bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual-polarization single-chord plasma interferometry in stellarators/torsatrons
Authors: Filippov V. , Grekov D.
Published: September 2020

The well known ordinary wave based interferometry is of frequent use for plasma diagnostics in fusion facilities. With the probing direction being perpendicular to the magnetic field of the facility, the ordinary wave phase shift is proportional to the average density along the probing path at frequencies much higher than the plasma frequency of electrons. In the case of extraordinary waves, the phase shift depends on both the plasma density and the confining magnetic field. For the facilities of stellarator/torsatron types, the magnetic field is known; therefore, the measurement of the extraordinary wave phase shift can also provide information on the plasma density profile. The plasma density measurements with the use of dual-polarization interferometers were carried out on the Uragan-3M and Uragan-2M torsatrons. For correct interpretation of the experimental results, numerical simulation was performed to describe the probing wave propagation through the plasma in the magnetic field of variable direction. The transmitting-to-receiving horn scattering matrix has been obtained in a wide range of plasma parameters. In the course of the interpretation of measurements, restrictions on the use of the Wentzel–Kramers–Brillouin approximation were determined. This has made it possible to develop the optimized layout of the dual-polarization interferometer for measuring the plasma density in stellarators/torsatrons. The here proposed upgrade of the interferometers on Uragan-2M will enable one to obtain additional information on the temporal evolution of the plasma density.
Subcycling of particle orbits in variational, geometric electromagnetic particle-in-cell methods
Authors: Hirvijoki Eero , Kormann Katharina , Zonta Filippo
Published: September 2020

This paper investigates the subcycling of particle orbits in variational, geometric particle-in-cell methods, addressing the Vlasov–Maxwell system in magnetized plasmas. The purpose of subcycling is to allow different time steps for different particle species and, ideally, time steps longer than the electron gyroperiod for the global field solves while sampling the local cyclotron orbits accurately. The considered algorithms retain the electromagnetic gauge invariance of the discrete action, guaranteeing a local charge conservation law, while the variational approach provides a bounded long-time energy behavior.
The effect of descriptor choice in machine learning models for ionic liquid melting point prediction
Authors: Low Kaycee , Kobayashi Rika , Izgorodina Ekaterina I.
Published: September 2020

The characterization of an ionic liquid’s properties based on structural information is a longstanding goal of computational chemistry, which has received much focus from ab initio and molecular dynamics calculations. This work examines kernel ridge regression models built from an experimental dataset of 2212 ionic liquid melting points consisting of diverse ion types. Structural descriptors, which have been shown to predict quantum mechanical properties of small neutral molecules within chemical accuracy, benefit from the addition of first-principles data related to the target property (molecular orbital energy, charge density profile, and interaction energy based on the geometry of a single ion pair) when predicting the melting point of ionic liquids. Out of the two chosen structural descriptors, ECFP4 circular fingerprints and the Coulomb matrix, the addition of molecular orbital energies and all quantum mechanical data to each descriptor, respectively, increases the accuracy of surrogate models for melting point prediction compared to using the structural descriptors alone. The best model, based on ECFP4 and molecular orbital energies, predicts ionic liquid melting points with an average mean absolute error of 29 K and, unlike group contribution methods, which have achieved similar results, is applicable to any type of ionic liquid.
Transmembrane potential of physiologically relevant model membranes: Effects of membrane asymmetry
Authors: Lin Xubo , Gorfe Alemayehu A.
Published: September 2020

Transmembrane potential difference (Vm) plays important roles in regulating various biological processes. At the macro level, Vm can be experimentally measured or calculated using the Nernst or Goldman–Hodgkin–Katz equation. However, the atomic details responsible for its generation and impact on protein and lipid dynamics still need to be further elucidated. In this work, we performed a series of all-atom molecular dynamics (MD) simulations of symmetric model membranes of various lipid compositions and cation contents to evaluate the relationship between membrane asymmetry and Vm. Specifically, we studied the impact of the asymmetric distribution of POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine), PIP2 (phosphatidylinositol 4,5-bisphosphate), as well as Na+ and K+ on Vm using atomically detailed MD simulations of symmetric model membranes. The results suggest that, for an asymmetric POPC-POPC/POPS bilayer in the presence of NaCl, the presence of the monovalent anionic lipid POPS in the inner leaflet polarizes the membrane (ΔVm < 0). Intriguingly, replacing a third of the POPS lipids by the polyvalent anionic signaling lipid PIP2 counteracts this effect, resulting in a smaller negative membrane potential. We also found that replacing Na+ ions in the inner region by K+ depolarizes the membrane (ΔVm > 0). These divergent effects arise from variations in the strength of cation–lipid interactions and are correlated with changes in lipid chain order and head-group orientation.
Laser-induced fluorescence of the trans-CHBrCHO radical
Authors: Masumoto Ichiro , Washida Nobuaki , Inomata Satoshi , Imamura Takashi , Muraoka Azusa , Yamashita Koichi
Published: September 2020

