bluuebunny/crossref_metadata_2025 huggingface dataset:
Unsteady flow past a square cylinder placed close to a free surface
Authors: Karmakar Avijit , Saha Arun K.
Published: December 2020

Two-dimensional flow past a square cylinder close to a free surface is studied numerically to investigate the effect of Froude numbers (0.0–0.6) and gap ratios (0.2–1.2) on the wake behavior and integral parameters. The multiphase approach with the modified volume of fluid method is employed to study the flow. InterFoam, a two-phase incompressible flow solver in OpenFOAM, has been used to simulate the flow field. The surface deformation is found to increase with the increasing Froude number, which, in turn, produces substantial surface vorticity to cross-cancel the vorticity of the separated shear layer generated near the top surface of the cylinder. At high Froude numbers, merging of shed vortices in the cylinder downstream was encountered that possessed a period twice that in the formation region. For a fixed Froude number, with a decrease in the gap ratio, the amount of cross-cancellation between the top shear layer and the free surface increases. This enhanced interaction leads to diffusion of the vortices from the top shear layer to smaller downstream distances as the cylinder moves close to the free surface. Under such effects, the integral parameters (drag and lift coefficients and Strouhal number) are found to be a strong function of the Froude number and gap ratio. A comparison study of the wake structures with that of a circular cylinder shows the close resemblance in the large scale structures of the two flow fields. In terms of integral parameters, both the bluff bodies possess a similar behavior with the variations of the Froude number and gap ratio, but the magnitudes are quite different due to the differences in the separation points.
Hamiltonian formulations for perturbed dissipationless plasma equations
Authors: Brizard A. J. , Chandre C.
Published: December 2020

The Hamiltonian formulations for the perturbed Vlasov–Maxwell equations and the perturbed ideal magnetohydrodynamics (MHD) equations are expressed in terms of the perturbation derivative ∂F/∂ϵ≡[F,S] of an arbitrary functional F[ψ] of the Vlasov–Maxwell fields ψ=(f,E,B) or the ideal MHD fields ψ=(ρ,u,s,B), which are assumed to depend continuously on the (dimensionless) perturbation parameter ϵ. Here, [ , ] denotes the functional Poisson bracket for each set of plasma equations and the perturbation action functional S is said to generate dynamically accessible perturbations of the plasma fields. The new Hamiltonian perturbation formulation introduces a framework for functional perturbation methods in plasma physics and highlights the crucial roles played by polarization and magnetization in Vlasov–Maxwell and ideal MHD perturbation theories. One application considered in this paper is a formulation of plasma stability that guarantees dynamical accessibility and leads to a natural generalization to higher-order perturbation theory.
Complete separability of the Hamilton–Jacobi equation for the charged particle orbits in a Liénard–Wiechert field
Authors: McLenaghan Raymond G. , Rastelli Giovanni , Valero Carlos
Published: December 2020

We classify all orthogonal coordinate systems in M4, allowing complete additively separated solutions of the Hamilton–Jacobi equation for a charged test particle in the Liénard–Wiechert field generated by any possible given motion of a point-charge Q. We prove that only the Cavendish–Coulomb field, corresponding to the uniform motion of Q, admits separation of variables, precisely in cylindrical spherical and cylindrical conical-spherical coordinates. We show also that for some fields, the test particle with motion constrained into certain planes admits complete orthogonal separation, and we determine the separable coordinates.
A three-fluid model for the dissipation of interfacial capillary-gravity waves
Authors: Rajan Girish Kumar
Published: December 2020

We investigate the dissipation of linear, two-dimensional, interfacial waves in a setting comprising three fluids (an upper fluid of semi-infinite depth, a middle fluid-layer of finite thickness, and a lower fluid of semi-infinite depth) separated by two distinct interfaces, which we consider to be elastic. We derive analytic expressions for the dissipation rate of capillary-gravity waves in such a system, in both the barotropic and baroclinic modes of propagation. Using the dissipation rate model formulated herein, we conduct parametric studies of barotropic gravity waves in an air–oil–water system. We consider six different wavenumbers within the range of 0.0165 m−1 (corresponding to ocean swell) to 44.5 m−1 (corresponding to a typical laboratory gravity wave) and investigate the effects of three major mechanisms of loss of energy, which are the dissipation due to the (i) dynamics in the upper fluid (air), (ii) elastic interfaces, and (iii) viscous middle fluid (oil) layer of finite thickness. For waves with wavenumbers of 0.0165 m−1 and 0.04 m−1, the dominant mechanism for the energy loss is that due to the dynamics in air. For waves with wavenumbers of 1 m−1 and 4 m−1, the oil layer acts to increase the dissipation rates significantly but only when its thickness is beyond a threshold value. For waves with wavenumbers of 36.2 m−1 and 44.5 m−1, the elastic interfaces cause significant increases in the dissipation rates, when their elasticities change from a value of 0.01 N/m to 0.0225 N/m. The three-fluid model developed herein is applicable to capillary-gravity waves propagating in a generic fluid system with arbitrary values for the densities, viscosities, interfacial elasticities, and with an arbitrary value for the middle fluid-layer thickness within an upper limit. This model is useful in predicting the dissipation rates of waves on the ocean surface, which is (in general) covered with biofilms and oil layers of thicknesses ranging from a few μm to a few mm, and in predicting the dissipation rates of waves such as swell, for which the dynamics in the upper fluid (air) are important.
Effect of dead layers on the ferroelectric property of ultrathin HfZrOx film
Authors: Oh Seungyeol , Kim Hyungwoo , Kashir Alireza , Hwang Hyunsang
Published: December 2020

