bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionospheric conductances and currents of a morning sector auroral arc from Swarm‐A electric and magnetic field measurements
Authors: Juusola L. , Archer W. E. , Kauristie K. , Burchill J. K. , Vanhamäki H. , Aikio A. T. 
Published: September 2016

AbstractWe show the first ionospheric Hall and Pedersen conductances derived from Swarm magnetic and electric field measurements during a crossing of a morning sector auroral arc. Only Swarm‐A was used, with assumptions of negligible azimuthal gradients and vanishing eastward electric field. We find upward field‐aligned current, enhanced Hall and Pedersen conductances, and relatively weak electric field coincident with the arc. Poleward of the arc, the field‐aligned current was downward, conductances lower, and the electric field enhanced. The arc was embedded in a westward electrojet, immediately equatorward of the peak current density. The equatorward portion of the electrojet could thus be considered conductance dominant and the poleward portion electric field dominant. Although the electric field measured by Swarm was intense, resulting in conductances lower than those typically reported, comparable electric fields have been observed earlier. These results demonstrate how Swarm data can significantly contribute to our understanding of the ionospheric electrodynamics.
Artificial bias typically neglected in comparisons of uncertain atmospheric data
Authors: Pitkänen Mikko R. A. , Mikkonen Santtu , Lehtinen Kari E. J. , Lipponen Antti , Arola Antti 
Published: September 2016

AbstractPublications in atmospheric sciences typically neglect biases caused by regression dilution (bias of the ordinary least squares line fitting) and regression to the mean (RTM) in comparisons of uncertain data. We use synthetic observations mimicking real atmospheric data to demonstrate how the biases arise from random data uncertainties of measurements, model output, or satellite retrieval products. Further, we provide examples of typical methods of data comparisons that have a tendency to pronounce the biases. The results show, that data uncertainties can significantly bias data comparisons due to regression dilution and RTM, a fact that is known in statistics but disregarded in atmospheric sciences. Thus, we argue that often these biases are widely regarded as measurement or modeling errors, for instance, while they in fact are artificial. It is essential that atmospheric and geoscience communities become aware of and consider these features in research.
Understanding the ion distributions near the boundaries of reconnection outflow region
Authors: Zhou Xu‐Zhi , Pan Dong‐Xiao , Angelopoulos Vassilis , Runov Andrei , Zong Qiu‐Gang , Pu Zu‐Yin 
Published: September 2016

AbstractAn interesting signature observed shortly after the onset of magnetotail reconnection is the gradual appearance of a local peak of ion phase space density (PSD) in the duskward and downstream direction separated from the colder, nearly isotropic ion population. Such a characteristic ion distribution, served as a diagnostic signature of magnetotail reconnection and well reproduced by a particle‐tracing Liouville simulation, are found to appear only near the off‐equatorial boundaries of the reconnection outflow region. Further analysis on ion trajectories suggests that the ions within the local peak and within the neighboring PSD cleft both belong to the outflowing population; on top of their outflowing motion, they both meander across the neutral sheet to exhibit duskward velocities near the off‐equatorial edges of their trajectories. The difference between them is that the local peak originates from ions previously constituting the preonset plasma sheet, whereas the cleft corresponds to the inflowing lobe ions before they are repelled in the downstream direction. As reconnection proceeds, the local PSD peak gradually attenuates and then disappears, which is a signature of reconnection flushing effect that depletes the ions in the preonset plasma sheet and eventually replaces them by lobe ions.
Magnetotelluric tensors, electromagnetic field scattering and distortion in three‐dimensional environments
Authors: Brown Colin 
Published: September 2016

AbstractThis paper describes how subsurface resistivity distributions can be estimated directly from the magnetotelluric (MT) tensor relationship between electric and magnetic fields observed on a three‐dimensional (3‐D) half‐space. It presents an inhomogeneous plane wave analogy where relationships between horizontal electric and magnetic fields, and an apparent current density define an apparent resistivity tensor constructed from a quadratic function of the MT tensor. An extended‐Born relationship allows the electric field to be normalized with respect to an apparent background current density. The model is generalized by including the vertical magnetic field in a 3 by 3 MT response tensor. A complex apparent wave number tensor, constructed from this tensor, has eigenvalues which, using the plane wave analogy, are the vertical wave numbers associated with the eigenpolarizations of propagating waves in the model half space. The elements associated with the vertical magnetic field transfer function define the horizontal wave numbers. An extended 3 by 3 phase tensor contains four elements of the conventional 2 by 2 phase tensor and two elements associated with the vertical magnetic transfer function. The extended phase tensor and a single real distortion tensor with six independent elements can be used to quantify static electric and magnetic field distortions. The approach provides a theoretical basis for visualization and migration of MT data, in comparison with results from other electrical and EM techniques, a starting point for constrained 3‐D inversions, and an assessment of results with other geophysical and geological data.
A method for determining transverse permeability of tight reservoir cores by radial pressure pulse decay measurement
Authors: Yang Zehao , Dong Mingzhe , Zhang Shaojie , Gong Houjian , Li Yajun , Long Feifei 
Published: September 2016

