bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling deformable capsules in viscous flow using immersed boundary method
Authors: Tran S. B. Q. , Le Q. T. , Leong F. Y. , Le D. V.
Published: September 2020

This paper presents an immersed boundary method (IBM) for deformable capsules in incompressible viscous flow. Unlike the conventional IBM, the present method utilizes an unstructured mesh coupled with the moving least squares method, which improves the performance for applications involving a complex geometry. We validate our method through independent studies on oscillation and deformation of spherical capsules in viscous flow. Our simulations on a deformable capsule flowing in an elbow channel show that the capsule capillary number affects its shape and deformation area significantly. The maximum deformation area is found to be linearly proportional to the capillary number. In addition, our simulation on soft capsule sorting using a pinched flow fractionation microfluidic device shows that smaller capsules tend to migrate toward the pinched wall region before streaming out in the expansion region. The result is that smaller capsules drift closer to the center plane of the device and can be efficiently separated from the larger ones using branching. For capsule sorting applications using T-junction, we found that the fate of a capsule depends on the relative position of its center of mass and the dividing streamline. Larger capsules are diverted from the main stream toward the side outlet, leading to effective size fractionation.
Bi-component symbiotic crystal
Authors: Huang Fei , Hu Chengpeng , Tan Peng , Meng Xiangda , Wang Yu , Xian Zhongzhao , Huang Xiaolin , Zhou Zhongxiang , Tian Hao
Published: September 2020

Compositional gradient ferroelectric materials can significantly influence both the microstructure and macro-electrical properties by introducing strain gradients. In this work, we design and fabricate bi-component symbiotic KTa1–xNbxO3 single crystals via growing at the liquid level using the top-seeded solution growth method. The bi-compositions lead to an integration of two sets of phase transition temperatures, coercive fields, and lattice parameters, etc. Interestingly, the polarization microscopy and piezoelectric force microscopy (PFM) results show that domain structures are coherent across the boundary. In addition, there are large flexoelectric fields (Eflexo) at the boundary, which can impact the polarization orientation and electric properties. Thus, the special crystal system provides some potential insights, such as the fabrication of both ferroelectric and metal materials and also the design and manufacture of piezoelectric and optical functional materials.
An extended trajectory-mechanics approach for calculating two-phase flow paths
Authors: Vasco D. W.
Published: September 2020

A technique originating in quantum dynamics is used to derive a trajectory-based, semi-analytical solution for two-phase flow. The partial differential equation governing the evolution of the aqueous phase is equivalent to a family of ordinary differential equations defined along a path through the porous medium. The trajectories may be found by solving the differential equations directly or by post-processing the output of a numerical solution to the full set of governing equations. The trajectories, which differ from conventional streamlines, are found to bend downward in response to gravitational forces. The curvature is more pronounced as the dip of the porous layer containing the flow increases. Subtle changes in the relative permeability curve can lead to significant variations in the trajectories. The ordinary differential equation for the trajectory provides an expression for the travel time along the path. The expression produces a semi-analytical approximation to the model parameter sensitivities, the partial derivatives of the travel times with respect to changes in the permeability model. The semi-analytical trajectory-based sensitivities generally agree with those computed using a numerical reservoir simulator and a perturbation approach. The sensitivities are useful in tomographic imaging algorithms designed to estimate the spatial variation in permeability within a porous medium using multiphase observations.
Ultrahigh emissivity of grating-patterned PDMS film from 8 to 13
μ
m wavelength regime
Authors: Song Jaeman , Seo Junyong , Han Jihye , Lee Jungchul , Lee Bong Jae
Published: September 2020

Polydimethylsiloxane (PDMS) is a prominent material for radiative cooling due to its promising optical properties in the mid-infrared spectral region as well as its fabrication easiness. Even though several works have reported that the mid-infrared emissivity of a PDMS film can be increased by surface modification, there is still room for further enhancement through global optimization. Here, we designed and fabricated the thin PDMS film patterned with two-dimensional gratings to obtain the highest emissivity in the wavelength range from 8 to 13 μm. A surrogate-model-based optimization was performed, and the optimum structure exhibited the averaged emissivity value of 0.99 in the wavelength of 8–13 μm, which is the highest value reported to date among polymer-based radiative coolers. For real-world applications, we also developed the fabrication method that is repeatable and applicable for various surfaces using a flexible master mold.
Two-dimensional numerical study of gap resonance coupling with motions of floating body moored close to a bottom-mounted wall
Authors: Lu Lin , Tan Lei , Zhou Zhongbing , Zhao Ming , Ikoma Tomoki
Published: September 2020

