bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Netherlands Twin Register: Longitudinal Research Based on Twin and Twin-Family Designs
Authors: Ligthart Lannie , van Beijsterveldt Catharina E.M. , Kevenaar Sofieke T. , de Zeeuw Eveline , van Bergen Elsje , Bruins Susanne , Pool René , Helmer Quinta , van Dongen Jenny , Hottenga Jouke-Jan , van’t Ent Dennis , Dolan Conor V. , Davies Gareth E. , Ehli Erik A. , Bartels Meike , Willemsen Gonneke , de Geus Eco J.C. , Boomsma Dorret I. 
Published: October 2019

AbstractThe Netherlands Twin Register (NTR) is a national register in which twins, multiples and their parents, siblings, spouses and other family members participate. Here we describe the NTR resources that were created from more than 30 years of data collections; the development and maintenance of the newly developed database systems, and the possibilities these resources create for future research. Since the early 1980s, the NTR has enrolled around 120,000 twins and a roughly equal number of their relatives. The majority of twin families have participated in survey studies, and subsamples took part in biomaterial collection (e.g., DNA) and dedicated projects, for example, for neuropsychological, biomarker and behavioral traits. The recruitment into the NTR is all inclusive without any restrictions on enrollment. These resources — the longitudinal phenotyping, the extended pedigree structures and the multigeneration genotyping — allow for future twin-family research that will contribute to gene discovery, causality modeling, and studies of genetic and cultural inheritance.
Temporal Variability in the Nutrient Biogeochemistry of the Surface North Atlantic: 15 Years of Ship of Opportunity Data
Authors: Macovei V. A. , Torres‐Valdés S. , Hartman S. E. , Schuster U. , Moore C. M. , Brown P. J. , Hydes D. J. , Sanders R. J. 
Published: October 2019

Ocean biological processes play an important role in the global carbon cycle via the production of organic matter and its subsequent export. Often, this flux is assumed to be in steady state; however, it is dependent on nutrients introduced to surface waters via multiple mechanisms, some of which are likely to exhibit both intra‐annual and interannual variability leading to comparable variability in ocean carbon uptake. Here we test this variability using surface (5 m) inorganic nutrient concentrations from voluntary observing ships and satellite‐derived estimates of chlorophyll and net primary production. At lower latitudes, the seasonality is small, and the monthly averages of nitrate:phosphate are lower than the canonical 16:1 Redfield ratio, implying nitrogen limitation, a situation confirmed via a series of nutrient limitation experiments conducted between Bermuda and Puerto Rico. The nutrient seasonal cycle is more pronounced at higher latitudes, with clear interannual variability. Over a large area of the midlatitude North Atlantic, the winters of 2009/2010 and 2010/2011 had nitrate values more than 1μmol L−1 higher than the 2002–2017 average, suggesting that during this period, the system may have shifted to phosphorus limitation. This nitrate increase meant that, in the region between 31° and 39° N, new production calculated from nitrate uptake was 20.5g C m−2 in 2010, more than four times higher than the median value of the whole observing period. Overall, we suggest that substantial variability in nutrient concentrations and biological carbon uptake occurs in the North Atlantic with interannual variability apparent over a number of different time scales.
Controls on the Thermomechanical Evolution of Hyperextended Lithosphere at Magma‐Poor Rifted Margins: The Example of Espirito Santo and the Kwanza Basins
Authors: Lavier L.L. , Ball P. J. , Manatschal G. , Heumann M. J. , MacDonald J. , Matt V. J. , Schneider C. 
Published: October 2019

