bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Time Evolution of Turbulence in the Space Environment by Neutral Beam Injection
Authors: Fletcher Alex C. , Crabtree Chris , Huba Joseph , Ganguli Gurudas , Siefring Carl 
Published: December 2019

AbstractThe Space Measurement of A Rocket‐released Turbulence mission will demonstrate the production and evolution of turbulence in the space environment via a cascade of plasma physics processes. A sounding rocket will inject neutral barium atoms into the upper ionosphere at high speed across the magnetic field. The barium atoms photoionize, and the magnetic field confines them, leading to an ion ring distribution in velocity space that is unstable to electrostatic lower hybrid waves. Nonlinear induced scattering of lower hybrid waves produces electromagnetic magnetosonic and whistler waves that rapidly escape the source region and propagate into the radiation belts. In this paper, we present models and simulations of early time parts of this cascade until the lower hybrid waves are generated. We study the neutral atom injection, expansion, and ionization analytically and computationally. In a realistic scenario, the velocity distribution function is found to be nongyrotropic instead of a perfect ring in the plane perpendicular to the magnetic field. Using these results, we examine a representative region of the barium cloud and perform particle‐in‐cell simulations of the excitation of the lower hybrid waves. Of particular interest is the energy extracted from the kinetic energy of the barium ions, as this will ultimately affect the amplitude of the electromagnetic waves in the radiation belts. We find that for velocity distribution functions that deviate from an ideal ring distribution, the energy extracted from the fast barium ions increases.
A New Volcanic Stratospheric Sulfate Aerosol Forcing Emulator (EVA_H): Comparison With Interactive Stratospheric Aerosol Models
Authors: Aubry Thomas J. , Toohey Matthew , Marshall Lauren , Schmidt Anja , Jellinek A. Mark 
Published: December 2019

AbstractIdealized models or emulators of volcanic aerosol forcing have been widely used to reconstruct the spatiotemporal evolution of past volcanic forcing. However, existing models, including the most recently developed Easy Volcanic Aerosol (EVA; Toohey et al., doi: 10.5194/gmd‐2016‐83), (i) do not account for the height of injection of volcanic SO
; (ii) prescribe a vertical structure for the forcing; and (iii) are often calibrated against a single eruption. We present a new idealized model, EVA_H, that addresses these limitations. Compared to EVA, EVA_H makes predictions of the global mean stratospheric aerosol optical depth that are (i) similar for the 1979–1998 period characterized by the large and high‐altitude tropical SO
injections of El Chichón (1982) and Mount Pinatubo (1991); (ii) significantly improved for the 1998–2015 period characterized by smaller eruptions with a large variety of injection latitudes and heights. Compared to EVA, the sensitivity of volcanic forcing to injection latitude and height in EVA_H is much more consistent with results from climate models that include interactive aerosol chemistry and microphysics, even though EVA_H remains less sensitive to eruption latitude than the latter models. We apply EVA_H to investigate potential biases and uncertainties in EVA‐based volcanic forcing data sets from phase 6 of the Coupled Model Intercomparison Project (CMIP6). EVA and EVA_H forcing reconstructions do not significantly differ for tropical high‐altitude volcanic injections. However, for high‐latitude or low‐altitude injections, our reconstructed forcing is significantly lower. This suggests that volcanic forcing in CMIP6 last millenium experiments may be overestimated for such eruptions.
Entangling three qubits without ever touching
Authors: Blasiak Pawel , Markiewicz Marcin 
Published: December 2019

