bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity in root growth responses to moisture deficit in young faba bean (Vicia faba L.) plants
Authors: Belachew Kiflemariam Yehuala , Nagel Kerstin A. , Fiorani Fabio , Stoddard Frederick L. 
Published: February 2018

Background
Soil moisture deficiency causes yield reduction and instability in faba bean (Vicia faba L.) production. The extent of sensitivity to drought stress varies across accessions originating from diverse moisture regimes of the world. Hence, we conducted successive greenhouse experiments in pots and rhizotrons to explore diversity in root responses to soil water deficit.

Methods
A set of 89 accessions from wet and dry growing regions of the world was defined according to the Focused Identification of Germplasm Strategy and screened in a perlite-sand medium under well watered conditions in a greenhouse experiment. Stomatal conductance, canopy temperature, chlorophyll concentration, and root and shoot dry weights were recorded during the fifth week of growth. Eight accessions representing the range of responses were selected for further investigation. Starting five days after germination, they were subjected to a root phenotyping experiment using the automated phenotyping platform GROWSCREEN-Rhizo. The rhizotrons were filled with peat-soil under well watered and water limited conditions. Root architectural traits were recorded five, 12, and 19 days after the treatment (DAT) began.

Results
In the germplasm survey, accessions from dry regions showed significantly higher values of chlorophyll concentration, shoot and root dry weights than those from wet regions. Root and shoot dry weight as well as seed weight, and chlorophyll concentration were positively correlated with each other. Accession DS70622 combined higher values of root and shoot dry weight than the rest. The experiment in GROWSCREEN-Rhizo showed large differences in root response to water deficit. The accession by treatment interactions in taproot and second order lateral root lengths were significant at 12 and 19 DAT, and the taproot length was reduced up to 57% by drought. The longest and deepest root systems under both treatment conditions were recorded by DS70622 and DS11320, and total root length of DS70622 was three times longer than that of WS99501, the shortest rooted accession. The maximum horizontal distribution of a root system and root surface coverage were positively correlated with taproot and total root lengths and root system depth. DS70622 and WS99501 combined maximum and minimum values of these traits, respectively. Thus, roots of DS70622 and DS11320, from dry regions, showed drought-avoidance characteristics whereas those of WS99501 and Mèlodie/2, from wet regions, showed the opposite.

Discussion
The combination of the germplasm survey and use of GROWSCREEN-Rhizo allowed exploring of adaptive traits and detection of root phenotypic markers for potential drought avoidance. The greater root system depth and root surface coverage, exemplified by DS70622 and DS11320, can now be tested as new sources of drought tolerance.
Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies
Authors: Haldrup Christa , Pedersen Anne L. , Øgaard Nadia , Strand Siri H. , Høyer Søren , Borre Michael , Ørntoft Torben F. , Sørensen Karina D. 
Published: February 2018

Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, leading to overdiagnosis and overtreatment. Aberrant promoter hypermethylation of specific genes has been suggested as novel candidate biomarkers for PC that may improve diagnosis and prognosis. We here analyzed ST6GALNAC3 and ZNF660 promoter methylation in prostate tissues, and ST6GALNAC3, ZNF660, CCDC181, and HAPLN3 promoter methylation in liquid biopsies. First, using four independent patient sample sets, including a total of 110 nonmalignant (NM) and 705 PC tissue samples, analyzed by methylation‐specific qPCR or methylation array, we found that hypermethylation of ST6GALNAC3 and ZNF660 was highly cancer‐specific with areas under the curve (AUC) of receiver operating characteristic (ROC) curve analysis of 0.917–0.995 and 0.846–0.903, respectively. Furthermore, ZNF660 hypermethylation was significantly associated with biochemical recurrence in two radical prostatectomy (RP) cohorts of 158 and 392 patients and remained significant also in the subsets of patients with Gleason score ≤7 (univariate Cox regression and log‐rank tests, P < 0.05), suggesting that ZNF660 methylation analysis can potentially help to stratify low‐/intermediate‐grade PCs into indolent vs. more aggressive subtypes. Notably, ZNF660 hypermethylation was also significantly associated with poor overall and PC‐specific survival in the RP cohort (n = 158) with long clinical follow‐up available. Moreover, as proof of principle, we successfully detected highly PC‐specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3, ZNF660, HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation‐specific PCR analysis. Finally, we generated a three‐gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity. In conclusion, we here for the first time demonstrate diagnostic biomarker potential of ST6GALNAC3 and ZNF660 methylation, as well as prognostic biomarker potential of ZNF660. Furthermore, we show that hypermethylation of four genes can be detected in ctDNA in liquid biopsies (serum) from patients with PC.
Violation of Field Line Conservation and Associated Spatial Scales in Particle‐in‐Cell Simulations and MMS Data
Authors: Wendel Deirdre E. , Liu Yi‐Hsin , Giles Barbara L. , Torbert Roy B. 
Published: February 2018

