bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of ion temperature gradient driven modes with 6D kinetic Vlasov code
Authors: Raeth M. , Hallatschek K. , Kormann K.
Published: April 2024

With the increase in computational capabilities over the last few years, it becomes possible to simulate more and more complex and accurate physical models. Gyrokinetic theory has been introduced in the 1960s and 1970s in the need of describing a plasma with more accurate models than fluid equations but eliminating the complexity of the fast gyration about the magnetic field lines. Although results from current gyrokinetic computer simulations are in fair agreement with experimental results in core physics, crucial assumptions made in the derivation make it unreliable in regimes of higher fluctuations and stronger gradient, such as the tokamak edge. With our novel optimized and scalable semi-Lagrangian solver, we are able to simulate ion temperature gradient modes with the 6D kinetic model including the turbulent saturation. After thoroughly testing our simulation code against analytical computations and gyrokinetic simulations (with the gyrokinetic code GYRO), it has been possible to show first plasma properties that go beyond standard gyrokinetic simulations. This includes the explicit description of the complete perpendicular energy fluxes and the excitation of high-frequency waves (around the Larmor frequency) in the nonlinear saturation phase.
Coherent phonon signal amplification technique based on a numerical differentiation method
Authors: Wu Junhui , Wang Shuai , Li Kang , Wang Jiawei , Duan Jianan , Xu Xiaochuan , He Feng
Published: April 2024

Coherent optical phonon (COP) and coherent acoustic phonon (CAP) play vital roles in probing ultrafast dynamics across various materials and systems. Their applications range from metamaterial diagnosis to manipulating ferroelectric polarization and self-trapping of carriers in perovskites. However, the inherently small signals associated with COP and CAP pose challenges in extracting valuable information. In this paper, we address this challenge by presenting a numerical differential method for signal amplification and deduction of phonon dephasing time. In addition, application of this method has been demonstrated in a superlattice system, establishing the validity and effectiveness of this technique.
Design of experiments to spectroscopically characterize radiation flow in stochastic media
Authors: Byvank T. , Coffing S. X. , Lioce D. A. , Fryer C. L. , Fontes C. J. , Kozlowski P. M. , Johns H. M. , Čamdžić Dž. , Elshafiey A. T. , Meyerhofer D. D. , Robey H. F. , Feltman J. M. , Recamier C. L. , Barnak D. H. , Hamilton C. E. , Edwards S. L. , Love K. N. , Patterson B. M. , Farhi B. Y. , Jones B. J. , Cleveland J. W. , Day T. H. , Quintana T. E. , Wong C. H. , Christiansen N. S. , Schmidt D. W. , Prinja A. K. , Urbatsch T. J.
Published: April 2024

Precise characterization of experimental radiation flow is required to validate the high energy density physics models, numerical methods, and codes that are used to simulate radiation-hydrodynamics phenomena such as thermal radiation transport in stochastic media. The Cassio code is used to simulate thermal radiation flow through inhomogeneous, stochastic-media-foam configurations containing optically thick clumps dispersed within an optically thin background aerogel. Cassio can model small inhomogeneous problems directly, but most problems require approximations to meet computer limitations on run-times and memory usage. Various examples of these approximations are methods that produce, in one calculation, an ensemble-averaged solution and associated standard deviation; reduced spatial dimensionality with approximate geometries; and full material homogenization with no geometric detail. Cassio simulations are used to design experiments at the OMEGA-60 Laser Facility that can measure the radiation flow using the spatially resolved COAX absorption spectroscopy diagnostic. The experimental platforms flow radiation through foam targets ranging from a background-only aerogel, to a single configuration of a specified stochastic medium, to a fully homogenized foam of the background and clump materials. Under constant total clump mass, larger clumps (here, larger than 10 μm diameter) will mix more slowly with the background such that the bulk radiation flow is faster than it would be in a fully homogenized material. The COAX platform can be used to infer temperature and density profiles in both the background material and clumps, simultaneously, and therefore to differentiate radiation flow in a range of stochastic and homogeneous media.
Numerical study on drag and heat flux reduction induced by a counterflowing jet for rarefied hypersonic flow over a blunt body
Authors: Guo Guangming , Luo Qin , Wu Jinwu
Published: April 2024

This paper focuses on the drag and heat flux reduction induced by a counterflowing jet located on the leading edge of the blunt body head in rarefied hypersonic flows using the direct simulation Monte Carlo method. Flow structures in the flowfield, such as detached shock wave, Mach disk, contact surface, jet layer, and recompression shock wave, are all weakened gradually with the increase in the freestream altitude, and they eventually disappear at the altitude of 90 km. The increase in the jet pressure provides a great drag reduction by up to 53% when it increases from 800 to 1600 Pa, but the proportion of drag on the blunt body head to the total drag is only affected slightly by the jet pressure. A noteworthy finding is that further increasing jet pressure almost have no effect on heat flux variation when it is larger than 1200 Pa. On the whole, jet temperature has a quite weak influence on both flow structures and drag, while heat flux on the blunt body head is closely related to jet temperature. The results suggest that jet temperature should vary with that of blunt body surface, and moreover, the optimal jet temperature should be moderately lower than the wall surface temperature. In addition, increasing freestream altitude can provide excellent performance of drag reduction, but it causes non-monotonic variation of heat flux. In view of this, it is worth noting that heat flux on the blunt body head actually increases with altitude when the blunt body is in a severely rarefied atmospheric environment, such as the altitude H > 70 km.
The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics
Authors: Bondanza Mattia , Nottoli Tommaso , Nottoli Michele , Cupellini Lorenzo , Lipparini Filippo , Mennucci Benedetta
Published: April 2024