The piston mode fluid resonance in the narrow gap between a moored floating body and a bottom-mounted vertical wall is numerically investigated based on a two-dimensional potential flow model and viscous numerical simulations. This study focuses on understanding the effect of mooring stiffness on the coupling dynamics of the gap resonance and the sway or heave motion of the floating body in regular waves. Numerical studies show that the resonant wave amplitude in the gap is reduced by the sway and heave motions. The reduction is highly dependent on the mooring stiffness. Two resonant frequencies are confirmed, and both increase with the mooring stiffness. Different modes of motions are identified in terms of the phase difference between the oscillatory motions of the gap flow and the floating body. Higher harmonic components of responses are found for the specific mooring stiffness. The performance of potential flow models in predicting resonant responses is revisited based on the understanding that the overall damping effect consists of two parts: (1) radiation damping and (2) viscous dissipation. It is confirmed that a potential model is also able to produce reasonable predictions as radiation damping plays a dominant role, for example, at the second resonant frequencies of coupling the gap resonance with the sway motion. Otherwise, as viscous dissipation dominates radiation damping, noticeable over-predictions by a potential model occur as recognized before, for example, the present results at the second peak response of gap resonance with the heave motion. The relative viscous dissipation is quantified with the reflection coefficient of viscous numerical results, while the radiation damping is quantified based on a specially designed radiation potential model with inputs of viscous numerical solutions.
Atmospheric He/O2 plasma jet fine etching with a scanning probe microscope
Authors: Nakazawa Kenta , Yamamoto Sho , Nakagawa Ei , Ogino Akihisa , Shimomura Masaru , Iwata Futoshi
Published: September 2020

In this study, we investigate a maskless fine etching technology using a He/O2 atmospheric pressure plasma jet (APPJ) assisted by a scanning probe microscope (SPM). The APPJ is localized in the submicrometer range by a nanopipette, which is also used as the probe of the SPM. We improve the rate of submicrometer-scale etching by adding O2 gas to the He source gas. The depth and full width at half maximum of a typical etched dot on a polymethylmethacrylate film were 475 nm and 235 nm, respectively. The etching rate was found to be six times faster with the added gas than without it. We also demonstrate line patterning; the width of the line was found to be 281 nm.
Tunable millimeter wave photonic crystal for limiting high power pulses using weakly ionized steady state plasma
Authors: Kim Hyunjun , Hopwood Jeffrey
Published: September 2020

We present the transmission characteristics of pulsed 44 GHz millimeter waves (MMWs) through a plasma formed within a photonic crystal. Initially, a low density plasma (ne=0.3×1018m−3) is sustained in a crystal vacancy defect using a continuous wave (cw) MMW power of 0.06 W. This weak plasma does not much attenuate wave transmission, but it does provide seed electrons such that dense plasma forms in response to incoming MMW pulses. The dense plasma formation limits the transmission of high power pulses through the photonic crystal. A high power pulse increases the plasma electron density and shifts the resonant frequency of the crystal vacancy in accordance with the plasma permittivity. A rapid decrease in the transmitted power is observed by following the time-evolution of the plasma. A numerical electromagnetic model estimates electron density and traces the time-evolution of the plasma during MMW pulsing. The plasma-filled photonic crystal is evaluated as a power limiter. As plasma properties are readily tunable, we observe an improved operational bandwidth for incoming pulse frequencies by controlling the cw power and gas pressure of the initial weak plasma.
Analysis of the effect of intermittency in a high-pressure turbine blade
Authors: Dupuy D. , Gicquel L. , Odier N. , Duchaine F. , Arts T.
Published: September 2020

High-pressure turbine blades are subject to large thermomechanical loads that may threaten their mechanical integrity. The prediction of the heat transfer on the blade surface, crucial to ensure its durability, thus requires an accurate description of the flow physics around the blade to be reliable. In an effort to better qualify the use of computational fluid dynamics in this design context as well as the need for an improved understanding of the flow physics, this paper investigates a transonic highly loaded linear turbine blade cascade that has been found difficult to predict in the literature using large-eddy simulations. Indeed, the configuration results in shocks and acoustic waves on the suction side of the blade, features that are commonly encountered in high-pressure turbines. Turbulent spots are observed on the suction-side boundary layer with an inlet turbulence intensity of 6%. The turbulent spots are shown to have a complex and highly unsteady effect on the shock/boundary-layer interaction, disrupting flow detachment and creating laminar spots downstream of the shock. To address these transient flow phenomena, conditional averages based on the intermittency level are introduced to show that accurate heat transfer predictions require an accurate prediction of the rate of turbulent-spot production. The analysis then focuses on the effect of intermittency on the turbulent kinetic energy exchanges in the near-wall region as the turbulent kinetic energy balance must be addressed in Reynolds-averaged Navier–Stokes models.
Photo-assisted deposited titanium dioxide for all-inorganic CsPbI2Br perovskite solar cells with high efficiency exceeding 13.6%
Authors: Lv Peiwen , Chen Shan-Ci , Xu Chaosheng , Peng Bei
Published: September 2020

All-inorganic perovskite solar cells advancing in phase and thermal stability are regarded as promising candidates for high-performance optoelectronic application. Herein, a photo-assisted deposited titanium dioxide was designed and utilized as the electron-transporting layer. Photo-assisted deposited titanium dioxide demonstrated a low interfacial recombination rate and high carrier extraction efficiency. Consequently, CsPbI2Br-based all inorganic perovskite solar cells exhibit power conversion efficiencies of up to a value of 13.69%. This photo-assisted deposition method is a promising approach for scalable, convenient, and inexpensive fabrication in the future.
Broadband operation of active terahertz quarter-wave plate achieved with vanadium-dioxide-based metasurface switchable by current injection
Authors: Nakanishi Toshihiro , Nakata Yosuke , Urade Yoshiro , Okimura Kunio
Published: September 2020

