bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of sudden electron density depletions observed in the dusk sector by the Poker Flat, Alaska incoherent scatter radar in summer
Authors: Richards P. G. , Nicolls M. J. , St.‐Maurice J.‐P. , Goodwin L. , Ruohoniemi J. M. 
Published: December 2014

AbstractThis paper investigates unusually deep and sudden electron density depletions (troughs) observed in the Poker Flat (Alaska) Incoherent Scatter Radar data in middle summer of 2007 and 2008. The troughs were observed in the premidnight sector during periods of weak magnetic and solar activity. The density recovered to normal levels around midnight. At the time when the electron density was undergoing its steep decrease, there was usually a surge of the order of 100 to 400 K in the ion temperature that lasted less than 1 h. The Ti surges were usually related to similar surges in the AE index, indicating that the high‐latitude convection pattern was expanding and intensifying at the time of the steep electron density drop. The convection patterns from the Super Dual Auroral Radar Network also indicate that the density troughs were associated with the expansion of the convection pattern to Poker Flat. The sudden decreases in the electron density are difficult to explain in summer because the high‐latitude region remains sunlit for most of the day. This paper suggests that the summer density troughs result from lower latitude plasma that had initially been corotating in darkness for several hours post sunset and brought back toward the sunlit side as the convection pattern expanded. The magnetic declination of ~22° east at 300 km at Poker Flat greatly facilitates the contrast between the plasma convecting from lower latitudes and the plasma that follows the high‐latitude convection pattern.
The effect of primary versus secondary processes on the volatile content of MORB glasses: An example from the equatorial Mid‐Atlantic Ridge (5°N–3°S)
Authors: Le Voyer Marion , Cottrell Elizabeth , Kelley Katherine A. , Brounce Maryjo , Hauri Erik H. 
Published: December 2014

AbstractWe report microanalysis of volatile and trace element compositions, as well as Fe3+/ΣFe ratios, from 45 basaltic glasses from cruise RC2806 along the equatorial Mid‐Atlantic Ridge. The along‐strike variations in volatiles result from the complex geodynamical setting of the area, including numerous transform faults, variations in ridge depth, melting degree, and source composition. The strongest gradient is centered on 1.7°N and encompasses an increase of H2O, Cl, and F contents as well as high F/Zr ratio spatially coincident with radiogenic isotope anomalies. We interpret these variations as source enrichment due to the influence of the nearby high‐μ‐type Sierra Leone plume. South of the St. Paul fracture zone, H2O and F contents, as well as H2O/Ce and F/Zr ratios, decrease progressively. This gradient in volatiles is consistent with progressive dilution of an enriched component in a heterogeneous mantle due to the progressive increase in the degree of melting. These two large‐scale gradients are interrupted by small‐scale anomalies in volatile contents attributed to (1) low‐degree melts preferentially sampling enriched heterogeneities near transform faults and (2) local assimilation of hydrothermal fluids in four samples from dredge 16D. Finally, 20 RC2806 samples described as “popping rocks” during collection do not show any difference in volatile content dissolved in the glass or in vesicularity when compared to the RC2806 “nonpopping” samples. Our observations lead us to question the interpretation of the CO2 content in the highly vesicular 2πD43 “popping rock” as being representative of the CO2 content of undegassed mid‐ocean ridge basalt.
Effects of three‐dimensional crustal structure and smoothing constraint on earthquake slip inversions: Case study of the Mw6.3 2009 L'Aquila earthquake
Authors: Gallovič František , Imperatori Walter , Mai P. Martin 
Published: December 2014