We present a new library designed to provide a simple and straightforward way to implement QM/AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) and other polarizable QM/MM (Molecular Mechanics) methods based on induced point dipoles. The library, herein referred to as OpenMMPol, is free and open-sourced and is engineered to address the increasing demand for accurate and efficient QM/MM simulations. OpenMMPol is specifically designed to allow polarizable QM/MM calculations of ground state energies and gradients and excitation properties. Key features of OpenMMPol include a modular architecture facilitating extensibility, parallel computing capabilities for enhanced performance on modern cluster architectures, a user-friendly interface for intuitive implementation, and a simple and flexible structure for providing input data. To show the capabilities offered by the library, we present an interface with PySCF to perform QM/AMOEBA molecular dynamics, geometry optimization, and excited-state calculation based on (time-dependent) density functional theory.
Rapid simulation of two-dimensional spectra with correlated anisotropic dimensions
Authors: Srivastava Deepansh J. , Baltisberger Jay H. , Grandinetti Philip J.
Published: April 2024

A new algorithm has been developed to simulate two-dimensional (2D) spectra with correlated anisotropic frequencies faster and more accurately than previous methods. The technique uses finite-element numerical integration on the sphere and an interpolation scheme based on the Alderman–Solum–Grant algorithm. This method is particularly useful for numerical calculations of joint probability distribution functions involving quantities with a parametric orientation dependence. The technique’s efficiency also allows for practical least-squares fitting of experimental 2D solid-state nuclear magnetic resonance (NMR) datasets. The simulation method is illustrated for select 2D NMR methods, and a least-squares analysis is demonstrated in the extraction of paramagnetic shift and quadrupolar coupling tensors and their relative orientation from the experimental shifting-d echo 2H NMR spectrum of a NiCl2 · 2D2O salt.
An analysis of double-quantum coherence ESR in an N-spin system: Analytical expressions and predictions
Authors: Sinha Roy Aritro , Marohn John A. , Freed Jack H.
Published: April 2024

Electron spin resonance pulsed dipolar spectroscopy (PDS) has become popular in protein 3D structure analysis. PDS studies yield distance distributions between a pair or multiple pairs of spin probes attached to protein molecules, which can be used directly in structural studies or as constraints in theoretical predictions. Double-quantum coherence (DQC) is a highly sensitive and accurate PDS technique to study protein structures in the solid state and under physiologically relevant conditions. In this work, we have derived analytical expressions for the DQC signal for a system with N-dipolar coupled spin-1/2 particles in the solid state. The expressions are integrated over the relevant spatial parameters to obtain closed form DQC signal expressions. These expressions contain the concentration-dependent “instantaneous diffusion” and the background signal. For micromolar and lower concentrations, these effects are negligible. An approximate analysis is provided for cases of finite pulses. The expressions obtained in this work should improve the analysis of DQC experimental data significantly, and the analytical approach could be extended easily to a wide range of magnetic resonance phenomena.
Master equation modeling of blackbody infrared radiative dissociation (BIRD) of hydrated peroxycarbonate radical anions
Authors: Salzburger Magdalena , Hütter Michael , van der Linde Christian , Ončák Milan , Beyer Martin K.
Published: April 2024

Molecular cluster ions, which are stored in an electromagnetic trap under ultra-high vacuum conditions, undergo blackbody infrared radiative dissociation (BIRD). This process can be simulated with master equation modeling (MEM), predicting temperature-dependent dissociation rate constants, which are very sensitive to the dissociation energy. We have recently introduced a multiple-well approach for master equation modeling, where several low-lying isomers are taken into account. Here, we experimentally measure the BIRD of CO4●–(H2O)1,2 and model the results with a slightly modified multiple-well MEM. In the experiment, we exclusively observe loss of water from CO4●–(H2O), while the BIRD of CO4●–(H2O)2 leads predominantly to loss of carbon dioxide, with water loss occurring to a lesser extent. The MEM of two competing reactions requires empirical scaling factors for infrared intensities and the sum of states of the loose transition states employed in the calculation of unimolecular rate constants so that the simulated branching ratio matches the experiment. The experimentally derived binding energies are ΔH0(CO4●––H2O) = 45 ± 3 kJ/mol, ΔH0(CO4●–(H2O)–H2O) = 41 ± 3 kJ/mol, and ΔH0(CO2–O2●–(H2O)2) = 37 ± 3 kJ/mol. Quantum chemical calculations on the CCSD(T)/aug-cc-pVTZ//CCSD/aug-cc-pVDZ level, corrected for the basis set superposition error, yield binding energies that are 2–5 kJ/mol higher than experiment, within error limits of both experiment and theory. The relative activation energies for the two competing loss channels are as well fully consistent with theory.
Global micro-tearing modes in the wide pedestal of an NSTX plasma
Authors: Dominski J. , Guttenfelder W. , Hatch D. , Goerler T. , Jenko F. , Munaretto S. , Kaye S.
Published: April 2024

