bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐Resolution40Ar/39Ar Geochronology of the Louisville Seamounts IODP Expedition 330 Drill Sites: Implications for the Duration of Hot Spot‐related Volcanism and Age Progressions
Authors: Heaton D. E. , Koppers A. A. P. 
Published: July 2019

AbstractThe Louisville Seamounts display age progressive volcanism and are thought to have formed as the Pacific Plate moved over a long‐lived primary hot spot. Here we present 70 new40Ar/39Ar age results from the Integrated Ocean Drilling Program (IODP) Sites U1372, U1375, U1376, and U1377 drilled and cored during Expedition 330 to the northern, older end of the Louisville Seamounts. The five seamounts drilled are flat‐topped guyots with ages ranging from ∼74 Ma (Canopus Guyot) to ∼51 Ma (Hadar Guyot) recovering up to ∼510 m of basaltic material beneath thin sediment interfaces. Our40Ar/39Ar measurements reveal that throughout each drill hole, most dates are constant within ∼500‐900 kyr at the 2σ confidence interval. In this study we use the new Louisville age information to compare against the Hawaiian‐Emperor trail on the Pacific Plate. The Louisville hot spot trail is low volume, dominantly alkali basalt, and seamounts have a relatively short lifespan up to ∼4 Myr, whereas the Hawaiian hot spot trail is high volume, has a tholeiitic shield‐building stage capped by an alkalic post‐shield stage, and has a lifespan up to ∼6‐7 Myr. Here we show a new approach to estimating a seamount's inception age based on the known cumulative age distributions for seamounts in the Louisville Seamount and Hawaii‐Emperor Seamount trails. Based on our new40Ar/39Ar analyses, we conclude that existing absolute plate motion models misrepresent the age progression of Louisville Seamounts and that the timing of the Hawaiian‐Emperor Bend and the 169°W bend in the Louisville Seamounts are asynchronous by ~3.7 Myr.
An Advanced Multiple‐Layer Canopy Model in the WRF Model With Large‐Eddy Simulations to Simulate Canopy Flows and Scalar Transport Under Different Stability Conditions
Authors: Ma Yulong , Liu Heping 
Published: July 2019

AbstractForest canopies play a critical role in affecting momentum and scalar transfer. Although there have been recent advances in numerical simulations of turbulent flows and scalar transfer across plant canopies and the atmosphere interface, few models have incorporated all important physical and physiological processes in subcanopy layers. Here we describe and evaluate an advanced multiple‐layer canopy module (MCANOPY), which is developed based largely on the Community Land Model version 4.5 and then coupled with the Weather Research and Forecasting model with large‐eddy simulations (WRF‐LES). The MCANOPY includes a suite of subcanopy processes, including radiation transfer, photosynthesis, canopy layer energy balance, momentum drag, and heat, water vapor, and CO2 exchange between canopy layers and the canopy atmosphere. Numerical schemes for heat and water transport in soil, ground surface energy balance, and soil respiration are also included. Both the stand‐alone MCANOPY and the coupled system (the WRF‐LES‐MCANOPY) are evaluated against data measured in the Canopy Horizontal Array Turbulence Study field experiment. The MCANOPY performs reasonably well in reproducing vertical profiles of mean and turbulent flows as well as second‐order statistical quantities including heat and scalar fluxes within the canopy under unstable stability conditions. The coupled WRF‐LES‐MCANOPY captures major features of canopy edge flows under both neutral and unstable conditions. Limitations of the MCANOPY are discussed for our further work. Our results suggest that our model can be a promising modeling system for a variety of applications to study canopy flows and scalar transport (e.g., CO2).
A Modified Particle Filter‐Based Data Assimilation Method for a High‐Precision 2‐D Hydrodynamic Model Considering Spatial‐temporal Variability of Roughness: Simulation of Dam‐Break Flood Inundation
Authors: Cao Yin , Ye Yuntao , Liang Lili , Zhao Hongli , Jiang Yunzhong , Wang Hao , Yi Zhenyan , Shang Yizi , Yan Dengming 
Published: July 2019