AbstractHigh‐quality, long offset seismic data from many distal rifted margins show evidence for hyper‐extended, <10‐km‐thick crust. Direct observation of such domains is challenging as they lie, at great water depth, buried beneath thick sedimentary sequences and formed by rock‐assemblages that are hydrated and geophysically indistinguishable. Only a few drill holes have penetrated basement at ultradistal rifted margins. These observations, together with outcrops of preserved analogs exposed in collisional orogens, suggest that the complex interaction of detachment faults rooted in a subhorizontal shear zone in the hyperextended crust or, in the serpentinized mantle controls the formation of the ocean continent transition. While depth‐dependent thinning controls the early phases of rifting conforming to classical rift models, we still have a superficial understanding of how normal faults and subhorizontal shear zones form and evolve during rifting and lithospheric breakup. Here we develop a rheological parameterization to simulate the formation of, and slip‐on, large offset normal faults rooted in growing brittle to ductile shear zones. The evolution of these structures leads to the creation of a hyperextended crust and eventually exhumed serpentinized mantle. We also propose a simplified formulation to simulate magmatic underplating and seafloor spreading. The resulting numerical models provide a self‐consistent picture for the evolution of magma‐poor rifted margins from initiation of rifting to seafloor spreading. The model results are compared with first‐order observations of the Kwanza and Espirito Santo conjugate margins in the South Atlantic as well as of magma‐poor margins globally.
MMS Observations of Whistler and Lower Hybrid Drift Waves Associated with Magnetic Reconnection in the Turbulent Magnetosheath
Authors: Vörös Zoltán , Yordanova Emilyia , Graham Daniel B. , Khotyaintsev Yuri V. , Narita Yasuhito 
Published: October 2019

AbstractMagnetic reconnection (MR) and the associated concurrently occurring waves have been extensively studied at large‐scale plasma boundaries, in quasi‐symmetric and asymmetric configurations in the terrestrial magnetotail and at the magnetopause. Recent high‐resolution observations by MMS (Magnetospheric Multiscale) spacecraft indicate that MR can occur also in the magnetosheath where the conditions are highly turbulent when the upstream shock geometry is quasi‐parallel. The strong turbulent motions make the boundary conditions for evolving MR complicated. In this paper it is demonstrated that the wave observations in localized regions of MR can serve as an additional diagnostic tool reinforcing our capacity for identifying MR events in turbulent plasmas. It is shown that in a close resemblance with MR at large‐scale boundaries, turbulent reconnection associated whistler waves occur at separatrix/outflow regions and at the outer boundary of the electron diffusion region, while lower hybrid drift waves are associated with density gradients during the crossing of the current sheet. The lower hybrid drift instability can make the density inhomogeneities rippled. The identification of MR associated waves in the magnetosheath represents also an important milestone for developing a better understanding of energy redistribution and dissipation in turbulent plasmas.
Periodic Excitation of Chorus and ECH Waves Modulated by Ultralow Frequency Compressions
Authors: Zhang Xiao‐Jia , Chen Lunjin , Artemyev Anton V. , Angelopoulos Vassilis , Liu Xu 
Published: October 2019

AbstractSpacecraft observations often reveal the presence of marginally stable chorus and electron cyclotron harmonic (ECH) waves across a spatial scale about several Earth radii (RE), which is much larger than the spatial scale of the localized injections that are thought to generate them. Given the importance of these waves for electron acceleration, scattering, and loss to the atmosphere, here we investigate how such broad, periodic wave excitation might occur. We show that it can be attributed to modulation of hot (resonant) electron distributions by ultralow frequency (ULF) waves, which transport electrons radially inward/outward by as much as ∼1.5 RE. Unstable electrons (and chorus waves generated by them) from higher L‐shells (presumably from the azimuthally extended flow‐braking region) are thus brought to lower L‐shells. Half a ULF cycle later, outward electron transport increases the loss cone anisotropy (the perpendicular velocity gradient near the loss cone), resulting in periodic generation of ECH waves with intensities that are anticorrelated with chorus wave intensity. Such wave generation and intermittent electron precipitation (modulated on the spatial/temporal scale of a ULF wavelength/wave period) across large spatial scales could explain the pulsating aurora.
Viscoelasticity of Liquid Iron at Conditions of the Earth's Outer Core
Authors: Xian Jia‐Wei , Sun Tao , Tsuchiya Taku 
Published: October 2019