Global linear electromagnetic gyrokinetic simulations of micro-tearing modes (MTMs) growing in the wide pedestal of the ELM-free NSTX discharge #132 588 are reported. Two micro-tearing branches growing near the surfaces of safety factor q = 4 (pedestal top) and q=5–6 (pedestal) are simulated. The frequencies of these MTMs with low toroidal mode number (n ranging from 3 to 6) are in agreement with the ones of quasi-coherent fluctuations present on the magnetic spectrogram. No kinetic ballooning mode (KBM) is observed at experimental values of β; instead, the experimental plasma lies 20% below the critical global KBM threshold. This confirms local simulation results stating that experimental NSTX profiles lie in the KBM stability region. Carbon impurities, which are abundant in this plasma, were found to play a significant role. Neglecting them leads to a ∼50% error in the growth rates.
Performance study of variational quantum linear solver with an improved ansatz for reservoir flow equations
Authors: Rao Xiang
Published: April 2024

This paper studies the performance of the variational quantum linear solver (VQLS) with an improved ansatz for discretized reservoir flow equations for the first time. First, we introduce the two typical flow equations in reservoir simulation, namely, the diffusion equation for pressure and the convection-dominated Buckley–Leverett equation for water saturation, and their commonly used finite volume or finite difference-based discretized linear equations. Then, we propose an improved ansatz in VQLS to enhance the convergence and accuracy of VQLS and a strategy of adjusting grid order to reduce the complexity of the quantum circuit for preparing the quantum state corresponding to the coefficient vector of the discretized reservoir flow equations. Finally, we apply the modified VQLS to solve the discretized reservoir flow equations by employing the Xanadu's PennyLane open-source library. Four numerical examples are implemented, and the results show that VQLS can calculate reservoir flow equations with high accuracy, and the improved ansatz significantly outperforms the original one. Moreover, we study the effects of reservoir heterogeneity, the number of ansatz layers, the equation type, and the number of shots on the computational performance. Limited by the current computing capacity, the number of grids subject to the involved number of quantum bits in the implemented examples is small; we will further explore this quantum algorithm to practical examples that require a large number of quantum bits in the future.
Anionic oxyl radical formed on CrVI-oxo anchored on the defect site of the UiO-66 node facilitates methane to methanol conversion
Authors: Qin Yuyao , Li Liwen , Liu Huixian , Han Jinyu , Wang Hua , Zhu Xinli , Ge Qingfeng
Published: April 2024

The direct conversion of methane to methanol has attracted increasing interest due to abundant and low-cost natural gas resources. Herein, by anchoring Cr-oxo/-oxyhydroxides on UiO-66 metal–organic frameworks, we demonstrate that reactive anionic oxyl radicals can be formed by controlling the coordination environment based on the results of density functional theory calculations. The anionic oxyl radicals produced at the completely oxidized CrVI site acted as the active species for facile methane activation. The thermodynamically stable CrVI-oxo/-oxyhydroxides with the anionic oxyl radicals catalyze the activation of the methane C–H bond through a homolytic mechanism. An analysis of the results showed that the catalytic performance of the active oxyl species correlates with the reaction energy of methane activation and H adsorption energies. Following methanol formation, N2O can regenerate the active sites on the most stable CrVI oxyhydroxides, i.e., the Cr(O)4Hf species. The present study demonstrated that the anionic oxyl radicals formed on the anchored CrVI oxyhydroxides by tuning the coordination environment enabled facile methane activation and facilitated methanol production.
Evolution of cooperation on reinforcement-learning driven-adaptive networks
Authors: Du Chunpeng , Lu Yikang , Meng Haoran , Park Junpyo
Published: April 2024