A new laser-induced fluorescence spectrum was observed in the region of 350 nm–360 nm. The spectrum was observed in the reaction between the CHBrCHBr and OH radicals and in the reaction of CHBrCHBr and CH2CHBr with atomic oxygen O(3P). The spectrum was assigned to the B̃−−X̃ transition of the trans-CHBrCHO (trans-2-bromovinoxy) radical. The B̃−−X̃ electronic transition energy (T0) was 28 542 cm−1, which was 242 cm−1 lower than that of the unsubstituted vinoxy radical (CH2CHO). From an analysis of the laser-induced single vibronic level fluorescence aided by ab initio calculations, some of the vibrational frequencies were assigned to the ground electronic state ν3 (C–O str.) = 1581 cm−1, ν6 (C–C str.) = 1130 cm−1, and ν8 (C–C–O bend.) = 409 cm−1. The fluorescence lifetimes of the excited B̃ state were 35 ns–75 ns, depending on the excited vibrational modes, implying that predissociation had accelerated as the energy level (v′) increased.
Spreading and retraction kinetics for impact of nanodroplets on hydrophobic surfaces
Authors: Wang Yi-Feng , Wang Yi-Bo , Xie Fang-Fang , Liu Jing-Yuan , Wang Shuo-Lin , Yang Yan-Ru , Gao Shu-Rong , Wang Xiao-Dong
Published: September 2020

Impact dynamics of nanodroplets has recently gained extensive attention because of its potential applications in nanoscale inkjet printing, nanodroplet spray cooling, and nanocoating. In this study, a nanodroplet impacting unheated, flat, smooth, and hydrophobic surfaces is investigated via molecular dynamics simulations. The emphasis is placed on spreading and retraction kinetics, i.e., time-dependent wetting radius or r–τ relation, where r and τ are the normalized wetting radius and time. On the basis of an energy conservation approach, an analytical model of r–τ kinetics is developed for impacting nanodroplets. Hypotheses of cylinder droplet and extensional flow are employed to calculate the transient kinetic energy and viscous dissipation rate, which are found to be the most appropriate for impacting nanodroplets. The model is tested in a range of Weber numbers from We = 15 to 60, Reynolds numbers from Re = 11.07 to 22.19, and surface wettability θ0 = 105° and 125°. The tests show that the mean relative deviation ranges from 2.22% to 5.47%, and hence, the developed model captures the spreading and retraction kinetics of a nanodroplet impacting hydrophobic surfaces with satisfactory accuracy. Furthermore, it is found that the model can also be extended to predict the retraction kinetics of nanodroplets on hydrophilic surfaces for high Weber numbers.
Reproducibility of potential energy surfaces of organic/metal interfaces on the example of PTCDA on Ag(111)
Authors: Hörmann Lukas , Jeindl Andreas , Hofmann Oliver T.
Published: September 2020

Molecular adsorption at organic/metal interfaces depends on a range of mechanisms: covalent bonds, charge transfer, Pauli repulsion, and van der Waals (vdW) interactions shape the potential energy surface (PES), making it key to understanding organic/metal interfaces. Describing such interfaces with density functional theory requires carefully selecting the exchange correlation (XC) functional and vdW correction scheme. To explore the reproducibility of the PES with respect to the choice of method, we present a benchmark of common local, semi-local, and non-local XC functionals in combination with various vdW corrections. We benchmark these methods using perylene-tetracarboxylic dianhydride on Ag(111), one of the most frequently studied organic/metal interfaces. For each method, we determine the PES using a Gaussian process regression algorithm, which requires only about 50 density functional theory calculations as input. This allows a detailed analysis of the PESs’ features, such as the positions and energies of minima and saddle points. Comparing the results from different combinations of XC functionals and vdW corrections enables us to identify trends and differences between the approaches. PESs for different computation methods are in qualitative agreement but also display significant quantitative differences. In particular, the lateral positions of adsorption geometries agree well with experiment, while adsorption heights, energies, and barriers show larger discrepancies.
Synthesis and Characterisation of Photolabile SPhNPPOC-Protected (R)-MiniPEG Containing Chiral γ-Peptide Nucleic Acid Monomers
Authors: Lai Qingteng , Dong Bo , Nie Kaixuan , Shi Huanhuan , Liang Bo , Liu Zhengchun
Published: September 2020

