bluuebunny/crossref_metadata_2025_split huggingface dataset:
Guidelines for standardization of bioprinting: a systematic study of process parameters and their effect on bioprinted structures
Authors: Kesti Matti , Fisch Philipp , Pensalfini Marco , Mazza Edoardo , Zenobi-Wong Marcy 
Published: May 2016

AbstractBiofabrication techniques including three-dimensional bioprinting could be used one day to fabricate living, patient-specific tissues and organs for use in regenerative medicine. Compared to traditional casting and molding methods, bioprinted structures can be much more complex, containing for example multiple materials and cell types in controlled spatial arrangement, engineered porosity, reinforcement structures and gradients in mechanical properties. With this complexity and increased function, however, comes the necessity to develop guidelines to standardize the bioprinting process, so printed grafts can safely enter the clinics. The bioink material must firstly fulfil requirements for biocompatibility and flow. Secondly, it is important to understand how process parameters affect the final mechanical properties of the printed graft. Using a gellan-alginate physically crosslinked bioink as an example, we show shear thinning and shear recovery properties which allow good printing resolution. Printed tensile specimens were used to systematically assess effect of line spacing, printing direction and crosslinking conditions. This standardized testing allowed direct comparison between this bioink and three commercially-available products. Bioprinting is a promising, yet complex fabrication method whose outcome is sensitive to a range of process parameters. This study provides the foundation for highly needed best practice guidelines for reproducible and safe bioprinted grafts.
Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae
Authors: Hooks Katarzyna B , Naseeb Samina , Parker Steven , Griffiths-Jones Sam , Delneri Daniela 
Published: May 2016

Abstract
The Saccharomyces cerevisiae genome has undergone extensive intron loss during its evolutionary history. It has been suggested that the few remaining introns (in only 5% of protein-coding genes) are retained because of their impact on function under stress conditions. Here, we explore the possibility that novel noncoding RNA structures (ncRNAs) are embedded within intronic sequences and are contributing to phenotype and intron retention in yeast. We employed de novo RNA structure prediction tools to screen intronic sequences in S. cerevisiae and 36 other fungi. We identified and validated 19 new intronic RNAs via RNA sequencing (RNA-seq) and RT-PCR. Contrary to the common belief that excised introns are rapidly degraded, we found that, in six cases, the excised introns were maintained intact in the cells. In another two cases we showed that the ncRNAs were further processed from their introns. RNA-seq analysis confirmed that introns in ribosomal protein genes are more highly expressed when they contain predicted RNA structures. We deleted the novel intronic RNA structure within the GLC7 intron and showed that this region, rather than the intron itself, is responsible for the cell’s ability to respond to salt stress. We also showed a direct association between the in cis presence of the intronic RNA and GLC7 expression. Overall, these data support the notion that some introns may have been maintained in the genome because they harbor functional RNA structures.
Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila
Authors: Hoi Charlene S L , Xiong Wenjun , Rebay Ilaria 
Published: May 2016

Abstract
The transcriptional coactivator and phosphatase eyes absent (Eya) is dynamically compartmentalized between the nucleus and cytoplasm. Although the nuclear transcriptional circuits within which Eya operates have been extensively characterized, understanding of its cytoplasmic functions and interactions remains limited. Our previous work showed that phosphorylation of Drosophila Eya by the Abelson tyrosine kinase can recruit Eya to the cytoplasm and that eya–abelson interactions are required for photoreceptor axons to project to correct layers in the brain. Based on these observations, we postulated that photoreceptor axon targeting might provide a suitable context for identifying the cytoplasmic signaling cascades with which Eya interacts. Using a dose-sensitive eya misexpression background, we performed an RNA interference-based genetic screen to identify suppressors. Included among the top 10 hits were nonreceptor tyrosine kinases and multiple members of the Jak/Stat signaling network (hop, Stat92E, Socs36E, and Socs44A), a pathway not previously implicated in axon targeting. Individual loss-of-function phenotypes combined with analysis of axonal projections in Stat92E null clones confirmed the importance of photoreceptor autonomous Jak/Stat signaling. Experiments in cultured cells detected cytoplasmic complexes between Eya and Hop, Socs36E and Socs44A; the latter interaction required both the Src homology 2 motif in Socs44A and tyrosine phosphorylated Eya, suggesting direct binding and validating the premise of the screen. Taken together, our data provide new insight into the cytoplasmic phosphotyrosine signaling networks that operate during photoreceptor axon guidance and suggest specific points of interaction with Eya.
Geochemistry of PM10 over Europe during the EMEP intensive measurement periods in summer 2012 and winter 2013
Authors: Alastuey Andrés , Querol Xavier , Aas Wenche , Lucarelli Franco , Pérez Noemí , Moreno Teresa , Cavalli Fabrizia , Areskoug Hans , Balan Violeta , Catrambone Maria , Ceburnis Darius , Cerro José C. , Conil Sébastien , Gevorgyan Lusine , Hueglin Christoph , Imre Kornelia , Jaffrezo Jean-Luc , Leeson Sarah R. , Mihalopoulos Nikolaos , Mitosinkova Marta , O'Dowd Colin D. , Pey Jorge , Putaud Jean-Philippe , Riffault Véronique , Ripoll Anna , Sciare Jean , Sellegri Karine , Spindler Gerald , Yttri Karl Espen 
Published: May 2016

