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At least 541 records · Page 30

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

47 OTHER INSTRUMENTATION↗

Optimization of a Lethal, Combat-Relevant Model of Sterile Inflammation in Mice for Drug Candidate Screening

ABSTRACT Introduction Extensive trauma, commonly seen in wounded military Service Members, often leads to a severe sterile inflammation termed systemic inflammatory response syndrome (SIRS), which can progress to multiple organ dysfunction syndrome (MODS) and death. MODS is a serious threat to wounded Service Members, historically causing 10% of all deaths in trauma admissions at a forward deployed combat hospital. The importance of this problem will be exacerbated in large-scale combat operations, in which evacuation will be delayed and care of complex injuries at lower echelons of care may be prolonged. The main goal of this study was to optimize an existing mouse model of lethal SIRS/MODS as a therapeutic screening platform for the evaluation of immunomodulatory drugs. Materials and Methods Male C57BL/6 mice were euthanized, and the bones and muscles were collected and blended into a paste termed tissue–bone matrix (TBX). The TBX at 12.5%–20% relative to body weight of each recipient mouse was implanted into subcutaneous pouches created on the dorsum of anesthetized animals. Mice were observed for clinical scores for up to 48 hours postimplantation and euthanized at the preset point of moribundity. To test effects of anesthetics on TBX-induced mortality, animals received isoflurane or ketamine/xylazine (K/X). In a separate set of studies, mice received TBX followed by intraperitoneal injection with 20 mg/kg or 40 mg/kg Eritoran or a placebo carrier. All Eritoran studies were performed in a blinded fashion. Results We observed that K/X anesthesia significantly increased the lethality of the implanted TBX in comparison to inhaled anesthetics. Although all the mice anesthetized with isoflurane and implanted with 12.5% TBX survived for 24 hours, 60% of mice anesthetized with K/X were moribund by 24 hours postimplantation. To mimic more closely the timing of lethal SIRS/MODS following polytrauma in human patients, we extended observation to 48 hours. We performed TBX dose–response studies and found that as low as 15%, 17.5%, and 20% TBX caused moribundity/mortality in 50%, 80%, and 100% mice, respectively, over a 48-hour time period. With 17.5% TBX, we tested if moribundity/mortality could be rescued by anti-inflammatory drug Eritoran, a toll-like receptor 4 antagonist. Neither 20 mg/kg nor 40 mg/kg doses of Eritoran were found to be effective in this model. Conclusions We optimized a TBX mouse model of SIRS/MODS for the purpose of evaluating novel therapeutic interventions to prevent trauma-related pathophysiologies in wounded Service Members. Negative effects of K/X on lethality of TBX should be further evaluated, particularly in the light of widespread use of ketamine in treatment of pain. By mimicking muscle crush, bone fracture, and necrosis, the TBX model has pleiotropic effects on physiology and immunology that make it uniquely valuable as a screening tool for the evaluation of novel therapeutics against trauma-induced SIRS/MODS.

General & Internal Medicine↗

The black hole weak gravity conjecture with multiple charges

We study the effect of higher-derivative corrections on asymptotically flat, fourdimensional, dyonic black holes in low-energy models of gravity coupled to N U(1) gauge fields. For large extremal black holes, the leading O (1/Q 2 ) correction to the extremality bound is calculated from the most general low-energy effective action containing operators with up to four derivatives. Motivated by the multi-charge generalization of the Weak Gravity Conjecture, we analyze the necessary kinematic conditions for an asymptotically large extremal black hole to decay into a multi-particle state of extremal black holes. In the large black hole regime, we show that the convex hull condition degenerates to the requirement that a certain quartic form constructed from the Wilson coefficients of the fourderivative effective operators, is everywhere positive. Using on-shell unitarity methods, we show that higher-derivative operators are renormalized at one-loop only if they generate local, on-shell matrix elements that are invariant tensors of the electromagnetic duality group U(N). The one-loop logarithmic running of the four-derivative Wilson coefficients is calculated and shown to imply the positivity of the extremality form at some finite value of Q 2 . This result generalizes an argument recently given by Charles [1], and shows that under the given assumptions the multi-charge Weak Gravity Conjecture is not a Swampland criterion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Scattering equations in AdS: scalar correlators in arbitrary dimensions

