bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Subsurface Indian Ocean Dipole Response to Tropical Volcanic Eruptions
Authors: Izumo Takeshi , Khodri Myriam , Lengaigne Matthieu , Suresh Iyyappan 
Published: August 2018

AbstractThe impacts of explosive volcanism on the densely populated Indian Ocean (IO) region remain elusive. Dedicated sensitivity experiments indicate that tropical volcanic eruptions induce a stronger surface cooling over Africa than of ocean, promoting westerlies in the equatorial IO. These westerlies drive a subsurface response reminiscent to that of a negative IO Dipole (IOD) during autumn in the year of eruption. The eruption also drives an enhanced cooling over the northwestern IO as a direct response to climatological cloud cover distribution. The resulting anomalous zonal sea surface temperature gradient contributes to enhance equatorial westerly anomalies in summer. The response is sensitive to the IO preconditioning, being larger when the system is favorable to a positive IOD development. Volcanic eruptions also induce a subsurface IOD‐like response in the multimodel database from the Coupled Model Intercomparison Project Phase 5 as well as a primary productivity decrease in the eastern IO.
Broadband Velocities and Displacements From Integrated GPS and Accelerometer Data for High‐Rate Seismogeodesy
Authors: Shu Yuanming , Fang Rongxin , Geng Jianghui , Zhao Qile , Liu Jingnan 
Published: August 2018

AbstractWe present a new method of integrating Global Positioning System (GPS) and accelerometer data for high‐rate seismogeodesy. This method is based on the GPS variometric approach which can obtain seismic waves in real time using only the readily available broadcast products and a single receiver. Collocated 1‐Hz GPS and 200‐Hz accelerometer data from the 2016 MW 7.8 Kaikōura earthquake were analyzed to verify the effectiveness of this method. Results reveal that this method can provide broadband and more accurate velocities and displacements qualified to detect P wave arrivals. Moreover, this method can effectively avoid the aliasing problem present in the 1‐Hz GPS waveforms. We therefore conclude that this new method can be a powerful tool to capture seismic waves in real time, which is crucial for the purpose of tsunami early warning and earthquake rapid response.
Seasonal and Solar Wind Control of the Reconnection Line Location on the Earth's Dayside Magnetopause
Authors: Hoshi Y. , Hasegawa H. , Kitamura N. , Saito Y. , Angelopoulos V. 
Published: August 2018

AbstractWe investigate the average location of magnetic reconnection on the Earth's dayside magnetopause, based on spatial distributions of northward and southward reconnection jets observed by the THEMIS spacecraft at the near‐noon (10–14 magnetic local time) magnetopause. A total of 711 reconnection jets were identified by applying the Walén relation, the tangential stress balance relation to be satisfied for a reconnected (rotational discontinuity) magnetopause, to magnetopause crossings identified from 10 years of THEMIS observations. The directions and positions of jets indicate that during southward interplanetary magnetic field (IMF) conditions, the dayside X‐line location shifts from the subsolar point toward the winter hemisphere by about 6 Earth radii under the largest tilt of the geomagnetic dipole axis. The X‐line location also shifts northward (southward) by at most 2.5 Earth radii when the IMF is predominantly radial and its x component is positive (negative). The dipole tilt effect on the shift of the X‐line location becomes smaller for higher solar wind Alfvén Mach numbers. The dipole tilt effect being larger than the IMF Bx effect suggests that the X‐line location has a seasonal dependence. Since models and theory show that the reconnection rate away from the subsolar magnetopause is lower than that at the subsolar magnetopause, the dipole tilt dependence of the X‐line location suggests that the efficiency of solar wind energy transfer into the magnetosphere may decrease under larger dipole tilt; this may partially account for seasonal variations of geomagnetic activity, which is known to decrease under larger dipole tilts.
The Study of Inland Eyewall Reformation of Typhoon Fanapi (2010) Using Numerical Experiments and Vorticity Budget Analysis
Authors: Yang Ming‐Jen , Wu Yao‐Chu , Liou Yu‐Chieng 
Published: August 2018

