bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dry Deposition of Ozone Over Land: Processes, Measurement, and Modeling
Authors: Clifton Olivia E. , Fiore Arlene M. , Massman William J. , Baublitz Colleen B. , Coyle Mhairi , Emberson Lisa , Fares Silvano , Farmer Delphine K. , Gentine Pierre , Gerosa Giacomo , Guenther Alex B. , Helmig Detlev , Lombardozzi Danica L. , Munger J. William , Patton Edward G. , Pusede Sally E. , Schwede Donna B. , Silva Sam J. , Sörgel Matthias , Steiner Allison L. , Tai Amos P. K. 
Published: February 2020

AbstractDry deposition of ozone is an important sink of ozone in near‐surface air. When dry deposition occurs through plant stomata, ozone can injure the plant, altering water and carbon cycling and reducing crop yields. Quantifying both stomatal and nonstomatal uptake accurately is relevant for understanding ozone's impact on human health as an air pollutant and on climate as a potent short‐lived greenhouse gas and primary control on the removal of several reactive greenhouse gases and air pollutants. Robust ozone dry deposition estimates require knowledge of the relative importance of individual deposition pathways, but spatiotemporal variability in nonstomatal deposition is poorly understood. Here we integrate understanding of ozone deposition processes by synthesizing research from fields such as atmospheric chemistry, ecology, and meteorology. We critically review methods for measurements and modeling, highlighting the empiricism that underpins modeling and thus the interpretation of observations. Our unprecedented synthesis of knowledge on deposition pathways, particularly soil and leaf cuticles, reveals process understanding not yet included in widely used models. If coordinated with short‐term field intensives, laboratory studies, and mechanistic modeling, measurements from a few long‐term sites would bridge the molecular to ecosystem scales necessary to establish the relative importance of individual deposition pathways and the extent to which they vary in space and time. Our recommended approaches seek to close knowledge gaps that currently limit quantifying the impact of ozone dry deposition on air quality, ecosystems, and climate.
The Interaction of the Eastward Extrusion of the Songpan‐Ganzi Terrane and the Crustal Rotational Movement of the Sichuan Basin Since the Late Paleogene: Evidence From Cretaceous and Paleogene Paleomagnetic Data Sets of the Sichuan Basin
Authors: Tong Yabo , Wu Zhonghai , Sun Yujun , Yang Zhenyu , Pei Junling , Yang Xiangdong , Li Jianfeng , Wang Chenxu 
Published: February 2020

AbstractSince ~40 Ma the eastward extrusion of the Songpan‐Ganzi Terrane (SGT), induced by the continuous convergence of the Indian Plate and Eurasia, was resisted by the Sichuan Basin which led to complex crustal rotational deformation of the basin edge. The interaction between the eastward extrusion of the SGT and crustal rotational movement of the Sichuan Basin is the key to understand the Cenozoic crustal deformation of the eastern edge of the Tibetan Plateau. However, we lack information about the dynamic mechanism of the branching of the eastward extrusion of the SGT and the characteristics of the crustal rotation of the Sichuan Basin. In the present study, the comprehensive analysis of Cretaceous and Paleogene paleomagnetic data from the southern edge of the Sichuan Basin shows a significant correlation between the locations of sampling sections on the edge of the basin and their corresponding amount of rotation. This indicates that since the time no earlier than 40 Ma (more likely since the Late Paleogene), the upper crust of the Sichuan Basin commenced passive integral clockwise rotation, relative to the eastern edge of the South China Block/Europe, which not only played an important role in promoting the eastward extrusion of the SGT dividing into the northeastern and southern branches at the eastern edge of the Tibetan Plateau, but was also probably correlative with the partial decoupling between the upper and lower crusts of the eastern edge of the Tibetan Plateau.
A Parsimonious Empirical Approach to Streamflow Recession Analysis and Forecasting
Authors: Delforge Damien , Muñoz‐Carpena Rafael , Van Camp Michel , Vanclooster Marnik 
Published: February 2020