In this study, we investigate the effects of various electrodes on the ferroelectric properties of ultrathin HfZrOx (HZO) films. The ferroelectric polarization is totally suppressed in the HZO films with TiN and W bottom electrodes when the film thickness is below 5 nm. These results can be attributed to the formation of a dead layer at the bottom electrode/HZO interface during the atomic layer deposition (ALD) and annealing processes. On the other hand, the HZO film with a Pt bottom electrode shows an excellent P–E loop with a very high switchable polarization (2Pr) of 42.5 μC/cm2 even at a film thickness of 2.5 nm. Through the short pulse switching technique, we confirm the formation of a thick dead layer in the HZO films with TiN and W electrodes, which inhibits the formation of the orthorhombic phase in these ultrathin HZO films. This implies that the ferroelectric property of ultrathin HZO films can be improved by choosing an appropriate electrode material capable of suppress ing the formation of a dead layer.
Existence of homoclinic orbits and heteroclinic cycle in a class of three-dimensional piecewise linear systems with three switching manifolds
Authors: Zhu Bin , Wei Zhouchao , Escalante-González R. J. , Kuznetsov Nikolay V.
Published: December 2020

In this article, we construct a kind of three-dimensional piecewise linear (PWL) system with three switching manifolds and obtain four theorems with regard to the existence of a homoclinic orbit and a heteroclinic cycle in this class of PWL system. The first theorem studies the existence of a heteroclinic cycle connecting two saddle-foci. The existence of a homoclinic orbit connecting one saddle-focus is investigated in the second theorem, and the third theorem examines the existence of a homoclinic orbit connecting another saddle-focus. The last one proves the coexistence of the heteroclinic cycle and two homoclinic orbits for the same parameters. Numerical simulations are given as examples and the results are consistent with the predictions of theorems.
Toward fully conservative hybrid lattice Boltzmann methods for compressible flows
Authors: Zhao S. , Farag G. , Boivin P. , Sagaut P.
Published: December 2020

This article presents a new numerical scheme designed to solve for any scalar equation coupled with a lattice Boltzmann solver (in so-called hybrid methods). Its most direct application is solving an energy equation, in parallel with a lattice Boltzmann solver, dealing with mass and momentum conservation. The numerical scheme is specifically designed to compute the energy flux consistently with the mass and momentum flux (as is carried out, for instance, using Riemann solvers). This scheme effectively eliminates a major limitation of the current compressible hybrid lattice Boltzmann method, in which the energy conservation is tackled under a non-conservative form, leading to discretization errors on jump conditions across shocks. Combined with our recently presented pressure-based solver [G. Farag et al., “A pressure-based regularized lattice-Boltzmann method for the simulation of compressible flows,” Phys. Fluids 32(6), 066106 (2020)], the resulting hybrid lattice Boltzmann scheme is, to the authors’ knowledge, the first to numerically conserve mass, momentum, and total energy simultaneously.
Reconfigurable and self-biased magnonic metamaterials
Authors: Haldar Arabinda , Adeyeye Adekunle Olusola
Published: December 2020

In magnonics, magnetic waves and oscillations are exploited for signal and information processing at microwave frequencies. A magnonic metamaterial is employed to configure different microwave bands by spatial engineering of magnetizations using different magnetic states or magnetic couplings. Magnetic field hysteretic variation of microwave responses has conventionally been used for tunable microwave operations. The use of such bias magnetic fields hinders the device integration of microwave magnonic devices. Here, we discuss a route to eliminating the requirement of bias magnetic field and simple initialization process for reconfigurable microwave operations. The distinct microwave responses are associated with different remanent magnetic states which are engineered by shape induced magnetic anisotropy rather than the conventional dipolar coupling driven magnetic states. However, the origin of the shift in the microwave spectra is associated with the variation of dipolar coupling for nanomagnetic networks, multilayer nanomagnets, and their arrays. This perspective provides an outlook on current challenges and potential future scopes of magnonic devices. We discuss some of our recent demonstrations toward the realizations of reconfigurable magnonic devices without any external bias magnetic field. Self-biased nanomagnets are also shown to have applications in designing a waveguide for spin wave transport and spin wave gating which operates without any bias magnetic field.
Effect of spin–orbit coupling on strong field ionization simulated with time-dependent configuration interaction
Authors: Lee Mi Kyung , Hoerner Paul , Li Wen , Schlegel H. Bernhard
Published: December 2020