Peptide nucleic acid (PNA) microarrays are expected to be developed as a new generation of gene detection tools. However, poor water solubility and the limitation of the sequence design of achiral PNA probes mainly hinder their application. Accordingly, (R)-diethylene glycol containing a chiral PNA (miniPEG-γPNA) has been developed to solve these problems. Light-directed synthesis is an effective method to fabricate high-density microarrays. Thiophenyl-2-(2-nitrophenyl)propoxycarbonyl (SPhNPPOC) is a newly synthesised photolabile protective group with high photolytic efficiency. Protecting the PNA monomers with SPhNPPOC may improve the preparation process of PNA microarrays by light-directed synthesis in terms of shortening the deprotection time and restraining side reactions. In this article, SPhNPPOC/carbobenzoxy (Cbz)-protected chiral miniPEG-γPNA monomers are synthesised, and the photo-deprotection rate is approximately twice that of a 2-(2-nitrophenyl)propyloxycarbonyl (NPPOC)-protected monomer. The monomers are expected to be used for the efficient and rapid fabrication of chiral miniPEG-γPNA microarrays through a photolithographic strategy.
Determining marine mammal detection functions for a stationary land-based survey site
Authors: Keen Eric M. , Wray Janie , Hendricks Benjamin , O'Mahony Éadin , Picard Chris R. , Alidina Hussein
Published: September 2020

Abstract ContextThe shore-based survey is a common, non-invasive, and low-cost method in marine mammal science, but its scientific applications are currently limited. Such studies typically target populations whose distributions are not random with respect to nearshore sites and involve repeated scans of the same area from single, stationary platforms. These circumstances prohibit the use of classic distance sampling techniques for estimating animal densities or distributions, particularly the derivation of a detection function that describes the probability of detecting targets at various distances from the observer. AimsHere, we present a technique for estimating land-based detection functions, as well as quantifying uncertainty in their parameterisation, on the basis of the range-specific variability of observations from one scan to the next. MethodsThis Bayesian technique uses Monte Carlo simulation to determine the likelihood of thousands of candidate detection functions, then conducts weighted sampling to generate a posterior distribution estimate of the detection function parameterisation. We tested the approach with both archival and artificial datasets built from known detection functions that reflect whale and porpoise detectability. Key resultsWhen the base distribution of targets was random, the whale detection function was estimated without error (i.e. the difference of the median of the posterior and the true value was 0.00), and the porpoise detection function was estimated with an error equal to 4.23% of the true value. When the target base distribution was non-random, estimation error remained low (2.57% for targets concentrated offshore, 1.14% when associated with nearshore habitats). When applied to field observations of humpback whales and Dall’s porpoises from a land-based study in northern British Columbia, Canada, this technique yielded credible results for humpback whales, but appeared to underestimate the detectability of Dall’s porpoises. ConclusionThe findings presented here indicate that this approach to detection function estimation is appropriate for long-running surveys in which scan regularity is high and the focus is on large, slow-moving, low herd-size, and easily detectable species. ImplicationsThe derivation of a detection function is a critical step in density estimation. The methodology presented here empowers land-based studies to contribute to quantitative monitoring and assessment of marine mammal populations in coastal habitats.
The pervasive threat of lead (Pb) in drinking water: Unmasking and pursuing scientific factors that govern lead release
Authors: Santucci Raymond J. , Scully John R.
Published: September 2020

The Flint water crisis raised questions about the factors resulting in unacceptable soluble lead concentrations in the city’s drinking water. Although water treatment strategies, failure to follow regulations, and unethical behavior were all factors, knowledge deficits at the intersection of several scientific fields also contributed to the crisis. Pursuit of opportunities to address unresolved scientific questions can help avert future lead poisoning disasters. Such advances will enable scientifically based, data-driven risk assessments that inform decisions involving drinking water systems. In this way, managers and decision makers can anticipate, monitor, and prevent future lead in water crises.
Synchrony matters more than species richness in plant community stability at a global scale
Authors: Valencia Enrique , de Bello Francesco , Galland Thomas , Adler Peter B. , Lepš Jan , E-Vojtkó Anna , van Klink Roel , Carmona Carlos P. , Danihelka Jiří , Dengler Jürgen , Eldridge David J. , Estiarte Marc , García-González Ricardo , Garnier Eric , Gómez‐García Daniel , Harrison Susan P. , Herben Tomáš , Ibáñez Ricardo , Jentsch Anke , Juergens Norbert , Kertész Miklós , Klumpp Katja , Louault Frédérique , Marrs Rob H. , Ogaya Romà , Ónodi Gábor , Pakeman Robin J. , Pardo Iker , Pärtel Meelis , Peco Begoña , Peñuelas Josep , Pywell Richard F. , Rueda Marta , Schmidt Wolfgang , Schmiedel Ute , Schuetz Martin , Skálová Hana , Šmilauer Petr , Šmilauerová Marie , Smit Christian , Song MingHua , Stock Martin , Val James , Vandvik Vigdis , Ward David , Wesche Karsten , Wiser Susan K. , Woodcock Ben A. , Young Truman P. , Yu Fei-Hai , Zobel Martin , Götzenberger Lars
Published: September 2020

