bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanical and electrical responses of natural-cooled high-temperature granite of different grain sizes
Authors: Jia Peng , Qian Yijin , Wang Qiwei , Mao Songze , Lu Jialiang
Published: December 2023

In order to understand the effect of grain size on the mechanical and electrical responses of natural-cooled high-temperature granite, uniaxial compression tests were carried out on natural cooled coarse- and fine-grained granite samples subjected to thermal treatment at room temperature, 200 °C, 400 °C, and 600 °C respectively. The resistivity and acoustic emission (AE) during the compression were monitored and changes in physical and mechanical properties, the AE and resistivity characteristics in the loading process were analyzed. Results show that high temperature exerts a more significant effect on deteriorating the coarse-grained granite. Changes in resistivity can reflect the development of rock damage. Corresponding to the compaction stage, crack initiation and stable propagation stage, and crack rapid propagation stage of rock under compressive load, changes in resistivity can be divided into three stages accordingly, including the initial rapid descent stage, the gentle descent stage, and the secondary rapid descent stage for the thermal-treated rock at 25–400 °C. The secondary rapid descent stage of resistivity can be used as a precursor for rock entering into the failure stage. The resistivity change is more sensitive to the damage development in coarse-grained granite.
Evolutionary Optimization of Convolutional Extreme Learning Machine for Remaining Useful Life Prediction
Authors: Mo Hyunho , Iacca Giovanni
Published: December 2023

Remaining useful life (RUL) prediction is a key enabler for making optimal maintenance strategies. Data-driven approaches, especially employing neural networks (NNs) such as multi-layer perceptrons (MLPs) and convolutional neural networks (CNNs), have gained increasing attention in the field of RUL prediction. Most of the past research has mainly focused on minimizing the RUL prediction error by training NNs with back-propagation (BP), which in general requires an extensive computational effort. However, in practice, such BP-based NNs (BPNNs) may not be affordable in industrial contexts that normally seek to save cost by minimizing access to expensive computing infrastructures. Driven by this motivation, here, we propose: (1) to use a very fast learning scheme called extreme learning machine (ELM) for training two different kinds of feed-forward neural networks (FFNNs), namely a single-layer feed-forward neural network (SL-FFNN) and a Convolutional ELM (CELM); and (2) to optimize the architecture of those networks by applying evolutionary computation. More specifically, we employ a multi-objective optimization (MOO) technique to search for the best network architectures in terms of trade-off between RUL prediction error and number of trainable parameters, the latter being correlated with computational effort. In our experiments, we test our methods on a widely used benchmark dataset, the C-MAPSS, on which we search such trade-off solutions. Compared to other methods based on BPNNs, our methods outperform a MLP and show a similar level of performance to a CNN in terms of prediction error, while using a much smaller (up to two orders of magnitude) number of trainable parameters.
“Radio Is a Blank Canvas for Youth Work”: Communication, Creative Agency, Compassion and Empathy
Authors: Howard Frances
Published: December 2023

Youth radio projects are firmly rooted in young people’s cultural and everyday experiences. Aligning with the open access, dialogic and participatory nature of youth work, youth radio programmes represent an ‘asset-based’ endeavour, which builds on young people’s cultural funds of knowledge. This article draws on data from two youth radio projects: Bolt FM, based in North East Glasgow, Scotland, and YMCA Digital, based in Nottingham, England. Youth workers and young people were interviewed about the affordances of radio as an outlet for creativity in their lives. In combination with youth work practice, radio as an art form can enable young people to tell stories, offer alternative narratives and more authentic modes of cultural production. Exploring creativity, this study theorises this mode of youth arts practice through Paul Willis’ Common Culture (1990). In the case of youth radio projects, communication, creative agency, compassion and empathy manifested. These findings strengthen existing research which highlights the value of youth work and radio programmes for young people.
Characterization of Thermal‐Hydraulic Coupling Behavior for Moraine Soil With Ice Inclusions in a Warming Environment
Authors: Zhou Jia‐Qing , Zhu Wen‐Yu , Li Qi‐Long , Wang Rui , Li Changdong , Gu Dongming , Wang Jiao
Published: December 2023

A warming environment is promoting the thawing process in ice‐rich moraine soils in cold alpine regions, thereby accelerating the formation/development of geohazards in these regions. The mechanism of these geohazards is closely related to the thermal‐hydraulic (TH) coupling behavior of moraine soils, which has rarely been investigated. Here, we conducted a series of bench‐scale TH coupling simulations of moraine soils with ice inclusions in a warming environment. The numerical model was conceptualized from a field survey on the Qinghai‐Tibet Plateau, which consists of a porous medium embedded with multilayer ice cubes with warmer water continuously flowing through it. A TH coupling framework considering ice‐water phase change was established to implement this coupled simulation with different initial ice contents and hydraulic gradients. The simulated results showed phased and nonlinear evolutionary features of temperature, ice content, and permeability for the moraine soil system. Further analyses showed that these complex evolutionary features can be reproduced by empirical formulas, with concise expressions following dimensional consistency and some coefficients having potential physical meanings. The discriminant models of two equilibrium states were finally developed to predict the critical times of structure stabilization and thermal equilibrium of the moraine soil system. This study presents the complex evolution of TH coupling properties of moraine soils, and simultaneously demonstrates that these properties can be predicted and characterized.
Decomposing the Precipitation Response to Climate Change in Convection Allowing Simulations Over the Conterminous United States
Authors: Wallace Brendan C. , Haberlie Alex M. , Ashley Walker S. , Gensini Vittorio A. , Michaelis Allison C.
Published: December 2023

