Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action
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Cannizzo, Michael D.↗
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Mode transitions and spoke structures in E × B Penning discharge
Two-dimensional particle-in-cell simulations in the (radial-azimuthal) plane perpendicular to the axial direction of a cylindrical $E$ x $B$ Penning discharge are presented. The low-pressure discharge is self-consistently supported by plasma ionization from the electron beam injected axially, along the direction of the external magnetic field. It is shown that with the increasing strength of the external magnetic field, the discharge undergoes a sequence of transitions between several azimuthal modes. Azimuthal m > 1 spiral arm structures are excited at low magnetic field values as plasma confinement improves and the radial density profile becomes peaked. With a larger field, spiral arms with m > 1 are replaced by the m = 1 spoke mode, most clearly seen in plasma density. A transition from spiral arms to the spoke regime occurs when the plasma potential in the center changes from weakly positive (or zero) to negative. Further increase in the magnetic field results in a well-developed m = 1 spoke mode with additional small-scale higher-frequency m > 1 structures inside and around the spoke. It is shown that while ionization and collisions affect some characteristics of the observed fluctuations, the basic features of the spoke and m > 1 spiral structure remained similar without ionization. The role of energy conservation in small-scale high-frequency modes and spoke dynamics is discussed. It is demonstrated that in regimes with the m = 1 spoke mode, additional m = 4 harmonics of the ion and electron fluxes to the wall appear due to the square boundary. The frequency of the m = 1 mode is weakly affected by the geometry of the boundary.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Plant defensin MtDef4–derived antifungal peptide with multiple modes of action and potential as a bio–inspired fungicide
Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). The sequence-divergent cysteine-rich antifungal defensins with multisite MoA are promising starting templates for design of novel peptide-based fungicides. Here, we experimentally tested such a set of 17-amino-acid peptides containing the γ-core motif of the antifungal plant defensin MtDef4. These designed peptides exhibited antifungal properties different from those of MtDef4. Focused analysis of a lead peptide, GMA4CG_V6, showed that it was a random coil in solution with little or no secondary structure elements. Additionally, it exhibited potent cation-tolerant antifungal activity against the plant fungal pathogen Botrytis cinerea, the causal agent of grey mould disease in fruits and vegetables. Its multisite MoA involved localization predominantly to the plasma membrane, permeabilization of the plasma membrane, rapid internalization into the vacuole and cytoplasm, and affinity for the bioactive phosphoinositides phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. The sequence motif RRRW was identified as a major determinant of the antifungal activity of this peptide. While topical spray application of GMA4CG_V6 on Nicotiana benthamiana and tomato plants provided preventive and curative suppression of grey mould disease symptoms, the peptide was not internalized into plant cells. Our findings open the possibility that truncated and modified defensin-derived peptides containing the γ-core sequence could serve as promising candidates for further development of bio-inspired fungicides.
54 ENVIRONMENTAL SCIENCES↗
Data-driven acceleration of thermal radiation transfer calculations with the dynamic mode decomposition and a sequential singular value decomposition
In this work, we present a method for accelerating discrete ordinates radiative transfer calculations for radiative transfer. Our method works with nonlinear positivity fixes, in contrast to most acceleration schemes. The method is based on the dynamic mode decomposition (DMD) and using a sequence of rank-one updates to compute the singular value decomposition needed for DMD. Using a sequential method allows us to automatically determine the number of solution vectors to include in the DMD acceleration. We present results for slab geometry discrete ordinates calculations with the standard temperature linearization. Compared with positive source iteration, our results demonstrate that our acceleration method reduces the number of transport sweeps required to solve the problem by a factor of about 3 on a standard diffusive Marshak wave problem, a factor of several thousand on a cooling problem where the effective scattering ratio approaches unity, and a factor of 20 improvement in a realistic, multimaterial radiating shock problem.
