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Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie↗

Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies

The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. Here, we analyze assemblies of an amphiphile (C 16 K 2 ), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson–Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson–Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.

ionization↗

A science-driven approach to optimize the design for a biological small-angle neutron scattering instrument

Biological small-angle neutron scattering (SANS) instruments facilitate critical analysis of the structure and dynamics of complex biological systems. However, with the growth of experimental demands and the advances in optical systems design, a new neutron optical concept is necessary to overcome the limitations of current instruments. This work presents an approach to include experimental objectives ( i.e. the science to be supported by a specific neutron scattering instrument) in the optimization of the neutron optical concept. The approach for a proposed SANS instrument at the Second Target Station of the Spallation Neutron Source at Oak Ridge National Laboratory, USA, is presented here. Further, the instrument is simulated with the McStas software package. The optimization process is driven by an evolutionary algorithm using McStas output data, which are processed to calculate an objective function designed to quantify the expected performance of the simulated neutron optical configuration for the intended purpose. Each McStas simulation covers the complete instrument, from source to detector, including realistic sample scattering functions. This approach effectively navigates a high-dimensional parameter space that is otherwise intractable; it allows the design of next-generation SANS instruments to address specific scientific cases and has the potential to increase instrument performance compared with traditional design approaches.

47 OTHER INSTRUMENTATION↗

Scattering-based structural inversion of soft materials via Kolmogorov–Arnold networks

Small-angle scattering techniques are indispensable tools for probing the structure of soft materials. However, traditional analytical models often face limitations in structural inversion for complex systems, primarily due to the absence of closed-form expressions of scattering functions. To address these challenges, we present a machine learning framework based on the Kolmogorov–Arnold Network (KAN) for directly extracting real-space structural information from scattering spectra in reciprocal space. This model-independent, data-driven approach provides a versatile solution for analyzing intricate configurations in soft matter. By applying the KAN to lyotropic lamellar phases and colloidal suspensions—two representative soft matter systems—we demonstrate its ability to accurately and efficiently resolve structural collectivity and complexity. Here, our findings highlight the transformative potential of machine learning in enhancing the quantitative analysis of soft materials, paving the way for robust structural inversion across diverse systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tunable Nanoscale Structure via Divalent Ion Identity in Charged-Neutral Polymer Blends

Charged-neutral polymer blends, wherein an ioncontaining polymer is blended with a neutral polymer, are potential candidates for battery electrolytes due to their improved ion transport properties and electrochemical stability. Though electrostatic interactions in charged polymer blends can theoretically stabilize ordered nanostructures analogous to those observed in neutral block copolymers, direct experimental evidence remains limited. Here, we investigate the effects of divalent cation identity on the nanoscale morphology of charged-neutral polymer blends composed of poly(ethylene oxide) (PEO) and Mg 2+ or Ca 2+ ioncontaining polymers, poly[3-(methylacryloxy)propylsulfonyl-1-(trifluoromethanesulfonylimide)] (P(Mg(MTFSI) 2 ) or P(Ca- (MTFSI) 2 ). By tuning the size of the divalent counterion, we are able to precisely tune the ion solvation between the free cation and PEO, which acts as a solvent in this system. Differential scanning calorimetry (DSC) and small-angle X-ray scattering (SAXS) measurements reveal that Mg 2+ and Ca 2+ ions induce distinct structural behavior. In both systems, the blends become more miscible as the concentration of ion-containing polymer is increased indicated by increased suppression of PEO crystallinity. At the highest concentrations of P(Mg(MTFSI) 2 ), the blends undergo microphase separation and generate nanostructures with shortranged ordering. In contrast, calcium ions, which are more readily solvated by PEO, produce more homogeneous blends characterized by a single glass-transition temperature and featureless SAXS data. The results demonstrate the novel experimental confirmation that charged-neutral polymer blends can undergo microphase separation and show that counterion identity can be exploited as a design parameter to control nanoscale morphology.

Ions↗

Machine learning inversion from scattering for mechanically driven polymers

A machine learning inversion method is developed for analyzing scattering functions of mechanically driven polymers and extracting the corresponding feature parameters, which include energy parameters and conformation variables. The polymer is modeled as a chain of fixed-length bonds constrained by bending energy, and it is subject to external forces such as stretching and shear. We generate a data set consisting of random combinations of energy parameters, including bending modulus, stretching and shear force, along with Monte Carlo-calculated scattering functions and conformation variables such as end-to-end distance, radius of gyration and off-diagonal component of the gyration tensor. The effects of the energy parameters on the polymer are captured by the scattering function, and principal component analysis ensures the feasibility of the machine learning inversion. Finally, we train a Gaussian process regressor using part of the data set as a training set and validate the trained regressor for inversion using the rest of the data. The regressor successfully extracts the feature parameters.