We demonstrate the broadband operation of a switchable terahertz quarter-wave plate achieved with an active metasurface employing vanadium dioxide. For this purpose, we utilize anisotropically deformed checkerboard structures, which present broadband characteristics compatible with deep modulation. Moreover, the metasurface is integrated with a current injection circuit to achieve state switching; this injection circuit can also be employed to monitor the electric state of vanadium dioxide. We estimate the Stokes parameters derived from the experimental transmission spectra of the fabricated metasurface and confirm the helicity switching of circularly polarized waves near a designed frequency of 0.66 THz. The relative bandwidth is evaluated to be 0.52, which is 4.2 times broader than that in a previous study.
Modeling of turbulent mixing with an improved K–L model
Authors: Xiao Mengjuan , Zhang Yousheng , Tian Baolin
Published: September 2020

Turbulent mixing, induced by Rayleigh–Taylor (RT), Richtmyer–Meshkov (RM), and Kelvin–Helmholtz (KH) instabilities, broadly occurs in both natural phenomena, such as supernova explosions, and engineering applications, such as inertial confinement fusion (ICF). These three instabilities usually simultaneously exist and are highly coupled to drive and affect turbulent mixing, which raises a great challenge for turbulence modeling. In this study, an improved version of the K–L model is proposed. The modifications include that: (i) the deviatoric shear stress is considered to describe the KH instability; (ii) the concept of characteristic acceleration is introduced to better distinguish RT and RM instabilities; and (iii) an enthalpy diffusion is directly derived from the internal energy equation to model the turbulent diffusion term. Then, a unified set of model coefficients is systematically derived based on the self-similar analysis and physical observations. This model is validated by canonical RT, RM, and KH mixings and further investigated for more complex cases, including the RM mixing with multiple reshocks, the two-dimensional RT mixing called “tilted-rig,” and the simple spherical implosion, a much simplified version of an ICF implosion. Good agreement with the corresponding experimental and numerical data is achieved, revealing the ability of the present model to describe combined buoyancy, shock, and shear effects, which will contribute to a further application in real problems.
The effect of a solid boundary on the propagation of thermodynamic disturbances in a rarefied gas
Authors: Ben-Ami Y. , Manela A.
Published: September 2020

We study the effect of a rigid boundary on the propagation of thermodynamic disturbances in a gas under non-continuum conditions. We consider a semi-infinite setup confined by an infinite planar wall and introduce initial gas disturbances in the form of density and temperature inhomogeneities. The problem is formulated for arbitrary small-amplitude perturbations and analyzed in the entire range of gas rarefaction rates, governed by the Knudsen (Kn) number. Our results describe the system relaxation to equilibrium, with specific emphasis on the effect of the solid surface. Analytical solutions are obtained in the free-molecular and near-continuum (based on the Navier–Stokes–Fourier and regularized 13 moment equations) regimes and compared with direct simulation Monte Carlo results. The impact of the solid wall is highlighted by comparing between diffuse (adiabatic or isothermal) and specular boundary reflections. Focusing on a case of an initial temperature disturbance, the results indicate that the system relaxation time shortens with increasing Kn. The isothermal boundary consistently reverberates the weakest acoustic disturbance, as the energy carried by the impinging wave is partially absorbed by the surface. The specular and adiabatic wall systems exhibit identical responses in the continuum limit while departing with increasing Kn due to higher-order moment effects. The unsteady normal force exerted by the gas on the surface is quantified and analyzed.
Lanthanum doping induced structural changes and their implications on ferroelectric properties of Hf1−xZrxO2 thin film
Authors: Mehmood Furqan , Mikolajick Thomas , Schroeder Uwe
Published: September 2020

Multiple polymorphs coexist in doped HfO2 ferroelectric material, and their relative fraction depends on the dopant concentration. The ferroelectric properties originate only from the polar orthorhombic Pca21 phase, which can be stabilized in a binary mixture of HfO2 and ZrO2 at a low thermal budget. However, this material suffers from limited field cycling endurance. Additional doping with La improves the field cycling endurance by several orders of magnitude. Hence, La doping is of interest to have better operational reliability. The dynamics of phase formation in Hf0.5Zr0.5O2 is well established, but they have not been investigated in the recently reported La:Hf0.5Zr0.5O2 in detail. In this work, a comprehensive analysis of stability dynamics of polymorphs in La:Hf1−xZrxO2 with different La doping concentrations and its implications on ferroelectric properties is reported.
Extraordinary acoustic transmission of a decorated window without ventilation
Authors: Tan Xihan , Xiang Xiao , Hu Chuandeng , Huang Yingzhou , Wang Shuxia , Wang Li , Wen Weijia
Published: September 2020