Abstract. The third intensive measurement period (IMP) organised by the European Monitoring and Evaluation Programme (EMEP) under the UNECE CLTRAP took place in summer 2012 and winter 2013, with PM10 filter samples concurrently collected at 20 (16 EMEP) regional background sites across Europe for subsequent analysis of their mineral dust content. All samples were analysed by the same or a comparable methodology. Higher PM10 mineral dust loadings were observed at most sites in summer (0.5–10 µg m−3) compared to winter (0.2–2 µg m−3), with the most elevated concentrations in the southern- and easternmost countries, accounting for 20–40 % of PM10. Saharan dust outbreaks were responsible for the high summer dust loadings at western and central European sites, whereas regional or local sources explained the elevated concentrations observed at eastern sites. The eastern Mediterranean sites experienced elevated levels due to African dust outbreaks during both summer and winter. The mineral dust composition varied more in winter than in summer, with a higher relative contribution of anthropogenic dust during the former period. A relatively high contribution of K from non-mineral and non-sea-salt sources, such as biomass burning, was evident in winter at some of the central and eastern European sites. The spatial distribution of some components and metals reveals the influence of specific anthropogenic sources on a regional scale: shipping emissions (V, Ni, and SO42−) in the Mediterranean region, metallurgy (Cr, Ni, and Mn) in central and eastern Europe, high temperature processes (As, Pb, and SO42−) in eastern countries, and traffic (Cu) at sites affected by emissions from nearby cities.
Sensitivity of snow density and specific surface area measured by microtomography to different image processing algorithms
Authors: Hagenmuller Pascal , Matzl Margret , Chambon Guillaume , Schneebeli Martin 
Published: May 2016

Abstract. Microtomography can measure the X-ray attenuation coefficient in a 3-D volume of snow with a spatial resolution of a few microns. In order to extract quantitative characteristics of the microstructure, such as the specific surface area (SSA), from these data, the greyscale image first needs to be segmented into a binary image of ice and air. Different numerical algorithms can then be used to compute the surface area of the binary image. In this paper, we report on the effect of commonly used segmentation and surface area computation techniques on the evaluation of density and specific surface area. The evaluation is based on a set of 38 X-ray tomographies of different snow samples without impregnation, scanned with an effective voxel size of 10 and 18 μm. We found that different surface area computation methods can induce relative variations up to 5 % in the density and SSA values. Regarding segmentation, similar results were obtained by sequential and energy-based approaches, provided the associated parameters were correctly chosen. The voxel size also appears to affect the values of density and SSA, but because images with the higher resolution also show the higher noise level, it was not possible to draw a definitive conclusion on this effect of resolution.
Extension of silicon emission model to silicon pillar oxidation
Authors: Kageshima Hiroyuki , Shiraishi Kenji , Endoh Tetsuo 
Published: May 2016