AbstractFor the first time, space flight technology exists to detect, in situ, violation of magnetic field line conservation. The violation of magnetic line conservation on scales smaller than the system size is a necessary and sufficient condition for finite magnetic field reconnection. We demonstrate that violation of line conservation produces a detectable, structured signature both in particle‐in‐cell simulations of reconnection and in data from the Magnetospheric Multi‐Scale mission. In particle‐in‐cell simulations of asymmetric reconnection, the quantity—which we call M—that identifies this violation achieves significant values in electron skin depth‐scale layers that extend away from the separator, with higher values emerging on the low‐density, high‐magnetic‐field side of the current sheet. At the separator, M owes largely to perpendicular gradients in the parallel electric field, while it attains its highest values away from the separator in dispersed, layered structures associated with gradients in the perpendicular nonideal electric field and electron transport. Sub‐ion scale bipolar forms of the quantity also appear further from the separator. In two MMS burst data intervals detecting the electron diffusion region, we find that M exceeds measurement uncertainties both at the separator and near the separatrices. One interval has highly sheared reconnecting fields and the other a stronger guide field. For one event, we determine the location and scale of M and the inner electron diffusion region relative to electron outflows and the magnetic separatrices. The measure can therefore serve as a potent diagnostic for magnetic reconnection in space measurements.
Determining L‐M‐N Current Sheet Coordinates at the Magnetopause From Magnetospheric Multiscale Data
Authors: Denton R. E. , Sonnerup B. U. Ö. , Russell C. T. , Hasegawa H. , Phan T.‐D. , Strangeway R. J. , Giles B. L. , Ergun R. E , Lindqvist P.‐A. , Torbert R. B. , Burch J. L , Vines S. K. 
Published: February 2018

AbstractWe discuss methods to determine L‐M‐N coordinate systems for current sheet crossings observed by the Magnetospheric Multiscale (MMS) spacecraft mission during ongoing reconnection, where eL is the direction of the reconnecting component of the magnetic field, B, and eN is normal to the magnetopause. We present and test a new hybrid method, with eL estimated as the maximum variance direction of B (MVAB) and eN as the direction of maximum directional derivative of B, and then adjust these directions to be perpendicular. In the best case, only small adjustment is needed. Results from this method, applied to an MMS crossing of the dayside magnetopause at 1305:45 UT on 16 October 2015, are discussed and compared with those from other methods for which eN is obtained by other means. Each of the other evaluations can be combined with eL from MVAB in a generalized hybrid approach to provide an L‐M‐N system. The quality of the results is judged by eigenvalue ratios, constancy of directions using different data segments and methods, and expected sign and magnitude of the normal component of B. For this event, the hybrid method appears to produce eN accurate to within less than 10°. We discuss variance analysis using the electric current density, J, or the J × B force, which yield promising results, and minimum Faraday residue analysis and MVAB alone, which can be useful for other events. We also briefly discuss results from our hybrid method and MVAB alone for a few other MMS reconnection events.
Observation and Numerical Simulation of Cavity Mode Oscillations Excited by an Interplanetary Shock
Authors: Takahashi Kazue , Lysak Robert , Vellante Massimo , Kletzing Craig A. , Hartinger Michael D. , Smith Charles W. 
Published: February 2018

