Distinct Modes Research Articles

Inhibition mechanism of α-amylase and amyloglucosidase by spherical nanocrystalline cellulose with varying particle sizes.

Inhibition mechanism of α-amylase and amyloglucosidase by spherical nanocrystalline cellulose with varying particle sizes.

Effect of dopant-induced local vibration modes on pressure-driven structural phase transition in Mn- and Co-doped ZnO

Effect of dopant-induced local vibration modes on pressure-driven structural phase transition in Mn- and Co-doped ZnO

Simultaneous and instrument-free detection of quinine and crystal violet based on a dual-emissive Eu3+-functionalized metal-organic framework.

Simultaneous and instrument-free detection of quinine and crystal violet based on a dual-emissive Eu3+-functionalized metal-organic framework.

An analytical model for customizing reinforcement plasticity to address the strength-ductility trade-off in staggered composites.

An analytical model for customizing reinforcement plasticity to address the strength-ductility trade-off in staggered composites.

Slow and steady: long-term evolution of the 76-second pulsar J0901−4046

Abstract PSR J0901−4046, a likely radio-loud neutron star with a period of 75.88 seconds, challenges conventional models of neutron star radio emission. Here, we showcase results from 46 hours of follow-up observations of PSR J0901−4046 using the MeerKAT, Murriyang, GMRT, and MWA radio telescopes. We demonstrate the intriguing stability of the source’s timing solution over more than three years, leading to an RMS arrival-time uncertainty of just ∼10−4 of the rotation period. Furthermore, non-detection below 500 MHz may indicate a low-frequency turnover in the source’s spectrum, while no secular decline in the flux density of the source over time, as was apparent from previous observations, has been observed. Using high time-resolution MeerKAT data, we demonstrate two distinct quasi-periodic oscillation modes present in single pulses, with characteristic time scales of 73 ms and 21 ms. We also observe a statistically significant change in the relative prevalence of distinct pulse morphologies compared to previous observations, possibly indicating a shift in the magnetospheric composition over time. Finally, we show that the W50 pulse width is nearly constant from 544–4032 MHz, consistent with zero radius-to-frequency mapping. The very short duty cycle (∼1.4○) is more similar to radio pulsars with periods >5 seconds than to radio-loud magnetars. This, along with the lack of magnetar-like outbursts or timing glitches, complicates the identification of the source with ultra-long period magnetar models.

Modes of Relevance in Research: Towards Understanding the Promises and Possibilities of Doing Relevance

Abstract In response to growing social, ecological and health-related challenges, scientists are increasingly expected to demonstrate the societal relevance of their work. This special issue critically examines the concept of “relevance” in scientific research, exploring how it is defined, enacted and contested across disciplines, institutions and collaborations. We propose a practice-oriented conceptualization of “doing relevance”, understanding it not as an inherent property of knowledge, but as a situated achievement shaped by various practices. To this end, we introduce four distinct modes of relevance: 1) relevance as reorienting research topics and disciplines; 2) relevance as engaging societal actors in user-driven research; 3) relevance as reshaping interactions between science and policy; and 4) relevance as transforming academic institutions. The contributions to this issue analyze how these four modes are enacted through the practices of diverse actors, demonstrating that relevance is not a static or self-evident concept, but is continually redefined in situated and context-specific engagements. Together, the articles illustrate how researchers navigate diverse expectations and institutional demands, leading them to enact relevance through concrete practices instead of following pre-determined criteria. We conclude by calling for future research that further explores how relevance is continually reconfigured in response to specific challenges, and how these reconfigurations enable and constrain science’s capacity to address pressing societal needs.

Investigation and design of the dual specificity of the PRDM9 protein lysine methyltransferase

The PRDM9 protein lysine methyltransferase is essential in meiotic recombination where it trimethylates H3K4 and H3K36 in chromatin. However, it is not known how this enzyme can specifically methylate these two substrates despite their dissimilar amino acid sequences. Using biochemical and molecular dynamics simulation approaches, we uncover that PRDM’s unique dual substrate specificity is based on distinct interaction modes of the enzyme with both substrates. Our data show that PRDM9 interacts with the H3K4 and H3K36 peptides through a bipartite peptide binding cleft, comprising one part specific for H3K4 but tolerating H3K36, and a second part with the opposite properties. Binding of the H3K4 and H3K36 peptide substrates occurs in slightly different conformations which enables the specific recognition of both substrates. While wildtype PRDM9 showed higher activity on H3K4 peptides, site-directed mutagenesis of residues involved in PRDM9-peptide contacts allowed us to strongly modulate the K4/K36 preferences creating mutants with elevated preference for H3K4, mutants with equal methylation of both substrates and even mutants with preference for H3K36. Our data illustrate evolutionary pathways to swap the sequence specificity of PKMTs by few amino acid exchanges, a process that happened several times in the divergent evolution of PKMTs.