AbstractA transverse pressure pulse decay (TPPD) method is presented to measure transverse permeability of tight reservoir cores in a cell with finite volume. Given appropriate assumptions, a mathematical model based on the specially designed experiment is formulated, and its general solution is proposed. Early‐time and late‐time techniques are further presented for convenient postprocessing applications of experimental data. Meanwhile, sensitivity analysis of TPPD method is given. It is found that a good TPPD experimental principle can be obtained by adjusting test gas, experimental pressure, dimension of core sample, and volume ratio (λ). The volume ratio error (λerror) analysis reveals the following: (1) a larger λerror results in increased transverse permeability error (kerror); (2) the volume ratio (λ) is better not very close to 0.754; (3) when λ is equal to or greater than 1, the kerror resulting from λerror is monotonic decreasing as the volume ratio increases. In practice, λ is usually equal to or greater than 1 due to the very small pore volume of a tight core. But this does not mean that the volume ratio should be as large as possible. The reason for this is that a pressure transducer with higher resolution is needed to record pressure change. That means experimental apparatus is much more costly. And such a TPPD experiment requires a much longer time to attain the late‐time straight line behavior. The best choice is to find an optimal balance point among experimental cost, time, and accuracy.
Enhanced waveguide effect for deep‐focus earthquakes in the subducting Pacific slab produced by a metastable olivine wedge
Authors: Furumura Takashi , Kennett Brian L. N. , Padhy Simanchal 
Published: September 2016

AbstractDeep‐focus (>400 km) earthquakes in the subducting Pacific slab produce areas of anomalously large and lengthy shaking along the fore‐arc (Pacific ocean) side of northern Japan. This effect arises because the slab acts as an efficient waveguide for seismic waves from earthquakes at depth within the slab. The mechanism of such slab‐induced waveguide effect can be explained by efficient propagation of seismic waves in a cold and low‐attenuation (high Q) slab, with multiple forward scattering of high‐frequency (>1 Hz) waves in a quasi‐laminar stochastic waveguide. In this study, we demonstrate an additional mechanism to enhance the waveguide effect for deeper events, which is caused by reduction of the seismic wave speed in a metastable olivine wedge (MOW) in the core of the slab for depths between 400 and 600 km. We present evidence for the presence of the low‐wave speed MOW from analysis of broadband waveforms of deep‐focus earthquakes in the Pacific slab descending beneath the Sea of Japan. For events below 400 km depth, low‐frequency and slightly dispersed P and S phases arrive ahead of the most energetic high‐frequency direct phases. Numerical simulations of high‐frequency seismic wave propagation for both 2‐D and 3‐D heterogeneous subduction zone models demonstrate a strong waveguide effect from the MOW due to focusing of high‐frequency seismic waves toward the up‐dip direction in the slab. The presence of the metastable olivine in slabs allows the development of very large and lengthy ground motion for stations on the fore‐arc side of northern Japan in good agreement with the observations.
Cross‐shelf water exchange in the East China Sea as estimated by satellite altimetry and in situ hydrographic measurement
Authors: Ding Ruibin , Huang Daji , Xuan Jiliang , Mayer Bernhard , Zhou Feng , Pohlmann Thomas 
Published: September 2016

AbstractCombining satellite altimetry and in situ hydrographic measurement, we estimated the cross‐shelf transport (CST) and its spatial and temporal variations across 200 m isobath in the East China Sea (ECS) from 1993 to 2014. The vertically integrated CST can be dynamically divided into three parts: surface Ekman transport, geostrophic transport, and bottom Ekman transport. The results show that the 22 year‐mean, sectionally integrated CST to be 1.7 ± 2.0 Sv (positive in the on‐shelf direction), comprised of bottom and surface Ekman transports of 2.7 ± 1.0 Sv and 0.6 ± 0.6 Sv, respectively, that are partially offset by a geostrophic transport of −1.5 ± 1.7 Sv. The sectionally integrated CST shows significantly high power at roughly annual period from 1999 to 2001, with lower power at intra‐annual period. The vertically integrated CST to the northeast of Taiwan is the main source of sectionally integrated CST. The vertically integrated CST also shows significant variations in the 6–15 month period band to the northeast of Taiwan as well. The temporal variations of the sectionally integrated and vertically integrated CST are both controlled primarily by geostrophic transport and modulated by bottom Ekman transport. In the upper 50 m, the geostrophic current to the northeast of Taiwan exhibits large mean and significant variability. The empirical orthogonal function analysis of vertical structure of geostrophic current shows two significant modes with strong annual signal. The first mode is associated with the migration of Kuroshio axis near Taiwan, while the second mode is associated with the variation of the meander of the Kuroshio to the northeast of Taiwan.
Chemical and dynamical impacts of stratospheric sudden warmings on Arctic ozone variability
Authors: Strahan S. E. , Douglass A. R. , Steenrod S. D. 
Published: September 2016

