bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of Dihydroanthracenes via Palladium-Catalyzed Tandem Mizoroki–Heck/Reductive Heck Reactions Using Cyclic Diaryliodoniums and Alkenes
Authors: Peng Xiaopeng , Yang Jianfeng , Qiu Xinhua , Duan Yuansheng , Bao Zeqing , Chen Jingfeng
Published: December 2020

An efficient Pd-catalyzed domino Mizoroki–Heck and reductive Heck reaction of terminal alkenes with six-membered cyclic diaryliodoniums is reported for the facile access to a diverse set of novel dihydroanthracenes. The scope of alkenes is general, leading to concise generation of 30 dihydroanthracenes which are not easily accessed by conventional methods. Furthermore, one of the newly synthesized dihydroanthracene displayed excellent antiproliferative activity against PANC-1 cancer cells (IC50 = 11.74 μM).
Peripherally Donor-Installed 7,8-Diaza[5]helicenes as a Platform for Helical Luminophores
Authors: Esser Birgit , Data Przemyslaw , Takeda Youhei , Ikari Yuta , Kaihara Takahito , Goto Shimpei , Bovenkerk Marcel , Grenz David C. , Ferreira Marli , Stachelek Patrycja , Yoshida Takumu , Ikai Tomoyuki , Tohnai Norimitsu , Minakata Satoshi
Published: December 2020

A new family of emissive donor–acceptor–donor (D-A-D) compounds has been developed by introducing two electron donors into the 7,8-diaza[5]helicene core as a novel helical electron acceptor. The X-ray crystallographic analyses revealed the uniquely twisted and helical structures of these compounds in the solid states. Notably, some D-A-D compounds developed herein display distinct mechanochromic luminescence (MCL) in the solid state, and a D-A-D helicene shows circularly polarized luminescence (CPL) with a relatively high luminescence dissymmetry factor g
lum of ca. 10–3. Time-resolved spectroscopic analysis revealed the aspects of thermally activated delayed fluorescence characters of the helicenes. Furthermore, the emissive helicenes were applied to organic light-emitting diodes as emitters.
Critical study of the effects and numerical simulations of boundary layer transition in lift-based wind turbines at moderate Reynolds numbers
Authors: Acarer Sercan
Published: December 2020

Early laminar-to-turbulent transition due to fouling typically degrades the lift and amplifies the drag of airfoils. Few studies of medium-size horizontal and vertical axis wind turbines (HAWTs and VAWTs, respectively) provide information on this turbulence. This reflects uncertainties in the reported power coefficients (Cp) and contradictory recommendations for computational fluid dynamics (CFD) models. This paper investigates the Cp degradation of wind turbines (Rechord = 0.7–1 × 106) and its CFD-modeling aspects. Published experimental data for the modern DU12W262 airfoil, for both the clean and dirty surface conditions, are taken as the baseline. CFD is employed to reproduce airfoil characteristics for both cases. Using the blade element momentum and computational fluid dynamics (CFD) models, the experimental and numerical HAWT and VAWT performances are assessed. Non-transition turbulence closure models [Spalart–Allmaras and Shear Stress Transport (SST)], which have been recommended against in previous works without due consideration for surface aspects, are shown to successfully mimic dirty surface conditions but to underpredict the dramatic experimental degradation of 82% in maximum CL/CD to 67% when uncalibrated. The resulting experimental Cp reductions for HAWTs and VAWTs are 34% and 65%, respectively, values that are also underpredicted by CFD as 17% and 34%, respectively, without calibration. The detailed findings may serve as pioneering data for transition effects and aspects of CFD for both HAWTs and VAWTs at moderate Reynolds numbers.
The MHD continuum with a radial electric field
Authors: Könies Axel , Slaby Christoph , Kleiber Ralf , Fehér Tamás , Borchardt Matthias , Mishchenko Alexey
Published: December 2020

The effects of a radial electric field, which is ubiquitous in stellarators, are considered when a system of reduced-MHD equations is derived from a gyro-kinetic Vlasov–Maxwell system. The resulting equations for the MHD continuum have been implemented into the continuum code CONTI. For a tokamak case, the MHD continuum is calculated and compared with a gyro-kinetic continuum calculated using the EUTERPE code, where good agreement of the obtained continua could be shown. Finally, MHD continua including the radial electric field are calculated for Wendelstein 7-X. Interestingly, for these examples, most of the gaps in the continuous spectrum of Alfvén waves below 200 kHz disappear.
Boris computational spintronics—High performance multi-mesh magnetic and spin transport modeling software
Authors: Lepadatu Serban
Published: December 2020

This work discusses the design and testing of a new computational spintronics research software. Boris is a comprehensive multi-physics open-source software, combining micromagnetics modeling capabilities with drift-diffusion spin transport modeling and a heat flow solver in multi-material structures. A multi-mesh paradigm is employed, allowing modeling of complex multi-layered structures with independent discretization and arbitrary relative positioning between different computational meshes. Implemented micromagnetics models include not only ferromagnetic materials modeling, but also two-sublattice models, allowing simulations of antiferromagnetic and ferrimagnetic materials, fully integrated into the multi-mesh and multi-material design approach. High computational performance is an important design consideration in Boris, and all computational routines can be executed on graphical processing units (GPUs), in addition to central processing units. In particular, a modified 3D convolution algorithm is used to compute the demagnetizing field on the GPU, termed pipelined convolution, and benchmark comparisons with existing GPU-accelerated software Mumax3 have shown performance improvements up to twice faster.
Lower-hybrid wave instability due to multiple fast heavy ion ring distributions in the SMART experiment
Authors: Soto A. Rualdo , Crabtree Chris , Ganguli Gurudas , Fletcher Alex C.
Published: December 2020