Complex networks are widespread in real-world environments across diverse domains. Real-world networks tend to form spontaneously through interactions between individual agents. Inspired by this, we design an evolutionary game model in which agents participate in a prisoner’s dilemma game (PDG) with their neighboring agents. Agents can autonomously modify their connections with neighbors using reinforcement learning to avoid unfavorable environments. Interestingly, our findings reveal some remarkable results. Exploiting reinforcement learning-based adaptive networks improves cooperation when juxtaposed with existing PDGs performed on homogeneous networks. At the same time, the network’s topology evolves from homogeneous to heterogeneous states. This change occurs as players gain experience from past games and become more astute in deciding whether to join PDGs with their current neighbors or disconnect from the least profitable neighbors. Instead, they seek out more favorable environments by establishing connections with second-order neighbors with higher rewards. By calculating the degree distribution and modularity of the adaptive network in a steady state, we confirm that the adaptive network follows a power law and has a clear community structure, indicating that the adaptive network is similar to networks in the real world. Our study reports a new phenomenon in evolutionary game theory on networks. It proposes a new perspective to generate scale-free networks, which is generating scale-free networks by the evolution of homogeneous networks rather than typical ways of network growth and preferential connection. Our results provide new aspects to understanding the network structure, the emergence of cooperation, and the behavior of actors in nature and society.
Geometry-dependent acoustic higher-order topological phases on a two-dimensional honeycomb lattice
Authors: Wu Shi-Qiao , Lin Zhi-Kang , Li Yongyao , Xie Jianing
Published: April 2024

Higher-order topological states, as emergent topological phases of matter, originating from condensed matter physics, have sparked a vibrant exploration of topological insulators. Their topologically protected multidimensional localized states are typically associated with nontrivial bulk band topology, and the significant impact of lattice geometry is unconsciously overlooked. Here, we construct coupled acoustic cavities on a two-dimensional honeycomb lattice to investigate the sensitivity of higher-order topological modes to the variations of edge contour. Fractional charge is utilized to accurately predict topological modes with distinct topological orders, in spite of the minimal bulk bandgaps inherent in the honeycomb lattice and bound states in the continuum. It is found that the presence and absence of the first-order and higher-order topological modes in the same topological phase are tightly linked to the sample boundaries, which can be demonstrated by both theoretical analysis and numerical calculation. Our study also discusses potential physical realization of geometry-dependent topological states across different platforms, providing inspiration for the prospective application of topological devices in acoustics.
Large eddy simulations of turbulence diffusion within the smoothed particle hydrodynamics
Authors: Meringolo Domenico Davide , Aristodemo Francesco , Servidio Sergio , Filianoti Pasquale Giuseppe F.
Published: April 2024

We present the modeling of the main facets of turbulence diffusion, i.e., diffusion of momentum, mass, density, and heat, within the smoothed particle hydrodynamics (SPH) method. The treatment is developed considering the large eddy simulation (LES) approach and is specifically founded on the δ-LES-SPH [A. Di Mascio et al., Phys. Fluids 29, 035102 (2017)], a model characterized by a turbulence closure for the continuity equation. The novelties introduced are the modeling of the advection–diffusion equation through turbulent mass diffusivity and the modeling of the internal energy equation through heat eddy diffusivity. Moreover, a calibration for the closure term of the continuity equation is also proposed, based on the physical assumption of equivalence between turbulent mass and density diffusion rates. Three test cases are investigated. The first test regards a two-dimensional (2D) problem with splashing and wave-breaking dynamics, which is used to investigate the proposed calibration for the turbulent density diffusion term. In the second test, a 2D jet in coflow condition without gravity is studied with particular emphasis on the advection–diffusion process. The last test regards the most general condition and reproduces three-dimensional (3D) jets in crossflow conditions, in which attention is given to both the mass and heat advection–diffusion processes. The proposed methodology, which allowed us to accurately reproduce the experimental tests considered, represents a promising approach for future investigation of problems characterized by complex dynamics with turbulence and mixing involved.
Measurements of dense fuel hydrodynamics in the NIF burning plasma experiments using backscattered neutron spectroscopy
Authors: Crilly A. J. , Schlossberg D. J. , Appelbe B. D. , Moore A. S. , Jeet J. , Kerr S. , Rubery M. , Lahmann B. , O'Neill S. , Forrest C. J. , Mannion O. M. , Chittenden J. P.
Published: April 2024

The hydrodynamics of the dense confining fuel shell is of great importance in defining the behavior of the burning plasma and burn propagation regimes of inertial confinement fusion experiments. However, it is difficult to probe due to its low emissivity in comparison with the central fusion core. In this work, we utilize the backscattered neutron spectroscopy technique to directly measure the hydrodynamic conditions of the dense fuel during fusion burn. Experimental data are fit to obtain dense fuel velocities and apparent ion temperatures. Trends of these inferred parameters with yield and velocity of the burning plasma are used to investigate their dependence on alpha heating and low mode drive asymmetry. It is shown that the dense fuel layer has an increased outward radial velocity as yield increases, showing that burn has continued into re-expansion, a key signature of hotspot ignition. A comparison with analytic and simulation models shows that the observed dense fuel parameters are displaying signatures of burn propagation into the dense fuel layer, including a rapid increase in dense fuel apparent ion temperature with neutron yield.
Revealing localized excitons in WSe2/β-Ga2O3
Authors: Cavalini Camila , Rabahi Cesar , de Brito Caique S. , Lee Eunji , Toledo José R. , Cazetta Felipe F. , Fernandes de Oliveira Raphael B. , Andrade Marcelo B. , Henini Mohamed , Zhang Yuhao , Kim Jeongyong , Barcelos Ingrid D. , Galvão Gobato Yara
Published: April 2024

