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At least 1,225 records · Page 68

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production of specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography–mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments’ ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Review of Particle Physics

The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,324 new measurements from 878 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on High Energy Soft QCD and Diffraction and one on the Determination of CKM Angles from B Hadrons. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 98 review articles. Volume 2 consists of the Particle Listings and contains also 22 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Pariicle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print and as a web version optimized for use on phones as well as an Android app.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Review of Particle Physics

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 2,143 new measurements from 709 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on Machine Learning, and one on Spectroscopy of Light Meson Resonances. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 97 review articles. Volume 2 consists of the Particle Listings and contains also 23 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print, as a web version optimized for use on phones, and as an Android app.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Deep medical image analysis with representation learning and neuromorphic computing

Deep learning is increasingly used in medical imaging, improving many steps of the processing chain, from acquisition to segmentation and anomaly detection to outcome prediction. Yet significant challenges remain: (i) image-based diagnosis depends on the spatial relationships between local patterns, something convolution and pooling often do not capture adequately; (ii) data augmentation, the de facto method for learning three-dimensional pose invariance, requires exponentially many points to achieve robust improvement; (iii) labelled medical images are much less abundant than unlabelled ones, especially for heterogeneous pathological cases; and (iv) scanning technologies such as magnetic resonance imaging can be slow and costly, generally without online learning abilities to focus on regions of clinical interest. To address these challenges, novel algorithmic and hardware approaches are needed for deep learning to reach its full potential in medical imaging.

60 APPLIED LIFE SCIENCES↗

Output-weighted sampling for multi-armed bandits with extreme payoffs

We present a new type of acquisition function for online decision-making in multi-armed and contextual bandit problems with extreme payoffs. Specifically, we model the payoff function as a Gaussian process and formulate a novel type of upper confidence bound acquisition function that guides exploration towards the bandits that are deemed most relevant according to the variability of the observed rewards. This is achieved by computing a tractable likelihood ratio that quantifies the importance of the output relative to the inputs and essentially acts as an attention mechanism that promotes exploration of extreme rewards. Our formulation is supported by asymptotic zero-regret guarantees, and its performance is demonstrated across several synthetic benchmarks, as well as two realistic examples involving noisy sensor network data. Finally, we provide a JAX library for efficient bandit optimization using Gaussian processes.

Science & Technology - Other Topics↗

Towards constraining cosmological parameters with SPT-3G observations of 25% of the sky

The South Pole Telescope (SPT), using its third-generation camera, SPT-3G, is conducting observations of the cosmic microwave background (CMB) in temperature and polarization across approximately 10 000 deg$^2$ of the sky at 95, 150, and 220 GHz. This comprehensive dataset should yield stringent constraints on cosmological parameters. In this work, we explore its potential to address the Hubble tension by forecasting constraints from temperature, polarization, and CMB lensing on early dark energy (EDE) and the variation in electron mass in spatially flat and curved universes. For this purpose, we investigate first whether analyzing the distinct SPT-3G observation fields independently, as opposed to as a single, unified region, results in a loss of information relevant to cosmological parameter estimation. We develop a realistic temperature and polarization likelihood pipeline capable of analyzing these fields in these two ways, and subsequently forecast constraints on cosmological parameters. Our findings indicate that any loss of constraining power from analyzing the fields separately is primarily concentrated at low multipoles ($\ell$ < 50) and the overall impact on the relative uncertainty on standard $Λ$ cold dark matter parameters is minimal (< 3%). Our forecasts suggest that SPT-3G data should improve by more than a factor of 90 and 190 the figure of merit of the EDE and the varying electron mass models, respectively, when combined with Planck data. The likelihood pipeline developed and used in this work is made publicly available online.