Abstract
Missing Si in the oxidation of Si pillar structures is investigated by extending the Si emission model to the oxidation of planar structures. The original Si emission model [H. Kageshima et al., Jpn. J. Appl. Phys. 38, L971 (1999)] assumes the emission of excess Si from the interface into the oxide during the oxidation process, the diffusion of the excess Si through the oxide, and the control of the oxidation rate by the concentration of remaining excess Si around the interface. By assuming the sublimation of the excess Si from the oxide surface in addition to the assumptions of the original Si emission model, the origin of the missing Si is consistently explained. It is suggested that the amount of the missing Si is enhanced by the geometrical effect of the pillar structure because the concentration of excess Si is inversely proportional to the radial position. This also suggests that the missing Si is inevitable for the thin pillar structures. Careful approaches to the oxidation process are recommended for pillar structures.
Quasi‐biennial oscillation modulation of the middle‐ and high‐latitude mesospheric semidiurnal tides during August–September
Authors: Laskar Fazlul I. , Chau Jorge L. , Stober Gunter , Hoffmann Peter , Hall Chris M. , Tsutsumi M. 
Published: May 2016

AbstractThe seasonal and interannual variabilities of mesospheric semidiurnal tides (SDT) are investigated using specular meteor radar‐based winds. The horizontal wind observations during 2003 to 2014 from a high‐latitude station, Andenes (69°N, 16°E), and during 2008 to 2014 from a midlatitude station, Juliusruh (54°N, 13°E), are used. It has been observed that the amplitudes of mesospheric SDTs are enhanced at both stations during August–September of all the years. These enhancements show a systematic behavior with that of the low‐latitude stratospheric quasi‐biennial oscillation (QBO), which is characterized based on winds from radiosonde data. The SDT amplitude values during enhancement are below/above mean level for those years in which the QBO wind at 50 hPa is westward/eastward (QBOw/QBOe). The average SDT amplitudes during the August–September enhancement duration are found to vary hand in hand with the low‐latitude QBO wind, suggesting QBO modulation of SDT. Stratospheric and lower mesospheric zonal wind perturbations from MERRA reanalysis data show weak local forcing in the Northern Hemisphere and indication of enhanced quasi‐stationary planetary waves (SPW) in the Southern Hemisphere. Based on these observations and some earlier results, we hypothesize that the QBOw/QBOe wind damp/enhance the southern hemispheric SPW of wave number 1 (SPW1). This modulated SPW1 then interacts with the northern midlatitude and high‐latitude SDTs to imprint the signature of QBO on them.
Control of slab width on subduction‐induced upper mantle flow and associated upwellings: Insights from analog models
Authors: Strak Vincent , Schellart Wouter P. 
Published: May 2016

AbstractThe impact of slab width W (i.e., trench‐parallel extent) on subduction‐induced upper mantle flow remains uncertain. We present a series of free subduction analog models where W was systematically varied to upscaled values of 250–3600 km to investigate its effect on subducting plate kinematics and upper mantle return flow around the lateral slab edges. We particularly focused on the upwelling component of mantle flow, which might promote decompression melting and could thereby produce intraplate volcanism. The models show that W has a strong control on trench curvature and on the trench retreat, subducting plate, and subduction velocities, generally in good agreement with previous modeling studies. Upper mantle flow velocity maps produced by means of a stereoscopic particle image velocimetry technique indicate that the magnitude of the subduction‐induced mantle flow around the lateral slab edges correlates positively with the product of W and trench retreat velocity. For all models an important upwelling component is always produced close to the lateral slab edges, with higher magnitudes for wider slabs. The trench‐parallel lateral extent of this upwelling component is the same irrespective of W, but its maximum magnitude gets located closer to the subducting plate in the trench‐normal direction and it is more focused when W increases. For W ≤ 2000 km the upwelling occurs laterally (in the trench‐parallel direction) next to the subslab domain and the mantle wedge domain, while for W ≥ 2000 km it is located only next to the subslab domain and focuses closer to the trench tip, because of stronger poloidal flow in the mantle wedge extending laterally.
On the stability and spatiotemporal variance distribution of salinity in the upper ocean
Authors: O'Kane Terence J. , Monselesan Didier P. , Maes Christophe 
Published: May 2016