AbstractFor more than a century, the study of streamflow recession has been dominated by seemingly physically based parametric methods that make assumptions on the nonlinear nature of the hydrograph recession. In practice, several studies have shown that various degrees of nonlinearity occur in the same time series and that parametric methods can underfit nonlinear recession patterns. As a result, these methods are often applied empirically to each recession segment. We propose a parsimonious data‐driven model, EDM‐Simplex, with two objectives: forecasting recession and characterizing its nonlinear behavior. We evaluate the new model through a global sensitivity analysis applied to three distinctive hydrograph series from a heterogeneous karstic catchment. The results show excellent 1‐day‐ahead forecasting performance (median Nash and Sutcliffe efficiency > 0.99) for all time series with four recession extraction methods. The sensitivity analysis also showed that empirical nonlinearity, that is, sensitivity to initial conditions, is best estimated through the absolute forecast performance and its decline over time. This indicator leads to different interpretations of nonlinearity compared to previous methods but is just as sensitive to the choice of recession extraction method. In particular, when forecasts were made for recession segments containing early stages of recession or flow anomalies, the upstream recession was significantly more linear than the downstream recession hydrographs affected by the karst. Consequently, our results support future research to interpret observed nonlinearities as a function of the catchment hydrological states for better integration of empirical, physical‐based, and operational approaches to recession analysis.
Partitioning Thresholds in Hybrid Implicit‐Explicit Representations of Naturally Fractured Reservoirs
Authors: Wong Daniel Lorng Yon , Doster Florian , Geiger Sebastian , Kamp Arjan 
Published: February 2020

AbstractFractures can have variable effects on fluid flow in a porous rock. Moderately conductive fractures may enhance the rock's overall effective permeability, while highly conductive fractures may completely dominate fluid transport. Fluid flow modeling is important to quantify the impact of fractures on the performance of a reservoir. However, simulating fluid flow is computationally intensive due to the heterogeneities introduced by the fracture network. In this work, complex fracture patterns are simplified using hybrid implicit‐explicit representations to yield a computationally tractable model. Hybrid modeling requires the selection of a partitioning size to group fractures by size. Small fractures are upscaled with the rock matrix; large fractures are explicitly represented. Our study shows that, given a naturally fractured reservoir, an upper limit exists for the partitioning size and that this threshold partitioning size can be determined without trial and error. Using artificial and realistic fracture patterns, we created hybrid models using different partitioning sizes and subjected them to pressure drawdowns. Simulated production rates were compared against reference results obtained from simulations on the original fracture patterns. Beyond a threshold partitioning size unique to each fracture pattern, hybrid model results deviate significantly from reference solutions. The threshold is identified from the relationship between upscaled permeabilities and partitioning sizes and corresponds to the point where the effective permeability of small fractures begins to increase rapidly. The permeability‐size relationship is obtained using numerical flow‐based upscaling. For uniformly distributed fractures with no abutment relationships, the effective medium theory is shown to generate accurate permeability‐size relationships.
Subcore Scale Fluid Flow Behavior in a Sandstone With Cataclastic Deformation Bands
Authors: Romano Carla R. , Zahasky Christopher , Garing Charlotte , Minto James M. , Benson Sally M. , Shipton Zoe K. , Lunn Rebecca J. 
Published: February 2020

AbstractAccurate determination of petrophysical and multiphase flow properties in sandstones is necessary for reservoir characterization, for instance for carbon dioxide and hydrogen storage in geological formations or for enhanced oil recovery. Several studies have examined the effect of heterogeneities, such as fractures, bedding planes, and laminae, on core‐scale fluid flow. However, the influence of deformation bands that commonly occur in high porosity sandstones is poorly understood. In this study, we consider a core sample of Navajo sandstone characterized by diagonally oriented deformation bands and two laminae perpendicular to the core axis, as determined from micro X‐ray computed tomography (micro‐CT). Positron emission tomography is used to derive the single phase hydrodynamic properties of the core. A CO2 drainage experiment is conducted in the water‐saturated core and imaged with a medical X‐ray CT scanner. Medical CT enables CO2 saturation quantification with increasing CO2 injection rate. Experimental results and the accompanying numerical simulations indicate that both the laminae and the deformation bands act as capillary barriers, with the laminae forming weaker capillary barriers than the deformation bands. The deformation bands have lower permeability and porosity due to grain crushing, and a very high capillary entry pressure that inhibits CO2 migration across the bands. At the reservoir scale, deformation bands form conjugate sets and are often present in thick anastomosing clusters that define lozenge‐shaped compartments. These findings have important consequences for subsurface fluid flow. For example, the presence of deformation bands may reduce the storage capacity and injectivity in carbon storage reservoirs.
Osteopontin contributes to late-onset asthma phenotypes in adult asthma patients
Authors: Trinh Hoang Kim Tu , Nguyen Thuy Van Thao , Kim Seo-Hee , Cao Thi Bich Tra , Luu Quoc Quang , Kim Seung-Hyun , Park Hae-Sim 
Published: February 2020

