bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and temporal variations in river terrace formation, preservation, and morphology in the Lower Meuse Valley, The Netherlands
Authors: Woolderink Hessel Antonius Gerardus , Kasse Cornelis , Cohen Kim Mikkel , Hoek Wim Zacharias , Van Balen Ronald Theodorus 
Published: August 2018

AbstractThe Lower Meuse Valley crosses the Roer Valley Rift System and provides an outstanding example of well-preserved late glacial and Holocene river terraces. The formation, preservation, and morphology of these terraces vary due to reach-specific conditions, a phenomenon that has been underappreciated in past studies. A detailed palaeogeographic reconstruction of the terrace series over the full length of the Lower Meuse Valley has been performed. This reconstruction provides improved insight into successive morphological responses to combined climatic and tectonic external forcing, as expressed and preserved in different ways along the river. New field data and data obtained from past studies were integrated using a digital mapping method in GIS. Results show that late glacial river terraces with diverse fluvial styles are best preserved in the Lower Meuse Valley downstream sub-reaches (traversing the Venlo Block and Peel Block), while Holocene terrace remnants are well-developed and preserved in the upstream sub-reaches (traversing the Campine Block and Roer Valley Graben). This reach-to-reach spatial variance in river terrace preservation and morphology can be ascribed to tectonically driven variations in river gradient and subsurface lithology, and to river-driven throughput of sediment supply.
A clinical guideline onDientamoeba fragilisinfections
Authors: van Gestel Rosanne SFE , Kusters Johannes G , Monkelbaan Jan F 
Published: August 2018

AbstractDientamoeba fragilis(D. fragilis) is an intestinal parasite frequently detected in humans with abdominal pain and diarrhoea, but it is also commonly found in asymptomatic subjects. Hence its clinical relevance is often disputed. The introduction of polymerase chain reaction (PCR) is a versatile and sensitive diagnostic technique for the detection of intestinal parasites, and in some Western world countries PCR has almost completely replaced microscopic diagnostics. PCR has however resulted in an increase in the number ofD. fragilis-positive patients. The disputed pathogenic nature of this intestinal parasite and an apparent increase in the incidence of patients with positive PCR results have renewed the discussions between clinicians and microbiologists on how to deal with an infected patient. Moreover, treatment guidelines differ throughout the world which makes it difficult for clinicians to choose an optimal therapeutic regimen.AimTo summarize and discuss the current knowledge on the pathogenicity, best diagnostic approach, treatment and follow-up of children and adults infected withD. fragilis.
Preliminary survival and movement data for a declining population of Flesh-footed Shearwater Ardenna carneipes in Western Australia provides insights into marine threats
Authors: LAVERS JENNIFER L. , LISOVSKI SIMEON , BOND ALEXANDER L. 
Published: August 2018

SummarySeabirds face diverse threats on their breeding islands and while at sea. Human activities have been linked to the decline of seabird populations, yet over-wintering areas typically receive little or no protection. Adult survival rates, a crucial parameter for population persistence in long-lived species, tend to be spatially or temporally restricted for many seabird species, limiting our understanding of factors driving population trends at some sites. We used bio-loggers to study the migration of Western Australian Flesh-footed Shearwaters Ardenna carneipes carneipes and estimated adult survival over five years. Western Australia is home to around 35% of the world’s breeding Flesh-footed Shearwaters, a population which was up-listed to Vulnerable in 2015. During the austral winter, shearwaters migrated across the central Indian Ocean to their non-breeding grounds off western Sri Lanka. Low site fidelity on breeding islands, mortality of adult birds at sea (e.g. fisheries bycatch), and low annual breeding frequency likely contributed to the low estimated annual adult survival (2011–2015: ϕ = 0.634-0.835).
Investigating the Onset of Strain Localization Within Anisotropic Shale Using Digital Volume Correlation of Time‐Resolved X‐Ray Microtomography Images
Authors: McBeck Jessica , Kobchenko Maya , Hall Stephen A. , Tudisco Erika , Cordonnier Benoit , Meakin Paul , Renard François 
Published: August 2018