AbstractAll identical particles are inherently correlated from the outset, regardless of how far apart their creation took place. In this paper, this fact is used for extraction of entanglement from independent particles unaffected by any interactions. Specifically, we are concerned with operational schemes for generation of all tripartite entangled states, essentially the GHZ state and the W state, which prevent the particles from touching one another over the entire evolution. The protocols discussed in the paper require only three particles in linear optical setups with equal efficiency for boson, fermion or anyon statistics. Within this framework indistinguishability of particles presents itself as a useful resource of entanglement accessible for practical applications.
Defect processes in F and Cl doped anatase TiO2
Authors: Filippatos Petros-Panagis , Kelaidis Nikolaos , Vasilopoulou Maria , Davazoglou Dimitris , Lathiotakis Nektarios N. , Chroneos Alexander 
Published: December 2019

AbstractTitanium dioxide represents one of the most widely studied transition metal oxides due to its high chemical stability, non-toxicity, abundance, electron transport capability in many classes of optoelectronic devices and excellent photocatalytic properties. Nevertheless, the wide bang gap of pristine oxide reduces its electron transport ability and photocatalytic activity. Doping with halides and other elements has been proven an efficient defect engineering strategy in order to reduce the band gap and maximize the photocatalytic activity. In the present study, we apply Density Functional Theory to investigate the influence of fluorine and chlorine doping on the electronic properties of TiO2. Furthermore, we present a complete investigation of spin polarized density functional theory of the (001) surface doped with F and Cl in order to elaborate changes in the electronic structure and compare them with the bulk TiO2.
Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover
Authors: Benevenuto Juliana , Bhakta Mehul , Lohr Daniel A. , Ferrão Luís Felipe V. , Resende Marcio F. R. , Kirst Matias , Quesenberry Kenneth , Munoz Patricio 
Published: December 2019

AbstractHerbicide resistance is a recurrent evolutionary event that has been reported across many species and for all major herbicide modes of action. The synthetic auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used since the 1940s, however the genetic variation underlying naturally evolving resistance remains largely unknown. In this study, we used populations of the forage legume crop red clover (Trifolium pratense L.) that were recurrently selected for 2,4-D resistance to detect genome-wide signatures of adaptation. Four susceptible and six derived resistant populations were sequenced using a less costly approach by combining targeted sequencing (Capture-Seq) with pooled individuals (Pool-Seq). Genomic signatures of selection were identified using: (i) pairwise allele frequency differences; (ii) genome scan for overly differentiated loci; and (iii) genome‐wide association. Fifty significant SNPs were consistently detected, most located in a single chromosome, which can be useful for marker assisted selection. Additionally, we searched for candidate genes at these genomic regions to gain insights into potential molecular mechanisms underlying 2,4-D resistance. Among the predicted functions of candidate genes, we found some related to the auxin metabolism, response to oxidative stress, and detoxification, which are also promising for further functional validation studies.
Time-course relationship between environmental factors and microbial diversity in tobacco soil
Authors: Wang Zhaobao , Yang Yan , Xia Yuzhen , Wu Tao , Zhu Jie , Yang Jianming , Li Zhengfeng 
Published: December 2019

AbstractSoil physicochemical properties and microbial diversity both play equally important roles in tobacco cultivation. However, the relationship between these factors remains unclear. In this study, we investigated their correlations through the whole tobacco growth period, including the pretransplanting (YX-p), root extending (R), flourishing (F), and mature (M) stages in the Yuxi region of the Yunnan-Guizhou Plateau by measuring physicochemical properties and conducting 16S/18S rRNA analysis. The analysis demonstrated that the microbial community richness and diversity continuously changed along with the growth course of the tobacco. Multiple environmental factors showed a certain correlation with the diversity of microbial communities. Some bacteria could accumulate nitrogen during the growth stages, and the diversity of the bacterial community also increased when the content of organic matter rose. In addition, the water content and available K also influenced the diversity of the microbial community. The dynamic changes in soil physicochemical properties and enzyme activities gave rise to differences in the microbial community composition and structure, all of which affected the growth of tobacco. This study revealed the time-course relationship between environmental factors and microbial diversity in tobacco soil. An understanding of this relationship provides guidance for research on the interaction system of plants, soil and microbes and on improving plant yield and quality.
Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2
Authors: Luzik Dmitrii A. , Rogacheva Olga N. , Izmailov Sergei A. , Indeykina Maria I. , Kononikhin Alexei S. , Skrynnikov Nikolai R. 
Published: December 2019