We have investigated the optical and magneto-optical properties of monolayer (ML) WSe2 on flakes of β-Ga2O3 under high magnetic fields. Remarkably, sharp emission peaks were observed and associated with localized excitons related to point defects. A detailed study of low-temperature photoluminescence (PL) and magneto-PL under high perpendicular magnetic field up to 9 T was carried out. Several sharp emission peaks have shown valley g-factors values close to −4, which is an unusual result for localized excitons in WSe2. Furthermore, some PL peaks have shown higher g-factor values of ≈−7 and ≈−12, which were associated with the hybridization of strain localized dark excitons and defects. The reported results suggest that β-Ga2O3 is, indeed, a promising dielectric substrate for ML WSe2 and also to explore fundamental physics in view of possible applications in quantum information technology.
Cross-influence of cavitation and flow rate on pressure pulsation of a volute mixed flow pump
Authors: Zheng Yunhao , Li Yanjun , Zhang Fan , Yuan Shouqi
Published: April 2024

Mixed-flow pump is a general purpose hydraulic machinery in many fields of fluid transport for its advantages of wide efficient operation flow rate range, but its operation stability is restricted by cavitation. To obtain the cross effect of cavitation and flow rate on its pressure pulsation, a high-precision experimental system was first established to monitor the pressure signals at four key positions, obtaining their time domain; second, based on this tested results, time frequency domain analysis technique based on continuous wavelet transform was adopted to capture the temporal evolution; third, wavelet coherence value analysis was further adopted to diagnose the cavitation development speed at different spatial positions. Primary findings are as follows: (1) the secondary peaks induced by cavitation generated the discrete disturbance in low-frequency range, and the amplitudes at shaft frequency and blade passing frequency were both increased, with a worse time continuity. (2) Under 1.0 QBEP, the mixed flow pump had a best anti-cavitation performance. Under 0.8 QBEP, its internal flow pattern was easily to be disturbed by cavitation flow, while that under 1.2 QBEP had the fastest cavitation development speed. (3) Under the action of unstable potential flow, within the flow field near the rotor–static interface and the downstream, a close flow exchange was established between the cavitation bubbles and mainstream; thus, the pressure pulsation inside the volute became more sensitive to the cavitation development.
Embracing interactive teaching methods
Authors: Chasteen Stephanie , Prather Edward , Scherr Rachel
Published: April 2024

New physics and astronomy faculty are excited about active teaching, but they still need support to implement the ideas in their classes.
The sinister side of weather data
Authors: Suits Robert
Published: April 2024

Immeasurable Weather: Meteorological Data and Settler Colonialism from 1820 to Hurricane Sandy, Sara J. Grossman
Attosecond analysis illuminates a watery mystery
Authors: Miller Johanna L.
Published: April 2024

With powerful x-ray free-electron lasers, researchers are making great strides in ultrafast spectroscopy—with lessons about how molecules arrange themselves at rest.
Significant shifts in latitudinal optima of North American birds
Authors: Martins Paulo Mateus , Anderson Marti J. , Sweatman Winston L. , Punnett Andrew J.
Published: April 2024

Changes in climate can alter environmental conditions faster than most species can adapt. A prediction under a warming climate is that species will shift their distributions poleward through time. While many studies focus on range shifts, latitudinal shifts in species’ optima can occur without detectable changes in their range. We quantified shifts in latitudinal optima for 209 North American bird species over the last 55 y. The latitudinal optimum (
m
) for each species in each year was estimated using a bespoke flexible non-linear zero-inflated model of abundance vs. latitude, and the annual shift in
m
through time was quantified. One-third (70) of the bird species showed a significant shift in their optimum. Overall, mean peak abundances of North American birds have shifted northward, on average, at a rate of 1.5 km per year (±0.58 SE), corresponding to a total distance moved of 82.5 km (±31.9 SE) over the last 55 y. Stronger poleward shifts at the continental scale were linked to key species’ traits, including thermal optimum, habitat specialization, and territoriality. Shifts in the western region were larger and less variable than in the eastern region, and they were linked to species’ thermal optimum, habitat density preference, and habitat specialization. Individual species’ latitudinal shifts were most strongly linked to their estimated thermal optimum, clearly indicating a climate-driven response. Displacement of species from their historically optimal realized niches can have dramatic ecological consequences. Effective conservation must consider within-range abundance shifts. Areas currently deemed “optimal” are unlikely to remain so.
Social media influences National Park visitation
Authors: Wichman Casey J.
Published: April 2024