AbstractDigital volume correlation analysis of time‐resolved X‐ray microtomography scans acquired during in situ triaxial compression of Green River shale cores provided time series of 3‐D incremental strain fields that elucidated evolving deformation processes by quantifying microscopic strain localization. With these data, we investigated the impact of mechanical anisotropy on microscopic strain localization culminating in macroscopic shear failure. We conducted triaxial compression experiments with the maximum compressive stress, σ1, aligned perpendicular and parallel to lamination planes in order to investigate end‐member stress states that arise within sedimentary basins. When the preexisting laminations were perpendicular to σ1, a lamination‐parallel region with high axial compaction developed within the macroscopically linear deformation phase of the experiment and then thickened with increasing applied differential stress. Scanning electron microscopy images indicate that this axial compaction occurred within a lower density lamination and that more axial compaction occurred within the center of the core than near its sides. Boundary element method simulations suggest that this compacting volume promoted shear fracture development within the upper portion of the shale. When the laminations were parallel to σ1, lamination‐parallel dilation bands formed, thickened, and intensified in dilation. Population densities of the distributions of incremental shear strain, radial dilation, and axial contraction calculated by digital volume correlation analysis enabled quantification of the evolving overall impact of, and interplay between, these various deformation modes.
Interdecadal Change of the Impact of Eurasian Snow on Spring Precipitation Over Southern China
Authors: Jia Xiaojing , Cao Ding Rui , Ge Jing Wen , Wang Min 
Published: August 2018

AbstractThis study investigates the interdecadal changes in the relationship between the Eurasian snow cover extent (SCE) and spring precipitation over southern China. The results show that the spring precipitation over southern China has experienced an obvious change from an active to a quiet period since the late 1980s. The entire data set is divided into two subperiods, that is, 1972–1987 (P1) and 1988–2009 (P2). The interannual variation of the spring precipitation of southern China is found to be significantly related to Eurasian SCE anomalies around northwest of Lake Baikal. Less‐than‐normal SCE northwest of Lake Baikal corresponds to more‐than‐normal spring precipitation over southern China. The result of a numerical experiment performed using a baroclinic atmospheric model indicates that the Eurasian snow anomalies around northwest of Lake Baikal can impact the variation of spring precipitation over southern China by modulating the atmospheric circulations over eastern Asia and the western North Pacific region. Further examination shows that the SCE anomalies around Lake Baikal contribute differently to the variation of spring precipitation over southern China before and after the late 1980s. During P1, the SCE anomalies around Lake Baikal contribute to the variation of spring precipitation over China in the form of a mono‐sign pattern, which is similar to the first empirical orthogonal function mode of spring precipitation, while in P2, the SCE anomalies around Lake Baikal favor a north‐south dipole mode of the spring precipitation variation, which bears considerable similarity to the second empirical orthogonal function mode of spring precipitation over China.
Falling Snow Radiative Effects Enhance the Global Warming Response of the Tropical Pacific Atmosphere
Authors: Chen Chao‐An , Li J.‐L. F. , Richardson Mark , Lee Wei‐Liang , Fetzer Eric , Stephens G. , Hsu Huang‐Hsiung , Wang Yi‐Hui , Yu Jia‐Yuh 
Published: August 2018

