bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visceral adiposity index is a better predictor of unhealthy metabolic phenotype than traditional adiposity measures: results from a population-based study
Authors: Ferreira Fabrícia Geralda , Juvanhol Leidjaira Lopes , da Silva Danielle Cristina Guimarães , Longo Giana Zarbato 
Published: December 2018

AbstractObjectiveThe present study aimed to investigate whether the visceral adiposity index (VAI) is an effective predictor to identify unhealthy metabolic phenotype by comparing normal-weight and overweight individuals.DesignA population-based cross-sectional study. Data were collected by interviews, anthropometric evaluation, dietetic, clinical and laboratory tests. The area under the receiver-operating characteristic curve (AUC) and prevalence ratio (PR), obtained from Poisson regression, were used to compare the predictive capacity of the obesity indicators evaluated (VAI, BMI, waist and neck circumference, waist-to-height and waist-to-hip ratios) and their association with the unhealthy metabolic phenotype. All analyses were stratified by sex and by nutritional status.SettingViçosa, Minas Gerais, Brazil.ParticipantsA total of 854 Brazilian adults (20–59 years old) of both sexes.ResultsVAI was the best predictor for unhealthy metabolic phenotype among men (AUC = 0·865) and women (AUC = 0·843) at normal weight. VAI also had the best predictive capacity among overweight women (AUC = 0·903). Among overweight men, its accuracy (AUC = 0·830) was higher than that of waist-to-hip ratio. In the adjusted regression models, VAI was the indicator most strongly associated with the unhealthy metabolic phenotype, especially among those with normal weight (PR = 6·74; 95 % CI 3·15, 14·42 for men; PR = 7·14; 95 % CI 3·79, 13·44 for women).ConclusionsVAI has better predictive capacity in detecting unhealthy metabolic phenotype than conventional anthropometric indicators, regardless of nutritional status and sex.
Increased copper levels inhibit denitrification in urban soils
Authors: LI Shun , YANG Xiaoru , BUCHNER Daniel , WANG Haitao , XU Huijuan , HADERLEIN Stefan B. , ZHU Yongguan 
Published: December 2018

ABSTRACTThe consequences of urbanisation for Earth's biogeochemical cycles are largely unexplored. Copper (Cu) in urban soils is being accumulated mainly due to anthropogenic activities under rapid urbanisation. The increasing Cu concentrations may contribute to altering soil nitrogen (N) cycling in urban ecosystems through modulating denitrification processes. This research aims to identify how Cu impacts urban soil denitrification functions and denitrifier abundance. An urban park soil with a background total Cu concentration of 7.9μgg–1 was incubated anaerobically with different Cu amendments (10, 20, 40, 80 and 160μg Cu g–1 soil), similar to prevalent Cu contents in urban soils. We evaluated the soil denitrification functions using the acetylene (C2H2) inhibition method and assessed the denitrifier abundance by quantitative polymerase chain reaction (qPCR) analyses of denitrifying marker genes (nirK, nirS and nosZ). At the function level, we observed that both the potential soil denitrification activity and the N2O emission rate due to denitrification were significantly (P<0.05) inhibited by Cu; even the lowest Cu addition (10μg Cu g–1 soil) drastically affected the denitrification function. Moreover, Cu significantly (P<0.05) decreased the abundance of nirK and nirS genes at the additions of 160μg Cu g–1 soil and 40μg Cu g–1 soil, respectively, whereas it had no clear impact on nosZ gene copies. Further correlation analyses revealed that the potential denitrification activity was positively correlated to the copy numbers of nirK and nirS genes, but it was not correlated to nosZ gene abundance. These findings indicate that Cu additions inhibited soil denitrification function and decreased denitrifier abundance in the investigated urban park soil. Our results suggest that Cu accumulation in urban soils, resulting from urbanisation, may generally influence denitrification in urban ecosystems.
Stress Triggering of the 2005 Eruption of Sierra Negra Volcano, Galápagos
Authors: Gregg P. M. , Le Mével H. , Zhan Y. , Dufek J. , Geist D. , Chadwick W. W. 
Published: December 2018