Visitation to National Parks in the United States increased by more than 25% since 2010, rising from roughly 70 to 90 million annual visitors. Anecdotes suggest that this increase was driven by the advent of social media in the early-to-mid 2010s, generating a new form of exposure for parks, and has led to concerns about overcrowding and degradation of environmental quality. However, there is little empirical evidence on the role of social media in influencing recreation decisions. Here, I construct a dataset on social media exposure (SME) for each National Park and relate that exposure to changes in visitation over the last two decades. High SME parks see visitation increase by 16 to 22% relative to parks with less exposure, which comes with a concomitant increase in revenue. Low SME parks have no, or negative, changes in visitation. These estimates account for unobserved park heterogeneity and are based on an instrumental variables strategy that predicts exposure with a park’s online popularity prior to the social media era. Additional analysis suggests that recent social media posts that include media attachments increase visitation, while posts with negative sentiment reduce visitation. These results provide insight for the National Park Service—which faces more than $22 billion in deferred maintenance costs and is considering policy options to manage demand—as well as for management of recreation on other public lands.
Deletion of the
TMEM30A
gene enables leukemic cell evasion of NK cell cytotoxicity
Authors: Kristenson Linnea , Badami Chiara , Ljungberg Angelica , Islamagic Erna , Tian Yarong , Xie Guojiang , Hussein Brwa Ali , Pesce Silvia , Tang Ka-Wei , Thorén Fredrik B.
Published: April 2024

Natural killer (NK) cell immunotherapy has gained attention as a promising strategy for treatment of various malignancies. In this study, we used a genome-wide CRISPR screen to identify genes that provide protection or susceptibility to NK cell cytotoxicity. The screen confirmed the role of several genes in NK cell regulation, such as genes involved in interferon-γ signaling and antigen presentation, as well as genes encoding the NK cell receptor ligands B7-H6 and CD58. Notably, the gene
TMEM30A
, encoding CDC50A–beta-subunit of the flippase shuttling phospholipids in the plasma membrane, emerged as crucial for NK cell killing. Accordingly, a broad range of
TMEM30A
knock-out (KO) leukemia and lymphoma cells displayed increased surface levels of phosphatidylserine (PtdSer).
TMEM30A
KO cells triggered less NK cell degranulation, cytokine production and displayed lower susceptibility to NK cell cytotoxicity. Blockade of PtdSer or the inhibitory receptor TIM-3, restored the NK cell ability to eliminate
TMEM30A
-mutated cells. The key role of the TIM-3 – PtdSer interaction for NK cell regulation was further substantiated by disruption of the receptor gene in primary NK cells, which significantly reduced the impact of elevated PtdSer in
TMEM30A
KO leukemic cells. Our study underscores the potential significance of agents targeting the interaction between PtdSer and TIM-3 in the realm of cancer immunotherapy.
Evidence of antigenic drift in the fusion machinery core of SARS-CoV-2 spike
Authors: Tan Timothy J. C. , Verma Abhishek K. , Odle Abby , Lei Ruipeng , Meyerholz David K. , Matreyek Kenneth A. , Perlman Stanley , Wong Lok-Yin Roy , Wu Nicholas C.
Published: April 2024

Antigenic drift of SARS-CoV-2 is typically defined by mutations in the N-terminal domain and receptor binding domain of spike protein. In contrast, whether antigenic drift occurs in the S2 domain remains largely elusive. Here, we perform a deep mutational scanning experiment to identify S2 mutations that affect binding of SARS-CoV-2 spike to three S2 apex public antibodies. Our results indicate that spatially diverse mutations, including D950N and Q954H, which are observed in Delta and Omicron variants, respectively, weaken the binding of spike to these antibodies. Although S2 apex antibodies are known to be nonneutralizing, we show that they confer protection in vivo through Fc-mediated effector functions. Overall, this study indicates that the S2 domain of SARS-CoV-2 spike can undergo antigenic drift, which represents a potential challenge for the development of more universal coronavirus vaccines.
The dawn of the tropical Atlantic invasion into the Mediterranean Sea
Authors: Albano Paolo G. , Schultz Lotta , Wessely Johannes , Taviani Marco , Dullinger Stefan , Danise Silvia
Published: April 2024

The Mediterranean Sea is a marine biodiversity hotspot already affected by climate-driven biodiversity collapses. Its highly endemic fauna is at further risk if global warming triggers an invasion of tropical Atlantic species. Here, we combine modern species occurrences with a unique paleorecord from the Last Interglacial (135 to 116 ka), a conservative analog of future climate, to model the future distribution of an exemplary subset of tropical West African mollusks, currently separated from the Mediterranean by cold upwelling off north-west Africa. We show that, already under an intermediate climate scenario (RCP 4.5) by 2050, climatic connectivity along north-west Africa may allow tropical species to colonize a by then largely environmentally suitable Mediterranean. The worst-case scenario RCP 8.5 leads to a fully tropicalized Mediterranean by 2100. The tropical Atlantic invasion will add to the ongoing Indo-Pacific invasion through the Suez Canal, irreversibly transforming the entire Mediterranean into a novel ecosystem unprecedented in human history.
Development of an aptamer capable of multidrug resistance reversal for tumor combination chemotherapy
Authors: Wen Xiaohong , Huang Zhixiang , Yang Xiaohai , He Xiaoxiao , Li Lie , Chen Haiyan , Wang Kemin , Guo Qiuping , Liu Jianbo
Published: April 2024

