bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a mechanistic dengue simulation model for Guangzhou
Authors: Mincham G. , Baldock K. L. , Rozilawati H. , Williams C. R. 
Published: March 2019

AbstractDengue infection in China has increased dramatically in recent years. Guangdong province (main city Guangzhou) accounted for more than 94% of all dengue cases in the 2014 outbreak. Currently, there is no existing effective vaccine and most efforts of control are focused on the vector itself. This study aimed to evaluate different dengue management strategies in a region where this disease is emerging. This work was done by establishing a dengue simulation model for Guangzhou to enable the testing of control strategies aimed at vector control and vaccination. For that purpose, the computer-based dengue simulation model (DENSiM) together with the Container-Inhabiting Mosquito Simulation Model (CIMSiM) has been used to create a working dengue simulation model for the city of Guangzhou. In order to achieve the best model fit against historical surveillance data, virus introduction scenarios were run and then matched against the actual dengue surveillance data. The simulation model was able to predict retrospective outbreaks with a sensitivity of 0.18 and a specificity of 0.98. This new parameterisation can now be used to evaluate the potential impact of different control strategies on dengue transmission in Guangzhou. The knowledge generated from this research would provide useful information for authorities regarding the historic patterns of dengue outbreaks, as well as the effectiveness of different disease management strategies.
“I'm gonna Spanglish it on you”: Self-reported vs. oral production of Spanish–English codeswitching
Authors: Cox Jessica G. , LaBoda Ashley , Mendes Najee 
Published: March 2019

AbstractMuch bilingualism research includes some consideration of codeswitching, which may be measured via self-report, an experimental task, or sociolinguistic interview; however, there is little triangulation across measures in either psycholinguistic or sociolinguistic approaches. To consider possible differences between self-report and oral production of codeswitching, Spanish–English bilinguals completed a codeswitching questionnaire and oral production in an autobiographical memory task. They also completed proficiency and executive function tests. We found that broad measures of self-reported and orally produced codeswitches were positively correlated, although relationships with proficiency and executive function were more complex. These findings may direct future studies’ operationalization of codeswitching.
The Influence of Isoconcentration Surface Selection in Quantitative Outputs from Proximity Histograms
Authors: Barton Dallin J , Hornbuckle B Chad , Darling Kristopher A , Thompson Gregory B 
Published: March 2019

AbstractIsoconcentration surfaces are commonly used to delineate phases in atom probe datasets. These surfaces then provide the spatial and compositional reference for proximity histograms, the number density of particles, and the volume fraction of particles within a multiphase system. This paper discusses the influence of the isoconcentration surface selection value on these quantitative outputs, using a simple oxide dispersive strengthened alloy, Fe91Ni8Zr1, as the case system. Zirconium reacted with intrinsic oxygen impurities in a consolidated ball-milled powder to precipitate nanoscale zirconia particles. The zirconia particles were identified by varying the Zr-isoconcentration values as well as by the maximum separation data mining method. The associated outputs mentioned above are elaborated upon in reference to the variation in this Zr isosurface value. Considering the dataset as a whole, a 10.5 at.% Zr isosurface provided a compositional inflection point for Zr between the particles and matrix on the proximity histogram; however, this value was unable to delineate all of the secondary oxide particles identified using the maximum separation method. Consequently, variations in the number density and volume fraction were observed as the Zr isovalue was changed to capture these particles resulting in a loss of the compositional accuracy. This highlighted the need for particle-by-particle analysis.
A printed multiband MIMO antenna with decoupling element
Authors: Xu Ziyu , Zhang Qisheng , Guo Linyan 
Published: March 2019

AbstractA printed multiband Multi-Input Multiple-Output (MIMO) antenna is proposed in this paper. This MIMO antenna system comprises two symmetric printed monopole antennas. Each antenna element consists of multiple bend lines, producing four resonant modes and covering the GSM900, PCS, LTE2300, and 5G bands. Simulated and measured results prove that the proposed MIMO antenna can be applied to traditional 2G, 3G, 4G, and present 5G mobile communication. By etching four invertedL-shaped grooves on its ground plate, mutual coupling between the adjacent antenna elements has been suppressed. This makes the |S21| at all four resonant modes is lower than −40 dB. In addition, its low coupling mechanism has been analyzed by surface current distribution. The designed multiband MIMO antenna provides an idea of reference to realize low mutual coupling between antenna elements, which is also realizable in infrared or optical regimes with appropriate designs.
A flexible wide band single fed slot antenna with circular polarizing rotated elliptical ground and impulse response
Authors: Zahran Sherif R. , Abdalla Mahmoud A. , Gaafar Abdelhamid 
Published: March 2019