Development and stability of heavy ion ring beams created by high speed neutral atom injection in the Earth's ionosphere is analyzed in view of the upcoming space measurement of a rocket-released turbulence (SMART) mission. It is found that due to velocity dispersion of the injected neutral atoms, an ensemble of ion ring beams will be formed at a given location upon photoionization. Associated with the multiple-ion ring beams, various beam and lower-hybrid (LH) waves develop. Wave dispersion analysis indicates that the beam energy is extracted through double resonances with beam and LH modes (i.e., ω∼kvr∼ωlh, where ωlh is the LH frequency, k is the wavenumber, and vr is the ring mean speed). For the SMART experimental conditions, we find that, far from the release point, the velocity spacing between the ion ring beams Δv will be much less than the mean speed of the beams themselves, vr. Therefore, we show that the system will behave essentially as if represented by a single ring with an effective alpha (α) parameter (a ratio of ring to background plasma density), that is larger by a factor that is equal to N, the total number of rings. A major difference from the traditional single beam analysis is that for the more realistic multiple beam case, the effective instability is more intense because the wave growth rate now scales as ∼(Nα)2/5.
Graphene oxide sensors of high sensitivity fabricated using cold atmospheric-pressure hydrogen plasma for use in the detection of small organic molecules
Authors: Homola Tomáš , Lorencova Lenka , Parráková Lucia , Gemeiner Pavol , Tkac Jan
Published: December 2020

A novel electrochemical sensor was fabricated by means of solution-processed graphene oxide (GO) ink on fluorine-doped tin oxide (FTO), followed by rapid reduction of the GO surface to reduced graphene oxide (rGO) by cold diffuse atmospheric plasma generated in pure hydrogen gas. The FTO/rGO electrode was then employed in the detection of ascorbic acid, uric acid, dopamine, and acetaminophen molecules with low limits of detection; in these cases, 0.03, 0.06, 0.07, and 0.04 μM, respectively. While traditional methods for the reduction of GO are time-consuming, in the order of tens of minutes, and involve high-temperature (450 °C) sintering in argon, the novelty of this work lies in the rapid manufacture of the sensing material through cold plasma-assisted reduction of a GO surface. Since the temperature of the plasma procedure is below 70 °C, with the elapsed time lesser than 10 s, and the plasma unit is capable of processing an area of up to 160 cm2, FTO/rGO electrode preparation can be performed at high throughput. This fabrication method may be easily deployed in rapid and low-cost roll-to-roll manufacture, a factor essential for the future commercialization of cost-effective flexible and printed electronics based on a wide range of sensors.
Identifying alternative ferroelectric materials beyond Hf(Zr)O2
Authors: Guo Jing , Clima Sergiu , Pourtois Geoffrey , Van Houdt Jan
Published: December 2020

A database-driven approach combined with ab initio density functional theory (DFT) simulations is used to identify and simulate alternative ferroelectric materials beyond Hf(Zr)O2. The database-driven screening method identifies a class of wurtzite ferroelectric materials. DFT simulations of wurtzite magnesium chalcogenides, including MgS, MgSe, and MgTe, show their potential to achieve improved ferroelectric (FE) stability, simple atomistic unit cell structure, and large FE polarization. Strain engineering can effectively modulate the FE switching barrier height for facilitating FE switching. The effect of the piezoelectric property on the FE switching barrier heights is also examined.
Polarization transfer from a laser to x rays via Thomson scattering with relativistic electrons: A dipole radiation perspective
Authors: Chi Zhijun
Published: December 2020

A Thomson scattering light source can produce polarization-controllable x rays with quasi-monochromaticity and high brightness, making it an excellent probe for x-ray imaging and nuclear physics research. In this paper, a clear physical picture of the polarization transfer process from a laser to x rays is given based on a dipole radiation model. For arbitrary interaction geometries between a laser and relativistic electrons, the electric field relation between the scattered x rays and the laser is derived analytically. The result shows that the polarization characteristics of the laser can be completely transferred into x rays, regardless of the interaction geometry. Meanwhile, the polarization of scattered x rays is dependent on the collecting angle. As the collecting angle increases, both the degree of polarization (DOP) and the bandwidth of scattered x rays will be degraded. A collecting angle confining scattered x rays of 5% rms bandwidth can guarantee a DOP higher than 97% for both linear and circular polarizations. A method for any polarization control of scattered x rays is demonstrated by using wave plates for the laser. Both the rotation of linear polarization and the switch of polarization state from linear polarization to circular polarization and from left-handed polarization to right-handed polarization can be easily realized.
Highly selective ozone-treated
β
-Ga2O3 solar-blind deep-UV photodetectors
Authors: Kim Suhyun , Kim Jihyun
Published: December 2020

