bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins
Authors: Sahu Nityananda , Khire Subodh S. , Gadre Shridhar R.
Published: July 2023

Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5–10 millihartrees and 5 cm−1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.
Characterization of non-Boltzmann CN X2Σ+ behind shock waves in CH4–N2 via broadband ultraviolet femtosecond absorption spectroscopy
Authors: Radhakrishna Vishnu , Tancin Ryan J. , Goldenstein Christopher S.
Published: July 2023

This article describes the temporal evolution of rotationally and vibrationally non-Boltzmann CN X2Σ+ formed behind reflected shock waves in N2–CH4 mixtures at conditions relevant to atmospheric entry into Titan. A novel ultrafast (i.e., femtosecond) laser absorption spectroscopy diagnostic was developed to provide broadband (≈400 cm−1) spectrally resolved (0.02 nm resolution) measurements of CN absorbance spectra belonging to its B2Σ+ ← X2Σ+ electronic system and its first four Δv = 0 vibrational bands (v″ = 0, 1, 2, 3). Measurements were acquired behind reflected shock waves in a mixture with 5.65% CH4 and 94.35% N2 at initial chemically and vibrationally frozen temperatures and pressures of 4400–5900 K and 0.55–0.75 bar, respectively. A six-temperature line-by-line absorption spectroscopy model for CN was developed to determine the rotational temperature of CN in v″ = 0, 1, 2, and 3, as well as two vibrational temperatures via least-squares fitting. The measured CN spectra revealed rotationally and vibrationally non-Boltzmann population distributions that strengthened with increasing shock speed and persisted for over 100 µs. The measured vibrational temperatures of CN initially increase in time with the increasing CN mole fraction and eventually exceed the expected post-shock rotational temperature of N2. The results suggest that strong chemical pumping is ultimately responsible for these trends and that, at the conditions studied, CN is primarily formed in high vibrational states within the A2Π or B2Σ+ state at characteristic rates, which are comparable to or exceed those of key vibrational equilibration processes.
Evaluation of the MACE force field architecture: From medicinal chemistry to materials science
Authors: Kovács Dávid Péter , Batatia Ilyes , Arany Eszter Sára , Csányi Gábor
Published: July 2023

The MACE architecture represents the state of the art in the field of machine learning force fields for a variety of in-domain, extrapolation, and low-data regime tasks. In this paper, we further evaluate MACE by fitting models for published benchmark datasets. We show that MACE generally outperforms alternatives for a wide range of systems, from amorphous carbon, universal materials modeling, and general small molecule organic chemistry to large molecules and liquid water. We demonstrate the capabilities of the model on tasks ranging from constrained geometry optimization to molecular dynamics simulations and find excellent performance across all tested domains. We show that MACE is very data efficient and can reproduce experimental molecular vibrational spectra when trained on as few as 50 randomly selected reference configurations. We further demonstrate that the strictly local atom-centered model is sufficient for such tasks even in the case of large molecules and weakly interacting molecular assemblies.
Design, fabrication, and characterization of picowell arrays on cyclic olefin copolymer surfaces generated with a 10.5 MeV N4+ ion microbeam
Authors: Bányász I. , Rajta I. , Havránek V. , Mackova A. , Laki A. J. , Kellermayer M. S. Z. , Szittner Z. , Kurunczi S. , Novák Sz. , Székács I. , Horváth R. , Fried M. , Nagy G. U. L.
Published: July 2023

Handling of picoliter-to-nanoliter-scale volumes and objects has increasing importance in life sciences. This is the volume scale of cell extractions and individual living cells. Here, we introduce a method of generating a picoliter-scale device by direct writing of picowell arrays on a ZEONOR™ copolymer surface with high-energy medium-mass ion microbeam. Arrays of various microstructures were written in the sample using a microbeam of 10.5 MeV N4+ ions at various implanted ion fluences. The best array was obtained by implantation of annuli of 10 and 11 μm of inner and outer diameters with a fluence of 7.8 × 1012 ions/cm2.
Evolution from the gradient drift instability to the formation of the spoke potential hump in a partially magnetized plasma
Authors: Xu Liang , Eremin Denis , Smolyakov Andrei , Krüger Dennis , Köhn Kevin , Brinkmann Ralf Peter
Published: July 2023

Rotating spokes commonly occur in partially magnetized plasma devices. This work explores the evolution from the gradient drift instability into an m = 1 rotating spoke mode in a magnetically enhanced hollow cathode discharge (with emissive cathode) by means of 2D radial-azimuthal particle-in-cell/Monte Carlo collision simulations. It is shown that the formation of the spoke potential hump region can be explained as a result of the local collapse of the anode sheath due to the gradient drift instability, which is triggered within the anode sheath. The sheath non-neutrality effect on the instability is considered and incorporated in the two-fluid linear theory of gradient drift instability. The unstable modes predicted by the theory are in good agreement with the fluctuation modes developed in the particle simulations.
Tsunami waveform forecasting at cooling water intakes of nuclear reactors with deep learning model
Authors: Kim Byung-Ho , Rehman Khawar , Cho Yong-Sik , Hong Seung Ho
Published: July 2023