We introduce a bosonic ambitwistor string theory in AdS space. Even though the theory is anomalous at the quantum level, one can nevertheless use it in the classical limit to derive a novel formula for correlation functions of boundary CFT operators in arbitrary space-time dimensions. The resulting construction can be treated as a natural extension of the CHY formalism for the flat-space S-matrix, as it similarly expresses tree-level amplitudes in AdS as integrals over the moduli space of Riemann spheres with punctures. These integrals localize on an operator-valued version of scattering equations, which we derive directly from the ambitwistor string action on a coset manifold. As a testing ground for this formalism we focus on the simplest case of ambitwistor string coupled to two cur- rent algebras, which gives bi-adjoint scalar correlators in AdS. In order to evaluate them directly, we make use of a series of contour deformations on the moduli space of punctured Riemann spheres and check that the result agrees with tree level Witten diagram computations to all multiplicity. We also initiate the study of eigenfunctions of scattering equations in AdS, which interpolate between conformal partial waves in different OPE channels, and point out a connection to an elliptic deformation of the Calogero-Sutherland model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nanoparticle-enabled increase of energy efficiency during laser metal additive manufacturing

The low energy efficiency of the laser metal additive manufacturing (AM) process is a potential sustainability concern for large-scale industrial production. Explicit investigation of the energy efficiency for laser melting requires the direct characterization of melt pool dimension and vapor depression, which is very difficult due to the opaque nature of the molten metal. Here we report the direct observation and quantification of effects of the TiC nanoparticles on the vapor depression and melt pool formation during laser powder bed fusion (LPBF) of Al6061 by in-situ high-speed high-energy x-ray imaging. Based on the quantification results, we calculated the laser melting energy efficiency (defined here as the ratio of the energy needed to melt the material to the energy delivered by the laser beam) with and without TiC nanoparticles during LPBF of Al6061. Here the results show that adding TiC nanoparticles into Al6061 leads to a significant increase of laser melting energy efficiency (114% increase on average, 521% increase under 312 W laser power, 0.4 m/s scan speed). Systematic property measurement, simulation, and x-ray imaging studies enable us, for the first time, to identify that three mechanisms work together to enhance the laser melting energy efficiency: (1) adding TiC nanoparticles increases the absorptivity; (2) adding TiC nanoparticles decreases the thermal conductivity, and (3) adding TiC nanoparticles enables the initiation of vapor depression and multiple reflection at lower laser power (i.e., lowers the laser power threshold for keyholing). The method and mechanisms of using TiC nanoparticles to increase the laser melting energy efficiency during LPBF of Al6061 we reported here may guide the development of feedstock materials for more energy efficient laser metal AM.