Time-dependent configuration interaction with a complex absorbing potential has been used to simulate strong field ionization by intense laser fields. Because spin–orbit coupling changes the energies of the ground and excited states, it can affect the strong field ionization rate for molecules containing heavy atoms. Configuration interaction with single excitations (CIS) has been employed for strong field ionization of closed shell systems. Single and double excitation configuration interaction with ionization (CISD-IP) has been used to treat ionization of degenerate states of cations on an equal footing. The CISD-IP wavefunction consists of ionizing single (one hole) and double (two hole/one particle) excitations from the neutral atom. Spin–orbit coupling has been implemented using an effective one electron spin–orbit coupling operator. The effective nuclear charge in the spin–orbit coupling operator has been optimized for Ar+, Kr+, Xe+, HX+ (X = Cl, Br, and I). Spin–orbit effects on angular dependence of the strong field ionization have been studied for HX and HX+. The effects of spin–orbit coupling are largest for ionization from the π orbitals of HX+. In a static field, oscillations are seen between the 2Π3/2 and 2Π1/2 states of HX+. For ionization of HX+ by a two cycle circularly polarized pulse, a single peak is seen when the maximum in the carrier envelope is perpendicular to the molecular axis and two peaks are seen when it is parallel to the axis. This is the result of the greater ionization rate for the π orbitals than for the σ orbitals.
Extrasynaptic acetylcholine signaling through a muscarinic receptor regulates cell migration
Authors: Kato Mihoko , Kolotuev Irina , Cunha Alexandre , Gharib Shahla , Sternberg Paul W.
Published: December 2020

Significance

Although ACh is best known for its role in neurotransmission, it also plays a role in cell migration. ACh promotes various cell migrations in vitro, but little is known how it affects cell migration inside an organism where multiple environmental cues are involved. We investigated the migration of an epithelial cell in
C. elegans
, the gonad leader cell, which expresses a muscarinic acetylcholine receptor. This leader cell migrates closely along the animal’s nerve cords and uses ACh secreted from cholinergic neurons. The muscarinic receptor helps the leader cell stay on its migratory path, but its overactivation causes a reversal in cell orientation. The leader cell may use the muscarinic receptor to adjust its orientation to stay on its migratory path.
Control of septum thickness by the curvature of SepF polymers
Authors: Wenzel Michaela , Celik Gulsoy Ilkay N. , Gao Yongqiang , Teng Zihao , Willemse Joost , Middelkamp Martijn , van Rosmalen Mariska G. M. , Larsen Per W. B. , van der Wel Nicole N. , Wuite Gijs J. L. , Roos Wouter H. , Hamoen Leendert W.
Published: December 2020

Significance

Many bacteria form a thick cell wall and divide by forming a cross wall. How they control the thickness of their cell wall and cross wall is unknown. In this study, we show that in these bacteria the cell division protein SepF forms very large protein rings with diameters that correspond to the diameter of their cross walls. Importantly, when we changed the diameter of SepF rings in the bacterial host
Bacillus subtilis
, the thickness of its cross wall changed accordingly. These results provide strong evidence that a large protein ring can function as a mold to control the thickness of the cell wall that divides these bacterial cells.
A rate threshold mechanism regulates MAPK stress signaling and survival
Authors: Johnson Amanda N. , Li Guoliang , Jashnsaz Hossein , Thiemicke Alexander , Kesler Benjamin K. , Rogers Dustin C. , Neuert Gregor
Published: December 2020

Significance

Signaling pathways must decide how to respond to extracellular stimulation patterns that vary widely in vivo. However, most experiments only explore how cells respond to one stimulation variable: concentration. By probing the model yeast osmostress mitogen-activated protein kinase pathway with diverse stimulation gradients we explore cellular sensitivity to multiple stimulation variables. We identify a rate threshold required for signaling and show that the timing of signaling initiation depends on both stimulation rate and concentration in finite-rate treatments. We connect our discovered limit on cell sensitivity to stimulation rate with a phenotype and molecular mechanism, demonstrating its biological relevance. Our results provide motivation and a blueprint for the dissection of other major stimulation-rate-dependent mechanisms in a variety of systems.
Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments
Authors: Dunham Eric C. , Dore John E. , Skidmore Mark L. , Roden Eric E. , Boyd Eric S.
Published: December 2020

Significance

In the absence of light, biomass production is driven by chemical energy through microbial chemosynthesis. H2, a potent reductant capable of supporting chemosynthesis, is readily generated by reactions between iron and silicate minerals and water. Here, we show that lithogenic H2produced by glacial comminution of iron- and silica-rich basaltic bedrock supports microbial chemosynthesis. Lithogenic production of H2in cold, dark subglacial environments and its use to generate chemosynthetic biomass suggest the potential for subglacial habitats to serve as refugia for microbial communities in the absence of sunlight, such as during Snowball Earth episodes or on icy planets where photosynthesis may not yet have evolved or where light is restricted.
GATA6 is a regulator of sinus node development and heart rhythm
Authors: Gharibeh Lara , Yamak Abir , Whitcomb Jamieson , Lu Aizhu , Joyal Mathieu , Komati Hiba , Liang Wenbin , Fiset Céline , Nemer Mona
Published: December 2020

Significance

GATA6 is a key regulator of sinus node (SAN) development. Loss of one
Gata6
allele disrupts patterning and size of the SAN. GATA6 plays cell autonomous as well as non-cell autonomous functions in several cell types required for proper SAN development and function. Haploinsufficiency of
Gata6
in mice leads to electrophysiological alterations and increases susceptibility to develop arrhythmias. GATA6 is critical for pacemaker cell differentiation and cardiac conduction.
Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs
Authors: Ragheb Mark N. , Merrikh Christopher , Browning Kaitlyn , Merrikh Houra
Published: December 2020

