bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turbulent Mixing in a Loop Current Eddy From Glider‐Based Microstructure Observations
Authors: Molodtsov S. , Anis A. , Amon R. M. W. , Perez‐Brunius P. 
Published: June 2020

AbstractTurbulence parameters have been estimated from microstructure velocity and temperature measurements in an anticyclonic Loop Current Eddy in the Gulf of Mexico for the very first time. Measurements were performed during a mission in October 2016, using a G2 Webb Research Slocum ocean glider instrumented with a microstructure sensors suite. Well‐defined turbulent kinetic energy dissipation rate patterns in the eddy and the surface mixed layer were clearly identified from both the velocity and temperature microstructure data. Higher dissipation rates were observed at the flanks and beneath the eddy core (up to 10−7 W/kg), while the core interior appeared to be very quiescent (~10−11 W/kg). Double diffusive thermohaline intrusions were detected on the side of the eddy, while the region below the eddy core was more conducive for salt fingering. Heat and salt fluxes associated with these processes suggest that a life span of such an eddy is ~1.5 years.
The Effect of Mineral Dissolution on the Effective Stress Law for Permeability in a Tight Sandstone
Authors: Ma Jin , Querci Lorenzo , Hattendorf Bodo , Saar Martin O. , Kong Xiang‐Zhao 
Published: June 2020

AbstractWe present flow‐through experiments to delineate the processes involved in permeability changes driven by effective stress variations and mineral cement dissolution in porous rocks. CO2‐enriched brine is injected continuously into a tight sandstone under in situ reservoir conditions for 455 hrs. Due to the dolomite cement dissolution, the bulk permeability of the sandstone specimen significantly increases, and two dissolution passages are identified near the fluid inlet by X‐ray CT imaging. Prereaction and postreaction examinations of the effective stress law for permeability suggest that after reaction, the bulk permeability is more sensitive to pore pressure changes and less sensitive to effective stress changes. These observations are corroborated by Scanning Electron Microscopy and X‐ray CT observations. This study deepens our understanding of the effect of mineral dissolution on the effective stress law for permeability, with implications for characterizing subsurface mass and energy transport, particularly during fluid injection/production into/from geologic reservoirs.
The Contribution of Methane Photoproduction to the Oceanic Methane Paradox
Authors: Li Y. , Fichot C. G. , Geng L. , Scarratt M. G. , Xie H. 
Published: June 2020

AbstractAlthough methanogenesis is considered a strictly anaerobic process, oxygen‐replete surface open‐ocean waters are usually supersaturated with methane (CH4), a phenomenon termed the oceanic methane paradox. Here, we report that abiotic methane photoproduction from chromophoric dissolved organic matter (CDOM) significantly contributes to this paradox. Methane photoproduction was observed during solar‐simulated irradiations of various waters collected along the land‐ocean continuum. Methane photoproduction rates decreased seaward, whereas its relative production efficiency and the methane‐to‐carbon‐monoxide (CO) photoproduction ratio (ΔCH4/ΔCO) both followed a reversed trend. Remote‐sensing modeling incorporating a ΔCH4/ΔCO–CDOM absorption relationship yielded an annual methane photoproduction of 118 Gg for the global open ocean, accounting for 20–60% of the open‐ocean methane efflux and being of comparable magnitude to the upper‐ocean methane microbial‐oxidation sink. The photodegradation of CDOM thus plays an important role in maintaining supersaturated methane concentrations in the oxygenated upper ocean and in sustaining oceanic methane emissions to the atmosphere.
Agile Adaptive Radar Sampling of Fast‐Evolving Atmospheric Phenomena Guided by Satellite Imagery and Surface Cameras
Authors: Kollias Pavlos , Luke Edward , Oue Mariko , Lamer Katia 
Published: June 2020