Explicit representation of finer‐scale processes can affect the sign and magnitude of the precipitation response to climate change between convection‐permitting and convection‐parameterizing models. We compare precipitation across two 15‐year epochs, a historical (HIST) and an end‐of‐21st‐century (EoC85), between a set of dynamically downscaled regional climate simulations at 3.75 km grid spacing (WRF) and bias‐corrected Community Earth System Model (CESM) output used to initialize and force the lateral boundaries of the downscaled simulations. In the historical climate, the downscaled simulations demonstrate less overall error than CESM when compared to observations for most portions of the conterminous United States. Both sets of simulations overestimate the incidence of environments with moderate to high precipitable water while CESM generally simulates rainfall that is too frequent but less intense. Within both sets of simulations, EoC85 rainfall amounts decrease in low‐moisture environments due to reduced rainfall frequency and intensity while rainfall amounts increase in high‐moisture environments as they occur more often. Overall, reductions in rainfall are stronger in WRF than in CESM, particularly during the warm season. This reduced drying in CESM is attributed to relatively higher rainfall frequency in environments with high concentrations of precipitable water and weak vertical motion. As a result, an increase in the occurrence of high moisture environments in EoC85 naturally favors more rainfall in CESM than WRF. Our results present an in‐depth examination of the characteristics of changes in overall accumulated precipitation and highlight an extra dimension of uncertainty when comparing convection‐permitting models against convection‐parameterizing models.
Atlantic Hurricanes Are Intensifying Faster
Authors: Scharping Nathaniel
Published: December 2023

Warmer waters and other factors are allowing Atlantic hurricanes to grow stronger faster.
Ocean Deserts Could Help Capture CO2 and Mitigate Global Warming
Authors: Dai Minhan , Luo Ya-Wei , Lin Hongyang , Achterberg Eric , Browning Thomas , Church Matthew , Lee Zhongping , Wang Wei-Leng
Published: December 2023

Various nutrient sources in the upper waters of oceanic subtropical gyres, which are the Earth's largest oligotrophic ecosystems, play a crucial role in governing the sequestration of atmospheric CO2.
Processes in the Surface Ocean Regulate Dissolved Organic Matter Distributions in the Deep
Authors: Bercovici Sarah K. , Dittmar Thorsten , Niggemann Jutta
Published: December 2023

Marine dissolved organic matter (DOM) is a major global carbon pool, consisting of thousands of compounds with distinct lifetimes. While marine DOM persists for millennia, its molecular and isotopic composition imply that it is dynamic on shorter timescales. To determine the extent to which DOM deviates from conservative water mass mixing, we conducted a two‐endmember mixing analysis on dissolved organic carbon (DOC) concentration and DOM molecular composition in the Atlantic and Pacific. Endmembers were the deep water masses near their formation sites. For DOM composition, we considered 6118 molecular formulae (MF) identified via Fourier‐transform ion cyclotron resonance mass spectrometry in solid‐phase extracts (SPE) of 837 samples. Bulk DOC and SPE‐DOC concentrations behaved conservatively in both basins and ≥70% of the MF (14–20 μM SPE‐DOC) mixed conservatively. However, a small fraction (10%–20%) of the MF (<3 μM SPE‐DOC) were added or removed during mixing. These MF were more reduced and oxidized, respectively, than the conservative fraction. There were also MF absent from the endmembers; these accounted for ≤1 μM of SPE‐DOC and positively correlated with DOM lability. Based on their distribution across the two basins, we conclude that the conserved MF are formed in the surface subtropical ocean and modified in overturning areas. In the deep ocean, however, these MF are solely controlled by mixing. This finding contrasts with the current paradigm of slow, continuous degradation of recalcitrant DOM in the deep ocean. Our analysis illustrates the importance of the surface ocean in controlling DOM cycling in the deep.
Fine‐Scale Structures of STEVE Revealed by 4K Imaging
Authors: Nishimura Y. , Dyer A. , Donovan E. F. , Angelopoulos V.
Published: December 2023