Statistical Context Learning in Visual Search: Distinct Electrophysiological Signatures of Contextual Guidance and Context Suppression.

Facilitation of visual search by repeated distractor contexts is typically studied employing distractor configurations that are 100% predictive of the target location. Yet, real-world contexts vary in predictivity. We used electroencephalography (EEG) in human participants of either sex to explore how visual search facilitation arises from two distinct processing modes-contextual guidance and context suppression-that depend on the predictivity of distractor contexts, comparing repeated distractor arrangements that were either predictive or nonpredictive of target location against a baseline of nonrepeated arrangements. In Experiment 1, we manipulated context predictivity by shifting repeated contexts from predictive to nonpredictive and vice versa, while in Experiment 2, we restricted repeated contexts to one side of the display to assess lateralized effects of the two processing modes. Both types of contexts behaviorally facilitated visual search, but facilitation was larger with predictive contexts. Making predictive contexts nonpredictive reduced the facilitation while rendering nonpredictive contexts predictive failed to produce gains. Half-display predictive contexts facilitated target detection on both sides, while nonpredictive contexts facilitated same-side target detection only. EEG analyses revealed that predictive contexts triggered an early N1pc (guidance signal), followed by an enhanced N2pc (attentional selection) and an increased contralateral delay activity (CDA, indexing working memory processing of the target) in occipitoparietal regions, indicative of contextual guidance boosting the entire processing chain. In contrast, nonpredictive contexts produced only an increased N2pc accompanied by reduced CDA, consistent with context suppression. These differential patterns demonstrate contextual guidance and context suppression to operate as electrophysiologically distinct processing modes.

Distinct non-canonical translation initiation modes arise for specific host and viral mRNAs during poxvirus-induced shutoff.

Many viruses potently inhibit host protein synthesis, termed host shutoff, while employing strategies to sustain their own translation. How and why certain host mRNAs continue to be translated at later infection stages remains unclear. Here, using RNAseq and polysome profiling, we show that during shutoff by vaccinia virus (VacV), several host mRNAs increase in polysome occupancy but only a few, primarily JUN that encodes the Jun transcription factor, result in increased protein abundance across multiple cell lines. While dispensable for Jun production, translation of viral mRNAs depended on the small ribosomal protein, Receptor for Activated C Kinase 1 (RACK1) and the eukaryotic Initiation Factor, eIF3. These differential eIF3 dependencies are associated with structurally distinct 5' untranslated regions in viral versus JUN mRNAs. Cryo-electron microscopy structures of 40S ribosomes from mock-infected or VacV-infected cells showed that when bound to eIF3, the rotational range of the RACK1-containing 40S head domain broadens during infection. Our data reveal how eIF3-bound 40S ribosomes are remodelled late in infection and the distinct strategies of translation initiation that arise during shutoff to produce host and viral proteins required for poxvirus spread.

Decoupling Self-Matching Effect Between Cathode and Anode in Hybrid Electrochemical Capacitors.

Hybrid electrochemical capacitors (HECs) are advanced energy storage devices that offer high energy density, high power density, and long cycle life by integrating the energy storage mechanisms of both batteries and supercapacitors. The electrochemical coupling resulting from the cathode-anode kinetic differences severely restricts the accuracy of predicting the performance of HECs based on electrode performance. However, no general method can decouple the effects of cathode-anode kinetics matching on electrochemical performance by integrating electrochemical coupling from an electrochemical perspective. Here, using an integrated method that combines two distinct three-electrode testing modes in the typical sodium-ion hybrid capacitors, the self-matching effect of cathode-anode working potential ranges is first refined as the foundation for kinetic matching and electrochemical coupling. The discrepancies and interdependencies in cathode-anode electrochemical coupling for an individual kinetic match are decoupled by examining the impact of the self-matching effect on the electrochemical results. The critical matching current density is introduced as a key kinetic parameter for evaluating the degree of cathode-anode matching in complex electrochemical systems. This advancement provides an innovative design principle for electrode matching and coupling in high-performance HECs.