The Fukushima nuclear disaster highlights the importance of accurate and fast predictions of tsunami hazard to critical coastal infrastructure to devise mitigation strategies in both long-term and real-time events. Recently, deep learning models allowed us to make accurate and rapid forecasts on high dimensional, non-linear, and non-stationary time series data such as that associated with tsunami waveforms. Thus, this study uses a one-dimensional convolutional neural network (CNN) model to predict waveforms at cooling water intakes of nuclear power plant at Uljin in South Korea. The site is particularly vulnerable to tsunamis originating from the west coast of Japan. Data for the CNN model are generated by numerical simulation of 1107 cases of tsunami propagation initiating from fault locations. The time series data for waveforms were predicted at 13 virtual gauges located in the nearshore region of the study area, 10 of which were classified as observation points and 3 gauges situated at the cooling water intakes were categorized as target locations. The performance assessment of the model's forecasts showed excellent results with rapid predictions. The study highlights two main points: (i) deep learning models can be based on sparse waveform in situ data (such as that recorded by deep-ocean assessment and reporting of tsunamis or any locally operating monitoring stations for ocean waves) or numerically simulated data at only a few points along the dominant wave propagation direction, and (ii) deep learning models are fully capable of accurate and fast predictions of complex geo-hazards that prompt rapid emergency response to coordinate mitigation efforts.
Research on the collapse dynamics of a restricted cavitation bubble near a right-angle wall based on Kelvin impulse theory
Authors: Wang Xiaoyu , Wu Guanhao , Shen Junwei , Sun Zhuo , Zhang Yuning , Zhang Lei , Zhang Yuning
Published: July 2023

In this paper, a Kelvin impulse theory model is constructed for a restricted bubble through conformal transformation. The collapse dynamics of a restricted bubble near a right-angle wall are systematically investigated based on the result of the new theoretical model and a high-speed photography experiment. In particular, the bubble collapse jet, characterized by the intensity and angle of the Kelvin impulse, is visualized and analyzed with experiment validations. The corresponding results for an unrestricted spherical bubble are also investigated for comparison purposes. The pivotal conclusions are as follows: (1) The Kelvin impulse intensity takes its maximum value at the position where the bubble is closest to the vertex of the right-angle wall. Furthermore, the intensity decreases with an increase in the dimensionless distance, and first decreases and then increases with an increase in the bubble azimuth angle. (2) The rates of change of the Kelvin impulse intensity and direction of the bubble are both very sensitive to the bubble position when the bubble is near one of the straight walls of the right-angle wall. (3) The trends of both the Kelvin impulse intensity and direction with the bubble position for restricted and unrestricted bubbles differ significantly because of the different characteristics of the Bjerknes force for the two kinds of bubbles.
Raising TC of ferromagnetic semiconductors through doping control: The case of GaMnAs
Authors: Lan Mu , Wang Rong , Song Yu , Wei Su-Huai
Published: July 2023

The difficulty of increasing the Curie temperature TC of magnetic semiconductors such as (Ga,Mn)As above the room temperature is related to the p-type doping bottleneck in this system, which has hindered the further development of dilute magnetic semiconductors. To overcome the p-type doping bottleneck, we investigate the doping properties of Mn in GaAs with hybrid functional calculations and propose strategies that can improve the p-type dopability in (Ga,Mn)As. We find that tensile strain and high temperature quenching are effective approaches to enhance p-type doping in epitaxial (Ga,Mn)As. The tensile strain applied, e.g., by the substrate with a larger lattice constant can decrease the formation energy of the substitutional dopant MnGa−, which is an acceptor with large size, and increase that of interstitial Mni2+, which is a small size compensating donor, thus improving the p-type dopability. The high temperature quenching also can achieve higher hole density by limiting the formation of compensating interstitial Mn. We suggest that the combination of these two schemes would effectively enhance the p-type dopability and further raise the Curie temperature TC of (Ga,Mn)As.
Plasmonically coupled semiconductor quantum dots for efficient hydrogen photoelectrocatalysis
Authors: Ijaz Mohsin , Zhang Hao , Chan Sanutep V. , Holt Robert , Davis Nathaniel J. L. K. , Blaikie Richard J.
Published: July 2023

Photocatalytic water splitting has attracted significant attention as a low-cost, clean, and green method for the conversion of solar energy into hydrogen, highlighting its potential to solve energy and environmental problems. In this work, we report the coupling of a plasmonic resonator with semiconductor quantum dots (QDs) for enhancement in photoelectrocatalytic water splitting toward hydrogen (H2) production. Specifically, cadmium selenide (CdSe) QDs were deposited on silver nano-gratings (Ag gratings). Plasmonic enhancement was observed in the absorption/emission of QDs using our angle-resolved steady-state optical spectroscopy. Furthermore, angle-resolved absorption spectra helped us to optimize the illumination conditions for resonant excitation using a setup for photoelectrochemical (PEC) experiments. Under the resonant pump, the emission of the QDs has been plasmonically enhanced with a Purcell factor (FP) of ∼1.5. Our numerical simulation revealed a strong near-field enhancement due to the excitation of surface plasmon resonances, contributing to FP. A similar enhancement order in the PEC experiments was also observed under resonant pump conditions, indicating the contribution of plasmon resonances to the enhanced photoelectrocatalysis. Switching the excitation's polarization further reinforces this, resulting in an enhanced photocurrent under p-polarization. These findings provide a proof of concept, thus laying the foundation for a practical device for efficient solar-to-H2 conversion.
Robust relativistic many-body Green’s function based approaches for assessing core ionized and excited states
Authors: Kehry Max , Klopper Wim , Holzer Christof
Published: July 2023