AbstractThe particle filter‐based data assimilation method is an effective tool to adjust model states based on observations. In this study, we proposed a modified particle filter‐based data assimilation method with a local weighting procedure (MPFDA‐LW) for a high‐precision two‐dimensional hydrodynamic model (HydroM2D) in dam‐break flood simulation. Moreover, a particle filter‐based data assimilation method with a global weighting procedure (PFDA‐GW) for the HydroM2D model was also investigated. The MPFDA‐LW and the PFDA‐GW for the HydroM2D model, respectively, adopted spatially nonuniform and uniform Manning's roughness coefficients. The MPFDA‐LW considering spatial‐temporal variability of Manning's roughness coefficient could significantly improve the performances of the HydroM2D model in simulating water stages at all gauges simultaneously, whereas the PFDA‐GW considering temporal variability of Manning's roughness coefficient could only slightly improve the performances of the HydroM2D model in simulating water stages at a few gauges. The MPFDA‐LW is more suitable for improving the performance of 2‐D hydrodynamic models in flood inundation simulation than the PFDA‐GW.
How Do Variably Striking Faults Reactivate During Rifting? Insights From Southern Malawi
Authors: Williams Jack N. , Fagereng Åke , Wedmore Luke N. J. , Biggs Juliet , Mphepo Felix , Dulanya Zuze , Mdala Hassan , Blenkinsop Thomas 
Published: July 2019

AbstractCrustal extension is commonly thought to be accommodated by faults that strike orthogonal and obliquely to the regional trend of the minimum compressive stress (σ3). Activation of oblique faults can, however, be conceptually problematic as under Andersonian faulting, it requires preexisting crustal weaknesses, high fluid pressures, and/or stress rotations. Furthermore, measurements of incremental fault displacements, which are typically used to identify oblique faulting, do not necessarily reflect regional stresses. Here, we assess oblique faulting by calculating the stress ratio (σ3/σ1, where σ1 is the maximum compressive stress), slip tendency, and effective coefficient of friction (μs′) required to reactivate variably striking normal faults under different trends of σ3. We apply this analysis to NW and NNE striking active faults at the southern end of the Malawi Rift, where NE‐SW, ENE‐WSW, E‐W, and SE‐NW σ3 trends have previously been proposed. A uniform σ3 trend is inferred for this region as recent joints sets do not rotate along the rift. With a NE‐SW trending σ3, NW‐striking faults are well oriented, however, NNE‐striking faults require μs′ < 0.6 to reactivate. This is inconsistent with a lack of frictionally weak phyllosilicates detected in the fault zone rocks. With an ENE‐WSW to E‐W trending σ3, all faults can reactivate at μs′ > 0.55. These σ3 trends are also comparable to a focal mechanism stress inversion, regional joint orientations, and previously reported geodetically derived extension directions. We therefore conclude that unlike typical models of oblique rifting, the southern Malawi Rift consists of faults that all strike slightly oblique to σ3.
Internal Tide Attenuation in the North Pacific
Authors: Alford Matthew H. , Simmons Harper L. , Marques Olavo B. , Girton James B. 
Published: July 2019

AbstractMultisatellite altimetry and an eddy‐resolving model with tides are used to quantify the attenuation of the mode‐1 M2 internal tide as it propagates from three major sources in the North Pacific. The model is used to correct the altimetric fluxes for the nonstationary signal that altimeters cannot detect. Because internal tides in the North Pacific are highly stationary, these corrections do not materially impact the decay rate estimates. Fluxes are integrated in wedges extending from the sources to account for interference and radial spreading. Observed attenuation rates are consistent with e‐folding scales between 750 and 3,000 km, suggesting weak dissipation rates (≤10−10 W/kg or 0.75×10−3 W/m2) compared to typical open‐ocean turbulence levels, implicating near‐inertial waves and higher‐mode internal tides in providing the balance of the dissipation in the ocean interior.
A 4,500‐Year‐Long Record of Southern Rocky Mountain Dust Deposition
Authors: Routson Cody C. , Arcusa Stéphanie H. , McKay Nicholas P. , Overpeck Jonathan T. 
Published: July 2019

AbstractDust emissions from southwestern North America (Southwest) impact human health and water resources. Whereas a growing network of regional dust reconstructions characterizes the long‐term natural variability of dustiness in the Southwest, short‐term fluctuations remain unexplored. We present a 4.5‐millennia near‐annual record of dust mass accumulation rates from the southern Rocky Mountains, CO. Using microscanning X‐ray fluorescence and a geochemical end‐member mixing model, the record confirms dust increased with human disturbance beginning around 1880 CE, reversing a long‐term decreasing trend potentially related to changes in effective moisture, wind, and vegetation. However, increases in dust mass accumulation rates do not correspond to years or periods of drought, as characterized by tree rings. This result suggests sediment supply and transport mechanisms have a strong influence on dust deposition. The record shows the Southwest is naturally prone to dustiness; however, human disturbances have a large influence on dust emissions, which can be mitigated by changing land use.
Constraints on Venus Lightning From Akatsuki's First 3 Years in Orbit
Authors: Lorenz Ralph D. , Imai Masataka , Takahashi Yukihiro , Sato Mitsuteru , Yamazaki Atsushi , Sato Takao M. , Imamura Takeshi , Satoh Takehiko , Nakamura Masato 
Published: July 2019