AbstractPatients with late-onset asthma (LOA) have poor clinical outcomes. Osteopontin (OPN) is associated with airway inflammation and remodeling. To investigate the role of OPN in LOA compared to early-onset asthma (EOA), serum OPN levels were compared between 131 adult asthma patients (48 LOA and 83 EOA patients) and 226 healthy controls (HCs). BALB/c mice were sensitized with ovalbumin with/without polyinosinic-polycytidylic acid (poly(I:C)) from week 6 (A6 mice) or week 12 (A12 mice) after birth. Airway hyperresponsiveness (AHR), bronchoalveolar lavage fluid (BALF), cell counts, histology, andSpp1expression were assessed. The levels of OPN, transforming growth factor β1 (TGF-β1), chitinase 3-like 1 (CH3L1), and interleukin (IL) 5 were measured by ELISA. The expression of Smad3 phosphorylation and tissue transglutaminase 2 (TGM2) was evaluated by Western blot. The serum OPN levels were significantly higher in asthma patients than in HCs and in LOA patients than in those with EOA (P < 0.05) and were positively correlated with serum TGF-β1 and CH3L1 (r = 0.174,r = 0.264;P < 0.05). A12 mice showed elevated AHR with increased levels of OPN/TGF-β1/IL-5 in BALF andSpp1compared to A6 mice. Poly(I:C) induced remarkable TGF-β1, CH3L1, Th2 cytokine, and OPN levels in BALF and the expression of phosphorylated Smad3, TGM2, andSpp1in the lungs. OPN triggered TGF-β1/Smad3 signaling in the lungs, which was suppressed by dexamethasone and anti-IL5 antibody. In conclusion, aging and exposure to viral infections may induce OPN release and consequently modulate inflammation and TGF-β1/Smad3-related remodeling, contributing to the development of LOA.
Clinical significance of TP53, BIRC3, ATM and MAPK-ERK genes in chronic lymphocytic leukaemia: data from the randomised UK LRF CLL4 trial
Authors: Blakemore Stuart J. , Clifford Ruth , Parker Helen , Antoniou Pavlos , Stec-Dziedzic Ewa , Larrayoz Marta , Davis Zadie , Kadalyayil Latha , Colins Andrew , Robbe Pauline , Vavoulis Dimitris , Forster Jade , Carr Louise , Morilla Ricardo , Else Monica , Bryant Dean , McCarthy Helen , Walewska Renata J. , Steele Andrew J. , Chan Jacqueline , Speight Graham , Stankovic Tanja , Cragg Mark S. , Catovsky Daniel , Oscier David G. , Rose-Zerilli Matthew J. J. , Schuh Anna , Strefford Jonathan C. 
Published: February 2020