AbstractMost models from the Coupled Model Intercomparison Project phase 5 (CMIP5) do not include the radiative effects of falling snow. This has been shown to bias simulations of radiation and circulation in the Pacific present‐day mean state. Here we explore how precipitating ice radiative effects contribute to simulated Pacific climate change via a pair of sensitivity experiments with and without snow radiative effects (SnowOn/SnowOff) using 1pctCO2 simulations of the Community Earth System Model version 1 (CESM1) climate model, in which atmospheric CO2 increases at 1% per year for 140 years. In addition, we compare our results with the CMIP5 ensemble mean. The initial climate state of each 1pctCO2 run shows similar patterns to present‐day simulations. Under global warming, the regions of convective activity tend to intensify and shift eastward. These changes are stronger in the SnowOn simulation, which also displays a stronger zonal gradient of sea surface temperature warming relative to SnowOff. The changes in convective activity and the associated precipitation are particularly notable: with reduced precipitation around the maritime continent, and an approximate doubling of the precipitation increase over parts of the western Pacific in SnowOn. CESM1 SnowOff patterns of change are similar to those in CMIP5 models that exclude snow radiative effects, hinting that future warming‐driven changes in precipitation and circulation over the Pacific might be stronger than those simulated by most CMIP5 models.
Precipitation Partitioning in Multiscale Atmospheric Simulations: Impacts of Stability Restoration Methods
Authors: He Jian , Alapaty Kiran 
Published: August 2018

AbstractProper simulation of high‐resolution surface precipitation distribution and variability is important to local aspects of environmental pollution and climate. Global and regional climate and weather models routinely evaluate total precipitation using available measurements, but quantitative evaluation of contributions by the individual components (convective and nonconvective) to the total precipitation is not routinely performed. Wet bias in one component can alleviate dry bias in the other component, making the total precipitation look comparable to measurements, leading to an invisible bias. To study this aspect, Tropical Rainfall Measuring Mission (TRMM) measurements for precipitation components were used to quantitatively evaluate convective fractions simulated by a cumulus parameterization scheme in a regional climate simulation using 12‐km grid spacing. Results indicated a wet bias in convective precipitation as compared to TRMM measurements. This wet bias helped to counter a dry bias in grid‐scale precipitation and led to a total precipitation comparable to Parameter‐elevation Regressions on Independent Slopes Model and TRMM measurements. A new formulation has been developed for convective cloud adjustment time scale alleviating wet bias in convective precipitation when compared to the old formulation and TRMM measurements. Results for different grid spacing also indicate that the new method produces lower subgrid‐scale precipitation with overall better precipitation estimates. Our results also suggest that evaluating both components of the surface precipitation rather than just the total itself can inform a need to improve cloud formulations, as demonstrated in this study. This study calls for the development of methods to routinely produce measurements for precipitation components that help evaluating global and regional climate and weather models.
Distinguishing Anthropogenic CO2 Emissions From Different Energy Intensive Industrial Sources Using OCO‐2 Observations: A Case Study in Northern China
Authors: Wang Songhan , Zhang Yongguang , Hakkarainen Janne , Ju Weimin , Liu Yongxue , Jiang Fei , He Wei 
Published: August 2018

AbstractEnergy intensive industries, such as iron and steel industry and coal‐processing industry, are one of the major anthropogenic fossil fuel carbon dioxide (CO2) emission sources, especially in China. Monitoring the localized CO2 emissions from these industrial point sources is valuable to improve emission estimates and inform on policy discussion. However, spatiotemporally explicit information on CO2 emissions from different energy intensive industrial sources is still limited. In this study, we use remote sensing data sets with high spatial resolution to detect the patterns of CO2 enhancements of carbon emission intensive industries, taking northern China as the case study area. CO2 anomalies are derived from spaceborne column‐averaged CO2 mixing ratio (XCO2) data measured by the Orbiting Carbon Observatory 2 (OCO‐2). The Gaussian plume model is used to select the XCO2 data when the CO2 emissions from plants are localized, which allows us to distinguish CO2 emissions from different industrial point sources. We demonstrate that high‐emission areas with industrial plants are detectable by CO2 anomalies compared to natural background area and the average enhancement is about 1.8 ppm. The XCO2 data also show a higher CO2 emission from a cluster of iron and steel plants than that of coal‐processing plants, which is consistent with emission inventories. Furthermore, anthropogenic CO2 emission hotspots are possible to be identified from surrounding natural background. Our results suggest the potential of satellite data for characterizing strong localized carbon emission from different industrial sources both in space and time.
Study of the Quasi‐5‐Day Wave in the MLT Region by a Meteor Radar Chain
Authors: Gong Yun , Li Chun , Ma Zheng , Zhang Shaodong , Zhou Qihou , Huang Chunming , Huang Kaiming , Li Guozhu , Ning Baiqi 
Published: August 2018