Vitrier, A. [Paris, Inst. Astrophys.]↗

Characterization and automated optimization of laser-driven proton beams from converging liquid sheet jet targets

Compact, stable, and versatile laser-driven ion sources hold great promise for applications ranging from medicine to materials science and fundamental physics. While single-shot sources have demonstrated favorable beam properties, including the peak fluxes necessary for several applications, high-repetition-rate operation will be necessary to generate and sustain the high average flux needed for many of the most exciting applications of laser-driven ion sources. Further, to navigate through the high-dimensional space of laser and target parameters toward experimental optima, it is essential to develop ion acceleration platforms compatible with machine learning techniques and capable of autonomous real-time optimization. Here, we present a multi-Hz ion acceleration platform employing a liquid sheet jet target. We characterize the laser-plasma interaction and the laser-driven proton beam across a variety of key parameters governing the interaction using an extensive suite of online diagnostics. We also demonstrate real-time, closed-loop optimization of the ion beam maximum energy by tuning the laser wave front using a Bayesian optimization scheme. This approach increased the maximum proton energy by 11% compared to a manually optimized wave front by enhancing the energy concentration within the laser focal spot, demonstrating the potential for closed-loop optimization schemes to tune future ion accelerators for robust high-repetition-rate operation.

Glenn, G. D. [SLAC National Accelerator Laboratory↗

Efficient atmospheric, solar, and supernova neutrino propagation through the Earth

Algorithms for computing neutrino oscillation probabilities in sharply varying matter potentials such as the Earth are becoming increasingly important. As the next generation of experiments, DUNE and HyperK as well as the IceCube upgrade and KM3NeT, come online, the computational cost for atmospheric and solar neutrinos will continue to increase. To address these issues, we expand upon our previous algorithm for long-baseline calculations to efficiently handle probabilities through the Earth for atmospheric, nighttime solar, and supernova neutrinos. The algorithm is fast, flexible, and accurate. It can handle arbitrary Earth models with two different schemes for varying density profiles. We also provide a c ++ implementation of the code called NUF ast- E arth along with a detailed user manual. The code intelligently keeps track of repeated calculations and only recalculates what is needed on each successive call which can also help provide significant speed-ups.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Greedy emulators for nuclear two-body scattering

Applications of reduced basis method emulators are increasing in low-energy nuclear physics because they enable fast and accurate sampling of high-fidelity calculations, enabling robust uncertainty quantification. Here, in this paper, we develop, implement, and test two model-driven emulators based on the (Petrov-)Galerkin projection using the prototypical test case of two-body scattering with the Minnesota potential and a more realistic local chiral potential. The high-fidelity scattering equations are solved with the matrix Numerov method, a reformulation of the popular Numerov recurrence relation for solving special second-order differential equations as a linear system of coupled equations. A novel error estimator based on reduced-space residuals is applied to an active learning approach (a greedy algorithm) to choosing training samples (“snapshots”) for the emulator and contrasted with a proper orthogonal decomposition (POD) approach. Both approaches allow for computationally efficient offline-online decompositions, but the greedy approach requires many fewer snapshot calculations. These developments set the groundwork for emulating scattering observables based on chiral nucleon-nucleon and three-nucleon interactions and optical models, where computational speed-ups are necessary for Bayesian uncertainty quantification. Our emulators and error estimators are widely applicable to linear systems.

Bayesian methods↗

Application of deep learning methods for beam size control during user operation at the Advanced Light Source

Past research at the Advanced Light Source (ALS) provided a proof-of-principle demonstration that deep learning methods could be effectively employed to compensate for the significant perturbations to the transverse electron beam size induced by user-controlled adjustments of the insertion devices. However, incorporating these methods into the ALS’ daily operations has faced notable challenges. The complexity of the system’s operational requirements and the significant upkeep demands has restricted their sustained application during user operation. Here, we introduce the development of a more robust neural network (NN)-based algorithm that utilizes a novel online fine-tuning approach and its systematic integration into the day-to-day machine operations. Our analysis emphasizes the process of NN model selection, demonstrates the superior performance of the NN-based method over traditional feedback methods, and examines the effectiveness and resilience of the new algorithm during user-operation scenarios. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