AbstractExtensive vertical deformation (>4.5 m) observed at Sierra Negra volcano Galápagos, Ecuador, between 1992 and the 2005 eruption led scientists to hypothesize that repeated faulting events relieved magma chamber overpressure and prevented eruption. To better understand the catalyst of the 2005 eruption, thermomechanical models are used to track the stress state and stability of the magma storage system during the 1992–2005 inflation events. Numerical experiments indicate that the host rock surrounding the Sierra Negra reservoir remained in compression with minimal changes in overpressure (~10 MPa) leading up to the 2005 eruption. The lack of tensile failure and minimal overpressure accumulation likely inhibited dike initiation and accommodated the significant inflation without the need for pressure relief through shallow trapdoor faulting events. The models indicate that static stress transfer due to the Mw 5.4 earthquake 3 hr prior to the eruption most likely triggered tensile failure and catalyzed the 2005 eruption.
Iron Isotope Systematics of the Panzhihua Mafic Layered Intrusion Associated With Giant Fe‐Ti Oxide Deposit in the Emeishan Large Igneous Province, SW China
Authors: Cao Yonghua , Wang Christina Yan , Huang Fang , Zhang Zhaofeng 
Published: December 2018

AbstractIn order to investigate how Fe was enriched from parental high‐Ti basaltic magma to form the stratigraphically thick Fe‐Ti oxide ore at the bottom layers, we present a systematic study for Fe isotopic compositions of whole rocks and mineral separates (clinopyroxene, magnetite, and ilmenite) throughout the Panzhihua intrusion. Whole rock δ56Fe ranges from 0 ± 0.02‰ to 0.15 ± 0.04‰, consistent with the range of clinopyroxene (0.01 ± 0.02‰ to 0.16 ± 0.05‰). On the contrary, magnetite (Mt) separates have δ56Fe ranging from 0.17 ± 0.05‰ to 0.62 ± 0.02‰, showing a strikingly complementary trend with coexisting ilmenite (Ilm) separates (−0.52 ± 0.03‰ to −0.09 ± 0.02‰) along the profile. The calculated bulk δ56Fe of Fe‐Ti oxides (Mt + Ilm), however, has a small range from 0.01‰ to 0.16‰, identical to those for clinopyroxene separates and whole rocks. The uniform δ56Fe of clinopyroxene may have resulted from the small Fe isotope fractionation between clinopyroxene and parental magma in early‐stage magma differentiation before substantial crystallization of Fe‐Ti oxides. The complementary trends of δ56Fe for Mt and Ilm along the profile and the uniform bulk δ56Fe of Fe‐Ti oxides are better interpreted as in situ crystallization of Fe‐Ti oxides from the interstitial liquid. Our Fe isotopic data and petrographic observations indicate that the thick Fe‐Ti oxide ore layers in the lower zone of the Panzhihua intrusion may be attributed to in situ crystallization of Mt and Ilm from the interstitial, immiscible Fe‐rich melt in the lower part of the magma chamber.
Assessing Superspheroids in Modeling the Scattering Matrices of Dust Aerosols
Authors: Lin Wushao , Bi Lei , Dubovik Oleg 
Published: December 2018

AbstractAtmospheric dust particles are known to have diverse and irregular morphologies. In order to account for nonsphericity, the spheroidal model with an aspect ratio distribution has been extensively used for modeling the optical properties of dust. The spheroidal model is superior to the spherical shape assumption, but it requires further improvement. In this study, superspheroids' modeling capabilities were systematically examined by comprehensively comparing the spheroid's and superspheroid's scattering matrices. Superspheroids have one more degree of freedom than spheroids and can be nonspherical at an aspect ratio of unity. The invariant imbedding T‐matrix and the improved geometrical optics methods were employed to compute superspheroids' single‐scattering properties with a wide distribution of aspect ratios and a number of roundness parameters. We then assessed the spheroidal and superspheroidal models' applicability for simulating the scattering matrices of 25 dust samples from the Amsterdam‐Granada Light Scattering Database. It was found that extreme aspect ratios for spheroids in reproducing the measurements were unnecessary if superspheroids were used. Even with equi‐probable aspect ratio distribution, superspheroids with constrained roundness parameters (from 2.4 to 3.0) could achieve better performances in concurrently matching six nonzero scattering matrix elements from the laboratory measurements. Moreover, superspheroids demonstrated better performances than spheroids in achieving spectral consistency for modeling dust scattering matrices. Therefore, superspheroids appear to be highly promising for atmospheric radiative transfer and remote sensing applications.
Analytical Solution for Anomalous Diffusion of Bedload Tracers Gradually Undergoing Burial
Authors: Wu Zi , Foufoula‐Georgiou Efi , Parker Gary , Singh Arvind , Fu Xudong , Wang Guangqian 
Published: December 2018