AbstractThe collection of high temporal resolution radar observations without compromising data quality requires adaptability and agility. So far, radar beam steering has been mostly guided by (i) expert judgment or (ii) stand‐alone automated identification and tracking algorithms operating on measurements collected by radar. The current study proposes a new paradigm, where external observations are used to optimize a radar's sampling strategy. Here the sampling strategy of a phased‐array radar and a polarimetric scanning cloud radar, two different yet uniquely complementary systems, is guided by an algorithm that uses observations from a geostationary satellite, a surface camera and the radars themselves to identify and track atmospheric phenomena. The tailored pointing and increase in sensitivity realized through this framework enables the steered radars to sample a diverse set of atmospheric phenomena such as shallow cumuli, lightning‐induced ice crystal orientation and a series of waterspouts.
Detailed Spatial Slip Distribution for Short‐Term Slow Slip Events Along the Nankai Subduction Zone, Southwest Japan
Authors: Kano Masayuki , Kato Aitaro 
Published: June 2020

AbstractMany short‐term slow slip events (S‐SSEs) occur at the transition zone along the Nankai subduction zone, southwest Japan. Because crustal deformation due to a single S‐SSE is small, the source fault is often represented using a planar uniform single‐fault slip model, resulting in little constraint on the spatial heterogeneity in amounts of slip. To comprehensively investigate the detailed cumulative spatial distribution of S‐SSEs in the entire Nankai subduction zone, we adopted a stacking approach of Global Navigation Satellite System data by referencing low‐frequency earthquakes. We extracted the cumulative displacements due to 12, 11, and 14 S‐SSEs that occurred between 2004 and 2009 in eastern Shikoku, Kii, and Tokai; coherent displacements nearly opposite to the direction of plate subduction were obtained. The inverted slip indicated significant slip laterally elongated along the transition zone at ~30–35 km depth. Small slip patches were inferred in the shallow portions at ~15–20 km depth in eastern Shikoku and at ~10–15 km depth in Tokai, respectively. The shallow patch in eastern Shikoku was located on the downdip edge of the coseismic slip area of the 1946 Nankai earthquake, while the Tokai small slip was located on the shallower side of the anticipated source area of a large earthquake. Large slip patches of S‐SSEs tend to avoid the spatially dense low‐frequency earthquake areas; in major S‐SSE areas, the number of low‐frequency earthquakes is small. This spatial dependence of fault slip style within the transition zone provides new insights on the generation mechanism of slow earthquakes.
Meltwater‐Enhanced Nutrient Export From Greenland's Glacial Fjords: A Sensitivity Analysis
Authors: Oliver Hilde , Castelao Renato M. , Wang Chuning , Yager Patricia L. 
Published: June 2020

AbstractAs mass loss from the Greenland Ice Sheet accelerates, this modeling study considers how meltwater inputs to the ocean can impact marine ecosystems using a simplified fjord scenario. At marine‐terminating glaciers in Greenland fjords, meltwater can be delivered far below the sea surface, both as subglacial runoff (from atmosphere‐driven surface melt) and as basal melt (from ocean heat). Such delivery can result in buoyancy‐driven upwelling and the upward entrainment of nutrient‐rich deep water, which can support phytoplankton growth in fjord surface waters. For this study, we use an idealized fjord‐scale model to investigate which properties of glaciers and fjords govern the transport of buoyantly upwelled nutrients from fjords. We model the influence of fjord geometry, hydrology, wind, tides, and phytoplankton growth within the fjord on meltwater‐driven nutrient export to the ocean. We use the Regional Ocean Modeling System (ROMS) coupled to a buoyant plume model and a biogeochemical model to simulate physical and biogeochemical processes within an idealized tidewater glacial fjord. Results show that meltwater‐driven nutrient export increases with larger subglacial discharge rates and deeper grounding lines, features that are both likely to change with continued ice sheet melting. Nutrient export decreases with longer residence times, allowing greater biological drawdown. While the absence of a coastal current in the model setup prevents the downstream advection of exported nutrients, results suggest that shelf‐forced flows could influence nutrient residence time within fjords. This simplified model highlights key uncertainties requiring further observation to understand ecological impacts of Greenland mass loss.
Reducing Numerical Diffusion in Dynamical Coupling Between Atmosphere and Ocean in Community Earth System Model Version 1.2.1
Authors: Ma Jialiang , Xu Shiming , Wang Bin 
Published: June 2020

AbstractClimate models contain atmospheric and oceanic components that are coupled together to simulate the thermodynamic and dynamic processes during air‐sea interactions. Community Earth System Model (CESM version 1.2.1) is a state‐of‐the‐art coupled model that is widely used and participates in Coupled Model Intercomparison Projects. Community Atmospheric Model (CAM), the atmospheric component of CESM, is based on the finite‐volume dynamic core, which utilizes staggered Arakawa‐D grids. However, the dynamics‐physics (D‐P) coupling in CAM causes the prognostic winds of the dynamic core be interpolated onto non‐staggered locations, which affects the wind structure for computing the air‐sea interaction and dynamical coupling. In this study we propose a new scheme that eliminates the extra interpolation during D‐P coupling for the atmosphere‐ocean interaction. We show that it improves the simulated climatology in key regions including eastern boundary upwelling regions and Southern Oceans. Compared with the default scheme, the new approach simulates strong surface wind near coast in eastern boundary upwelling regions. As a result, existing problems of the model, such as warm SST biases in these regions, are reduced. Meanwhile, for Southern Ocean, the prevailing westerlies are enhanced in new scheme, resulting in meridional sea ice transport. As a result, the overestimation of sea ice extent and negative bias in SST is reduced. This new scheme is generally applicable to coupled models with staggered dynamics‐physics, such as spectral‐element method based CAM.
Quantifying Fluid Retention Due to Natural Vegetation in a Forest Floodplain Analogue Using the Aggregated Dead Zone (ADZ) Dilution Approach
Authors: Carling Paul A. , Leyland Julian , Kleinhans Maarten G. , Besozzi Louison , Duranton Pierre , Trieu Hai , Teske Roy 
Published: June 2020

AbstractFluid retention and flow resistance due to natural vegetation remain poorly understood despite the importance of understanding these for flow routing and floodplain revegetation projects. Experiments were undertaken in a shallow earthen channel containing a natural cover of small trees, herbaceous plants, and leaf litter, which were sequentially removed and subjected to a range of flows. A dilution monitoring approach within the Aggregated Dead Zone framework was applied to a series of floodplain vegetated flows, yielding information on bulk flow parameters including tracer dispersion, fluid retention, and flow resistance at the reach scale. The primary response of flow to vegetation removal was a small increase in bulk velocity, with depth and wetted width decreasing only slightly. Reach mean travel time and the advective time delay decreased by about a factor of 2 with the removal of herbs, grass, and leaf litter, leaving only trees. Removing the trees, leaving a bare earthen channel, only slightly decreased travel times. Flow resistance and retention exhibited large values for low discharge and converged on a constant low value for relatively high discharges. It is concluded that flow resistance during low flow is higher than in a high flow with the same vegetation. Consequently, sparse vegetation has a prominent effect on hydraulic retention compared with an unvegetated channel at low discharges but this becomes negligible during high discharges as momentum increasingly dominates the flow. This outcome casts doubt on the efficacy of scrubby vegetation to impede higher‐velocity floodplain flows, showing need for field‐scale determination of integral floodplain resistance.
The Utility of Optical Satellite Winter Snow Depths for Initializing a Glacio‐Hydrological Model of a High‐Elevation, Andean Catchment
Authors: Shaw Thomas E. , Caro Alexis , Mendoza Pablo , Ayala Álvaro , Pellicciotti Francesca , Gascoin Simon , McPhee James 
Published: June 2020