The ultra-wide energy bandgap (4.6–4.9 eV) of the β-Ga2O3 semiconductor offers intrinsic solar blindness, which is a great advantage as the absorber material of a deep ultraviolet (UV) photodetector. Although the band-to-band excitation transition in β-Ga2O3 is allowed solely by the UV-C wavelength, the defective sites including oxygen vacancies can induce sub-bandgap absorption, resulting in high background noise. The UV-ozone treatment was performed at elevated temperatures to investigate its effect on removing these oxygen vacancies; it creates reactive oxygen radicals that can reach the β-Ga2O3 lattice and passivate the defective sites. The chemical analysis through x-ray photoelectron and micro-Raman spectroscopies revealed an increase in Ga–O bonding after UV-ozone treatment. The optoelectrical measurements on the β-Ga2O3 UV-C photodetectors showed that the UV-ozone treatment significantly decreased the response to UV-A light. Thus, the photodetector performance (photo-to-dark current ratio, responsivity, detectivity, and rejection ratio) was greatly enhanced; especially, the rejection ratio was increased to 4.56 × 108 by eight orders of magnitude after UV-ozone treatment. The remarkably improved UV-C selectivity in the β-Ga2O3 solar-blind photodetector highlights its potential of realizing truly solar-blind photodetectors using a simple UV-ozone treatment technique.
Fine structures of acoustic emission spectra: How to separate dislocation movements and entanglements in 316L stainless steel
Authors: Chen Yan , Gou Boyuan , Fu Wei , Chen Can , Ding Xiangdong , Sun Jun , Salje Ekhard K. H.
Published: December 2020

Intermittent avalanches in a multitude of materials are characterized by acoustic emission, AE, where local events lead to strain relaxations and generate shock waves (so-called “jerks”), which are measured at the sample surface. The bane of this approach is that several avalanche mechanisms may contribute to the same AE spectrum so that a detailed analysis of each individual contribution becomes virtually impossible. It is, hence, essential to develop tools to separate signals from different dynamical processes, such as ferroic domain switching, collapse of porous inclusions, dislocation movements, entanglements, and so on. Particularly, difficult cases are dynamical microstructures in fcc alloys where the AE signal strength is weak. Nevertheless, using profile analysis of AE signals, we can distinguish between two mechanisms, namely, dislocation movements and dynamic entanglements in fcc 316L stainless steel. In this approach, we are able to measure the statistical AE durations of both subsets separately. The fingerprint for superposed avalanches with different durations is seen by the scaling between the energy E and the maximum amplitude A of each avalanche E ∼ Ax with x = 2. While the same exponent x applies for both mechanisms, the scaling relation shows two branches with different absolute energy values. The two mechanisms are then confirmed by separating the energy distributions P(E) ∼ E−ε for the two mechanisms with ε = 1.55 for dislocation movements and ε = 1.36 for entanglements.
Electronic degeneracy conduction in highly Si-doped Al0.6Ga0.4N layers based on the carrier compensation effect
Authors: Kataoka Keita , Narita Tetsuo , Nagata Kengo , Makino Hiroaki , Saito Yoshiki
Published: December 2020

Electronic degeneracy to express metallic conduction in Al-rich AlGaN for the electron injection layer enhances the efficiencies of deep ultraviolet light emitters. This study systematically demonstrates the Si doping range and conditions to realize degenerate n-type Al0.6Ga0.4N layers based on the electron compensation effect. The temperature-independent electron concentrations resulting from the degenerate band appear in high Si doping conditions to overcome the electron compensation due to carbon on nitrogen sites (CN). However, excessive Si doping of over 4.0 × 1019 cm−3 leads to the collapse of the electronic degeneracy and a switch to the temperature-dependent electron transport via the impurity bands, where the luminescence bands originating from III vacancy-Si complexes (VIII-nSi) are dominant. The key parameter is the effective donor concentration, Nd − Na, based on the reduction in electron concentrations via acceptor-like deep levels such as CN and VIII-nSi. The Hall-effect analyses for n-type Al0.6Ga0.4N layers with various Si concentrations yielded an Nd − Na value of (9.5 ± 2.9) × 1018 cm−3 to vanish the ionization energy of Si donors, which is approximately six times higher than that in GaN. The results suggest not only the optimal doping range to obtain an Al-rich AlGaN layer with metallic conduction but also the necessity of the growth condition to minimize electron compensation.
Unsteady flow of Carreau fluids around an impulsively moving cylinder
Authors: Yun Yeji , Jee Solkeun , Lee Junseong
Published: December 2020

Unsteady flow of Carreau fluids around an impulsively moving circular cylinder is numerically investigated in this study. Both shear-thinning and shear-thickening fluids are used with the range of the power-index number 0.4 ≤ n ≤ 2. Unsteady laminar flow with the influence of shear-dependent viscosity and impulsive motions of the cylinder are analyzed with various Carreau numbers 10 ≤ Cu ≤ 40 and Reynolds numbers 10 ≤ Re ≤ 100. Both starting and stopping flows are numerically simulated. Systematic validation is conducted for current numerical approaches using literature data before the investigation of the unsteady flow. The effects of major Carreau fluid flow parameters, namely, n, Cu, and Re, on the unsteady vortical flow are studied with a focus on the formation of vortices, zero-shear point on the cylinder, and transitory hydrodynamic loads. In general, increased shear-thickening (n > 1 with higher Cu and lower Re) leads to higher viscous effect, delaying the formation of additional vortices and promoting the drag force due to the dominant viscous drag. More interesting flow aspects are noticed with shear-thinning fluids. Increased shear-thinning (n < 1 with higher Cu and higher Re) results in complicated vortical flow including secondary, tertiary, quaternary vortices, and even more. Highly oscillated drag force is obtained in such vortical flow due to the oscillated pressure drag, which dominates the total drag in the current unsteady flow. It is expected that the results reported in this study could be used for a better understanding of unsteady non-Newtonian fluid flow and for the validation of numerical simulation of unsteady non-Newtonian fluid flow.
Air flow quality analysis of an open-circuit boundary layer wind tunnel and comparison with a closed-circuit wind tunnel
Authors: Jiménez-Portaz María , Chiapponi Luca , Clavero María , Losada Miguel A.
Published: December 2020