A two-component contour deformation (CD) based GW method that employs frequency sampling to drastically reduce the computational effort when assessing quasiparticle states far away from the Fermi level is outlined. Compared to the canonical CD-GW method, computational scaling is reduced by an order of magnitude without sacrificing accuracy. This allows for an efficient calculation of core ionization energies. The improved computational efficiency is used to provide benchmarks for core ionized states, comparing the performance of 15 density functional approximations as Kohn–Sham starting points for GW calculations on a set of 65 core ionization energies of 32 small molecules. Contrary to valence states, GW calculations on core states prefer functionals with only a moderate amount of Hartree–Fock exchange. Moreover, modern ab initio local hybrid functionals are also shown to provide excellent generalized Kohn–Sham references for core GW calculations. Furthermore, the core–valence separated Bethe–Salpeter equation (CVS-BSE) is outlined. CVS-BSE is a convenient tool to probe core excited states. The latter is tested on a set of 40 core excitations of eight small inorganic molecules. Results from the CVS-BSE method for excitation energies and the corresponding absorption cross sections are found to be in excellent agreement with those of reference damped response BSE calculations.
Data-driven Reynolds stress models based on the frozen treatment of Reynolds stress tensor and Reynolds force vector
Authors: Amarloo Ali , Cinnella Paola , Iosifidis Alexandros , Forooghi Pourya , Abkar Mahdi
Published: July 2023

For developing a reliable data-driven Reynold stress tensor (RST) model, successful reconstruction of the mean velocity field based on high-fidelity information (i.e., direct numerical simulations or large-eddy simulations) is crucial and challenging, considering the ill-conditioning problem of Reynolds-averaged Navier–Stokes (RANS) equations. It is shown that the frozen treatment of the Reynolds force vector (RFV) reduced the ill-conditioning problem even for the cases with a very high Reynolds number; therefore, it has a better potential to be used in the data-driven development of the RANS models. In this study, we compare the algebraic RST correction models that are trained based on the frozen treatment of both RFV and RST for the aforementioned potential. We derive a vector-based framework for the RFV similar to the tensor-based framework for the RST. Regarding the complexity of the models, we compare sparse regression on a set of candidate functions and a multi-layer perceptron network. The training process is applied to the high-fidelity data of three cases, including square-duct secondary flow, roughness-induced secondary flow, and periodic hills flow. The results showed that using the RFV discrepancy values, instead of the RST discrepancy values, generally does not improve the reconstruction of the mean velocity field despite the fact that the propagation of the RFV discrepancy data shows lower errors in the propagation process of all three cases. Regarding the complexity, using multi-layer perceptron improves the prediction of the cases with secondary flows, but it shows similar performance in the case of periodic hills.
Benchmarking of different optimizers in the variational quantum algorithms for applications in quantum chemistry
Authors: Singh Harshdeep , Majumder Sonjoy , Mishra Sabyashachi
Published: July 2023

Classical optimizers play a crucial role in determining the accuracy and convergence of variational quantum algorithms; leading algorithms use a near-term quantum computer to solve the ground state properties of molecules, simulate dynamics of different quantum systems, and so on. In the literature, many optimizers, each having its own architecture, have been employed expediently for different applications. In this work, we consider a few popular and efficacious optimizers and assess their performance in variational quantum algorithms for applications in quantum chemistry in a realistic noisy setting. We benchmark the optimizers with critical analysis based on quantum simulations of simple molecules, such as hydrogen, lithium hydride, beryllium hydride, water, and hydrogen fluoride. The errors in the ground state energy, dissociation energy, and dipole moment are the parameters used as yardsticks. All the simulations were carried out with an ideal quantum circuit simulator, a noisy quantum circuit simulator, and finally a noisy simulator with noise embedded from the IBM Cairo quantum device to understand the performance of the classical optimizers in ideal and realistic quantum environments. We used the standard unitary coupled cluster ansatz for simulations, and the number of qubits varied from two starting from the hydrogen molecule to ten qubits in hydrogen fluoride. Based on the performance of these optimizers in the ideal quantum circuits, the conjugate gradient, limited-memory Broyden—Fletcher—Goldfarb—Shanno bound, and sequential least squares programming optimizers are found to be the best-performing gradient-based optimizers. While constrained optimization by linear approximation (COBYLA) and Powell's conjugate direction algorithm for unconstrained optimization (POWELL) perform most efficiently among the gradient-free methods, in noisy quantum circuit conditions, simultaneous perturbation stochastic approximation, POWELL, and COBYLA are among the best-performing optimizers.
Effects of the organic selenium sources with/without probiotics on broiler chicken growth, meat quality and meat selenium content
Authors: Shokrinejad Gerdin A. , Afsharmanesh M. , Salarmoini M. , Khajeh Bami M.
Published: July 2023