Significance

The bacterial DNA translocase Mfd binds to stalled RNA polymerases (RNAPs) and is generally thought to facilitate transcription-coupled DNA repair. Most of our knowledge about Mfd is based on data from biochemical studies. However, little is known about Mfd’s function in living cells, especially in the absence of exogenous DNA damage. Here, we show that Mfd modulates RNAP association and alters transcription at a variety of chromosomal loci, especially those containing highly structured, regulatory RNAs. As such, this work improves our understanding of Mfd’s function in living cells and assigns it a function as a transcription regulator.
Sarcomeres regulate murine cardiomyocyte maturation through MRTF-SRF signaling
Authors: Guo Yuxuan , Cao Yangpo , Jardin Blake D. , Sethi Isha , Ma Qing , Moghadaszadeh Behzad , Troiano Emily C. , Mazumdar Neil , Trembley Michael A. , Small Eric M. , Yuan Guo-Cheng , Beggs Alan H. , Pu William T.
Published: December 2020

Significance

Mature cardiomyocytes are highly adapted to pump efficiently over billions of cycles. The mechanisms that regulate and coordinate the acquisition of the specialized features of mature cardiomyocytes in the postnatal period are not well understood. This knowledge gap hinders studies of disease pathogenesis and the maturation of stem cell–derived cardiomyocytes for cardiac regenerative medicine. Here, we studied the roles of sarcomeres, the contractile machinery of cardiomyocytes, in regulating cardiomyocyte maturation. Using an in vivo genetic mosaic approach to circumvent animal lethality and secondary consequences of cardiac dysfunction, we analyzed the contribution of sarcomeres to cardiomyocyte maturation in a physiological context. We identified an important role of sarcomeres in the regulation of signal transduction and gene transcription.
In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1
Authors: Duellberg Christian , Auer Albert , Canigova Nikola , Loibl Katrin , Loose Martin
Published: December 2020

Significance

The complex morphology of neurons relies on a tight control of protein localization and activation. How spatiotemporal activity patterns emerge from the interplay between diverse intracellular components is often not known. Here, we addressed this question for the neuronal protein ADAP1, which catalyzes GTP hydrolysis in the small G protein ARF6 and binds to the motor protein KIF13B. Using in vitro reconstitutions from purified proteins, we were able to propose a model where the motor and the signaling lipid PIP
3
act in concert to distribute, deposit, and activate ADAP1, which in turn regulates ARF6. This regulatory pathway offers a mechanism for how small GTPases are controlled in space and time to control dendrite branching, which is important for neuronal development.
Real-time observation of Cas9 postcatalytic domain motions
Authors: Wang Yanbo , Mallon John , Wang Haobo , Singh Digvijay , Hyun Jo Myung , Hua Boyang , Bailey Scott , Ha Taekjip
Published: December 2020

Significance

Cas9 complexed with a programmable guide RNA has been repurposed for genome-engineering applications. Mechanistic understanding of Cas9-mediated DNA cleavage provides opportunities for rational engineering of Cas9 to improve its efficiency and specificity. Domain movements of Cas9 have been well studied before DNA cleavage but not after. In this study, we observed the HNH nuclease domain motions from DNA binding to post-DNA cleavage in real time using single-molecule fluorescence techniques. The coupling between DNA cleavage activity and Cas9 conformation demonstrated in our study provides insights and motivation for future applications.
Convective isolation of Hadean mantle reservoirs through Archean time
Authors: Tusch Jonas , Münker Carsten , Hasenstab Eric , Jansen Mike , Marien Chris S. , Kurzweil Florian , Van Kranendonk Martin J. , Smithies Hugh , Maier Wolfgang , Garbe-Schönberg Dieter
Published: December 2020

Significance

Geological processes like mantle convection or plate tectonics are an essential factor controlling Earth’s habitability. Our study provides insights into timescales of convective homogenization of Earth’s early mantle, employing the novel tool of high-precision
182
W isotope measurements to rocks from the Pilbara Craton in Australia, that span an age range from 3.5 billion years to 2.7 billion years. Previous
182
W studies mostly covered snapshots through geologic time, so the long-term
182
W evolution of the mantle has been ambiguous. Together with sophisticated trace element approaches, we can now provide an improved insight into such timescales, arguing for local preservation of primordial geochemical heterogeneities within Earth’s mantle as late as around 3.0 billion years, the putative onset of widespread plate tectonics on Earth.
Operando measurement of lattice strain in internal combustion engine components by neutron diffraction
Authors: Wissink Martin L. , Chen Yan , Frost Matthew J. , Curran Scott J. , Rios Orlando , Sims Zachary C. , Weiss David , Stromme Eric T. , An Ke
Published: December 2020

Significance

Internal combustion engine components experience extreme thermomechanical cycling during operation, and the continuing need to improve engine efficiency while maintaining or improving reliability drives the development of lightweight materials with improved thermal and mechanical integrity. Understanding the behavior of new materials in dynamic operation requires operando characterization tools, but conventional in situ measurements of material behavior during real engine operation are very limited, and no practical means exist to replicate such extreme dynamics for ex situ study. In this work, we demonstrate that the penetrating power of neutrons can provide noninvasive measurement of lattice strains inside components of a firing engine, enabling the operando study of complex load states and thermal gradients throughout the solid materials.
Association of aerobic glycolysis with the structural connectome reveals a benefit–risk balancing mechanism in the human brain
Authors: Chen Yuhan , Lin Qixiang , Liao Xuhong , Zhou Changsong , He Yong
Published: December 2020

