bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tapered Optical Fiber-Based LSPR Biosensor for Ascorbic Acid Detection
Authors: Zhu Guo , Singh Lokendra , Wang Yu , Singh Ragini , Zhang Bingyuan , Liu Fengzhen , Kaushik Brajesh Kumar , Kumar Santosh 
Published: October 2020

AbstractThe ascorbic acid (AA) is a biomarker that can be used to detect the symptoms of severe disorders such as scurvy, Parkinson’s, Alzheimer’s, and cardiovascular diseases. In this work, a simple and effective sensor model is developed to diagnose the presence of AA samples. To develop the sensor, a tapered single-mode optical fiber has been used with the well-known phenomenon of localized surface plasmon resonance (LSPR). For LSPR, the tapered region is immobilized with synthesized gold nanoparticles (AuNPs) and zinc oxide nanoparticles (ZnO-NPs) whose absorbance peak wavelengths appear at 519nm and 370nm, respectively. On the basis of nanoparticles (NPs) configurations, two different biosensor probes are developed. In the first one, the sensing region is immobilized with AuNPs and named Probe I. In the second probe, the immobilized layer of AuNPs is further coated with a layer of ZnO-NPs, and a resultant probe is termed as Probe II. The characterizations of synthesized AuNPs and developed fiber probes are done by the ultraviolet-visible (UV-vis) spectrophotometer, high-resolution transmission electron microscope (HR-TEM), atomic force microscopy (AFM), and scanning electron microscope (SEM). To enhance the selectivity, a sensing region of probes is functionalized with ascorbate oxidase enzyme that oxidizes the AA in the presence of oxygen. The response of developed sensor probes is authenticated by sensing the samples of AA in the range from 500 nM to 1 mM, which covers the range of AA found in human bodies, i.e., 40µM–120µM. The performance analysis of the developed sensor probes has been done in terms of their stability, reproducibility, reusability, and selectivity. To observe the stability of AA, a pH-test has also been done that results in a better solubility of AA molecules in phosphate-buffered saline (PBS) solution.
Improving topic modeling through homophily for legal documents
Authors: Ashihara Kazuki , El Vaigh Cheikh Brahim , Chu Chenhui , Renoust Benjamin , Okubo Noriko , Takemura Noriko , Nakashima Yuta , Nagahara Hajime 
Published: October 2020

AbstractTopic modeling that can automatically assign topics to legal documents is very important in the domain of computational law. The relevance of the modeled topics strongly depends on the legal context they are used in. On the other hand, references to laws and prior cases are key elements for judges to rule on a case. Taken together, these references form a network, whose structure can be analysed with network analysis. However, the content of the referenced documents may not be always accessed. Even in that case, the reference structure itself shows that documents share latent similar characteristics. We propose to use this latent structure to improve topic modeling of law cases using document homophily. In this paper, we explore the use of homophily networks extracted from two types of references: prior cases and statute laws, to enhance topic modeling on legal case documents. We conduct in detail, an analysis on a dataset consisting of rich legal cases, i.e., the COLIEE dataset, to create these networks. The homophily networks consist of nodes for legal cases, and edges with weights for the two families of references between the case nodes. We further propose models to use the edge weights for topic modeling. In particular, we propose a cutting model and a weighting model to improve the relational topic model (RTM). The cutting model uses edges with weights higher than a threshold as document links in RTM; the weighting model uses the edge weights to weight the link probability function in RTM. The weights can be obtained either from the co-citations or from the cosine similarity based on an embedding of the homophily networks. Experiments show that the use of the homophily networks for topic modeling significantly outperforms previous studies, and the weighting model is more effective than the cutting model.
Exploring the Emission Characteristics and Reduction Potential of Air Pollutants From Chinese Aluminum Industry: 2005–2025
Authors: Cheng Ke , Zhang Jiayu , Yi Peng , Zhu Guifen , Hao Weiwei , Ji Wanwan , Tian Hezhong , Wang Yan 
Published: October 2020