36 MATERIALS SCIENCE↗

FY24 Report on Water NSTF Testing: Lower Tank Inlet Piping Configuration

The following report serves as a summary of the accomplishments and testing results by the Natural convection Shutdown heat removal Test Facility (NSTF) experimental program over the past 12-month period. A major activity included reconfiguration of the chimney piping geometry which altered the discharge position into the tank from the original 50% tank height to a new lower position at a 10.9% tank height. This modification increases the volume of available coolant thus extending long-term operating capacity, however also results in a decreased liquid driving head which has the potential to reduce the natural circulation efficiency and decrease overall performance. Examination of the tradeoffs for these two configurations is an area of interest for RCCS designers and drove planned test activities this year. Ten matrix tests were performed in FY24, totaling 195 hours of heated operations and 12.9 MWh of electrical heating throughout the year, with eight classified as Accepted per NQA-1 and two classified as Trending. Testing prior to the facility reconfiguration examined the facility response to throttling at the tank inlet, demonstrating increased sensitivity of flow instabilities to throttling within the two-phase region when compared to throttling at the lower sensitivity single-phase inlet region. Testing after the chimney reconfiguration began with a baseline test at conditions of 80% inventory fill and prototypic thermal power input of 2.1 MW t . In addition to establishing a reference for nominal system behavior and performance, repeat testing with multiple subsequent runs demonstrated strong repeatability between tests performed at the same conditions in this new configuration. These tests also examined if influences would occur to system behavior with installation of new higher-resolution instrumentation within the upper chimney. In this critical region where boiling and flashing phenomena dominate, the test results provided confidence that the new instrumentation does not uncharacteristically influence the observed behaviors. An inventory parametric series was then initiated to examine system behavior with the new chimney configuration at six varying initial inventory levels, ranging from high 80% to low 20% fill. Two-phase oscillations with similar peak and mean flow rates were observed when comparing to the previous mid tank configuration. Generally, similar system response trends with inventory were also observed, such as two phase oscillations suppressing as inventories were lowered. However, in one absolute inventory comparison at the highest fill of 80%, flow oscillations saw a gradual growth over the 4 hours of two-phase operation in the new lower tank inlet configuration, opposite of the gradual dampening observed in the mid tank inlet configuration. This can be attributed to, in part, a greater hydrostatic head pressure above the two-phase discharge region where the boiling front is developed. Furthermore, the change resulted in greater sensitivity to liquid degassing phenomena during single-phase heating, causing loop instabilities to form which trigged moderate flow degradation during the period approaching saturation and boiling conditions. This behavior had been observed previously under some conditions but was a common occurrence in recent testing with the newer lower tank inlet configuration. Initial observations from these first data sets suggest an overall larger window of stability for the mid tank inlet configuration compared to the lower tank inlet. Lastly, the lowest inventory fill test was repeated over an extended testing window to examine depletion behavior. Natural circulation flow and effective heat removal performance were observed during most of the testing period; only after the tank became fully drained (0% fill) did flow stagnate and violent geysering events occur. This early observation confirms one relative advantage over the mid tank inlet configuration, which stagnated under comparable conditions at ~20% inventory remaining in the tank.

42 ENGINEERING↗

TiNi-Based Bi-Metallic Shape-Memory Alloy by Laser-Directed Energy Deposition

In this study, laser-directed energy deposition was applied to build a Ti-rich ternary Ti–Ni–Cu shape-memory alloy onto a TiNi shape-memory alloy substrate to realize the joining of the multifunctional bi-metallic shape-memory alloy structure. The cost-effective Ti, Ni, and Cu elemental powder blend was used for raw materials. Various material characterization approaches were applied to reveal different material properties in two sections. The as-fabricated Ti–Ni–Cu alloy microstructure has the TiNi phase as the matrix with Ti2Ni secondary precipitates. The hardness shows no high values indicating that the major phase is not hard intermetallics. A bonding strength of 569.1 MPa was obtained by tensile testing, and digital image correlation reveals the different tensile responses of the two sections. Differential scanning calorimetry was used to measure the phase-transformation temperatures. The austenite finishing temperature of higher than 80 °C was measured for the Ti–Ni–Cu alloy section. For the TiNi substrate, the austenite finishing temperature was tested to be near 47 °C at the bottom and around 22 °C at the upper substrate region, which is due to the repeated laser scanning that acts as annealing on the substrate. Finally, the multiple shape-memory effect of two shape-memory alloy sides was tested and identified.

36 MATERIALS SCIENCE↗

Faster network disruption from layered oscillatory dynamics

Nonlinear complex network-coupled systems typically have multiple stable equilibrium states. Following perturbations or due to ambient noise, the system is pushed away from its initial equilibrium, and, depending on the direction and the amplitude of the excursion, it might undergo a transition to another equilibrium. It was recently demonstrated [M. Tyloo, J. Phys. Complex. 3 03LT01 (2022)] that layered complex networks may exhibit amplified fluctuations. Here, I investigate how noise with system-specific correlations impacts the first escape time of nonlinearly coupled oscillators. Interestingly, I show that, not only the strong amplification of the fluctuations is a threat to the good functioning of the network but also the spatial and temporal correlations of the noise along the lowest-lying eigenmodes of the Laplacian matrix. Finally, I analyze first escape times on synthetic networks and compare noise originating from layered dynamics to uncorrelated noise.