AbstractNumerical simulations of Typhoon Fanapi (2010) interacting with the terrain of Taiwan are conducted using the Advanced Research Weather Research and Forecasting model (ARW, version 3.3.1) on a triply nested grid (with the finest grid size of 1 km and 55 vertical levels). Fanapi made landfall on eastern Taiwan at 0000 UTC 19 September and left Taiwan at 1200 UTC 19 September 2010, producing heavy rainfall and severe floods. After landfall, the Fanapi eyewall weakened and broke down over the Central Mountain Range. Vortical hot towers (VHTs) occurred along the Fanapi rainband, and the VHTs in land have weaker maximum updrafts (7.0–8.0 m/s), narrower diameter (7.0–11.5 km), and shallower depth (6.5–9.0 km), compared with oceanic VHTs over the Taiwan Strait. The VHTs over the Taiwan Strait remained organized along the rainband and propagated toward the southeast quadrant of the Fanapi circulation over land by the tangential flow. These organized VHTs in the southeast quadrant help transport cyclonic vorticity from lower into middle levels and then cooperate with the rich vorticity within the rainband by horizontal vorticity advection to rebuild the Fanapi eyewall upward from the bottom. The vorticity balance within the entire Fanapi circulation is largely dominated by its southeast quadrant with organized VHTs over Taiwan Island. In the simulation with no latent heat release, the VHTs quickly decay and radiate outward from the eyewall as gravity‐wave perturbations.
Modeling of Atmospheric Aerosol Properties in the São Paulo Metropolitan Area: Impact of Biomass Burning
Authors: Vara‐Vela Angel , de Fátima Andrade Maria , Zhang Yang , Kumar Prashant , Ynoue Rita Yuri , Souto‐Oliveira Carlos Eduardo , da Silva Lopes Fábio Juliano , Landulfo Eduardo 
Published: August 2018

AbstractSmoke particles ejected into the atmosphere from biomass burning can modify the atmospheric composition around and even far from the sources. In late winter and early spring, biomass burning emissions from inland regions can be efficiently transported to urban areas in southeastern South America, thus affecting air quality in those areas. In this study, the Weather Research and Forecasting with Chemistry model was applied in order to investigate the impact of biomass burning sources on aerosol loadings and properties over the São Paulo Metropolitan Area (SPMA), in southeastern Brazil, during the period from 19 August to 3 September 2014. The model performance was evaluated using available aerosol measurements from the Narrowing the Uncertainties on Aerosol and Climate Change in São Paulo State project. The combined application of aerosol data and Weather Research and Forecasting with Chemistry simulations made it possible to represent some of the most important aerosol properties, such as particle number concentration and cloud condensation nuclei activation, in addition to evaluation of the impact of biomass burning by analyzing a 5‐day transport event, from 22 to 26 August 2014. During this transport event, differences in the average predicted PM2.5 concentration reached 15 μg/m3 (peaking at 20 μg/m3 during the nighttime hours) over the SPMA, compared with 35 μg/m3 over inland areas northwest and north of the SPMA. Biomass burning accounted for up to 20% of the baseline particle number concentration‐ and cloud condensation nuclei‐weighted relative differences over the SPMA (2,300 and 1,400 cm−3, respectively).
Simulated Lightning in a Convection Permitting Global Model
Authors: Field P. R. , Roberts M. J. , Wilkinson J. M. 
Published: August 2018

AbstractHigh‐resolution (grid spacing 10 km in midlatitudes) model simulations using explicitly resolved convection in the Met Office Unified Model, as part of the Horizon 2020 PRIMAVERA project, are used to provide a global lightning climatology. The results show for the first time that global simulations can capture the strong diurnal flash rate variation as well as the seasonal variation. The lightning parametrization uses information about the graupel and ice water path to estimate a total lightning flash rate. Comparisons are made with the World Lightning Location Network (that mainly detects cloud to ground lightning) and combined Lightning Imaging Sensor and Optical Transients Detector data set (that provides an estimate of total flash rate). The model results generally capture the temporal behavior and spatial distribution of the lightning over land. Over the ocean, the lightning in the Intertropical Convergence Zone appears excessive.
Effects of Phase Scintillation on the GNSS Positioning Error During the September 2017 Storm at Svalbard
Authors: Linty Nicola , Minetto Alex , Dovis Fabio , Spogli Luca 
Published: August 2018

