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At least 1,117 records · Page 62

Forecasting constraints on the high-z IGM thermal state from the Lyman-α forest flux autocorrelation function

ABSTRACT The autocorrelation function of the Lyman-$\alpha$ (Ly $\alpha$) forest flux from high-z quasars probes the small-scale structure of the intergalactic medium (IGM). The thermal state of the IGM, determined by the physics of reionization, sets the small-scale power observed in the Ly $\alpha$ forest. To explore the sensitivity of the autocorrelation function to the IGM’s thermal state, we compute the autocorrelation function from a cosmological hydrodynamical simulation with an instantaneous reionization model and 135 post-processed thermal states. Using mock data sets of 20 quasars, we forecast constraints on $T_0$ and $\gamma$, which characterize the post-processed IGM thermal state, at $5.4 \le z \le 6$. While this model simplifies the IGM’s thermal state, it serves as a key first step in assessing future observational prospects. We also perform an inference test on mocks and re-weight out posterior distributions to guarantee that they exhibit statistically correct behaviour. At $z = 5.4$, we find that an idealized data set constrains $T_0$ to 59 per cent and $\gamma$ to 16 per cent at the 1$\sigma$ equivalent confidence level. To explore more realistic, non-instantaneous reionization scenarios, we analyse four models combining temperature and ultraviolet background (UVB) fluctuations at $z = 5.8$. We find that mock data generated from a model with both temperature and UVB fluctuations can rule out a model with only temperature fluctuations at the $> 1\sigma$ level 73.9 per cent of the time.

Wolfson, Molly↗

X-ray fluorescence microscopy methods for biological tissues

Abstract Synchrotron-based X-ray fluorescence microscopy is a flexible tool for identifying the distribution of trace elements in biological specimens across a broad range of sample sizes. The technique is not particularly limited by sample type and can be performed on ancient fossils, fixed or fresh tissue specimens, and in some cases even live tissue and live cells can be studied. The technique can also be expanded to provide chemical specificity to elemental maps, either at individual points of interest in a map or across a large field of view. While virtually any sample type can be characterized with X-ray fluorescence microscopy, common biological sample preparation methods (often borrowed from other fields, such as histology) can lead to unforeseen pitfalls, resulting in altered element distributions and concentrations. A general overview of sample preparation and data-acquisition methods for X-ray fluorescence microscopy is presented, along with outlining the general approach for applying this technique to a new field of investigation for prospective new users. Considerations for improving data acquisition and quality are reviewed as well as the effects of sample preparation, with a particular focus on soft tissues. The effects of common sample pretreatment steps as well as the underlying factors that govern which, and to what extent, specific elements are likely to be altered are reviewed along with common artifacts observed in X-ray fluorescence microscopy data.

Pushie, M. Jake (ORCID:0000000174945427)↗

Structural basis for a highly conserved RNA-mediated enteroviral genome replication

Abstract Enteroviruses contain conserved RNA structures at the extreme 5′ end of their genomes that recruit essential proteins 3CD and PCBP2 to promote genome replication. However, the high-resolution structures and mechanisms of these replication-linked RNAs (REPLRs) are limited. Here, we determined the crystal structures of the coxsackievirus B3 and rhinoviruses B14 and C15 REPLRs at 1.54, 2.2 and 2.54 Å resolution, revealing a highly conserved H-type four-way junction fold with co-axially stacked sA-sD and sB-sC helices that are stabilized by a long-range A•C•U base-triple. Such conserved features observed in the crystal structures also allowed us to predict the models of several other enteroviral REPLRs using homology modeling, which generated models almost identical to the experimentally determined structures. Moreover, our structure-guided binding studies with recombinantly purified full-length human PCBP2 showed that two previously proposed binding sites, the sB-loop and 3′ spacer, reside proximally and bind a single PCBP2. Additionally, the DNA oligos complementary to the 3′ spacer, the high-affinity PCBP2 binding site, abrogated its interactions with enteroviral REPLRs, suggesting the critical roles of this single-stranded region in recruiting PCBP2 for enteroviral genome replication and illuminating the promising prospects of developing therapeutics against enteroviral infections targeting this replication platform.

Biochemistry & Molecular Biology↗

The Gene Ontology knowledgebase in 2026

Abstract The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.