AbstractViscosity and elasticity are material properties essential for understanding the composition, dynamics, and evolution of the Earth's core, yet their intrinsic connection as embedded in the general theory of viscoelasticity is not well explored. Here we use molecular dynamics to determine the viscoelasticity of liquid iron at conditions of the Earth's outer core. The frequency‐dependent viscosity and shear modulus are determined from the power spectrum of the stress autocorrelation function. We find that the stress autocorrelation function is well characterized by a generalized Maxwell model containing two relaxation modes. The mode with shorter relaxation time (τ1) corresponds to the motion of individual atoms; the other with longer relaxation time (τ2) is associated with collective motions. As temperature (T ) decreases, the slow‐decaying mode becomes more prominent with increasingly larger τ2. In contrast, τ1 remains nearly constant (∼0.016 ps). The infinite frequency shear modulus (G∞), which characterizes the instantaneous shear response, is found to be larger than the static shear modulus of hexagonal close‐packed (hcp) iron of the same density and increases linearly with T. Based on these findings as well as seismic analyses (Tsuboi & Saito, 2002, https://doi.org/10.1186/BF03351717; Krasnoshchekov et al., 2005, https://doi.org/10.1038/nature03613), the zero frequency viscosity (η0) of the lowermost outer core is inferred as 109 Pa·s. The likely material states exhibiting such viscosities are discussed. Moreover, we show that to retain the rigidity consistent with seismic observations, the η0 of the inner core should be at least 1013 Pa·s.
A Novel Hybrid Finite Element‐Spectral Boundary Integral Scheme for Modeling Earthquake Cycles: Application to Rate and State Faults With Low‐Velocity Zones
Authors: Abdelmeguid Mohamed , Ma Xiao , Elbanna Ahmed 
Published: October 2019

AbstractWe present a novel hybrid finite element‐spectral boundary integral (SBI) scheme that enables efficient simulation of earthquake cycles. This combined finite element‐SBI approach captures the benefits of finite elements in modeling problems with nonlinearities, as well as the computational superiority of SBI. The domain truncation enabled by this scheme allows us to utilize high‐resolution finite elements discretization to capture inhomogeneities or complexities that may exist in a narrow region surrounding the fault. Combined with an adaptive time stepping algorithm, this framework opens new opportunities for modeling earthquake cycles with high‐resolution fault zone physics. In this initial study, we consider a two‐dimensional antiplane model with a vertical strike‐slip fault governed by rate and state friction in the quasi‐dynamic limit under the radiation damping approximation. The proposed approach is first verified using the benchmark problem BP‐1 from the Southern California Earthquake Center sequence of earthquake and aseismic slip community verification effort. The computational framework is then utilized to model the earthquake sequence and aseismic slip of a fault embedded within a low‐velocity fault zone (LVFZ) with different widths and compliance levels. Our results indicate that sufficiently compliant LVFZs contribute to the emergence of subsurface events that fail to penetrate to the free surface and may experience earthquake clusters with nonuniform interseismic time. Furthermore, the LVFZ leads to slip rate amplification relative to the homogeneous elastic case. We discuss the implications of our results for understanding earthquake complexity as an interplay of fault friction and bulk heterogeneities.
Modeling Sediment Flocculation in Langmuir Turbulence
Authors: Liu Jinliang , Liang Jun‐Hong , Xu Kehui , Chen Qin , Ozdemir Celalettin Emre 
Published: October 2019

AbstractCohesive sediments exist as flocs of different sizes, which are built and destroyed through flocculation processes including both aggregation and breakup. This study investigates sediment flocculation processes in wave‐driven Langmuir turbulence that is commonly observed in coastal ocean through embedding a size‐resolving flocculation model into a turbulence‐resolving hydrodynamic model. The specific research questions are how Langmuir turbulence affects flocculation processes and how flocculation processes impact the spatial and size distributions of suspended cohesive sediment. The results show that Langmuir turbulence suspends flocs in the water column and organizes flocs of different sizes. By modulating the encounter of flocs and redistributing flocs in the turbulence field, Langmuir turbulence enhances the aggregation and breakup rates of flocs that are located in similar regions with high turbulent dissipation rates and suppresses those of others. As an outcome of modulated flocculation processes, floc size distribution changes with depth and floc mass concentration profiles change with floc size. The addition of wave breaking increases the shear rate near the surface and reduces the median floc size and averaged settling velocity, leading to increase in total floc mass concentration in the whole water column. Wave breaking also increases cross‐shelf sediment transport by more than 15% under the simulated conditions, which is comparable to that due to Langmuir turbulence compared to shear turbulence. Both floc size distribution and floc concentration vary with wind and wave conditions.
Ural Blocking Driving Extreme Arctic Sea Ice Loss, Cold Eurasia, and Stratospheric Vortex Weakening in Autumn and Early Winter 2016–2017
Authors: Tyrlis Evangelos , Manzini Elisa , Bader Jürgen , Ukita Jinro , Nakamura Hisashi , Matei Daniela 
Published: October 2019