AbstractObservations by the Lightning and Airglow Camera on Japan's Venus Climate Orbiter “Akatsuki” over its first 3 years in orbit are reported. Forty‐two opportunities during low‐altitude nightside passes have accumulated 16.8 hr of observation, yielding an area‐time product of 81.6 ×106 km2‐hr, by far the largest at Venus itself to date. No flashes attributable to lightning have been detected, whereas similar observations at Earth would yield thousands of detections. A low flash rate of ~0.005 per million km2‐hr indicated in ground‐based observations is not excluded (but would require that there are not many more smaller flashes). The allowable flash rate is incompatible with the much higher rates of bursts recorded by magnetic and electric field sensors at Venus, indicating that electrical discharges at Venus lack optical emission or that the electromagnetic detections have a nonlightning explanation or both.
A Fast Fermi Acceleration at Mars Bow Shock
Authors: Meziane K. , Mazelle C. X. , Mitchell D. L. , Hamza A. M. , Penou E. , Jakosky B. M. 
Published: July 2019

AbstractWe report, for the first time, strong evidences that a fast Fermi mechanism is taking place at the Mars bow shock. The MAVEN spacecraft observations from the Solar Wind Electron Analyzer instrument show electron flux spikes with energies up to ∼1.5 keV. These spikes are associated with sunward propagating electrons and appear when the interplanetary field line threading the spacecraft is connected near the Martian bow shock tangency point. The observed loss cone distribution is a salient feature of these backstreaming electrons as the phase space density peaks on a ring centered along the magnetic field direction. Moreover, the data show no evidence of any effect due to a hypothetical cross‐shock electric potential on the observed angular distributions. Although similar distributions are seen at the terrestrial bow shock, the quantitative analysis of the measurements strongly indicates that the electrons are produced at the shock foot and escape upstream before exploring the entire shock structure.
Density‐Driven Convection in a Fractured Porous Media: Implications for Geological CO2 Storage
Authors: Kim Minji , Kim Kue‐Young , Han Weon Shik , Oh Junho , Park Eungyu 
Published: July 2019

AbstractDissolution trapping is one of the primary mechanisms of carbon dioxide (CO2) storage in a geological formation. In this study, a numerical model was used to examine the impacts of single and multiple fractures on the transport of dissolved CO2 plumes in various geological settings. The effects of the fracture angle, fracture‐matrix permeability ratio, fracture intersection, and matrix heterogeneity on density‐driven CO2 convection were systematically investigated. The fractures were found to play time‐varying roles in both homogeneous and heterogeneous media by serving as preferential pathways for both CO2‐rich plumes (fingers) and CO2‐free water. The competition between the enhancement of convective mixing and the inhibition of finger growth by the upward flow of freshwater generated a complex flow system. The interaction between the strong upward flow of freshwater through the fractures and the falling CO2‐rich fingers through the porous matrix induced a positive feedback, resulting in accelerated domain‐scale circulation and CO2 dissolution. While the CO2‐rich fingers grew relatively evenly at the top boundary in the homogeneous media, they selectively developed through the high permeable zones in the heterogeneous media. Compared with homogeneous media, the heterogeneous media preserving fractures particularly generated a more dynamic fracture‐matrix mass transfer, resulting in more rapid CO2 dissolution. The findings of this study were extended to examine the effects of fracture connectivity on the enhancement of CO2 transport and dissolution on a field scale.
Multichannel direct transmissions of near-field information
Authors: Wan Xiang , Zhang Qian , Yi Chen Tian , Zhang Lei , Xu Wei , Huang He , Kun Xiao Chao , Xiao Qiang , Jun Cui Tie 
Published: July 2019

