bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dust Emission Modeling Using a New High‐Resolution Dust Source Function in WRF‐Chem With Implications for Air Quality
Authors: Parajuli Sagar P. , Stenchikov Georgiy L. , Ukhov Alexander , Kim Hyunglok 
Published: August 2019

AbstractAir‐borne dust affects all aspects of human life. The sources of dust have high spatial variation and a better quantification of dust emission helps to identify remediation measures. Orographic and statistical source functions allow a better estimation of dust emission fluxes in coarse‐scale modeling, but a high‐resolution source function is necessary to represent the highly heterogeneous nature of dust sources at the finer scale. Here we use a newly developed high‐resolution (~500 m) source function in Weather Research and Forecasting model, coupled with chemistry (WRF‐Chem) to simulate dust emission over the Middle East and North Africa and evaluate our simulated results against observations. Using a 4‐km grid spacing, we also simulate the emission and transport of dust originating from the Tigris‐Euphrates basin, one of the most important regional dust sources, and quantify the effects of this source on the air quality of the entire Arabian Peninsula. Results show that the use of new source function effectively represents the key dust sources and provides reasonable estimates of dust optical depth and concentrations. We find that the atmospheric dust originating from the Tigris‐Euphrates basin alone exceeds the particulate matter 10 air quality standards in several downwind cities. Our results have broader environmental implications and indicate that the mobilization of depleted uranium deposited in Kuwait and Southern Iraq during the Gulf War (1991) could potentially affect the urban centers over the peninsula, albeit in low concentrations. Our results suggest that an integrated and coordinated management of the Tigris‐Euphrates basin is necessary to maintain good air quality across the Arabian Peninsula.
Understanding the Radio Spectrum of Thunderstorm Narrow Bipolar Events
Authors: Liu Ningyu , Dwyer Joseph R. , Tilles Julia N. , Stanley Mark A. , Krehbiel Paul R. , Rison William , Brown Robert G. , Wilson Jennifer G. 
Published: August 2019

AbstractThis paper reports a study to understand the radio spectrum of thunderstorm narrow bipolar events (NBEs) or compact intracloud discharges, which are powerful sources of high‐frequency (HF) and very high frequency (VHF) electromagnetic radiation. The radio spectra from 10 kHz to about 100 MHz are obtained for three NBEs, including one caused by fast positive breakdown and two by fast negative breakdown. The results indicate that the two polarities of fast breakdown have similar spectra, with a relatively flat spectrum in the HF and VHF band. The ratio of energy spectral densities in the very low frequency and HF bands is (0.9–5) × 105. We develop a statistical modeling approach to investigate if a system of streamers can explain the main features of fast breakdown. Assuming that the current moment peak and charge moment change of individual streamers vary in the ranges of 5–10 A‐m and 5–20 μC‐m, respectively, the modeling results indicate that a system of 107–108 streamers can reproduce the current moment, charge transfer, and radio spectrum of fast breakdown. The rapid current variation on a time scale of nanoseconds required for fast breakdown to produce strong HF/VHF emissions is provided by exponentially accelerating and expanding streamers. Our study therefore supports the hypothesis that fast breakdown is a system of streamers. Finally, suggestions are given regarding future streamer simulations and NBE measurements in order to further develop our understanding of NBEs and lightning initiation.
Humid Subtropical Forests Constitute a Net Methane Source: A Catchment‐Scale Study
Authors: Yu Longfei , Zhu Jing , Zhang Xiaoshan , Wang Zhangwei , Dörsch Peter , Mulder Jan 
Published: August 2019