Context Selenium is an essential trace micronutrient that plays an important biological role in maintenance of animal health. Aims The purpose of this study was to compare the effects of dietary supplementation of selenium (Se)-enriched yeast (SeY), Se–chitosan (SeCh), and selenised glucose (SeGlu) as organic forms of Se, as well as the interaction of these compounds with probiotics, on broiler chicken growth, carcass characteristics, meat quality, and meat Se concentration. Methods In total, 300 1-day-old Ross 308 broiler chickens were randomly assigned to six experimental groups in a 3 × 2 factorial treatment arrangement. Factors tested included Se sources (SeY, SeCh, and SeGlu at a concentration of 0.3 mg/kg) and probiotics (a mixture of probiotic bacteria containing Bacillus coagulans, Bacillus subtilis, Bacillus lichen formis, Lactobacillus faecium, Lactobacillus rhamnosus, and Lactobacillus plantarum, at concentrations of 0 and 100 mg/kg). The treatments were replicated in five floor pens, with 10 broiler chickens per pen. Key results For the entire period (1–42 days), broiler chickens given SeCh or SeGlu showed a lower feed conversion ratio than did broiler chickens fed SeY (P < 0.05). Furthermore, broiler chickens fed diets supplemented with SeGlu without or with probiotics had considerably higher breast relative weight than did those fed SeY without probiotics. In comparison to SeY-fed birds, those fed SeCh or SeGlu had lower thiobarbituric acid-reactive substances, drip loss, cooking loss, and higher water-holding capacity values in the breast muscle (P < 0.05). Birds fed diets supplemented with SeCh and SeGlu with probiotics had higher yellowness and lower thiobarbituric acid-reactive substances and cooking loss in breast meat than did birds fed diets supplemented with SeY without or with probiotics. Furthermore, the concentration of Se in meat was higher in birds fed a SeGlu diet with probiotics than in other treatments, except in birds fed a SeCh diet with probiotics. Conclusions Compared to the use of SeY, the use of SeCh and SeGlu as new Se forms is a simple, unique, and cost-effective technique for improving broiler chicken growth performance, carcass characteristics, and meat quality. Implications These findings provide a basis for the application of SeCh and SeGlu in chicken broiler diets.
Quantum reality with negative-mass particles
Authors: Waegell Mordecai , Cohen Eliahu , Elitzur Avshalom , Tollaksen Jeff , Aharonov Yakir
Published: July 2023

Physical interpretations of the time-symmetric formulation of quantum mechanics, due to Aharonov, Bergmann, and Lebowitz are discussed in terms of weak values. The most direct, yet somewhat naive, interpretation uses the time-symmetric formulation to assign eigenvalues to unmeasured observables of a system, which results in logical paradoxes, and no clear physical picture. A top–down ontological model is introduced that treats the weak values of observables as physically real during the time between pre- and post-selection (PPS), which avoids these paradoxes. The generally delocalized rank-1 projectors of a quantum system describe its fundamental ontological elements, and the highest-rank projectors corresponding to individual localized objects describe an emergent particle model, with unusual particles, whose masses and energies may be negative or imaginary. This retrocausal top–down model leads to an intuitive particle-based ontological picture, wherein weak measurements directly probe the properties of these exotic particles, which exist whether or not they are actually measured.
MBTD1 preserves adult hematopoietic stem cell pool size and function
Authors: Takubo Keiyo , Htun Phyo Wai , Ueda Takeshi , Sera Yasuyuki , Iwasaki Masayuki , Koizumi Miho , Shiroshita Kohei , Kobayashi Hiroshi , Haraguchi Miho , Watanuki Shintaro , Honda Zen-ichiro , Yamasaki Norimasa , Nakamura-Ishizu Ayako , Arai Fumio , Motoyama Noboru , Hatta Tomohisa , Natsume Tohru , Suda Toshio , Honda Hiroaki
Published: July 2023

Mbtd1 (mbt domain containing 1
) encodes a nuclear protein containing a zinc finger domain and four malignant brain tumor (MBT) repeats. We previously generated
Mbtd1
-deficient mice and found that MBTD1 is highly expressed in fetal hematopoietic stem cells (HSCs) and sustains the number and function of fetal HSCs. However, since
Mbtd1
-deficient mice die soon after birth possibly due to skeletal abnormalities, its role in adult hematopoiesis remains unclear. To address this issue, we generated
Mbtd1
conditional knockout mice and analyzed adult hematopoietic tissues deficient in
Mbtd1
. We observed that the numbers of HSCs and progenitors increased and
Mbtd1
-deficient HSCs exhibited hyperactive cell cycle, resulting in a defective response to exogenous stresses. Mechanistically, we found that MBTD1 directly binds to the promoter region of
FoxO3a
, encoding a forkhead protein essential for HSC quiescence, and interacts with components of TIP60 chromatin remodeling complex and other proteins involved in HSC and other stem cell functions. Restoration of FOXO3a activity in
Mbtd1-
deficient HSCs in vivo rescued cell cycle and pool size abnormalities. These findings indicate that MBTD1 is a critical regulator for HSC pool size and function, mainly through the maintenance of cell cycle quiescence by FOXO3a.
Bacterial chemoreceptor signaling complexes control kinase activity by stabilizing the catalytic domain of CheA
Authors: Tran Thomas , Karunanayake Mudiyanselage Aruni P. K. K. , Eyles Stephen J. , Thompson Lynmarie K.
Published: July 2023