AbstractAmidst the rising desire for environmental governance in China, the aluminum industry has aroused more extensive attention because of the intensive energy consumption. Based on the process‐based life cycle assessment (PLCA) method, emissions of nine typical air pollutants (PM, SO2, NOX, VOCs, CO, CO2, fluoride, asphalt fume, and PFCs) by the primary aluminum industry in China over the period 2005–2017 were calculated. The production process of aluminum industry was decomposed into three primary processes (alumina, carbon for aluminum, and electrolytic aluminum), and corresponding emission sources (fuel combustion, power consumption, and production process) were identified. The contributions of different processes and emission sources were then compared and spatiotemporal changes and their relation with existing policies were determined. The results show that the production of aluminum and the indirect source of electricity power are the dominant driving forces of air pollutants emissions of China's primary aluminum industry and aluminum production process, respectively. Pollutant‐emitting areas of the aluminum industry differed considerably. The country's industrial policies were discovered to strongly influence the emissions of aluminum industry. Based on the emission inventory, three scenarios were established to project the potential of emission reduction of air pollutants from the aluminum industry in China until the year 2025. In addition, the effectiveness of China's heavy pollution emergency response policy was evaluated. It suggests differentiated emergency control mode would be a more effective pathway for reducing the emissions of air pollutants by the aluminum industry.
Cosmic Ray Neutron Soil Moisture Estimation Using Physically Based Site‐Specific Conversion Functions
Authors: Andreasen Mie , Jensen Karsten H. , Bogena Heye , Desilets Darin , Zreda Marek , Looms Majken C. 
Published: October 2020

AbstractIn order to advance the use of the cosmic ray neutrons (CRNs) to map soil moisture in heterogeneous landscapes, we need to develop a methodology that reliably estimates soil moisture without having to collect 100+ soil samples for each point along the survey route. In this study, such an approach is developed using physically based modeling with the numerical MCNP neutron transport code. The objective is to determine site‐specific conversion functions to estimate soil moisture from CRNs for the dominant land covers. Here, we assess this methodology at three field sites with similar mineral soil composition, but different land covers. First, we ensure that the developed models capture the most important differences in neutron transport behavior across sites. For this, we use measured time series and height profiles of thermal and epithermal neutrons. Then, we compare the estimates obtained from the site‐specific conversion functions with the standard N0‐calibration function. Finally, we compare the CRN soil moisture estimates with independent soil moisture estimates. Overall, the site‐specific models are in agreement with the observed trends in neutron intensities. The site‐specific soil moisture is similar to the N0‐estimated soil moisture, which results in comparable statistical measures. We show that various land covers have a significant impact on the amount and soil moisture sensitivity of epithermal neutrons, while the thermal neutrons are affected to a less degree. Thereby, thermal‐to‐epithermal neutron ratios can be used to identify the land cover type and thereby the appropriate conversion function for soil moisture estimation for each point along the survey route.
Constraining Mantle Viscosity Structure From a Statistical Analysis of Slab Stagnation Events
Authors: Wang Yongming , Li Mingming 
Published: October 2020

AbstractThe viscosity structure of Earth's mantle, even the 1‐D radial viscosity profile, remains not well constrained. The dynamics of the subducting slabs is strongly affected by, and can be used to constrain, the viscosity structure of the mantle. Here, we perform fully dynamic, self‐consistent mantle convection models to study the dynamics of subducted slabs in the deep mantle. We use a statistical analysis approach to quantify how the depth distribution of flat‐lying slabs is affected by the depth‐dependence of mantle viscosity. We find that, for cases in which the viscosity increases at 660 km depth, whether sharply or gradually, flat‐lying slabs preferentially occur above this depth, and importantly, up to ∼30% of the subducted slabs previously flatted at this depth later sink to the deep lower mantle and maintain a flat‐lying morphology. The frequency of (or the probability to have) flat‐lying slabs at ∼1,000 km depth in these cases is similar to cases in which the viscosity jump occurs at 1,000 km depth. Therefore, to explain the presence of flat‐lying slabs at ∼1,000 km depth for the Earth does not require a viscosity jump at this depth. In contrast, a viscosity jump merely occurring at ∼1,000 km depth causes a lack of flat‐lying slabs in the uppermost lower mantle at ∼700–900 km depth and is inconsistent with seismic observations. The presence of flat‐lying slab materials in the Earth's uppermost lower mantle requires a viscosity increase at 660 km depth.
A Statistical Study of Polar Cap Flow Channels and Their IMF By Dependence
Authors: Herlingshaw K. , Baddeley L. J. , Oksavik K. , Lorentzen D. A. 
Published: October 2020