AbstractWe use the Global Modeling Initiative (GMI) chemistry and transport model with Modern‐Era Retrospective Analysis for Research and Applications (MERRA) meteorological fields to quantify heterogeneous chemical ozone loss in Arctic winters 2005–2015. Comparisons to Aura Microwave Limb Sounder N2O and O3 observations show the GMI simulation credibly represents the transport processes and net heterogeneous chemical loss necessary to simulate Arctic ozone. We find that the maximum seasonal ozone depletion varies linearly with the number of cold days and with wave driving (eddy heat flux) calculated from MERRA fields. We use this relationship and MERRA temperatures to estimate seasonal ozone loss from 1993 to 2004 when inorganic chlorine levels were in the same range as during the Aura period. Using these loss estimates and the observed March mean 63–90°N column O3, we quantify the sensitivity of the ozone dynamical resupply to wave driving, separating it from the sensitivity of ozone depletion to wave driving. The results show that about 2/3 of the deviation of the observed March Arctic O3 from an assumed climatological mean is due to variations in O3 resupply and 1/3 is due to depletion. Winters with a stratospheric sudden warming (SSW) before mid‐February have about 1/3 the depletion of winters without one and export less depletion to the midlatitudes. However, a larger effect on the spring midlatitude ozone comes from dynamical differences between warm and cold Arctic winters, which can mask or add to the impact of exported depletion.
Atmospheric structure favoring high sea surface temperatures in the western equatorial Pacific
Authors: Wirasatriya Anindya , Kawamura Hiroshi , Shimada Teruhisa , Hosoda Kohtaro 
Published: September 2016

AbstractWe investigated the atmospheric processes over high sea surface temperature called Hot Event (HE) in the western equatorial Pacific from climatological analysis and a case study of the HE which began on 28 May 2003 (hereafter, HE030528). Climatological analysis shows that during the development stage of HE, solar radiation inside the HE area is higher than its climatology and wind speed is lower than the decay stage. During the decay stage, strong westerly wind often occurs inside HE area. The case study of HE030528 shows that the suppressed convection above high SST area resulted from the deep convection from the northern and southern areas outside HE. The suppressed convection created a band‐shaped structure of low cloud cover along HE area increasing solar radiation during the development stage. Thus, the theory of “remote convection” was supported for the HE030528 formation mechanisms. The large sea level pressure gradient magnitude between the southern side of the terrain gap and the northern coast of the Solomon Islands, through which strong wind blew, indicated the role of land topography for the increase of wind speed during the decay of HE030528. Moreover, surface wind had an important role to influence the variability of solar radiation during the occurrence of HE030528 by controlling the water vapor supply in the upper troposphere through surface evaporation and surface convergence variation. Thus, surface wind was the key factor for HE030528 occurrence. The representativeness of HE030528 and the possible relation between HE and Madden‐Julian Oscillation are also discussed.
Percolation theory for solute transport in porous media: Geochemistry, geomorphology, and carbon cycling
Authors: Hunt Allen G. , Ghanbarian Behzad 
Published: September 2016

AbstractUnderstanding the time‐dependent scaling of chemical weathering has been a significant research goal for over a decade. A percolation theoretical treatment of nonreactive solute transport that was previously shown compatible with the scaling of chemical weathering rates is here shown to be compatible with soil formation rates, and with C and N sequestration rates in the soil as well. In this theoretical framework, the percolation backbone fractal dimensionality, which generates the long‐time tail of the solute arrival time distribution, also predicts the scaling of the reaction rates, while laboratory proportionality to the fluid flow velocity translates to an analogous relevance of the vertical infiltration rate in the field. The predicted proportionality of solute transport to net infiltration generates simultaneously the variability in soil formation rates across 4 orders of magnitude of precipitation and 12 orders of magnitude of time scales.
Disordered Proteins
Authors: DeForte Shelly , Uversky Vladimir N 
Published: September 2016

Abstract

Intrinsically disordered proteins (IDPs) and disordered protein regions (IDPRs) do not have a specific three‐dimensional (3D) structure in their unbound states under physiological conditions, existing instead as dynamic structural ensembles. There are also subtler categories of disorder, such as conditional (or dormant) disorder and partial disorder. Both the ability of a protein/region to fold and the predisposition to stay intrinsically disordered are encoded in the amino acid sequence. Structurally, IDPs/IDPRs are characterised by high spatiotemporal heterogeneity. It is important to remember, however, that although structure and disorder are often treated as binary states, they actually sit on a structural continuum. Functionally, IDPs/IDPRs are often characterised by the ability to multitask and be promiscuous binders. The field of unstructural biology has arisen to explain proteins that fall outside of the classical structure–function paradigm. A major goal in the coming years will be to understand sequence‐to‐function relationships for disordered proteins.