Multidrug resistance (MDR) is a major factor in the failure of many forms of tumor chemotherapy. Development of a specific ligand for MDR-reversal would enhance the intracellular accumulation of therapeutic agents and effectively improve the tumor treatments. Here, an aptamer was screened against a doxorubicin (DOX)-resistant human hepatocellular carcinoma cell line (HepG2/DOX) via cell-based systematic evolution of ligands by exponential enrichment. A 50 nt truncated sequence termed d3 was obtained with high affinity and specificity for HepG2/DOX cells. Multidrug resistance protein 1 (MDR1) is determined to be a possible recognition target of the selected aptamer. Aptamer d3 binding was revealed to block the MDR of the tumor cells and increase the accumulation of intracellular anticancer drugs, including DOX, vincristine, and paclitaxel, which led to a boost to the cell killing of the anticancer drugs and lowering their survival of the tumor cells. The aptamer d3-mediated MDR-reversal for effective chemotherapy was further verified in an in vivo animal model, and combination of aptamer d3 with DOX significantly improved the suppression of tumor growth by treating a xenograft HepG2/DOX tumor in vivo. This work demonstrates the feasibility of a therapeutic DNA aptamer as a tumor MDR-reversal agent, and combination of the selected aptamer with chemotherapeutic drugs shows great potential for liver cancer treatments.
Assessment and report of individual symptoms in studies of delirium in postoperative populations: a systematic review
Authors: Bowman Emily M L , Sweeney Aoife M , McAuley Danny F , Cardwell Chris , Kane Joseph , Badawi Nadine , Jahan Nusrat , Iqbal Halla Kiyan , Mitchell Callum , Ballantyne Jessica A , Cunningham Emma L
Published: April 2024

Objectives

Delirium is most often reported as present or absent. Patients with symptoms falling short of the diagnostic criteria for delirium fall into ‘no delirium’ or ‘control’ groups. This binary classification neglects individual symptoms and may be hindering identification of the pathophysiology underlying delirium. This systematic review investigates which individual symptoms of delirium are reported by studies of postoperative delirium in adults.

Methods

Medline, EMBASE and Web of Science databases were searched on 03 June 2021 and 06 April 2023. Two reviewers independently examined titles and abstracts. Each paper was screened in duplicate and conflicting decisions settled by consensus discussion. Data were extracted, qualitatively synthesised and narratively reported. All included studies were quality assessed.

Results

These searches yielded 4,367 results. After title and abstract screening, 694 full-text studies were reviewed, and 62 deemed eligible for inclusion. This review details 11,377 patients including 2,049 patients with delirium. In total, 78 differently described delirium symptoms were reported. The most reported symptoms were inattention (N = 29), disorientation (N = 27), psychomotor agitation/retardation (N = 22), hallucination (N = 22) and memory impairment (N = 18). Notably, psychomotor agitation and hallucinations are not listed in the current Diagnostic and Statistical Manual for Mental Disorders-5-Text Revision delirium definition.

Conclusions

The 78 symptoms reported in this systematic review cover domains of attention, awareness, disorientation and other cognitive changes. There is a lack of standardisation of terms, and many recorded symptoms are synonyms of each other. This systematic review provides a library of individual delirium symptoms, which may be used to inform future reporting.
Social complexity affects cognitive abilities but not brain structure in a Poeciliid fish
Authors: Triki Zegni , Zhou Tunhe , Argyriou Elli , Sousa de Novais Edson , Servant Oriane , Kolm Niclas
Published: April 2024

Some cognitive abilities are suggested to be the result of a complex social life, allowing individuals to achieve higher fitness through advanced strategies. However, most evidence is correlative. Here, we provide an experimental investigation of how group size and composition affect brain and cognitive development in the guppy (Poecilia reticulata). For 6 months, we reared sexually mature females in one of 3 social treatments: a small conspecific group of 3 guppies, a large heterospecific group of 3 guppies and 3 splash tetras (Copella arnoldi)—a species that co-occurs with the guppy in the wild, and a large conspecific group of 6 guppies. We then tested the guppies’ performance in self-control (inhibitory control), operant conditioning (associative learning), and cognitive flexibility (reversal learning) tasks. Using X-ray imaging, we measured their brain size and major brain regions. Larger groups of 6 individuals, both conspecific and heterospecific groups, showed better cognitive flexibility than smaller groups but no difference in self-control and operant conditioning tests. Interestingly, while social manipulation had no significant effect on brain morphology, relatively larger telencephalons were associated with better cognitive flexibility. This suggests alternative mechanisms beyond brain region size enabled greater cognitive flexibility in individuals from larger groups. Although there is no clear evidence for the impact on brain morphology, our research shows that living in larger social groups can enhance cognitive flexibility. This indicates that the social environment plays a role in the cognitive development of guppies.
EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery
Authors: Schmitz Johanna Elena , Aggarwal Nihit , Laufer Lukas , Walter Jörn , Salhab Abdulrahman , Rahmann Sven
Published: April 2024

Motivation

Automated chromatin segmentation based on ChIP-seq (chromatin immunoprecipitation followed by sequencing) data reveals insights into the epigenetic regulation of chromatin accessibility. Existing segmentation methods are constrained by simplifying modeling assumptions, which may have a negative impact on the segmentation quality.