AbstractAn algorithm to detect high‐speed ionospheric flow channels (FCs) in the polar cap was applied to data from the Longyearbyen radar of the Super Dual Auroral Radar Network. The Longyearbyen radar is at high latitude (78.2°N, 16.0°E geographic coordinates) and points northeast; therefore, it is in an ideal position for measuring zonal flows in the polar cap. The algorithm detected 998 events in the dayside polar cap region over 2 years of observations. The detected FCs typically were between 200 and 300 km latitudinal width, 1.1–1.3 km s−1 peak velocity, and 3 min in duration. The FC location shows an interplanetary magnetic field (IMF) By dependency, moving dawnward/duskward for a +By/−By. The FC monthly occurrence shows a bimodal distribution with peaks around the spring and autumn equinoxes, likely due to increased coupling between the solar wind‐magnetosphere‐ionosphere system at these times. The highest peak velocities show an absence of broad FC widths, suggesting that as the flow speed increases in the polar cap, the channels become more localized and narrow.
Prediction of Elastic Properties Within CO2 Plume at Sleipner Field Using AVS Inversion Modified for Thin‐Layer Reflections Guided by Uncertainty Estimation
Authors: Ghosh Ranjana , Ojha Maheswar 
Published: October 2020

AbstractExisting amplitude variation with offset (AVO) and slowness (AVS) theories fail to interpret observed amplitudes in terms of actual elastic properties of the media for a reflection event resulting from a stack of thin layers. We propose a method to replace the stack of thin layers with an equivalent medium of elastic properties using the Backus averaging theory. Numerical examples show considerable deviation in intercept calculated from the modified AVO and AVS theories from the conventional methods. AVS theory is preferred as it can be applied irrespective of impedance contrast in both precritical and postcritical reflections, and no spherical divergence correction is required. P and S wave velocities, density, and thickness of thin layers are determined using the inversion scheme of very fast simulated annealing (VFSA). Uncertainty in prediction is evaluated using an approximate marginal posterior probability density function and a parameter correlation matrix. We demonstrate our methodology on synthetic and real seismic data from the Sleipner field, which is a good example of enhanced seismic amplitudes due to interference among reflections from thin layers. We select 11 common depth point (CDP) gathers for amplitude analysis of four identified reflectors along a line of 3‐D seismic data acquired in 2008. Predicted mean models of CO2‐saturated sand layers at all locations show that the thickness, density, and P and S wave velocities vary from 5–7 m, 1.8–2.0 g/cm3, and 1,460–1,490 and 630–650 m/s, respectively. Our analysis suggests that the model parameters are well constrained and independent except at a few locations.
Magnetic Cr‐Rich Spinel in Serpentinized Ultramafic Complexes
Authors: Yu Yongjae , Tikoff Basil 
Published: October 2020