AbstractIn this paper, a flexible single fed planar circular polarized slot antenna is proposed for Internet of Things wideband applications. The antenna flexibility is achieved by employing a mechanically bendable liquid crystalline polymer substrate. The overall antenna volume is 50 mm × 42 mm × 0.1 mm. The antenna design uses 45° rotated elliptical ground structure for generating circular polarized radiation over wideband spectrum. Two parametrical analyses targeting the slot ground are introduced in order to achieve the most efficient design. The final antenna design demonstrates a good matching in terms of reflection coefficient (<−10 dB), semi-omnidirectional radiation patterns, average gain of 4 dB, and <3 dB axial ratio over entire frequency band of operation. All antenna parameters are studied in both straight and bent antenna setup scenarios. Good agreement between simulation and measurement results of the antenna parameters are achieved. For both straight and bent antenna scenarios, the antenna receiving functionality in time domain is confirmed by retrieving highly correlated impulse responses.
Surface Imaging Functions for Elastic Reverse Time Migration
Authors: Pollitz Fred F. 
Published: March 2019

AbstractReverse time migration is often used to interpret acoustic or three‐component seismic recordings by creating an image of subsurface seismic reflectors. Here I describe elastic reverse time migration imaging functions that are cast as waveform misfit sensitivity kernels of contrasts in material parameters across hypothetical seismic discontinuities, that is, specular reflectors. The proposed “surface” imaging functions are theoretically applicable to either reflected or converted waves in order to estimate the location and reflectivity of these discontinuities. The surface imaging functions, as well as volumetric sensitivity kernels that target point diffractors, are tested on sets of synthetic surface array recordings that sample the 3‐D seismic wavefield on simple 2‐D structures generated using a 2.5‐D spectral element method. These tests illustrate that in contrast with the volumetric sensitivity kernels, the reflectivity is generally dominated by a high‐amplitude peak that coincides with input locations of discontinuities. Passive recordings of microseismicity, shot gathers, or a combination thereof can be potentially interpreted with the new surface imaging functions to yield useful reflectivity images.
Response of the Diurnal Cycle of Summer Rainfall to Large‐Scale Circulation and Coastal Upwelling at Hainan, South China
Authors: Shi Rui , Cai Qinbo , Dong Lingyu , Guo Xinyu , Wang Dongxiao 
Published: March 2019

AbstractThe modulation of coastal rainfall at Hainan by large‐scale circulation and coastal upwelling is studied using observations and numerical modeling. Tropical Rainfall Measuring Mission data show that the monthly mean rainfall off southern Hainan was considerably higher in August 2010 than in August 2011. The main cause of this difference is an intensification of offshore rainfall from midnight to early morning. Compared with the multiyear (2000–2017) average field, reanalysis data show that there is an apparent increase in atmospheric humidity in August 2010. During this time, a moderate El Niño was decaying and a new La Niña event was developing, so a significant adjustment of the large‐scale circulation was observed in the western Pacific. The resulting anomalous onshore wind depresses the development of upwelling, leading to a relatively warm sea surface temperature off the south coast of Hainan, which in turn enhances the land‐sea thermal contrast and land breeze at night. Decreases in upwelling intensity and asymmetric intensification of nocturnal and daytime offshore rainfall are confirmed not only in the summer of 2010 but also in the summer of 2003. Numerical simulations using the Weather Research and Forecasting model verify that the enhanced land breeze ultimately leads to pronounced coastal rainfall off southern Hainan at night. The results indicate that localized surface convergence associated with the sea and land breezes may be more important than the atmospheric humidity and convective instability in modulating the diurnal cycle of rainfall for tropical islands.
Modulation of Lateral Transport by Submesoscale Flows and Inertia‐Gravity Waves
Authors: Sinha Anirban , Balwada Dhruv , Tarshish Nathaniel , Abernathey Ryan 
Published: March 2019