AbstractEarthquake slip inversions aiming to retrieve kinematic rupture characteristics typically assume 1‐D velocity models and a flat Earth surface. However, heterogeneous nature of the crust and presence of rough topography lead to seismic scattering and other wave propagation phenomena, introducing complex 3‐D effects on ground motions. Here we investigate how the use of imprecise Green's functions—achieved by including 3‐D velocity perturbations and topography—affect slip‐inversion results. We create sets of synthetic seismograms, including 3‐D heterogeneous Earth structure and topography, and then invert these synthetics using Green's functions computed for a horizontally layered 1‐D Earth model. We apply a linear inversion, regularized by smoothing and positivity constraint, and examine in detail how smoothing effects perturb the solution. Among others, our tests and resolution analyses demonstrate how imprecise Green's functions introduce artificial slip rate multiples especially at shallow depths and that the timing of the peak slip rate is hardly affected by the chosen smoothing. The investigation is extended to recordings of the 2009 Mw6.3 L'Aquila earthquake, considering both strong motion and high‐rate GPS stations. We interpret the inversion results taking into account the lessons learned from the synthetic tests. The retrieved slip model resembles previously published solutions using geodetic data, showing a large‐slip asperity southeast of the hypocenter. In agreement with other studies, we find evidence for fast but subshear rupture propagation in updip direction, followed by a delayed propagation along strike. We conjecture that rupture was partially inhibited by a deep localized velocity‐strengthening patch that subsequently experienced afterslip.
Three‐dimensional shear velocity anisotropic model of Piton de la Fournaise Volcano (La Réunion Island) from ambient seismic noise
Authors: Mordret Aurélien , Rivet Diane , Landès Matthieu , Shapiro Nikolaï M. 
Published: December 2014

AbstractWe cross correlate 4 years of seismic noise from the seismic network of Piton de la Fournaise Volcano (La Réunion Island) to measure the group velocity dispersion curves of Rayleigh and Love waves. We average measurements from vertical and radial components to obtain 577 Rayleigh wave dispersion curves. The transverse components provided 395 Love wave dispersion curves. We regionalize the group velocities measurements into 2‐D velocity maps between 0.4 and 8 s. Finally, we locally inverted these maps for a pseudo 3‐D anisotropic shear‐velocity model down to 3 km below the sea level using a Neighborhood Algorithm. The 3‐D isotropic shear‐wave model shows three distinct high‐velocity anomalies surrounded by a low‐velocity ring. The anomaly located below the present “Plaine des Sables” could be related to an old intrusive body at the location of the former volcanic center before it migrated toward its present location. The second high‐velocity body located below the summit of the volcano likely corresponds to the actual preferential dyke intrusion zone as highlighted by the seismicity. The third high‐velocity anomaly located below the “Grandes Pentes” and the “Grand Brûlé” areas and is an imprint of the solidified magma chamber of the dismantled “Les Alizés” Volcano. Radial anisotropy shows two main anomalies: positive anisotropy above sea level highlighting the recent edifice of Piton de la Fournaise with an accumulation of horizontal lava flows and the second one below the sea level with a negative anisotropy corresponding to the ancient edifice of Piton de la Fournaise dominated by intrusions of vertical dykes.
Moored observations of synoptic and seasonal variability in the East Greenland Coastal Current
Authors: Harden B. E. , Straneo F. , Sutherland D. A. 
Published: December 2014

AbstractWe present a year‐round assessment of the hydrographic variability within the East Greenland Coastal Current on the Greenland shelf from five synoptic crossings and 4 years of moored hydrographic data. From the five synoptic sections the current is observed as a robust, surface intensified flow with a total volume transport of 0.66 ± 0.18 Sv and a freshwater transport of 42 ± 12 mSv. The moorings showed heretofore unobserved variability in the abundance of Polar and Atlantic water masses in the current on synoptic scales. This is exhibited as large vertical displacement of isotherms (often greater than 100 m). Seasonally, the current is hemmed into the coast during the fall by a full depth Atlantic Water layer that has penetrated onto the inner shelf. The Polar Water layer in the current then thickens through the winter and spring seasons increasing the freshwater content in the current; the timing implies that this is probably driven by the seasonally varying export of freshwater from the Arctic and not the local runoff from Greenland. The measured synoptic variability is enhanced during the winter and spring period due to a lower halocline and a concurrent enhancement in the along‐coast wind speed. The local winds force much of the high‐frequency variability in a manner consistent with downwelling, but variability distinct from downwelling is also visible.
Seasonal and interannual oxygen variability on the Washington and Oregon continental shelves
Authors: Siedlecki S. A. , Banas N. S. , Davis K. A. , Giddings S. , Hickey B. M. , MacCready P. , Connolly T. , Geier S. 
Published: December 2014