We introduce a kind of acoustic metamaterial, which can greatly enhance the transmission at subwavelength ranges and keep its hyaline and air-proof characteristics simultaneously. In contrast to the state of the art, this originally conceived passive metamaterial makes full use of the resonance of glass plates without any complex or expensive materials. We provide the design of the decorated window, numerical simulation, and experimental demonstrations for this kind of metamaterial and analyze the underlying physical mechanism. Furthermore, we show that more transmission peaks can be realized by introducing multilayer resonance coupling of this decorated window. This meta-window should have many potential applications where both the sound and visible light transmission are required without any ventilation.
Multi-temperature vibrational energy relaxation rates in CO2
Authors: Kustova E. , Mekhonoshina M.
Published: September 2020

Rates of vibrational energy relaxation in carbon dioxide are studied in the framework of the three-temperature kinetic-theory approach. Vibrational–translational transitions in the bending mode and inter-mode exchange of vibrational quanta are considered. In the zero-order approximation of the generalized Chapman–Enskog method, the energy relaxation rates in the coupled symmetric–bending and asymmetric modes are expressed in terms of thermodynamic forces similar to chemical reaction affinities, and a compact representation for the vibrational energy production rates is proposed. Linearized theory is developed, and analytical ratios of linearized relaxation rates to those defined by the original Landau–Teller (LT) theory are obtained. The relaxation rates are calculated using the Schwartz–Slawsky–Herzfeld (SSH) and forced harmonic oscillator models for the vibrational energy transition probabilities in the temperature range 200 K–10 000 K. For inter-mode exchanges, using the SSH theory yields significantly underpredicted relaxation rates. The ranges of applicability for the LT formula and linearized theory are estimated; the original LT formula for inter-mode vibrational energy exchanges is not capable of accounting for the excitation of both vibrational modes; linearized models yield better results. Possible steps for improving the numerically efficient LT model are proposed.
Mechanically stressed phytoplankton light up
Authors: Berkowitz Rachel
Published: September 2020

The bioluminescent intensity depends on the rate and amplitude of the microorganism’s deformation.
Modelling evacuation decision-making in the 2016 Chimney Tops 2 fire in Gatlinburg, TN
Authors: Kuligowski Erica D. , Walpole Emily H. , Lovreglio Ruggiero , McCaffrey Sarah
Published: September 2020

As wildfires occurring at the wildland–urban interface (WUI) continue to become more severe, there is an increasing need to understand human behaviour in these situations, and evacuation decision-making in particular. To contribute to this understanding, an online survey (using both mail and online sampling methods) was disseminated to households impacted by the 2016 Chimney Tops 2 fire in Tennessee. The survey instrument measured pre-event variables such as awareness of fire risks and previous experience with evacuations as well as the types of warnings and fire cues received during the event, with a focus on factors known to impact evacuation decisions and risk perception. Using linear and logistic regression analyses, it was found that fire cues and receiving warnings from a trusted source influenced risk perceptions leading up to an evacuation decision. In line with the Protective Action Decision Model, risk perception also highly influenced evacuation decisions, along with other variables, i.e. gender and prior preparation actions. Results from this work provide support for findings from previous wildfire evacuation research as well as produce some novel findings, along with several methodological recommendations, which will be further explored.
Understanding the role of individual units in a deep neural network
Authors: Bau David , Zhu Jun-Yan , Strobelt Hendrik , Lapedriza Agata , Zhou Bolei , Torralba Antonio
Published: September 2020

Deep neural networks excel at finding hierarchical representations that solve complex tasks over large datasets. How can we humans understand these learned representations? In this work, we present network dissection, an analytic framework to systematically identify the semantics of individual hidden units within image classification and image generation networks. First, we analyze a convolutional neural network (CNN) trained on scene classification and discover units that match a diverse set of object concepts. We find evidence that the network has learned many object classes that play crucial roles in classifying scene classes. Second, we use a similar analytic method to analyze a generative adversarial network (GAN) model trained to generate scenes. By analyzing changes made when small sets of units are activated or deactivated, we find that objects can be added and removed from the output scenes while adapting to the context. Finally, we apply our analytic framework to understanding adversarial attacks and to semantic image editing.
Early evolutionary loss of the lipid A modifying enzyme PagP resulting in innate immune evasion inYersinia pestis
Authors: Chandler Courtney E. , Harberts Erin M. , Pelletier Mark R. , Thaipisuttikul Iyarit , Jones Jace W. , Hajjar Adeline M. , Sahl Jason W. , Goodlett David R. , Pride Aaron C. , Rasko David A. , Trent M. Stephen , Bishop Russell E. , Ernst Robert K.
Published: September 2020

Significance

Immune evasion is a hallmark ofYersinia pestispathogenesis, including loss of pathogen-associated patterns recognized by Toll-like receptors. During its life cycle,Y. pestisalternates between mammalian hosts and arthropod transmission vectors and concurrently remodels its membrane, specifically modifying the structure of the lipid A portion of its lipopolysaccharide recognized by TLR4-MD2. Genomic analysis identified a single-nucleotide polymorphism that results in a premature stop in translation of the lipid A acyltransferasepagP, resulting in synthesis of a stealthy, hypoacylated lipid A structure absent in other Yersiniaceae. This provides evidence of lipid A as a crucial determinant inY. pestisinfectivity, pathogenesis, and host innate immune evasion and represents one of the earliest identified adaptations ofY. pestisfromYersinia pseudotuberculosis.
Active vision shapes and coordinates flight motor responses in flies
Authors: Cellini Benjamin , Mongeau Jean-Michel
Published: September 2020

