bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complexity of Fault Rupture and Fluid Leakage in Shale: Insights From a Controlled Fault Activation Experiment
Authors: Guglielmi Yves , Nussbaum Christophe , Jeanne Pierre , Rutqvist Jonny , Cappa Frédéric , Birkholzer Jens 
Published: January 2020

AbstractWe observed rupture growth caused by controlled fluid injections at 340‐m depth within a fault zone in the low‐permeability Opalinus Clay in the Mont Terri Underground Research Laboratory (Switzerland). The rupture mechanisms were evaluated using measurements of the three‐component borehole wall displacements and fluid pressure in two sections of the fault zone and located horizontally 3 m apart from each other. One section was set across a secondary segment of the fault and used for stepwise fluid injection intended to trigger rupture growth. The other section was set across the principal shear zone of the fault for monitoring. After stepwise pressure increase up to 5.95 MPa at injection, rupture initiated as slip activation, followed by an overall opening of the fault planes connected to the injection. After 19 s of continued injection, displacements arrived at the monitoring point on the principal shear zone. These displacements are about 2.4 times larger than in the secondary fault segment. Overall, the displacements corresponded to a normal fault activation. About 9 s after the displacement front arrived, a strong pressure increase of 4.17 MPa was measured at the monitoring point, indicating a hydraulic connection had formed along the initially very low permeability fault planes between the injection and the monitoring points. Our analyses highlight that the fault activation is consistent with the state of stress but that injection pressure must be close to the normal stress acting on the fault for permeability to be generated and for fluid leakage to occur.
Atmospheric Forcing Drives the Winter Sea Ice Thickness Asymmetry of Hudson Bay
Authors: Kirillov S. , Babb D. , Dmitrenko I. , Landy J. , Lukovich J. , Ehn J. , Sydor K. , Barber D. , Stroeve J. 
Published: January 2020

AbstractRecently, we highlighted the presence of a strong west‐east asymmetry in sea ice thickness across Hudson Bay that is driven by cyclonic circulation. Building on this work, we use satellite altimetry and a unique set of in situ observations of ice thickness from three moored upward looking sonars to examine the role of atmospherically driven ice dynamics in producing contrasting regional ice thickness patterns. Ultimately, north‐northwesterly winds coupled with numerous reversals during winter 2016/2017 led to thicker ice in southern Hudson Bay, while enhanced west‐northwesterly winds during winter 2017/2018 led to thicker ice in eastern Hudson Bay that delayed breakup and onset of the summer shipping season to coastal communities. Extending the analysis over the 40‐year satellite observation period, we find that these two different patterns of atmospheric forcing alter the timing of breakup by 30 days in eastern Hudson Bay and offer some skill in seasonal predictions of breakup.
Anomalous δ13C in Particulate Organic Carbon at the Chemoautotrophy Maximum in the Cariaco Basin
Authors: Scranton Mary I. , Taylor Gordon T. , Thunell Robert C. , Muller‐Karger Frank E. , Astor Yrene , Swart Peter , Edgcomb Virginia P. , Pachiadaki Maria G. 
Published: January 2020

AbstractA chemoautotrophy maximum is present in many anoxic basins at the sulfidic layer's upper boundary, but the factors controlling this feature are poorly understood. In 13 of 31 cruises to the Cariaco Basin, particulate organic carbon (POC) was enriched in 13C (δ13CPOC as high as −16‰) within the oxic/sulfidic transition compared to photic zone values (−23 to −26‰). During “heavy” cruises, fluxes of O2 and [NO3− + NO2−] to the oxic/sulfidic interface were significantly lower than during “light” cruises. Cruises with isotopically heavy POC were more common between 2013 and 2015 when suspended particles below the photic zone tended to be nitrogen rich compared to later cruises. Within the chemoautotrophic layer, nitrogen‐rich particles (molar ratio C/N< 10) were more likely to be 13C‐enriched than nitrogen‐poor particles, implying that these inventories were dominated by living cells and fresh detritus rather than laterally transported or extensively decomposed detritus. During heavy cruises, 13C enrichments persisted to 1,300 m, providing the first evidence of downward transport of chemoautotrophically produced POC. Dissolved inorganic carbon assimilation during heavy cruises (n = 3) was faster and occurred deeper than during light cruises (n = 2). Metagenomics data from the chemoautotrophic layer during two cruises support prevalence of microorganisms carrying RuBisCO form II genes, which encode a carbon fixation enzyme that discriminates less against heavy isotopes than most other carbon fixation enzymes, and metatranscriptomics data indicate that higher expression of form II RuBisCO genes during the heavy cruises at depths where essential reactants coexist are responsible for the isotopically heavier POC.
A Multiyear Gridded Data Ensemble of Surface Biogenic Carbon Fluxes for North America: Evaluation and Analysis of Results
Authors: Zhou Yu , Williams Christopher A. , Lauvaux Thomas , Davis Kenneth J. , Feng Sha , Baker Ian , Denning Scott , Wei Yaxing 
Published: January 2020