AbstractThe coastal waters of the northern portion of the California Current System experience a seasonal decline in oxygen concentrations and hypoxia over the summer upwelling season that results in negative impacts on habitat for many organisms. Using a regional model extending from 43°N to 50°N, with an oxygen component developed in this study, drivers of seasonal and regional oxygen variability are identified. The model includes two pools of detritus, which was an essential addition in order to achieve good agreement with the observations. The model was validated using an extensive array of hydrographic and moored observations. The model captures the observed seasonal decline as well as spatial trends in bottom oxygen. Spatially, three regions of high respiration are identified as locations where hypoxia develops each modeled year. Two of the regions are previously identified recirculation regions. The third region is off of the Washington coast. Sediment oxygen demand causes the region on the Washington coast to be susceptible to hypoxia and is correlated to the broad area of shallow shelf (<60 m) in the region. Respiration and circulation‐driven divergence contribute similar (60, 40%, respectively) amounts to the integrated oxygen budget on the Washington coast while respiration dominates the Oregon coast. Divergence, or circulation, contributes to the oxygen dynamics on the shelf in two ways: first, through the generation of retention features, and second, by determining variability.
Comprehensive study of emission source contributions for tropospheric ozone formation over East Asia
Authors: Itahashi Syuichi , Hayami Hiroshi , Uno Itsushi 
Published: December 2014

AbstractEmission source contributions of tropospheric ozone (O3) were comprehensively investigated by using the higher‐order decoupled direct method (HDDM) for sensitivity analysis and the ozone source apportionment technology (OSAT) for mass balance analysis in the comprehensive air‐quality model with extensions (CAMx). The response of O3 to emissions reductions at various levels in mainland China, Korea, and Japan were estimated and compared with results calculated by the brute force method (BFM) where one model parameter is varied at a time. Emissions were assessed at three receptor sites in Japan that experienced severe pollution events in May 2009. For emissions from China, HDDM assessed O3 response with a bias of only up to 3 ppbv (a relative error of 4.5%) even for a 50% reduction but failed to assess a more extreme reduction. OSAT was reasonably accurate at 100% reduction, with a −4 ppbv (−7%) bias, but was less accurate at moderate ranges of reduction (∼50–70%). For emissions from Korea and Japan, HDDM captured the nonlinear response at all receptor sites and at all reduction levels to within 1% in all but one case; however, the bias of OSAT increased with the increasing reduction of emissions. One possible reason for this is that OSAT does not account for NO titration. To address this, a term for potential ozone (PO; O3 and NO2 together) was introduced. Using of PO instead of O3 improved the performance of OSAT, especially for emissions reductions from Korea and Japan. The proposed approach with PO refined the OSAT results and did not degrade HDDM performance.
The Victoria mode in the North Pacific linking extratropical sea level pressure variations to ENSO
Authors: Ding Ruiqiang , Li Jianping , Tseng Yu‐heng , Sun Cheng , Guo Yipeng 
Published: December 2014

AbstractThe Victoria mode (VM) represents the second dominant mode (empirical orthogonal function, EOF2) of North Pacific variability, independent of the Pacific Decadal Oscillation and is defined as the EOF2 of SST anomalies in the North Pacific poleward of 20°N. The present study indicates that the VM is closely linked to the development of El Niño–Southern Oscillation (ENSO). The VM may effectively act as an ocean bridge (or conduit) through which the extratropical atmospheric variability in the North Pacific influences ENSO. The VM can trigger the onset of ENSO via the following two dominant processes: (1) surface air‐sea coupling associated with the VM in the subtropical/tropical Pacific and (2) evolution of subsurface ocean temperature anomalies along the equator associated with the VM. These two processes may force sufficient surface warming to occur in the central eastern equatorial Pacific from spring to summer, which in turn initiates an ENSO event. The VM influence on ENSO relies on a basin‐scale air‐sea interaction dynamic, as opposed to more local‐scale dynamics typically associated with the seasonal footprinting mechanism or Pacific meridional mode. The majority of VM events are followed by ENSO events. These ENSO events triggered by VM include El Niño Modoki (EM) as well as conventional El Niño. There is no evidence that the VM tends to be more conducive to the initialization of EM than conventional El Niño.
Toward quantification and source sector identification of fossil fuel CO2 emissions from an urban area: Results from the INFLUX experiment
Authors: Turnbull Jocelyn C. , Sweeney Colm , Karion Anna , Newberger Timothy , Lehman Scott J. , Tans Pieter P. , Davis Kenneth J. , Lauvaux Thomas , Miles Natasha L. , Richardson Scott J. , Cambaliza Maria Obiminda , Shepson Paul B. , Gurney Kevin , Patarasuk Risa , Razlivanov Igor 
Published: December 2014