Gaussian process regressors↗

Colloidal Dispersions of Sterically and Electrostatically Stabilized PbS Quantum Dots: Structure Factors, Second Virial Coefficients, and Film-Forming Properties

Electrostatically stabilized nanocrystals (NCs) and, in particular, quantum dots (QDs) hold promise for forming strongly coupled superlattices due to their compact and electronically conductive surface ligands. However, studies of the colloidal dispersion and interparticle interactions of electrostatically stabilized sub-10 nm NCs have been limited, hindering the optimization of their colloidal stability and self-assembly. In this study, we employed small-angle X-ray scattering (SAXS) experiments to investigate the interparticle interactions and arrangement of PbS QDs with thiostannate ligands (PbS-Sn2S64-) in polar solvents. The study reveals significant deviations from the ideal solution behavior in electrostatically stabilized QD dispersions. Our results demonstrate that PbS-Sn2S64- QDs exhibit long-range interactions within the solvent, in contrast to the short-range steric repulsion characteristic of PbS QDs with oleate ligands (PbS-OA). Introducing highly charged multivalent electrolytes screens electrostatic interactions between charged QDs, reducing the length scale of the repulsive interactions. Furthermore, we calculated the second virial (B2) coefficients from SAXS data, providing insights into how surface chemistry, solvent, and size influence pair potentials. Finally, we explore the influence of long-range interparticle interactions of PbS-Sn2S64- QDs on the morphology of films produced by drying or spin-coating colloidal solutions. The long-range repulsive term of PbS-Sn2S64- QDs promotes the formation of amorphous films, and screening the electrostatic repulsion by the addition of an electrolyte enables the formation of crystalline domains. These findings highlight the critical role of NC-NC interactions in tailoring the properties of functional materials made of colloidal NCs.

SAXS↗

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗

Machine learning inversion from small-angle scattering for charged polymers

We develop Monte Carlo simulations for uniformly charged polymers and a machine learning algorithm to interpret the intra-polymer structure factor of the charged polymer system, which can be obtained from small-angle scattering experiments. The polymer is modeled as a chain of fixed-length bonds, where the connected bonds are subject to bending energy, and there is also a screened Coulomb potential for charge interaction between all joints. The bending energy is determined by the intrinsic bending stiffness, and the charge interaction depends on the interaction strength and screening length. All three contribute to the stiffness of the polymer chain and lead to longer and larger polymer conformations. The screening length also introduces a second length scale for the polymer besides the bending persistence length. To obtain the inverse mapping from the structure factor to these polymer conformation and energy-related parameters, we generate a large data set of structure factors by running simulations for a wide range of polymer energy parameters. We use principal component analysis to investigate the intra-polymer structure factors and determine the feasibility of the inversion using the nearest neighbor distance. We employ Gaussian process regression to achieve the inverse mapping and extract the characteristic parameters of polymers from the structure factor with low relative error.

36 MATERIALS SCIENCE↗

10 Boron-film-based gas detectors at ESS

The development of detectors for the European Spallation Source is an important parallel element to the effort put into the design and construction of the neutron source and instruments. The 10Boron-film-based detector developments that started over a decade ago as basic detector concepts have now reached technical maturity after intense prototyping work and numerous testing campaigns. Several of the ESS beamlines that will soon enter the commissioning phase started welcoming the detector systems built with the 10 B-film converter technology. The real-size demonstrators evolved in the last 2–3 years into a diverse suite of gas proportional counters for use in diffraction, reflectometry and small-angle scattering studies in spite of the operational complexity posed by the requirements for large-area coverage, low material budget and robustness for operation in the high-flux and high-radiation environment of ESS. The detectors are now being shipped to ESS or undergoing the last performance and calibration tests before being handed over to the instrument teams for installation in the host beamlines. A common feature of these detector systems is the very large number of readout channels that they are instrumented with in order to fulfill the demanding requirements for sensitivity, spatial resolution and count-rate capability. Across all of the detector types that will operate at ESS, the integration, testing and commissioning of the read-out technologies and software tools for data reduction, calibration and analysis are the focus of the detector and integration teams. These will yield a wealth of knowledge about their operation as well as initial results on the in-situ performance, a very important asset to ensure rapid commissioning of the detectors when neutrons from the ESS source become available. In this paper we will give an overview of the 10 B-film-based detector technologies included in the ESS detector suite that are currently facing the transition from the production phase to installation and integration with the other beamline components, which comes with its own specific challenges of both organizational and technical nature.