AbstractA digital-coding programmable metasurface (DCPM) is a type of functional system that is composed of subwavelength-scale digital coding elements with opposite phase responses. By configuring the digital coding elements, a DCPM can construct dynamic near-field image patterns in which the intensity of each pixel of the image can be dynamically and independently modulated. Thus, a DCPM can perform both spatial and temporal modulations. Here, this advantage is used to realize multichannel direct transmissions of near-field information. Three points are selected in the near-field region to form three independent channels. By applying various digital phase codes on the DCPM, independent binary digital symbols defined by amplitude codes (namely, weak and strong amplitudes) are transmitted through the three channels. The measured near-field distributions and temporal transmissions of the system agree with numerical calculations. Compared with the conventional multichannel transmission, the proposed mechanism achieves simultaneous spatial and temporal modulations by treating DCPM as an energy radiator and information modulator, thereby enduing DCPM with high potential in near-field information processing and communications.
Mendelian randomisation analysis of the effect of educational attainment and cognitive ability on smoking behaviour
Authors: Sanderson Eleanor , Davey Smith George , Bowden Jack , Munafò Marcus R. 
Published: July 2019

AbstractRecent analyses have shown educational attainment to be associated with a number of health outcomes. This association may, in part, be due to an effect of educational attainment on smoking behaviour. In this study, we apply a multivariable Mendelian randomisation design to determine whether the effect of educational attainment on smoking behaviour is due to educational attainment or general cognitive ability. We use individual data from the UK Biobank study (N = 120,050) and summary data from large GWA studies of educational attainment, cognitive ability and smoking behaviour. Our results show that more years of education are associated with a reduced likelihood of smoking that is not due to an effect of general cognitive ability on smoking behaviour. Given the considerable physical harms associated with smoking, the effect of educational attainment on smoking is likely to contribute to the health inequalities associated with differences in educational attainment.
An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa
Authors: Huang Hao , Shao Xiaolong , Xie Yingpeng , Wang Tingting , Zhang Yingchao , Wang Xin , Deng Xin 
Published: July 2019

AbstractThe virulence of Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is regulated by many transcriptional factors (TFs) that control the expression of quorum sensing and protein secretion systems. Here, we report a genome-wide, network-based approach to dissect the crosstalk between 20 key virulence-related TFs. Using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), as well as RNA-seq, we identify 1200 TF-bound genes and 4775 differentially expressed genes. We experimentally validate 347 of these genes as functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that we call ‘Pseudomonas aeruginosa genomic regulatory network’ (PAGnet). Analysis of the network led to the identification of novel functions for two TFs (ExsA and GacA) in quorum sensing and nitrogen metabolism. Furthermore, we present an online platform and R package based on PAGnet to facilitate updating and user-customised analyses.
Design and fabrication of flexible DNA polymer cocoons to encapsulate live cells
Authors: Gao Tao , Chen Tianshu , Feng Chang , He Xiang , Mu Chaoli , Anzai Jun-ichi , Li Genxi 
Published: July 2019

AbstractThe capability to encapsulate designated live cells into a biologically and mechanically tunable polymer layer is in high demand. Here, an approach to weave functional DNA polymer cocoons has been proposed as an encapsulation method. By developing in situ DNA-oriented polymerization (isDOP), we demonstrate a localized, programmable, and biocompatible encapsulation approach to graft DNA polymers onto live cells. Further guided by two mutually aided enzymatic reactions, the grafted DNA polymers are assembled into DNA polymer cocoons at the cell surface. Therefore, the coating of bacteria, yeast, and mammalian cells has been achieved. The capabilities of this approach may offer significant opportunities to engineer cell surfaces and enable the precise manipulation of the encapsulated cells, such as encoding, handling, and sorting, for many biomedical applications.
E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family
Authors: Hsu Jenny , Arand Julia , Chaikovsky Andrea , Mooney Nancie A. , Demeter Janos , Brison Caileen M. , Oliverio Romane , Vogel Hannes , Rubin Seth M. , Jackson Peter K. , Sage Julien 
Published: July 2019

AbstractE2F transcription factors are central regulators of cell division and cell fate decisions. E2F4 often represents the predominant E2F activity in cells. E2F4 is a transcriptional repressor implicated in cell cycle arrest and whose repressive activity depends on its interaction with members of the RB family. Here we show that E2F4 is important for the proliferation and the survival of mouse embryonic stem cells. In these cells, E2F4 acts in part as a transcriptional activator that promotes the expression of cell cycle genes. This role for E2F4 is independent of the RB family. Furthermore, E2F4 functionally interacts with chromatin regulators associated with gene activation and we observed decreased histone acetylation at the promoters of cell cycle genes and E2F targets upon loss of E2F4 in RB family-mutant cells. Taken together, our findings uncover a non-canonical role for E2F4 that provide insights into the biology of rapidly dividing cells.
DNA assembly for nanopore data storage readout
Authors: Lopez Randolph , Chen Yuan-Jyue , Dumas Ang Siena , Yekhanin Sergey , Makarychev Konstantin , Racz Miklos Z , Seelig Georg , Strauss Karin , Ceze Luis 
Published: July 2019