Significance

Many animals, including humans, move their eyes, head, and/or body to stabilize visual gaze. Revealing how the nervous system relays visual information to control the eyes, head, and/or body together is critical to understanding gaze stabilization. Here, we studied how tethered, flying fruit flies combine head movements and wing steering efforts to stabilize gaze. By combining experimental and theoretical approaches we show that head movements shape visual information, which in turn increases the strength of wing steering responses. Moreover, head movements preceded and coordinated downstream wing steering responses, establishing a temporal order. Taken together, head movements and their influence on visual inputs must be considered to fully appreciate the potential of visual information processing for flight control.
Structures of
Arabidopsis thaliana
oxygen-sensing plant cysteine oxidases 4 and 5 enable targeted manipulation of their activity
Authors: White Mark D. , Dalle Carbonare Laura , Lavilla Puerta Mikel , Iacopino Sergio , Edwards Martin , Dunne Kate , Pires Elisabete , Levy Colin , McDonough Michael A. , Licausi Francesco , Flashman Emily
Published: September 2020

Significance

The plant cysteine oxidases (PCOs) have been identified as oxygen-sensing enzymes in plants, controlling hypoxia-dependent processes, including adaptive responses to flooding. As such, they are potential targets for engineering plants with enhanced flood tolerance. To approach this in a rational manner requires an understanding of how PCO structure relates to their ability to trigger hypoxic adaptation. We report the structures of two PCOs from
Arabidopsis
and show that the effects of mutagenesis of key amino acids at their active site are seen both in vitro and, importantly, in planta. This work provides a platform for further efforts to manipulate PCO structure and function to improve the ability of crops to withstand future climate extremes.
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
Authors: Heckmann David , Campeau Anaamika , Lloyd Colton J. , Phaneuf Patrick V. , Hefner Ying , Carrillo-Terrazas Marvic , Feist Adam M. , Gonzalez David J. , Palsson Bernhard O.
Published: September 2020

Significance

Enzyme kinetic parameters are crucial for a quantitative understanding of metabolism, but traditionally have to be measured in laborious low-throughput assays. To solve this problem, the enzyme turnover number,
k
cat
, can be estimated in vivo, but it is unclear whether in vivo estimates represent stable systems parameters that can be used for metabolic modeling. We present the data-driven estimation of in vivo
k
cat
s using proteomics and flux data of metabolic knock out strains of
Escherichia coli
. Our results show that in vivo
k
cat
s are stable parameters that can be used for metabolic modeling. We use the estimated in vivo
k
cat
s to parameterize metabolic models and show that model performance for gene expression predictions increases drastically compared to in vitro parameters.
B cells expressing authentic naive human VRC01-class BCRs can be recruited to germinal centers and affinity mature in multiple independent mouse models
Authors: Huang Deli , Abbott Robert K. , Havenar-Daughton Colin , Skog Patrick D. , Al-Kolla Rita , Groschel Bettina , Blane Tanya R. , Menis Sergey , Tran Jenny Tuyet , Thinnes Theresa C. , Volpi Sabrina A. , Liguori Alessia , Schiffner Torben , Villegas Sophia M. , Kalyuzhniy Oleksandr , Pintea Mark , Voss James E. , Phelps Nicole , Tingle Ryan , Rodriguez Alberto R. , Martin Greg , Kupryianov Sergey , deCamp Allan , Schief William R. , Nemazee David , Crotty Shane
Published: September 2020

Significance

Rational development of successful vaccines requires utilization of predictive models of vaccination. One approach for development of an HIV vaccine has been to study broadly neutralizing antibodies (bnAbs) and revert the mutations back to germline. However, there are limitations to such models. Therefore, we generated three knockin mice expressing B cell receptors (BCRs) from authentic naive VRC01-class B cells from healthy human donors (“HuGL” mice). This approach revealed that human VRC01-class naive B cell BCRs are indeed competent for antigen-specific responses in vivo. Additionally, a series of experiments shows the importance of precursor frequency and affinity on B cell responses to vaccine antigens. Overall, these HuGL mouse models validate a central tenet of the germline-targeting approach to vaccine design.
Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription
Authors: Wang Yan , Chen Yaoyi , Hu Yanping , Fang Xianyang
Published: September 2020

Significance

We present a site-specific NP labeling strategy for large RNAs by transcription using the TPT3-NaM UBP system. The applicability of this labeling strategy is validated by XSI measurements on 97-nt and 719-nt RNAs with site-specific Nanogold labels. This strategy is generally applicable to any natural and artificial RNAs that can be transcribed by T7 RNA polymerase (RNAP) or covalent conjugation of RNAs with other metal NPs. The usage of a far upstream forward primer during PCR enables easy purification of RNA from DNA templates, and the nondenaturing conditions for conjugation reactions and subsequent purification steps avoids potential large RNA misfolding. This labeling strategy expands our capability to site-specifically conjugate RNAs with NPs for many applications.
RubyACRs, nonalgal anion channelrhodopsins with highly red-shifted absorption
Authors: Govorunova Elena G. , Sineshchekov Oleg A. , Li Hai , Wang Yumei , Brown Leonid S. , Spudich John L.
Published: September 2020