47 OTHER INSTRUMENTATION↗

Deciphering supramolecular and polymer-like behavior in metallogels: real-time insights into temperature-modulated gelation and rapid self-assembly dynamics

Bis(pyridyl) urea-based gelators, namely L2 and its isomeric mixture ( L1 + L2 ), are known to self-assemble into 1D architectures capable of inducing supramolecular gelation. Coordination with metal ions such as Ag( I ), Cu( II ), and Fe( III ) introduces structural reinforcement, enabling the formation of distinct 3D networks governed by metal-specific coordination geometries. Here, we present a comprehensive investigation into the temperature-responsive behavior (20–60 °C) of L2 and L1 + L2 , both in the absence and presence of Ag( I ), Dy( III ), Fe( III ), Cu( II ), and Ho( III ), using real-time small-angle neutron scattering (SANS). To probe long-term structural evolution/kinetics of self-assembly, real-time small-angle X-ray scattering (SAXS) was employed on L2 + Ag gels, complemented by differential scanning calorimetry (DSC) to evaluate thermal transitions. Our results reveal strikingly divergent gelation behaviors: L2 forms a highly rigid, covalent polymer-like network, while L1 + L2 exhibits remarkable thermal adaptability. Upon metal coordination, the assemblies exhibit pronounced crystallinity and exceptional thermal stability, as evidenced by persistent Bragg reflections and invariant d-spacings. Intriguingly, L2 : Fe (2 : 1) and L1 : L2 : Fe (0.5 : 0.5 : 1) in acetonitrile-d 3 (ACN-d 3 ) deviate from this trend, forming thermally labile amorphous gels. These systems show a complete loss of crystalline order, reduced Porod exponents—indicative of collapsed or branched fiber morphologies—and prominent melting and glass transition events in DSC. Fitting SANS and SAXS data to the correlation length model unveiled insightful nanostructural features. While most systems displayed minimal temperature-induced variation in mesh size or surface morphology, L2 : Ag in dimethyl sulfoxide-d 6 (DMSO-d 6 )/D 2 O and L2 : Fe (1 : 1) in ACN-d 3 exhibited a rare combination of thermally stable correlation lengths and increasing high- q exponents—strongly suggesting progressive fiber densification or surface smoothing within a robust gel framework. These findings highlight the tunability and structural resilience of supramolecular gels through precise control of ligand architecture, metal coordination, and temperature, offering valuable design principles for functional soft materials.

Pajoubpong, Jinnipha [Univ. of Cincinnati, OH (Uni↗

Machine-learning-informed scattering correlation analysis of sheared colloids

We have carried out theoretical analysis, Monte Carlo simulations and machine-learning analysis to quantify microscopic rearrangements of dilute dispersions of spherical colloidal particles from coherent scattering intensity. Both monodisperse and polydisperse dispersions of colloids were created and underwent a rearrangement consisting of an affine simple shear and non-affine rearrangement using the Monte Carlo method. We calculated the coherent scattering intensity of the dispersions and the correlation function of intensity before and after the rearrangement and generated a large data set of angular correlation functions for varying system parameters, including number density, polydispersity, shear strain and non-affine rearrangement. Singular value decomposition of the data set shows the feasibility of machine-learning inversion from the correlation function for the polydispersity, shear strain and non-affine rearrangement using only three parameters. A Gaussian process regressor is then trained on the data set and can retrieve the affine shear strain, non-affine rearrangement and polydispersity with relative errors of 3%, 1% and 6%, respectively. Altogether, our model provides a framework for quantitative studies of both steady and non-steady microscopic dynamics of colloidal dispersions using coherent scattering methods.

Gaussian process regression↗

Multiplexing and Demultiplexing Signals for Radiography Application Using the Discrete Fourier Transform

Our goal is to develop an X-ray phase-contrast imaging system that can provide excellent soft tissue contrast of phase, attenuation, and small-angle scatter. We propose to replace the common system of G0, G1, and G2 gradings with a biprism array to replace the G1 grading and introduce a novel X-ray tube designed to replace the motion of the phase stepping grading G2. The proposed X-ray tube uses temporal multiplexing to provide simultaneous virtual “electronic phase stepping.” In this work the discrete Fourier transform is used to separate from the composite measurement individual X-ray phase contrast measurements sampled at different frequencies. The method performs a discrete Fourier transform of a composite refence sequence to obtain using the frequency amplitudes calibration factors needed to extract the X-ray phase contrast measurement amplitudes from the composite image. The composite reference sequence is the sum of the individual sequences, at different frequencies, with amplitudes of one. The method takes the discrete Fourier transform of this composite reference sequence; whereby, the amplitude of each frequency component is compared with the total sum of its stand-alone sequence amplitude. A calibration factor is determined so that the amplitude of this composite reference frequency times the calibration factor must equal the total sum of the sequence amplitude—the zero-frequency amplitude of the discrete Fourier transform of its stand-alone sequence. To demultiplex the composite measured signal these calibration factors are multiplied by the amplitudes of the frequency components of the discrete Fourier transform of the composite X-phase-contrast measurement to obtain the amplitude of each frequency encoded measurement. Using these calibration factors, we demonstrate with the discrete Fourier transform in Mathematica the extraction of individual images from a composite image that one would expect obtaining from our proposed new X-ray phase contrast imaging system. We then demonstrate as an example how using images from X-ray phase contrast data one can calculate phase, attenuation and the dark field images using grading phase step data supplied to use from Microworks, GmbH in Karlsruhe, Germany.