Groundwater influence on vegetation: water source, waterlogging, or both?

From a broad, global-to-hillslope perspective, I will discuss some observational evidence and model results suggesting that the groundwater can directly influence vegetation through three mechanisms: as a water source for plant root uptake in dry places/times where/when the water table is accessible, as a cause for waterlogging and soil anoxia where/when the water table is too near the surface, and as a double-stressor if the water table fluctuates wildly, too deep in dry times but too shallow in wet times. as a water source for plant root uptake in dry places/times where/when the water table is accessible, as a cause for waterlogging and soil anoxia where/when the water table is too near the surface, and as a double-stressor if the water table fluctuates wildly, too deep in dry times but too shallow in wet times. The dominance of each mechanism, and the resulting mode of vegetation feedback, can be analyzed in a 2D space, with the climate on one axis, and the topographic structure on the other, forming a climotopo-matrix to frame the distinct modes of groundwater-vegetation interactions. On top of this framework, the subsurface structure of the Critical Zone forms a 3rd dimension that regulates the infiltration and water table depths, further enriching the models of groundwater-vegetation interactions. I will end by posing a set of hypotheses as food for further thoughts.

Discharge modes of self-pulsing discharges in argon at atmospheric pressure

Abstract Self-pulsing discharges are an intriguing method to generate non-thermal plasma using DC high voltages. However, the sophisticated interaction between the electrical circuit and the actual plasma characteristics is still not well explored. Therefore, this study presents a modelling study on self-pulsing discharges in pure argon at atmospheric pressure in a 1.5 mm gas gap. A time-resolved, one-dimensional fluid-Poisson model coupled to an equivalent circuit with variable parameters is applied to analyse the impact of circuit parameters like internal resistance and applied negative DC high voltage on basic discharge properties. This includes the analysis of the spatio-temporal development of the densities of charge carriers and excited species, the electric field and ionisation rates in combination with the synchronised electrical quantities like discharge current, discharge voltage and self-pulsing frequency. In particular, three distinct periodic self-pulsing modes of the discharge are found, i.e., a transient spark, a transient glow and a modulated DC glow mode. The transition between these modes is related to different recharging times of the circuit capacitance for different external resistances in series with the gas gap. It leads to changes in the predominance of the different ionisation processes together with the crucial impact of pre-ionisation on the discharge inception. These insights provide essential knowledge on tunability within a selection of self-pulsing DC discharge modes for generating non-thermal plasma with desired effects, e.g. for material processing and environmental or medical applications.

Improved Corrosion Resistance and Thermal Stability for Carbon Fiber‐Based Composites by Molten Salt

Carbon fiber/carbon fiber‐based (C/C) composites have attracted significant attention in nuclear energy systems. Especially in molten salt reactors (MSRs) for usage of green energy, this material shows exceptional mechanical properties, high‐temperature resistance, and corrosion resistance. However, in molten salt environments, there is lack of structural failure modes of C/C composites under tensile loading. It is crucial to evaluate the rationality of structural design for in‐service MSR. Herein, synergistic effects of molten salt infiltration and thermal stability are explored on mechanical behaviors of C/C composites, employing acoustic emission (AE) and synchrotron radiation grazing‐incidence wide‐angle X‐ray scattering (GIWAXS) to monitor corresponding structure and morphology evolution. AE identified four distinct damage modes of C/C composites: fiber‐matrix debonding, matrix cracking, individual fiber breakage, and fiber bundle fracture, corroborating by scanning electron microscopy, revealing microstructural reduction. Furthermore, the effects of high‐temperature thermal treatment and molten salt infiltration on the crystal structure of C/C composites are confirmed by in situ high‐temperature synchrotron‐based GIWAXS . These findings suggest that both treatments improve the corrosion resistance, mechanical integrity, and thermal stability of C/C composites.