Significance

Aerobic glycolysis (AG) is the nonoxidative metabolism of glucose despite abundant oxygen. High AG is critical for various biological processes in the brain, such as biosynthesis and rapid ATP production, but also identifies regions most vulnerable to amyloid-β deposition. Currently, the wiring mechanisms underlying the metabolic benefits and risks of AG are largely unknown. Using advanced neuroimaging techniques and computational modelling, we systematically examined the relationship between AG and the connectome. Our results delineate large yet optimized wiring costs in high-AG regions (e.g., default-mode and prefrontal cortices), revealing a balancing mechanism that satisfies metabolic demand while reducing vulnerability risk. This research highlights wiring rules in high-AG regions and deepens our understanding of the relationship between brain metabolism and the connectome.
Probabilistic structure of events controlling the after-storm recovery of coastal dunes
Authors: Rinaldo Tobia , Ramakrishnan Kiran Adhithya , Rodriguez-Iturbe Ignacio , Durán Vinent Orencio
Published: December 2020

Significance

Coastal dunes help stabilize barrier islands by reducing the frequency of overwashes and promoting vertical accretion. In doing so, they build unique habitats and protect coastal infrastructure. The after-storm recovery of coastal dunes thus underpins the short-term resiliency of sandy coasts to storm impacts and sea-level rise. Here, we show that this recovery is controlled by the size and frequency of random high-water events too small to overtop a mature dune, but large enough to prevent the development of small embryo dunes. Using data from several locations around the world, we find that the statistical properties of high-water events change surprisingly little and do not depend on tidal range and wave regime.
Stochastic dynamics of barrier island elevation
Authors: Vinent Orencio Durán , Schaffer Benjamin E. , Rodriguez-Iturbe Ignacio
Published: December 2020

Significance

Barrier islands sustain important coastal ecosystems and are our first line of defense from storm impacts. However, they are threatened by sea level rise and lack of sand supply and could undergo rapid deterioration. The uncertainty in barrier response is amplified by the complexity of the processes involved and their stochastic nature. Here we find that barrier stochastic behavior can be described by a stochastic equation that suggests the presence of a tipping point in barrier response to external drivers. The solution of this equation allows the quantitative estimation of after-storm recovery, the rate of barrier landward migration, the effectiveness of dune protection in reducing back-barrier flooding, and the effects of potential interventions to accelerate after-storm recovery.
Transfer of information across repeated decisions in general and in obsessive–compulsive disorder
Authors: Solway Alec , Lin Zhen , Vinaik Ekansh
Published: December 2020

Significance

Real-life decisions are often repeated. Whether considering taking a new job, or doing something mundane like checking if the stove is off, people frequently revisit decisions. This mode of behavior takes a particularly pathological form in obsessive–compulsive disorder (OCD). Surprisingly, little is known about how information is transferred across decisions, and whether and how such transfer is disrupted in OCD. Data from a repeated decision-making task and computational modeling revealed that different memory systems separately biased repeated decisions toward previous choices by changing how people weigh evidence. Transfer specifically driven by implicit memory was reduced in individuals with higher levels of OCD symptoms on top of other baseline decision-making deficits, offering computational insight into checking behavior.
Staphylococcus aureus
binds to the N-terminal region of corneodesmosin to adhere to the stratum corneum in atopic dermatitis
Authors: Towell Aisling M. , Feuillie Cécile , Vitry Pauline , Da Costa Thaina M. , Mathelié-Guinlet Marion , Kezic Sanja , Fleury Orla M. , McAleer Maeve A. , Dufrêne Yves F. , Irvine Alan D. , Geoghegan Joan A.
Published: December 2020

Significance

Staphylococcus aureus
colonizes skin of patients with atopic dermatitis (AD), increasing disease severity. Colonization involves bacterial adhesion to skin corneocytes, and elucidating the molecular basis of interactions governing adhesion is crucial to further our understanding of pathogenesis and inform targeted therapies. We identify host and pathogen factors that enable adhesion. We demonstrate that
S. aureus
interacts with the N-terminal region of corneodesmosin on the surface of patient corneocytes. This interaction is mediated by two bacterial cell wall-anchored proteins (fibronectin binding protein B and clumping factor B). Frequency and force of bacterial binding to AD corneocytes decreased when the N-terminal region of corneodesmosin was blocked with an antibody, indicating the contribution of this interaction during
S. aureus
adhesion to human skin.
Cerebellar Purkinje cells can differentially modulate coherence between sensory and motor cortex depending on region and behavior
Authors: Lindeman Sander , Hong Sungho , Kros Lieke , Mejias Jorge F. , Romano Vincenzo , Oostenveld Robert , Negrello Mario , Bosman Laurens W. J. , De Zeeuw Chris I.
Published: December 2020

Significance

Coordinated activity of sensory and motor cortices is essential for adjusting movements based on sensory feedback. Sensory and motor cortices communicate directly as well as via the thalamus and also receive indirect input from the cerebellum. We show here that cerebellar activity can affect the amplitude and coherence of fast sensorimotor responses in the primary somatosensory and motor cortices upon whisker stimulation. The cerebellum can differentially alter sensory-induced theta- and gamma-band cortical coherences via a fast ascending pathway. In line with the functional heterogeneity of its modular organization, cerebellar impact is region-specific and tuned to ongoing motor responses. Our data highlight site-specific and context-dependent cerebello-cerebral interactions that can come into play during a plethora of sensorimotor functions.
College roommates have a modest but significant influence on each other’s political ideology
Authors: Strother Logan , Piston Spencer , Golberstein Ezra , Gollust Sarah E. , Eisenberg Daniel
Published: December 2020