AbstractAccurate and fine‐scale estimates of biogenic carbon fluxes are critical for measuring and monitoring the biosphere's responses and feedback to the climate system. Currently available data products from flux towers and model‐intercomparison projects struggle to adequately represent spatiotemporal dynamics of surface biogenic carbon fluxes, and to quantify their uncertainties, which also are crucial to atmospheric inversion systems. To address these gaps, we introduce a new perturbed‐parameter model ensemble with the CASA model to estimate surface biogenic carbon fluxes at monthly and 3‐hourly scales for North America at ~500‐m and 5‐km resolutions. We first use the Extended Fourier Amplitude Sensitivity Testing to choose the three most sensitive parameters to be perturbed, maximum light use efficiency (Emax), optimal temperature of photosynthesis (Topt), and temperature response of respiration (Q10). The initial range for each parameter is broadly sampled for the L1 ensemble, but then we pruned Emax with site‐level primary productivity to derive an L2 ensemble with narrower uncertainty ranges. Ensembles are strongly correlated with site‐level results at both monthly and 3‐hourly scales, and the spread across L1/L2 ensemble members encompasses the range of AmeriFlux observations. Monthly variability in the L2 ensemble mean is 85% of the observed variability. The L2 ensemble outperforms diverse data products with the highest Taylor skill scores at diurnal to annual scales. The ensemble's seasonality agrees well with other models for most biome types and in high and middle latitudes, but inconsistencies are found in subtropical and tropical ecoregions and for annual totals over North America.
An ~130 kyr Record of Surface Water Temperature and δ18O From the Northern Bay of Bengal: Investigating the Linkage Between Heinrich Events and Weak Monsoon Intervals in Asia
Authors: Lauterbach Stefan , Andersen Nils , Wang Yiming V. , Blanz Thomas , Larsen Thomas , Schneider Ralph R. 
Published: January 2020

AbstractMillennial‐scale reductions in monsoon precipitation, so‐called Weak Monsoon Intervals (WMIs), have been identified in numerous paleoclimate records across the Afro‐Asian monsoon domain throughout the last glacial‐interglacial cycle. These are considered the regional response to cooling during Heinrich events in the North Atlantic realm and several mechanisms have been suggested to explain this hemisphere‐scale climatic teleconnection. In particular, reductions in Indian Ocean sea surface temperature (SST) have been proposed as the linking element between Heinrich events and WMIs. However, the validity of this relationship has only been demonstrated for the last ~20 kyr, leaving unresolved whether it also holds on longer time scales. Here we present a new paired record of planktonic foraminifera‐based δ18Osw‐ivc and UK'37‐based SST from the northern Bay of Bengal, covering the last ~130 kyr. The δ18Osw‐ivc record clearly reflects orbitally paced changes of Indian Summer Monsoon intensity superimposed by centennial‐ to millennial‐scale WMIs that occurred synchronously to North Atlantic Heinrich events. Comparison with the UK'37‐based SST reconstruction reveals, however, that WMIs in most cases were not paralleled by ocean surface cooling, questioning whether Indian Ocean SST lowering was the linking element between Heinrich events and reductions in monsoon precipitation in Asia also during the last glacial period.
Using Hydrological‐Biogeochemical Linkages to Elucidate Carbon Dynamics in Coastal Marshes Subject to Relative Sea Level Rise
Authors: Guimond Julia A. , Yu Xuan , Seyfferth Angelia L. , Michael Holly A. 
Published: January 2020