AbstractCommonly, well‐drained forest soils are net methane (CH4) sinks, whereas poorly drained soils in groundwater discharge zones could contribute significant CH4emissions. Climate change is projected to bring more summer precipitation extremes to subtropics, which may affect forest CH4balance. Chinese forests often have a hilly topography with well‐drained hillslopes and pronounced groundwater discharge zones. Although different landscape elements are likely to have different source and sink functions for CH4, the climatic influence on CH4budget at the catchment scale remains poorly studied. Here, we measured CH4fluxes over three years along a topographic gradient in a subtropical forested catchment in SW China. CH4fluxes exhibited a clear spatial pattern indicating moderate CH4uptake or emission from the well‐drained soils on the hillslope (−5.8 to +1.0 kg CH4‐C·ha−1·year−1) and significant CH4emission from the wetter soils in the groundwater discharge zone (94.3 to 479.5 kg CH4‐C·ha−1·year−1). Despite its small area contribution to the catchment (0.6%), the groundwater discharge zone emitted substantial amounts of CH4in monsoonal summers, affecting the whole‐catchment budget. Hillslope soils showed weaker CH4uptake or even turned into a small CH4source under wet climatic conditions. Estimates of catchment‐scale CH4budgets indicate that subtropical forest catchments can tip from a net CH4sink in drier years to a net CH4source in wetter years, highlighting the importance of interannual climate variabilities. Our findings suggest that subtropical forests under projected climate change could contribute a net CH4source with consequences for the regional CH4balance.
Compositional Characteristics of Fluvial Particulate Organic Matter Exported From the World's Largest Alpine Wetland
Authors: Dai Guohua , Zhu Erxiong , Liu Zongguang , Wang Yiyun , Zhu Shanshan , Wang Simin , Ma Tian , Jia Juan , Wang Xin , Hou Shengjie , Fu Pingqing , Peterse Francien , Feng Xiaojuan 
Published: August 2019

AbstractWetlands are hot spots for particulate organic matter (POM) supply into rivers, which link the land‐ocean transfer in the global carbon cycle. However, the source, composition, and seasonal variability of POM carried by wetland‐draining rivers are poorly constrained. Here we combine bulk and source‐specific biomarker analyses to investigate the fluvial POM biogeochemistry of the Black and White Rivers draining from the Zoige wetland. We find that POM was dominated by terrestrial organic matter including high‐molecular‐weight (HMW) lipids, branched glycerol dialkyl glycerol tetraethers, and lignin phenols. However, fluvial POM was rich in HMW lipids and poor in lignin phenols compared to the catchment soils, possibly due to hydrodynamic sorting and dissolution processes. While lignin phenol concentrations were higher in the wet season, HMW lipid concentrations were lower. Additionally, lignin phenols increased with total suspended solids, while HMW lipids decrease. These contrasts imply an enhanced input of lignin‐rich particles from soil surface layers in the wet season, diluting HMW lipids. Compared with that in other rivers around the world with a higher forest coverage in the catchment, POM in the Black and White Rivers draining grass‐dominated wetlands had a much higher ratio of HMW fatty acids to lignin phenols. Our results represent a benchmark study highlighting compositional characteristics of fluvial POM exported from the Zoige wetland and the divergent behavior of molecular components during fluvial transfer. Such information is vital for assessing future changes in the Zoige wetland, given its high vulnerability to climatic and land use changes.
Does an Early Spring Indicate an Early Summer? Relationships Between Intraseasonal Growing Degree Day Thresholds
Authors: Crimmins M. A. , Crimmins T. M. 
Published: August 2019

AbstractSpring heat accumulation plays a major role in the timing of events such as leaf‐out, leaf expansion, flowering, and insect hatch in temperate systems. Accordingly, heat accumulation can serve as a proxy for the timing of plant and insect phenological activity and can be used in a predictive way when the timing of heat accumulation thresholds being reached can be anticipated. This has strong value for a host of planning and management applications. If relationships exist between earlier‐ and later‐season thresholds at a location, then the timing of later‐season phenological events that are forced by the accumulation of warmth could be anticipated based on when earlier‐season thresholds are met. Using high‐resolution daily temperature data, we calculated the coherence in pairs of spring‐season heat accumulation (growing degree day) threshold anomalies over 1948–2016. Overall, relationships between thresholds spanning the entire spring season were relatively low, while later season thresholds exhibited much higher correlations. This pattern is generally the result of decreasing variability in heat accumulation with season progression. However, correlation strengths did not follow latitudinal or gradients, revealing that within‐season heat accumulation and interannual variability in threshold timing are unique to the specified base temperature and thresholds being compared. We show that the relationships between earlier‐ and later‐season heat accumulation thresholds were sufficient to accurately predict the timing of phenological events in plants in two case examples.
Application of Individual Foraminifera Mg/Ca and δ18O Analyses for Paleoceanographic Reconstructions in Active Depositional Environments
Authors: Fritz‐Endres Theresa , Dekens Petra S. , Fehrenbacher Jennifer , Spero Howard J. , Stine Alexander 
Published: August 2019