Aleksander, Suzi A (ORCID:0000000167872901)↗

Galaxy Cruise: Deep Insights into Interacting Galaxies in the Local Universe

Abstract We present the first results from GALAXY CRUISE, a community (or citizen) science project based on data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). The current paradigm of galaxy evolution suggests that galaxies grow hierarchically via mergers, but our observational understanding of the role of mergers is still limited. The data from HSC-SSP are ideally suited to improve our understanding with improved identifications of interacting galaxies thanks to the superb depth and image quality of HSC-SSP. We launched a community science project, GALAXY CRUISE, in 2019 and have collected over two million independent classifications of 20686 galaxies at z < 0.2. We first characterize the accuracy of the participants’ classifications and demonstrate that it surpasses previous studies based on shallower imaging data. We then investigate various aspects of interacting galaxies in detail. We show that there is a clear sign of enhanced activities of super-massive black holes and star formation in interacting galaxies compared to those in isolated galaxies. The enhancement seems particularly strong for galaxies undergoing violent mergers. We also show that the mass growth rate inferred from our results is roughly consistent with the observed evolution of the stellar mass function. The second season of GALAXY CRUISE is currently underway and we conclude with future prospects. We make the morphological classification catalog used in this paper publicly available at the GALAXY CRUISE website, which will be particularly useful for machine-learning applications.

Tanaka, Masayuki↗

Respiratory energy demands and scope for demand expansion and destruction

Photosynthesis is the primary energy input to plants, but most plant metabolic processes are powered much or all of the time by ATP and NAD(P)H that come from respiratory oxidation of photosynthetically produced carbohydrates, that is, “dark respiration” (Amthor, 1994). The processes of growth, nutrient uptake and assimilation, active transport, and maintenance are thus all clients of respiration and compete for their share of a respiratory energy budget that is capped by photosynthate income. The economic principle of opportunity cost applies to these clients’ competing demands: spending respiratory energy on process A means missing the benefit of investing that energy in process B (Mahmoudabadi et al., 2019). This principle is key to assessing prospects for crop improvement by metabolic engineering. As de Lorenzo (2015) put it: “metabolism…frames and ultimately resolves whether a given genetic program (existing…or engineered) can be deployed or not.” Foreign or reconfigured native processes bolted on to a crop-plant’s metabolic chassis must compete for respiratory energy with native ones without crashing the energy economy. A proviso on plant carbon budgets is that photosynthetic carbon fixation (“source activity”) can in certain cases increase to meet increased carbon demand (“sink activity”), that is, budget envelopes are not always fixed (Smith et al., 2018). However, as there is some consensus that productivity is most often limited or co-limited by carbon supply (Ainsworth and Long, 2005; Körner, 2015; Sonnewald and Fernie, 2018), we make this our basal assumption in the analyses below.

59 BASIC BIOLOGICAL SCIENCES↗

The Belle II Physics Book

The Belle II Theory Interface Platform (B2TiP) was created as a physics prospects working group of the Belle II collaboration in June 2014. It offered a platform where theorists and experimentalists could work together to elucidate the potential impacts of the Belle II program, which includes a wide scope of physics topics: B physics, charm, τ, quarkonium physics, electroweak precision measurements, and dark sector searches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Gravitational wave physics and astronomy in the nascent era

The detections of gravitational waves (GW) by the LIGO/Virgo collaborations provide various possibilities for both physics and astronomy. We are quite sure that GW observations will develop a lot, both in precision and in number, thanks to the continuous work on the improvement of detectors, including the expected new detector, KAGRA, and the planned detector, LIGO-India. On this occasion, we review the fundamental outcomes and prospects of gravitational wave physics and astronomy. We survey the development, focusing on representative sources of gravitational waves: binary black holes, binary neutron stars, and supernovae. We also summarize the role of gravitational wave observations as a probe of new physics.

79 ASTRONOMY AND ASTROPHYSICS↗

Drug-induced kidney injury: challenges and opportunities

Abstract Drug-induced kidney injury (DIKI) is a frequently reported adverse event, associated with acute kidney injury, chronic kidney disease, and end-stage renal failure. Prospective cohort studies on acute injuries suggest a frequency of around 14%–26% in adult populations and a significant concern in pediatrics with a frequency of 16% being attributed to a drug. In drug discovery and development, renal injury accounts for 8 and 9% of preclinical and clinical failures, respectively, impacting multiple therapeutic areas. Currently, the standard biomarkers for identifying DIKI are serum creatinine and blood urea nitrogen. However, both markers lack the sensitivity and specificity to detect nephrotoxicity prior to a significant loss of renal function. Consequently, there is a pressing need for the development of alternative methods to reliably predict drug-induced kidney injury (DIKI) in early drug discovery. In this article, we discuss various aspects of DIKI and how it is assessed in preclinical models and in the clinical setting, including the challenges posed by translating animal data to humans. We then examine the urinary biomarkers accepted by both the US Food and Drug Administration (FDA) and the European Medicines Agency for monitoring DIKI in preclinical studies and on a case-by-case basis in clinical trials. We also review new approach methodologies (NAMs) and how they may assist in developing novel biomarkers for DIKI that can be used earlier in drug discovery and development.