Significance

Our identification and characterization of two anion channelrhodopsins families, one from nonphotosynthetic microorganisms, shows that light-gated anion conductance is more widely spread among eukaryotic lineages than previously thought. The strongly red-shifted absorption spectra of the subset that we designate RubyACRs make them promising candidates for the long-sought inhibitory optogenetic tools producing large passive currents activated by red light, enabling deep tissue penetration. Previously only low-efficiency ion-pumping rhodopsins were available for neural inhibition at similar long wavelengths. The unusual residue composition of the retinal-binding pocket in RubyACRs expands our understanding of color tuning in rhodopsins. Finally, activation of chloride currents by energy transfer from a cytoplasmic fluorescent tag on RubyACRs introduces a potential dimension in molecular engineering of optogenetic tools.
Avoiding ventilator-associated pneumonia: Curcumin-functionalized endotracheal tube and photodynamic action
Authors: Zangirolami Amanda C. , Dias Lucas D. , Blanco Kate C. , Vinagreiro Carolina S. , Inada Natalia M. , Arnaut Luis G. , Pereira Mariette M. , Bagnato Vanderlei S.
Published: September 2020

Significance

Hospital-acquired infections also caused by multidrug-resistant bacteria are currently one of the most severe problems that our society faces, which constitute an excellent risk for humankind. The absence of alternatives to combat these types of infections leaves humanity highly vulnerable. Therefore, it becomes imperative to develop new technologies to fight bacterial infections, with alternative mechanisms of action relative to the classical antibiotics. Since ventilator-associated pneumonia (VAP) occurs in patients under mechanical ventilation, an urgent need is needed to prevent, decrease, and combat infectious pathogens at the endotracheal tube (ETT). In this paper, we demonstrate a practical methodology to prepare a regular photosensitizer-containing ETT, with effective photodynamic activity for microbial inactivation. The process is efficient and safe for the patient.
Dark noise and retinal degeneration from D190N-rhodopsin
Authors: Silverman Daniel , Chai Zuying , Yue Wendy W. S. , Ramisetty Sravani Keerthi , Bekshe Lokappa Sowmya , Sakai Kazumi , Frederiksen Rikard , Bina Parinaz , Tsang Stephen H. , Yamashita Takahiro , Chen Jeannie , Yau King-Wai
Published: September 2020

Significance

Rhodopsin mutations account for ∼30% of autosomal-dominant retinitis pigmentosa cases. While dozens of distinct mutations have been identified, the reported detriments that they cause in cell culture are not necessarily all consistent across studies and have often not been evaluated in animal models. Even when an animal model is available, it is typically not straightforward to isolate mutant-rhodopsin signals from related endogenous-rhodopsin signals. Here, we introduce an approach employing a largely “functionally silenced” endogenous rhodopsin in rods as background for isolating activity due to D190N-rhodopsin (D190N-Rho). We conclude that, despite D190N-Rho’s elevated molecular rate constant of spontaneous activation, it does not increase the overall cellular dark noise of the rod, thus excluding its increased noise as the reason for disease.
Engineering carboxylic acid reductase for selective synthesis of medium-chain fatty alcohols in yeast
Authors: Hu Yating , Zhu Zhiwei , Gradischnig David , Winkler Margit , Nielsen Jens , Siewers Verena
Published: September 2020

Significance

The yeast
Saccharomyces cerevisiae
has been utilized extensively as a cell factory to produce numerous products. The de novo synthesis of medium-chain fatty alcohols (MCFOHs) through conversion of free fatty acids by carboxylic acid reductase (CAR) has been studied in yeast. However, the broad substrate specificity of CAR is one of the biggest challenges to improve MCFOH production. Here, different protein engineering strategies were employed to modify the CAR enzyme toward a more specific catalytic activity on shorter chain fatty acids. For this, we created a high-throughput screening assay relying on the detoxification of the toxic substrate to select for efficient enzyme variants. This study represents an important step forward in the selective synthesis of MCFOHs in yeast.
Summertime stationary waves integrate tropical and extratropical impacts on tropical cyclone activity
Authors: Wang Zhuo , Zhang Gan , Dunkerton Timothy J. , Jin Fei-Fei
Published: September 2020

Significance

Skillful seasonal prediction of tropical cyclone (TC) activity helps hurricane preparedness and mitigation, especially when the storm impacts are expected to worsen with increasing sea level and water vapor capacity in a warming climate. Slowly varying tropical oceanic conditions have been regarded as a primary source of predictability for TC activity, but recent studies suggest that TC activity is also subject to some long-range impacts of extratropical processes. We show that summertime stationary waves in the Northern Hemisphere, including tropical upper-tropospheric troughs, integrate tropical and extratropical impacts into a unified framework and provide a hemispheric perspective that helps in understanding the variability and predictability of TC activity over the North Atlantic and North Pacific.
Beyond the Tip of the Iceberg: A Narrative Review to Identify Research Gaps on Comorbid Psychiatric Disorders in Adolescents with Methamphetamine use Disorder or Chronic Methamphetamine Use
Authors: Kuitunen-Paul Sören , Roessner Veit , Basedow Lukas A. , Golub Yulia
Published: September 2020

Background

Methamphetamine use disorder (MUD) frequently begins in adolescence, often accompanied by other psychiatric or mental disorders. Up to now, no comprehensive review about MUD and comorbid disorders in adolescents is available. We thus aimed to review the literature on comorbid mental disorders and MUD in adolescents in order to identify future research topics.