AbstractMarine and terrestrial material deposited together in Integrated Ocean Discovery Program Expedition 354 cores in the Bay of Bengal offer the opportunity to link the evolution of monsoonal climate and tectonic erosional history. We test the utility of foraminiferal climate reconstructions in this active depositional environment in which turbidity currents transport material to Expedition 354 sites and may mix foraminiferal shells from higher up on the Bengal Fan with local shells. Mg/Ca and δ18O in ~80 modern (<1 kyr) individual Trilobatus sacculifer specimens reconstruct seasonal sea surface temperature (SST) and sea surface salinity (SSS) at three locations: lower fan Expedition 354 Site U1454 near the modern active channel and more likely to be influenced by turbidity currents, lower fan Expedition 354 Site U1449 far from channel activity, and Site 342KL on the continental slope. Because the lower Bengal Fan locations have less seasonally variable SST and SSS than conditions closer to the continental slope, we can determine if foraminiferal populations are local or have been transported from a distal source. Mg/Ca and δ18O from Site U1449 are not likely to be affected by turbidity currents and reflect local conditions. In contrast, Mg/Ca and δ18O from Site U1454 show strong evidence that foraminifera from the active channel record a mixture of local conditions and distal conditions recorded at higher latitudes. Our results suggest that foraminifera can be used to reconstruct SST and δ18O in this complex depositional environment, but caution must be taken when the downcore lithology indicates turbidites and possible sediment transport.
Baltic Sea methanogens compete with acetogens for electrons from metallic iron
Authors: Palacios Paola Andrea , Snoeyenbos-West Oona , Löscher Carolin Regina , Thamdrup Bo , Rotaru Amelia-Elena 
Published: August 2019

Abstract
Microbially induced corrosion of metallic iron (Fe0)-containing structures is an environmental and economic hazard. Methanogens are abundant in low-sulfide environments and yet their specific role in Fe0 corrosion is poorly understood. In this study, Sporomusa and Methanosarcina dominated enrichments from Baltic Sea methanogenic sediments that were established with Fe0 as the sole electron donor and CO2 as the electron acceptor. The Baltic-Sporomusa was phylogenetically affiliated to the electroactive acetogen S. silvacetica. Baltic-Sporomusa adjusted rapidly to growth on H2. On Fe0, spent filtrate enhanced growth of this acetogen suggesting that it was using endogenous enzymes to retrieve electrons and produce acetate. Previous studies have proposed that acetate produced by acetogens can feed commensal acetoclastic methanogens such as Methanosarcina. However, Baltic-methanogens could not generate methane from acetate, plus the decrease or absence of acetogens stimulated their growth. The decrease in numbers of Sporomusa was concurrent with an upsurge in Methanosarcina and increased methane production, suggesting that methanogens compete with acetogens for electrons from Fe0. Furthermore, Baltic-methanogens were unable to use H2 (1.5 atm) for methanogenesis and were inhibited by spent filtrate additions, indicating that enzymatically produced H2 is not a favorable electron donor. We hypothesize that Baltic-methanogens retrieve electrons from Fe0 via a yet enigmatic direct electron uptake mechanism.
Orthogonal monoterpenoid biosynthesis in yeast constructed on an isomeric substrate
Authors: Ignea Codruta , Raadam Morten H. , Motawia Mohammed S. , Makris Antonios M. , Vickers Claudia E. , Kampranis Sotirios C. 
Published: August 2019