AbstractThe Indianapolis Flux Experiment (INFLUX) aims to develop and assess methods for quantifying urban greenhouse gas emissions. Here we use CO2, 14CO2, and CO measurements from tall towers around Indianapolis, USA, to determine urban total CO2, the fossil fuel derived CO2 component (CO2ff), and CO enhancements relative to background measurements. When a local background directly upwind of the urban area is used, the wintertime total CO2 enhancement over Indianapolis can be entirely explained by urban CO2ff emissions. Conversely, when a continental background is used, CO2ff enhancements are larger and account for only half the total CO2 enhancement, effectively representing the combined CO2ff enhancement from Indianapolis and the wider region. In summer, we find that diurnal variability in both background CO2 mole fraction and covarying vertical mixing makes it difficult to use a simple upwind‐downwind difference for a reliable determination of total CO2 urban enhancement. We use characteristic CO2ff source sector CO:CO2ff emission ratios to examine the contribution of the CO2ff source sectors to total CO2ff emissions. This method is strongly sensitive to the mobile sector, which produces most CO. We show that the inventory‐based emission product (“bottom up”) and atmospheric observations (“top down”) can be directly compared throughout the diurnal cycle using this ratio method. For Indianapolis, the top‐down observations are consistent with the bottom‐up Hestia data product emission sector patterns for most of the diurnal cycle but disagree during the nighttime hours. Further examination of both the top‐down and bottom‐up assumptions is needed to assess the exact cause of the discrepancy.
Diagenesis and clay mineral formation at Gale Crater, Mars
Authors: Bridges J. C. , Schwenzer S. P. , Leveille R. , Westall F. , Wiens R. C. , Mangold N. , Bristow T. , Edwards P. , Berger G. 
Published: December 2014

AbstractThe Mars Science Laboratory rover Curiosity found host rocks of basaltic composition and alteration assemblages containing clay minerals at Yellowknife Bay, Gale Crater. On the basis of the observed host rock and alteration minerals, we present results of equilibrium thermochemical modeling of the Sheepbed mudstones of Yellowknife Bay in order to constrain the formation conditions of its secondary mineral assemblage. Building on conclusions from sedimentary observations by the Mars Science Laboratory team, we assume diagenetic, in situ alteration. The modeling shows that the mineral assemblage formed by the reaction of a CO2‐poor and oxidizing, dilute aqueous solution (Gale Portage Water) in an open system with the Fe‐rich basaltic‐composition sedimentary rocks at 10–50°C and water/rock ratio (mass of rock reacted with the starting fluid) of 100–1000, pH of ~7.5–12. Model alteration assemblages predominantly contain phyllosilicates (Fe‐smectite, chlorite), the bulk composition of a mixture of which is close to that of saponite inferred from Chemistry and Mineralogy data and to that of saponite observed in the nakhlite Martian meteorites and terrestrial analogues. To match the observed clay mineral chemistry, inhomogeneous dissolution dominated by the amorphous phase and olivine is required. We therefore deduce a dissolving composition of approximately 70% amorphous material, with 20% olivine, and 10% whole rock component.
Protein Databases: Operations, Possibilities and Challenges
Authors: Valencia Alfonso 
Published: December 2014

Abstract

The information on protein function, as essential component of biological systems, is essential for the development of biology and biomedicine. The information on proteins is organised in databases that store their sequences, domain organisation, three‐dimensional structures, posttranslational modifications, interactions, molecular functions and other protein features. This information is combined with the proper bioinformatics methods to address complex biological problems. The annotation of splice isoforms is used as a current example of the use of information from central protein databases. Instead of offering a mere catalogue of the many protein databases, which status is periodically reviewed and maintained in ‘The Molecular Biology Database Collection’ (
http://www.oxfordjournals.org/nar/database/c/
), this article reviews the operations necessary to organise and make openly accessible their information as part of the complex ecosystems of bioinformatics infrastructures. Finally, this article revises the main challenges that their sustainability represents.