We utilized a 4K imaging to examine properties of fine‐scale structures of Strong Thermal Emission Velocity Enhancement (STEVE) near the magnetic zenith. Its high spatial (0.09 km at 200 km altitude) and temporal (24 Hz) resolution provided unprecedented details of fine‐scale structures in the subauroral ionosphere. Although the STEVE emission was seen as a homogeneous purple/mauve arc in the all‐sky images, the high‐speed imaging revealed that STEVE contained substantial multi‐scale structures. The characteristic wavelength and period were 12.4 ± 7.4 km and 1.4 ± 0.8 s, and they drifted westward at 8.9 ± 0.7 km/s. The speed is comparable to the reported magnitude of the intense subauroral ion drifts (SAID), suggesting that the fine‐scale structures are an optical manifestation of the E × B drift in the intense SAID. A spectral analysis identified multiple peaks at >10, 4, 2, 1.1, and <1/5 s period (>83, 33, 16, 9, and <1.7 km wavelength). Although most of the fine‐scale structures were stable during the drift across the field of view, some of the structures dynamically evolved within a few tens of km. The fine‐scale structures have a power law spectrum with a slope of −1, indicating that shear flow turbulence cascade structures to smaller scales. The fine‐scale structures pose a challenge to the subauroral ionosphere‐thermosphere interaction about how the ionosphere creates such fine‐scale structures and how the thermosphere reacts much faster than expected from a typical chemical reaction time.
Nonlinear Internal Tides in a Realistically Forced Global Ocean Simulation
Authors: Solano Miguel S. , Buijsman Maarten C. , Shriver Jay F. , Magalhaes Jorge , da Silva Jose , Jackson Christopher , Arbic Brian K. , Barkan Roy
Published: December 2023

The decay of the low‐mode internal tide due to the superharmonic energy cascade is investigated in a realistically forced global Hybrid Coordinate Ocean Model simulation with 1/25° (4 km) horizontal grid spacing. Time‐mean and depth‐integrated supertidal kinetic energy is found to be largest near low‐latitude internal tide generation sites, such as the Bay of Bengal, Amazon Shelf, and Mascarene Ridge. The supertidal kinetic energy can make up to 50% of the total internal tide kinetic energy several hundred kilometers from the generation sites. As opposed to the tidal flux divergence, the supertidal flux divergence does not correlate with the barotropic to baroclinic energy conversion. Instead, the time‐mean and depth‐integrated supertidal flux divergence correlates with the nonlinear kinetic energy transfers from (sub)tidal to supertidal frequency bands as estimated with a novel coarse‐graining approach. The regular spaced banding patterns of the surface‐intensified nonlinear energy transfers are attributed to semidiurnal mode 1 and mode 2 internal waves that interfere constructively at the surface. This causes patches where both surface tidal kinetic energy and nonlinear energy transfers are elevated. The simulated internal tide off the Amazon Shelf steepens significantly near these patches, generating solitary‐like waves in good agreement with Synthetic Aperture Radar imagery. Globally, we find that regions of high supertidal energy flux also show a high correlation with observed instances of internal solitary waves.
Atmospheric Refraction Delay Toward Millimeter‐Level Lunar Laser Ranging: Correcting the Temperature‐Induced Error With Real‐Time and Co‐Located Lidar Measurements
Authors: He Yun , Jing Dongzhe , Liu Qi , Liu Fuchao , Yi Fan
Published: December 2023

Next‐generation lunar laser ranging (LLR) aims for mm‐level accuracy, significantly promoting the study of gravitational physics. However, atmospheric refraction delay causes an unacceptable ranging error that can be efficiently corrected by neither the atmospheric delay models nor ray‐tracing calculation. Here we report on an improved ray‐tracing method, in which temperature profiles measured by radiosonde are replaced by those measured by a pure rotational Raman lidar, to realize real‐time and co‐located delay correction. Using 9‐night lidar observations, temperature‐induced delays of ±15 mm can be corrected for laser ranging, which is the largest residual in the LLR error budget.
A computational framework for resolving the microbiome diversity conundrum
Authors: Daybog Itay , Kolodny Oren
Published: December 2023

Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term ‘the microbial β- diversity conundrum’. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals’ microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host’s fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
Enhanced TARP-γ8-PSD-95 coupling in excitatory neurons contributes to the rapid antidepressant-like action of ketamine in male mice
Authors: Xue Shi-Ge , He Jin-Gang , Lu Ling-Li , Song Shi-Jie , Chen Mei-Mei , Wang Fang , Chen Jian-Guo
Published: December 2023

Ketamine produces rapid antidepressant effects at sub-anesthetic dosage through early and sustained activation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), however, the exact molecular mechanism still remains unclear. Transmembrane AMPAR regulatory protein-γ8 (TARP-γ8) is identified as one of AMPAR auxiliary subunits, which controls assemblies, surface trafficking and gating of AMPARs. Here, we show that ketamine rescues both depressive-like behaviors and the decreased AMPARs-mediated neurotransmission by recruitment of TARP-γ8 at the postsynaptic sites in the ventral hippocampus of stressed male mice. Furthermore, the rapid antidepressant effects of ketamine are abolished by selective blockade of TARP-γ8-containing AMPAR or uncoupling of TARP-γ8 from PSD-95. Overexpression of TARP-γ8 reverses chronic stress-induced depressive-like behaviors and attenuation of AMPARs-mediated neurotransmission. Conversely, knockdown of TARP-γ8 in excitatory neurons prevents the rapid antidepressant effects of ketamine.
Sharp zero-phonon lines of single organic molecules on a hexagonal boron-nitride surface
Authors: Smit Robert , Tebyani Arash , Hameury Jil , van der Molen Sense Jan , Orrit Michel
Published: December 2023