AbstractSynthetic DNA is becoming an attractive substrate for digital data storage due to its density, durability, and relevance in biological research. A major challenge in making DNA data storage a reality is that reading DNA back into data using sequencing by synthesis remains a laborious, slow and expensive process. Here, we demonstrate successful decoding of 1.67 megabytes of information stored in short fragments of synthetic DNA using a portable nanopore sequencing platform. We design and validate an assembly strategy for DNA storage that drastically increases the throughput of nanopore sequencing. Importantly, this assembly strategy is generalizable to any application that requires nanopore sequencing of small DNA amplicons.
Iron-dependent histone 3 lysine 9 demethylation controls B cell proliferation and humoral immune responses
Authors: Jiang Yuhang , Li Cuifeng , Wu Qian , An Peng , Huang Laiquan , Wang Jia , Chen Chen , Chen Xi , Zhang Fan , Ma Li , Liu Sanhong , He Hanqing , Xie Shuyun , Sun Yangbai , Liu Hanshao , Zhan Yu , Tao Yu , Liu Zhi , Sun Xiaohua , Hu Yiming , Wang Qi , Ye Deji , Zhang Jie , Zou Shanhua , Wang Ying , Wei Gang , Liu Yongzhong , Shi Yufang , Eugene Chin Y. , Hao Yongqiang , Wang Fudi , Zhang Xiaoren 
Published: July 2019

AbstractTrace elements play important roles in human health, but little is known about their functions in humoral immunity. Here, we show an important role for iron in inducing cyclin E and B cell proliferation. We find that iron-deficient individuals exhibit a significantly reduced antibody response to the measles vaccine when compared to iron-normal controls. Mice with iron deficiency also exhibit attenuated T-dependent or T-independent antigen-specific antibody responses. We show that iron is essential for B cell proliferation; both iron deficiency and α-ketoglutarate inhibition could suppress cyclin E1 induction and S phase entry of B cells upon activation. Finally, we demonstrate that three demethylases, KDM2B, KDM3B and KDM4C, are responsible for histone 3 lysine 9 (H3K9) demethylation at the cyclin E1 promoter, cyclin E1 induction and B cell proliferation. Thus, our data reveal a crucial role of H3K9 demethylation in B cell proliferation, and the importance of iron in humoral immunity.
Neuroepigenetic signatures of age and sex in the living human brain
Authors: Gilbert Tonya M. , Zürcher Nicole R. , Catanese Mary C. , Tseng Chieh-En J. , Di Biase Maria A. , Lyall Amanda E. , Hightower Baileigh G. , Parmar Anjali J. , Bhanot Anisha , Wu Christine J. , Hibert Matthew L. , Kim Minhae , Mahmood Umar , Stufflebeam Steven M. , Schroeder Frederick A. , Wang Changning , Roffman Joshua L. , Holt Daphne J. , Greve Douglas N. , Pasternak Ofer , Kubicki Marek , Wey Hsiao-Ying , Hooker Jacob M. 
Published: July 2019

AbstractAge- and sex-related alterations in gene transcription have been demonstrated, however the underlying mechanisms are unresolved. Neuroepigenetic pathways regulate gene transcription in the brain. Here, we measure in vivo expression of the epigenetic enzymes, histone deacetylases (HDACs), across healthy human aging and between sexes using [11C]Martinostat positron emission tomography (PET) neuroimaging (n = 41). Relative HDAC expression increases with age in cerebral white matter, and correlates with age-associated disruptions in white matter microstructure. A post mortem study confirmed that HDAC1 and HDAC2 paralogs are elevated in white matter tissue from elderly donors. There are also sex-specific in vivo HDAC expression differences in brain regions associated with emotion and memory, including the amygdala and hippocampus. Hippocampus and white matter HDAC expression negatively correlates with emotion regulation skills (n = 23). Age and sex are associated with HDAC expression in vivo, which could drive age- and sex-related transcriptional changes and impact human behavior.