Motile bacteria have a chemotaxis system that enables them to sense their environment and direct their swimming toward favorable conditions. Chemotaxis involves a signaling process in which ligand binding to the extracellular domain of the chemoreceptor alters the activity of the histidine kinase, CheA, bound ~300 Å away to the distal cytoplasmic tip of the receptor, to initiate a phosphorylation cascade that controls flagellar rotation. The cytoplasmic domain of the receptor is thought to propagate this signal via changes in dynamics and/or stability, but it is unclear how these changes modulate the kinase activity of CheA. To address this question, we have used hydrogen deuterium exchange mass spectrometry to probe the structure and dynamics of CheA within functional signaling complexes of the
Escherichia coli
aspartate receptor cytoplasmic fragment, CheA, and CheW. Our results reveal that stabilization of the P4 catalytic domain of CheA correlates with kinase activation. Furthermore, differences in activation of the kinase that occur during sensory adaptation depend on receptor destabilization of the P3 dimerization domain of CheA. Finally, hydrogen exchange properties of the P1 domain that bears the phosphorylated histidine identify the dimer interface of P1/P1’ in the CheA dimer and support an ordered sequential binding mechanism of catalysis, in which dimeric P1/P1’ has productive interactions with P4 only upon nucleotide binding. Thus stabilization/destabilization of domains is a key element of the mechanism of modulating CheA kinase activity in chemotaxis, and may play a role in the control of other kinases.
Plasma membrane association and resistosome formation of plant helper immune receptors
Authors: Wang Zaiqing , Liu Xiaoxiao , Yu Jie , Yin Shuining , Cai Wenjuan , Kim Nak Hyun , El Kasmi Farid , Dangl Jeffery L. , Wan Li
Published: July 2023

Intracellular plant immune receptors, termed NLRs (Nucleotide-binding Leucine-rich repeat Receptors), confer effector-triggered immunity. Sensor NLRs are responsible for pathogen effector recognition. Helper NLRs function downstream of sensor NLRs to transduce signaling and induce cell death and immunity. Activation of sensor NLRs that contain TIR (Toll/interleukin-1receptor) domains generates small molecules that induce an association between a downstream heterodimer signalosome of EDS1 (EnhancedDisease Susceptibility 1)/SAG101 (Senescence-AssociatedGene 101) and the helper NLR of NRG1 (NRequired Gene 1). Autoactive NRG1s oligomerize and form calcium signaling channels largely localized at the plasma membrane (PM). The molecular mechanisms of helper NLR PM association and effector-induced NRG1 oligomerization are not well characterized. We demonstrate that helper NLRs require positively charged residues in their N-terminal domains for phospholipid binding and PM association before and after activation, despite oligomerization and conformational changes that accompany activation. We demonstrate that effector activation of a TIR-containing sensor NLR induces NRG1 oligomerization at the PM and that the cytoplasmic pool of EDS1/SAG101 is critical for cell death function. EDS1/SAG101 cannot be detected in the oligomerized NRG1 resistosome, suggesting that additional unknown triggers might be required to induce the dissociation of EDS1/SAG101 from the previously described NRG1/EDS1/SAG101 heterotrimer before subsequent NRG1 oligomerization. Alternatively, the conformational changes resulting from NRG1 oligomerization abrogate the interface for EDS1/SAG101 association. Our data provide observations regarding dynamic PM association during helper NLR activation and underpin an updated model for effector-induced NRG1 resistosome formation.
Fossil leaves reveal drivers of herbivore functional diversity during the Cenozoic
Authors: Albrecht Jörg , Wappler Torsten , Fritz Susanne A. , Schleuning Matthias
Published: July 2023

Herbivorous arthropods are the most diverse group of multicellular organisms on Earth. The most discussed drivers of their inordinate taxonomic and functional diversity are high niche availability associated with the diversity of host plants and dense niche packing due to host partitioning among herbivores. However, the relative contributions of these two factors to dynamics in the diversity of herbivores throughout Earth’s history remain unresolved. Using fossil data on herbivore-induced leaf damage from across the Cenozoic, we infer quantitative bipartite interaction networks between plants and functional feeding types of herbivores. We fit a general model of diversity to these interaction networks and discover that host partitioning among functional groups of herbivores contributed twice as much to herbivore functional diversity as host diversity. These findings indicate that niche packing primarily shaped the dynamics in the functional diversity of herbivores during the past 66 my. Our study highlights how the fossil record can be used to test fundamental theories of biodiversity and represents a benchmark for assessing the drivers of herbivore functional diversity in modern ecosystems.
SARS-CoV-2 mouse adaptation selects virulence mutations that cause TNF-driven age-dependent severe disease with human correlates
Authors: Bader Stefanie M. , Cooney James P. , Sheerin Dylan , Taiaroa George , Harty Leigh , Davidson Kathryn C. , Mackiewicz Liana , Dayton Merle , Wilcox Stephen , Whitehead Lachlan , Rogers Kelly L. , Georgy Smitha Rose , Coussens Anna K. , Grimley Samantha L. , Corbin Vincent , Pitt Miranda , Coin Lachlan , Pickering Raelene , Thomas Merlin , Allison Cody C. , McAuley Julie , Purcell Damian F. J. , Doerflinger Marcel , Pellegrini Marc
Published: July 2023