Single fluorescent molecules embedded in the bulk of host crystals have proven to be sensitive probes of the dynamics in their nano environment, thanks to their narrow (about 30–50 MHz or 0.1–0.2 μeV) optical linewidth of the 0-0 zero-phonon line (0-0 ZPL) at cryogenic temperatures. However, the optical linewidths of the 0-0 ZPL have been found to increase dramatically as the single molecules are located closer to a surface or interface, while no 0-0 ZPL has been detected for single molecules on any surface. Here we study single terrylene molecules adsorbed on the surface of hexagonal boron-nitride (hBN) substrates. Our low-temperature results show that it is possible to observe the 0-0 ZPL of fluorescent molecules on a surface. We compare our results for molecules deposited on the surfaces of annealed and non-annealed hBN flakes and we see a marked improvement in the spectral stability of the emitters after annealing.
Accurate de novo peptide sequencing using fully convolutional neural networks
Authors: Liu Kaiyuan , Ye Yuzhen , Li Sujun , Tang Haixu
Published: December 2023

De novo peptide sequencing, which does not rely on a comprehensive target sequence database, provides us with a way to identify novel peptides from tandem mass spectra. However, current de novo sequencing algorithms suffer from low accuracy and coverage, which hinders their application in proteomics. In this paper, we present PepNet, a fully convolutional neural network for high accuracy de novo peptide sequencing. PepNet takes an MS/MS spectrum (represented as a high-dimensional vector) as input, and outputs the optimal peptide sequence along with its confidence score. The PepNet model is trained using a total of 3 million high-energy collisional dissociation MS/MS spectra from multiple human peptide spectral libraries. Evaluation results show that PepNet significantly outperforms current best-performing de novo sequencing algorithms (e.g. PointNovo and DeepNovo) in both peptide-level accuracy and positional-level accuracy. PepNet can sequence a large fraction of spectra that were not identified by database search engines, and thus could be used as a complementary tool to database search engines for peptide identification in proteomics. In addition, PepNet runs around 3x and 7x faster than PointNovo and DeepNovo on GPUs, respectively, thus being more suitable for the analysis of large-scale proteomics data.
Targeted mutagenesis of the herpesvirus fusogen central helix captures transition states
Authors: Zhou Momei , Vollmer Benjamin , Machala Emily , Chen Muyuan , Grünewald Kay , Arvin Ann M. , Chiu Wah , Oliver Stefan L.
Published: December 2023

Herpesviruses remain a burden for animal and human health, including the medically important varicella-zoster virus (VZV). Membrane fusion mediated by conserved core glycoproteins, the fusogen gB and the heterodimer gH-gL, enables herpesvirus cell entry. The ectodomain of gB orthologs has five domains and is proposed to transition from a prefusion to postfusion conformation but the functional relevance of the domains for this transition remains poorly defined. Here we describe structure-function studies of the VZV gB DIII central helix targeting residues 526EHV528. Critically, a H527P mutation captures gB in a prefusion conformation as determined by cryo-EM, a loss of membrane fusion in a virus free assay, and failure of recombinant VZV to spread in cell monolayers. Importantly, two predominant cryo-EM structures of gB[H527P] are identified by 3D classification and focused refinement, suggesting they represented gB conformations in transition. These studies reveal gB DIII as a critical element for herpesvirus gB fusion function.
Multi-step nucleation pathway of C-S-H during cement hydration from atomistic simulations
Authors: Aretxabaleta Xabier M. , López-Zorrilla Jon , Etxebarria Iñigo , Manzano Hegoi
Published: December 2023

The Calcium Silicate Hydrate (C-S-H) nucleation is a crucial step during cement hydration and determines to a great extent the rheology, microstructure, and properties of the cement paste. Recent evidence indicates that the C-S-H nucleation involves at least two steps, yet the underlying atomic scale mechanism, the nature of the primary particles and their stability, or how they merge/aggregate to form larger structures is unknown. In this work, we use atomistic simulation methods, specifically DFT, evolutionary algorithms (EA), and Molecular Dynamics (MD), to investigate the structure and formation of C-S-H primary particles (PPs) from the ions in solution, and then discuss a possible formation pathway for the C-S-H nucleation. Our simulations indicate that even for small sizes the most stable clusters encode C-S-H structural motifs, and we identified a C4S4H2 cluster candidate to be the C-S-H basic building block. We suggest a formation path in which small clusters formed by silicate dimers merge into large elongated aggregates. Upon dehydration, the C-S-H basic building blocks can be formed within the aggregates, and eventually crystallize.
A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers
Authors: Wranik Maximilian , Kepa Michal W. , Beale Emma V. , James Daniel , Bertrand Quentin , Weinert Tobias , Furrer Antonia , Glover Hannah , Gashi Dardan , Carrillo Melissa , Kondo Yasushi , Stipp Robin T. , Khusainov Georgii , Nass Karol , Ozerov Dmitry , Cirelli Claudio , Johnson Philip J. M. , Dworkowski Florian , Beale John H. , Stubbs Scott , Zamofing Thierry , Schneider Marco , Krauskopf Kristina , Gao Li , Thorn-Seshold Oliver , Bostedt Christoph , Bacellar Camila , Steinmetz Michel O. , Milne Christopher , Standfuss Jörg
Published: December 2023

Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.
Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone
Authors: Nam Donggeon , Bacik John-Paul , Khade Rahul L. , Aguilera Maria Camila , Wei Yang , Villada Juan D. , Neidig Michael L. , Zhang Yong , Ando Nozomi , Fasan Rudi
Published: December 2023

Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.
Diversification of division mechanisms in endospore-forming bacteria revealed by analyses of peptidoglycan synthesis in Clostridioides difficile
Authors: Shrestha Shailab , Taib Najwa , Gribaldo Simonetta , Shen Aimee
Published: December 2023

The bacterial enzymes FtsW and FtsI, encoded in the highly conserved dcw gene cluster, are considered to be universally essential for the synthesis of septal peptidoglycan (PG) during cell division. Here, we show that the pathogen Clostridioides difficile lacks a canonical FtsW/FtsI pair, and its dcw-encoded PG synthases have undergone a specialization to fulfill sporulation-specific roles, including synthesizing septal PG during the sporulation-specific mode of cell division. Although these enzymes are directly regulated by canonical divisome components during this process, dcw-encoded PG synthases and their divisome regulators are dispensable for cell division during normal growth. Instead, C. difficile uses a bifunctional class A penicillin-binding protein as the core divisome PG synthase, revealing a previously unreported role for this class of enzymes. Our findings support that the emergence of endosporulation in the Firmicutes phylum facilitated the functional repurposing of cell division factors. Moreover, they indicate that C. difficile, and likely other clostridia, assemble a distinct divisome that therefore may represent a unique target for therapeutic interventions.
Operando analysis of a solid oxide fuel cell by environmental transmission electron microscopy
Authors: Jeangros Q. , Bugnet M. , Epicier T. , Frantz C. , Diethelm S. , Montinaro D. , Tyukalova E. , Pivak Y. , Van herle J. , Hessler-Wyser A. , Duchamp M.
Published: December 2023

Correlating the microstructure of an energy conversion device to its performance is often a complex exercise, notably in solid oxide fuel cell research. Solid oxide fuel cells combine multiple materials and interfaces that evolve in time due to high operating temperatures and reactive atmospheres. We demonstrate here that operando environmental transmission electron microscopy can identify structure-property links in such devices. By contacting a cathode-electrolyte-anode cell to a heating and biasing microelectromechanical system in a single-chamber configuration, a direct correlation is found between the environmental conditions (oxygen and hydrogen partial pressures, temperature), the cell open circuit voltage, and the microstructural evolution of the fuel cell, down to the atomic scale. The results shed important insights into the impact of the anode oxidation state and its morphology on the cell electrical properties.
Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis
Authors: Sharma Meenakshi , de Alba Eva
Published: December 2023

Pathogenic dsDNA prompts AIM2 assembly leading to the formation of the inflammasome, a multimeric complex that triggers the inflammatory response. The recognition of foreign dsDNA involves AIM2 self-assembly concomitant with dsDNA binding. However, we lack mechanistic and kinetic information on the formation and propagation of the assembly, which can shed light on innate immunity’s time response and specificity. Combining optical traps and confocal fluorescence microscopy, we determine here the association and dissociation rates of the AIM2-DNA complex at the single molecule level. We identify distinct mechanisms for oligomer growth via the binding of incoming AIM2 molecules to adjacent dsDNA or direct interaction with bound AIM2 assemblies, resembling primary and secondary nucleation. Through these mechanisms, the size of AIM2 oligomers can increase fourfold in seconds. Finally, our data indicate that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2.
Programmable de novo designed coiled coil-mediated phase separation in mammalian cells
Authors: Ramšak Maruša , Ramirez Dominique A. , Hough Loren E. , Shirts Michael R. , Vidmar Sara , Eleršič Filipič Kristina , Anderluh Gregor , Jerala Roman
Published: December 2023