The wide use of wind tunnels, as a tool to measure the flow properties and the flow effects on different structures/ecosystems, makes it necessary to guarantee the correct functioning of the facility and to carry out a continuous monitoring. The aim of this work is (i) to check the homogeneity and quality of the air flow in an open-circuit boundary layer wind tunnel, (ii) to provide data and ideas that could help other researchers to improve similar tunnels, and (iii) to compare some of the results with the behavior of a classic closed-circuit wind tunnel. Experiments are carried out working with a constant reference velocity, using a hot cross wire anemometry system to obtain high resolution measurements, in the entrance and test sections for different longitudinal and cross planes. The results concern the characteristics of the mean and turbulent flow. In this manuscript, we report the analysis of the turbulence production, the Reynolds stresses, the vertical velocity skewness, the vorticity, and the spectral properties, and a quadrant decomposition is also performed. Finally, comparing the results with respect to a closed-circuit wind tunnel, it is shown that the turbulence intensity is generally higher and the mean flow is more homogeneous in the present open-circuit wind tunnel. Moreover, the Reynolds number is similar in both tunnels, which indicates that both tunnels are mechanically similar.
High-volume and -adiabat capsule (“HVAC”) ignition: Lowered fuel compression requirements using advanced Hohlraums
Authors: Amendt Peter , Ho Darwin , Nora Ryan , Ping Yuan , Smalyuk Vladimir
Published: December 2020

Lower-than-expected deuterium–tritium fuel areal densities have been experimentally inferred across a variety of high-convergence, nominally low-adiabat implosion campaigns at the National Ignition Facility (NIF) using cylinder-shaped Hohlraums [Hurricane et al., Phys. Plasmas 26, 052704 (2019)]. A leading candidate explanation is the presence of atomic mix between the fuel and ablator from hydrodynamic instability growth [Clark et al., Phys. Plasmas 26, 050601 (2019)], leading to reduced fuel compressibility and an effectively higher (in-flight) fuel adiabat α. Tolerating a high-α implosion can be obtained with significantly higher capsule absorbed energy Ecap according to the one-dimensional (1-D) ignition-threshold-factor analytic scaling [S. Atzeni and J. Meyer-ter-Vehn, Nucl. Fusion 41, 465 (2001)], ITF∼Ecap·α−1.8. Recent experiments with large Al shells in rugby-shaped Hohlraums have established high laser-capsule coupling efficiencies of ≽ 30% [Ping et al., Nat. Phys. 15, 138 (2019)], enabling a path to Ecap≽ 0.5 MJ at the NIF and increased performance margin M ≡ ITF − 1. The ability to operate at high adiabat with large capsules using nonstandard Hohlraums leads to the predicted onset of a volume-ignition mode, defined as when both the entire fuel is the “hot spot” and inertial confinement is principally provided by the ablator compared with the compressed fuel. Such an ignition mode, normally reserved for high-Z targets, e.g., double shells [Amendt et al., Phys. Plasmas 14, 056312 (2007)], is predicted to lead to lower fuel convergence and less exposure to mix due to the intended high adiabat—but at the expense of ∼3–4 × reduced (1-D) yield compared with conventional central hot-spot ignition designs.
GaN/AlGaN 2DEGs in the quantum regime: Magneto-transport and photoluminescence to 60 tesla
Authors: Crooker S. A. , Lee M. , McDonald R. D. , Doorn J. L. , Zimmermann I. , Lai Y. , Winter L. E. , Ren Y. , Cho Y.-J. , Ramshaw B. J. , Xing H. G. , Jena D.
Published: December 2020

Using high magnetic fields up to 60 T, we report magneto-transport and photoluminescence (PL) studies of a two-dimensional electron gas (2DEG) in a GaN/AlGaN heterojunction grown by molecular-beam epitaxy. Transport measurements demonstrate that the quantum limit can be exceeded (Landau level filling factor ν<1) and show evidence for the ν=2/3 fractional quantum Hall state. Simultaneous optical and transport measurements reveal synchronous quantum oscillations of both the PL intensity and the longitudinal resistivity in the integer quantum Hall regime. PL spectra directly reveal the dispersion of occupied Landau levels in the 2DEG and, therefore, the electron mass. These results demonstrate the utility of high (pulsed) magnetic fields for detailed measurements of quantum phenomena in high-density 2DEGs.
Energy and analytic gradients for the orbital-optimized coupled-cluster doubles method with the density-fitting approximation: An efficient implementation
Authors: Bozkaya Uğur , Ünal Aslı , Alagöz Yavuz
Published: December 2020