Connor, Skylar (ORCID:0000000233479180)↗

Predicting oncology drug-induced cardiotoxicity with donor-specific iPSC-CMs—a proof-of-concept study with doxorubicin

Abstract Many oncology drugs have been found to induce cardiotoxicity in a subset of patients, which significantly limits their clinical use and impedes the benefit of lifesaving anticancer treatments. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) carry donor-specific genetic information and have been proposed for exploring the interindividual difference in oncology drug-induced cardiotoxicity. Herein, we evaluated the inter- and intraindividual variability of iPSC-CM-related assays and presented a proof of concept to prospectively predict doxorubicin (DOX)-induced cardiotoxicity (DIC) using donor-specific iPSC-CMs. Our findings demonstrated that donor-specific iPSC-CMs exhibited greater line-to-line variability than the intraindividual variability in impedance cytotoxicity and transcriptome assays. The variable and dose-dependent cytotoxic responses of iPSC-CMs resembled those observed in clinical practice and largely replicated the reported mechanisms. By categorizing iPSC-CMs into resistant and sensitive cell lines based on their time- and concentration-related phenotypic responses to DOX, we found that the sensitivity of donor-specific iPSC-CMs to DOX may predict in vivo DIC risk. Furthermore, we identified a differentially expressed gene, DND microRNA-mediated repression inhibitor 1 (DND1), between the DOX-resistant and DOX-sensitive iPSC-CMs. Our results support the utilization of donor-specific iPSC-CMs in assessing interindividual differences in DIC. Further studies will encompass a large panel of donor-specific iPSC-CMs to identify potential novel molecular and genetic biomarkers for predicting DOX and other oncology drug-induced cardiotoxicity.

Toxicology↗

Preparations for a European R&D roadmap for an inertial fusion demo reactor

A European consortium of 15 laboratories across nine nations have worked together under the EUROFusion Enabling Research grants for the past decade with three principle objectives. These are: (a) investigating obstacles to ignition on megaJoule-class laser facilities; (b) investigating novel alternative approaches to ignition, including basic studies for fast ignition (both electron and ion-driven), auxiliary heating, shock ignition, etc.; and (c) developing technologies that will be required in the future for a fusion reactor. This paperr presents a brief overview of these activities, along with new calculations relates the concept of auxiliary heating of inertial fusion targets, and provides possible future directions of research and development for the updated European Roadmap that is due at the end of 2020. This article is part of a discussion meeting issue ‘Prospects for high gain inertial fusion energy (part 2)’.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fast electron transport dynamics and energy deposition in magnetized, imploded cylindrical plasma

Inertial confinement fusion approaches involve the creation of high-energy-density states through compression. High gain scenarios may be enabled by the beneficial heating from fast electrons produced with an intense laser and by energy containment with a high-strength magnetic field. Here, we report experimental measurements from a configuration integrating a magnetized, imploded cylindrical plasma and intense laser-driven electrons as well as multi-stage simulations that show fast electrons transport pathways at different times during the implosion and quantify their energy deposition contribution. The experiment consisted of a CH foam cylinder, inside an external coaxial magnetic field of 5 T, that was imploded using 36 OMEGA laser beams. Two-dimensional (2D) hydrodynamic modelling predicts the CH density reaches 9.0 g cm − 3 , the temperature reaches 920 eV and the external B-field is amplified at maximum compression to 580 T. At pre-determined times during the compression, the intense OMEGA EP laser irradiated one end of the cylinder to accelerate relativistic electrons into the dense imploded plasma providing additional heating. The relativistic electron beam generation was simulated using a 2D particle-in-cell (PIC) code. Finally, three-dimensional hybrid-PIC simulations calculated the electron propagation and energy deposition inside the target and revealed the roles the compressed and self-generated B-fields play in transport. During a time window before the maximum compression time, the self-generated B-field on the compression front confines the injected electrons inside the target, increasing the temperature through Joule heating. For a stronger B-field seed of 20 T, the electrons are predicted to be guided into the compressed target and provide additional collisional heating. This article is part of a discussion meeting issue ‘Prospects for high gain inertial fusion energy (part 2)’.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Taylor–Couette flow for astrophysical purposes

