PVR). This study expands our knowledge of affected molecular pathways in CAPN5-NIV using unbiased, shotgun proteomic analysis rather than targeted detection platforms. The high-levels and representation of acute phase response proteins suggests a functional role for the innate immune system in CAPN5-NIV pathogenesis.