AbstractAn extensive analysis of quasi 5‐day waves (5DWs) in the mesosphere and lower thermosphere and their responses to a major sudden stratospheric warming (SSW) event (January 2013) are presented. The analysis is based on data conducted from a meteor radar chain in the period from December 2008 to November 2017 and Aura Microwave Limb Sounder satellite. The radar chain includes three stations located at Mohe (MH, 53.5°N, 122.3°E), Beijing (BJ, 40.3°N, 116.2°E), and Wuhan (WH, 30.5°N, 114.6°E). The 5DWs present clear interannual and seasonal variations, which are observed by both the radar wind data and Aura‐temperature data. Interestingly, the ter‐annual oscillation is found to be as important as the commonly recognized annual oscillation and semiannual oscillation at the three stations in both neutral wind components. The 5DWs are strong mainly during the August/September in the meridional component, while they are primarily enhanced in the period of January, April/May, and late summer in the zonal component. An enhancement of 5DWs is observed during the 2013 SSW event in the mesosphere and lower thermosphere region at the three stations. The amplitudes during the SSW are more than 2 times larger than the January average. The strength of the amplification is most prominent at MH and reduces as latitude decreases. According to the results obtained from the radar wind and Aura temperature, the enhanced 5DW modes are W1 at MH, and W2 at BJ and WH. Our results indicate that the amplification of the 5DWs is very likely associated with the 2013 SSW.
Modal energy transfer by thermally induced refractive index gratings in Yb-doped fibers
Authors: Stihler Christoph , Jauregui Cesar , Tünnermann Andreas , Limpert Jens 
Published: August 2018

AbstractThermally induced refractive index gratings in Yb-doped fibers lead to transverse mode instability (TMI) above an average power threshold, which represents a severe problem for many applications. To obtain a deeper understanding of TMI, the evolution of the strength of the thermally induced refractive index grating with the average output power in a fiber amplifier is experimentally investigated for the first time. This investigation is performed by introducing a phase shift between the refractive index grating and modal interference pattern, which is obtained by applying a pump power variation to the fiber amplifier. It is demonstrated that the refractive index grating is sufficiently strong to enable modal energy coupling at powers that are significantly below the TMI threshold if the induced phase shift is sufficiently large. The experiments indicate that at higher powers, the refractive index grating becomes more sensitive to such phase shifts, which will ultimately trigger TMI. Furthermore, the experimental results demonstrate beam cleaning above the TMI threshold via the introduction of a positive phase shift. This finding paves the way for the development of a new class of mitigation strategies for TMI that are based on controlling the phase shift between the thermally induced refractive index grating and modal interference pattern.
Localized recombination drives diversification of killing spectra for phage-derived syringacins
Authors: Baltrus David A , Clark Meara , Smith Caitlin , Hockett Kevin L 
Published: August 2018

Abstract
To better understand the potential for antagonistic interactions between members of the same bacterial species, we have surveyed bacteriocin killing activity across a diverse suite of strains of the phytopathogen Pseudomonas syringae. Our data demonstrate that killing activity from phage-derived bacteriocins of P. syringae (R-type syringacins) is widespread. Despite a high overall diversity of bacteriocin activity, strains can broadly be classified into five main killing types and two main sensitivity types. Furthermore, we show that killing activity switches frequently between strains and that switches correlate with localized recombination of two genes that together encode the proteins that specify bacteriocin targeting. Lastly, we demonstrate that phage-derived bacteriocin killing activity can be swapped between strains simply through expression of these two genes in trans. Overall, our study characterizes extensive diversity of killing activity for phage-derived bacteriocins of P. syringae across strains and highlights the power of localized recombination to alter phenotypes that mediate strain interactions during evolution of natural populations and communities.
Unexpected stability of aqueous dispersions of raspberry-like colloids
Authors: Lan Yang , Caciagli Alessio , Guidetti Giulia , Yu Ziyi , Liu Ji , Johansen Villads E. , Kamp Marlous , Abell Chris , Vignolini Silvia , Scherman Oren A. , Eiser Erika 
Published: August 2018