97 MATHEMATICS AND COMPUTING↗

Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation

This Final Scientific and Technical Report summarizes work performed under the Phase IIA SBIR project “Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation” (DE-SC0020906) from August 2023 through August 2025. The objective of the Phase IIA effort was to mature and harden capabilities developed during Phase II, with the goal of enabling practical interoperability between Coreform’s isogeometric analysis (IGA) technologies and the Multiphysics Object-Oriented Simulation Environment (MOOSE), while improving robustness, performance, and scalability for complex, nuclear-relevant geometries. Over the course of Phase IIA, the project established and validated an extraction-based interoperability pathway between Coreform tools and MOOSE. A combined mesh and matrix format was defined collaboratively with MOOSE developers and integrated into the solver, enabling standard MOOSE workflows to operate on data exported from Coreform’s IGA and Flex Representation Method (FRM) pipelines. Early demonstrations validated architectural compatibility using linear solid mechanics problems, while later efforts focused on benchmark testing and external use. By the end of the project period, engineers at BWXT were able to independently set up and execute a simulation using the Coreform–MOOSE workflow and provide direct feedback that informed further refinement. In parallel, substantial effort was devoted to improving the robustness of trimmed U-spline construction for complex CAD geometries. A growing test suite of nuclear-relevant models was compiled through collaboration with multiple stakeholders and used to drive extensive bug fixing and reliability improvements. These efforts resulted in improved robustness and performance, including the addition of fallback capabilities that enhance reliability when the underlying commercial CAD kernel fails. Performance-oriented work progressed later in the project, with the development and demonstration of methods to decompose complex geometries into structured subregions and updated data representations to support more efficient solver processing. Additionally, extensive enhancements to threadsafe parallel data structures and trimming operations established a foundation for scalable processing of large assemblies. Collaboration with Sandia National Laboratories on the SGM geometric modeling kernel advanced to a functioning interface test case, positioning the workflow for future kernel integration. Overall, the Phase IIA effort successfully transitioned the project from architectural proof-of-concept to externally exercised, solver-integrated capability, while clarifying remaining technical challenges related to standardization, performance optimization, and kernel integration.

42 ENGINEERING↗

Two-Dimensional Silk Crystal Films as Matrix Layer for High-Performance Microelectronics

This study explores a bio-inspired approach for memristive devices by combining Keggin-type polyoxometalates (POMs)-[SiW 12 O 40 ] 4 (POM-T) and [PW 12 O 40 ] 3 (POM-P), with silk fibroin (SF) to create 2D SF–POM layers on highly ordered pyrolytic graphite (HOPG) as resistive switching layers for memristors. We propose that the ordered SF layer template 0D POMs facilitate the formation of conductive filaments, thereby enhancing the variability of the manufactured memristors. AFM analysis revealed that both SF and SF–POM layers shared similar morphologies, while SF–POM–T formed larger aggregates, likely due to the stronger acidity of POM-T, which probably caused SF to aggregate and alter its secondary structure. Scanning Kelvin probe microscopy (SKPM) revealed that POMs reduced the contact potential difference of HOPG, resulting in lower work functions. Compared to an SF device, the SF–POM–P device showed improved memristive behavior, with a larger current gap and good repeatability over multiple sweeps; whereas the SF–POM–T device did not exhibit memristor activity, likely due to acidity-induced disruption of the SF template’s order and CF formation. More importantly, SF–POM–P devices also demonstrated programmable memristive states. Finally, combining simulation-driven memristor modeling, we showcase a co-design workflow for advancing bioinspired memristors through new materials design, synthesis, and device modeling and development.