Significance

Understanding the relationship between college and political ideology is of increasing importance in the United States in the context of intense partisan polarization. Leveraging a quasi-experiment and a panel survey, we find no evidence that a sample of students moves leftward along the political spectrum during the first year of college. However, we find strong evidence of a causal effect of roommates: Students move toward their randomly assigned roommates’ political ideology over the course of their first year of college. Our study identifies causal evidence of social network effects for political views and identifies these causal effects for college students specifically. Our findings are inconsistent with claims that college makes students more liberal.
E3 ubiquitin ligase Mindbomb 1 facilitates nuclear delivery of adenovirus genomes
Authors: Sarbanes Stephanie L. , Blomen Vincent A. , Lam Eric , Heissel Søren , Luna Joseph M. , Brummelkamp Thijn R. , Falck-Pedersen Erik , Hoffmann H.-Heinrich , Rice Charles M.
Published: December 2020

Significance

Adenoviruses (AdVs) are DNA viruses that can cause severe respiratory illness in humans. A better understanding of the complex ways AdVs utilize cellular processes in service of their replication is critical to the development of new therapies to counter viral infection and disease. Using a genome-wide screen, we identified a cellular protein Mindbomb 1 (MIB1) required for AdV infection and show that it functions in the AdV entry process to mediate release of the viral genome into the nucleus. We further show that MIB1, as an E3 ubiquitin ligase, mediates AdV capsid disassembly and genome release through ubiquitination of a target protein(s), demonstrating the importance of this rapid posttranslational modification to virus infection.
The Ligand of Ate1 is intrinsically disordered and participates in nucleolar phase separation regulated by Jumonji Domain Containing 6
Authors: Arva Akshaya , Kasu Yasar Arfat T. , Duncan Jennifer , Alkhatatbeh Mosleh A. , Brower Christopher S.
Published: December 2020

Significance

Due to the difficulty in their biochemical characterization, until recently intrinsically disordered proteins have gone largely unannotated. However, an appreciation for their biological significance is emerging, as they are now known to facilitate liquid–liquid phase separation (LLPS), which can produce membrane-lacking organelles that enable the spatial regulation of important cellular processes. This report characterizes the Ligand of Ate1 (Liat1) as an intrinsically disordered protein that participates in LLPS in the nucleolus, a prominent membrane-lacking organelle specialized in ribosome biogenesis. Furthermore, it shows that the lysyl-hydroxylase activity of Jumonji Domain Containing 6 modifies Liat1 and inhibits its nucleolar targeting and potential functions.
Global silicate weathering flux overestimated because of sediment–water cation exchange
Authors: Tipper Edward T. , Stevenson Emily I. , Alcock Victoria , Knight Alasdair C. G. , Baronas J. Jotautas , Hilton Robert G. , Bickle Mike J. , Larkin Christina S. , Feng Linshu , Relph Katy E. , Hughes Genevieve
Published: December 2020

Significance

Large rivers transport water and sediment to floodplains and oceans, supplying the nutrients that sustain life. They also transport carbon, removed from the atmosphere during mineral dissolution reactions, which is thought to provide a key negative climate feedback on long timescales. We demonstrate that the (million-year) carbon flux associated with mineral dissolution has been overestimated by up to 28% because of a reactive pool of elements transported with river-borne suspended sediment. This is most acute in regions of high erosion, where silicate weathering is thought to be most intense.
DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes
Authors: Pfab Jonas , Phan Nhut Minh , Si Dong
Published: December 2020

Significance

Electron cryomicroscopy (cryo-EM), a 2017 Nobel prize-awarded technology, provides direct 3D maps of macromolecules and explains the shape and interactions of protein complexes such as SARS-CoV-2 viral proteins and human cell receptors. This understanding can be combined with detailed structural information gathered using other technologies to form the basis for modeling course of diseases and for designing therapeutic drugs. However, ab initio modeling of protein complex structure remains a challenging problem. Here, we present DeepTracer, a fully automated and robust tool that determines the all-atom structure of a protein complex based solely on its cryo-EM map and amino acid sequence, with improved accuracy and efficiency compared to previous methods. We also provide a web service for global access.
Drosophila melanogaster
sex peptide regulates mated female midgut morphology and physiology
Authors: White Melissa A. , Bonfini Alessandro , Wolfner Mariana F. , Buchon Nicolas
Published: December 2020

Significance

We describe a role for the seminal fluid protein Sex Peptide (SP) in regulating the post-mating morphology and physiology of the female digestive tract. We show that females must receive SP to increase their midgut size following mating, a response that is important for female fecundity. Receiving SP is also important for post-mating changes in the expression of digestive enzyme and metabolic genes in the midgut. This is a significant step in our understanding of how female physiology shifts to cope with the metabolic demands of reproduction. Our study reveals another mechanism through which the male can alter female post-mating physiology to enhance reproductive output.
Endogenous membrane stress induces T6SS activity in
Pseudomonas aeruginosa
Authors: Stolle Anne-Sophie , Meader Bradley Thomas , Toska Jonida , Mekalanos John J.
Published: December 2020