AbstractAqueous colloidal suspensions, both man-made and natural, are part of our everyday life. The applicability of colloidal suspensions, however, is limited by the range of conditions over which they are stable. Here we report a novel type of highly monodisperse raspberry-like colloids, which are prepared in a single-step synthesis that relies on simultaneous dispersion and emulsion polymerisation. The resulting raspberry colloids behave almost like hard spheres. In aqueous solutions, such prepared raspberries show unexpected stability against aggregation over large variations of added salt concentrations without addition of stabilisers. We present simple Derjaguin–Landau–Verwey–Overbeek (DLVO) calculations performed on raspberry-like and smooth colloids showing that this stability results from our raspberries’ unique morphology, which extends our understanding of colloidal stability against salting. Further, the raspberries’ stability facilitates the formation of superspheres and thin films in which the raspberry colloids self-assemble into hexagonally close-packed photonic crystals with exquisite reproducibility.
LY6E mediates an evolutionarily conserved enhancement of virus infection by targeting a late entry step
Authors: Mar Katrina B. , Rinkenberger Nicholas R. , Boys Ian N. , Eitson Jennifer L. , McDougal Matthew B. , Richardson R. Blake , Schoggins John W. 
Published: August 2018

AbstractInterferons (IFNs) contribute to cell-intrinsic antiviral immunity by inducing hundreds of interferon-stimulated genes (ISGs). In a screen to identify antiviral ISGs, we unexpectedly found that LY6E, a member of the LY6/uPAR family, enhanced viral infection. Here, we show that viral enhancement by ectopically expressed LY6E extends to several cellular backgrounds and affects multiple RNA viruses. LY6E does not impair IFN antiviral activity or signaling, but rather promotes viral entry. Using influenza A virus as a model, we narrow the enhancing effect of LY6E to uncoating after endosomal escape. Diverse mammalian orthologs of LY6E also enhance viral infectivity, indicating evolutionary conservation of function. By structure-function analyses, we identify a single amino acid in a predicted loop region that is essential for viral enhancement. Our study suggests that LY6E belongs to a class of IFN-inducible host factors that enhance viral infectivity without suppressing IFN antiviral activity.
Imaging of Murine Whole Lung Fibrosis by Large Scale 3D Microscopy aided by Tissue Optical Clearing
Authors: Ochoa Lorenzo F. , Kholodnykh Alexander , Villarreal Paula , Tian Bing , Pal Rahul , Freiberg Alexander N. , Brasier Allan R. , Motamedi Massoud , Vargas Gracie 
Published: August 2018

AbstractPulmonary fibrosis, characterized by excessive collagen deposition in the lungs, comprises a key and debilitating component of chronic lung diseases. Methods are lacking for the direct visualization of fibrillar collagen throughout the whole murine lung, a capability that would aid the understanding of lung fibrosis. We combined an optimized organ-level optical clearing (OC) approach with large-scale, label-free multiphoton microscopy (MPM) and second harmonic generation microscopy (SHGM) to reveal the complete network of fibrillar collagen in whole murine lungs. An innate inflammation-driven model based on repetitive poly(I:C) challenge was evaluated. Following OC, mosaic MPM/SHGM imaging with 3D reconstruction and whole organ quantitative analysis revealed significant differences in collagen deposition between PBS and poly(I:C) treated lungs. Airway specific analysis in whole lung acquisitions revealed significant sub-epithelial fibrosis evident throughout the proximal conductive and distal airways with higher collagen deposition in the poly(I:C) group vs PBS group. This study establishes a new, powerful approach based on OC and MPM/SHGM imaging for 3D analysis of lung fibrosis with macroscopic views of lung pathology based on microscopy and providing a new way to analyze the whole lung while avoiding regional sampling bias.