AbstractIn comparison to the six spinel end‐members in the spinel prism, magnetic information on the intermediate spinel compositions is relatively poorly established. To investigate magnetic properties of intermediate compositions of Cr‐rich spinel, we collected 12 samples that might contain potentially magnetic Cr‐rich spinel. On the basis of chemical composition analysis and physical magnetic behavior, magnetic Group A Fe‐rich spinel (i.e., magnetite), magnetic Group B Cr‐rich spinel, and paramagnetic Group C Cr‐Al‐rich spinel were identified. Magnetite is solely responsible for the natural remanent magnetization (NRM) in severely serpentinized samples from intraoceanic island arcs, orogenic exposures of ultramafics, and back‐arc continental lithosphere settings. Magnetic Group B Cr‐rich spinel shows maximum unblocking temperatures of 200–280°C. Such temperatures permit Cr‐rich spinel to contribute to magnetic anomalies up to about 8–12 km in terrestrial lithosphere settings, given a normal geothermal gradient of 25 K/km. The existence of magnetic Cr‐rich spinel requires certain compositional conditions including a cation ratio of [Cr]/[Fe2+ + Fe3+] from 1.33 to 1.56 as well as a low oxide ratio of (Al2O3 + MgO)/(Cr2O3 + FeO + Fe2O3) less than 10%. It is evident that compositions of spinels are related with the degree of serpentinization as Group A spinel is observed along the fractures between/among olivine grains in heavily serpentinized rocks. Spinels in Groups B and C seem to experience less severe metasomatic or hydrothermal alteration during serpentinization. Distribution of magnetic Cr‐rich spinel along the fractures of silicates (mostly olivine) may support a chemical origin of the NRM. Thus, Cr‐rich spinel is a potential NRM carrier and a source of magnetic anomalies in ultramafic complexes.
Machine Learning Accelerates Parameter Optimization and Uncertainty Assessment of a Land Surface Model
Authors: Sawada Yohei 
Published: October 2020

AbstractThe performance of land surface models (LSMs) significantly affects the understanding of atmospheric and related processes. Many of the LSMs' soil and vegetation parameters were highly uncertain so that it is crucially important to efficiently optimize them. Here I present a globally applicable and computationally efficient method for parameter optimization and uncertainty assessment of the LSM by combining Markov Chain Monte Carlo (MCMC) with machine learning. First, I performed the long‐term (decadal‐scale) ensemble simulation of the LSM, in which each ensemble member has different parameters' values, and calculated the gap between simulation and observation, or the cost function, for each ensemble member. Second, I developed the statistical machine learning‐based surrogate model, which is computationally cheap but accurately mimics the relationship between parameters and the cost function, by applying the Gaussian process regression to learn the model simulation. Third, I applied MCMC by repeatedly evaluating the surrogate model to get the posterior probabilistic distribution of parameters. Using satellite passive microwave brightness temperature observations, both synthetic and real‐data experiments in the Sahel region of west Africa were performed to optimize unknown soil and vegetation parameters of the LSM. The primary findings are (1) the proposed method is 50,000 times as fast as the direct application of MCMC to the full LSM; (2) the skill of the LSM to simulate both soil moisture and vegetation dynamics can be improved; and (3) I successfully quantify the characteristics of equifinality by obtaining the full nonparametric probabilistic distribution of parameters.
Morphology, Bedload, and Sorting Process Variability in Response to Lateral Confinement: Results From Physical Models of Gravel‐bed Rivers
Authors: Carbonari Costanza , Recking Alain , Solari Luca 
Published: October 2020

This paper uses flume experiments to investigate the influence of lateral width confinement on channel morphology, sediment sorting, and bedload transport. Three runs of about 60 hr were carried out under constant feeding rate equal to 0.6 l/s and 8 g/s, with a bimodal mixture of natural sediments, a fixed flume slope of 3%, and width imposed by lateral walls from 0.12 to 0.50 m in order to model three different flow confinement configurations. Despite the three runs transporting at the same rate on average, they presented different gravel‐bed river morphologies and different degrees of bed complexity. The three runs also presented differences in bedload transport rate fluctuations associated with different magnitude and mechanisms of bed storage and release of sediments. The intermediate width configuration (Run 2) was found to have a minimum storage and release of sediments compared with both the wider configuration (Run 1) and the narrower configuration (Run 3). Runs 1 and 3 were characterized by a significant storage and release of sediments resulting in a highly fluctuating bedload transport rate; however, while Run 1 (braiding morphology) stored and released sediments through lateral deposits and bed variations with planimetric sorting, Run 3 (single‐thread channel) stored and released sediments through variations in bed elevation accompanied by vertical sorting. We extrapolated this concept to the full set of gravel‐bed river morphologies, thus speculating about the channel morphology for optimal sediment transfer.
On the Use of the Term “Evapotranspiration”
Authors: Miralles D. G. , Brutsaert W. , Dolman A. J. , Gash J. H. 
Published: October 2020