Method

A PubMed search was conducted in July 2019. Relevant comorbidities were defined as attention-deficit disorder with/without hyperactivity, anxiety disorders, depression, eating disorders, post-traumatic stress disorder, psychosis, borderline personality disorder, conduct disorder and antisocial personality disorder, as well as other substance use disorders. For each comorbidity, we summarized prevalence rates, findings on comorbidity mechanisms, and recommended treatment options, if applicable.

Results

Few articles focused on MUD in adolescents. Prevalence rates differed largely between comorbid disorders, with tobacco use disorder, conduct disorder, post-traumatic stress disorder, anxiety disorders, and attention-deficit disorders being the most prevalent comorbidities while eating disorders were rare. Examined onset patterns and comorbidity mechanisms indicated three groups of comorbidities: preexisting disorders self-medicated with methamphetamine, disorders induced by chronic methamphetamine use, and disorders arising due to risk factors shared with MUD. Reviewed comorbidities were frequently associated with worse treatment outcomes.

Conclusions

The limited evidence is in stark contrast to the presumably high prevalence and relevance of comorbid mental disorders in adolescents with MUD. Suggestions for future research topics, informed by adult findings, include genetic vulnerabilities, biological changes, and consequences of different use patterns. Surprisingly few MUD treatment programs explicitly integrate comorbid mental disorder modules.
People with disabilities in the margins in Nigeria
Authors: Etieyibo Edwin , Omiegbe Odirin
Published: September 2020

With the emergence of numerous human rights groups as well as legal instruments in the international arena, the rights and protection of people with disabilities are increasingly being guaranteed. However, in Nigeria, people with disabilities still live at the margins due to some cultural practices that continue to discriminate against them and undermine their rights and general wellbeing. The paper is an empirical study combined with some historical investigation of some of the extant literature to make a case that (a) there is connection between culture and the discrimination, neglect and abuse of person with disabilities; and, (b) that cultural practices undermine the rights and general wellbeing of persons living with disabilities in Nigeria.
A partial data inverse problem for the electro-magnetic wave equation and application to the related Borg–Levinson theorem
Authors: Bellassoued Mourad , Mannoubi Yosra
Published: September 2020

In this article we study the stability in an inverse problem of recovering the magnetic field and the electric potential in a bounded smooth domain from boundary observation of the corresponding wave equation. We prove that the knowledge of the partial Dirichlet-to-Neumann map measured on arbitrary subset of the boundary determines the electric potential and the magnetic field. Next, we apply this result to prove the uniqueness for the multidimensional Borg–Levinson theorem for the electro-magnetic potential from partial data.
A new 3D model for magnetic particle imaging using realistic magnetic field topologies for algebraic reconstruction
Authors: Bringout Gaël , Erb Wolfgang , Frikel Jürgen
Published: September 2020

We derive a new 3D model for magnetic particle imaging (MPI) that is able to incorporate realistic magnetic fields in the reconstruction process. In real MPI scanners, the generated magnetic fields have distortions that lead to deformed magnetic low-field volumes with the shapes of ellipsoids or bananas instead of ideal field-free points (FFP) or lines (FFL), respectively. Most of the common model-based reconstruction schemes in MPI use however the idealized assumption of an ideal FFP or FFL topology and, thus, generate artifacts in the reconstruction. Our model-based approach is able to deal with these distortions and can generally be applied to dynamic magnetic fields that are approximately parallel to their velocity field. We show how this new 3D model can be discretized and inverted algebraically in order to recover the magnetic particle concentration. To model and describe the magnetic fields, we use decompositions of the fields in spherical harmonics. We complement the description of the new model with several simulations and experiments, exploring the effects of magnetic fields distortion and reconstruction parameters on the reconstruction.
Numerical solution of inverse problems by weak adversarial networks
Authors: Bao Gang , Ye Xiaojing , Zang Yaohua , Zhou Haomin
Published: September 2020

In this paper, a weak adversarial network approach is developed to numerically solve a class of inverse problems, including electrical impedance tomography and dynamic electrical impedance tomography problems. The weak formulation of the partial differential equation for the given inverse problem is leveraged, where the solution and the test function are parameterized as deep neural networks. Then, the weak formulation and the boundary conditions induce a minimax problem of a saddle function of the network parameters. As the parameters are alternatively updated, the network gradually approximates the solution of the inverse problem. Theoretical justifications are provided on the convergence of the proposed algorithm. The proposed method is completely mesh-free without any spatial discretization, and is particularly suitable for problems with high dimensionality and low regularity on solutions. Numerical experiments on a variety of test inverse problems demonstrate the promising accuracy and efficiency of this approach.
Skyrmion racetrack memory with an antidot
Authors: Kumar Behera Aroop , Murapaka Chandrasekhar , Mallick Sougata , Bhusan Singh Braj , Bedanta Subhankar
Published: September 2020