A concise review is given of astrophysically motivated experimental and theoretical research on Taylor–Couette flow. The flows of interest rotate differentially with the inner cylinder faster than the outer, but are linearly stable against Rayleigh’s inviscid centrifugal instability. At shear Reynolds numbers as large as 10 6 , hydrodynamic flows of this type (quasi-Keplerian) appear to be nonlinearly stable: no turbulence is seen that cannot be attributed to interaction with the axial boundaries, rather than the radial shear itself. Direct numerical simulations agree, although they cannot yet reach such high Reynolds numbers. This result indicates that accretion-disc turbulence is not purely hydrodynamic in origin, at least insofar as it is driven by radial shear. Theory, however, predicts linear magnetohydrodynamic (MHD) instabilities in astrophysical discs: in particular, the standard magnetorotational instability (SMRI). MHD Taylor–Couette experiments aimed at SMRI are challenged by the low magnetic Prandtl numbers of liquid metals. High fluid Reynolds numbers and careful control of the axial boundaries are required. The quest for laboratory SMRI has been rewarded with the discovery of some interesting inductionless cousins of SMRI, and with the recently reported success in demonstrating SMRI itself using conducting axial boundaries. Some outstanding questions and near-future prospects are discussed, especially in connection with astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗

Toward a Robust Confirmation or Refutation of the Sterile-Neutrino Explanation of Short-Baseline Anomalies

The sterile neutrino interpretation of the LSND and MiniBooNE neutrino anomalies is currently being tested at three liquid argon detectors: MicroBooNE, SBND, and ICARUS. It has been argued that a degeneracy between 𝜈 𝜇 → 𝜈 𝑒 and 𝜈 𝑒 → 𝜈 𝑒 oscillations significantly degrades their sensitivity to sterile neutrinos. Through an independent study, we show two methods to eliminate this concern. First, we resolve this degeneracy by including external constraints on 𝜈𝑒 disappearance from the PROSPECT reactor experiment. Second, by properly analyzing the full three-dimensional parameter space, we demonstrate that the stronger-than-sensitivity exclusion from MicroBooNE alone already covers the entire 2⁢𝜎 preferred regions of MiniBooNE at the level of 2−3⁢𝜎. We show that upcoming searches at SBND and ICARUS can improve on this beyond the 4⁢𝜎 level, thereby providing a rigorous test of short-baseline anomalies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tau tridents at accelerator neutrino facilities

We present the first detailed study of Standard Model neutrino tridents involving tau leptons at the near detectors of accelerator neutrino facilities. The rates of these processes were previously thought to be negligible, even at future facilities. Our full 2 → 4 calculation, including both coherent and incoherent scatterings, reveals that the DUNE near detector could observe a considerable number of tau tridents—an important background to new physics searches. We identify promising kinematic features that may allow distinction of tau tridents from the usual neutrino charged-current background at DUNE, and thus establish the observation of tau tridents for the first time. We also comment on the detection prospects at other accelerator and collider neutrino experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Ferromagnetic moment in the magnetoelectric antiferromagnet Co 4 ⁢Ta 2 ⁢O 9 : Evidence of the 𝑃⁢1 magnetic space group

Exploring ferromagnetic moments in magnetoelectric materials is of both fundamental and technological importance. It enables the control of the correlated state using an uncompensated moment. However, its material realization is challenging owing to its exclusive microscopic mechanisms. Here, we report a nearly isotropic ferromagnetic moment in the magnetoelectric antiferromagnet Co 4 ⁢Ta 2 ⁢O 9 , by performing dc and ac magnetic susceptibility, magnetization, and neutron diffraction measurements on identical single crystals. Combined with the group theory analysis, we demonstrate a 𝑃⁢1 magnetic space group. This implies that physical activities can occur along any crystallographic direction, which explains the unusual magnetoelectric property of Co 4⁢ Ta 2⁢ O 9 . The ground state is classified as the M-type altermagnet based on the magnetic point group. Our study provides essential information to resolve the debate on the magnetic ground state and understand the magnetoelectric properties of the related compound with the prospect of observing and examining the 𝑃⁢1 magnetic space group or ferromagnet in ferroelectrics.

Antiferromagnets↗

Phases of dark matter from inverse decays

Inverse decays are an interesting avenue for producing dark matter in the early Universe. We study in detail various phases of dark matter parameter space where inverse decays control its abundance, expanding on our work of inverse decay (INDY) dark matter and going beyond. The role of initial conditions and the impact of departure from kinetic equilibrium are investigated as well. We show how these inverse decay phases can arise in theories of a kinetically mixed dark photon and dark Higgs, with promising prospects for detection at upcoming experiments.

Cosmology↗