AbstractSynthetic biology efforts for the production of valuable chemicals are frequently hindered by the structure and regulation of the native metabolic pathways of the chassis. This is particularly evident in the case of monoterpenoid production in Saccharomyces cerevisiae, where the canonical terpene precursor geranyl diphosphate is tightly coupled to the biosynthesis of isoprenoid compounds essential for yeast viability. Here, we establish a synthetic orthogonal monoterpenoid pathway based on an alternative precursor, neryl diphosphate. We identify structural determinants of isomeric substrate selectivity in monoterpene synthases and engineer five different enzymes to accept the alternative substrate with improved efficiency and specificity. We combine the engineered enzymes with dynamic regulation of metabolic flux to harness the potential of the orthogonal substrate and improve the production of industrially-relevant monoterpenes by several-fold compared to the canonical pathway. This approach highlights the introduction of synthetic metabolism as an effective strategy for high-value compound production.
Detonation synthesis of carbon nano-onions via liquid carbon condensation
Authors: Bagge-Hansen M. , Bastea S. , Hammons J. A. , Nielsen M. H. , Lauderbach L. M. , Hodgin R. L. , Pagoria P. , May C. , Aloni S. , Jones A. , Shaw W. L. , Bukovsky E. V. , Sinclair N. , Gustavsen R. L. , Watkins E. B. , Jensen B. J. , Dattelbaum D. M. , Firestone M. A. , Huber R. C. , Ringstrand B. S. , Lee J. R. I. , van Buuren T. , Fried L. E. , Willey T. M. 
Published: August 2019

AbstractTransit through the carbon liquid phase has significant consequences for the subsequent formation of solid nanocarbon detonation products. We report dynamic measurements of liquid carbon condensation and solidification into nano-onions over ∽200 ns by analysis of time-resolved, small-angle X-ray scattering data acquired during detonation of a hydrogen-free explosive, DNTF (3,4-bis(3-nitrofurazan-4-yl)furoxan). Further, thermochemical modeling predicts a direct liquid to solid graphite phase transition for DNTF products ~200 ns post-detonation. Solid detonation products were collected and characterized by high-resolution electron microscopy to confirm the abundance of carbon nano-onions with an average diameter of ∽10 nm, matching the dynamic measurements. We analyze other carbon-rich explosives by similar methods to systematically explore different regions of the carbon phase diagram traversed during detonation. Our results suggest a potential pathway to the efficient production of carbon nano-onions, while offering insight into the phase transformation kinetics of liquid carbon under extreme pressures and temperatures.
Multi-level patterning nucleic acid photolithography
Authors: Hölz Kathrin , Schaudy Erika , Lietard Jory , Somoza Mark M. 
Published: August 2019

AbstractThe versatile and tunable self-assembly properties of nucleic acids and engineered nucleic acid constructs make them invaluable in constructing microscale and nanoscale devices, structures and circuits. Increasing the complexity, functionality and ease of assembly of such constructs, as well as interfacing them to the macroscopic world requires a multifaceted and programmable fabrication approach that combines efficient and spatially resolved nucleic acid synthesis with multiple post-synthetic chemical and enzymatic modifications. Here we demonstrate a multi-level photolithographic patterning approach that starts with large-scale in situ surface synthesis of natural, modified or chimeric nucleic acid molecular structures and is followed by chemical and enzymatic nucleic acid modifications and processing. The resulting high-complexity, micrometer-resolution nucleic acid surface patterns include linear and branched structures, multi-color fluorophore labeling and programmable targeted oligonucleotide immobilization and cleavage.
Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans
Authors: Floc’h Kevin , Lacroix Françoise , Servant Pascale , Wong Yung-Sing , Kleman Jean-Philippe , Bourgeois Dominique , Timmins Joanna 
Published: August 2019