AbstractInformation about end‐of‐winter spatial distribution of snow depth is important for seasonal forecasts of spring/summer streamflow in high‐mountain regions. Nevertheless, such information typically relies upon extrapolation from a sparse network of observations at low elevations. Here, we test the potential of high‐resolution snow depth data derived from optical stereophotogrammetry of Pléiades satellites for improving the representation of snow depth initial conditions (SDICs) in a glacio‐hydrological model and assess potential improvements in the skill of snowmelt and streamflow simulations in a high‐elevation Andean catchment. We calibrate model parameters controlling glacier mass balance and snow cover evolution using ground‐based and satellite observations, and consider the relative importance of accurate estimates of SDICs compared to model parameters and forcings. We find that Pléiades SDICs improve the simulation of snow‐covered area, glacier mass balance, and monthly streamflow compared to alternative SDICs based upon extrapolation of meteorological variables or statistical methods to estimate SDICs based upon topography. Model simulations are found to be sensitive to SDICs in the early spring (up to 48% variability in modeled streamflow compared to the best estimate model), and to temperature gradients in all months that control albedo and melt rates over a large elevation range (>2,400 m). As such, appropriately characterizing the distribution of total snow volume with elevation is important for reproducing total streamflow and the proportions of snowmelt. Therefore, optical stereo‐photogrammetry offers an advantage for obtaining SDICs that aid both the timing and magnitude of streamflow simulations, process representation (e.g., snow cover evolution) and has the potential for large spatial domains.
Rapid diversification of wild social groups driven by toxin-immunity loci on mobile genetic elements
Authors: Vassallo Christopher N , Troselj Vera , Weltzer Michael L , Wall Daniel 
Published: June 2020

Abstract
Many species form distinct social groups that provide fitness advantages to individuals. However, the evolutionary processes that generate new social groups are not well understood. Here we examined recently diverged natural isolates of the model social bacterium, Myxococcus xanthus, to probe the genetic mechanisms and evolutionary processes of kin discrimination that occurred naturally in soil. We show that social incompatibilities were formed from horizontal gene transfer of effectors belonging to three distinct polymorphic toxin systems; outer membrane exchange, type VI secretion and rearrangement hotspot systems. Strikingly, the unique toxin effectors and their respective immunity genes that are responsible for social incompatibilities reside on mobile genetic elements, which make up nearly all of the genotypic variation between isolates within clades. By disrupting these three toxin systems, we engineered social harmony between strains that were originally incompatible. In addition, a horizontal allele swap of a single kin recognition receptor changed social interactions and competition outcomes. Our results provide a case study for how horizontal gene transfer led to social diversification in a natural context. Finally, we show how genomic information of kin discriminatory loci can be used to predict social interactions.
Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits
Authors: Ren Fei-Rong , Sun Xiang , Wang Tian-Yu , Yao Ya-Lin , Huang Yan-Zhen , Zhang Xue , Luan Jun-Bo 
Published: June 2020

Abstract
Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.
Signaling Inhibitors Accelerate the Conversion of mouse iPS Cells into Cancer Stem Cells in the Tumor Microenvironment
Authors: Du Juan , Xu Yanning , Sasada Saki , Oo Aung Ko Ko , Hassan Ghmkin , Mahmud Hafizah , Khayrani Apriliana Cahya , Alam Md Jahangir , Kumon Kazuki , Uesaki Ryo , Afify Said M. , Mansour Hager M. , Nair Neha , Zahra Maram H. , Seno Akimasa , Okada Nobuhiro , Chen Ling , Yan Ting , Seno Masaharu 
Published: June 2020