Efficient implementations of the orbital-optimized coupled-cluster doubles (or simply “optimized CCD,” OCCD, for short) method and its analytic energy gradients with the density-fitting (DF) approach, denoted by DF-OCCD, are presented. In addition to the DF approach, the Cholesky-decomposed variant (CD-OCCD) is also implemented for energy computations. The computational cost of the DF-OCCD method (available in a plugin version of the DFOCC module of PSI4) is compared with that of the conventional OCCD (from the Q-CHEM package). The OCCD computations were performed with the Q-CHEM package in which OCCD are denoted by OD. In the conventional OCCD method, one needs to perform four-index integral transformations at each of the CCD iterations, which limits its applications to large chemical systems. Our results demonstrate that DF-OCCD provides dramatically lower computational costs compared to OCCD, and there are almost eightfold reductions in the computational time for the C6H14 molecule with the cc-pVTZ basis set. For open-shell geometries, interaction energies, and hydrogen transfer reactions, DF-OCCD provides significant improvements upon DF-CCD. Furthermore, the performance of the DF-OCCD method is substantially better for harmonic vibrational frequencies in the case of symmetry-breaking problems. Moreover, several factors make DF-OCCD more attractive compared to CCSD: (1) for DF-OCCD, there is no need for orbital relaxation contributions in analytic gradient computations; (2) active spaces can readily be incorporated into DF-OCCD; (3) DF-OCCD provides accurate vibrational frequencies when symmetry-breaking problems are observed; (4) in its response function, DF-OCCD avoids artificial poles; hence, excited-state molecular properties can be computed via linear response theory; and (5) symmetric and asymmetric triples corrections based on DF-OCCD [DF-OCCD(T)] have a significantly better performance in near degeneracy regions.
On conservation laws in quantum mechanics
Authors: Aharonov Yakir , Popescu Sandu , Rohrlich Daniel
Published: December 2020

Significance

Conservation laws are one of the most important aspects of nature. As such, they have been intensively studied and extensively applied, and are considered to be perfectly well established. We, however, raise fundamental question about the very meaning of conservation laws in quantum mechanics. We argue that, although the standard way in which conservation laws are defined in quantum mechanics is perfectly valid as far as it goes, it misses essential features of nature and has to be revisited and extended.
Massively parallel discovery of human-specific substitutions that alter enhancer activity
Authors: Uebbing Severin , Gockley Jake , Reilly Steven K. , Kocher Acadia A. , Geller Evan , Gandotra Neeru , Scharfe Curt , Cotney Justin , Noonan James P.
Published: December 2020

Significance

Uniquely human biology is the result of genetic differences between humans and other primates, but identifying the critical changes still poses a major challenge. We screened >32,000 human-specific substitutions in two classes of putative transcriptional enhancers implicated in human evolution for their effects on enhancer activity in human neural stem cells, a cell type fundamental for cortical development and expansion. We identify hundreds of substitutions that modify enhancer activity either alone or in combination with other variants. We find different patterns of substitution effects in different enhancer types. Our data support substitutions often interacting by modifying the same transcription factor binding sites. The functional substitutions we identify provide a rich set of candidate loci for studies of human-specific regulatory evolution.
The intestinal parasite
Cryptosporidium
is controlled by an enterocyte intrinsic inflammasome that depends on NLRP6
Authors: Sateriale Adam , Gullicksrud Jodi A. , Engiles Julie B. , McLeod Briana I. , Kugler Emily M. , Henao-Mejia Jorge , Zhou Ting , Ring Aaron M. , Brodsky Igor E. , Hunter Christopher A. , Striepen Boris
Published: December 2020

Significance

The intestinal immune system is able to control pathogens while tolerating and interpreting microbial cues from an abundant microbiome. The mechanisms of innate recognition are crucial to differentiating between pathogen and commensal in this tissue and to mounting an appropriate inflammatory response. Persistent inflammation can alter the cellular architecture and physiology of the gut and have lasting impact on the nutritional state of children who face frequent infection with certain enteric pathogens. We demonstrate that the widespread parasite
Cryptosporidium
acts as a potent trigger for an enterocyte-intrinsic inflammasome that depends on the NOD-like receptor pyrin domain-6 and results in the local release of the proinflammatory cytokine IL-18.
SCAMP5 plays a critical role in axonal trafficking and synaptic localization of NHE6 to adjust quantal size at glutamatergic synapses
Authors: Lee Unghwi , Choi Chunghon , Ryu Seung Hyun , Park Daehun , Lee Sang-Eun , Kim Kitae , Kim Yujin , Chang Sunghoe
Published: December 2020

Significance

As a vesicular Na
+
(K
+
)/H
+
exchanger, NHE6 promotes glutamate filling into synaptic vesicles (SVs). Thus, proper localization of NHE6 is critical for determining synaptic strength at glutamatergic synapses, but the underlying mechanism remains unknown. We found that an SV-enriched protein, SCAMP5, is a key determinant for axonal trafficking and synaptic localization of NHE6. By perturbing their interaction, NHE6 fails to be localized at synaptic sites, resulting in hyperacidification of the SV lumen and a significant reduction in the quantal size of glutamate released. Since both are autism candidate genes, our results suggest that impaired interaction between two proteins could relate to the synaptic dysfunction observed in autism.
UFMylation inhibits the proinflammatory capacity of interferon-γ–activated macrophages
Authors: Balce Dale R. , Wang Ya-Ting , McAllaster Michael R. , Dunlap Bria F. , Orvedahl Anthony , Hykes Barry L. , Droit Lindsay , Handley Scott A. , Wilen Craig B. , Doench John G. , Orchard Robert C. , Stallings Christina L. , Virgin Herbert W.
Published: December 2020