The diversity of COVID-19 disease in otherwise healthy people, from seemingly asymptomatic infection to severe life-threatening disease, is not clearly understood. We passaged a naturally occurring near-ancestral SARS-CoV-2 variant, capable of infecting wild-type mice, and identified viral genomic mutations coinciding with the acquisition of severe disease in young adult mice and lethality in aged animals. Transcriptomic analysis of lung tissues from mice with severe disease elucidated a host antiviral response dominated mainly by interferon and IL-6 pathway activation in young mice, while in aged animals, a fatal outcome was dominated by TNF and TGF-β signaling. Congruent with our pathway analysis, we showed that young TNF-deficient mice had mild disease compared to controls and aged TNF-deficient animals were more likely to survive infection. Emerging clinical correlates of disease are consistent with our preclinical studies, and our model may provide value in defining aberrant host responses that are causative of severe COVID-19.
Whole-soil-profile warming does not change microbial carbon use efficiency in surface and deep soils
Authors: Zhang Qiufang , Qin Wenkuan , Feng Jiguang , Li Xiaojie , Zhang Zhenhua , He Jin-Sheng , Schimel Joshua P. , Zhu Biao
Published: July 2023

The paucity of investigations of carbon (C) dynamics through the soil profile with warming makes it challenging to evaluate the terrestrial C feedback to climate change. Soil microbes are important engines driving terrestrial biogeochemical cycles; their carbon use efficiency (CUE), defined as the proportion of metabolized organic C allocated to microbial biomass, is a key regulator controlling the fate of soil C. It has been theorized that microbial CUE should decline with warming; however, empirical evidence for this response is scarce, and data from deeper soils are particularly scarce. Here, based on soil samples from a whole-soil-profile warming experiment (0 to 1 m, +4 °C) and
18
O tracing approach, we examined the vertical variation of microbial CUE and its response to ~3.3-y experimental warming in an alpine grassland on the Qinghai–Tibetan Plateau. Microbial CUE decreased with soil depth, a trend that was primarily controlled by soil C availability. However, warming had limited effects on microbial CUE regardless of soil depth. Similarly, warming had no significant effect on soil C availability, as characterized by extractable organic C, enzyme-based lignocellulose index, and lignin phenol–based ratios of vanillyls, syringyls, and cinnamyls. Collectively, our work suggests that short-term warming does not alter microbial CUE in either surface or deep soils, and emphasizes the regulatory role of soil C availability on microbial CUE.
SEC61G assists
EGFR
-amplified glioblastoma to evade immune elimination
Authors: Zeng Kunlin , Zeng Yu , Zhan Hongchao , Zhan Ziling , Wang Li , Xie Yuxin , Tang Yanqing , Li Cuiying , Chen Yanwen , Li Shangbiao , Liu Ming , Chen Xiaoxia , Liang Li , Deng Fan , Song Ye , Zhou Aidong
Published: July 2023

Amplification of chromosome 7p11 (7p11) is the most common alteration in primary glioblastoma (GBM), resulting in gains of epidermal growth factor receptor (
EGFR
) copy number in 50 to 60% of GBM tumors. However, treatment strategies targeting EGFR have thus far failed in clinical trials, and the underlying mechanism remains largely unclear. We here demonstrate that
EGFR
amplification at the 7p11 locus frequently encompasses its neighboring genes and identifies SEC61G as a critical regulator facilitating GBM immune evasion and tumor growth. We found that
SEC61G
is always coamplified with
EGFR
and is highly expressed in GBM. As an essential subunit of the SEC61 translocon complex, SEC61G promotes translocation of newly translated immune checkpoint ligands (ICLs, including PD-L1, PVR, and PD-L2) into the endoplasmic reticulum and promotes their glycosylation, stabilization, and membrane presentation. Depletion of SEC61G promotes the infiltration and cytolytic activity of CD8
+
T cells and thus inhibits GBM occurrence. Further, SEC61G inhibition augments the therapeutic efficiency of EGFR tyrosine kinase inhibitors in mice. Our study demonstrates a critical role of SEC61G in GBM immune evasion, which provides a compelling rationale for combination therapy of
EGFR
-amplified GBMs.
Genome-wide kinase-MAM interactome screening reveals the role of CK2A1 in MAM Ca2+dynamics linked to DEE66
Authors: Thi My Nhung Truong , Phuoc Long Nguyen , Diem Nghi Tran , Suh Yeongjun , Hoang Anh Nguyen , Jung Cheol Woon , Minh Triet Hong , Jung Minkyo , Woo Youngsik , Yoo Jinyeong , Noh Sujin , Kim Soo Jeong , Lee Su Been , Park Seongoh , Thomas Gary , Simmen Thomas , Mun Jiyoung , Rhee Hyun-Woo , Kwon Sung Won , Park Sang Ki
Published: July 2023

The endoplasmic reticulum (ER) and mitochondria form a unique subcellular compartment called mitochondria-associated ER membranes (MAMs). Disruption of MAMs impairs Ca2+homeostasis, triggering pleiotropic effects in the neuronal system. Genome-wide kinase-MAM interactome screening identifies casein kinase 2 alpha 1 (CK2A1) as a regulator of composition and Ca2+transport of MAMs. CK2A1-mediated phosphorylation of PACS2 at Ser207/208/213 facilitates MAM localization of the CK2A1–PACS2–PKD2 complex, regulating PKD2-dependent mitochondrial Ca2+influx. We further reveal that mutations of PACS2 (E209K and E211K) associated with developmental and epileptic encephalopathy-66 (DEE66) impair MAM integrity through the disturbance of PACS2 phosphorylation at Ser207/208/213. This, in turn, causes the reduction of mitochondrial Ca2+uptake and the dramatic increase of the cytosolic Ca2+level, thereby, inducing neurotransmitter release at the axon boutons of glutamatergic neurons. In conclusion, our findings suggest a molecular mechanism that MAM alterations induced by pathological PACS2 mutations modulate Ca2+-dependent neurotransmitter release.
Escherichia coli
small heat shock protein IbpA plays a role in regulating the heat shock response by controlling the translation of σ
32
Authors: Miwa Tsukumi , Taguchi Hideki
Published: July 2023