AbstractWe investigate the role of small‐scale, high‐frequency motions on lateral transport in the ocean, by using velocity fields and particle trajectories from an ocean general circulation model (MITgcm‐llc4320) that permits submesoscale flows, inertia‐gravity waves, and tides. Temporal averaging/filtering removes most of the submesoscale turbulence, inertia‐gravity waves, and tides, resulting in a largely geostrophic flow, with a rapid drop‐off in energy at scales smaller than the mesoscales. We advect two types of Lagrangian particles: (a) 2‐D particles (surface restricted) and (b) 3‐D particles (advected in full three dimensions) with the filtered and unfiltered velocities and calculate Lagrangian diagnostics. At large length/time scales, Lagrangian diffusivity is comparable for filtered and unfiltered velocities, while at short scales, unfiltered velocities disperse particles much faster. We also calculate diagnostics of Lagrangian coherent structures:rotationally coherent Lagrangian vortices detected from closed contours of the Lagrangian‐averaged vorticity deviation and material transport barriers formed by ridges of maximum finite‐time Lyapunov exponent. For temporally filtered velocities, we observe strong material coherence, which breaks down when the level of temporal filtering is reduced/removed, due to vigorous small‐scale mixing. In addition, for the lowest temporal resolution, the 3‐D particles experience very little vertical motion, suggesting that degrading temporal resolution greatly reduces vertical advection by high‐frequency motions. Our study suggests that Lagrangian diagnostics based on satellite‐derived surface geostrophic velocity fields, even with higher spatial resolutions as in the upcoming Surface Water and Ocean Topography mission, may overestimate the presence of mesoscale coherent structures and underestimate dispersion.
The Single Column Atmosphere Model Version 6 (SCAM6): Not a Scam but a Tool for Model Evaluation and Development
Authors: Gettelman A. , Truesdale J. E. , Bacmeister J. T. , Caldwell P. M. , Neale R. B. , Bogenschutz P. A. , Simpson I. R. 
Published: March 2019

AbstractThe Single Column Atmosphere Model (SCAM) is a single column model version of the Community Atmosphere Model (CAM). Here we describe the functionality and features of SCAM6, available as part of CAM6 in the Community Earth System Model, version 2 (CESM2). SCAM6 features a wide selection of standard cases, as well as the ability to easily configure a case specified by the user based on a particular point in a CAM 3‐D simulation. This work illustrates how SCAM6 reproduces CAM6 results for physical parameterizations, mostly of moisture and clouds. We demonstrate how SCAM6 can be used for model development through different physics selections, as well as with parameter sweep experiments to highlight the sensitivity of cloud properties to the specification of the vapor deposition process in the cloud microphysics. Furthermore, we use SCAM6 to illustrate the sensitivity of CAM6 cloud radiative properties and precipitation to variable drop number (cloud microphysics properties). Finally, we illustrate how SCAM6 can be used to explore critical emergent processes such as cloud feedbacks and show that CAM6 cloud responses to surface warming in stratus and stratocumulus regimes are similar to those in CAM5. CAM6 has a larger response in the shallow cumulus regime than CAM5. CAM6 cloud feedbacks in the shallow cumulus regime are sensitive to turbulence parameters. SCAM6 is thus a valuable tool for model development, evaluation, and scientific analy sis and an important part of the model hierarchy in Community Earth System Model, version 2.
Crescent‐Shaped Electron Distributions at the Nonreconnecting Magnetopause: Magnetospheric Multiscale Observations
Authors: Tang B.‐B. , Li W. Y. , Graham D. B. , Rager A. C. , Wang C. , Khotyaintsev Yu. V. , Lavraud B. , Hasegawa H. , Zhang Y.‐C. , Dai L. , Giles B. L. , Dorelli J. C. , Russell C. T. , Lindqvist P.‐A. , Ergun R. E. , Burch J. L. 
Published: March 2019