Significance

The stability of ecological communities under ongoing climate and land-use change is fundamental to the sustainable management of natural resources through its effect on critical ecosystem services. Biodiversity is hypothesized to enhance stability through compensatory effects (decreased synchrony between species). However, the relative importance and interplay between different biotic and abiotic drivers of stability remain controversial. By analyzing long-term data from natural and seminatural ecosystems across the globe, we found that the degree of synchrony among dominant species was the main driver of stability, rather than species richness per se. These biotic effects overrode environmental drivers, which influenced the stability of communities by modulating the effects of richness and synchrony.
Spatiotemporal dissociation of fMRI activity in the caudate nucleus underlies human de novo motor skill learning
Authors: Choi Yera , Shin Emily Yunha , Kim Sungshin
Published: September 2020

Significance

Numerous real-world motor skills require learning arbitrary relationships between actions and their consequences from scratch. However, little is understood about the neural signatures of de novo motor learning and associated individual variability. In a longitudinal fMRI experiment, where participants learned to control a cursor by moving fingers, we found a gradual transition of performance-related activity from the head to tail of the caudate nucleus. This finding reflects the flexible and stable reward representations in the head and tail, respectively. Additionally, intrinsic cortico-caudate connectivity predicted better learners with weaker head–prefrontal and stronger tail–sensorimotor interactions. The present study provides unprecedented insight into de novo motor learning, which may contribute to the understanding of motor-related disorders, and infant learning.
Short Vi-polysaccharide abrogates T-independent immune response and hyporesponsiveness elicited by long Vi-CRM197conjugate vaccine
Authors: Micoli Francesca , Bjarnarson Stefania P. , Arcuri Melissa , Aradottir Pind Audur Anna , Magnusdottir Gudbjorg J. , Necchi Francesca , Di Benedetto Roberta , Carducci Martina , Schiavo Fabiola , Giannelli Carlo , Pisoni Ivan , Martin Laura B. , Del Giudice Giuseppe , MacLennan Calman A. , Rappuoli Rino , Jonsdottir Ingileif , Saul Allan
Published: September 2020

Significance

Our results suggest a rational way of designing and developing an improved typhoid conjugate vaccine and, by extension, to conjugate vaccines in general: first, modify a T-independent polysaccharide so that it no longer induces a T-independent response, then conjugate the polysaccharide to a suitable carrier protein restoring immunogenicity, thus creating a pure T-dependent antigen that induces a strongly boostable and long-lived response at an early age.
Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes
Authors: Painter Mark M. , Zimmerman Gretchen E. , Merlino Madeline S. , Robertson Andrew W. , Terry Valeri H. , Ren Xuefeng , McLeod Megan R. , Gomez-Rodriguez Lyanne , Garcia Kirsten A. , Leonard Jolie A. , Leopold Kay E. , Neevel Andrew J. , Lubow Jay , Olson Eli , Piechocka-Trocha Alicja , Collins David R. , Tripathi Ashootosh , Raghavan Malini , Walker Bruce D. , Hurley James H. , Sherman David H. , Collins Kathleen L.
Published: September 2020

Significance

This study describes the discovery of a class of drug that can help the immune system eliminate hard-to-kill cells infected with HIV. HIV establishes a persistent infection for which there is no cure, necessitating the development of new approaches to enhance the clearance of HIV-infected cells. HIV encodes Nef, which down-regulates MHC-I expression in infected cells to impair immune-mediated clearance by cytotoxic T lymphocytes. We identified the plecomacrolide family of natural products as potent inhibitors of Nef, and concanamycin A restored MHC-I and enhanced the clearance of HIV-infected primary cells by cytotoxic T lymphocytes. Concanamycin A counteracted Nef from diverse clades of HIV targeting multiple allotypes of MHC-I, indicating the potential for broad therapeutic utility.
Synaptic secretion from human natural killer cells is diverse and includes supramolecular attack particles
Authors: Ambrose Ashley R. , Hazime Khodor S. , Worboys Jonathan D. , Niembro-Vivanco Olatz , Davis Daniel M.
Published: September 2020

Significance

Cytotoxic immune cells kill cancer and virally infected cells through secretion of perforin and granzymes at immune synapses. It has recently been shown that cytotoxic T cells secrete membraneless protein structures, termed SMAPs, comprising perforin and granzyme within a shell of the glycoprotein TSP-1. Here, using a novel imaging technique termed "shadow imaging," we quantitatively assessed synaptic secretion from individual human NK cells. Upon ligation of activating receptors, NK cells secreted vesicles as well as membraneless SMAPs containing TSP-1, perforin, and granzyme B. Super-resolution microscopy revealed that NK cell SMAPs were larger than those secreted by T cells. Heterogeneity in NK cell synaptic secretion is likely important for the different effector functions of NK cell subtypes.
Structure of the dimeric ATP synthase from bovine mitochondria
Authors: Spikes Tobias E. , Montgomery Martin G. , Walker John E.
Published: September 2020