Small heat shock proteins (sHsps) act as ATP-independent chaperones that prevent irreversible aggregate formation by sequestering denatured proteins. IbpA, an
Escherichia coli
sHsp, functions not only as a chaperone but also as a suppressor of its own expression through posttranscriptional regulation, contributing to negative feedback regulation. IbpA also regulates the expression of its paralog, IbpB, in a similar manner, but the extent to which IbpA regulates other protein expressions is unclear. We have identified that IbpA down-regulates the expression of many Hsps by repressing the translation of the heat shock transcription factor σ
32
. The IbpA regulation not only controls the σ
32
level but also contributes to the shutoff of the heat shock response. These results revealed an unexplored role of IbpA to regulate heat shock response at a translational level, which adds an alternative layer for tightly controlled and rapid expression of σ
32
on demand.
Chromatin conformational changes at human satellite II contribute to the senescence phenotype in the tumor microenvironment
Authors: Miyata Kenichi , Zhou Xiangyu , Nishio Mika , Hanyu Aki , Chiba Masatomo , Kawasaki Hiroko , Osako Tomo , Takeuchi Kengo , Ohno Shinji , Ueno Takayuki , Maruyama Reo , Takahashi Akiko
Published: July 2023

Cellular senescence and senescence-associated secretory phenotype (SASP) in stromal cells within the tumor microenvironment promote cancer progression. Although cellular senescence has been shown to induce changes in the higher-order chromatin structure and abnormal transcription of repetitive elements in the genome, the functional significance of these changes is unclear. In this study, we examined the human satellite II (hSATII) loci in the pericentromere to understand these changes and their functional significance. Our results indicated that the hSATII loci decompact during senescence induction, resulting in new DNA–DNA interactions in distinct genomic regions, which we refer to as DRISR (Distinctive Regions Interacted with Satellite II in Replicative senescent Fibroblasts). Interestingly, decompaction occurs before the expression of hSATII RNA. The DRISR with altered chromatin accessibility was enriched for motifs associated with cellular senescence and inflammatory SASP genes. Moreover, DNA-fluorescence in situ hybridization analysis of the breast cancer tissues revealed hSATII decompaction in cancer and stromal cells. Furthermore, we reanalyzed the single-cell assay for transposase-accessible chromatin with sequencing data and found increased SASP-related gene expression in fibroblasts exhibiting hSATII decompaction in breast cancer tissues. These findings suggest that changes in the higher-order chromatin structure of the pericentromeric repetitive sequences during cellular senescence might directly contribute to the cellular senescence phenotype and cancer progression via inflammatory gene expression.
Atomic coordination environment engineering of bimetallic alloy nanostructures for efficient ammonia electrosynthesis from nitrate
Authors: Wang Yunhao , Sun Mingzi , Zhou Jingwen , Xiong Yuecheng , Zhang Qinghua , Ye Chenliang , Wang Xixi , Lu Pengyi , Feng Tianyi , Hao Fengkun , Liu Fu , Wang Juan , Ma Yangbo , Yin Jinwen , Chu Shengqi , Gu Lin , Huang Bolong , Fan Zhanxi
Published: July 2023

Electrochemical nitrate reduction reaction (NO
3
RR) to ammonia has been regarded as a promising strategy to balance the global nitrogen cycle. However, it still suffers from poor Faradaic efficiency (FE) and limited yield rate for ammonia production on heterogeneous electrocatalysts, especially in neutral solutions. Herein, we report one-pot synthesis of ultrathin nanosheet-assembled RuFe nanoflowers with low-coordinated Ru sites to enhance NO
3
RR performances in neutral electrolyte. Significantly, RuFe nanoflowers exhibit outstanding ammonia FE of 92.9% and yield rate of 38.68 mg h
−1
mg
cat
−1
(64.47 mg h
−1
mg
Ru
−1
) at −0.30 and −0.65 V (vs. reversible hydrogen electrode), respectively. Experimental studies and theoretical calculations reveal that RuFe nanoflowers with low-coordinated Ru sites are highly electroactive with an increased d-band center to guarantee efficient electron transfer, leading to low energy barriers of nitrate reduction. The demonstration of rechargeable zinc-nitrate batteries with large-specific capacity using RuFe nanoflowers indicates their great potential in next-generation electrochemical energy systems.
Multiple constraints, multiple avenues
Authors: Gagné Anne-Marie
Published: July 2023

