bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Positive‐Definite, WENO‐Limited, High‐Order Finite Volume Solver for 2‐D Transport on the Cubed Sphere Using an ADER Time Discretization
Authors: Norman M. R. , Nair R. D. 
Published: June 2018

AbstractModern computer architectures reward added computation if it reduces algorithmic dependence, reduces data movement, increases accuracy/robustness, and improves memory accesses. The driving motive for this study is to develop a numerical algorithm that respects these constraints while improving accuracy and robustness. This study introduces the ADER‐DT (Arbitrary DERivatives in time and space‐differential transform) time discretization to positive‐definite, weighted essentially nonoscillatory (WENO)‐limited, finite volume transport on the cubed sphere in lieu of semidiscrete integrators. The cost of the ADER‐DT algorithm is significantly improved from previous implementations without affecting accuracy. A new function‐based WENO implementation is also detailed for use with the ADER‐DT time discretization. While ADER‐DT costs about 1.5 times more than a fourth‐order, five‐stage strong stability preserving Runge‐Kutta (SSPRK4) method, it is far more computationally dense (which is advantageous on accelerators such as graphics processing units), and it has a larger effective maximum stable time step. ADER‐DT errors converge more quickly with grid refinement than SSPRK4, giving 6.5 times less error in the
norm than SSPRK4 at the highest refinement level for smooth data. For nonsmooth data, ADER‐DT resolves C0 discontinuities more sharply. For a complex flow field, ADER exhibits less phase error than SSPRK4. Improving both accuracy and robustness as well as better respecting modern computational efficiency requirements, we believe the method presented herein is competitive for efficiently transporting tracers over the sphere for applications targeting modern computing architectures.
Regionalization of Groundwater Residence Time Using Metamodeling
Authors: Starn J. J. , Belitz K. 
Published: June 2018

AbstractGroundwater residence‐time distributions (RTDs) are critical for assessing susceptibility of water resources to degradation. A novel combination of numerical modeling and statistical methods allows estimation of regional RTDs with unprecedented speed. In this method, particle RTDs are generated in 30 type locales in the northeastern glaciated U.S. by using automated generalized finite‐difference groundwater flow and advective transport models. Targets for statistical learning were created from particle RTDs by fitting Weibull, gamma, and inverse Gaussian distributions. Whole‐basin flux‐weighted RTDs were well fit by one‐component Weibull distributions. Flux‐weighted RTDs at stressed receptors such as wells often produced more complicated RTDs that required a two‐component mixture to fit. A Multitask LASSO regression was trained on the parametric RTDs using hydrogeographic features of the modeled areas as explanatory features. In this way, RTDs are regionalized with mappable physical features such as recharge and aquifer volume. The shape, location, and scale parameters of the parametric RTDs are strongly related to the mean exponential age. The shape parameter of the distribution, which controls deviation from exponential, is additionally a function of aquifer heterogeneity and hydrologic features. Regionalized RTDs provide useful metrics with respect to groundwater lag times and solute loading to streams. The lag time between input and output contained in the RTD is critical to understanding the relation between the land surface and human and ecological receptors.
Satellite‐Observed Major Greening and Biomass Increase in South China Karst During Recent Decade
Authors: Brandt Martin , Yue Yuemin , Wigneron Jean Pierre , Tong Xiaowei , Tian Feng , Jepsen Martin Rudbeck , Xiao Xiangming , Verger Aleixandre , Mialon Arnaud , Al‐Yaari Amen , Wang Kelin , Fensholt Rasmus 
Published: June 2018

AbstractAbove‐ground vegetation biomass is one of the major carbon sinks and provides both provisioning (e.g., forestry products) and regulating ecosystem services (by sequestering carbon). Continuing deforestation and climate change threaten this natural resource but can effectively be countered by national conservation policies. Here we present time series (1999–2017) derived from complementary satellite systems to describe a phenomenon of global significance: the greening of South China Karst. We find a major increase in growing season vegetation cover from 69% in 1999 to 81% in 2017 occurring over ~1.4 million km2. Over 1999–2012, we report one of the globally largest increases in biomass to occur in the South China Karst region (on average +4% over 0.9 million km2), which accounts for ~5% of the global areas characterized with increases in biomass. These increases in southern China's vegetation have occurred despite a decline in rainfall (−8%) and soil moisture (−5%) between 1999 and 2012 and are derived from effects of forestry and conservation activities at an unprecedented spatial scale in human history (~20,000 km2 yr−1 since 2002). These findings have major implications for the provisioning of ecosystem services not only for the Chinese karst ecosystem (e.g., carbon storage, water filtration, and timber production) but also for the study of global carbon cycles.
Multipathing Rayleigh Waves From Long‐Distance Noise Cross Correlation Along an Ocean‐Continent Boundary (Alaska to California)
Authors: Xia Yingjie , Ni Sidao , Tape Carl 
Published: June 2018