Significance

Interferon-γ (IFN-γ)–dependent macrophage activation is an important component of the innate immune response. Although critical for cellular defenses against intracellular pathogens and activation of the adaptive immune system, overactive responses to IFN-γ could be harmful to the host. We conducted a genome-wide CRISPR knockout screen to identify pathways that, if perturbed, could lead to increased responses to IFN-γ and identify the UFMylation system as a negative regulator of IFN-γ activation. Increased responses to IFN-γ in UFMylation-deficient cells was dependent on the endoplasmic reticulum stress signal transducer Ern1 and myeloid-specific deletion of a UFMylation gene led to altered responses to infection in vivo. This work highlights the importance of maintaining endoplasmic reticulum homeostasis in macrophages during exposure to proinflammatory stimuli.
T
FH
cells depend on Tcf1-intrinsic HDAC activity to suppress CTLA4 and guard B-cell help function
Authors: Li Fengyin , Zhao Xin , Zhang Yali , Shao Peng , Ma Xiaoke , Paradee William J. , Liu Chengyu , Wang Jianmin , Xue Hai-Hui
Published: December 2020

Significance

A successful vaccine depends on productive T follicular helper (T
FH
) and B-cell responses to elicit protective immunity. Vaccines are delivered as live-attenuated viruses, inactivated organisms, or protein subcomponents via different routes. In the context of protein immunization, we demonstrate that Tcf1 and Lef1 transcription factors play critical roles in suppressing excessive induction of CTLA4 and LAG3 coinhibitory receptors in T
FH
cells and, hence, preventing undue inhibition of B cells. This function is in contrast to the requirement for Tcf1 and Lef1 in induction of Bcl6 in T
FH
cells elicited by viral or bacterial infections. These findings highlight that the same protein factors could be utilized to regulate distinct aspects of T
FH
cell differentiation depending on vaccination routes and regimens.
Statistical finite elements for misspecified models
Authors: Duffin Connor , Cripps Edward , Stemler Thomas , Girolami Mark
Published: December 2020

Significance

Science and engineering have benefited greatly from the ability of finite element methods (FEMs) to simulate nonlinear, time-dependent complex systems. The recent advent of extensive data collection from such complex systems now raises the question of how to systematically incorporate these data into finite element models, consistently updating the solution in the face of mathematical model misspecification with physical reality. This article describes general and widely applicable methodology for the coherent synthesis of data with FEM models, providing a data-driven probability distribution that captures all sources of uncertainty in the pairing of FEM with measurements.
Gigantic vortical differential scattering as a monochromatic probe for multiscale chiral structures
Authors: Ni Jincheng , Liu Shunli , Wu Dong , Lao Zhaoxin , Wang Zhongyu , Huang Kun , Ji Shengyun , Li Jiawen , Huang Zhixiang , Xiong Qihua , Hu Yanlei , Chu Jiaru , Qiu Cheng-Wei
Published: December 2020

Significance

Optical chirality by light–matter interaction is a powerful strategy for discriminating the chirality of materials in modern physics. Here we present a vortex-dependent approach to yield a direct chiroptical response with monochromatic light. The chiroptical signal of ∼120% is obtained on intrinsically chiral microstructures by optical vortices in the visible range. The chiroptical properties of microstructures can be flexibly controlled by tuning their geometric features. We further demonstrate the strong chiral light–matter interaction by optical vortices for sensitively detecting optical chirality of molecules.
The in-situ XAS study on the formation of Pd nanoparticles via thermal decomposition of palladium (II) acetate in hydroxyl functionalized ionic liquids
Authors: Yao Siyu , Sun Haolin , Ma Ding
Published: December 2020

The formation of palladium nanoparticles (NPs) via thermal decomposition of palladium (II) acetate in hydroxyl functionalized ionic liquid (IL) [C2OHmim]+[NTf2]− was studied using in-situ energy dispersive x-ray absorption fine structure spectroscopy (DXAFS) and complementary methods such as transmission electron microscopy (TEM) and inductively coupled plasma mass spectrometry. Detailed XAFS spectra analysis unraveled that the palladium acetate trimer precursor underwent dissociation after being dispersed in ILs, which accelerated the thermal decomposition compared with other organic solvents. Based on the reaction kinetics, extened x-ray absorption fine structure spectroscopy fitting and TEM characterization results, the thermal decomposition process can be divided three successive stages namely the explosive nucleation, autocatalytic surface growth and NP attachment growth.
Fabrication of CsPbBr3 films with high quality using a simple method
Authors: Yang Xingming , Li Mengmeng , Jiang Junjie , Ma Ligang , Tang Wenchao , Xu Cuiping , Cai H L , Zhang F M , Wu X S
Published: December 2020