Significance

Adenosine triphosphate (ATP), the fuel of life, is produced in inner membranes of the mitochondria of eukaryotic cells by an embedded molecular machine with a rotary action, called ATP synthase. Single ATP synthases associate into dimers and form long rows, influencing the formation of characteristic cristae which change shape constantly. Our structure of bovine dimers has a wedge made of small proteins and specific lipids in the membrane domain of each monomer that imposes a range of acute angles on the central axes of the monomers, and a pivot between the wedges accommodates rocking motions of the machine accompanying catalysis and other movements that happen independently. It also throws light on how the membrane rotor is made to turn.
Indium segregation mechanism and V-defect formation at the [0001] InAlN surface: an ab-initio investigation
Authors: Mohamad Ranim , Ruterana Pierre
Published: September 2020

First-principle calculations were performed to investigate adsorption and diffusion of indium and aluminum atoms on (0001) and (0001) In (18%) AlN surfaces. First, it was shown that these surfaces are most stable when they contain complex defects. The presence of vacancies causes the In to be strongly bound to the surface with the adsorption energy increasing by 0.11 eV for metal-polar and by 0.78 eV N-polar. In contrast, the adsorption strength of Al to the surface with defects decreases; the corresponding energy goes from 3.96 eV–2.29 eV (metal-polar) and from 8.30 eV–5.05 eV (N-polar). Simultaneously, the diffusion of In is enhanced; its energy barrier decreases by 0.74 eV (0.06 eV) for the N-polar (metal-polar) InAlN surface, whereas that of the Al adatom increases by 0.32 eV for metal-polar (0.08 eV for N-polar), which should limit its diffusion on the surface. Therefore, the indium atoms will tend to migrate towards the complex defects. Eventually, during epitaxial growth, this aggregation of indium atoms around the defects and the low mobility of Al atoms could be the origin of the observed V defects, the phase separation and the crystallographic degradation of the InAlN epitaxial layers with increasing thickness.
Multisection step-impedance modeling and analysis of broadband microwave honeycomb absorbing structures
Authors: He Fan , Zhao Yong , Si Kaixuan , Zha Dace , Li Rui , Dong Jianxiong , Bie Shaowei , Jiang Jianjun
Published: September 2020

A multisection step-impedance honeycomb absorbing structure is investigated both theoretically and experimentally. Excellent intrinsic impedance matching and low reflection are realized by providing a step-impedance transition between air and metal in the microwave band. The wideband absorption mechanism of the honeycomb absorbing structure is analyzed using a step-impedance model, and the particle swarm optimization algorithm is used to obtain the optimal step impedance. Two absorbing structures were simulated: The double-layer structure had an absorption frequency band of 3.9–12.4 GHz and a thickness of 9 mm, and the triple-layer structure had an absorption frequency band of 2.2–12.4 GHz and a thickness of 15 mm. The measured reflectivity values were consistent with the calculated results, thereby confirming the validity of our designs for the absorbing structure.
Effect of a non-thermal atmospheric pressure plasma jet on four different yeasts
Authors: Siadati Seyedehneda , Pet’ková Mária , Kenari Ali Jamaati , Kyzek Stanislav , Gálová Eliška , Zahoranová Anna
Published: September 2020

Non-thermal atmospheric pressure plasmas are known to be an effective method for the inactivation of microorganisms. However, yeasts have proved to be more resistant to provided treatments. We investigated the influence of an Argon plasma jet on the inactivation of four different yeasts; Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida parapsilosis and Magnusiomyces magnusii. Results from direct plasma treatment on the yeasts in distilled water, as the most effective technique we found, are presented here. The surviving yeasts after 5, 7, and 10 min plasma exposures were evaluated visually and quantitatively. Quantitative results showed strong reductions in the survival rates after the plasma treatment. The longest plasma exposure time yielded the least survival. Moreover, how long the inactivations lasted was evaluated by assessing the treated samples after 1 h and again after 2 h. The survival rates were further decreased within these storage times. In the 10 min treated-2 h stored samples, the rates dropped to 5% or even below, depending on the yeast species. High concentrations of reactive oxygen and nitrogen species in the plasma-air-water interacting system were detected by optical emission spectroscopy of the plasma jet and also by measuring concentrations of H2O2, NO2
− and NO3
− in plasma activated water (as the surrounding liquid for the yeasts). The conductivity and pH of the treated water was measured as well. The level of the conductivity increased along with the decrease in pH. Synergistic effects of these chemical reactive species in acidified water resulted in the yeast inactivation.
An atomic-layer NiO-BaTiO3 nanocomposite for use in electrochemical sensing of serotonin
Authors: Ran Gu , Xia Ying , Zhang Hengchang , Kuang Wei , Fu Chuan
Published: September 2020