Skyrmion racetrack memory has a lot of potential in future non-volatile solid state devices. By application of current in such devices, both spin-orbit torque and spin-transfer torques are proven to be useful to nucleate and propagate skyrmions. However, the current applied during nucleation of successive skyrmions may have unwanted perturbation viz. Joule heating and the skyrmion Hall effect, on the propagation of previously generated skyrmions. Therefore, new methodology is desired to decouple the generation and propagation of skyrmions. Here, we present a novel route via micromagnetic simulations for generation of skyrmions from triangular antidot structure in a ferromagnetic nanotrack using local Oersted field. Antidots are holes in a magnetic nanoelement. Multiple skyrmions can be simultaneously generated by incorporating a greater number of antidots. Controlled skyrmion injection can be achieved by tuning the separation between the antidots that are placed at either end of the nanotrack. Here, we propose a novel design to realise skyrmionic racetrcak memory, where one can individually generate and manipulate the skyrmions within the nanotrack.
Two-particle correlations at high-energy nuclear collisions, peripheral-tube model revisited
Authors: Hama Yogiro , Kodama Takeshi , Qian Wei-Liang
Published: September 2020

In this paper, we give an account of the peripheral-tube model, which has been developed to give an intuitive and dynamical description of the so-called ridge effect in two-particle correlations in high-energy nuclear collisions. Starting from a realistic event-by-event fluctuating hydrodynamical model calculation, we first show the emergence of ridge + shoulders in the so-called two-particle long-range correlations, reproducing the data. In contrast to the commonly used geometric picture of the origin of the anisotropic flow, we can explain such a structure dynamically in terms of the presence of high energy-density peripheral tubes in the initial conditions. These tubes violently explode and deflect the near radial flow coming from the interior of the hot matter, which in turn produces a two-ridge structure in single-particle distribution, with approximately two units opening in azimuth. When computing the two-particle correlation, this will result in characteristic three-ridge structure, with a high near-side ridge and two symmetric lower away-side ridges or shoulders. Several anisotropic flows, necessary to producing ridge + shoulder structure, appear naturally in this dynamical description. Using this simple idea, we can understand several related phenomena, such as centrality dependence and trigger-angle dependence.
Parametrization of the surface energy in the ETF approximation
Authors: Furtado U J , Gulminelli F
Published: September 2020

We perform extended Thomas–Fermi calculations in the Wigner–Seitz cell below and above neutron drip with realistic functionals. The resulting energy density is decomposed as a sum of bulk terms and a surface term, and a compressible liquid drop analytical formula is used to fit the surface tension. The effect of curvature terms and neutron skin is studied in detail. A very good reproduction of the microscopic data is obtained using an expression that depends only on the mass and charge of the cluster, showing that the in-medium modifications of the nuclear energy in the presence of an external neutron gas can be effectively accounted for in the isospin dependence of the surface tension. In this first application, aimed at establishing the fitting protocol, we concentrate on the Sly4 energy functional, but the study can be easily generalized to different functionals, and the resulting parametrizations can be used for direct applications in pasta calculations in neutron star crusts and supernova matter.
Revisiting Majorana neutrino textures in the light of dark LMA
Authors: Borgohain Happy , Borah Debasish
Published: September 2020

We study the possibility of texture zeros in Majorana light neutrino mass matrix in the light of dark large mixing angle (DLMA) solution to solar neutrino problem where solar mixing angle (sin2
θ
12 ≃ 0.7) lies in the second octant instead of first octant in standard large mixing angle (LMA) scenario (sin2
θ
12 ≃ 0.3). In three neutrino scenario, we find that LMA and DLMA solutions lead to different set of allowed and disallowed textures with one and two zeros. While being consistent with existing bounds from neutrino oscillation data, neutrinoless double beta decay and cosmology these allowed textures also lead to interesting correlations among light neutrino parameters which can distinguish LMA from DLMA solution. We also check the implications for texture zeros in 3 + 1 neutrino scenario using both LMA and DLMA solutions. While LMA and DLMA solutions do not play decisive role in ruling out texture zeros in this case, they do give rise to distinct predictions and correlations between light neutrino parameters.
Revisiting the rare H → q

i

q

j
decays in the standard model
Authors: Aranda J I , González-Estrada G , Montaño J , Ramírez-Zavaleta F , Tututi E S
Published: September 2020

We revisit the rare decays of the Higgs boson to two different quarks in the standard model (SM), which arise at the one-loop level. We perform Taylor series expansions to the complete form factors of the decay amplitudes, according to their different mass hierarchies, this allow us to take full advantage of the Glashow–Iliopoulos–Maiani (GIM) mechanism to eliminate spurious contributions and retain those that truly contribute. We found that Br(H → uc) = 5.00 × 10−20, Br(H → ds) = 1.19 × 10−11, Br(H → db) = 5.16 × 10−9 and Br(H → sb) = 1.15 × 10−7. Our predictions for the H → uc, ds decays disagree with previous results in the literature.