AbstractEvaporation is the phenomenon by which a substance is converted from its liquid into its vapor phase, independently of where it lies in nature. However, language is alive, and just like regular speech, scientific terminology changes. Frequently, those changes are grounded on a solid rationale, but sometimes these semantic transitions have a fragile foundation. That is the case with “evapotranspiration.” A growing generation of scientists have been educated on using this terminology and are unaware of the historical controversy and physical inconsistency that surrounds it. Here, we present what may appear to some as an esoteric linguistic discussion, yet it was originally triggered by the increasing time some of us have devoted to justifying our word choice to reviewers, editors, and peers. By clarifying our arguments for using the term “evaporation,” we also seek to prevent having to revive this discussion every time a new article is submitted, so that we can move directly on to more scientifically relevant matters.
Aberrant super-enhancer landscape reveals core transcriptional regulatory circuitry in lung adenocarcinoma
Authors: Zhang Te , Song Xuming , Zhang Zeyu , Mao Qixing , Xia Wenjie , Xu Lin , Jiang Feng , Dong Gaochao 
Published: October 2020

AbstractLung adenocarcinoma (LUAD) relies on dysregulated gene expression to sustain its infinite growth and progression. Emerging evidence indicates that aberrant transcriptional program results from core transcriptional regulatory circuitry (CRC) which is driven by super-enhancers (SEs). In this study, by integrating profiles of H3K27Ac chromatin immunoprecipitation sequencing (ChIP-seq) from normal adult lung and LUAD cell lines, we revealed that widespread alterations of the super-enhancer were presence during lung carcinogenesis. With SE-based modeling of regulatory circuits and assessments of transcription factor (TF) dependencies, we reconstructed an interconnected transcriptional regulation network formed by three master TFs, including ELF3, EHF, and TGIF1, all of which promoted each other’s expression that confirmed by ChIP-qPCR and western blot. Loss-of function assay revealed that each of them is essential for LUAD cells survival, invasion and metastasis. Meanwhile, the rescue assay also illustrated the transacting transcriptional regulatory circuitry. In addition, the mRNA levels of ELF3, EHF, and TGIF1 were differentially expressed in LUAD tumors and peritumoral tissue. IHC of serial sections revealed that high expressions of CRC (ELF3/EHF/TGIF1-High) were closely associated with high proliferative activity in tumor tissue and poor prognosis on patients with LUAD. Finally, we used small molecular inhibitors to perturb the transcriptional circuitry, also exhibited a prominent anti-cancer effect in vitro. Our findings reveal the mechanism of the transcriptional dysregulation and addiction of LUAD.
The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis
Authors: Wegwitz Florian , Prokakis Evangelos , Pejkovska Anastasija , Kosinsky Robyn Laura , Glatzel Markus , Pantel Klaus , Wikman Harriet , Johnsen Steven A. 
Published: October 2020

AbstractThe HER2-positive breast cancer subtype (HER2+-BC) displays a particularly aggressive behavior. Anti-HER2 therapies have significantly improved the survival of patients with HER2+-BC. However, a large number of patients become refractory to current targeted therapies, necessitating the development of new treatment strategies. Epigenetic regulators are commonly misregulated in cancer and represent attractive molecular therapeutic targets. Monoubiquitination of histone 2B (H2Bub1) by the heterodimeric ubiquitin ligase complex RNF20/RNF40 has been described to have tumor suppressor functions and loss of H2Bub1 has been associated with cancer progression. In this study, we utilized human tumor samples, cell culture models, and a mammary carcinoma mouse model with tissue-specific Rnf40 deletion and identified an unexpected tumor-supportive role of RNF40 in HER2+-BC. We demonstrate that RNF40-driven H2B monoubiquitination is essential for transcriptional activation of RHO/ROCK/LIMK pathway components and proper actin-cytoskeleton dynamics through a trans-histone crosstalk with histone 3 lysine 4 trimethylation (H3K4me3). Collectively, this work demonstrates a previously unknown essential role of RNF40 in HER2+-BC, revealing the H2B monoubiquitination axis as a possible tumor context-dependent therapeutic target in breast cancer.