Membraneless liquid compartments based on phase-separating biopolymers have been observed in diverse cell types and attributed to weak multivalent interactions predominantly based on intrinsically disordered domains. The design of liquid-liquid phase separated (LLPS) condensates based on de novo designed tunable modules that interact in a well-understood, controllable manner could improve our understanding of this phenomenon and enable the introduction of new features. Here we report the construction of CC-LLPS in mammalian cells, based on designed coiled-coil (CC) dimer-forming modules, where the stability of CC pairs, their number, linkers, and sequential arrangement govern the transition between diffuse, liquid and immobile condensates and are corroborated by coarse-grained molecular simulations. Through modular design, we achieve multiple coexisting condensates, chemical regulation of LLPS, condensate fusion, formation from either one or two polypeptide components or LLPS regulation by a third polypeptide chain. These findings provide further insights into the principles underlying LLPS formation and a design platform for controlling biological processes.
Colliding heavy nuclei take multiple identities on the path to fusion
Authors: Cook Kaitlin J. , Rafferty Dominic C. , Hinde David J. , Simpson Edward C. , Dasgupta Mahananda , Corradi Lorenzo , Evers Maurits , Fioretto Enrico , Jeung Dongyun , Lobanov Nikolai , Luong Duc Huy , Mijatović Tea , Montagnoli Giovanna , Stefanini Alberto M. , Szilner Suzana
Published: December 2023

The properties of superheavy elements probe extremes of physics and chemistry. They are synthesised at accelerator laboratories using nuclear fusion, where two atomic nuclei collide, stick together (capture), then with low probability evolve to a compact superheavy nucleus. The fundamental microscopic mechanisms controlling fusion are not fully understood, limiting predictive capability. Even capture, considered to be the simplest stage of fusion, is not matched by models. Here we show that collisions of 40Ca with 208Pb, experience an ‘explosion’ of mass and charge transfers between the nuclei before capture, with unexpectedly high probability and complexity. Ninety different partitions of the protons and neutrons between the projectile-like and target-like nuclei are observed. Since each is expected to have a different probability of fusion, the early stages of collisions may be crucial in superheavy element synthesis. Our interpretation challenges the current view of fusion, explains both the successes and failures of current capture models, and provides a framework for improved models.
Single-crystal ZrCo nanoparticle for advanced hydrogen and H-isotope storage
Authors: Li Zhenyang , Liu Shiyuan , Pu Yanhui , Huang Gang , Yuan Yingbo , Zhu Ruiqi , Li Xufeng , Chen Chunyan , Deng Gao , Zou Haihan , Yi Peng , Fang Ming , Sun Xin , He Junzhe , Cai He , Shang Jiaxiang , Liu Xiaofang , Yu Ronghai , Shui Jianglan
Published: December 2023

Hydrogen-isotope storage materials are essential for the controlled nuclear fusion. However, the currently used smelting-ZrCo alloy suffers from rapid degradation of performance due to severe disproportionation. Here, we reveal a defect-derived disproportionation mechanism and report a nano-single-crystal strategy to solve ZrCo’s problems. Single-crystal nano-ZrCo is synthesized by a wet-chemistry method and exhibits excellent comprehensive hydrogen-isotope storage performances, including ultrafast uptake/release kinetics, high anti-disproportionation ability, and stable cycling, far superior to conventional smelting-ZrCo. Especially, a further incorporation of Ti into nano-ZrCo can almost suppress the disproportionation reaction. Moreover, a mathematical relationship between dehydrogenation temperature and ZrCo particle size is established. Additionally, a microwave method capable of nondestructively detecting the hydrogen storage state of ZrCo is developed. The proposed disproportionation mechanism and anti-disproportionation strategy will be instructive for other materials with similar problems.
Precise synthesis and photovoltaic properties of giant molecule acceptors
Authors: Zhuo Hongmei , Li Xiaojun , Zhang Jinyuan , Zhu Can , He Haozhe , Ding Kan , Li Jing , Meng Lei , Ade Harald , Li Yongfang
Published: December 2023

Series of giant molecule acceptors DY, TY and QY with two, three and four small molecule acceptor subunits are synthesized by a stepwise synthetic method and used for systematically investigating the influence of subunit numbers on the structure-property relationship from small molecule acceptor YDT to giant molecule acceptors and to polymerized small molecule acceptor PY-IT. Among these acceptors-based devices, the TY-based film shows proper donor/acceptor phase separation, higher charge transfer state yield and longer charge transfer state lifetime. Combining with the highest electron mobility, more efficient exciton dissociation and lower charge carrier recombination properties, the TY-based device exhibits the highest power conversion efficiency of 16.32%. These results indicate that the subunit number in these acceptors has significant influence on their photovoltaic properties. This stepwise synthetic method of giant molecule acceptors will be beneficial to diversify their structures and promote their applications in high-efficiency and stable organic solar cells.
Synthesizing evidence for the external cycling of NOx in high- to low-NOx atmospheres
Authors: Ye Chunxiang , Zhou Xianliang , Zhang Yingjie , Wang Youfeng , Wang Jianshu , Zhang Chong , Woodward-Massey Robert , Cantrell Christopher , Mauldin Roy L. , Campos Teresa , Hornbrook Rebecca S. , Ortega John , Apel Eric C. , Haggerty Julie , Hall Samuel , Ullmann Kirk , Weinheimer Andrew , Stutz Jochen , Karl Thomas , Smith James N. , Guenther Alex , Song Shaojie
Published: December 2023