Inorganic perovskite CsPbBr3 is a material used for fabricating highly efficient and stable perovskite solar cells. In this work, a two-step infiltration-spinning method is proposed to obtain CsPbBr3 films with pure phase. Phase transformations between CsPb2Br5, CsPbBr3 and Cs4PbBr6 are investigated by controlling the contact time between the CsBr solution and the PbBr2 substrate. CsPbBr3 films with large grain sizes are obtained after high temperature post-treatment. The CsPbBr3-based solar cells show a high efficiency (approximately 7%) with a short-circuit current density of 6.68 mA cm−2, an open-circuit voltage of 1.47 V and a fill factor of 70.9% under standard solar illumination.
Effect of helium concentration on irradiation damage of Fe-ion irradiated SIMP steel at 300 °C and 450 °C*
Authors: Yang Zhen , Yang Junyuan , Liao Qing , Xu Shuai , Li Bingsheng
Published: December 2020

SIMP steel is newly developed fully martensitic steel for lead-cooled fast reactors and accelerator-driven systems. It is important to evaluate its radiation resistance via high flux neutron irradiation, where dense He atoms can be formed via (n, α) transmutation reaction. Co-irradiation with Fe and He ions, instead of neutron, was performed. Specimens were irradiated with 6.4-MeV Fe ions to the damage dose of 5 dpa at a depth of 600 nm. Three different helium injection ratios of 60-appm He/dpa (dpa: displacements per atom), 200-appm He/dpa and 600-appm He/dpa at a depth of 600 nm, were performed. Two different irradiation temperatures of 300 °C and 450 °C were carried out. The effect of helium concentration on the microstructure of Fe-irradiated SIMP steel was investigated. Microstructural damage was observed using transmission electron microscopy. The formed dislocation loops and bubbles depended on the helium injection ratio and irradiation temperature. Lots of dislocation loops and helium bubbles were homogeneously distributed at 300 °C, but not at 450 °C. The causes of observed effects are discussed.
Kant on Aesthetic Attention
Authors: Williams Jessica J
Published: December 2020

In this paper, I examine the role of attention in Kant’s aesthetic theory in the Critique of the Power of Judgment. While broadly Kantian aestheticians have defended the claim that there is a distinct way that we attend to objects in aesthetic experience, Kant himself is not usually acknowledged as offering an account of aesthetic attention. On the basis of Kant’s more general account of attention in other texts and his remarks on attention in the Critique of the Power of Judgment, I reconstruct Kant’s account of aesthetic attention. On his account, aesthetic attention is simultaneously directed at the form of an object and at the judging subject’s own mental states as she attends to the object. In the experience of beauty, we specifically attend to the harmonious relation between the faculties of imagination and understanding.
Machine learning application for patient stratification and phenotype/genotype investigation in a rare disease
Authors: Spiga Ottavia , Cicaloni Vittoria , Dimitri Giovanna Maria , Pettini Francesco , Braconi Daniela , Bernini Andrea , Santucci Annalisa
Published: December 2020

Alkaptonuria (AKU, OMIM: 203500) is an autosomal recessive disorder caused by mutations in the Homogentisate 1,2-dioxygenase (HGD) gene. A lack of standardized data, information and methodologies to assess disease severity and progression represents a common complication in ultra-rare disorders like AKU. This is the reason why we developed a comprehensive tool, called ApreciseKUre, able to collect AKU patients deriving data, to analyse the complex network among genotypic and phenotypic information and to get new insight in such multi-systemic disease. By taking advantage of the dataset, containing the highest number of AKU patient ever considered, it is possible to apply more sophisticated computational methods (such as machine learning) to achieve a first AKU patient stratification based on phenotypic and genotypic data in a typical precision medicine perspective. Thanks to our sufficiently populated and organized dataset, it is possible, for the first time, to extensively explore the phenotype–genotype relationships unknown so far. This proof of principle study for rare diseases confirms the importance of a dedicated database, allowing data management and analysis and can be used to tailor treatments for every patient in a more effective way.
SoluProt: prediction of soluble protein expression inEscherichia coli
Authors: Hon Jiri , Marusiak Martin , Martinek Tomas , Kunka Antonin , Zendulka Jaroslav , Bednar David , Damborsky Jiri
Published: December 2020

Motivation

Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase solubility are plagued by low success rates and often reduce biological activity. Computational prediction of protein expressibility and solubility in Escherichia coli using only sequence information could reduce the cost of experimental studies by enabling prioritization of highly soluble proteins.

Results

A new tool for sequence-based prediction of soluble protein expression in E.coli, SoluProt, was created using the gradient boosting machine technique with the TargetTrack database as a training set. When evaluated against a balanced independent test set derived from the NESG database, SoluProt’s accuracy of 58.5% and AUC of 0.62 exceeded those of a suite of alternative solubility prediction tools. There is also evidence that it could significantly increase the success rate of experimental protein studies. SoluProt is freely available as a standalone program and a user-friendly webserver at https://loschmidt.chemi.muni.cz/soluprot/.