CrazyKhoreia: A Robotic Perception System for MAV Path Planning From Digital Images

Micro Air Vehicles (MAVs) can be used for a wide range of applications, such as drone-based light shows for cultural or marketing purposes, or as a replacement for fireworks. However, more widespread usage of this technology is precluded by the usability gap between choreography design and deployment on target drones. Seamless deployment of MAV choreographies requires the building of computational interfaces that can obtain drone trajectories from conventional media such as digital images. In this paper, we propose CrazyKhoreia, a low-cost, computationally efficient approach to MAV choreography design. CrazyKhoreia is a robotic perception system that obtains a safe, traversable, and accurate waypoint matrix from a digital image. We validate our trajectory generation system through two distinct modes of operation: light painting, where an MAV flies through all waypoints, and multi-drone formation, in which multiple MAVs are arranged to emulate a given image. The utility of each mode is evaluated differently, using the full resolution CrazyKhoreia output as a reference for comparison. For the light painting mode, we logged the MAV’s pose at a frequency of 10 Hz and compared it with the reference for different levels of detail in the reproduced path. The Root Mean Squared Error (RMSE) ranges from 0.1287 to 0.3190 m. For multi-drone formation, where the swarm remains stationary, we computed the RMSE by comparing observed positions with the reference across multiple tests, resulting in a mean RMSE value of 0.1360 m.

Seven-core trench-assisted-graded-index ring fiber for orbital angular momentum modes

Abstract To meet the ever-increasing demand for data rate and bandwidth, mode-division-multiplexing technology utilizing orbital angular momentum (OAM) emerges as a promising solution to substantially expand the transmission capacity of optical fiber communication systems. In this work, we propose and numerically investigate a refractive index profile for multi-core fiber, termed the seven-core trench-assisted-graded-index ring fiber. This designed fiber introduces a graded-index profile to enhance OAM mode purity and increase the number of supported modes within a multi-ring core structure. A trench-assisted design is implemented to further suppress the crosstalk between multiple ring cores. To our knowledge, the seven-core trench-assisted-graded-index ring fiber is adopted for the first time to simultaneously maximize OAM purity and minimize the inter-core crosstalk. Through systematic numerical analysis using the finite element method (FEM), the optimized fiber can support 266 distinct OAM modes within the C-band. The purity of these OAM modes, synthesized from intrinsic EH modes, exceeds 99.27%. The effective mode area (A eff) for most supported OAM modes reaches 190 µm2, significantly surpassing that of step-index ring core fiber (SIRCF). Through careful optimization of structural parameters, the crosstalk between adjacent cores can be maintained below -90 dB after a 100-km transmission distance for the majority of modes.

Tri-Mode CRISPR-Based Biosensor for miRNA Detection: Enhancing Clinical Diagnostics with Cross-Validation.

In vitro diagnostics require the accurate detection of disease-associated target biomolecules at ultralow concentrations. A multimode sensing strategy is considered as a potential method for in vitro diagnosis because it allows cross-validation of test results through data complementation and self-calibration, and provides double confirmation. Here, we present a CRISPR/Cas12a-powered trimode biosensor (CPTMB) for ultrasensitive and reliable analysis of miRNA. Briefly, the presence of target miRNA initiates rolling circle extension-driven loop-mediated isothermal amplification (R-LAMP), which subsequently activates the trans-cleavage activity of CRISPR/Cas12a. Then, the hairpin probe (HP) biogate on nucleic acid-functionalized MB@Fe-MOF signal probe was degraded by Cas12a, leading to the release of methylene blue (MB) signal molecules encapsulated within Fe-MOF nanocarriers. Due to the capability of MB to generate output responses across three distinct modes: electrochemical (EC), fluorescence (FL), and ultraviolet-visible spectroscopy (UV-vis), a trimodal sensing system is achieved. Benefiting from the efficient signal amplification capabilities of R-LAMP and CRISPR/Cas12a, this strategy enables rapid detection of target miRNA at femtomolar levels within 70 min. Furthermore, the detection results across the three modes cross-validate one another, thereby enhancing the reliability of the analysis. More importantly, the platform has been successfully applied to miRNA analysis in real samples, and the detection results are in good agreement with those of the standard method RT-qPCR, indicating its great potential in the clinical diagnosis of early-stage cancer.