AbstractThis study investigates the dynamics that led to the repeated cold surges over midlatitude Eurasia, exceptionally warm conditions and sea ice loss over the Arctic, and the unseasonable weakening of the stratospheric polar vortex in autumn and early winter 2016–2017. We use ERA‐Interim reanalysis data and COBE sea ice and sea surface temperature observational data to trace the dynamical pathways that caused these extreme phenomena. Following abnormally low sea ice conditions in early autumn over the Pacific sector of the Arctic basin, blocking anticyclones became dominant over Eurasia throughout autumn. Ural blocking (UB) activity was four times above climatological levels and organized in several successive events. UB episodes played a key role in the unprecedented sea ice loss observed in late autumn 2016 over the Barents‐Kara Seas and the weakening of the stratospheric vortex. Each blocking induced circulation anomalies that resulted in cold air advection to its south and warm advection to its north. The near‐surface warming anomalies over the Arctic and cooling anomalies over midlatitude Eurasia varied in phase with the life cycles of UB episodes. The sea ice cover minimum over the Barents‐Kara Seas in 2016 was not observed in late summer but rather in mid‐November and December shortly after the two strongest UB episodes. Each UB episode drove intense upward flux of wave activity that resulted in unseasonable weakening of the stratospheric vortex in November. The surface impact of this weakening can be linked to the migration of blocking activity and cold spells toward Europe in early winter 2017.
Wetter Global Arid Regions Driven by Volcanic Eruptions
Authors: Zuo Meng , Zhou Tianjun , Man Wenmin 
Published: October 2019

AbstractArid regions are among the most sensitive areas to climate change; a better understanding of the impact of volcanic eruptions on the hydroclimate over global arid regions is helpful for adaptation but is not well studied. Here we show evidences that arid regions exhibit a wetter condition after volcanic eruptions based on reconstructions and observations, especially for volcanoes located in the Northern hemisphere and tropics. Such “dry gets wetter” response is further supported by climate model simulations driven by volcanic aerosol forcing. The dynamic processes related to changes in atmospheric circulation are found to play a dominant role in precipitation responses. The wetter condition over northern hemispheric (southern hemispheric) (NH (SH)) arid regions after southern (northern) hemispheric volcanic eruptions is caused by enhanced cross‐equator flow, while the increased precipitation over global arid regions and NH (SH) arid regions following tropical volcanic eruptions and northern (southern) eruptions, respectively, are mainly controlled by the monsoon‐desert coupling mechanism. The response of the extreme precipitation is consistent with that of the mean precipitation but more sensitive on a regional scale. The results indicate that volcanic eruptions at different latitudes should be considered in the design of near‐term decadal climate prediction experiments and the implementation of geoengineering activities.
UKESM1: Description and Evaluation of the U.K. Earth System Model
Authors: Sellar Alistair A. , Jones Colin G. , Mulcahy Jane P. , Tang Yongming , Yool Andrew , Wiltshire Andy , O'Connor Fiona M. , Stringer Marc , Hill Richard , Palmieri Julien , Woodward Stephanie , de Mora Lee , Kuhlbrodt Till , Rumbold Steven T. , Kelley Douglas I. , Ellis Rich , Johnson Colin E. , Walton Jeremy , Abraham Nathan Luke , Andrews Martin B. , Andrews Timothy , Archibald Alex T. , Berthou Ségolène , Burke Eleanor , Blockley Ed , Carslaw Ken , Dalvi Mohit , Edwards John , Folberth Gerd A. , Gedney Nicola , Griffiths Paul T. , Harper Anna B. , Hendry Maggie A. , Hewitt Alan J. , Johnson Ben , Jones Andy , Jones Chris D. , Keeble James , Liddicoat Spencer , Morgenstern Olaf , Parker Robert J. , Predoi Valeriu , Robertson Eddy , Siahaan Antony , Smith Robin S. , Swaminathan Ranjini , Woodhouse Matthew T. , Zeng Guang , Zerroukat Mohamed 
Published: October 2019