AbstractCavity mode oscillations (CMOs) are basic magnetohydrodynamic eigenmodes in the magnetosphere predicted by theory and are expected to occur following the arrival of an interplanetary shock. However, observational studies of shock‐induced CMOs have been sparse. We present a case study of a dayside ultralow‐frequency wave event that exhibited CMO properties. The event occurred immediately following the arrival of an interplanetary shock at 0829 UT on 15 August 2015. The shock was observed in the solar wind by the Time History of Events and Macroscale Interactions during Substorms‐B and ‐C spacecraft, and magnetospheric ultralow‐frequency waves were observed by multiple spacecraft including the Van Allen Probe‐A and Van Allen Probe‐B spacecraft, which were located in the dayside plasmasphere at L ∼1.4 and L ∼ 2.4, respectively. Both Van Allen Probes spacecraft detected compressional poloidal mode oscillations at ∼13 mHz (fundamental) and ∼26 mHz (second harmonic). At both frequencies, the azimuthal component of the electric field (Eϕ) lagged behind the compressional component of the magnetic field (Bμ) by ∼90°. The frequencies and the Eϕ‐Bμ relative phase are in good agreement with the CMOs generated in a dipole magnetohydrodynamic simulation that incorporates a realistic plasma mass density distribution and ionospheric boundary condition. The oscillations were also detected on the ground by the European quasi‐Meridional Magnetometer Array, which was located near the magnetic field footprints of the Van Allen Probes spacecraft.
Jovian Auroral Ion Precipitation: Field‐Aligned Currents and Ultraviolet Emissions
Authors: Houston S. J. , Ozak N. , Young J. , Cravens T. E. , Schultz D. R. 
Published: February 2018

AbstractA model is described for the transport of magnetospheric oxygen ions with low charge state and energies up to several MeV/nucleon (MeV/u) as they precipitate into Jupiter's polar atmosphere. A revised and updated hybrid Monte Carlo model originally developed by Ozak et al. (2010, https://doi.org/10.1029/2010JA015635) is used to model the Jovian X‐ray aurora. The current model uses a wide range of incident oxygen ion energies (10 keV/u to 5 MeV/u) and the most up‐to‐date collision cross sections. In addition, the effects of the secondary electrons generated from the heavy ion precipitation are included using a two‐stream transport model that computes the secondary electron fluxes and their escape from the atmosphere. The model also determines H2 Lyman‐Werner band emission intensities, including a predicted spectrum and the associated color ratio. Implications of the new model results for interpretation of data from National Aeronautics and Space Administration's Juno mission are discussed. In particular, the model predicts that for a 2 MeV/u oxygen ion energy input of 10 mW/m2: (1) escaping electrons are produced with an energy range from 1 eV to 4 keV, which is a smaller range than previous models by Ozak et al. (2013, https://doi.org/10.1002/2013GL50812) predicted, (2) H2 band emission rates of 75 kR are generated, similar to previous estimates, and (3) a newly calculated Lyman and Werner band color ratio of 10 is expected. The color ratios are put into a context of various methane number density distributions.
A Census of Plasma Waves and Structures Associated With an Injection Front in the Inner Magnetosphere
Authors: Malaspina David M. , Ukhorskiy Aleksandr , Chu Xiangning , Wygant John 
Published: February 2018