Significance

In this study, we applied a CRISPR interference approach to knock down expression of essential genes involved in cell envelope biogenesis and determined if this can trigger
Pseudomonas aeruginosa
T6SS apparatus assembly. We found that disruption of envelope biogenesis can be sensed by the bacteria via a sensory pathway that involves phosphorylation leading to profound T6SS dynamic activation. Our data provide further evidence that membrane disruption is a key signal that drives T6SS organelle assembly. This process likely mimics natural activation pathways that allow
P. aeruginosa
to detect the attack by other aggressive bacteria species and thus sheds further light on the potential key signals that control T6SS organelle biogenesis.
IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues
Authors: Radtke Andrea J. , Kandov Evelyn , Lowekamp Bradley , Speranza Emily , Chu Colin J. , Gola Anita , Thakur Nishant , Shih Rochelle , Yao Li , Yaniv Ziv Rafael , Beuschel Rebecca T. , Kabat Juraj , Croteau Joshua , Davis Jeremy , Hernandez Jonathan M. , Germain Ronald N.
Published: December 2020

Significance

Single-cell flow cytometry and genomic methods are rapidly increasing our knowledge of the diversity of cell types in metazoan tissues. However, suitably robust methods for placing these cells in a spatial context that reveals how their localization and putative interactions contribute to tissue physiology and pathology are still lacking. Here we provide a readily accessible pipeline (IBEX) for highly multiplex immunofluorescent imaging that enables a fine-grained analysis of cells in their tissue context. Additionally, we describe extensions of the IBEX workflow to handle hard-to-image tissue preparations and a method to facilitate direct integration of the imaging data with flow cytometry and sequencing technologies.
Oral administration of PEGylated TLR7 ligand ameliorates alcohol-associated liver disease via the induction of IL-22
Authors: Wang Qinglan , Kim So Yeon , Matsushita Hiroshi , Wang Zhijun , Pandyarajan Vijay , Matsuda Michitaka , Ohashi Koichiro , Tsuchiya Takashi , Roh Yoon Seok , Kiani Calvin , Zhao Yutong , Chan Michael , Devkota Suzanne , Lu Shelly C. , Hayashi Tomoko , Carson Dennis A. , Seki Ekihiro
Published: December 2020

Significance

Alcoholic hepatitis (AH) is a severe form of alcohol-associated liver disease (ALD) that is characterized by chronic liver injury and inflammation. The current treatment strategy for AH involves the use of corticosteroids, despite a lack of evidence supporting their efficacy, because other effective therapeutic agents are not available. Here, we demonstrate that activation of TLR7 signaling via the oral administration of 1Z1, which is a synthetic TLR7 ligand that does not elicit systemic side effects, protects against liver injury in an AH mouse model. The therapeutic effect of 1Z1 requires TLR7 expression and is mediated by intestinal IL-22 upregulation. Our study suggests that 1Z1-induced TLR7 activation and IL-22 induction may be a therapeutic approach for the treatment of AH.
Precise genome engineering in
Drosophila
using prime editing
Authors: Bosch Justin A. , Birchak Gabriel , Perrimon Norbert
Published: December 2020

Significance

Precise genome engineering allows researchers to modify gene function, tag endogenous proteins, or model human disease mutations. Here, we adapt prime editing, a new CRISPR-based technology that uses reverse transcription to write precise changes into a target genomic location, for the model organism
Drosophila melanogaster
. We created and optimized genetic tools to edit three genes (
ebony
,
white
, and
forked
) in cultured cells and in vivo. Importantly, we demonstrate efficient germ-line transmission of a precise edit in
ebony
. As
Drosophila
is the first nonmammalian animal to be tested using this method, this study demonstrates the potential wide impact and translatability of prime editing in other animal species.
HMGB1-mediated chromatin remodeling attenuates
Il24
gene expression for the protection from allergic contact dermatitis
Authors: Senda Naoyuki , Yanai Hideyuki , Hibino Sana , Li Lei , Mizushima Yu , Miyagaki Tomomitsu , Saeki Mai , Kishi Yusuke , Hangai Sho , Nishio Junko , Sugaya Makoto , Taniguchi Tadatsugu , Sato Shinichi
Published: December 2020

Significance

High-mobility group box 1 protein (HMGB1) protein gained attention for its proinflammatory function in a number of pathological conditions, such as skin inflammation. In this study, a Cre/loxP-engineered mouse strain allowed for HMGB1 conditionally ablated in keratinocytes. When allergic contact dermatitis was induced in the HMGB1 mutant mice, skin inflammation was exacerbated in the mutant mice. Expression of interleukin-24 (IL-24), a proinflammatory cytokine associated to skin inflammatory disorders, was elevated in skin lesions of these mice. We also adduced evidence that that HMGB1 represses the binding of histone H3 (lys4) (H3K4me3) to the
Il24
gene promoter in keratinocytes. Therefore, our study revealed a facet of nuclear HMGB1 that represses the
Il24
gene for the suppression of allergic inflammatory skin disorders.
Political orientation and system justification: the moderating role of national identity in a Spanish sample (Orientación política y justificación del sistema: el rol moderador de la identidad nacional en una muestra española)
Authors: Moscato Gianluigi , Caricati Luca , Bonetti Chiara
Published: December 2020