AbstractSeismic interferometry can reliably extract interstation surface waves in homogeneous or smooth media. We test the validity of this technique in the case of sharp lateral heterogeneity, by examining paths along the western edge of continental North America. After cross correlating several years of time series of ambient seismic noise, we extract interstation Rayleigh waves with different arrivals in the frequency of 0.04 to 0.06 Hz (periods 17 to 25 s). Using beamforming and seismic wavefield simulations, we show that the different Rayleigh wave arrivals are related to the oceanic and continental paths, respectively. This multipathing of Rayleigh waves that is identified from ambient noise is also identified from earthquakes. Our results demonstrate that seismic noise interferometry is capable of extracting realistic surface waves for complex structural paths such as along the continental margin of North America. Additional studies from other regions may demonstrate the potential for using multipathing surface waves within full waveform inversion.
Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota
Authors: Kearney Sean M , Gibbons Sean M , Poyet Mathilde , Gurry Thomas , Bullock Kevin , Allegretti Jessica R , Clish Clary B , Alm Eric J 
Published: June 2018

Abstract
Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.
A rapid method for assessing the accumulation of microplastics in the sea surface microlayer (SML) of estuarine systems
Authors: Anderson Zachary T. , Cundy Andrew B. , Croudace Ian W. , Warwick Phillip E. , Celis-Hernandez Omar , Stead Jessica L. 
Published: June 2018

AbstractMicroplastics are an increasingly important contaminant in the marine environment. Depending on their composition and degree of biofouling, many common microplastics are less dense than seawater and so tend to float at or near the ocean surface. As such, they may exhibit high concentrations in the sea surface microlayer (SML – the upper 1–1000 μm of the ocean) relative to deeper water. This paper examines the accumulation of microplastics, in particular microfibres, in the SML in two contrasting estuarine systems – the Hamble estuary and the Beaulieu estuary, southern U.K., via a novel and rapid SML-selective sampling method using a dipped glass plate. Microplastic concentrations (for identified fibres, of 0.05 to 4.5 mm length) were highest in the SML-selective samples (with a mean concentration of 43 ± 36 fibres/L), compared to <5 fibres/L for surface and sub-surface bulk water samples. Data collected show the usefulness of the dipped glass plate method as a rapid and inexpensive tool for sampling SML-associated microplastics in estuaries, and indicate that microplastics preferentially accumulate at the SML in estuarine conditions (providing a potential transfer mechanism for incorporation into upper intertidal sinks). Fibres are present (and readily sampled) in both developed and more pristine estuarine systems.
Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours
Authors: Burnett Kyra , Edsinger Eric , Albrecht Dirk R. 
Published: June 2018

AbstractImaging living organisms at high spatial resolution requires effective and innocuous immobilization. Long-term imaging places further demands on sample mounting with minimal perturbation of the organism. Here we present a simple, inexpensive method for rapid encapsulation of small animals of any developmental stage within a photo-crosslinked polyethylene glycol (PEG) hydrogel, gently restricting movement within their confined spaces. Immobilized animals maintain their original morphology in a hydrated environment compatible with chemical treatment, optical stimulation, and light-sheet microscopy. We demonstrate prolonged three-dimensional imaging of neural responses in the nematode Caenorhabditis elegans, recovery of viable organisms after 24 h, and imaging of larger squid hatchlings. We characterize a range of hydrogel and illumination conditions for immobilization quality, and identify paralytic-free conditions suitable for high-resolution single-cell imaging. Overall, PEG hydrogel encapsulation provides fast, versatile, and gentle mounting of small living organisms, from yeast to zebrafish, for continuous observation over hours.
Magnetic activity evolution on Sun-like stars
Authors: Gondoin P. 
Published: June 2018