AbstractCrescent‐shaped electron distributions perpendicular to the magnetic field are an important indicator of the electron diffusion region in magnetic reconnection. They can be formed by the electron finite gyroradius effect at plasma boundaries or by demagnetized electron motion. In this study, we present Magnetospheric Multiscale mission observations of electron crescents at the flank magnetopause on 20 September 2017, where reconnection signatures are not observed. These agyrotropic electron distributions are generated by electron gyromotion at the thin electron‐scale magnetic boundaries of a magnetic minimum after magnetic curvature scattering. The variation of their angular range in the perpendicular plane is in good agreement with predictions. Upper hybrid waves are observed to accompany the electron crescents at all four Magnetospheric Multiscale spacecraft as a result of the beam‐plasma instability associated with these agyrotropic electron distributions. This study suggests electron crescents can be more frequently formed at the magnetopause.
Maternal hyperglycemia disturbs neocortical neurogenesis via epigenetic regulation in C57BL/6J mice
Authors: Ji Shufang , Zhou Wenjuan , Li Xian , Liu Shangming , Wang Fuwu , Li Xinyue , Zhao Tiantian , Ji Guangyu , Du Jingyi , Hao Aijun 
Published: March 2019

AbstractOffspring of mothers with hyperglycemia during pregnancy have a higher incidence of long-term neuropsychiatric disorders than offspring from a normal pregnancy, indicating that neocortical neurogenesis might be affected by maternal hyperglycemia. A paucity of study evaluating the effects of hyperglycemia on neocortical neurogenetic differentiation of neural stem cells, and the mechanism remains unclear. We sought to investigate the the roles and possible molecular mechanism of maternal hyperglycemia on neocortical neurogenetic differentiation of neural stem cells. We established a mouse model of a hyperglycemic pregnancy to study effects of intrauterine exposure to maternal hyperglycemia on neocortical neurogenesis. We observed morphological changes in the neocortex and detected the neurogenetic differentiation of neural stem cells in offspring affected by high glucose levels. We investigated the regulatory network between epigenetic modification and transcription factors in differentiated neural stem cells under hyperglycemic conditions. Maternal hyperglycemia disturbs neocortical lamination in some non-malformed offspring. Our results suggested that hyperglycemia altered the early-born neuron fate and the distribution of newborn neurons in deep layers by promoting the earlier differentiation of neural stem cells. Altered histone acetylation and its regulation on the transcription of proneural genes might be correlated to the disrupted differentiation of neural stem cells and altered distribution of newborn projection neurons in the neocortex. Our data raised the possibility that maternal hyperglycemia in pregnancy disturbs the laminar distribution of neocortical projection neurons in some non-malformed offspring via epigenetic regulation on neural stem cell differentiation and the birthdate of neocortical neurons.
Quantitative proteomic analyses of dynamic signalling events in cortical neurons undergoing excitotoxic cell death
Authors: Hoque Ashfaqul , Williamson Nicholas A. , Ameen S. Sadia , Ciccotosto Giuseppe D. , Hossain M. Iqbal , Oakhill Jonathan S. , Ng Dominic C. H. , Ang Ching-Seng , Cheng Heung-Chin 
Published: March 2019

AbstractExcitotoxicity, caused by overstimulation or dysregulation of ionotropic glutamate receptors (iGluRs), is a pathological process directing neuronal death in many neurological disorders. The aberrantly stimulated iGluRs direct massive influx of calcium ions into the affected neurons, leading to changes in expression and phosphorylation of specific proteins to modulate their functions and direct their participation in the signalling pathways that induce excitotoxic neuronal death. To define these pathways, we used quantitative proteomic approaches to identify these neuronal proteins (referred to as the changed proteins) and determine how their expression and/or phosphorylation dynamically changed in association with excitotoxic cell death. Our data, available in ProteomeXchange with identifier PXD008353, identified over 100 changed proteins exhibiting significant alterations in abundance and/or phosphorylation levels at different time points (5–240 min) in neurons after glutamate overstimulation. Bioinformatic analyses predicted that many of them are components of signalling networks directing defective neuronal morphology and functions. Among them, the well-known neuronal survival regulators including mitogen-activated protein kinases Erk1/2, glycogen synthase kinase 3 (GSK3) and microtubule-associated protein (Tau), were selected for validation by biochemical approaches, which confirmed the findings of the proteomic analysis. Bioinformatic analysis predicted Protein Kinase B (Akt), c-Jun kinase (JNK), cyclin-dependent protein kinase 5 (Cdk5), MAP kinase kinase (MEK), Casein kinase 2 (CK2), Rho-activated protein kinase (Rock) and Serum/glucocorticoid-regulated kinase 1 (SGK1) as the potential upstream kinases phosphorylating some of the changed proteins. Further biochemical investigation confirmed the predictions of sustained changes of the activation states of neuronal Akt and CK2 in excitotoxicity. Thus, future investigation to define the signalling pathways directing the dynamic alterations in abundance and phosphorylation of the identified changed neuronal proteins will help elucidate the molecular mechanism of neuronal death in excitotoxicity.
Ultrafast energy relaxation dynamics of amide I vibrations coupled with protein-bound water molecules
Authors: Tan Junjun , Zhang Jiahui , Li Chuanzhao , Luo Yi , Ye Shuji 
Published: March 2019