Right-wing people usually justify the system more than left-wing people. The social identity approach suggests that system justification may be an ingroup bias at overarching national levels and that differences between leftists and rightists could be linked to differences in party norms in promoting national identification. A cross-sectional design was used in which 192 adults (64.6% men, mean age of 35.61 years) were enrolled. Political orientation, national identification and general and economic system justification were collected. Results from structural equation modelling indicated that rightists, as compared with leftists, were higher in national identification and both general and economic system justification. National identification mostly mediated the relationship between political orientation and general system justification, while mediation on the relationship between political orientation and economic system justification was less marked. The social identity approach expectation that differences in system justification could be linked to the extent to which people identify with their overarching social category appears to be supported.
ZFP91 is required for the maintenance of regulatory T cell homeostasis and function
Authors: Wang Aiting , Ding Lei , Wu Zhongqiu , Ding Rui , Teng Xiao-Lu , Wang Feixiang , Hu Zhilin , Chen Lei , Yu Xiaoyan , Zou Qiang
Published: December 2020

Autophagy programs the metabolic and functional fitness of regulatory T (T reg) cells to establish immune tolerance, yet the mechanisms governing autophagy initiation in T reg cells remain unclear. Here, we show that the E3 ubiquitin ligase ZFP91 facilitates autophagy activation to sustain T reg cell metabolic programming and functional integrity. T reg cell–specific deletion of Zfp91 caused T reg cell dysfunction and exacerbated colonic inflammation and inflammation-driven colon carcinogenesis. TCR-triggered autophagy induction largely relied on T reg cell–derived ZFP91 to restrict hyperglycolysis, which is required for the maintenance of T reg cell homeostasis. Mechanistically, ZFP91 rapidly translocated from the nucleus to the cytoplasm in response to TCR stimulation and then mediated BECN1 ubiquitination to promote BECN1–PIK3C3 complex formation. Therefore, our results highlight a ZFP91-dependent mechanism promoting TCR-initiated autophagosome maturation to maintain T reg cell homeostasis and function.
Accuracy of Machine Learning Potential for Predictions of Multiple-Target Physical Properties*
Authors: Ouyang Yulou , Zhang Zhongwei , Yu Cuiqian , He Jia , Yan Gang , Chen Jie
Published: December 2020

The accurate and rapid prediction of materials’ physical properties, such as thermal transport and mechanical properties, are of particular importance for potential applications of featuring novel materials. We demonstrate, using graphene as an example, how machine learning potential, combined with the Boltzmann transport equation and molecular dynamics simulations, can simultaneously provide an accurate prediction of multiple-target physical properties, with an accuracy comparable to that of density functional theory calculation and/or experimental measurements. Benchmarked quantities include the Grüneisen parameter, the thermal expansion coefficient, Young’s modulus, Poisson’s ratio, and thermal conductivity. Moreover, the transferability of commonly used empirical potential in predicting multiple-target physical properties is also examined. Our study suggests that atomic simulation, in conjunction with machine learning potential, represents a promising method of exploring the various physical properties of novel materials.
Fano Effect and Spin-Polarized Transport in a Triple-Quantum-Dot Interferometer Attached to Two Ferromagnetic Leads
Authors: Bai Jiyuan , Chen Kongfa , Ren Pengyu , Li Jianghua , He Zelong , Li Li
Published: December 2020

We report the conductance and average current through a triple-quantum-dot interferometer coupled with two ferromagnetic leads using the nonequilibrium Green’s function. The results show that the interference between the resonant process and the non-resonant process leads to the formation of Fano resonance. More Fano resonances can be observed by applying a time-dependent external field. As a Zeeman magnetic field is applied, the spin-up electron transport is depressed in a certain range of electron energy levels. A spin-polarized pulse device can be realized by adjusting the spin polarization parameters of ferromagnetic leads. Moreover, the I–V characteristic curves show that under the influence of Fano resonance, the spin polarization is significantly enhanced by applying a relatively large reverse bias voltage. These results strongly suggest that the spin-polarized pulse device can be potentially applied as a spin-dependent quantum device.
Trion-Facilitated Dexter-Type Energy Transfer in a Cluster of Single Perovskite CsPbBr3 Nanocrystals*
Authors: Cao Zengle , Hu Fengrui , Man Zaiqin , Zhang Chunfeng , Zhang Weihua , Wang Xiaoyong , Xiao Min
Published: December 2020

Semiconductor colloidal nanocrystals (NCs) can interact with each other to profoundly influence the charge transfer, transport and extraction processes after they have been assembled into a high-density film for optoelectronic device applications. These interactions normally occur among several nearby single colloidal NCs, which should be effectively separated from their surroundings to remove the ensemble average effect for fine optical characterizations. By means of atomic force microscopy (AFM) nanoxerography, here we prepare individual clusters of perovskite CsPbBr3 NCs and perform single-particle measurements on their optical properties at the cryogenic temperature. While discrete photoluminescence bands can be resolved from the several single CsPbBr3 NCs that are contained within an individual cluster, the shorter- and longer-wavelength bands are dramatically different in that their intensities show sub- and superlinear dependences on the laser excitation powers, respectively. This can be explained by the generation of charged excitons (trions) at high laser excitation powers, and their subsequent Dexter-type energy transfer from smaller- to larger-sized CsPbBr3 NCs. Our findings not only suggest that these individual clusters prepared by AFM nanoxerography can serve as a potent platform to explore few-NC interactions but they also reveal the long-neglected role played by trions in channeling photo-excited energies among neighboring NCs.