97 MATHEMATICS AND COMPUTING↗
On the Low Risk of Subsynchronous Resonance (SSR) in Type III Wind Turbines Operating in Grid-Forming Control
We have shown in a previous work that the risk of sub-synchronous resonance (SSR) between a wind power plant with Type III wind turbines and series-compensated transmission lines is low when the wind turbines in the plant are operated in grid-forming mode, instead of the standard grid-following mode. The fundamental mechanism behind the improved damping characteristics is explained in this paper by modeling the positive and negative sequence impedances of Type III wind turbines for GFM operation mode. It is discovered that the GFM control naturally acts against the negative resistance of Type III wind turbines that results from an interaction between the proportional gain of the rotor-side converter current controller and negative slip. The developed sequence impedance models and improved damping behavior are verified using PSCAD simulations of a 2.5-MW Type III GFM wind turbine. The modeling predictions are also supported by experimentally measuring the sequence impedance response of a 2.5-MW Type III wind turbine during operation in GFL and GFM modes.
grid-following turbine↗
The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11
SARS-CoV-2, the virus behind the COVID-19 pandemic, has changed over time to the extent that the current virus is substantially different from what originally led to the pandemic in 2019–2020. Viral variants have modified the severity and transmissibility of the disease and continue do so. How much of this change is due to viral fitness versus a response to immune pressure is hard to define. One class of antibodies that continues to afford some level of protection from emerging variants are those that closely overlap the binding site for angiotensin-converting enzyme 2 (ACE2) on the receptor binding domain (RBD). Some members of this class that were identified early in the course of the pandemic arose from the VH 3-53 germline gene (IGHV3-53*01) and had short heavy chain complementarity-determining region 3s (CDR H3s). Here, we describe the molecular basis of the SARS-CoV-2 RBD recognition by the anti-RBD monoclonal antibody CoV11 isolated early in the COVID-19 pandemic and show how its unique mode of binding the RBD determines its neutralization breadth. CoV11 utilizes a heavy chain VH 3-53 and a light chain VK 3-20 germline sequence to bind to the RBD. Two of CoV11’s four heavy chain changes from the VH 3-53 germline sequence, $Thr^{28}_{FWRH1}$ to Ile and $Ser^{31}_{CDRH1}$ to Arg, and some unique features in its CDR H3 increase its affinity to the RBD, while the four light chain changes from the VK 3-20 germline sequence sit outside of the RBD binding site. Antibodies of this type can retain significant affinity and neutralization potency against variants of concern (VOCs) that have diverged significantly from original virus lineage such as the prevalent omicron variant. We also discuss the mechanism by which VH 3-53 encoded antibodies recognize spike antigen and show how minimal changes to their sequence, their choice of light chain, and their mode of binding influence their affinity and impact their neutralization breadth.
60 APPLIED LIFE SCIENCES↗
On the Low Risk of SSR in Type III Wind Turbines Operating with Grid-Forming Control
We have shown in previous work that the risk of subsynchronous resonance between wind power plants with Type III wind turbines and series-compensated transmission lines is low when the wind turbines are operated in grid-forming (GFM) mode instead of the standard grid-following mode. This paper explains the fundamental mechanism behind the improved damping characteristics by modeling the positive- and negative-sequence impedances of Type III wind turbines in GFM control mode. Here it is discovered that the GFM control naturally acts against the negative resistance behavior of Type III wind turbines at subsynchronous frequencies that results from an interaction between the rotor-side converter current controller and negative slip. The developed impedance models in the sequence domain and the improved damping behavior are verified using PSCAD simulations of a 2.5-MW Type III GFM wind turbine. The modeling predictions are also supported by experimentally measuring the impedance response of a 2.5-MW Type III wind turbine in GFM mode.