AbstractDespite recent advances in ocean observing arrays and satellite sensors, there remains great uncertainty in the large‐scale spatial variations of upper ocean salinity on the interannual to decadal timescales. Consonant with both broad‐scale surface warming and the amplification of the global hydrological cycle, observed global multidecadal salinity changes typically have focussed on the linear response to anthropogenic forcing but not on salinity variations due to changes in the static stability and or variability due to the intrinsic ocean or internal climate processes. Here, we examine the static stability and spatiotemporal variability of upper ocean salinity across a hierarchy of models and reanalyses. In particular, we partition the variance into time bands via application of singular spectral analysis, considering sea surface salinity (SSS), the Brunt Väisälä frequency (N2), and the ocean salinity stratification in terms of the stabilizing effect due to the haline part of N2 over the upper 500m. We identify regions of significant coherent SSS variability, either intrinsic to the ocean or in response to the interannually varying atmosphere. Based on consistency across models (CMIP5 and forced experiments) and reanalyses, we identify the stabilizing role of salinity in the tropics—typically associated with heavy precipitation and barrier layer formation, and the role of salinity in destabilizing upper ocean stratification in the subtropical regions where large‐scale density compensation typically occurs.
The potassic sedimentary rocks in Gale Crater, Mars, as seen by ChemCam on board Curiosity
Authors: Le Deit L. , Mangold N. , Forni O. , Cousin A. , Lasue J. , Schröder S. , Wiens R. C. , Sumner D. , Fabre C. , Stack K. M. , Anderson R. B. , Blaney D. , Clegg S. , Dromart G. , Fisk M. , Gasnault O. , Grotzinger J. P. , Gupta S. , Lanza N. , Le Mouélic S. , Maurice S. , McLennan S. M. , Meslin P.‐Y. , Nachon M. , Newsom H. , Payré V. , Rapin W. , Rice M. , Sautter V. , Treiman A. H. 
Published: May 2016

AbstractThe Mars Science Laboratory rover Curiosity encountered potassium‐rich clastic sedimentary rocks at two sites in Gale Crater, the waypoints Cooperstown and Kimberley. These rocks include several distinct meters thick sedimentary outcrops ranging from fine sandstone to conglomerate, interpreted to record an ancient fluvial or fluvio‐deltaic depositional system. From ChemCam Laser‐Induced Breakdown Spectroscopy (LIBS) chemical analyses, this suite of sedimentary rocks has an overall mean K2O abundance that is more than 5 times higher than that of the average Martian crust. The combined analysis of ChemCam data with stratigraphic and geographic locations reveals that the mean K2O abundance increases upward through the stratigraphic section. Chemical analyses across each unit can be represented as mixtures of several distinct chemical components, i.e., mineral phases, including K‐bearing minerals, mafic silicates, Fe‐oxides, and Fe‐hydroxide/oxyhydroxides. Possible K‐bearing minerals include alkali feldspar (including anorthoclase and sanidine) and K‐bearing phyllosilicate such as illite. Mixtures of different source rocks, including a potassium‐rich rock located on the rim and walls of Gale Crater, are the likely origin of observed chemical variations within each unit. Physical sorting may have also played a role in the enrichment in K in the Kimberley formation. The occurrence of these potassic sedimentary rocks provides additional evidence for the chemical diversity of the crust exposed at Gale Crater.
Near‐axis crustal structure and thickness of the Endeavour Segment, Juan de Fuca Ridge
Authors: Soule Dax , Wilcock William S. D. , Toomey Douglas R. , Hooft Emilie E. E. , Weekly Robert T. 
Published: May 2016

AbstractA model of crustal thickness and lower crustal velocities is obtained for crustal ages of 0.1–1.2 Ma on the Endeavour Segment of the Juan de Fuca Ridge by inverting travel times of crustal paths and non‐ridge‐crossing wide‐angle Moho reflections obtained from a three‐dimensional tomographic experiment. The crust is thicker by 0.5–1 km beneath a 200 m high plateau that extends across the segment center. This feature is consistent with the influence of the proposed Heckle melt anomaly on the spreading center. The history of ridge propagation on the Cobb overlapping spreading center may also have influenced the formation of the plateau. The sharp boundaries of the plateau and crustal thickness anomaly suggest that melt transport is predominantly upward in the crust. Lower crustal velocities are lower at the ends of the segment, likely due to increased hydrothermal alteration in regions influenced by overlapping spreading centers, and possibly increased magmatic differentiation.
Diminishing high‐frequency directivity due to a source effect: Empirical evidence from small earthquakes in the Abruzzo region, Italy
Authors: Pacor F. , Gallovič F. , Puglia R. , Luzi L. , D'Amico M. 
Published: May 2016