42 ENGINEERING↗

Exploring small-angle emissions in charm quark jets in proton-proton collisions at $\sqrt{s}=5.02$ TeV

A measurement of the angular structure of inclusive jets and those containing a prompt D 0 meson in proton-proton collisions at the LHC at a center-of-mass energy of 5.02 TeV is presented. The data corresponding to an integrated luminosity of 301 pb −1 were collected by the CMS experiment in 2017. Two jet grooming algorithms, late-k T and soft drop, are used to study the intrajet radiation pattern using iterative Cambridge-Aachen declustering. The splitting-angle distributions of jets with transverse momentum (p T ) of around 100 GeV, obtained with these two algorithms, show that there is a shift of the distribution for jets containing a prompt D 0 meson with respect to inclusive jets. The suppression of emissions at small angles observed in the late-k T grooming approach is consistent with the dead-cone effect, whereas the similar suppression for splittings selected with the soft-drop algorithm appears to be induced by gluon splitting to charm quark-antiquark pairs at large angles. The measured distributions are corrected to the particle level and can be used to constrain model predictions for the substructure of high-p T charm quark jets.

Charm Physics↗

Desmearing Bonse–Hart USANS data using Bayesian Gaussian process regression

Ultra-small-angle neutron scattering (USANS) enables access to micrometer-scale structures but is intrinsically affected by strong, anisotropic resolution smearing arising from slit-geometry optics. As a result, recovery of the intrinsic scattering intensity constitutes an ill-posed inverse problem, and commonly used iterative desmearing methods lack rigorous uncertainty quantification. We present a Bayesian desmearing framework for slit-geometry USANS based on Gaussian process regression. In this approach, the scattering intensity is modeled as a smooth random function, and the instrumental point spread function is incorporated explicitly as a forward operator. The resulting formulation yields a closed-form maximum a posteriori solution with well-defined credibility intervals. Computational benchmarks and experimental validation using combined USANS and small-angle neutron scattering (SANS) measurements demonstrate that the framework enables stable desmearing, suppresses experimental noise, and preserves physically meaningful structural features under realistic conditions.

Tung, Chi-Huan [Oak Ridge National Laboratory (ORN↗

Energy-energy correlators in 𝑒 + ⁢𝑒 − annihilation and deep inelastic scattering

We study energy-energy correlators (EECs) in 𝑒 + ⁢𝑒 − annihilation and deep inelastic lepton-hadron scattering (DIS), focusing on aspects of nonperturbative physics in these observables. We introduce the EEC jet functions and investigate the infrared behavior of both small-angle EECs and angle-integrated EECs by performing explicit one-loop calculations. The factorization and universality of the EECs in these processes are demonstrated. A matching scheme is proposed to smoothly connect kinematic regions where different scaling behaviors with jet energy are observed. In combination with the next-to-leading order correction, this matching provides a good description of the EEC data and pythia simulations in high-energy 𝑒 + ⁢𝑒 − annihilation. Predictions for DIS processes for future electron-ion collider kinematics are also presented.

Guo, Yuxun [Lawrence Berkeley National Laboratory ↗

Correlation-aware binning for small-angle neutron scattering via Gaussian-process inference

Binning in small-angle neutron scattering (SANS) is typically performed empirically, with fixed parameters chosen for convenience rather than statistical optimality. Such practices often fail to balance statistical precision and spatial resolution, leading to inconsistencies across instruments and datasets. Here we establish a correlation-aware framework that determines the optimal bin width from first principles by extending the classical Freedman–Diaconis (FD) rule to account for inter-bin correlations with a Gaussian process. In this formulation, the scattering intensity is treated as a smooth stochastic field whose statistical coherence is described by a covariance matrix. Analytical expressions of errors derived from this model yield closed-form criteria that separate the total deviation into contributions from counting noise, aliasing distortion and curvature-dependent correlation effects. Expressed in reduced variables, the resulting dimensionless error surface reveals a continuous transition from the uncorrelated FD regime to the correlation-dominated limit, providing a unified description of noise suppression and resolution control. Because the formulation depends only on the profile characteristics of scattering intensity I(Q), specifically its average intensity and first- and second-order derivatives, it applies generally to any SANS measurement regardless of sample, instrument or geometry. Experimental validation using small- and ultra-small-angle neutron scattering data confirms the predicted scaling behavior, demonstrating that correlation-aware inference systematically reduces mean-squared error and enables information-efficient reproducible data reduction across materials and instruments.

Tung, Chi-Huan [ORNL] (ORCID:0000000221972074)↗