17 WIND ENERGY↗
Coherent Transfer of Lattice Entropy via Extreme Nonlinear Phononics in Metal Halide Perovskites
Entropy transfer in metal halide perovskites, characterized by significant lattice anharmonicity and low stiffness, underlies the remarkable properties observed in their optoelectronic applications, ranging from solar cells to lasers. The conventional view of this transfer involves stochastic processes occurring within a thermal bath of phonons, where the lattice arrangement and energy flow from higher- to lower-frequency modes. Here, we unveil a comprehensive chronological sequence detailing a conceptually distinct coherent transfer of entropy in a prototypical perovskite CH 3 NH 3 Pbl 3 . The terahertz periodic modulation imposes vibrational coherence into electronic states, leading to the emergence of mixed (vibronic) quantum beat between approximately 3 and 0.3 THz. We highlight a well-structured bidirectional time-frequency transfer of these diverse phonon modes, each developing at different times and transitioning from high to low frequencies from 3 to 0.3 THz, before reversing direction and ascending to around 0.8 THz. First-principles molecular dynamics simulations disentangle a complex web of coherent-phononic coupling pathways and identify the salient roles of the initial modes in shaping entropy evolution at later stages. Capitalizing on coherent entropy transfer and dynamic anharmonicity presents a compelling opportunity to exceed the fundamental thermodynamic (Shockley-Queisser) limit of photoconversion efficiency and to pioneer novel optoelectronic functionalities. Published by the American Physical Society 2024
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry
Tousled-like kinases (TLKs) are nuclear serine-threonine kinases essential for genome maintenance and proper cell division in animals and plants. A major function of TLKs is to phosphorylate the histone chaperone proteins ASF1a and ASF1b to facilitate DNA replication-coupled nucleosome assembly, but how TLKs selectively target these critical substrates is unknown. Here, we show that TLK2 selectivity towards ASF1 substrates is achieved in two ways. First, the TLK2 catalytic domain recognizes consensus phosphorylation site motifs in the ASF1 C-terminal tail. Second, a short sequence at the TLK2 N-terminus docks onto the ASF1a globular N-terminal domain in a manner that mimics its histone H3 client. Disrupting either catalytic or non-catalytic interactions through mutagenesis hampers ASF1 phosphorylation by TLK2 and cell growth. Our results suggest that the stringent selectivity of TLKs for ASF1 is enforced by an unusual interaction mode involving mutual recognition of a short sequence motifs by both kinase and substrate.
59 BASIC BIOLOGICAL SCIENCES↗
Radial oscillations of viscous neutron stars: Zero diffusion case
In this article, the spectrum of radial oscillations of neutron stars is systematically studied within two frameworks of viscous relativistic hydrodynamics: the relativistic Navier-Stokes and Israel-Stewart theories. A correspondence is established between the discrete stellar eigenmodes and the continuous dispersion relation of perturbations around a homogeneous fluid, providing a basis for interpreting our numerical results. We analyze the Newtonian limit and assess the impact of relativistic corrections, such as the gravitational redshifting of microscopic relaxation timescales. We show that bulk viscosity can significantly affect the behavior of both hydrodynamic and nonhydrodynamic fundamental modes, and that, depending on the magnitude of the viscous effects, it is the nonhydrodynamic mode that becomes unstable beyond the turning point in a sequence of equilibrium configurations. These results provide a useful step toward systematic studies of neutron star quasinormal modes in the presence of viscosity.
79 ASTRONOMY AND ASTROPHYSICS↗
Why the observed spin evolution of older-than-solar-like stars might not require a dynamo mode change
ABSTRACT The spin evolution of main-sequence stars has long been of interest for basic stellar evolution, stellar ageing, stellar activity, and consequent influence on companion planets. Observations of older-than-solar late-type main-sequence stars have been interpreted to imply that a change from a dipole-dominated magnetic field to one with more prominent higher multipoles might be necessary to account for the data. The spin-down models that lead to this inference are essentially tuned to the Sun. Here, we take a different approach that considers individual stars as fixed points rather than just the Sun. We use a time-dependent theoretical model to solve for the spin evolution of low-mass main-sequence stars that includes a Parker-type wind and a time-evolving magnetic field coupled to the spin. Because the wind is exponentially sensitive to the stellar mass over radius and the coronal base temperature, the use of each observed star as a separate fixed point is more appropriate and, in turn, produces a set of solution curves that produces a solution envelope rather than a simple line. This envelope of solution curves, unlike a single line fit, is consistent with the data and does not unambiguously require a modal transition in the magnetic field to explain it.