36 MATERIALS SCIENCE↗

Quantum error correction in the black hole interior

We study the quantum error correction properties of the black hole interior in a toy model for an evaporating black hole: Jackiw-Teitelboim gravity entangled with a non-gravitational bath. After the Page time, the black hole interior degrees of freedom in this system are encoded in the bath Hilbert space. We use the gravitational path integral to show that the interior density matrix is correctable against the action of quantum operations on the bath which (i) do not have prior access to details of the black hole microstates, and (ii) do not have a large, negative coherent information with respect to the maximally mixed state on the bath, with the lower bound controlled by the black hole entropy and code subspace dimension. Thus, the encoding of the black hole interior in the radiation is robust against generic, low-rank quantum operations. For erasure errors, gravity comes within an O (1) distance of saturating the Singleton bound on the tolerance of error correcting codes. For typical errors in the bath to corrupt the interior, they must have a rank that is a large multiple of the bath Hilbert space dimension, with the precise coefficient set by the black hole entropy and code subspace dimension.

2D gravity↗

A framework to measure the properties of intergalactic metal systems with two-point flux statistics

ABSTRACT The abundance, temperature, and clustering of metals in the intergalactic medium are important parameters for understanding their cosmic evolution and quantifying their impact on cosmological analysis with the Ly α forest. The properties of these systems are typically measured from individual quasar spectra redward of the quasar’s Ly α emission line, yet that approach may provide biased results due to selection effects. We present an alternative approach to measure these properties in an unbiased manner with the two-point statistics commonly employed to quantify large-scale structure. Our model treats the observed flux of a large sample of quasar spectra as a continuous field and describes the one-dimensional, two-point statistics of this field with three parameters per ion: the abundance (column density distribution), temperature (Doppler parameter), and clustering (cloud–cloud correlation function). We demonstrate this approach on multiple ions (e.g. ${\rm C\, \small {\rm IV}}$ , ${\rm Si\, \small {\rm IV}}$ , and ${\rm Mg\, \small {\rm II}}$ ) with early data from the Dark Energy Spectroscopic Instrument (DESI) and high-resolution spectra from the literature. Our initial results show some evidence that the ${\rm C\, \small {\rm IV}}$ abundance is higher than previous measurements and evidence for abundance evolution over time. The first full year of DESI observations will have over an order of magnitude more quasar spectra than this study. In a future paper, we will use those data to measure the growth of clustering and its impact on the Ly α forest, as well as test other DESI analysis infrastructure such as the pipeline noise estimates and the resolution matrix.

79 ASTRONOMY AND ASTROPHYSICS↗

Non-invertible symmetries and LSM-type constraints on a tensor product Hilbert space

We discuss the exact non-invertible Kramers-Wannier symmetry of 1+1d lattice models on a tensor product Hilbert space of qubits. This symmetry is associated with a topological defect and a conserved operator, and the latter can be presented as a matrix product operator. Importantly, unlike its continuum counterpart, the symmetry algebra involves lattice translations. Consequently, it is not described by a fusion category. In the presence of this defect, the symmetry algebra involving parity/time-reversal is realized projectively, which is reminiscent of an anomaly. Different Hamiltonians with the same lattice non-invertible symmetry can flow in their continuum limits to infinitely many different fusion categories (with different Frobenius-Schur indicators), including, as a special case, the Ising CFT. The non-invertible symmetry leads to a constraint similar to that of Lieb-Schultz-Mattis, implying that the system cannot have a unique gapped ground state. It is either in a gapless phase or in a gapped phase with three (or a multiple of three) ground states, associated with the spontaneous breaking of the lattice non-invertible symmetry.