AbstractDespite advances in chronic lymphocytic leukaemia (CLL) treatment, globally chemotherapy remains a central treatment modality, with chemotherapy trials representing an invaluable resource to explore disease-related/genetic features contributing to long-term outcomes. In 499 LRF CLL4 cases, a trial with >12 years follow-up, we employed targeted resequencing of 22 genes, identifying 623 mutations. After background mutation rate correction, 11/22 genes were recurrently mutated at frequencies between 3.6% (NFKBIE) and 24% (SF3B1). Mutations beyond Sanger resolution (<12% VAF) were observed in all genes, withKRASmutations principally composed of these low VAF variants. Firstly, employing orthogonal approaches to confirm <12% VAFTP53mutations, we assessed the clinical impact ofTP53clonal architecture. Whilst ≥ 12% VAFTP53mut cases were associated with reduced PFS and OS, we could not demonstrate a difference between <12% VAFTP53mutations and either wild type or ≥12% VAFTP53mut cases. Secondly, we identified biallelicBIRC3lesions (mutation and deletion) as an independent marker of inferior PFS and OS. Finally, we observed that mutatedMAPK-ERKgenes were independent markers of poor OS in multivariate survival analysis. In conclusion, our study supports using targeted resequencing of expanded gene panels to elucidate the prognostic impact of gene mutations.
Chronic activation of endothelial MAPK disrupts hematopoiesis via NFKB dependent inflammatory stress reversible by SCGF
Authors: Ramalingam Pradeep , Poulos Michael G. , Lazzari Elisa , Gutkin Michael C. , Lopez David , Kloss Christopher C. , Crowley Michael J. , Katsnelson Lizabeth , Freire Ana G. , Greenblatt Matthew B. , Park Christopher Y. , Butler Jason M. 
Published: February 2020

AbstractInflammatory signals arising from the microenvironment have emerged as critical regulators of hematopoietic stem cell (HSC) function during diverse processes including embryonic development, infectious diseases, and myelosuppressive injuries caused by irradiation and chemotherapy. However, the contributions of cellular subsets within the microenvironment that elicit niche-driven inflammation remain poorly understood. Here, we identify endothelial cells as a crucial component in driving bone marrow (BM) inflammation and HSC dysfunction observed following myelosuppression. We demonstrate that sustained activation of endothelial MAPK causes NF-κB-dependent inflammatory stress response within the BM, leading to significant HSC dysfunction including loss of engraftment ability and a myeloid-biased output. These phenotypes are resolved upon inhibition of endothelial NF-κB signaling. We identify SCGF as a niche-derived factor that suppresses BM inflammation and enhances hematopoietic recovery following myelosuppression. Our findings demonstrate that chronic endothelial inflammation adversely impacts niche activity and HSC function which is reversible upon suppression of inflammation.
Mirrored entanglement witnesses
Authors: Bae Joonwoo , Chruściński Dariusz , Hiesmayr Beatrix C. 
Published: February 2020