The NiO films were deposited on the surface of BaTiO3 (BTO) by atomic layer deposition (ALD). The thickness of NiO film was controlled by the number of ALD cycles, which the optimum number of ALD cycles were 400 cycles. The morphology of NiO-BTO nanocomposite was observed by x-ray diffraction, scanning electron microscope, and transmission electron microscopy. The sensor based on NiO-BTO nanocomposite displays good electrocatalytic activity and high sensitivity for serotonin (at 0.36 V vs. Ag/AgCl). In the range of 0.05–5 μM, the concentrations of serotonin are linearly related to current intensity and the detection limit is 0.03 μM (S/N = 3). The NiO-BTO/GCE was successfully applied in serum samples. It shows that the NiO-BTO nanocomposite prepared by ALD can serve as electrochemical sensor devices and applications in the fields of biosensors.
Selective growth and upconversion photoluminescence of Y-based fluorides: from NaYF4: Yb/Er to YF3: Yb/Er crystals
Authors: Xie Juan , Hu Wenbo , Tian Dan , Wei Yang , Zheng Guangchao , Huang Ling , Liang Erjun
Published: September 2020

Y-based fluorides have been recognized as most efficient host materials for upconversion photoluminescence (UC-PL). Herein, we have produced a series of Yb/Er doped Y-based fluorides with specific crystal structures, shapes and sizes. The selective growth process is governed by our pre-designed surfactant 4, 4′-((2,5-bi’s (2-(diethylamino) ethoxy) −1,4-phenylene) bis (ethyne-2,1-diyl)) dibenzoic acid (DBA) and selective solvents. It is shown that highly pure hexagonal microprisms and cubic microspheres of NaYF4: Yb/Er could be selectively grown in water at low and high content of DBA, respectively, while only orthorhombic nanowires and microflowers of YF3: Yb/Er could be obtained in ethanol. Finally, all these materials obtained exhibit strong UC-PL signal while the UC emission intensity of the NaYF4: Yb/Er hexagonal microprisms is much higher than those of the cubic microspheres and orthorhombic YF3 nanowires and microflowers. This work provides a novel method for selective crystal growth of Y-based fluorides with specific shape, size, crystal phase and highly UC-PL efficiency by breaking the intrinsic limitation of crystal growth habit, which could be possibly extended to the controlled synthesis of other related materials.
Scattering in gapped graphene quantum dot with magnetic flux
Authors: Lemaalem Bouchaib , Belouad Abdelhadi , Mekkaoui Miloud , Jellal Ahmed
Published: September 2020

We study the propagation of electrons in a circular quantum dot of gapped graphene subject to the magnetic flux ϕ. We present analytical expressions for the eigenstates, scattering coefficients, scattering efficiency and radial component of the reflected current. We identify different scattering regimes as a function of the physical parameters such as the incident electronic energy, potential barrier, radius of quantum dot, gap and ϕ. We choose two values of the flux ϕ = 1/2, 3/2 and show that for low energy of the incident electron, the scattering resonances appear and the far-field scattered current presents distinct preferred scattering directions.
Acoustoelectric imaging of deep dipoles in a human head phantom for guiding treatment of epilepsy
Authors: Barragan Andres , Preston Chet , Alvarez Alex , Bera Tushar , Qin Yexian , Weinand Martin , Kasoff Willard , Witte Russell S
Published: September 2020

Objective. This study employs a human head model with real skull to demonstrate the feasibility of transcranial acoustoelectric brain imaging (tABI) as a new modality for electrical mapping of deep dipole sources during treatment of epilepsy with much better resolution and accuracy than conventional mapping methods. Approach. This technique exploits an interaction between a focused ultrasound (US) beam and tissue resistivity to localize current source densities as deep as 63 mm at high spatial resolution (1 to 4 mm) and resolve fast time-varying currents with sub-ms precision. Main results. Detection thresholds through a thick segment of the human skull at biologically safe US intensities was below 0.5 mA and within range of strong currents generated by the human brain. Significance. This work suggests that 4D tABI may emerge as a revolutionary modality for real-time high-resolution mapping of neuronal currents for the purpose of monitoring, staging, and guiding treatment of epilepsy and other brain disorders characterized by abnormal rhythms.
Comparison of signal decomposition techniques for analysis of human cortical signals
Authors: Duraivel Suseendrakumar , Rao Akshay T , Lu Charles W , Bentley J Nicole , Stacey William C , Chestek Cynthia A , Patil Parag G
Published: September 2020