Results

We introduce EpiSegMix, a novel segmentation method based on a hidden Markov model with flexible read count distribution types and state duration modeling, allowing for a more flexible modeling of both histone signals and segment lengths. In a comparison with existing tools, ChromHMM, Segway, and EpiCSeg, we show that EpiSegMix is more predictive of cell biology, such as gene expression. Its flexible framework enables it to fit an accurate probabilistic model, which has the potential to increase the biological interpretability of chromatin states.

Availability and implementation

Source code: https://gitlab.com/rahmannlab/episegmix.
Digital tools for youth health promotion: principles, policies and practices in sub-Saharan Africa
Authors: Ferretti Agata , Adjei Kwame K , Ali Joseph , Atuire Caesar , Ayuk Betrand Tambe , Banougnin Boladé Hamed , Cengiz Nezerith , Gichoya Judy , Jjingo Daudi , Juma Damian Omari , Kotze Wiaan , Krubiner Carleigh , Littler Katherine , McCradden Melissa D , Moodley Keymanthri , Naidoo Meshandren , Nair Gonasagrie , Obeng-Kyereh Kingsley , Oliver Kedebone , Ralefala Dimpho , Toska Elona , Wekesah Frederick M , Wright Jonty , Vayena Effy
Published: April 2024

Although digital health promotion (DHP) technologies for young people are increasingly available in low- and middle-income countries (LMICs), there has been insufficient research investigating whether existing ethical and policy frameworks are adequate to address the challenges and promote the technological opportunities in these settings. In an effort to fill this gap and as part of a larger research project, in November 2022, we conducted a workshop in Cape Town, South Africa, entitled ‘Unlocking the Potential of Digital Health Promotion for Young People in Low- and Middle-Income Countries’. The workshop brought together 25 experts from the areas of digital health ethics, youth health and engagement, health policy and promotion and technology development, predominantly from sub-Saharan Africa (SSA), to explore their views on the ethics and governance and potential policy pathways of DHP for young people in LMICs. Using the World Café method, participants contributed their views on (i) the advantages and barriers associated with DHP for youth in LMICs, (ii) the availability and relevance of ethical and regulatory frameworks for DHP and (iii) the translation of ethical principles into policies and implementation practices required by these policies, within the context of SSA. Our thematic analysis of the ensuing discussion revealed a willingness to foster such technologies if they prove safe, do not exacerbate inequalities, put youth at the center and are subject to appropriate oversight. In addition, our work has led to the potential translation of fundamental ethical principles into the form of a policy roadmap for ethically aligned DHP for youth in SSA.
Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae
Authors: Aneli Serena , Ceccatelli Berti Camilla , Gilea Alexandru Ionut , Birolo Giovanni , Mutti Giacomo , Pavesi Angelo , Baruffini Enrico , Goffrini Paola , Capelli Cristian
Published: April 2024

Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
Safety and Immunogenicity of the H56:IC31 Tuberculosis Vaccine Candidate in Adults Successfully Treated for Drug-Susceptible Pulmonary Tuberculosis: A Phase 1 Randomized Trial
Authors: Tait Dereck , Diacon Andreas , Borges Álvaro H , van Brakel Elana , Hokey David , Rutkowski Kathryn T , Hunt Devin J , Russell Marisa , Andersen Peter L , Kromann Ingrid , Ruhwald Morten , Churchyard Gavin , Dawson Rodney
Published: April 2024

Background

H56:IC31 is a candidate vaccine against tuberculosis (TB) with the potential to reduce TB recurrence rate. It is thus important for future clinical trials to demonstrate safety and immunogenicity of H56:IC31 in individuals treated for TB.

Methods

Twenty-two adults confirmed to be Mycobacterium tuberculosis negative (by 2 GeneXpert tests or 2 sputum cultures) after 4–5 months of TB treatment, and not more than 28 days after completion of TB treatment, were randomized to receive 2 doses of H56:IC31 (5 mg H56:500 nmol IC31; n = 16) or placebo (n = 6) 56 days apart. Participants were followed for 420 days for safety and immunogenicity.

Results

H56:IC31 vaccination was associated with an acceptable safety profile, consisting mostly of mild self-limited injection site reactions. No serious adverse events or vaccine-related severe adverse events were reported. H56:IC31 induced a CD4+ T-cell response for Ag85B and ESAT-6, with ESAT-6 being immunodominant, which persisted through 6 months after the last vaccination. There was some evidence of CD8+ T-cell responses for both Ag85B and ESAT-6, but to a lesser extent than CD4+ responses.

Conclusions

H56:IC31 was associated with an acceptable safety profile, and induced a predominant CD4+ T-cell response, in adults recently treated for drug-susceptible, uncomplicated pulmonary TB.

Clinical Trials Registration

NCT02375698.