AbstractCoastal marshes are an important component of the global carbon cycle, yet our understanding of how these ecosystems will respond to sea level rise (SLR) is limited. Coastal marsh hydrology varies based on elevation, distance from channel, and hydraulic properties, resulting in zones of unique water level oscillation patterns. These zones impact ecology and geochemistry and correspond to differences in carbon accumulation rates. These physical‐biogeochemical linkages enable use of a hydrological model to predict changes in marsh zonation, and in turn carbon accumulation, as well as groundwater‐surface water exchange under SLR. Here, we developed a calibrated hydrological model of a Delaware coastal marsh using HydroGeoSphere. We simulated three scenarios each of SLR, sediment accretion, and upland hydrologic response, and we quantified changes in the spatial coverage of different hydrologic zonations and groundwater‐surface water exchange. Results show that relative SLR reduces marsh area, carbon burial, and lateral water fluxes. However, the magnitudes of change are linked to the terrestrial groundwater table response as well as relative SLR. In scenarios where the upland water table does not change with SLR, the magnitude of decline in marsh area and carbon accumulation is reduced compared to scenarios where the upland water table keeps pace with SLR. In contrast, the reduction in lateral water flux is minimized in scenarios with an upland water table rise equal to SLR compared to scenarios where the upland water table is held at present‐day levels. This study highlights the importance of regional hydrologic setting in the fate of coastal marsh dynamics.
Molecular signatures of aneuploidy-driven adaptive evolution
Authors: Kaya Alaattin , Mariotti Marco , Tyshkovskiy Alexander , Zhou Xuming , Hulke Michelle L. , Ma Siming , Gerashchenko Maxim V. , Koren Amnon , Gladyshev Vadim N. 
Published: January 2020

AbstractAlteration of normal ploidy (aneuploidy) can have a number of opposing effects, such as unbalancing protein abundances and inhibiting cell growth but also accelerating genetic diversification and rapid adaptation. The interplay of these detrimental and beneficial effects remains puzzling. Here, to understand how cells develop tolerance to aneuploidy, we subject disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution under strong selection, by forcing disomy maintenance and daily population dilution. We characterize mutations, karyotype alterations and gene expression changes, and dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates and displayed diverse adaptive events. They tended to evolve towards normal ploidy through chromosomal DNA loss and gene expression changes. We identify genes with recurrent mutations and altered expression in multiple lines, revealing a variant that improves growth under genotoxic stresses. These findings support rapid evolvability of disomic strains that can be used to characterize fitness effects of mutations under different stress conditions.
Targeting p53 and histone methyltransferases restores exhausted CD8+ T cells in HCV infection
Authors: Barili Valeria , Fisicaro Paola , Montanini Barbara , Acerbi Greta , Filippi Anita , Forleo Giovanna , Romualdi Chiara , Ferracin Manuela , Guerrieri Francesca , Pedrazzi Giuseppe , Boni Carolina , Rossi Marzia , Vecchi Andrea , Penna Amalia , Zecca Alessandra , Mori Cristina , Orlandini Alessandra , Negri Elisa , Pesci Marco , Massari Marco , Missale Gabriele , Levrero Massimo , Ottonello Simone , Ferrari Carlo 
Published: January 2020

AbstractHepatitis C virus infection (HCV) represents a unique model to characterize, from early to late stages of infection, the T cell differentiation process leading to exhaustion of human CD8+ T cells. Here we show that in early HCV infection, exhaustion-committed virus-specific CD8+ T cells display a marked upregulation of transcription associated with impaired glycolytic and mitochondrial functions, that are linked to enhanced ataxia-telangiectasia mutated (ATM) and p53 signaling. After evolution to chronic infection, exhaustion of HCV-specific T cell responses is instead characterized by a broad gene downregulation associated with a wide metabolic and anti-viral function impairment, which can be rescued by histone methyltransferase inhibitors. These results have implications not only for treatment of HCV-positive patients not responding to last-generation antivirals, but also for other chronic pathologies associated with T cell dysfunction, including cancer.
Comprehensive T cell repertoire characterization of non-small cell lung cancer
Authors: Reuben Alexandre , Zhang Jiexin , Chiou Shin-Heng , Gittelman Rachel M. , Li Jun , Lee Won-Chul , Fujimoto Junya , Behrens Carmen , Liu Xiaoke , Wang Feng , Quek Kelly , Wang Chunlin , Kheradmand Farrah , Chen Runzhe , Chow Chi-Wan , Lin Heather , Bernatchez Chantale , Jalali Ali , Hu Xin , Wu Chang-Jiun , Eterovic Agda Karina , Parra Edwin Roger , Yusko Erik , Emerson Ryan , Benzeno Sharon , Vignali Marissa , Wu Xifeng , Ye Yuanqing , Little Latasha D. , Gumbs Curtis , Mao Xizeng , Song Xingzhi , Tippen Samantha , Thornton Rebecca L. , Cascone Tina , Snyder Alexandra , Wargo Jennifer A. , Herbst Roy , Swisher Stephen , Kadara Humam , Moran Cesar , Kalhor Neda , Zhang Jianhua , Scheet Paul , Vaporciyan Ara A. , Sepesi Boris , Gibbons Don L. , Robins Harlan , Hwu Patrick , Heymach John V. , Sharma Padmanee , Allison James P. , Baladandayuthapani Veera , Lee Jack J. , Davis Mark M. , Wistuba Ignacio I. , Futreal P. Andrew , Zhang Jianjun 
Published: January 2020