AbstractAccounting for the burial of tracer particles during bedload transport is an important component in the formulation of tracer dispersal in rivers. Herein we propose a modified active layer formulation, which accounts for the effect of burial and admits analytical solutions, enabling insightful exploration of the phenomenon of superdiffusion of bedload tracers at the intermediate timescale. This phenomenon has been observed in recent numerical results using the 2‐D Exner‐Based Master Equation. By assuming that tracers in the active layer can exchange with nontracer particles in the substrate layer to preserve mass, and that tracers entering the substrate layer get permanently trapped during the timescale of analysis, we are able to deduce governing equations for the tracer concentration in both layers. The active layer tracer concentration is shown to be governed by an advection‐diffusion equation with a sink term, and the increase of tracers in the substrate layer is driven by a corresponding source term. The solution for the variance of tracer population is analytically determined and can be approximated by the sum of a diffusion‐induced scaling (∝t1) and an advection‐induced scaling (∝t3) terms at the intermediate timescale, which explains the phenomenon of superdiffusion. The proposed formulation is shown to be able to capture the key characteristics of tracer transport as inferred by comparison with available results of numerical simulations.
Comparison of Soil Organic Matter Transformation Processes in Different Alpine Ecosystems in the Qinghai‐Tibet Plateau
Authors: Chen Qiuyu , Lei Tianzhu , Wu Yingqin , Si Guicai , Xi Chuanwu , Zhang Gengxin 
Published: December 2018

AbstractSoils in the Qinghai‐Tibet Plateau are young in terms of development and form a thin, skeletal soil layer because the gravel parent materials are glaciofluvial deposit, eluvium, and fluvial sediment, which are extremely sensitive to global climate change. The lack of understanding of soil organic matter (SOM) transformation processes in this region hinders the prediction of SOM stocks under future climate conditions. In this study, SOM transformation processes were investigated by density groupings and pyrolysis‐gas chromatography/tandem‐mass spectrometry (Py‐GC–MS/MS) in five alpine ecosystems: alpine desert, alpine grassland, alpine meadow, alpine wetland, and alpine forest. The roles of microbial community in different density fractions were elucidated. Soil samples were separated into three fractions with NaI solution: labile fraction (FL; ρ ≤ 1.6 g/cm3), moderate fraction (FM; 1.6 < ρ < 2.25 g/cm3), and recalcitrant fraction (FR; ρ ≥ 2.25 g/cm3). The following results were obtained. (1) The ratios of different fractions (FM/FL, FR/FM, and FR/FL) indicated the transformation processes of SOM, and ratios less than 1 represented degradation. The transformation processes were similar in alpine grassland and meadow and were similar in alpine desert, wetland, and forest but differed from each other. (2) Fungi preferred to degrade plant detritus, which mainly affected FL, whereas bacteria chiefly affected FM. (3) Precipitation altered vegetation type and soil pH, thus affecting communities and microorganism activities and resulting in the above differences. These findings highlight the importance of understanding the limited transformation processes of SOM in ecosystems to predict the impact of climate change on SOM preservation.
Modeling Gas Migration, Sustained Casing Pressure, and Surface Casing Vent Flow in Onshore Oil and Gas Wells
Authors: Lackey G. , Rajaram H. 
Published: December 2018

AbstractFaulty oil and gas wellbores are a primary pathway of concern for gas migration from the deep subsurface into shallow freshwater aquifers. Leaked gases migrating vertically along wellbores either collect and build a pressure at the wellhead known as sustained casing pressure (SCP) or escape into the atmosphere as surface casing vent flow (SCVF). SCP and SCVF are valuable indicators of integrity loss that provide insight into the potential for groundwater contamination through gas migration. Previous models of SCP and SCVF have focused on offshore wells and have not considered the relationship between SCP/SCVF and gas migration away from onshore wells. We present the first modeling framework for SCP and SCVF that is applicable to onshore oil and gas wells constructed with outermost annuli that are hydraulically connected or “open” to the surrounding formation. Our results show that SCP behavior is unique in onshore wells with open annuli, because steady state SCP is not achieved in an open annulus unless gas escapes the wellbore via gas migration (Darcy Flow), a wellhead leak, or a controlled bleed‐off test. We show that appropriately modeling gas leakage along the wellbore and SCP/SCVF helps to constrain methane leakage fluxes from faulty wells and could be integrated with subsurface flow and transport models of stray gas contamination. By relating gas fluxes to SCP/SCVF, our model can provide information used to support regulatory actions informed by SCP/SCVF, which are easy to measure and monitor.
First principles calculation of spin-related quantities for point defect qubit research
Authors: Ivády Viktor , Abrikosov Igor A. , Gali Adam 
Published: December 2018