AbstractOur knowledge of bacterial nucleoids originates mostly from studies of rod- or crescent-shaped bacteria. Here we reveal that Deinococcus radiodurans, a relatively large spherical bacterium with a multipartite genome, constitutes a valuable system for the study of the nucleoid in cocci. Using advanced microscopy, we show that D. radiodurans undergoes coordinated morphological changes at both the cellular and nucleoid level as it progresses through its cell cycle. The nucleoid is highly condensed, but also surprisingly dynamic, adopting multiple configurations and presenting an unusual arrangement in which oriC loci are radially distributed around clustered ter sites maintained at the cell centre. Single-particle tracking and fluorescence recovery after photobleaching studies of the histone-like HU protein suggest that its loose binding to DNA may contribute to this remarkable plasticity. These findings demonstrate that nucleoid organization is complex and tightly coupled to cell cycle progression in this organism.
Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor-resistant HER2-positive breast cancer
Authors: Wang Qingfei , Guldner Ian H. , Golomb Samantha M. , Sun Longhua , Harris Jack A. , Lu Xin , Zhang Siyuan 
Published: August 2019

AbstractAcquired resistance to targeted cancer therapy is a significant clinical challenge. In parallel with clinical trials combining CDK4/6 inhibitors to treat HER2+ breast cancer, we sought to prospectively model tumor evolution in response to this regimen in vivo and identify a clinically actionable strategy to combat drug resistance. Despite a promising initial response, acquired resistance emerges rapidly to the combination of anti-HER2/neu antibody and CDK4/6 inhibitor Palbociclib. Using high-throughput single-cell profiling over the course of treatments, we reveal a distinct immunosuppressive immature myeloid cell (IMC) population to infiltrate the resistant tumors. Guided by single-cell transcriptome analysis, we demonstrate that combination of IMC-targeting tyrosine kinase inhibitor cabozantinib and immune checkpoint blockade enhances anti-tumor immunity, and overcomes the resistance. Furthermore, sequential combinatorial immunotherapy enables a sustained control of the fast-evolving CDK4/6 inhibitor-resistant tumors. Our study demonstrates a translational framework for treating rapidly evolving tumors through preclinical modeling and single-cell analyses.
The regulatory landscape of a core maize domestication module controlling bud dormancy and growth repression
Authors: Dong Zhaobin , Xiao Yuguo , Govindarajulu Rajanikanth , Feil Regina , Siddoway Muriel L. , Nielsen Torrey , Lunn John E. , Hawkins Jennifer , Whipple Clinton , Chuck George 
Published: August 2019

AbstractMany domesticated crop plants have been bred for increased apical dominance, displaying greatly reduced axillary branching compared to their wild ancestors. In maize, this was achieved through selection for a gain-of-function allele of the TCP transcription factor teosinte branched1 (tb1). The mechanism for how a dominant Tb1 allele increased apical dominance, is unknown. Through ChIP seq, RNA seq, hormone and sugar measurements on 1 mm axillary bud tissue, we identify the genetic pathways putatively regulated by TB1. These include pathways regulating phytohormones such as gibberellins, abscisic acid and jasmonic acid, but surprisingly, not auxin. In addition, metabolites involved in sugar sensing such as trehalose 6-phosphate were increased. This suggests that TB1 induces bud suppression through the production of inhibitory phytohormones and by reducing sugar levels and energy balance. Interestingly, TB1 also putatively targets several other domestication loci, including teosinte glume architecture1, prol1.1/grassy tillers1, as well as itself. This places tb1 on top of the domestication hierarchy, demonstrating its critical importance during the domestication of maize from teosinte.
Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening
Authors: Mayran Alexandre , Sochodolsky Kevin , Khetchoumian Konstantin , Harris Juliette , Gauthier Yves , Bemmo Amandine , Balsalobre Aurelio , Drouin Jacques 
Published: August 2019

AbstractPioneer transcription factors are characterized by having the unique property of enabling the opening of closed chromatin sites, for implementation of cell fates. We previously found that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire, which allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigate the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes are defined by scRNAseq and chromatin accessibility profiling. We find that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors.