bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Electric Field Models in Reproducing Observed Ring Current Ion Spectra During Two Geomagnetic Storms
Authors: Menz A.M. , Kistler L.M. , Mouikis C.G. , Matsui H. , Spence H.E. , Thaller S.A. , Wygant J.R. 
Published: October 2019

AbstractWe use the UNH‐IMEF, Weimer 1996, https://doi.org/10.1029/96GL02255 and Volland‐Stern electric field models along with a dipole magnetic field to calculate drift paths for particles that reach the Van Allen Probes' orbit for two inbound passes during two large geomagnetic storms. We compare the particle access in the models with the observed particle access using both realistic and enhanced solar wind model parameters. To test the accuracy of the drift paths, we estimate the H+ charge exchange loss along these drift paths. While increasing the strength of the model electric field drives particles further inward, improving agreement, energy‐dependent cutoffs in the spectra do not agree, indicating that potential patterns for highly disturbed times are inaccurate. While none of the models were able to reproduce the observed features of the more dawnward pass during the 17 March 2013 storm, the UNH‐IMEF model with enhanced inputs was able to adequately reproduce the access, charge exchange loss, and H+ particle pressure during the 17 March 2015 storm.
Theoretical Time Evolution of Numerical Errors When Using Floating Point Numbers in Shallow‐Water Models
Authors: Yamaura Tsuyoshi , Nishizawa Seiya , Tomita Hirofumi 
Published: October 2019

AbstractWe carried out a theoretical investigation of the impact of the numerical errors caused by using floating point numbers (FPNs) in simulations, such as rounding errors. Under the presupposition that model variables can be written as the linear sum of the true value and the numerical error, equations governing the time evolution of numerical errors due to FPNs (FPN errors) are obtained by considering the total errors of the results of simulations of shallow‐water models and estimating the errors incurred by using FPNs with varying precision. We can use the time evolution equations to estimate the behavior of the FPN errors, then confirm these estimations by carrying out numerical simulations. In a geostrophic wind balance state, the FPN error oscillates and gradually increases in proportion to the square root of the number of time steps, like a random walk. We found that the error introduced by using FPNs can be considered as stochastic forcing. In a state of barotropic instability, the FPN error initially evolves as stochastic forcing, as in the case of the geostrophic wind balance state. However, it then begins to increase exponentially, like a barotropic instability wave. These numerical results are obtained by using a staggered‐grid arrangement and stable time‐integration method to retain near‐neutral numerical stability in the simulations. The FPN error tends to behave as theoretically predicted if the numerical stability is close to neutral.
“Hot” electrons in metallic nanostructures—non-thermal carriers or heating?
Authors: Dubi Yonatan , Sivan Yonatan 
Published: October 2019

AbstractUnderstanding the interplay between illumination and the electron distribution in metallic nanostructures is a crucial step towards developing applications such as plasmonic photocatalysis for green fuels, nanoscale photodetection and more. Elucidating this interplay is challenging, as it requires taking into account all channels of energy flow in the electronic system. Here, we develop such a theory, which is based on a coupled Boltzmann-heat equations and requires only energy conservation and basic thermodynamics, where the electron distribution, and the electron and phonon (lattice) temperatures are determined uniquely. Applying this theory to realistic illuminated nanoparticle systems, we find that the electron and phonon temperatures are similar, thus justifying the (classical) single-temperature models. We show that while the fraction of high-energy “hot” carriers compared to thermalized carriers grows substantially with illumination intensity, it remains extremely small (on the order of 10−8). Importantly, most of the absorbed illumination power goes into heating rather than generating hot carriers, thus rendering plasmonic hot carrier generation extremely inefficient. Our formulation allows for the first time a unique quantitative comparison of theory and measurements of steady-state electron distributions in metallic nanostructures.
Reassessing the pathogenicity of c.2858G>T(p.(G953V)) in COL4A5 Gene: report of 19 Chinese families
Authors: Zhang Yanqin , Ding Jie , Wang Suxia , Zhang Hongwen , Zhong Xuhui , Liu Xiaoyu , Xu Ke , Wang Fang 
Published: October 2019

AbstractX-linked Alport syndrome (XLAS) is an inherited renal disease caused by mutations inCOL4A5gene. The c.2858G>T(p.(G953V)) inCOL4A5gene (rs78972735) has been considered pathogenic previously. However, there are conflicting interpretations of its pathogenicity recently. Here we presented 19 Chinese families, out of which 36 individuals (18 probands and 18 family members) carried the c.2858G>T(p.(G953V)) inCOL4A5gene. The clinical manifestations and genetic findings of them were analyzed. We found there were no clinical features of Alport syndrome not only in six probands with c.2858G>T(p.(G953V)) inCOL4A5plus pathogenic variants in other genes (e.g.,WT1,ADCK4,NPHP1,TRPC6,COL4A4,andPAX2) but also in another six probands with only the c.2858G>T(p.(G953V)) variant. The other six probands with a combination of c.2858G>T(p.(G953V)) and another pathogenic variant inCOL4A5had XLAS. Eleven family members (11/18, nine females and two males) who had only the c.2858G>T(p.(G953V)) variant were asymptomatic. These two males (at age of 42 and 35 years) had normal result of urine analysis and no more clinical traits of Alport syndrome. We conclude c.2858G>T(p.(G953V)) inCOL4A5gene is not a pathogenic variant for XLAS. Individuals should not be diagnosed as XLAS only based on the detection of c.2858G>T(p.(G953V)) inCOL4A5gene.
Synthesis of clathrate cerium superhydride CeH9 at 80-100 GPa with atomic hydrogen sublattice
Authors: Salke Nilesh P. , Davari Esfahani M. Mahdi , Zhang Youjun , Kruglov Ivan A. , Zhou Jianshi , Wang Yaguo , Greenberg Eran , Prakapenka Vitali B. , Liu Jin , Oganov Artem R. , Lin Jung-Fu 
Published: October 2019

AbstractHydrogen-rich superhydrides are believed to be very promising high-Tc superconductors. Recent experiments discovered superhydrides at very high pressures, e.g. FeH5 at 130 GPa and LaH10 at 170 GPa. With the motivation of discovering new hydrogen-rich high-Tc superconductors at lowest possible pressure, here we report the prediction and experimental synthesis of cerium superhydride CeH9 at 80–100 GPa in the laser-heated diamond anvil cell coupled with synchrotron X-ray diffraction. Ab initio calculations were carried out to evaluate the detailed chemistry of the Ce-H system and to understand the structure, stability and superconductivity of CeH9. CeH9 crystallizes in a P63/mmc clathrate structure with a very dense 3-dimensional atomic hydrogen sublattice at 100 GPa. These findings shed a significant light on the search for superhydrides in close similarity with atomic hydrogen within a feasible pressure range. Discovery of superhydride CeH9 provides a practical platform to further investigate and understand conventional superconductivity in hydrogen rich superhydrides.
Glycan-mediated enhancement of reovirus receptor binding
Authors: Koehler Melanie , Aravamudhan Pavithra , Guzman-Cardozo Camila , Dumitru Andra C. , Yang Jinsung , Gargiulo Serena , Soumillion Patrice , Dermody Terence S. , Alsteens David 
Published: October 2019

AbstractViral infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by interactions between viral proteins and their cell surface receptors. Despite recent progress, the molecular mechanisms underlying the multistep reovirus entry process are poorly understood. Using atomic force microscopy, we investigated how the reovirus σ1 attachment protein binds to both α-linked sialic acid (α-SA) and JAM-A cell-surface receptors. We discovered that initial σ1 binding to α-SA favors a strong multivalent anchorage to JAM-A. The enhanced JAM-A binding by virions following α-SA engagement is comparable to JAM-A binding by infectious subvirion particles (ISVPs) in the absence of α-SA. Since ISVPs have an extended σ1 conformer, this finding suggests that α-SA binding triggers a conformational change in σ1. These results provide new insights into the function of viral attachment proteins in the initiation of infection and open new avenues for the use of reoviruses as oncolytic agents.
Framework engineering to produce dominant T cell receptors with enhanced antigen-specific function
Authors: Thomas Sharyn , Mohammed Fiyaz , Reijmers Rogier M. , Woolston Annemarie , Stauss Theresa , Kennedy Alan , Stirling David , Holler Angelika , Green Louisa , Jones David , Matthews Katherine K. , Price David A. , Chain Benjamin M. , Heemskerk Mirjam H. M. , Morris Emma C. , Willcox Benjamin E. , Stauss Hans J. 
Published: October 2019

AbstractTCR-gene-transfer is an efficient strategy to produce therapeutic T cells of defined antigen specificity. However, there are substantial variations in the cell surface expression levels of human TCRs, which can impair the function of engineered T cells. Here we demonstrate that substitutions of 3 amino acid residues in the framework of the TCR variable domains consistently increase the expression of human TCRs on the surface of engineered T cells.The modified TCRs mediate enhanced T cell proliferation, cytokine production and cytotoxicity, while reducing the peptide concentration required for triggering effector function up to 3000-fold. Adoptive transfer experiments in mice show that modified TCRs control tumor growth more efficiently than wild-type TCRs. Our data indicate that simple variable domain modifications at a distance from the antigen-binding loops lead to increased TCR expression and improved effector function. This finding provides a generic platform to optimize the efficacy of TCR gene therapy in humans.
Transcriptome-wide association study of attention deficit hyperactivity disorder identifies associated genes and phenotypes
Authors: Liao Calwing , Laporte Alexandre D. , Spiegelman Dan , Akçimen Fulya , Joober Ridha , Dion Patrick A. , Rouleau Guy A. 
Published: October 2019

AbstractAttention deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental psychiatric disorder. Genome-wide association studies (GWAS) have identified several loci associated with ADHD. However, understanding the biological relevance of these genetic loci has proven to be difficult. Here, we conduct an ADHD transcriptome-wide association study (TWAS) consisting of 19,099 cases and 34,194 controls and identify 9 transcriptome-wide significant hits, of which 6 genes were not implicated in the original GWAS. We demonstrate that two of the previous GWAS hits can be largely explained by expression regulation. Probabilistic causal fine-mapping of TWAS signals prioritizes KAT2B with a posterior probability of 0.467 in the dorsolateral prefrontal cortex and TMEM161B with a posterior probability of 0.838 in the amygdala. Furthermore, pathway enrichment identifies dopaminergic and norepinephrine pathways, which are highly relevant for ADHD. Overall, our findings highlight the power of TWAS to identify and prioritize putatively causal genes.
Selective crack suppression during deformation in metal films on polymer substrates using electron beam irradiation
Authors: Lee So-Yeon , Park Kyung Ryoul , Kang Sung-gyu , Lee Ji-Hoon , Jeon Eun-chae , Shim Cheol-Hwee , Ahn Jae-Pyoung , Kim Dong-Ik , Han Heung Nam , Joo Young-Chang , Kim Changsoon , Choi In-Suk 
Published: October 2019

AbstractWhile cracks are usually considered detrimental, crack generation can be harnessed for various applications, for example in ceramic materials, via directing crack propagation and crack opening. Here, we find that electron beam irradiation prompts a crack suppression phenomenon in a copper (Cu) thin film on a polyimide substrate, allowing for the control of crack formation in terms of both location and shape. Under tensile strain, cracks form on the unirradiated region of the Cu film whereas cracks are prevented on the irradiated region. We attribute this to the enhancement of the adhesion at the Cu–polyimide interface by electrons transmitted through the Cu film. Finally, we selectively form conductive regions in a Cu film on a polyimide substrate under tension and fabricate a strain-responsive organic light-emitting device.
Sleep quality, duration, and consistency are associated with better academic performance in college students
Authors: Okano Kana , Kaczmarzyk Jakub R. , Dave Neha , Gabrieli John D. E. , Grossman Jeffrey C. 
Published: October 2019

AbstractAlthough numerous survey studies have reported connections between sleep and cognitive function, there remains a lack of quantitative data using objective measures to directly assess the association between sleep and academic performance. In this study, wearable activity trackers were distributed to 100 students in an introductory college chemistry class (88 of whom completed the study), allowing for multiple sleep measures to be correlated with in-class performance on quizzes and midterm examinations. Overall, better quality, longer duration, and greater consistency of sleep correlated with better grades. However, there was no relation between sleep measures on the single night before a test and test performance; instead, sleep duration and quality for the month and the week before a test correlated with better grades. Sleep measures accounted for nearly 25% of the variance in academic performance. These findings provide quantitative, objective evidence that better quality, longer duration, and greater consistency of sleep are strongly associated with better academic performance in college. Gender differences are discussed.
Competitive Interactions between PIRT, the Cold Sensing Ion Channel TRPM8, and PIP2 Suggest a Mechanism for Regulation
Authors: Sisco Nicholas J. , Helsell Cole V. M. , Van Horn Wade D. 
Published: October 2019

AbstractTRPM8 is a member of the transient receptor potential ion channel family where it functions as a cold and pain sensor in humans and other higher organisms. Previous studies show that TRPM8 requires the signaling phosphoinositide lipid PIP2 to function. TRPM8 function is further regulated by other diverse mechanisms, including the small modulatory membrane protein PIRT (phosphoinositide regulator of TRP). Like TRPM8, PIRT also binds PIP2 and behavioral studies have shown that PIRT is required for normal TRPM8-mediated cold-sensing. To better understand the molecular mechanism of PIRT regulation of TRPM8, solution nuclear magnetic resonance (NMR) spectroscopy was used to assign the backbone resonances of full-length human PIRT and investigate the direct binding of PIRT to PIP2 and the human TRPM8 S1-S4 transmembrane domain. Microscale thermophoresis (MST) binding studies validate the NMR results and identify a competitive PIRT interaction between PIP2 and the TRPM8 S1-S4 domain. Computational PIP2 docking to a human TRPM8 comparative model was performed to help localize where PIRT may bind TRPM8. Taken together, our data suggest a mechanism where TRPM8, PIRT, and PIP2 form a regulatory complex and PIRT modulation of TRPM8 arises, at least in part, by regulating local concentrations of PIP2 accessible to TRPM8.
Climate change, range shifts, and the disruption of a pollinator-plant complex
Authors: Gómez-Ruiz Emma P. , Lacher Thomas E. 
Published: October 2019

AbstractClimate change has significant impacts on the distribution of species and alters ecological processes that result from species interactions. There is concern that such distribution shifts will affect animal-plant pollination networks. We modelled the potential future (2050 and 2070) distribution of an endangered migratory bat species (Leptonycteris nivalis) and the plants they pollinate (Agavespp) during their annual migration from central Mexico to the southern United States. Our models show that the overlap between theAgaveand the endangered pollinating bat will be reduced by at least 75%. The reduction of suitable areas forAgavespecies will restrict the foraging resources available for the endangered bat, threatening the survival of its populations and the maintenance of their pollination service. The potential extinction of the batL. nivaliswill likely have negative effects on the sexual reproduction and genetic variability ofAgaveplants increasing their vulnerability to future environmental changes.
Effects of arbuscular mycorrhizal fungi on rice-herbivore interactions are soil-dependent
Authors: Bernaola Lina , Stout Michael J. 
Published: October 2019

AbstractThe effect of soil type on establishment of arbuscular mycorrhizal (AM) fungi, and their effects on plant growth and resistance to rice pests are poorly understood. We investigated the effects of inoculation with AM fungi on rice plants in two different unsterilized field soils under greenhouse and field conditions in two consecutive years in Louisiana, United States. We tested whether inoculation with AM fungi in the two soils changed plant biomass, nutrient concentration, resistance to pests, and yields. Inoculation with a commercial formulation of AM fungi increased root colonization by fungi in all soils, regardless of soil P availability; it also increased densities of root-feeding rice water weevil larvae and growth of leaf-feeding fall armyworm larvae, but these effects were soil-dependent. Inoculation with AM fungi had no effect on N and P concentrations or rice yields. The effect on plant biomass was also soil-dependent. Our study provides evidence for the first time that inoculation with AM fungi can increase colonization of roots of rice plants, but the effects of colonization on resistance to pests and plant biomass appear to be soil dependent. Moreover, the increased susceptibility to pests of rice colonized by AM fungi does not appear to be related to nutrient concentrations.
Bactericera cockerelli resistance in the wild tomato Solanum habrochaites is polygenic and influenced by the presence of Candidatus Liberibacter solanacearum
Authors: Avila Carlos A. , Marconi Thiago G. , Viloria Zenaida , Kurpis Julianna , Del Rio Sonia Y. 
Published: October 2019

AbstractThe tomato-potato psyllid (TPP), Bactericera cockerelli, is a vector for the phloem-limited bacterium Candidatus Liberibacter solanacearum (Lso), the causative agent of economically important diseases including tomato vein-greening and potato zebra chip. Here, we screened 11 wild tomato relatives for TPP resistance as potential resources for tomato (Solanum lycopersicum) cultivar development. Six accessions with strong TPP resistance (survival <10%) were identified within S. habrochaites, S. pennelli, S. huaylasense, S. chmielewskii, S. corneliomulleri, and S. galapagense. Two S. pennelli and S. corneliomulleri accessions also showed resistance to Lso. We evaluated recombinant inbred lines (RILs) carrying resistance from S. habrochaites accession LA1777 in the S. lycopersicum background and identified major quantitative trait loci (QTLs) responsible for adult TPP mortality and fecundity in several RILs carrying insertions in different chromosomes, indicating the polygenic nature of these traits. Analysis of a major resistance QTL in RIL LA3952 on chromosome 8 revealed that the presence of Lso is required to increase adult TPP mortality. By contrast, the reduced TPP oviposition trait in LA3952 is independent of Lso. Therefore, resistance traits are available in wild-tomato species, although their complex inheritance and modes of action require further characterisation to optimise their utilisation for tomato improvement.
Diversity of vaginal microbiome and metabolome during genital infections
Authors: Ceccarani Camilla , Foschi Claudio , Parolin Carola , D’Antuono Antonietta , Gaspari Valeria , Consolandi Clarissa , Laghi Luca , Camboni Tania , Vitali Beatrice , Severgnini Marco , Marangoni Antonella 
Published: October 2019

AbstractWe characterized the vaginal ecosystem during common infections of the female genital tract, as vulvovaginal candidiasis (VVC, n = 18) and Chlamydia trachomatis infection (CT, n = 20), recruiting healthy (HC, n = 21) and bacterial vaginosis-affected (BV, n = 20) women as references of eubiosis and dysbiosis. The profiles of the vaginal microbiome and metabolome were studied in 79 reproductive-aged women, by means of next generation sequencing and proton based-nuclear magnetic resonance spectroscopy. Lactobacillus genus was profoundly depleted in all the genital infections herein considered, and species-level analysis revealed that healthy vaginal microbiome was dominated by L. crispatus. In the shift from HC to CT, VVC, and BV, L. crispatus was progressively replaced by L. iners. CT infection and VVC, as well as BV condition, were mainly characterised by anaerobe genera, e.g. Gardnerella, Prevotella, Megasphaera, Roseburia and Atopobium. The changes in the bacterial communities occurring during the genital infections resulted in significant alterations in the vaginal metabolites composition, being the decrease of lactate a common marker of all the pathological conditions. In conclusion, according to the taxonomic and metabolomics analysis, we found that each of the four conditions is characterized by a peculiar vaginal microbiome/metabolome fingerprint.
Realization of broadband negative refraction in visible range using vertically stacked hyperbolic metamaterials
Authors: Bang Sanghun , So Sunae , Rho Junsuk 
Published: October 2019

AbstractNegative refraction has generated much interest recently with its unprecedented optical phenomenon. However, a broadband negative refraction has been challenging because they mainly involve optical resonances. This paper reports the realization of broadband negative refraction in the visible spectrum by using vertically-stacked metal-dielectric multilayer structures. Such structure exploits the characteristics of the constituent metal and dielectric materials, and does not require resonance to achieve negative refraction. Broadband negative refraction (wavelength 270–1300 nm) is numerically demonstrated. Compared to conventional horizontally-stacked multilayer structures, the vertically-stacked multilayer structure has a broader range of working wavelength in the visible range, with higher transmittance. We also report a variety of material combinations with broad working wavelength. The broadband negative refraction metamaterial provides an effective way to manipulate light and may have applications in super-resolution imaging, and invisibility cloaks.