External cycling regenerating nitrogen oxides (NOx ≡ NO + NO2) from their oxidative reservoir, NOz, is proposed to reshape the temporal–spatial distribution of NOx and consequently hydroxyl radical (OH), the most important oxidant in the atmosphere. Here we verify the in situ external cycling of NOx in various environments with nitrous acid (HONO) as an intermediate based on synthesized field evidence collected onboard aircraft platform at daytime. External cycling helps to reconcile stubborn underestimation on observed ratios of HONO/NO2 and NO2/NOz by current chemical model schemes and rationalize atypical diurnal concentration profiles of HONO and NO2 lacking noontime valleys specially observed in low-NOx atmospheres. Perturbation on the budget of HONO and NOx by external cycling is also found to increase as NOx concentration decreases. Consequently, model underestimation of OH observations by up to 41% in low NOx atmospheres is attributed to the omission of external cycling in models.
Potential window alignment regulating ion transfer in faradaic junctions for efficient photoelectrocatalysis
Authors: Dong Hongzheng , Pan Xiangyu , Gong Yuancai , Xue Mengfan , Wang Pin , Ho-Kimura SocMan , Yao Yingfang , Xin Hao , Luo Wenjun , Zou Zhigang
Published: December 2023

In the past decades, a band alignment theory has become a basis for designing different high-performance semiconductor devices, such as photocatalysis, photoelectrocatalysis, photoelectrostorage and third-generation photovoltaics. Recently, a faradaic junction model (coupled electron and ion transfer) has been proposed to explain charge transfer phenomena in these semiconductor heterojunctions. However, the classic band alignment theory cannot explain coupled electron and ion transfer processes because it only regulates electron transfer. Therefore, it is very significant to explore a suitable design concept for regulating coupled electron and ion transfer in order to improve the performance of semiconductor heterojunctions. Herein, we propose a potential window alignment theory for regulating ion transfer and remarkably improving the photoelectrocatalytic performance of a MoS2/Cd-Cu2ZnSnS4 heterojunction photocathode. Moreover, we find that a faradaic potential window, rather than the band position of the intermediate layer, is a criterion for identifying interface charge transfer direction. This finding can offer different perspectives for designing high-performance semiconductor heterojunctions with suitable potential windows for solar energy conversion and storage.
Real-time speech MRI datasets with corresponding articulator ground-truth segmentations
Authors: Ruthven Matthieu , Peplinski Agnieszka M. , Adams David M. , King Andrew P. , Miquel Marc Eric
Published: December 2023

The use of real-time magnetic resonance imaging (rt-MRI) of speech is increasing in clinical practice and speech science research. Analysis of such images often requires segmentation of articulators and the vocal tract, and the community is turning to deep-learning-based methods to perform this segmentation. While there are publicly available rt-MRI datasets of speech, these do not include ground-truth (GT) segmentations, a key requirement for the development of deep-learning-based segmentation methods. To begin to address this barrier, this work presents rt-MRI speech datasets of five healthy adult volunteers with corresponding GT segmentations and velopharyngeal closure patterns. The images were acquired using standard clinical MRI scanners, coils and sequences to facilitate acquisition of similar images in other centres. The datasets include manually created GT segmentations of six anatomical features including the tongue, soft palate and vocal tract. In addition, this work makes code and instructions to implement a current state-of-the-art deep-learning-based method to segment rt-MRI speech datasets publicly available, thus providing the community and others with a starting point for developing such methods.
MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects
Authors: Wang He , Lim Kai Peng , Kong Weijia , Gao Huanhuan , Wong Bertrand Jern Han , Phua Ser Xian , Guo Tiannan , Goh Wilson Wen Bin
Published: December 2023

Mass spectrometry-based proteomics plays a critical role in current biological and clinical research. Technical issues like data integration, missing value imputation, batch effect correction and the exploration of inter-connections amongst these technical issues, can produce errors but are not well studied. Although proteomic technologies have improved significantly in recent years, this alone cannot resolve these issues. What is needed are better algorithms and data processing knowledge. But to obtain these, we need appropriate proteomics datasets for exploration, investigation, and benchmarking. To meet this need, we developed MultiPro (Multi-purpose Proteome Resource), a resource comprising four comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent Acquisition (DDA) and Data Independent Acquisition (DIA) modes. Each dataset contains a balanced two-class design based on well-characterized and widely studied cell lines (A549 vs K562 or HCC1806 vs HS578T) with 48 or 36 biological and technical replicates altogether, allowing for investigation of a multitude of technical issues. These datasets allow for investigation of inter-connections between class and batch factors, or to develop approaches to compare and integrate data from DDA and DIA platforms.
A nomogram based on psoas muscle index predicting long-term cirrhosis incidence in non-cirrhotic patients with HBV-related acute‑on‑chronic liver failure
Authors: Bai Jie , Xu Manman , Peng Fengling , Gong Junwei , Song Xiaodong , Li Yongguo
Published: December 2023