AbstractIn early September 2017, several space weather events triggered disturbed conditions of the near‐Earth space. The combination of two coronal mass ejection arrivals, associated with an X‐class flare, caused a strong geomagnetic storm on 7 and 8 September, thus inducing diffuse ionospheric phase scintillations on Global Navigation Satellite System (GNSS) signals. This work analyzes the effects and the actual impact of such phase scintillations on transionospheric Global Positioning System (GPS) signals and on related positioning accuracy. The research focuses in particular on high‐latitude GPS L1 data, recorded during a test campaign in Svalbard, Norway. The joint effect of satellites at low elevation and the exposure of ionosphere to the geospace forcing make navigation a critical task for such a challenging environment. Data analysis shows that the performance of carrier smoothing algorithms was affected by the presence of moderate and strong phase scintillation. It is shown in this study that positioning errors double when GPS signals affected by scintillation are used. This work shows that scintillations induce a considerable clustering effect on the smoothed positioning solutions; therefore, a methodology to automatically and autonomously detect the boundaries of the scintillation event is suggested according to such an high‐level effect. The use of software‐defined radio receivers for automatically capturing and processing GNSS data affected by scintillation is an added value to the analysis, as it offers the possibility to implement advanced signal processing techniques and a deeper observation of the impact of scintillations on the signals.
The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes
Authors: Chen Juan , Cai Zhaokui , Bai Meizhu , Yu Xiaohua , Zhang Chao , Cao Changchang , Hu Xihao , Wang Lei , Su Ruibao , Wang Di , Wang Lei , Yao Yingpeng , Ye Rong , Hou Baidong , Yu Yang , Yu Shuyang , Li Jinsong , Xue Yuanchao 
Published: August 2018

AbstractActivation-induced cytidine deaminase (AID) mediates class switching by binding to a small fraction of single-stranded DNA (ssDNA) to diversify the antibody repertoire. The precise mechanism for highly selective AID targeting in the genome has remained elusive. Here, we report an RNA-binding protein, ROD1 (also known as PTBP3), that is both required and sufficient to define AID-binding sites genome-wide in activated B cells. ROD1 interacts with AID via an ultraconserved loop, which proves to be critical for the recruitment of AID to ssDNA using bi-directionally transcribed nascent RNAs as stepping stones. Strikingly, AID-specific mutations identified in human patients with hyper-IgM syndrome type 2 (HIGM2) completely disrupt the AID interacting surface with ROD1, thereby abolishing the recruitment of AID to immunoglobulin (Ig) loci. Together, our results suggest that bi-directionally transcribed RNA traps the RNA-binding protein ROD1, which serves as a guiding system for AID to load onto specific genomic loci to induce DNA rearrangement during immune responses.
Reconciling glacial Antarctic water stable isotopes with ice sheet topography and the isotopic paleothermometer
Authors: Werner Martin , Jouzel Jean , Masson-Delmotte Valérie , Lohmann Gerrit 
Published: August 2018

AbstractStable water isotope records from Antarctica are key for our understanding of Quaternary climate variations. However, the exact quantitative interpretation of these important climate proxy records in terms of surface temperature, ice sheet height and other climatic changes is still a matter of debate. Here we report results obtained with an atmospheric general circulation model equipped with water isotopes, run at a high-spatial horizontal resolution of one-by-one degree. Comparing different glacial maximum ice sheet reconstructions, a best model data match is achieved for the PMIP3 reconstruction. Reduced West Antarctic elevation changes between 400 and 800 m lead to further improved agreement with ice core data. Our modern and glacial climate simulations support the validity of the isotopic paleothermometer approach based on the use of present-day observations and reveal that a glacial ocean state as displayed in the GLAMAP reconstruction is suitable for capturing the observed glacial isotope changes in Antarctic ice cores.
Density-functional fluctuation theory of crowds
Authors: Méndez-Valderrama J. Felipe , Kinkhabwala Yunus A. , Silver Jeffrey , Cohen Itai , Arias T. A. 
Published: August 2018