Context. Characterising the time evolution of magnetic activity on Sun-like stars is important not only for stellar physics but also for determining the environment in which planets evolve.
Aims. In recent decades, many surveys of open clusters have produced extensive rotation periods measurements on Sun-like stars of different ages. The present study uses this information with the aim to improve the description of their magnetic activity evolution.
Methods. I present a method that infers the long-term evolution of Ca II chromospheric (R′HK) and X-ray coronal (LX) emission on solar mass stars by combining a best fit parametric model of their rotation evolution with empirical rotation-activity relationships.
Results. The inferred scenario reproduces the high chromospheric and coronal emission levels around R′HK ≈ 10−4 and LX ≈ 1030 erg s−1 that are observed on pre-main sequence (PMS) stars. At the end of the PMS contraction phase around the age of ~30 Myr, the slowest rotating stars experience a rapid transition of their magnetic activity to more moderate levels around R′HK ≈ 4 × 10−5 and L5 ≈ 1029 erg s−1. This transition occurs later on more rapidly rotating stars, up to an age of ~600 Myr for the fastest rotators. After this brief episode of large magnetic activity decay, the average chromospheric and coronal emission levels of solar-mass stars decrease steadily converging towards similar values (R′HK ≈ 10−5 and LX ≈ 1027 erg s−1) by the age of the Sun.
Conclusion. The study suggests that solar mass stars in open clusters with ages between ~30 and ~600 Myr exhibit bimodal distributions of their R′HK chromospheric activity indices and coronal X-ray to bolometric luminosity ratios that can be traced back to their rotation evolution. This conclusion is consistent with available measurements of activity indices from Sun-like stars in nearby open clusters.
Opposition effect on S-type asteroid (25143) Itokawa
Authors: Lee Mingyeong , Ishiguro Masateru 
Published: June 2018

Aims.The opposition effect has been detected on solar system bodies such as asteroids and comets. Two mechanisms have been proposed to explain the effect: the shadow-hiding opposition effect (SHOE) and the coherent backscattering opposition effect (CBOE). The Hayabusa asteroid sample return mission provides a unique opportunity to investigate the opposition effect on disk-resolved images of the S-type asteroid (25413) Itokawa at very small phase anglesα.Methods.We made use of the data taken atα= 0.°04–2.°54 using the Asteroid Multi-band Imaging Camera (AMICA) on UT 2005 October 13. Comparing sets of two images taken at different phase angles, we derived the opposition slope parameter (SOE) that characterizes a linear increase in the reflectanceI∕Fper unit phase angle.Results.We found that (i)SOEis less dependent on the incidence and emission angles; (ii) the reflectance increases nonlinearly toward the opposition at small angles withα≲ 1.°4, showing a good correlation between meanI∕FandSOE; and (iii)SOEbecomes nearly constant atα≳ 1.°4 and shows no clear correlation betweenI∕FandSOE.Conclusions.From these results, we conjecture that CBOE is dominant atα≲ 1.°4, while SHOE is dominant atα≳ 1.°4.
Magnoflorine Enhances LPS-Activated Pro-Inflammatory Responses via MyD88-Dependent Pathways in U937 Macrophages
Authors: Haque Md. Areeful , Jantan Ibrahim , Harikrishnan Hemavathy , Abdul Wahab Siti Mariam 
Published: June 2018

AbstractMagnoflorine, a major bioactive metabolite isolated from Tinospora crispa, has been reported for its diverse biochemical and pharmacological properties. However, there is little report on its underlying mechanisms of action on immune responses, particularly on macrophage activation. In this study, we aimed to investigate the effects of magnoflorine, isolated from T. crispa on the pro-inflammatory mediators generation induced by LPS and the concomitant NF-κB, MAPKs, and PI3K-Akt signaling pathways in U937 macrophages. Differentiated U937 macrophages were treated with magnoflorine and the release of pro-inflammatory mediators was evaluated through ELISA, while the relative mRNA expression of the respective mediators was quantified through qRT-PCR. Correspondingly, western blotting was executed to observe the modulatory effects of magnoflorine on the expression of various markers related to NF-κB, MAPK and PI3K-Akt signaling activation in LPS-primed U937 macrophages. Magnoflorine significantly enhanced the upregulation of TNF-α, IL-1β, and PGE2 production as well as COX-2 protein expression. Successively, magnoflorine prompted the mRNA transcription level of these pro-inflammatory mediators. Magnoflorine enhanced the NF-κB activation by prompting p65, IκBα, and IKKα/β phosphorylation as well as IκBα degradation. Besides, magnoflorine treatments concentration-dependently augmented the phosphorylation of JNK, ERK, and p38 MAPKs as well as Akt. The immunoaugmenting effects were further confirmed by investigating the effects of magnoflorine on specific inhibitors, where the treatment with specific inhibitors of NF-κB, MAPKs, and PI3K-Akt proficiently blocked the magnoflorine-triggered TNF-α release and COX-2 expression. Magnoflorine furthermore enhanced the MyD88 and TLR4 upregulation. The results suggest that magnoflorine has high potential on augmenting immune responses.
Disruptive Hearing Technologies and Mild Sensorineural Hearing Loss I: Accessibility and Affordability Issues
Authors: Johnson Carole , Danhauer Jeffrey , Jilla Anna 
Published: June 2018