AbstractThe influence of hydration water on the vibrational energy relaxation in a protein holds the key to understand ultrafast protein dynamics, but its detection is a major challenge. Here, we report measurements on the ultrafast vibrational dynamics of amide I vibrations of proteins at the lipid membrane/H2O interface using femtosecond time-resolved sum frequency generation vibrational spectroscopy. We find that the relaxation time of the amide I mode shows a very strong dependence on the H2O exposure, but not on the D2O exposure. This observation indicates that the exposure of amide I bond to H2O opens up a resonant relaxation channel and facilitates direct resonant vibrational energy transfer from the amide I mode to the H2O bending mode. The protein backbone motions can thus be energetically coupled with protein-bound water molecules. Our findings highlight the influence of H2O on the ultrafast structure dynamics of proteins.
Author Correction: Runx/Cbfβ complexes protect group 2 innate lymphoid cells from exhausted-like hyporesponsiveness during allergic airway inflammation
Authors: Miyamoto Chizuko , Kojo Satoshi , Yamashita Motoi , Moro Kazuyo , Lacaud Georges , Shiroguchi Katsuyuki , Taniuchi Ichiro , Ebihara Takashi 
Published: March 2019

The original version of this Article contained an error in the author affiliations. Affiliation 5 incorrectly read ‘Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Suite, Hyogo 565-0874, Japan.’ This has now been corrected in both the PDF and HTML versions of the Article.
Structural dynamics of a metal–organic framework induced by CO2 migration in its non-uniform porous structure
Authors: Zhao Pu , Fang Hong , Mukhopadhyay Sanghamitra , Li Aurelia , Rudić Svemir , McPherson Ian J. , Tang Chiu C. , Fairen-Jimenez David , Tsang S. C. Edman , Redfern Simon A. T. 
Published: March 2019

AbstractStimuli-responsive behaviors of flexible metal–organic frameworks (MOFs) make these materials promising in a wide variety of applications such as gas separation, drug delivery, and molecular sensing. Considerable efforts have been made over the last decade to understand the structural changes of flexible MOFs in response to external stimuli. Uniform pore deformation has been used as the general description. However, recent advances in synthesizing MOFs with non-uniform porous structures, i.e. with multiple types of pores which vary in size, shape, and environment, challenge the adequacy of this description. Here, we demonstrate that the CO2-adsorption-stimulated structural change of a flexible MOF, ZIF-7, is induced by CO2 migration in its non-uniform porous structure rather than by the proactive opening of one type of its guest-hosting pores. Structural dynamics induced by guest migration in non-uniform porous structures is rare among the enormous number of MOFs discovered and detailed characterization is very limited in the literature. The concept presented in this work provides new insights into MOF flexibility.
Purification of cross-linked RNA-protein complexes by phenol-toluol extraction
Authors: Urdaneta Erika C. , Vieira-Vieira Carlos H. , Hick Timon , Wessels Hans-Herrmann , Figini Davide , Moschall Rebecca , Medenbach Jan , Ohler Uwe , Granneman Sander , Selbach Matthias , Beckmann Benedikt M. 
Published: March 2019

AbstractRecent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well as the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria). We have developed the Phenol Toluol extraction (PTex) protocol that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to RNA as short as 30 nt, RNPs directly from animal tissue and can be used to simplify complex workflows such as PAR-CLIP. Finally, we provide a global RNA-bound proteome of human HEK293 cells and the bacterium Salmonella Typhimurium.