AbstractA primary goal of collective population behavior studies is to determine the rules governing crowd distributions in order to predict future behaviors in new environments. Current top-down modeling approaches describe, instead of predict, specific emergent behaviors, whereas bottom-up approaches must postulate, instead of directly determine, rules for individual behaviors. Here, we employ classical density functional theory (DFT) to quantify, directly from observations of local crowd density, the rules that predict mass behaviors under new circumstances. To demonstrate our theory-based, data-driven approach, we use a model crowd consisting of walking fruit flies and extract two functions that separately describe spatial and social preferences. The resulting theory accurately predicts experimental fly distributions in new environments and provides quantification of the crowd “mood”. Should this approach generalize beyond milling crowds, it may find powerful applications in fields ranging from spatial ecology and active matter to demography and economics.
Identification of a novel anoikis signalling pathway using the fungal virulence factor gliotoxin
Authors: Haun Florian , Neumann Simon , Peintner Lukas , Wieland Katrin , Habicht Jüri , Schwan Carsten , Østevold Kristine , Koczorowska Maria Magdalena , Biniossek Martin , Kist Matthias , Busch Hauke , Boerries Melanie , Davis Roger J. , Maurer Ulrich , Schilling Oliver , Aktories Klaus , Borner Christoph 
Published: August 2018

AbstractAnoikis is a form of apoptosis induced by cell detachment. Integrin inactivation plays a major role in the process but the exact signalling pathway is ill-defined. Here we identify an anoikis pathway using gliotoxin (GT), a virulence factor of the fungusAspergillus fumigatus, which causes invasive aspergillosis in humans. GT prevents integrin binding to RGD-containing extracellular matrix components by covalently modifying cysteines in the binding pocket. As a consequence, focal adhesion kinase (FAK) is inhibited resulting in dephosphorylation of p190RhoGAP, allowing activation of RhoA. Sequential activation of ROCK, MKK4/MKK7 and JNK then triggers pro-apoptotic phosphorylation of Bim. Cells in suspension or lacking integrin surface expression are insensitive to GT but are sensitised to ROCK-MKK4/MKK7-JNK-dependent anoikis upon attachment to fibronectin or integrin upregulation. The same signalling pathway is triggered by FAK inhibition or inhibiting integrin αV/β3 with Cilengitide. Thus, GT can target integrins to induce anoikis on lung epithelial cells.
Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation
Authors: Benzinger Dirk , Khammash Mustafa 
Published: August 2018

AbstractMany natural transcription factors are regulated in a pulsatile fashion, but it remains unknown whether synthetic gene expression systems can benefit from such dynamic regulation. Here we find, using a fast-acting, optogenetic transcription factor in Saccharomyces cerevisiae, that dynamic pulsatile signals reduce cell-to-cell variability in gene expression. We then show that by encoding such signals into a single input, expression mean and variability can be independently tuned. Further, we construct a light-responsive promoter library and demonstrate how pulsatile signaling also enables graded multi-gene regulation at fixed expression ratios, despite differences in promoter dose-response characteristics. Pulsatile regulation can thus lead to beneficial functional behaviors in synthetic biological systems, which previously required laborious optimization of genetic parts or the construction of synthetic gene networks.
Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors
Authors: Pareja Fresia , Brandes Alissa H. , Basili Thais , Selenica Pier , Geyer Felipe C. , Fan Dan , Da Cruz Paula Arnaud , Kumar Rahul , Brown David N. , Gularte-Mérida Rodrigo , Alemar Barbara , Bi Rui , Lim Raymond S. , de Bruijn Ino , Fujisawa Sho , Gardner Rui , Feng Elvin , Li Anqi , da Silva Edaise M. , Lozada John R. , Blecua Pedro , Cohen-Gould Leona , Jungbluth Achim A. , Rakha Emad A. , Ellis Ian O. , Edelweiss Maria I. A. , Palazzo Juan , Norton Larry , Hollmann Travis , Edelweiss Marcia , Rubin Brian P. , Weigelt Britta , Reis-Filho Jorge S. 
Published: August 2018

AbstractGranular cell tumors (GCTs) are rare tumors that can arise in multiple anatomical locations, and are characterized by abundant intracytoplasmic granules. The genetic drivers of GCTs are currently unknown. Here, we apply whole-exome sequencing and targeted sequencing analysis to reveal mutually exclusive, clonal, inactivating somatic mutations in the endosomal pH regulatorsATP6AP1orATP6AP2in 72% of GCTs. Silencing of these genes in vitro results in impaired vesicle acidification, redistribution of endosomal compartments, and accumulation of intracytoplasmic granules, recapitulating the cardinal phenotypic characteristics of GCTs and providing a novel genotypic–phenotypic correlation. In addition, depletion of ATP6AP1 or ATP6AP2 results in the acquisition of oncogenic properties. Our results demonstrate that inactivating mutations ofATP6AP1andATP6AP2are likely oncogenic drivers of GCTs and underpin the genesis of the intracytoplasmic granules that characterize them, providing a genetic link between endosomal pH regulation and tumorigenesis.
Luciferase-induced photoreductive uncaging of small-molecule effectors
Authors: Lindberg Eric , Angerani Simona , Anzola Marcello , Winssinger Nicolas 
Published: August 2018