Variety of coil sets for the compact stellarator-tokamak hybrid

Abstract A first of-its-kind quasi-axisymmetric stellarator-tokamak hybrid design concept has recently been presented. Here we will provide an overview of various coil configurations that can be employed in this hybrid design, showcasing the versatility of possible topologies. A device based on this design method could be operated either as a tokamak or as a low-aspect-ratio, quasi-axisymmetric stellarator. The volumes and aspect ratios of the two distinct modes of operation are kept approximately constant, thereby ensuring that no volume is lost due to the shaping of the stellarator coils. It is notable that the number of coils required for this optimized stellarator can be reduced to a single additional type of unlinked modular coil (``banana coil''), as compared to the tokamak scenario. However, the use of multiple, smaller banana coils is also a viable option, as demonstrated in this study.

Viral fusion proteins of classes II and III recognize and reorganize complex biological membranes

Viral infection requires stable binding of viral fusion proteins to host membranes, which contain hundreds of lipid species. The mechanisms by which fusion proteins utilize specific host lipids to drive virus–host membrane fusion remains elusive. We conducted molecular simulations of classes I, II, and III fusion proteins interacting with membranes of diverse lipid compositions. Free energy calculations reveal that class I fusion proteins generally exhibit stronger membrane binding compared to classes II and III — a trend consistent across 74 fusion proteins from 13 viral families as suggested by sequence analysis. Class II fusion proteins utilize a lipid binding pocket formed by fusion protein monomers, stabilizing the initial binding of monomers to the host membrane prior to assembling into fusogenic trimers. In contrast, class III fusion proteins form a lipid binding pocket at the monomer–monomer interface through a unique fusion loop crossover. The distinct lipid binding modes correlate with the differing maturation pathways of classes II and III proteins. Binding affinity was predominantly controlled by cholesterol and gangliosides as well as via local enrichment of polyunsaturated lipids, thereby locally enhancing membrane disorder. Our study reveals energetics and atomic details underlying lipid recognition and reorganization by different viral fusion protein classes, offering insights into their specialized membrane fusion pathways.

Design, Synthesis and Biological Evaluation of N6-Substituted-C2-Alkynyl-4'-Thionucleoside and 4'-Trucatedthionucleoside Derivatives as Novel A3 Adenosine Receptor Ligands.

Design, Synthesis and Biological Evaluation of N6-Substituted-C2-Alkynyl-4'-Thionucleoside and 4'-Trucatedthionucleoside Derivatives as Novel A3 Adenosine Receptor Ligands.

Distinct modes of interaction within eIF4F-like complexes and susceptibility to the RocA inhibitor for the Trypanosoma brucei EIF4AI translation initiation factor.

Trypanosomatids are parasitic protozoa responsible for major human diseases which are characterized by unique gene expression mechanisms. mRNA translation in these parasites is associated with multiple eIF4F-like complexes, required for mRNA recruitment and ribosome binding. The eukaryotic eIF4F is generally known to require the action of eIF4A, an ATP-dependent RNA helicase, in order to function properly, but not all trypanosomatid eIF4F complexes might require EIF4AI, their single eIF4A homologue. In mammals, eIF4A is known to be targeted by specific inhibitors and can thus be considered a potential target for a selective inhibition of translation in these parasites. Here, aiming to better define the EIF4AI functionality, we started by investigating its interactome in Trypanosoma brucei, confirming a strong interaction with only one of five eIF4F-like complexes found in trypanosomatids, based on the EIF4E4/EIF4G3 subunits. Nevertheless, when the interactome of a mutant EIF4AI (DEAD/DQAD), known to be impacted on its ATPase activity, was investigated, the only eIF4F-like complex found was based on the EIF4E3/EIF4G4 pair, with many translation-related and other proteins also found with the mutant protein. When both wild-type and mutant proteins were also investigated through a fluorescent-based tethering assay, a stimulatory effect on mRNA expression was confirmed for EIF4AI, but not for the mutant protein. Sensitivity to the Rocaglamide A (RocA) inhibitor, which targets the mammalian eIF4A, was also investigated, with the inhibitor blocking the stimulation seen on the tethering assay. Parasite susceptibility to RocA was further assessed in T. brucei and Leishmania infantum, with both, and specially T. brucei, being much less susceptible to the drug than mammalian cells. This phenotype correlates with changes in EIF4AI within the RocA binding pocket where, in comparison with the mammalian eIF4A, a phenylalanine to valine substitution in the T. brucei EIF4AI likely impairs RocA binding. Our results help better define the EIF4AI mode of action in T. brucei and provide relevant data which might support future searches for specific EIF4AI inhibitors.