AbstractWe document the development of the first version of the U.K. Earth System Model UKESM1. The model represents a major advance on its predecessor HadGEM2‐ES, with enhancements to all component models and new feedback mechanisms. These include a new core physical model with a well‐resolved stratosphere; terrestrial biogeochemistry with coupled carbon and nitrogen cycles and enhanced land management; tropospheric‐stratospheric chemistry allowing the holistic simulation of radiative forcing from ozone, methane, and nitrous oxide; two‐moment, five‐species, modal aerosol; and ocean biogeochemistry with two‐way coupling to the carbon cycle and atmospheric aerosols. The complexity of coupling between the ocean, land, and atmosphere physical climate and biogeochemical cycles in UKESM1 is unprecedented for an Earth system model. We describe in detail the process by which the coupled model was developed and tuned to achieve acceptable performance in key physical and Earth system quantities and discuss the challenges involved in mitigating biases in a model with complex connections between its components. Overall, the model performs well, with a stable pre‐industrial state and good agreement with observations in the latter period of its historical simulations. However, global mean surface temperature exhibits stronger‐than‐observed cooling from 1950 to 1970, followed by rapid warming from 1980 to 2014. Metrics from idealized simulations show a high climate sensitivity relative to previous generations of models: Equilibrium climate sensitivity is 5.4 K, transient climate response ranges from 2.68 to 2.85 K, and transient climate response to cumulative emissions is 2.49 to 2.66 K TtC−1.
Characterizing Evaporation Ducts Within the Marine Atmospheric Boundary Layer Using Artificial Neural Networks
Authors: Sit Hilarie , Earls Christopher J. 
Published: October 2019

AbstractWe apply a multilayer perceptron machine learning (ML) regression approach to infer electromagnetic (EM) duct heights within the marine atmospheric boundary layer (MABL) using sparsely sampled EM propagation data obtained within a bistatic context. This paper explains the rationale behind the selection of the ML network architecture, along with other model hyperparameters, in an effort to demystify the process of arriving at a useful ML model. The resulting speed of our ML predictions of EM duct heights, using sparse data measurements within MABL, indicates the suitability of the proposed method for real‐time applications.
Patient-derived organoids as a potential model to predict response to PD-1/PD-L1 checkpoint inhibitors
Authors: Scognamiglio Giosue , De Chiara Annarosaria , Parafioriti Antonina , Armiraglio Elisabetta , Fazioli Flavio , Gallo Michele , Aversa Laura , Camerlingo Rosa , Cacciatore Francesco , Colella Gianluca , Pili Roberto , de Nigris Filomena 
Published: October 2019

Abstract
Selection of cancer patients for treatment with immune checkpoint inhibitors remains a challenge due to tumour heterogeneity and variable biomarker detection. PD-L1 expression in 24 surgical chordoma specimen was determined immunohistochemically with antibodies 28-8 and E1L3N. The ability of patient-derived organoids to detect treatment effects of nivolumab was explored by quantitative and qualitative immunofluorescence and FACS analysis. The more sensitive antibody, E1L3N (ROC = 0.896, p = 0.001), was associated with greater tumour diameters (p = 0.014) and detected both tumour cells and infiltrating lymphocytes in 54% of patients, but only 1–15% of their cells. Organoids generated from PD-L1-positive patients contained both tumour cells and PD-1/CD8-positive lymphocytes and responded to nivolumab treatment with marked dose-dependent diameter reductions of up to 50% and increased cell death in both PD-L1-positive and negative organoids. Patient-derived organoids may be valuable to predict individual responses to immunotherapy even in patients with low or no immunohistochemical PD-L1 expression.
Single cell analysis to dissect molecular heterogeneity and disease evolution in metastatic melanoma
Authors: Fattore Luigi , Ruggiero Ciro Francesco , Liguoro Domenico , Mancini Rita , Ciliberto Gennaro 
Published: October 2019

AbstractOriginally described as interpatient variability, tumour heterogeneity has now been demonstrated to occur intrapatiently, within the same lesion, or in different lesions of the same patient. Tumour heterogeneity involves both genetic and epigenetic changes. Intrapatient heterogeneity is responsible for generating subpopulations of cancer cells which undergo clonal evolution with time. Tumour heterogeneity develops also as a consequence of the selective pressure imposed by the immune system. It has been demonstrated that tumour heterogeneity and different spatiotemporal interactions between all the cellular compontents within the tumour microenvironment lead to cancer adaptation and to therapeutic pressure. In this context, the recent advent of single cell analysis approaches which are able to better study tumour heterogeneity from the genomic, transcriptomic and proteomic standpoint represent a major technological breakthrough. In this review, using metastatic melanoma as a prototypical example, we will focus on applying single cell analyses to the study of clonal trajectories which guide the evolution of drug resistance to targeted therapy.