Key Concepts

Many biologically important protein regions fail to form specific three‐dimensional (3D) structures in their unbound states under physiological conditions.

Amino acid sequences of these intrinsically disordered proteins (IDPs) are noticeably different from sequences of ordered proteins and reliable predictors can be developed to distinguish the tendency of a protein to be structured or disordered.

IDPs are highly abundant in nature and have numerous functions that complement the functional repertoire of ordered proteins.

IDPs are characterised by high structural heterogeneity, and there is a structural continuum, with highly ordered proteins on one end and highly disordered proteins on the other.

IDPs/IDPRs are commonly found in various human diseases where they often play crucial roles in pathogenesis.

IDPs are crucial constituents of various membraneless organelles abundantly found in the cytoplasm and nucleoplasm of eukaryotic cells.
Cystic Fibrosis: Modifier Genes
Authors: Saferali Aabida , Turvey Stuart E , Sandford Andrew J 
Published: September 2016

Abstract

Cystic fibrosis (CF) is a rare autosomal recessive disease that causes early death through respiratory failure. Although it is known that CF is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (
CFTR
) it has been found that other genetic factors make a large contribution to the severity of lung disease as well as several other CF traits. Several large‐scale genomewide association studies have been performed for CF lung disease severity, body mass index/nutritional status, CF‐related diabetes, meconium ileus and age of onset of chronic
Pseudomonas aeruginosa
infection. Several genes have been identified that modulate CF disease severity. In particular, apical membrane constituents have been associated with several phenotypes including lung function, meconium ileus and age of onset of
P. aeruginosa
infection. The results of these studies have provided insight into the pathophysiology of CF and have identified novel therapeutic targets.

Key Concepts

Lung disease severity in CF, along with several other CF traits, is influenced by non‐
CFTR
genetic factors.

Genomewide association studies and linkage analysis have identified several genes associated with CF severity.

Meta‐analysis of several patient cohorts is required to identify reproducible findings.

Apical membrane constituents, in particular
SLC6A14
,
SLC26A9
and
SLC9A3
, are a class of molecules associated with several CF phenotypes.

Exome‐wide sequencing can be used as an alternative approach to discover novel modifier genes.
Phloem Long‐Distance Trafficking of
RNAs
and Proteins
Authors: Xoconostle‐Cázares Beatriz , Martínez‐Navarro Angélica C , Ruiz‐Medrano Roberto 
Published: September 2016

Abstract

The vascular tissue has been essential for the evolutionary radiation of land plants, and has allowed them to colonise a wide range of habitats. The phloem is involved in the distribution of fixed carbon throughout the whole plant. The concept of this tissue as a central distributor of signals that regulate plant development and responses to environmental cues has emerged recently. Indeed, several phenomena, such as post‐transcriptional gene silencing, flowering and tuber induction, as well as systemic acquired resistance to pathogens rely on signals, originating in source leaves, and transported via the phloem to systemic tissues. Considering that the phloem translocation stream contains a large array of macromolecules. Given that the functional phloem consists of interconnected enucleate cells, the sieve elements (SEs), the majority of proteins and ribonucleic acids (RNAs) found in phloem sap exudates must originate from the adjoining companion cell (CC). While several proteins play a role in the maintenance of the SEs, it is possible that several species of proteins and RNAs function in long‐distance signalling. In this article the current state of the art of this subject is described, as well as perspectives and possible applications for crop improvement.

Key Concepts

The vascular tissue consists of xylem and phloem.

The xylem is composed of vessels that are dead cells upon maturity that transport mineral nutrients from roots to shoots.

The phloem is composed of vessels formed from enucleated living cells involved in the transport of fixed carbon from photosynthetic to heterotrophic organs.

The phloem is involved in the delivery of signals that control development as well as responses to external stimuli, such as defence response, post‐transcriptional gene silencing and response to phosphate starvation.

Viruses and viroids are transported through the phloem during systemic infection.

These probably take advantage of a system enabling long‐distance transport of endogenous proteins and RNAs.

The phloem translocation stream contains a wide variety of proteins and RNAs, some of which appear to have a signalling function.

RNA and protein exchange can occur between plant pathogenic fungi and parasitic plants and their hosts.

Knowledge of this RNA and protein phloem transport system can have applications for crop improvement.