Key Concepts:

Functional annotation is a process of assigning function to a protein based on the experimental evidence published in the literature or transferred from other proteins with similar sequences.

Process of adding information to database entries by groups of experts typically associated to large databases is known as database curation.

Information transfer is a process of assigning functions or functional characteristics to protein sequences based on the annotations of similar – in most cases orthologos – sequences.

Combining annotations from different publications and database to produce a representative description of protein characteristics and functional properties is known as information integration.

Bioinformatics infrastructure is the collection of databases, bioinformatics methods, and computational resources that provide the essential support to the work of biologists.
Decoding upper limb residual muscle activity in severe chronic stroke
Authors: Ramos‐Murguialday Ander , García‐Cossio Eliana , Walter Armin , Cho Woosang , Broetz Doris , Bogdan Martin , Cohen Leonardo G. , Birbaumer Niels 
Published: December 2014

AbstractObjectiveStroke is a leading cause of long‐term motor disability. Stroke patients with severe hand weakness do not profit from rehabilitative treatments. Recently, brain‐controlled robotics and sequential functional electrical stimulation allowed some improvement. However, for such therapies to succeed, it is required to decode patients' intentions for different arm movements. Here, we evaluated whether residual muscle activity could be used to predict movements from paralyzed joints in severely impaired chronic stroke patients.MethodsMuscle activity was recorded with surface‐electromyography (EMG) in 41 patients, with severe hand weakness (Fugl‐Meyer Assessment [FMA] hand subscores of 2.93 ± 2.7), in order to decode their intention to perform six different motions of the affected arm, required for voluntary muscle activity and to control neuroprostheses. Decoding of paretic and nonparetic muscle activity was performed using a feed‐forward neural network classifier. The contribution of each muscle to the intended movement was determined.ResultsDecoding of up to six arm movements was accurate (>65%) in more than 97% of nonparetic and 46% of paretic muscles.InterpretationThese results demonstrate that some level of neuronal innervation to the paretic muscle remains preserved and can be used to implement neurorehabilitative treatments in 46% of patients with severe paralysis and extensive cortical and/or subcortical lesions. Such decoding may allow these patients for the first time after stroke to control different motions of arm prostheses through muscle‐triggered rehabilitative treatments.
Smoothed estimation of unknown inputs and states in dynamic systems with application to oceanic flow field reconstruction
Authors: Fang Huazhen , de Callafon Raymond A. , Franks Peter J. S. 
Published: December 2014

SummaryForward‐backward smoothing based unknown input and state estimation for dynamic systems is studied in this paper, motivated by reconstruction of an oceanographic flow field using a swarm of buoyancy‐controlled drifters. The development is conducted in a Bayesian framework. A Bayesian paradigm is constructed first to offer a probabilistic view of the unknown quantities given the measurements. Then a maximum a posteriori is established to build a means for simultaneous input and state smoothing, which can be solved by the classical Gauss–Newton method in the nonlinear case. Application to reconstruction of a complex three‐dimensional flow field is presented and investigated via simulation studies. Copyright © 2014 John Wiley & Sons, Ltd.
Lewis Acid‐Catalyzed Generation of CC and CN Bonds on π‐Deficient Heterocyclic Substrates
Authors: Staderini Matteo , Bolognesi Maria Laura , Menéndez J. Carlos 
Published: December 2014

AbstractFocused microwave irradiation of a series of halogenated nitrogen heterocycles and different kinds of nucleophiles in the presence of a catalytic amount of indium trichloride leads to the efficient and completely regioselective generation of aromatic CC and CN bonds. The method is simple, rapid, general and inexpensive, and can be performed without the use of dried solvents. Most of the synthetized compounds are new and in many cases the work‐up required only filtration. Furthermore, this is the first example of the use of a Lewis acid as a catalyst for heteroarylation, vinylation and amination reactions on π‐deficient heterocyclic substrates.magnified image