AbstractNow that observations have conclusively established that the inner magnetosphere is abundantly populated with kinetic electric field structures and nonlinear waves, attention has turned to quantifying the ability of these structures and waves to scatter and accelerate inner magnetospheric plasma populations. A necessary step in that quantification is determining the distribution of observed structure and wave properties (e.g., occurrence rates, amplitudes, and spatial scales). Kinetic structures and nonlinear waves have broadband signatures in frequency space, and consequently, high‐resolution time domain electric and magnetic field data are required to uniquely identify such structures and waves as well as determine their properties. However, most high‐resolution fields data are collected with a strong bias toward high‐amplitude signals in a preselected frequency range, strongly biasing observations of structure and wave properties. In this study, an ∼45 min unbroken interval of 16,384 samples/s field burst data, encompassing an electron injection event, is examined. This data set enables an unbiased census of the kinetic structures and nonlinear waves driven by this electron injection, as well as determination of their “typical” properties. It is found that the properties determined using this unbiased burst data are considerably different than those inferred from amplitude‐biased burst data, with significant implications for wave‐particle interactions due to kinetic structures and nonlinear waves in the inner magnetosphere.
Stimulated Mirror Instability From the Interplay of Anisotropic Protons and Electrons, and their Suprathermal Populations
Authors: Shaaban S. M. , Lazar M. , Astfalk P. , Poedts S. 
Published: February 2018

AbstractMirror instability driven by the temperature anisotropy of protons can offer a plausible explanation for the mirror‐like fluctuations observed in planetary magnetosheaths. In the present paper we invoke a realistic kinetic approach which can reproduce nonthermal features of plasma particles reported by the observations, i.e., temperature anisotropies and suprathermal populations. Seeking accuracy, a numerical analysis is performed using an advanced code named DSHARK, recently proposed to resolve the linear dispersion and stability for an arbitrary propagation in bi‐Kappa distributed electron‐proton plasmas. The stimulating effect of the anisotropic bi‐Maxwellian electrons reported in Remya et al. (2013, https://doi.org/10.1002/jgra.50091) is markedly enhanced in the presence of suprathermal electrons described by the bi‐Kappa distribution functions. The influence of suprathermal protons is more temperate, but overall, present results demonstrate that these sources of free energy provide natural conditions for a stimulated mirror instability, more efficient than predicted before and capable to compete with other instabilities (e.g., the electromagnetic ion‐cyclotron instability) and mechanisms of relaxation.
Toward a Global Horizontal and Vertical Elastic Load Deformation Model Derived from GRACE and GNSS Station Position Time Series
Authors: Chanard Kristel , Fleitout Luce , Calais Eric , Rebischung Paul , Avouac Jean‐Philippe 
Published: February 2018

AbstractWe model surface displacements induced by variations in continental water, atmospheric pressure, and nontidal oceanic loading, derived from the Gravity Recovery and Climate Experiment (GRACE) for spherical harmonic degrees two and higher. As they are not observable by GRACE, we use at first the degree‐1 spherical harmonic coefficients from Swenson et al. (2008, https://doi.org/10.1029/2007JB005338). We compare the predicted displacements with the position time series of 689 globally distributed continuous Global Navigation Satellite System (GNSS) stations. While GNSS vertical displacements are well explained by the model at a global scale, horizontal displacements are systematically underpredicted and out of phase with GNSS station position time series. We then reestimate the degree 1 deformation field from a comparison between our GRACE‐derived model, with no a priori degree 1 loads, and the GNSS observations. We show that this approach reconciles GRACE‐derived loading displacements and GNSS station position time series at a global scale, particularly in the horizontal components. Assuming that they reflect surface loading deformation only, our degree‐1 estimates can be translated into geocenter motion time series. We also address and assess the impact of systematic errors in GNSS station position time series at the Global Positioning System (GPS) draconitic period and its harmonics on the comparison between GNSS and GRACE‐derived annual displacements. Our results confirm that surface mass redistributions observed by GRACE, combined with an elastic spherical and layered Earth model, can be used to provide first‐order corrections for loading deformation observed in both horizontal and vertical components of GNSS station position time series.
Crustal Structure of the Ionian Basin and Eastern Sicily Margin: Results From a Wide‐Angle Seismic Survey
Authors: Dellong David , Klingelhoefer Frauke , Kopp Heidrun , Graindorge David , Margheriti Lucia , Moretti Milena , Murphy Shane , Gutscher Marc‐Andre 
Published: February 2018