AbstractPoint defect research in semiconductors has gained remarkable new momentum due to the identification of special point defects that can implement qubits and single photon emitters with unique characteristics. Indeed, these implementations are among the few alternatives for quantum technologies that may operate even at room temperature, and therefore discoveries and characterization of novel point defects may highly facilitate future solid state quantum technologies. First principles calculations play an important role in point defect research, since they provide a direct, extended insight into the formation of the defect states. In the last decades, considerable efforts have been made to calculate spin-dependent properties of point defects from first principles. The developed methods have already demonstrated their essential role in quantitative understanding of the physics and application of point defect qubits. Here, we review and discuss accuracy aspects of these novel ab initio methods and report on their most relevant applications for existing point defect qubits in semiconductors. We pay attention to the advantages and limitations of the methodological solutions and highlight additional developments that are expected in the near future. Moreover, we discuss the opportunity of a systematic search for potential point defect qubits, as well as the possible development of predictive spin dynamic simulations facilitated by ab initio calculations of spin-dependent quantities.
Tailoring properties of hybrid perovskites by domain-width engineering with charged walls
Authors: Chen Lan , Paillard Charles , Zhao Hong Jian , Íñiguez Jorge , Yang Yurong , Bellaiche Laurent 
Published: December 2018

AbstractCharged ferroelectric domain walls are fascinating electrical topological defects that can exhibit unusual properties. Here, in the search for novel phenomena, we perform and analyze first-principles calculations to investigate the effect of domain width on properties of domains with charged walls in the photovoltaic material consisting of methylammonium lead iodide hybrid perovskite. We report that such domains are stable and have rather low domain wall energy for any investigated width (that is, up to 13 lattice constants). Increasing the domain width first linearly decreases the electronic band gap from ≃1.4 eV to about zero (which therefore provides an efficient band-gap engineering), before the system undergoes an insulator-to-metal transition and then remains metallic (with both the tail-to-tail and head-to-head domain walls being conductive) for the largest widths. All these results can be understood in terms of: (i) components of polarization along the normal of the domain walls being small in magnitude; (ii) an internal electric field that is basically independent of the domain width; and (iii) rather negligible charge transfer between walls. These findings deepen the knowledge of charged ferroelectric domain walls and can further broaden their potential for applications, particularly in the context of halide perovskites for photovoltaics.
Spike sorting based on shape, phase, and distribution features, and K-TOPS clustering with validity and error indices
Authors: Caro-Martín Carmen Rocío , Delgado-García José M. , Gruart Agnès , Sánchez-Campusano R. 
Published: December 2018

AbstractSpike sorting is one of the most important data analysis problems in neurophysiology. The precision in all steps of the spike-sorting procedure critically affects the accuracy of all subsequent analyses. After data preprocessing and spike detection have been carried out properly, both feature extraction and spike clustering are the most critical subsequent steps of the spike-sorting procedure. The proposed spike sorting approach comprised a new feature extraction method based on shape, phase, and distribution features of each spike (hereinafter SS-SPDF method), which reveal significant information of the neural events under study. In addition, we applied an efficient clustering algorithm based on K-means and template optimization in phase space (hereinafter K-TOPS) that included two integrative clustering measures (validity and error indices) to verify the cohesion-dispersion among spike events during classification and the misclassification of clustering, respectively. The proposed method/algorithm was tested on both simulated data and real neural recordings. The results obtained for these datasets suggest that our spike sorting approach provides an efficient way for sorting both single-unit spikes and overlapping waveforms. By analyzing raw extracellular recordings collected from the rostral-medial prefrontal cortex (rmPFC) of behaving rabbits during classical eyeblink conditioning, we have demonstrated that the present method/algorithm performs better at classifying spikes and neurons and at assessing their modulating properties than other methods currently used in neurophysiology.
Rotational direction of flagellar motor from the conformation of FliG middle domain in marine Vibrio
Authors: Nishikino Tatsuro , Hijikata Atsushi , Miyanoiri Yohei , Onoue Yasuhiro , Kojima Seiji , Shirai Tsuyoshi , Homma Michio 
Published: December 2018