AbstractCancer stem cells (CSCs) are a class of cancer cells characterized by self-renewal, differentiation and tumorigenic potential. We previously established a model of CSCs by culturing mouse induced pluripotent stem cells (miPSCs) for four weeks in the presence of a conditioned medium (CM) of cancer cell lines, which functioned as the tumor microenvironment. Based on this methodology of developing CSCs from miPSCs, we assessed the risk of 110 non-mutagenic chemical compounds, most of which are known as inhibitors of cytoplasmic signaling pathways, as potential carcinogens. We treated miPSCs with each compound for one week in the presence of a CM of Lewis lung carcinoma (LLC) cells. However, one-week period was too short for the CM to convert miPSCs into CSCs. Consequently, PDO325901 (MEK inhibitor), CHIR99021 (GSK-3β inhibitor) and Dasatinib (Abl, Src and c-Kit inhibitor) were found to confer miPSCs with the CSC phenotype in one week. The tumor cells that survived exhibited stemness markers, spheroid formation and tumorigenesis in Balb/c nude mice. Hence, we concluded that the three signal inhibitors accelerated the conversion of miPSCs into CSCs. Similarly to our previous study, we found that the PI3K-Akt signaling pathway was upregulated in the CSCs. Herein, we focused on the expression of relative genes after the treatment with these three inhibitors. Our results demonstrated an increased expression of pik3ca, pik3cb, pik3r5 and pik3r1 genes indicating class IA PI3K as the responsible signaling pathway. Hence, AKT phosphorylation was found to be up-regulated in the obtained CSCs. Inhibition of Erk1/2, tyrosine kinase, and/or GSK-3β was implied to be involved in the enhancement of the PI3K-AKT signaling pathway in the undifferentiated cells, resulting in the sustained stemness, and subsequent conversion of miPSCs into CSCs in the tumor microenvironment.
Derivation of oocyte-like cells from putative embryonic stem cells and parthenogenetically activated into blastocysts in goat
Authors: Malik Hruda Nanda , Singhal Dinesh Kumar , Saini Sikander , Malakar Dhruba 
Published: June 2020

AbstractGerm cells are responsible for the propagation of live animals from generation to generation, but to surprise, a steep increase in infertile problems among livestock poses great threat for economic development of human race. An alternative and robust approach is essential to combat these ailments. Here, we demonstrate that goat putative embryonic stem cells (ESCs) were successfullyin vitrodifferentiated into primordial germ cells and oocyte-like cells using bone morphogenetic protein-4 (BMP-4) and trans-retinoic acid (RA). Oocyte-like cells having distinct zonapellucida recruited adjacent somatic cells in differentiating culture to form cumulus-oocyte complexes (COCs). The putative COCs were found to express the zonapellucida specific (ZP1 and ZP2) and oocyte-specific markers. Primordial germ cell-specific markers VASA, DAZL, STELLA, and PUM1 were detected at protein and mRNA level. In addition to that, the surface architecture of these putative COCs was thoroughly visualized by the scanning electron microscope. The putative COCs were further parthenogenetically activated to develop into healthy morula, blastocysts and hatched blastocyst stage like embryos. Our findings may contribute to the fundamental understanding of mammalian germ cell biology and may provide clinical insights regarding infertility ailments.
Carbon nanoparticles induce endoplasmic reticulum stress around blood vessels with accumulation of misfolded proteins in the developing brain of offspring
Authors: Onoda Atsuto , Kawasaki Takayasu , Tsukiyama Koichi , Takeda Ken , Umezawa Masakazu 
Published: June 2020

AbstractNano-particulate air pollution threatens developing brains and is epidemiologically related to neurodegenerative diseases involving deposition of misfolded proteins. However, the mechanism underlying developmental neurotoxicity by nanoparticles remains unknown. Here, we report that maternal exposure to low doses of carbon black nanoparticle (CB-NP) induces endoplasmic reticulum (ER) stress associated with accumulation of misfolded proteins. Notably, offspring specifically showed high induction of ER stress in perivascular macrophages and reactive astrocytes only around brain blood vessels, along with accumulation of β-sheet-rich proteins regarded as misfolded proteins. Our results suggest that maternal CB-NP exposure induced ER stress in PVMs and reactive astrocytes around blood vessels in the brain of offspring in mice. The induction of ER stress accompanied by the perivascular accumulation of misfolded proteins is likely to be associated with perivascular abnormalities and neurodegeneration, and development of neurodegenerative diseases related to particulate air pollution.