Astronomy & Astrophysics↗
Stochastic transition in synchronized spiking nanooscillators
This work reports that synchronization of Mott material-based nanoscale coupled spiking oscillators can be drastically different from that in conventional harmonic oscillators. We investigated the synchronization of spiking nanooscillators mediated by thermal interactions due to the close physical proximity of the devices. Controlling the driving voltage enables in-phase 1:1 and 2:1 integer synchronization modes between neighboring oscillators. Transition between these two integer modes occurs through an unusual stochastic synchronization regime instead of the loss of spiking coherence. In the stochastic synchronization regime, random length spiking sequences belonging to the 1:1 and 2:1 integer modes are intermixed. The occurrence of this stochasticity is an important factor that must be taken into account in the design of large-scale spiking networks for hardware-level implementation of novel computational paradigms such as neuromorphic and stochastic computing.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Deformation and fracture behavior of a laser powder bed fusion processed stainless steel: In situ synchrotron x-ray computed microtomography study
Tensile plastic deformation and fracture behavior of a laser powder bed fusion processed 316L stainless steel alloy was investigated in situ using high-resolution synchrotron x-ray computed microtomography (sXCT). Three different cases were studied: (1) specimen A1, near full-density with initial porosity of 0.04%, (2) specimen B1, initial lack-of-fusion (LOF) porosity of about 3% with the major axis of defects aligned nearly perpendicular to the tensile loading direction (LD), and (3) specimen B, similar to B1 but with the major axis of LOF defects aligned nearly parallel to LD. The effects of type, density, and orientation of defects in as-printed samples on plastic deformation and failure modes were studied by analyzing sXCT image sequences and quantitative defect properties. Specifically, the evolutions of porosity, size, aspect ratio, and angle of gas pores and LOF defects were characterized as a function of applied strain. Moreover, interactions between as-printed defects and deformation-induced crack propagation were investigated. The tensile behavior of specimen A1 was comparable to that of a commercial wrought plate. Furthermore, the quantitative in-situ sXCT results showed a void-growth phenomenon in A1 but without noticeable coalescence, resulting in a ductile cup-cone failure. Specimen B1 showed damage-driven brittle failure with limited plasticity due to early and rapid propagation of open voids. On the other hand, specimen B, with a similar amount of LOF defects as B1, showed deceivingly strong and ductile tensile behavior similar to A1 without any major crack propagations due to the favorable orientation relationship between LOF defects and the LD.
36 MATERIALS SCIENCE↗
Heteroepitaxial chemistry of zinc chalcogenides on InP nanocrystals for defect-free interfaces with atomic uniformity
Heteroepitaxy on colloidal semiconductor nanocrystals is an essential strategy for manipulating their optoelectronic functionalities. However, their practical synthesis typically leads to scattered and unexpected outcomes due to the intervention of multiple reaction pathways associated with complicated side products of reactants. Here, the heteroepitaxy mechanism of zinc chalcogenide initiated on indium phosphide (InP) colloidal nanocrystals is elucidated using the precursors, zinc carboxylate and trialkylphosphine selenide. The high magnetic receptivity of 77 Se and the characteristic longitudinal optical phonon mode of ZnSe allowed for monitoring the sequence of epilayer formation at the molecular level. The investigation revealed the sterically hindered acyloxytrialkylphosphonium and diacyloxytrialkylphosphorane to be main intermediates in the surface reaction, which retards the metal ion adsorption by a large steric hindrance. The transformation of adsorbates to the crystalline epilayer was disturbed by surface oxides. Raman scattering disclosed the pathway of secondary surface oxidation triggered by carboxylate ligands migrated from zinc carboxylate. The surface-initiated heteroepitaxy protocol is proposed to fabricate core/shell heterostructured nanocrystals with atomic-scale uniformity of epilayers. Despite the large lattice mismatch of ZnS to InP, we realised a uniform and interface defect-free ZnS epilayer (~0.3 nm thickness) on InP nanocrystals, as evidenced by a high photoluminescence quantum yield of 97.3%.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Direct observation of the exotic β – γ – α decay mode in the T z = – 1 nucleus Na 20