AbstractBioluminescence resonance energy transfer (BRET) is extensively used to study dynamic systems and has been utilized in sensors for studying protein proximity, metabolites, and drug concentrations. Herein, we demonstrate that BRET can activate a ruthenium-based photocatalyst which performs bioorthogonal reactions. BRET from luciferase to the ruthenium photocatalyst is used to uncage effector molecules with up to 64 turnovers of the catalyst, achieving concentrations >0.6 μM effector with 10 nM luciferase construct. Using a BRET sensor, we further demonstrate that the catalysis can be modulated in response to an analyte, analogous to allosterically controlled enzymes. The BRET-induced reaction is used to uncage small-molecule drugs (ibrutinib and duocarmycin) at biologically effective concentrations in cellulo.
Quantitative mappings between symmetry and topology in solids
Authors: Song Zhida , Zhang Tiantian , Fang Zhong , Fang Chen 
Published: August 2018

AbstractThe study of spatial symmetries was accomplished during the last century and had greatly improved our understanding of the properties of solids. Nowadays, the symmetry data of any crystal can be readily extracted from standard first-principles calculation. On the other hand, the topological data (topological invariants), the defining quantities of nontrivial topological states, are in general considerably difficult to obtain, and this difficulty has critically slowed down the search for topological materials. Here we provide explicit and exhaustive mappings from symmetry data to topological data for arbitrary gapped band structure in the presence of time-reversal symmetry and any one of the 230 space groups. The mappings are completed using the theoretical tools of layer construction and symmetry-based indicators. With these results, finding topological invariants in any given gapped band structure reduces to a simple search in the mapping tables provided.
NF1 deficiency correlates with estrogen receptor signaling and diminished survival in breast cancer
Authors: Dischinger Patrick S. , Tovar Elizabeth A. , Essenburg Curt J. , Madaj Zachary B. , Gardner Eve E. , Callaghan Megan E. , Turner Ashley N. , Challa Anil K. , Kempston Tristan , Eagleson Bryn , Kesterson Robert A. , Bronson Roderick T. , Bowman Megan J. , Graveel Carrie R. , Steensma Matthew R. 
Published: August 2018

AbstractThe key negative regulatory gene of the RAS pathway, NF1, is mutated or deleted in numerous cancer types and is associated with increased cancer risk and drug resistance. Even though women with neurofibromatosis (germline NF1 mutations) have a substantially increased breast cancer risk at a young age and NF1 is commonly mutated in sporadic breast cancers, we have a limited understanding of the role of NF1 in breast cancer. We utilized CRISPR–Cas9 gene editing to create Nf1 rat models to evaluate the effect of Nf1 deficiency on tumorigenesis. The resulting Nf1 indels induced highly penetrant, aggressive mammary adenocarcinomas that express estrogen receptor (ER) and progesterone receptor (PR). We identified distinct Nf1 mRNA and protein isoforms that were altered during tumorigenesis. To evaluate NF1 in human breast cancer, we analyzed genomic changes in a data set of 2000 clinically annotated breast cancers. We found NF1 shallow deletions in 25% of sporadic breast cancers, which correlated with poor clinical outcome. To identify biological networks impacted by NF1 deficiency, we constructed gene co-expression networks using weighted gene correlation network analysis (WGCNA) and identified a network connected to ESR1 (estrogen receptor). Moreover, NF1-deficient cancers correlated with established RAS activation signatures. Estrogen-dependence was verified by estrogen-ablation in Nf1 rats where rapid tumor regression was observed. Additionally, Nf1 deficiency correlated with increased estrogen receptor phosphorylation in mammary adenocarcinomas. These results demonstrate a significant role for NF1 in both NF1-related breast cancer and sporadic breast cancer, and highlight a potential functional link between neurofibromin and the estrogen receptor.