Objective. Conventional neural signal analysis methods assume that features of interest are linear, time-invariant signals confined to well-delineated spectral bands. However, new evidence suggests that neural signals exhibit important non-stationary characteristics with ill-defined spectral distributions. These features pose a need for signal processing algorithms that can characterize temporal and spectral features of non-linear time series. This study compares the effectiveness of four algorithms in extracting neural information for use in decoding cortical signals: Fast Fourier Transform bandpass filtering (FFT), principal spectral component analysis (PSCA), wavelet analysis (WA), and empirical mode decomposition (EMD). Approach. Electrocorticographic signals were recorded from the motor and sensory cortex of two epileptic patients performing finger movements. Each signal processing algorithm was used to extract beta (10–30 Hz) and gamma (66–114 Hz) band power to detect thumb movement and decode finger flexions, respectively. Naïve-Bayes (NB), support vector machine (SVM), and linear discriminant analysis (LDA) classifiers using each signal were validated using leave-one-out cross-validation. Main results. Decoders using all four signal decompositions achieved above 90% average accuracy in finger movement detection using beta power. When decoding individual finger flexion using gamma, the PSCA NB classifiers achieved 78 ± 4% accuracy while FFT, WA, and EMD analysis achieved accuracies of 73 ± 8%, 68 ± 7%, and 62 ± 3% respectively, with similar results using SVM and LDA. Significance. These results illustrate the relative levels of useful information contributed by each decomposition method in the case of finger movement decoding, which can inform the development of effective neural decoding pipelines. Further analyses could compare performance using more specific non-sinusoidal features, such as transients and phase-amplitude coupling.
A combination of hydrogen bonding and chemical covalent crosslinking to fabricate a novel swim-bladder-derived dry heart valve material yields advantageous mechanical and biological properties
Authors: Lan Xiaorong , Zhao Qianting , Zhang Jiayi , Lei Yang , Wang Yunbing
Published: September 2020

The current biological valve products used in transcatheter aortic valve replacement (TAVR) are mainly made of glutaraldehyde (GLUT)-crosslinked porcine and bovine pericardia, which need to be transported and stored in GLUT solution. This leads to prolonged preparation time and the presence of GLUT residue. Therefore, there has been interest in developing TAVR valves using a pre-crimped valve (also known as a dry valve). Herein, a natural, inexpensive, and widely available swim bladder was selected as the source of a biological valve functioning as a dry valve and was obtained via acellular processes and crosslinking fixation. With the help of multiple hydrogen bonds between polyphenols (represented by procyanidin and curcumin) and tissue, as well as the chemical crosslinking of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) with tissue, we found that this novel combined crosslinking method was able to successfully crosslink with an acellular swim bladder. The stabilities, mechanical properties, resistance to pre-folding/pre-compressing, flattening capability in water, hemocompatibility, cytocompatibility, and anti-calcification capability were systematically measured via a series of experiments. We demonstrated that this dry valve resulting from a combination of EDC/polyphenols exhibited superior properties compared with those of a control pericardial-based valve.
Use of Ethanol-Based Hand Disinfectants: Source of Increased Ethyl Glucuronide Levels in Hair?
Authors: Scholz Clementine , Baumgartner Markus R , Madry Milena M
Published: September 2020

Aim

Due to the COVID-19 pandemic increasing the use of hand disinfectants, we investigated the effect of frequent use of ethanol-based hand disinfectants (EBHD) on the levels of the alcohol marker ethyl glucuronide (EtG) in hair.

Method

Hair samples were collected from 10 health professionals (8 nondrinkers, 2 rarely drinking individuals) and EtG was examined in hair.

Result

EtG (~2 pg/mg) was only detected in the hair sample of a nondrinker using EBHD 60–70 times per working day.

Conclusion

Our data provide no evidence that frequent EBHD use results in hair EtG levels above the recommended Society of Hair Testing cutoff for repeated alcohol consumption (5 pg/mg).
Irregular adaxial–abaxial polarity rearrangement contributes to the monosymmetric-to-asymmetric transformation of Canna indica stamen
Authors: Tian Xueyi , Li Xiaorong , Yu Qianxia , Zhao Haichan , Song Juanjuan , Liao Jingping
Published: September 2020

In flowering plants, lateral organs including stamens develop according to the precise regulation of adaxial–abaxial polarity. However, the polarity establishment process is poorly understood in asymmetric stamens. Canna indica (Zingiberales: Cannaceae) is a common ornamental plant with an asymmetric stamen comprising a one-theca anther and a petaloid appendage. In this study, we depicted the monosymmetric-to-asymmetric morphogenesis of C. indica stamen, and the morphogenesis of the monosymmetric stamen of a sister species was used as a contrast. We chose a HD-ZIP III gene family member and a YABBY family member as the adaxial and abaxial polarity marker genes, respectively, and tested their expression using mRNA in situ hybridization. The expression patterns of the two genes changed dynamically and asymmetrically during the stamen development process. Compared with their homologues in Arabidopsis thaliana, these two genes exhibited some specific expression patterns. We hypothesize that the distinctive adaxial–abaxial polarity participates in the irregular morphogenesis of C. indica stamen, which mediates the putative stamen-to-petaloid staminode conversion in this species.
History in Person: A Longitudinal Study of a Language Learner’s Experience at Home and Abroad
Authors: Lee Sheng-Hsun
Published: September 2020