There is a lack of scoring system to predict the occurrence of cirrhosis in individuals with acute-on-chronic liver failure (ACLF) in the absence of cirrhosis. The goal of this study was to develop a psoas muscle index (PMI)-based nomogram for cirrhosis risk in non-cirrhotic patients with HBV-related ACLF. We included 274 non-cirrhotic HBV-ACLF patients who were randomly assigned to training and validation groups. Logistic analyses were performed to identify risk factors for cirrhosis. A nomogram was then constructed. The predictive performance of the nomogram was assessed using the area under the receiver operating characteristic curve (AUROC), calibration curve, and decision curve analysis (DCA). During the 360-day follow-up, 44.5% (122/274) of non-cirrhotic HBV-ACLF patients developed cirrhosis. A higher PMI at the L3 level was correlated with a decreased risk of long-term cirrhosis occurrence (OR 0.677, 95% CI 0.518–0.885, P = 0.004). The nomogram incorporating PMI, age, neutrophil-to-lymphocyte ratio (NLR), and international normalized ratio (INR), indicated satisfactory predictive performance for cirrhosis risk stratification in ACLF population. The nomograms had an AUROC of 0.812 (95% CI 0.747–0.866) and 0.824 (95% CI 0.730–0.896) in the training and validation cohorts, respectively. The calibration curves displayed excellent predictive accuracy of the nomogram in both sets. In both cohorts, the DCA verified the nomogram's clinical efficacy. In non-cirrhotic HBV-ACLF patients, a greater PMI appears to protect against long-term cirrhosis occurrence. Strong predictive performance has been demonstrated by PMI-based nomograms in assessing the likelihood of 1-year cirrhosis in those with HBV-ACLF.
Ratios of monocytes and neutrophils to lymphocytes in the blood predict benefit of CDK4/6 inhibitor treatment in metastatic breast cancer
Authors: Moukas Stefanos Ioannis , Kasimir-Bauer Sabine , Tewes Mitra , Kolberg Hans-Christian , Hoffmann Oliver , Kimmig Rainer , Keup Corinna
Published: December 2023

Biomarkers to identify metastatic breast cancer (mBC) patients resistant to CDK4/6 inhibition (CDK4/6i) are currently missing. We evaluated the usefulness of the monocyte-to-lymphocyte ratio (MLR), the neutrophil–to-lymphocyte ratio (NLR) and the platelet-to-lymphocyte ratio (PLR) as predictive markers for de novo resistance to CDK4/6i. Various blood cell counts and MLR, NLR, PLR were recorded before treatment initiation (baseline) and four weeks later from 97 mBC patients receiving endocrine therapy (ET) alone or in combination with CDK4/6i. Binary blood cell count/ratios (mean = cut-off) were related to outcome using Cox regression. High MLR (p = 0.001) and high NLR (p = 0.01) at baseline significantly correlated with a shorter progression-free survival (PFS) in the CDK4/6i cohort, independent of any other clinical parameter as determined by multivariate Cox regression. Both, high MLR (p = 0.008) and high NLR (p = 0.043) as well as a decrease in PLR after four weeks of CDK4/6i first line treatment (p = 0.01) indicated a shorter overall survival. Moreover, decreasing PLR (p = 0.043) and increasing mean corpuscular volume (MCV; p = 0.011) within the first cycle of CDK4/6i correlated with a shorter PFS and decreasing MLR (p = 0.039) within the first cycle of first-line CDK4/6i was also correlated with shorter PFS. In summary, easily assessable blood cell parameter were shown to have predictive, monitoring and prognostic value and thus, could, in future, be used for individualized CDK4/6i therapy management. Most importantly, the imbalance of NLR and MLR at baseline might serve as predictive marker for de novo resistance to CDK4/6i in mBC patients.
Nutritional status of pediatric patients with inflammatory bowel diseases is related to disease duration and clinical picture at diagnosis
Authors: Pawłowska-Seredyńska Katarzyna , Akutko Katarzyna , Umławska Wioleta , Śmieszniak Bartłomiej , Seredyński Rafał , Stawarski Andrzej , Pytrus Tomasz , Iwańczak Barbara
Published: December 2023

This cross-sectional study presents the nutritional status of newly diagnosed pediatric patients with Crohn’s disease (CD) and ulcerative colitis (UC) and its association with the duration of the disease and selected clinical features. We analyzed the data of 41 pediatric patients with CD and 29 with UC (mean age: 13.1 y, range: 5.2–18.0 y) up to 3 mo. from diagnosis. Anthropometry included body weight, body height, body mass index (BMI), three skinfold thicknesses, mid-upper arm circumference and mid-upper arm muscle circumference adjusted for age and sex using national standards. Anthropometry was linked to the disease duration, location of the disease, symptoms, and blood test results. Both studied groups presented significantly lower BMI compared to the reference population, but only children with CD characterized with significantly worse nutritional status according to arm anthropometry. In CD, better nutritional status was associated mainly with longer disease duration and, to a lesser extent, with extraintestinal manifestations, perianal disease, and small intestinal lesions. In UC, anemia at diagnosis was associated with poor nutritional status. Our finding emphasizes the need for more attentive diagnostic care for pediatric patients who exhibit extraintestinal symptoms or perianal disease with no obvious signs of malnutrition, to avoid diagnostic delays.