AbstractImmunotherapy targeting T cells is increasingly utilized to treat solid tumors including non-small cell lung cancer (NSCLC). This requires a better understanding of the T cells in the lungs of patients with NSCLC. Here, we report T cell repertoire analysis in a cohort of 236 early-stage NSCLC patients. T cell repertoire attributes are associated with clinicopathologic features, mutational and immune landscape. A considerable proportion of the most prevalent T cells in tumors are also prevalent in the uninvolved tumor-adjacent lungs and appear specific to shared background mutations or viral infections. Patients with higher T cell repertoire homology between the tumor and uninvolved tumor-adjacent lung, suggesting a less tumor-focused T cell response, exhibit inferior survival. These findings indicate that a concise understanding of antigens and T cells in NSCLC is needed to improve therapeutic efficacy and reduce toxicity with immunotherapy, particularly adoptive T cell therapy.
Targeting FROUNT with disulfiram suppresses macrophage accumulation and its tumor-promoting properties
Authors: Terashima Yuya , Toda Etsuko , Itakura Meiji , Otsuji Mikiya , Yoshinaga Sosuke , Okumura Kazuhiro , Shand Francis H. W. , Komohara Yoshihiro , Takeda Mitsuhiro , Kokubo Kana , Chen Ming-Chen , Yokoi Sana , Rokutan Hirofumi , Kofuku Yutaka , Ohnishi Koji , Ohira Miki , Iizasa Toshihiko , Nakano Hirofumi , Okabe Takayoshi , Kojima Hirotatsu , Shimizu Akira , Kanegasaki Shiro , Zhang Ming-Rong , Shimada Ichio , Nagase Hiroki , Terasawa Hiroaki , Matsushima Kouji 
Published: January 2020

AbstractTumor-associated macrophages affect tumor progression and resistance to immune checkpoint therapy. Here, we identify the chemokine signal regulator FROUNT as a target to control tumor-associated macrophages. The low level FROUNT expression in patients with cancer correlates with better clinical outcomes. Frount-deficiency markedly reduces tumor progression and decreases macrophage tumor-promoting activity. FROUNT is highly expressed in macrophages, and its myeloid-specific deletion impairs tumor growth. Further, the anti-alcoholism drug disulfiram (DSF) acts as a potent inhibitor of FROUNT. DSF interferes with FROUNT-chemokine receptor interactions via direct binding to a specific site of the chemokine receptor-binding domain of FROUNT, leading to inhibition of macrophage responses. DSF monotherapy reduces tumor progression and decreases macrophage tumor-promoting activity, as seen in the case of Frount-deficiency. Moreover, co-treatment with DSF and an immune checkpoint antibody synergistically inhibits tumor growth. Thus, inhibition of FROUNT by DSF represents a promising strategy for macrophage-targeted cancer therapy.
Error-mitigated quantum gates exceeding physical fidelities in a trapped-ion system
Authors: Zhang Shuaining , Lu Yao , Zhang Kuan , Chen Wentao , Li Ying , Zhang Jing-Ning , Kim Kihwan 
Published: January 2020