Bayesian optimization algorithms for accelerator physics

Accelerator physics relies on numerical algorithms to solve optimization problems in online accelerator control and tasks such as experimental design and model calibration in simulations. The effectiveness of optimization algorithms in discovering ideal solutions for complex challenges with limited resources often determines the problem complexity these methods can address. The accelerator physics community has recognized the advantages of Bayesian optimization algorithms, which leverage statistical surrogate models of objective functions to effectively address complex optimization challenges, especially in the presence of noise during accelerator operation and in resource-intensive physics simulations. In this review article, we offer a conceptual overview of applying Bayesian optimization techniques toward solving optimization problems in accelerator physics. We begin by providing a straightforward explanation of the essential components that make up Bayesian optimization techniques. We then give an overview of current and previous work applying and modifying these techniques to solve accelerator physics challenges. Finally, we explore practical implementation strategies for Bayesian optimization algorithms to maximize their performance, enabling users to effectively address complex optimization challenges in real-time beam control and accelerator design. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

Passive and active neutron signatures of 233 U for nondestructive assay

The thorium fuel cycle is emerging as an attractive alternative to conventional nuclear fuel cycles, as it does not require the enrichment of uranium for long-term sustainability. The operating principle of this fuel cycle is the irradiation of 232 Th to produce 233 U, which is fissile and sustains the fission chain reaction. 233 U poses unique challenges for nuclear safeguards, as it is associated with a uniquely extreme γ-ray environment from 232 U contamination, which limits the feasibility of the γ-ray-based assay, as well as more conservative accountability requirements than for 235 U set by the International Atomic Energy Agency. Consequently, instrumentation used for safeguarding 235 U in traditional fuel cycles may be inapplicable. It is essential that the nondestructive signatures of 233 U be characterized so that nuclear safeguards can be applied to thorium fuel-cycle facilities as they come online. In this work, a set of 233 U 3 O 8 plates, containing 984 g 233 U, was measured at the National Criticality Experiments Research Center. A high-pressure 4 He gaseous scintillation detector, which is insensitive to γ-rays, was used to perform a passive fast neutron spectral signature measurement of 233 U 3 O 8 , and was used in conjunction with a pulsed deuterium-tritium neutron generator to demonstrate the differential die-away signature of this material. Furthermore, an array of 3 He detectors was used in conjunction with the same neutron generator to measure the delayed neutron time profile of 233 U, which is unique to this nuclide. These measurements provide a benchmark for future nondestructive assay instrumentation development, and demonstrate a set of key neutron signatures to be leveraged for nuclear safeguards in the thorium fuel cycle.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Experimental studies of the two-step scheme with an intense radioactive 132 Sn beam for next-generation production of very neutron-rich nuclei

The study of nuclei in the yet-unexplored, very neutron-rich, mid- to heavy-mass region of the nuclear chart, comprising perhaps half of all nuclei predicted to exist, is leading to new and/or upgraded facilities, as well as to research into the underlying production processes. In the present study, the usefulness of the two-step scheme, an alternate method to produce very neutron-rich nuclei, by a combination of an isotope-separation online (ISOL) system as a first step, and in-beam fragmentation of re-accelerated radioactive isotopes (RIs) as a second step, was investigated with a 132 Sn beam. In this work, very neutron-rich RIs around the neutron-rich neutron number N = 82 region were produced from the 278-MeV/nucleon 132 Sn beam impinging on a 5.97-mm Be target, and their production cross sections were measured. Yields were then estimated for the two-step scheme with the 132 Sn beam relative to the ones by a one-step scheme, in-flight fission of a 238 U beam, for 1-MW proton and 238 U beams at respective RI-beam facilities. This comparison suggests that the two-step scheme with the 132 Sn beam provides yields >40-times higher than those with the one-step scheme for the very neutron-rich N = 82 region. Moreover, by using various RI beams over the nuclear chart from ISOL, certain kinds of very neutron-rich RIs around the supernova r-process path can be produced with greater yields than by the one-step approach.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Direct observation of the exotic β – γ – α decay mode in the T z = – 1 nucleus Na 20