Availability and implementation

https://loschmidt.chemi.muni.cz/soluprot/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Damage to Broca’s area does not contribute to long-term speech production outcome after stroke
Authors: Gajardo-Vidal Andrea , Lorca-Puls Diego L , team PLORAS , Warner Holly , Pshdary Bawan , Crinion Jennifer T , Leff Alexander P , Hope Thomas M H , Geva Sharon , Seghier Mohamed L , Green David W , Bowman Howard , Price Cathy J
Published: December 2020

Broca’s area in the posterior half of the left inferior frontal gyrus has long been thought to be critical for speech production. The current view is that long-term speech production outcome in patients with Broca’s area damage is best explained by the combination of damage to Broca’s area and neighbouring regions including the underlying white matter, which was also damaged in Paul Broca’s two historic cases. Here, we dissociate the effect of damage to Broca’s area from the effect of damage to surrounding areas by studying long-term speech production outcome in 134 stroke survivors with relatively circumscribed left frontal lobe lesions that spared posterior speech production areas in lateral inferior parietal and superior temporal association cortices. Collectively, these patients had varying degrees of damage to one or more of nine atlas-based grey or white matter regions: Brodmann areas 44 and 45 (together known as Broca’s area), ventral premotor cortex, primary motor cortex, insula, putamen, the anterior segment of the arcuate fasciculus, uncinate fasciculus and frontal aslant tract. Spoken picture description scores from the Comprehensive Aphasia Test were used as the outcome measure. Multiple regression analyses allowed us to tease apart the contribution of other variables influencing speech production abilities such as total lesion volume and time post-stroke. We found that, in our sample of patients with left frontal damage, long-term speech production impairments (lasting beyond 3 months post-stroke) were solely predicted by the degree of damage to white matter, directly above the insula, in the vicinity of the anterior part of the arcuate fasciculus, with no contribution from the degree of damage to Broca’s area (as confirmed with Bayesian statistics). The effect of white matter damage cannot be explained by a disconnection of Broca’s area, because speech production scores were worse after damage to the anterior arcuate fasciculus with relative sparing of Broca’s area than after damage to Broca’s area with relative sparing of the anterior arcuate fasciculus. Our findings provide evidence for three novel conclusions: (i) Broca’s area damage does not contribute to long-term speech production outcome after left frontal lobe strokes; (ii) persistent speech production impairments after damage to the anterior arcuate fasciculus cannot be explained by a disconnection of Broca’s area; and (iii) the prior association between persistent speech production impairments and Broca’s area damage can be explained by co-occurring white matter damage, above the insula, in the vicinity of the anterior part of the arcuate fasciculus.
Assessment of the greenness of new stability indicating micellar UPLC and HPTLC methods for determination of tenofovir alafenamide in dosage forms
Authors: Said Noha S , Nasr Zeinab Adel , Abdel-Razeq Sawsan A
Published: December 2020

In this study, a green stability indicating chromatographic methods were developed and validated for the quantitative determination of tenofovir alafenamide in the presence of its degradation products in bulk powder as well as in dosage forms. The first method was micellar UPLC in which separation was achieved on kinetex ® 1.7 μm HILIC 100A, LC column using an ecofriendly micellar mobile phase consisting (0.05 M sodium dodecyl sulphate and 0.05 M sodium dihydrogen phosphate, (pH 5.5) and 10% 1-propanol (70:30) at a flow rate of 1 mL min−1 with a UV detection at 210 nm. The second method depended on HPTLC method performed on HPTLC plates pre-coated with silica gel 60 F254 using a mobile phase consisting of n-butanol—acetic acid (7:3, v/v) and detection at 260 nm. Tenofovir alafenamide was subjected to stress conditions including alkaline and acidic degradation. Beer’ law was obeyed over the concentration range of 1–18 μg mL−1 and 0.1–4 μg/spot for micellar UPLC and HPTLC methods, respectively. Both methods are successfully applied to the analysis of the drug in its tablets and validated according to ICH guidelines. In addition, their greenness was assessed using three different tools indicating their least hazardous effect on the environment.
Proton-Pump Inhibitor Use and the Risk of Community-Associated Clostridium difficile Infection
Authors: Inghammar Malin , Svanström Henrik , Voldstedlund Marianne , Melbye Mads , Hviid Anders , Mølbak Kåre , Pasternak Björn
Published: December 2020

Background

Proton-pump inhibitors (PPIs) have been reported to increase the risk of community-associated Clostridium difficile infection (CDI), but the association remains disputed.

Methods

A nationwide cohort study among adults in Denmark, 2010–2013, linking register data on C. difficile testing, filled prescriptions, and patient characteristics. All incident episodes of community-associated CDI (ie, positive culture, molecular assay, or toxin test in individuals without previous hospitalization in the prior 12 weeks and without a positive test for C. difficile in the prior 8 weeks) were identified in the Danish National Microbiological Database. Self-controlled case-series analyses were used to estimate incidence rate ratios (IRRs) for community-associated CDI, comparing periods with and without exposure to PPIs. By design, models took fixed confounders such as chronic disease, genetics, and socioeconomic status into account; further, time-varying confounders, including hospital stay and antibiotic and corticosteroid use were adjusted for.

Results

3583 episodes of community-associated CDI were identified, of which 964 occurred during current use of PPIs, 324 occurred 0–6 months after treatment cessation, 123 occurred 6–12 months after treatment cessation, and 2172 occurred during time periods without use of PPIs. The adjusted IRR was 2.03 (95% confidence interval, 1.74–2.36), comparing use of PPI with nonuse. The increased risk remained elevated in later time periods: 1.54 (1.31–1.80) for 0–6 months, 1.24 (1.00–1.53) for 6–12 months after current use.

Conclusions

Use of PPIs was associated with moderately increased risk of community-associated CDI. The risk remained elevated up to 1 year after PPI treatment had ended.
Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer
Authors: Metze Dennis , Popp Denny , Schwab Laura , Keller Nina-Sophie , da Rocha Ulisses Nunes , Richnow Hans-Hermann , Vogt Carsten
Published: December 2020

High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12–80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.