Seiberg, Nathan (ORCID:000000033897046X)↗

QuDPy: A Python-based tool for computing ultrafast non-linear optical responses

Nonlinear Optical Spectroscopy is a well-developed field with theoretical and experimental advances that have benefited multiple disciplines, including chemistry, biology, and physics. However, for the accurate interpretation of the corresponding multi-dimensional spectra, there is a need for precise quantum dynamical simulations based on model Hamiltonians. In this article, we present the initial release of our code, QuDPy (Quantum Dynamics in Python), which provides a robust numerical platform for performing quantum dynamics simulations based on model systems, including open quantum systems. Furthermore, a distinguishing feature of our approach is the ability to specify various high-order optical response pathways in the form of double-sided Feynman diagrams through a straightforward input syntax. This syntax outlines the time-ordering of ket-sided or bra-sided optical interactions acting on the time-evolving density matrix of the system. We utilize the quantum dynamics capabilities of QuTip to simulate the spectral response of complex systems, allowing us to compute virtually any $n$-th order optical response of the model system. To illustrate the utility of our approach, we provide a series of example calculations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structural Insights into Low and High Recalcitrance Natural Poplar Variants Using Neutron and X-ray Scattering

Here, we used small-angle neutron scattering (SANS) and wide-angle X-ray scattering (WAXS) to study two Populus trichocarpa variants, GW-11012 and BESC-316, with lignin contents of 17.8 and 23.2%, respectively, to understand why the low lignin variant has increased sugar release during liquid hot water (LHW) pretreatment. SANS showed differences in cell wall polymer arrangement in the variants. In GW-11012, the cellulose microfibrils were similar in size to BESC-316 but were not equally spaced and lignin was aggregated rather than homogenously interspersed with other matrix co-polymers. However, after LHW pretreatments, the SANS profiles of the pretreated variants were almost indistinguishable, indicating that the nanoscale structural features could not adequately explain the increased sugar release observed in GW-11012. WAXS analysis revealed higher cellulose crystallinity and larger crystallite size in native and pretreated GW-11012. However, the most significant difference was that the crystallite orientation was approximately 2-fold higher in GW-11012. This suggests that higher crystallite orientation may be favorable for the action of processive cellulases leading to increased sugar release from GW-11012. Our study shows that there is a complex interplay between cell wall polymers during their deposition resulting in changes in lignin distribution and cellulose structure, highlighting the importance of investigating plant cell wall architecture across multiple length scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An IIPG-based finite element framework in MOOSE for modeling fiber reinforced composite failure governed by extrinsic cohesive laws

Fiber reinforced composites (FRC) are widely applied to many important engineering structures such as silicon carbide ceramic matrix composite (SiC CMC) of nuclear fuel claddings. Many material and structure failures are initiated at the interface between two distinctive materials, such as the debonding of interfaces of matrix/fiber of composites or bulk matrix/inclusion in metals at micro-scales. Accurate and robust modeling of these interface failures is critical to the development of novel material and structure with improved functionality. This paper presents a discontinuous Galerkin (DG) finite element method based on the Incomplete Interior Penalty scheme and its implementation in MOOSE for modeling material interface behaviors. The proposed method naturally accommodates important extrinsic cohesive zone material models and is capable of modeling the failures of material interfaces across which material properties are highly distinctive. We demonstrate a good performance of the proposed method using single fiber and multiple fiber debonding problems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Resonant Landau-Zener conversion in multi-axion systems

Multiple axions may emerge in the low-energy effective theory of Nature. Generically, the potentials describing these axion fields are non-diagonal, leading to mass mixing between axion states which can be temperature-dependent due to QCD instanton effects. As the temperature of the Universe drops, level crossing can occur, causing resonant conversion between axion states. In this work, we present an analytic study of the cosmological evolution of multi-axion systems including adiabatic and non-adiabatic resonant conversion from one axion state into another during the misalignment process. We show how the Landau-Zener formalism accurately captures the non-adiabatic resonant conversion, permitting an analytic description of the relic abundances of each axion field for nearly any arbitrary two-state axion mass matrix. As an application, we study the mixing of a QCD axion with an axion-like-particle for specific potentials to identify the predictions for haloscope experiments. We conclude that the detection of an axion off the expected QCD mass-coupling line predicts other haloscope targets if it mixes with the QCD axion.

Axions and ALPs↗