AbstractWe have investigated covalent conjugation of VPPPVPPRRRX′ peptide (where X′ denotes Nε-chloroacetyl lysine) to N-terminal SH3 domain from adapter protein Grb2. Our experimental results confirmed that the peptide first binds to the SH3 domain noncovalently before establishing a covalent linkage through reaction of X′ with the target cysteine residue C32. We have also confirmed that this reaction involves a thiolate-anion form of C32 and follows the SN2 mechanism. For this system, we have developed a new MD-based protocol to model the formation of covalent conjugate. The simulation starts with the known coordinates of the noncovalent complex. When two reactive groups come into contact during the course of the simulation, the reaction is initiated. The reaction is modeled via gradual interpolation between the two sets of force field parameters that are representative of the noncovalent and covalent complexes. The simulation proceeds smoothly, with no appreciable perturbations to temperature, pressure or volume, and results in a high-quality MD model of the covalent complex. The validity of this model is confirmed using the experimental chemical shift data. The new MD-based approach offers a valuable tool to explore the mechanics of protein-peptide conjugation and build accurate models of covalent complexes.
Accumulation, morpho-physiological and oxidative stress induction by single and binary treatments of fluoride and low molecular weight phthalates in Spirodela polyrhiza L. Schleiden
Authors: Sharma Ritika , Kumari Arpna , Rajput Sneh , Nishu  , Arora Saroj , Rampal Rajkumar , Kaur Rajinder 
Published: December 2019

AbstractThe present study examined the interactive effects of fluoride and phthalates on their uptake, generation of reactive oxygen species and activation of antioxidative defence responses inSpirodela polyrhizaL. Schleiden. A hydroponic study was conducted in whichS. polyrhizacultured in Hoagland’s nutrient medium, was exposed to fluoride (50 ppm) and different concentrations viz., 75, 150 300 ppm of diethyl phthalate (DEP) and diallyl phthalate (DAP) individually as well as in combination for the time period of 24, 72, 120 and 168 h respectively. A significant decline in fresh weight, dry to fresh weight ratio, total chlorophyll, carotenoid content and increased anthocyanin content was observed. Fluoride and phthalates was found to be readily accumulated byS. polyrhizain all the exposure periods. Interestingly, when binary treatments were given in nutrient medium, uptake of both fluoride and phthalate was found to be influenced by each other. In combined treatments, DEP stimulated fluoride uptake, while its own uptake was restricted by fluoride. In contrary to this, fluoride stimulated DAP uptake. Moreover, combined stress further caused significant decrement in carbohydrate, protein content and increment in MDA levels, phenolic content and electrolyte leakage. Nevertheless, phthalates showed more pronounced oxidative stress and growth inhibition compared to fluoride. To cope up with the oxidative damage, enhanced level of antioxidant enzymatic activities was observed inS. polyrhizaunder both fluoride and phthalate stress as compared to control. Scanning electron microscope imaging of leaf stomata revealed that combined stress of fluoride with phthalates caused distortion in the shape of guard cells. Confocal micrographs confirmed the generation of reactive oxygen species, cell damage, disruption in membrane integrity, and enhanced levels of glutathione in plant cells. This study focussed on ecotoxicological and interactive significance of fluoride led phthalate uptake or vice versa which was also assumed to confer tolerance attributes.
c-Cbl targets PD-1 in immune cells for proteasomal degradation and modulates colorectal tumor growth
Authors: Lyle Chimera , Richards Sean , Yasuda Kei , Napoleon Marc Arthur , Walker Joshua , Arinze Nkiruka , Belghasem Mostafa , Vellard Irva , Yin Wenqing , Ravid Jonathan D. , Zavaro Elias , Amraei Razie , Francis Jean , Phatak Uma , Rifkin Ian R. , Rahimi Nader , Chitalia Vipul C. 
Published: December 2019