This study explores the longitudinal pathway of social identification traveled by a US learner of Chinese, Tom. Focusing on the historical production of persons, I analyze interactional recordings, instructional artifacts, and participant interviews collected over three years of qualitative inquiry. The analysis articulates how Tom’s narrative of intercultural encounters was reframed, rekeyed, and recycled at home and abroad. Along the way, Tom was identified as (i) an avid learner of Chinese in a language classroom in the USA; (ii) an ignorant foreigner while studying in China; and (iii) a political outcast upon his return to the USA whose intercultural experience abroad, nevertheless, afforded his classmates an opportunity to appreciate a more ethno-relative perspective. The consonance and dissonance of identification are results of interplay between history in person and history in institutionalized struggles. This interplay must be considered to understand the (re)making of language-learning identities across historical time, social space, and communicative modes. The findings illustrate how history, social identification, and engagement in intercultural communication mutually inform each other in and beyond transnational mobility.
Brief iPad-Based Assessment of Cognitive Functioning with ImPACT® Quick Test: Prevalence of Low Scores Using Multivariate Base Rates
Authors: Wallace Jessica , Schatz Philip , Covassin Tracey , Iverson Grant L
Published: September 2020

Objective

The ImPACT® Quick Test is a brief iPad-based battery of neurocognitive tests that has been standardized on a sample of children, adolescents, and adults (ages 12–70). This study provides information on the prevalence of ImPACT® Quick Test scores falling below specific percentiles in the normative sample to aid in clinical interpretation and reduce the risk of over-interpreting, or misinterpreting, a single low score.

Method

Participants were 683 individuals ranging in age from 12 to 70, who were assessed individually. The ImPACT® Quick Test includes five subtests, contributing to three factor scores: motor speed, memory, and attention tracker. The prevalence of low factor scores, stratified by age and sex, were calculated using multivariate base rates.

Results

In the total sample, obtaining 1 or more scores below the 25th percentile was common (base rate, BR = 47.2%), but obtaining 2 or more scores in this range was uncommon (BR = 15.3%). Similarly, obtaining 1 or more scores below the 16th percentile was common (BR = 31.4%), but obtaining two or more scores in this range was uncommon (BR = 6.9%). There were small differences in BRs between sexes and the number of low scores was fairly similar across the age groups.

Conclusion

Results from this study parallel previous work illustrating that a substantial percentage of healthy individuals will obtain one or more low test scores when administered a brief battery of cognitive tests. Given that some healthy individuals will obtain a single score below expected cut-offs, clinicians should caution against overinterpreting a single low test score.
A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear
Authors: Cai Jinpu , Xu Yuyang , Zhang Wen , Ding Shiying , Sun Yuewei , Lyu Jingyi , Duan Meiyu , Liu Shuai , Huang Lan , Zhou Fengfeng
Published: September 2020

Motivation: DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated. Methods: This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels. Results: A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.
3-Dimensional Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for Coronavirus Disease 2019 Testing
Authors: Decker Summer J , Goldstein Todd A , Ford Jonathan M , Teng Michael N , Pugliese Robert S , Berry Gregory J , Pettengill Matthew , Silbert Suzane , Hazelton Todd R , Wilson Jason W , Shine Kristy , Wang Zi-Xuan , Hutchinson Morgan , Castagnaro Joseph , Bloom Ona E , Breining Dwayne A , Goldsmith Barbara M , Sinnott John T , O’Donnell Donna Gentile , Crawford James M , Lockwood Charles J , Kim Kami
Published: September 2020

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), can be detected in respiratory samples by real-time reverse transcriptase polymerase chain reaction (RT-PCR) or other molecular methods. Accessibility of diagnostic testing for COVID-19 has been limited by intermittent shortages of supplies required for testing, including flocked nasopharyngeal (FLNP) swabs.

Methods

We developed a 3-dimensional printed nasopharyngeal (3DP) swab as a replacement of the FLNP swab. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at 3 clinical sites (n = 291) using 3 SARS-CoV-2 emergency use authorization tests: a modified version of the Centers for Disease Control and Prevention (CDC) RT-PCR Diagnostic Panel and 2 commercial automated formats, Roche Cobas and NeuMoDx.

Results

The cycle threshold—C(t)—values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (P = .152 and P = .092), with the RNase P target performing significantly better in the 3DP swabs (P < .001). The C(t) values showed no significant differences between swabs for both viral gene targets in the Roche cobas assay (P = .05 and P = .05) as well as the NeuMoDx assay (P = .401 and P = .484). The overall clinical correlation of COVID-19 diagnosis between all methods was 95.88% (Kappa 0.901).

Conclusions

The 3DP swabs were equivalent to standard FLNP in 3 testing platforms for SARS-CoV-2. Given the need for widespread testing, 3DP swabs printed onsite are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits.
Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression
Authors: de Vries Sophie , de Vries Jan , Archibald John M , Slamovits Claudio H
Published: September 2020

Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.