AbstractIn the Ionian Sea (central Mediterranean) the slow convergence between Africa and Eurasia results in the formation of a narrow subduction zone. The nature of the crust of the subducting plate remains debated and could represent the last remnants of the Neo‐Tethys ocean. The origin of the Ionian basin is also under discussion, especially concerning the rifting mechanisms as the Malta Escarpment could represent a remnant of this opening. This subduction retreats toward the south‐east (motion occurring since the last 35 Ma) but is confined to the narrow Ionian basin. A major lateral slab tear fault is required to accommodate the slab roll‐back. This fault is thought to propagate along the eastern Sicily margin but its precise location remains controversial. This study focuses on the deep crustal structure of the eastern Sicily margin and the Malta Escarpment. We present two two‐dimensional P wave velocity models obtained from forward modeling of wide‐angle seismic data acquired onboard the R/V Meteor during the DIONYSUS cruise in 2014. The results image an oceanic crust within the Ionian basin as well as the deep structure of the Malta Escarpment, which presents characteristics of a transform margin. A deep and asymmetrical sedimentary basin is imaged south of the Messina strait and seems to have opened between the Calabrian and Peloritan continental terranes. The interpretation of the velocity models suggests that the tear fault is located east of the Malta Escarpment, along the Alfeo fault system.
Land Ice Freshwater Budget of the Arctic and North Atlantic Oceans: 1. Data, Methods, and Results
Authors: Bamber J. L. , Tedstone A. J. , King M. D. , Howat I. M. , Enderlin E. M. , van den Broeke M. R. , Noel B. 
Published: February 2018

AbstractThe freshwater budget of the Arctic and sub‐polar North Atlantic Oceans has been changing due, primarily, to increased river runoff, declining sea ice and enhanced melting of Arctic land ice. Since the mid‐1990s this latter component has experienced a pronounced increase. We use a combination of satellite observations of glacier flow speed and regional climate modeling to reconstruct the land ice freshwater flux from the Greenland ice sheet and Arctic glaciers and ice caps for the period 1958–2016. The cumulative freshwater flux anomaly exceeded 6,300 ± 316 km3by 2016. This is roughly twice the estimate of a previous analysis that did not include glaciers and ice caps outside of Greenland and which extended only to 2010. From 2010 onward, the total freshwater flux is about 1,300 km3/yr, equivalent to 0.04 Sv, which is roughly 40% of the estimated total runoff to the Arctic for the same time period. Not all of this flux will reach areas of deep convection or Arctic and Sub‐Arctic seas. We note, however, that the largest freshwater flux anomalies, grouped by ocean basin, are located in Baffin Bay and Davis Strait. The land ice freshwater flux displays a strong seasonal cycle with summer time values typically around five times larger than the annual mean. This will be important for understanding the impact of these fluxes on fjord circulation, stratification, and the biogeochemistry of, and nutrient delivery to, coastal waters.
Lower‐Stratospheric Control of the Frequency of Sudden Stratospheric Warming Events
Authors: Martineau Patrick , Chen Gang , Son Seok‐Woo , Kim Joowan 
Published: February 2018

AbstractThe sensitivity of stratospheric polar vortex variability to the basic‐state stratospheric temperature profile is investigated by performing a parameter sweep experiment with a dry dynamical core general circulation model where the equilibrium temperature profiles in the polar lower and upper stratosphere are systematically varied. It is found that stratospheric variability is more sensitive to the temperature distribution in the lower stratosphere than in the upper stratosphere. In particular, a cold lower stratosphere favors a strong time‐mean polar vortex with a large daily variability, promoting frequent sudden stratospheric warming events in the model runs forced with both wavenumber‐1 and wavenumber‐2 topographies. This sensitivity is explained by the control exerted by the lower‐stratospheric basic state onto fluxes of planetary‐scale wave activity from the troposphere to the stratosphere, confirming that the lower stratosphere can act like a valve for the upward propagation of wave activity. It is further shown that with optimal model parameters, stratospheric polar vortex climatology and variability mimicking Southern and Northern Hemisphere conditions are obtained with both wavenumber‐1 and wavenumber‐2 topographies.