AbstractCasitas B lymphoma (c-Cbl) is an E3 ubiquitin ligase and a negative regulator of colorectal cancer (CRC). Despite its high expression in immune cells, the effect of c-Cbl on the tumor microenvironment remains poorly understood. Here we demonstrate that c-Cbl alters the tumor microenvironment and suppresses Programmed cell death-1 (PD-1) protein, an immune checkpoint receptor. Using syngeneic CRC xenografts, we observed significantly higher growth of xenografts and infiltrating immune cells in c-Cbl+/− compared to c-Cbl+/+ mice. Tumor-associated CD8+ T-lymphocytes and macrophages of c-Cbl+/− mice showed 2–3-fold higher levels of PD-1. Functionally, macrophages from c-Cbl+/− mice showed a 4–5-fold reduction in tumor phagocytosis, which was restored with an anti-PD-1 neutralizing antibody suggesting regulation of PD-1 by c-Cbl. Further mechanistic probing revealed that C-terminus of c-Cbl interacted with the cytoplasmic tail of PD-1. c-Cbl destabilized PD-1 through ubiquitination- proteasomal degradation depending on c-Cbl’s RING finger function. This data demonstrates c-Cbl as an E3 ligase of PD-1 and a regulator of tumor microenvironment, both of which were unrecognized components of its tumor suppressive activity. Advancing immune checkpoint and c-Cbl biology, our study prompts for probing of PD-1 regulation by c-Cbl in conditions driven by immune checkpoint abnormalities such as cancers and autoimmune diseases.
Symmetry selected quantum dynamics of few electrons in nanopillar transistors
Authors: Wan Yue-Min , Lin Heng-Tien 
Published: December 2019

AbstractStudy on single electron tunnel using current-voltage characteristics in nanopillar transistors at 298 K show that the mapping between the Nth electron excited in the central box ∼8.5 × 8.5 × 3 nm3 and the Nth tunnel peak is not in the one-to-one correspondence to suggest that the total number N of electrons is not the best quantum number for characterizing the quality of single electron tunnel in a three-dimensional quantum box transistor. Instead, we find that the best number is the sub-quantum number nz of the conduction z channel. When the number of electrons in nz is charged to be even and the number of electrons excited in the nx and ny are also even at two, the adding of the third electron into the easy nx/ny channels creates a weak symmetry breaking in the parity conserved x-y plane to assist the indirect tunnel of electrons. A comprehensive model that incorporates the interactions of electron-electron, spin-spin, electron-phonon, and electron-hole is proposed to explain how the excited even electrons can be stabilized in the electric-field driving channel. Quantum selection rules with hierarchy for the ni (i = x, y, z) and N = Σni are tabulated to prove the superiority of nz over N.
Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds
Authors: Ebrahimzadegan Rahman , Houben Andreas , Mirzaghaderi Ghader 
Published: December 2019

AbstractHere, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (−B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.
Thermal and efficiency droop in InGaN/GaN light-emitting diodes: decoupling multiphysics effects using temperature-dependent RF measurements
Authors: Rashidi Arman , Monavarian Morteza , Aragon Andrew , Feezell Daniel 
Published: December 2019