The exotic β – γ – α decay mode of 20 Na has been directly observed for the first time in the Day-one experiment at the Beijing Radioactive Ion-beam Facility. The 20 Na source was produced by using a 100-MeV proton beam bombarding a stack of microporous MgO thick target and delivered as an intense mass separated beam after online ionization. A high-efficiency simultaneous measurement of β, γ, and α transitions enables the β-delayed γ – γ and α – γ coincidence spectroscopy. Here three β – γ – α exotic decay sequences in 20 Na are discovered, which expands the rare decay modes observed in β decay. Moreover, a β – α –decay sequence to the 6130-keV 3 – state of 16 O is observed, which is likely through the 12367-keV 1 + state in 20 Ne. The experimentally deduced B(F) and B(GT) are compared to the shell-model calculation, the allowed β transition strengths can be well accounted for by using sd shell-model space interactions.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
On resistive interchange, double tearing, and resonant and non-resonant infernal modes in spherical tokamak negative central shear discharges
We examine the linear and nonlinear stability of a sequence of reversed shear NSTX equilibria with the same toroidal current density and pressure profile but with different toroidal field strengths. All equilibria have two q = 2 surfaces and have q > 1 everywhere. For this sequence, which all have β P ∼ 0.5, as the minimum value of q decreases below about 1.4, the localized resistive interchange criterion is strongly violated, and the unstable mode with toroidal mode number n=1 changes its dominant poloidal mode number m from a (m,n)=(2,1) double tearing mode to a non-resonant (1,1) infernal mode. This (1,1) mode nonlinearly flattens both the current density and the pressure near the magnetic axis. The higher-n unstable modes are all resistive infernal modes localized around the surface where q has a minimum and the magnetic shear vanishes. They generally saturate nonlinearly at low amplitude but can cause magnetic surface breakup near the axis.
Spitzer resistivity↗
Collective modes of excitation in 64 Cu
Medium and high-spin level sequences in 64 Cu were investigated using the complex 26 Mg( 48 Ca, αp5nγ ) multinucleon transfer reaction. The experiment was performed at the ATLAS accelerator facility at the Argonne National Laboratory using the Gammasphere array and the fragment mass analyzer (FMA). Two high-spin, quasirotational bands consisting of stretched-E2 transitions were observed in coincidence with the known low-spin structure for the first time. These bands share remarkable similarities with highly deformed and/or superdeformed bands observed in the A ≈ 60–70 mass region. In addition, a regular dipole sequence with weak E2 crossover transitions was observed. A general discussion of the observed structures, complemented by theoretical calculations carried out within the framework of the adiabatic and configuration-fixed constrained covariant density functional theory and the quantum particle-rotor model, are presented. Furthermore, the results are interpreted in the context of shell-structure evolution and the collectivity in the mass region.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Granger Causality for prediction in Dynamic Mode Decomposition: Application to power systems
Here, the dynamic mode decomposition (DMD) technique extracts the dominant modes characterizing the innate dynamical behavior of the system within the measurement data. For appropriate identification of dominant modes from the measurement data, the DMD algorithm necessitates ensuring the quality of the input measurement data sequences. On that account, for validating the usability of the dataset for the DMD algorithm, the paper proposed two conditions: Persistence of excitation (PE) and the Granger Causality Test (GCT). The virtual data sequences are designed with the hankel matrix representation such that the dimensions of the subspace spanning the essential system modes are increased with the addition of new state variables. The PE condition provides the lower bound for the trajectory length, and the GCT provides the order of the model. Satisfying the PE condition enables estimating an approximate linear model, but the predictability with the identified model is only assured with the temporal causation among data searched with GCT. The proposed methodology is validated with the application for coherency identification (CI) in a multi-machine power system (MMPS), an essential phenomenon in transient stability analysis. The significance of PE condition and GCT is demonstrated through various case studies implemented on 22 bus six generator system.
24 POWER TRANSMISSION AND DISTRIBUTION↗