AbstractVarious quantum applications can be reduced to estimating expectation values, which are inevitably deviated by operational and environmental errors. Although errors can be tackled by quantum error correction, the overheads are far from being affordable for near-term technologies. To alleviate the detrimental effects of errors on the estimation of expectation values, quantum error mitigation techniques have been proposed, which require no additional qubit resources. Here we benchmark the performance of a quantum error mitigation technique based on probabilistic error cancellation in a trapped-ion system. Our results clearly show that effective gate fidelities exceed physical fidelities, i.e., we surpass the break-even point of eliminating gate errors, by programming quantum circuits. The error rates are effectively reduced from (1.10 ± 0.12) × 10−3 to (1.44 ± 5.28) × 10−5 and from (0.99 ± 0.06) × 10−2 to (0.96 ± 0.10) × 10−3 for single- and two-qubit gates, respectively. Our demonstration opens up the possibility of implementing high-fidelity computations on a near-term noisy quantum device.
Imaging brain activity during complex social behaviors in Drosophila with Flyception2
Authors: Grover Dhruv , Katsuki Takeo , Li Jinfang , Dawkins Thomas J. , Greenspan Ralph J. 
Published: January 2020

AbstractOptical in vivo recordings from freely walking Drosophila are currently possible only for limited behaviors. Here, we expand the range of accessible behaviors with a retroreflective marker-based tracking and ratiometric brain imaging system, permitting brain activity imaging even in copulating male flies. We discover that P1 neurons, active during courtship, are inactive during copulation, whereas GABAergic mAL neurons remain active during copulation, suggesting a countervailing role of mAL in opposing P1 activity during mating.
Embedding physics domain knowledge into a Bayesian network enables layer-by-layer process innovation for photovoltaics
Authors: Ren Zekun , Oviedo Felipe , Thway Maung , Tian Siyu I. P. , Wang Yue , Xue Hansong , Dario Perea Jose , Layurova Mariya , Heumueller Thomas , Birgersson Erik , Aberle Armin G. , Brabec Christoph J. , Stangl Rolf , Li Qianxiao , Sun Shijing , Lin Fen , Peters Ian Marius , Buonassisi Tonio 
Published: January 2020

AbstractProcess optimization of photovoltaic devices is a time-intensive, trial-and-error endeavor, which lacks full transparency of the underlying physics and relies on user-imposed constraints that may or may not lead to a global optimum. Herein, we demonstrate that embedding physics domain knowledge into a Bayesian network enables an optimization approach for gallium arsenide (GaAs) solar cells that identifies the root cause(s) of underperformance with layer-by-layer resolution and reveals alternative optimal process windows beyond traditional black-box optimization. Our Bayesian network approach links a key GaAs process variable (growth temperature) to material descriptors (bulk and interface properties, e.g., bulk lifetime, doping, and surface recombination) and device performance parameters (e.g., cell efficiency). For this purpose, we combine a Bayesian inference framework with a neural network surrogate device-physics model that is 100× faster than numerical solvers. With the trained surrogate model and only a small number of experimental samples, our approach reduces significantly the time-consuming intervention and characterization required by the experimentalist. As a demonstration of our method, in only five metal organic chemical vapor depositions, we identify a superior growth temperature profile for the window, bulk, and back surface field layer of a GaAs solar cell, without any secondary measurements, and demonstrate a 6.5% relative AM1.5G efficiency improvement above traditional grid search methods.
Immunization with full-length Plasmodium falciparum merozoite surface protein 1 is safe and elicits functional cytophilic antibodies in a randomized first-in-human trial
Authors: Blank Antje , Fürle Kristin , Jäschke Anja , Mikus Gerd , Lehmann Monika , Hüsing Johannes , Heiss Kirsten , Giese Thomas , Carter Darrick , Böhnlein Ernst , Lanzer Michael , Haefeli Walter E. , Bujard Hermann 
Published: January 2020

AbstractA vaccine remains a priority in the global fight against malaria. Here, we report on a single-center, randomized, double-blind, placebo and adjuvant-controlled, dose escalation phase 1a safety and immunogenicity clinical trial of full-lengthPlasmodium falciparummerozoite surface protein 1 (MSP1) in combination with GLA-SE adjuvant. Thirty-two healthy volunteers were vaccinated at least three times with MSP1 plus adjuvant, adjuvant alone, or placebo (24:4:4) to evaluate the safety and immunogenicity. MSP1 was safe, well tolerated and immunogenic, with all vaccinees sero-converting independent of the dose. The MSP1-specific IgG and IgM titers persisted above levels found in malaria semi-immune humans for at least 6 months after the last immunization. The antibodies were variant- and strain-transcending and stimulated respiratory activity in granulocytes. Furthermore, full-length MSP1 induced memory T-cells. Our findings encourage challenge studies as the next step to evaluate the efficacy of full-length MSP1 as a vaccine candidate against falciparum malaria (EudraCT 2016-002463-33).