The exotic β – γ – α decay mode of 20 Na has been directly observed for the first time in the Day-one experiment at the Beijing Radioactive Ion-beam Facility. The 20 Na source was produced by using a 100-MeV proton beam bombarding a stack of microporous MgO thick target and delivered as an intense mass separated beam after online ionization. A high-efficiency simultaneous measurement of β, γ, and α transitions enables the β-delayed γ – γ and α – γ coincidence spectroscopy. Here three β – γ – α exotic decay sequences in 20 Na are discovered, which expands the rare decay modes observed in β decay. Moreover, a β – α –decay sequence to the 6130-keV 3 – state of 16 O is observed, which is likely through the 12367-keV 1 + state in 20 Ne. The experimentally deduced B(F) and B(GT) are compared to the shell-model calculation, the allowed β transition strengths can be well accounted for by using sd shell-model space interactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Investigation of 48 Ca-induced reactions with 242 Pu and 238 U targets at the JINR Superheavy Element Factory

Experiments using a 48 Ca beam on 238 U and 242 Pu targets to produce superheavy nuclei were performed at the gas-filled separator DGFRS-2 online to the new cyclotron DC280 at the SHE Factory at JINR. The decay properties of 286 Fl and 287 Fl, as well as their α-decay products, were refined after the detection of 25 and 69 new decay chains, respectively. In addition, 16 decay chains of 283 Cn were observed in the 238 U+ 48 Ca reaction. The possibility of existing of isomeric states in the 287 Fl consecutive α decays is discussed. A new α line with an energy of 100–200 keV lower than the main one at 10.19 MeV was observed for the first time for even-even 286 Fl decay. A maximum cross section of $10.4^{+3.5}_{-2.1}$pb was measured for the 242 Pu( 48 Ca,3n) 287 Fl reaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

First experiment at the Super Heavy Element Factory: High cross section of Mc 288 in the Am 243 + Ca 48 reaction and identification of the new isotope Lr 264

Here, we present results of the first experiment aimed at the synthesis of Mc isotopes in the 243 Am+ 48 Ca reaction performed at the new gas-filled separator DGFRS-2 online to the new cyclotron DC280 at the Super Heavy Element Factory at JINR. Fifty-five new decay chains of 288 Mc and six chains assigned to 289 Mc were detected. The α decay of 268 Db with an energy of 7.6–8.0 MeV, half-life of 16$^{+6}_{-4}$h, and a branch of 55$^{+20}_{-15}$% was registered for the first time, and a new spontaneously fissioning isotope 264 Lr with a half-life of 4.9$^{+2.1}_{-1.3}$h was identified. The cross section for the 243 Am( 48 Ca,3n) 288 Mc reaction was measured to be 17.1$^{+6.3}_{-4.7}$ pb, which is the largest value for the known superheavy nuclei at the island of stability.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Densities and momentum distributions in A ≤ 12 nuclei from chiral effective field theory interactions

Current and future electron and neutrino scattering experiments will be greatly aided by a better understanding of the role played by short-range correlations in nuclei. Two-body physics, including nucleon-nucleon correlations and two-body electroweak currents, is required to explain the body of experimental data for both static and dynamical nuclear properties. In this work, we focus on examining nucleon-nucleon correlations from a chiral effective field theory perspective and provide a comprehensive set of new variational Monte Carlo calculations of one- and two-body densities and momentum distributions based on the Norfolk many-body nuclear Hamiltonians for A ≤ 12 systems. Here, online access to detailed tables and figures is available.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Momentum distribution of the uniform electron gas at finite temperature: Effects of spin polarization

We carry out extensive direct path integral Monte Carlo (PIMC) simulations of the uniform electron gas (UEG) at finite temperature for different values of the spin-polarization ξ. This allows us to unambiguously quantify the impact of spin effects on the momentum distribution function n(k) and related properties. We find that interesting physical effects like the interaction-induced increase in the occupation of the zero-momentum state n(0) substantially depend on ξ. Our results further advance the current understanding of the UEG as a fundamental model system, and are of practical relevance for the description of transport properties of warm dense matter in an external magnetic field. All PIMC results are freely available online and can be used as a benchmark for the development of methods and applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