AbstractFliG, which is composed of three distinctive domains, N-terminal (N), middle (M), and C-terminal (C), is an essential rotor component that generates torque and determines rotational direction. To determine the role of FliG in determining flagellar rotational direction, we prepared rotational biased mutants of fliG in Vibrio alginolyticus. The E144D mutant, whose residue is belonging to the EHPQR-motif in FliGM, exhibited an increased number of switching events. This phenotype generated a response similar to the phenol-repellent response in chemotaxis. To clarify the effect of E144D mutation on the rotational switching, we combined the mutation with other che mutations (G214S, G215A and A282T) in FliG. Two of the double mutants suppressed the rotational biased phenotype. To gain structural insight into the mutations, we performed molecular dynamic simulations of the FliGMC domain, based on the crystal structure of Thermotoga maritima FliG and nuclear magnetic resonance analysis. Furthermore, we examined the swimming behavior of the fliG mutants lacking CheY. The results suggested that the conformation of FliG in E144D mutant was similar to that in the wild type. However, that of G214S and G215A caused a steric hindrance in FliG. The conformational change in FliGM triggered by binding CheY may lead to a rapid change of direction and may occur in both directional states.
Rational truncation of aptamer for cross-species application to detect krait envenomation
Authors: Dhiman Abhijeet , Anand Anjali , Malhotra Anita , Khan Eshan , Santra Vishal , Kumar Amit , Sharma Tarun Kumar 
Published: December 2018

AbstractIn majority of snakebite cases, the snake responsible for the bite remains unidentified. The traditional snakebite diagnostics method relies upon clinical symptoms and blood coagulation assays that do not provide accurate diagnosis which is important for epidemiological as well as diagnostics point of view. On the other hand, high batch-to-batch variations in antibody performance limit its application for diagnostic assays. In recent years, nucleic acid aptamers have emerged as a strong chemical rival of antibodies due to several obvious advantages, including but not limited to in vitro generation, synthetic nature, ease of functionalization, high stability and adaptability to various diagnostic formats. In the current study, we have rationally truncated an aptamer developed for α-Toxin of Bungarus multicinctus and demonstrated its utility for the detection of venom of Bungarus caeruleus. The truncated aptamer α-Tox-T2 (26mer) is found to have greater affinity than its 40-mer parent counterpart α-Tox-FL. The truncated aptamers are characterized and compared with parent aptamer for their binding, selectivity, affinity, alteration in secondary structure and limit of detection. Altogether, our findings establish the cross-species application of a DNA aptamer generated for α-Toxin of Bungarus multicinctus (a snake found in Taiwan and China) for the reliable detection of venom of Bungarus caeruleus (a snake found in the Indian subcontinent).
Quantitative evaluation of comb-structure correction methods for multispectral fibrescopic imaging
Authors: Waterhouse Dale J. , Luthman A. Siri , Yoon Jonghee , Gordon George S. D. , Bohndiek Sarah E. 
Published: December 2018

AbstractRemoving the comb artifact introduced by imaging fibre bundles, or ‘fibrescopes’, for example in medical endoscopy, is essential to provide high quality images to the observer. Multispectral imaging (MSI) is an emerging method that combines morphological (spatial) and chemical (spectral) information in a single data ‘cube’. When a fibrescope is coupled to a spectrally resolved detector array (SRDA) to perform MSI, comb removal is complicated by the demosaicking step required to reconstruct the multispectral data cube. To understand the potential for using SRDAs as multispectral imaging sensors in medical endoscopy, we assessed five comb correction methods with respect to five performance metrics relevant to biomedical imaging applications: processing time, resolution, smoothness, signal and the accuracy of spectral reconstruction. By assigning weights to each metric, which are determined by the particular imaging application, our results can be used to select the correction method to achieve best overall performance. In most cases, interpolation gave the best compromise between the different performance metrics when imaging using an SRDA.