AbstractLimited accessibility to and affordability of hearing health care (HHC) and hearing aids (HAs) are two reasons why people do not seek treatment for their hearing losses. This article is the first in a series of two and discusses affordability issues (i.e., billing models, cost-effectiveness, insurance coverage, and reimbursement) related to and provides a historical context for the Over-the-Counter Hearing Aid Act of 2017. This piece of legislation supports development of a new class of over-the-counter HAs that represents a disruptive technology that may transform the HHC industry by reducing costs specific to the device. A discussion of ethical issues and the importance of using evidence-based practice guidelines set the stage for the second article in this series, which reviews relevant research on issues pertaining to persons with mild hearing loss.
Effectiveness of Auditory Measures for Detecting Hidden Hearing Loss and/or Cochlear Synaptopathy: A Systematic Review
Authors: James Jessica , Park Jin , Smith Emily , Johnson Carole , Clifton Shari , Danhauer Jeffrey , Barbee Christi 
Published: June 2018

AbstractStandard audiometric evaluations are not sensitive enough to identify hidden hearing loss (HHL) and/or cochlear synaptopathy (CS). Patients with either of these conditions frequently present with difficulty understanding speech in noise or other complaints such as tinnitus. The purpose of this systematic review is to identify articles in peer-reviewed journals that assessed the sensitivity of audiologic measures for detecting HHL and/or CS, and which showed potential for use in a clinical test battery for these disorders. A reference librarian submitted specific boolean terminology to MEDLINE, Embase, and Web of Science. The authors used a consensus approach with specially designed score sheets for the selection of titles, abstracts, and then articles for inclusion in the systematic review and for quality assessment. Fifteen articles were included in the systematic review. Seven articles involved humans; seven involved animals, and one study used both humans and animals. Results showed that pure-tone audiometry to 20 kHz, otoacoustic emissions, electrocochleography, auditory brainstem response (ABR), electrophysiological tests, speech recognition in noise with and without temporal distortion, interviews, and self-report measures have been used to assess HHL and/or CS. For HHL, ultra-high-frequency audiometry may help identify persons with sensory hair cell loss that does not show up on standard audiograms. Promising nonbehavioral measures for CS included ABR wave I amplitude, the summating potential-to-action potential ratio, and speech recognition in noise with and without temporal distortion. Self-report questionnaires also may help identify auditory dysfunction in persons with normal hearing.
Re-centering Central Asia: China’s “New Great Game” in the old Eurasian Heartland
Authors: Chen Xiangming , Fazilov Fakhmiddin 
Published: June 2018

AbstractChina’s President Xi Jinping’s Central Asian tour in fall 2013 marked Beijing’s unprecedented (re)turn to Central Asia as a lynchpin of the “Silk Road Economic Belt” of the globally ambitious Belt and Road Initiative (BRI). China’s BRI positions Central Asia as the crucial nexus for the cross-regional long-distance loops of trade, investment, and infrastructure development. By revisiting the classical geopolitical theory about the original Eurasian Heartland and its contemporary offshoots, we extract some insights for understanding the new China-Central Asia transboundary regional nexus. In a double-pronged empirical analysis of China’s development strategies regarding Central Asia, we examine: (1) the construction of oil and gas pipelines from Central Asia to transmit energy all the way to China’s east coast, and (2) the launch and expansion of the Eurasian Railroad to transport goods from China’s manufacturing bases in both coastal and inland regions to Europe and Central Asia. In synthesizing the findings from this coupled analysis through classical and contemporary theoretical lenses, we discuss how China’s growing influence in Central Asia via the BRI can reshape the region’s diverse national interests, development opportunities and constraints while fostering closer China-Central Asia bilateral cooperation across multiple national boundaries. In light of the analysis, we also offer an updated view and critique of the classical Heartland/Rimland theories and discuss how a China-centric “New Great Game” differs from its original nineteenth century antecedent while pointing to similar underpinnings.
ICBdocker: a Docker image for proteome annotation and visualization
Authors: Bordin Nicola , Devos Damien P 
Published: June 2018

Abstract

Summary
We introduce ICBdocker, a Docker environment that allows the annotation of functional and structural features of proteomes through a Python/Perl pipeline. DataTables pages make it easy to set up a web-resource for research groups with a focus on the same organisms or datasets. The results are available as tab-separated values files and HTML, allowing data analysis and browsing. The pipeline focuses on modularity and scalability, with capability of integrating with multi-processing and high-performance computing clusters.

Availability and implementation
ICBdocker is freely available on DockerHub at https://hub.docker.com/r/bordin89/icb/ Source code and documentation are available on GitHub at: https://github.com/bordin89/ICB_docker.