The abstract nature of human agency, as a capacity or a possibility to exert power, complicates its empirical
examination. While translated and revised texts represent the cumulative result of the agents’ decisions, they offer limited
information on their motivation, goals and sense of agency. In this paper, we employ a multi-method approach to examine the
revised edition (Galeano rev. Sánchez 2013) of Mémoire du feu (Galeano transl. Couffon 1985; transl. Binard 1985, 1988), the French translation of
Memoria del Fuego (Galeano 1982, 1984, 1986). Through a dialogue between semi-structured
interviews (focused on the agent’s choices, motivations and sense of agency) and comparative textual analysis (focused on the
result of her decisions), we investigate why Mémoire du feu was revised and how this project unfolded. The
interaction taking place during semi-structured interviews allowed for the exploration of some dimensions of the reviser’s work
that would otherwise have remained unarticulated discursively and helped us understand the textual results of her decisions. The
revision appears as an agent-based process, as constraints were negotiated by the reviser, and resources were selected by her.
Finally, the reviser’s sense of agency, widened by her multipositionality, emerged as a crucial factor in shaping the textual
product.
Effects of dielectric layer on ductility for dielectric/Au/dielectric multilayers on polycarbonate substrate
Authors: Zhou Jiali , Zhang Xuan , Zhang Xiaofeng , Zhang Wenqiao , Chen Yuandong , Shi Huilei , Yan Yue
Published: July 2023

The ductility of transparent conductive films on polycarbonate (PC) substrate is of great concern as it significantly affects the stability and longevity of aeronautic equipment. Three types of dielectric/Au/dielectric multilayers, including ITO/Au/ITO (IAI), IZO/Au/IZO (ZAZ) and AZO/Au/AZO (AAA) were fabricated to obtain highly ductile films on thick rigid PC substrate. The ductility of multilayers was comparatively investigated using in situ scanning electron microscopy test and in situ electrical resistance test under uniaxial tension. The effect of dielectric layer on ductility was elucidated according to the results of film stress and elastic modulus, and analyzed using the energy release rate approach based on the mechanics model. The results of in situ tests revealed that the crack initiation strain by morphology and the conductive failure strain of AAA were found to be 1.04 ± 0.04% and 1.47 ± 0.07%, which were superior to those of IAI and ZAZ. This result can be attributed to differences in layer stress state and layer-substrate mechanical contrast induced by different dielectric layers. Although AAA has the lower fracture toughness, the higher compressive residual stress and the smaller elastic mismatch give AAA the smallest crack driving force under the same conditions, resulting in excellent ductility.
Reconstruction of three-dimensional strain field in an asymmetrical curved core–shell hetero-nanowire
Authors: Kryvyi Serhii , Kret Slawomir , Domagala Jaroslaw Z , Wojnar Piotr
Published: July 2023

Crystal orientation and strain mapping of an individual curved and asymmetrical core–shell hetero-nanowire (NW) is performed based on transmission electron microscopy. It relies on a comprehensive analysis of scanning nanobeam electron diffraction data obtained for 1.3 nm electron probe size. The proposed approach also handles the problem of appearing twinning defects on diffraction patterns and allows for the investigation of materials with high defect densities. Based on the experimental maps and their comparison with finite element simulations, the entire core–shell geometry including full three-dimensional strain distribution within the curved core–shell NW are obtained. Our approach represents, therefore, a low-dose quasi-tomography of the strain field within a nanoobject using only a single zone axis diffraction experiment. Our approach is applicable also for electron beam-sensitive materials for which performing conventional tomography is a difficult task.
Relativistic quantum heat engine with the presence of minimal length
Authors: Sukamto Heru , Yuwana Lila , Purwanto Agus
Published: July 2023

The presence of a minimal length has a significant effect on relativistic physical systems. This paper discusses how minimal length affects the efficiency of a relativistic quantum heat engine. The working substance chosen is a Dirac particle trapped in a one-dimensional infinite potential well. In this paper, we calculate the efficiency of a quantum heat engine in three thermodynamic cycles, namely the Carnot, Otto, and Brayton cycles. The engine efficiency is calculated analytically and numerically. In this research, the minimal length is a correction factor for the relativistic energy. The result is that the minimal length could increase or decrease the efficiency of the relativistic quantum heat engine on the small potential width according to the particle mass, the expansion parameter, and the thermodynamic cycle.
Narrow linewidth fiber laser with multiple unpumped EDF fiber loops and self-injection feedback
Authors: Li Huinan , Yang Feng , Sui Xiaolin , Wang Bo , Wu Ziyan , Wang Sha
Published: July 2023

In this paper, we proposed a narrow linewidth single-longitudinal-mode (SLM) fiber laser, which was realized by employing a triple-cascaded unpumped erbium doped fiber (EDF) Sagnac loops structure with Rayleigh backscattering (RBS) feedback. Narrow linewidth SLM laser output can be achieved by using the unpumped EDF loops. However, it is generally difficult to achieve laser emission with a linewidth below 1 kHz and a power of tens of milliwatts. In this paper, we propose a fiber laser with multiple unpumped Er-doped fiber loops and self-injection feedback. The cascade of multi-unpumped Er-doped fiber rings is employed to reduce the linewidth of the laser, while the self-injection feedback based on RBS is used to improve the stability of the laser and further compress the laser linewidth. By only utilizing three unpumped Er-doped fiber rings cascaded, we obtain an output beam with a linewidth of 723.05 Hz and laser power of 21.52 mW with 0.30 dB fluctuation during a period time of 30 min at the pump power of 170.6 mW. After introducing the feedback mechanism based on RBS into the fiber laser, an output laser with a linewidth of 530.11 Hz and a laser power of 8.57 mW with 0.23 dB fluctuation in 30 min can be obtained at the pump power of 268.68 mW. Compared with the fiber laser with one unpumped Er-doped fiber ring, the linewidth is reduced more than two times.