AbstractMultiphysics processes such as recombination dynamics in the active region, carrier injection and transport, and internal heating may contribute to thermal and efficiency droop in InGaN/GaN light-emitting diodes (LEDs). However, an unambiguous methodology and characterization technique to decouple these processes under electrical injection and determine their individual roles in droop phenomena is lacking. In this work, we investigate thermal and efficiency droop in electrically injected single-quantum-well InGaN/GaN LEDs by decoupling the inherent radiative efficiency, injection efficiency, carrier transport, and thermal effects using a comprehensive rate equation approach and a temperature-dependent pulsed-RF measurement technique. Determination of the inherent recombination rates in the quantum well confirms efficiency droop at high current densities is caused by a combination of strong non-radiative recombination (with temperature dependence consistent with indirect Auger) and saturation of the radiative rate. The overall reduction of efficiency at elevated temperatures (thermal droop) results from carriers shifting from the radiative process to the non-radiative processes. The rate equation approach and temperature-dependent pulsed-RF measurement technique unambiguously gives access to the true recombination dynamics in the QW and is a useful methodology to study efficiency issues in III-nitride LEDs.
Feasibility of improving vascular imaging in the presence of metallic stents using spectral photon counting CT and K-edge imaging
Authors: Sigovan Monica , Si-Mohamed Salim , Bar-Ness Daniel , Mitchell Julia , Langlois Jean-Baptiste , Coulon Philippe , Roessl Ewald , Blevis Ira , Rokni Michal , Rioufol Gilles , Douek Philippe , Boussel Loic 
Published: December 2019

AbstractCorrect visualization of the vascular lumen is impaired in standard computed tomography (CT) because of blooming artifacts, increase of apparent size, induced by metallic stents and vascular calcifications. Recently, due to the introduction of photon-counting detectors in the X-ray imaging field, a new prototype spectral photon-counting CT (SPCCT) based on a modified clinical CT system has been tested in a feasibility study for improving vascular lumen delineation and visualization of coronary stent architecture. Coronary stents of different metal composition were deployed inside plastic tubes containing hydroxyapatite spheres to simulate vascular calcifications and in the abdominal aorta of one New Zealand White (NZW) rabbit. Imaging was performed with an SPCCT prototype, a dual-energy CT system, and a conventional 64-channel CT system (B64). We found the apparent widths of the stents significantly smaller on SPCCT than on the other two systems in vitro (p < 0.01), thus closer to the true size. Consequently, the intra-stent lumen was significantly larger on SPCCT (p < 0.01). In conclusion, owing to the increased spatial resolution of SPCCT, improved lumen visualization and delineation of stent metallic mesh is possible compared to dual-energy and conventional CT.
The Prognostic Importance of CD20+ B lymphocytes in Colorectal Cancer and the Relation to Other Immune Cell subsets
Authors: Edin Sofia , Kaprio Tuomas , Hagström Jaana , Larsson Pär , Mustonen Harri , Böckelman Camilla , Strigård Karin , Gunnarsson Ulf , Haglund Caj , Palmqvist Richard 
Published: December 2019

AbstractThe anti-tumour immune response is critical to patient prognosis in colorectal cancer (CRC). The aim of this study was to investigate infiltration of B lymphocytes into CRC tumours, and their clinical relevance, prognostic value and relation to other immune cell subsets. We used multiplexed immunohistochemistry and multispectral imaging to assay the amount of infiltrating CD20+ B lymphocytes along with infiltration of CD8+ cytotoxic T cells, FOXP3+ T regulatory cells, CD68+ macrophages and CD66b+ neutrophils, in 316 archival CRC tissue specimens. A higher density of infiltrating CD20+ B lymphocytes was associated with tumours of the right colon (P = 0.025) and of lower stages (P = 0.009). Furthermore, patients whose tumours were highly infiltrated by CD20+ B lymphocytes had a significantly improved disease-specific survival (HR = 0.45, 95% CI 0.28–0.73, P = 0.001), which remained significant in multivariable analysis. CD20+ B lymphocytes were highly and positively associated with CD8+ T lymphocytes (P < 0.001), and part of the prognostic role was found to be a cooperative effect between these lymphocyte subsets. Our results support a favourable prognostic value of tumour-infiltrating CD20+ B lymphocytes in CRC. Furthermore, a cooperative prognostic effect between CD20+ B lymphocytes and CD8+ T lymphocytes is suggested.