AbstractThe aim of this study is to investigate the directivity effects of ~250 aftershocks (magnitudes 3–5.5) of the Mw 6.1 2009 L'Aquila earthquake (central Italy). To this end, we estimate the apparent source spectra at each station removing path and site effects inferred by standard Generalized Inversion Technique. Then, we evaluate the residuals between the apparent source spectra and the event mean source spectrum at selected frequencies. We investigate azimuthal and frequency dependence of the residuals for 40 events with the best station coverage. For most of events with the strongest directivity effect (Mw 3.4–4.0), we observe a remarkable decrease of the directivity amplification at high frequencies, which has not yet been documented for such relatively small‐magnitude events. Since there is negligible distance dependence, we ascribe this observation to a source phenomenon such as significant small‐scale rupture propagation complexity.
Magnetospheric Multiscale observations of large‐amplitude, parallel, electrostatic waves associated with magnetic reconnection at the magnetopause
Authors: Ergun R. E. , Holmes J. C. , Goodrich K. A. , Wilder F. D. , Stawarz J. E , Eriksson S. , Newman D. L. , Schwartz S. J. , Goldman M. V. , Sturner A. P. , Malaspina D. M. , Usanova M. E. , Torbert R. B. , Argall M. , Lindqvist P.‐A. , Khotyaintsev Y. , Burch J. L. , Strangeway R. J. , Russell C. T. , Pollock C. J. , Giles B. L. , Dorelli J. J. C. , Avanov L. , Hesse M. , Chen L. J. , Lavraud B. , Le Contel O. , Retino A. , Phan T. D. , Eastwood J. P. , Oieroset M. , Drake J. , Shay M. A. , Cassak P. A. , Nakamura R. , Zhou M. , Ashour‐Abdalla M. , André M. 
Published: May 2016

AbstractWe report observations from the Magnetospheric Multiscale satellites of large‐amplitude, parallel, electrostatic waves associated with magnetic reconnection at the Earth's magnetopause. The observed waves have parallel electric fields (E||) with amplitudes on the order of 100 mV/m and display nonlinear characteristics that suggest a possible net E||. These waves are observed within the ion diffusion region and adjacent to (within several electron skin depths) the electron diffusion region. They are in or near the magnetosphere side current layer. Simulation results support that the strong electrostatic linear and nonlinear wave activities appear to be driven by a two stream instability, which is a consequence of mixing cold (<10 eV) plasma in the magnetosphere with warm (~100 eV) plasma from the magnetosheath on a freshly reconnected magnetic field line. The frequent observation of these waves suggests that cold plasma is often present near the magnetopause.
Observation of high‐frequency electrostatic waves in the vicinity of the reconnection ion diffusion region by the spacecraft of the Magnetospheric Multiscale (MMS) mission
Authors: Zhou M. , Ashour‐Abdalla M. , Berchem J. , Walker R. J. , Liang H. , El‐Alaoui M. , Goldstein M. L. , Lindqvist P.‐A. , Marklund G. , Khotyaintsev Y. V. , Ergun R. E. , Wilder F. D. , Russell C. T. , Strangeway R. J. , Zhao C. , Paterson W. R. , Giles B. L. , Pollock C. J. , Torbert R. B. , Burch J. L. , Dorelli J. C. , Gershman D. J. , Avanov L. A. , Lavraud B. , Chandler M. O. 
Published: May 2016

AbstractWe report Magnetospheric Multiscale observations of high‐frequency electrostatic waves in the vicinity of the reconnection ion diffusion region on the dayside magnetopause. The ion diffusion region is identified during two magnetopause crossings by the Hall electromagnetic fields, the slippage of ions with respect to the magnetic field, and magnetic energy dissipation. In addition to electron beam modes that have been previously detected at the separatrix on the magnetospheric side of the magnetopause, we report, for the first time, the existence of electron cyclotron harmonic waves at the magnetosheath separatrix. Broadband waves between the electron cyclotron and electron plasma frequencies, which were probably generated by electron beams, were found within the magnetopause current sheet. Contributions by these high‐frequency waves to the magnetic energy dissipation were negligible in the diffusion regions as compared to those of lower‐frequency waves.