AbstractEntanglement detection, which signifies the task of distinguishing entangled states from separable states, can be generally performed by realizing entanglement witnesses via local measurements on a single-copy level and classical communication, and are known to be experimenter friendly. We introduce a framework of constructing mirrored entanglement witnesses by showing that an experimental observable is twice as effective since it generally provides bounds from above and below for separable states. Differently stated, a pair of witnesses, mirrored witnesses, exists for the characterization of the bounds, which are two faces of one observable. We show how to generally construct those witnesses and provide examples for bipartite and multipartite systems. We also show that both mirrored witnesses can be improved by introducing nonlinearities, by which a larger set of entangled states can be certified.
SciPy 1.0: fundamental algorithms for scientific computing in Python
Authors: Virtanen Pauli , Gommers Ralf , Oliphant Travis E. , Haberland Matt , Reddy Tyler , Cournapeau David , Burovski Evgeni , Peterson Pearu , Weckesser Warren , Bright Jonathan , van der Walt Stéfan J. , Brett Matthew , Wilson Joshua , Millman K. Jarrod , Mayorov Nikolay , Nelson Andrew R. J. , Jones Eric , Kern Robert , Larson Eric , Carey C J , Polat İlhan , Feng Yu , Moore Eric W. , VanderPlas Jake , Laxalde Denis , Perktold Josef , Cimrman Robert , Henriksen Ian , Quintero E. A. , Harris Charles R. , Archibald Anne M. , Ribeiro Antônio H. , Pedregosa Fabian , van Mulbregt Paul ,   SciPy 1.0 Contributors, Vijaykumar Aditya , Bardelli Alessandro Pietro , Rothberg Alex , Hilboll Andreas , Kloeckner Andreas , Scopatz Anthony , Lee Antony , Rokem Ariel , Woods C. Nathan , Fulton Chad , Masson Charles , Häggström Christian , Fitzgerald Clark , Nicholson David A. , Hagen David R. , Pasechnik Dmitrii V. , Olivetti Emanuele , Martin Eric , Wieser Eric , Silva Fabrice , Lenders Felix , Wilhelm Florian , Young G. , Price Gavin A. , Ingold Gert-Ludwig , Allen Gregory E. , Lee Gregory R. , Audren Hervé , Probst Irvin , Dietrich Jörg P. , Silterra Jacob , Webber James T , Slavič Janko , Nothman Joel , Buchner Johannes , Kulick Johannes , Schönberger Johannes L. , de Miranda Cardoso José Vinícius , Reimer Joscha , Harrington Joseph , Rodríguez Juan Luis Cano , Nunez-Iglesias Juan , Kuczynski Justin , Tritz Kevin , Thoma Martin , Newville Matthew , Kümmerer Matthias , Bolingbroke Maximilian , Tartre Michael , Pak Mikhail , Smith Nathaniel J. , Nowaczyk Nikolai , Shebanov Nikolay , Pavlyk Oleksandr , Brodtkorb Per A. , Lee Perry , McGibbon Robert T. , Feldbauer Roman , Lewis Sam , Tygier Sam , Sievert Scott , Vigna Sebastiano , Peterson Stefan , More Surhud , Pudlik Tadeusz , Oshima Takuya , Pingel Thomas J. , Robitaille Thomas P. , Spura Thomas , Jones Thouis R. , Cera Tim , Leslie Tim , Zito Tiziano , Krauss Tom , Upadhyay Utkarsh , Halchenko Yaroslav O. , Vázquez-Baeza Yoshiki 
Published: February 2020

AbstractSciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.
RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root
Authors: Safavi-Rizi Vajiheh , Herde Marco , Stöhr Christine 
Published: February 2020

AbstractDue to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar ‘Moneymaker’, in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.
Spatio-temporal genetic tagging of a cosmopolitan planktivorous shark provides insight to gene flow, temporal variation and site-specific re-encounters
Authors: Lieber Lilian , Hall Graham , Hall Jackie , Berrow Simon , Johnston Emmett , Gubili Chrysoula , Sarginson Jane , Francis Malcolm , Duffy Clinton , Wintner Sabine P. , Doherty Philip D. , Godley Brendan J. , Hawkes Lucy A. , Witt Matthew J. , Henderson Suzanne M. , de Sabata Eleonora , Shivji Mahmood S. , Dawson Deborah A. , Sims David W. , Jones Catherine S. , Noble Leslie R. 
Published: February 2020

AbstractMigratory movements in response to seasonal resources often influence population structure and dynamics. Yet in mobile marine predators, population genetic consequences of such repetitious behaviour remain inaccessible without comprehensive sampling strategies. Temporal genetic sampling of seasonally recurring aggregations of planktivorous basking sharks, Cetorhinus maximus, in the Northeast Atlantic (NEA) affords an opportunity to resolve individual re-encounters at key sites with population connectivity and patterns of relatedness. Genetic tagging (19 microsatellites) revealed 18% of re-sampled individuals in the NEA demonstrated inter/multi-annual site-specific re-encounters. High genetic connectivity and migration between aggregation sites indicate the Irish Sea as an important movement corridor, with a contemporary effective population estimate (Ne) of 382 (CI = 241–830). We contrast the prevailing view of high gene flow across oceanic regions with evidence of population structure within the NEA, with early-season sharks off southwest Ireland possibly representing genetically distinct migrants. Finally, we found basking sharks surfacing together in the NEA are on average more related than expected by chance, suggesting a genetic consequence of, or a potential mechanism maintaining, site-specific re-encounters. Long-term temporal genetic monitoring is paramount in determining future viability of cosmopolitan marine species, identifying genetic units for conservation management, and for understanding aggregation structure and dynamics.