Showing papers by "Nagoya University published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Observation of Gravitational Waves from Two Neutron Star–Black Hole Coalescences

Abstract: We report the observation of gravitational waves from two compact binary coalescences in LIGO’s and Virgo’s third observing run with properties consistent with neutron star–black hole (NSBH) binaries. The two events are named GW200105_162426 and GW200115_042309, abbreviated as GW200105 and GW200115; the first was observed by LIGO Livingston and Virgo and the second by all three LIGO–Virgo detectors. The source of GW200105 has component masses 8.9−1.5+1.2 and 1.9−0.2+0.3M⊙ , whereas the source of GW200115 has component masses 5.7−2.1+1.8 and 1.5−0.3+0.7M⊙ (all measurements quoted at the 90% credible level). The probability that the secondary’s mass is below the maximal mass of a neutron star is 89%–96% and 87%–98%, respectively, for GW200105 and GW200115, with the ranges arising from different astrophysical assumptions. The source luminosity distances are 280−110+110 and 300−100+150Mpc , respectively. The magnitude of the primary spin of GW200105 is less than 0.23 at the 90% credible level, and its orientation is unconstrained. For GW200115, the primary spin has a negative spin projection onto the orbital angular momentum at 88% probability. We are unable to constrain the spin or tidal deformation of the secondary component for either event. We infer an NSBH merger rate density of 45−33+75Gpc−3yr−1 when assuming that GW200105 and GW200115 are representative of the NSBH population or 130−69+112Gpc−3yr−1 under the assumption of a broader distribution of component masses.

International Geomagnetic Reference Field: the thirteenth generation

Abstract: In December 2019, the International Association of Geomagnetism and Aeronomy (IAGA) Division V Working Group (V-MOD) adopted the thirteenth generation of the International Geomagnetic Reference Field (IGRF). This IGRF updates the previous generation with a definitive main field model for epoch 2015.0, a main field model for epoch 2020.0, and a predictive linear secular variation for 2020.0 to 2025.0. This letter provides the equations defining the IGRF, the spherical harmonic coefficients for this thirteenth generation model, maps of magnetic declination, inclination and total field intensity for the epoch 2020.0, and maps of their predicted rate of change for the 2020.0 to 2025.0 time period.

The trans-ancestral genomic architecture of glycemic traits

Abstract: Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10-8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.

Leading hadronic contribution to the muon magnetic moment from lattice QCD

Abstract: The standard model of particle physics describes the vast majority of experiments and observations involving elementary particles. Any deviation from its predictions would be a sign of new, fundamental physics. One long-standing discrepancy concerns the anomalous magnetic moment of the muon, a measure of the magnetic field surrounding that particle. Standard-model predictions1 exhibit disagreement with measurements2 that is tightly scattered around 3.7 standard deviations. Today, theoretical and measurement errors are comparable; however, ongoing and planned experiments aim to reduce the measurement error by a factor of four. Theoretically, the dominant source of error is the leading-order hadronic vacuum polarization (LO-HVP) contribution. For the upcoming measurements, it is essential to evaluate the prediction for this contribution with independent methods and to reduce its uncertainties. The most precise, model-independent determinations so far rely on dispersive techniques, combined with measurements of the cross-section of electron–positron annihilation into hadrons3–6. To eliminate our reliance on these experiments, here we use ab initio quantum chromodynamics (QCD) and quantum electrodynamics simulations to compute the LO-HVP contribution. We reach sufficient precision to discriminate between the measurement of the anomalous magnetic moment of the muon and the predictions of dispersive methods. Our result favours the experimentally measured value over those obtained using the dispersion relation. Moreover, the methods used and developed in this work will enable further increased precision as more powerful computers become available. A precise theoretical computation of the anomalous magnetic moment of the muon based on ab initio quantum chromodynamics and quantum electrodynamics calculations is presented, which favours the existing experimental values.

Constraining the atmospheric limb of the plastic cycle.

Abstract: Plastic pollution is one of the most pressing environmental and social issues of the 21st century. Recent work has highlighted the atmosphere’s role in transporting microplastics to remote locations [S. Allen et al., Nat. Geosci. 12, 339 (2019) and J. Brahney, M. Hallerud, E. Heim, M. Hahnenberger, S. Sukumaran, Science 368, 1257–1260 (2020)]. Here, we use in situ observations of microplastic deposition combined with an atmospheric transport model and optimal estimation techniques to test hypotheses of the most likely sources of atmospheric plastic. Results suggest that atmospheric microplastics in the western United States are primarily derived from secondary re-emission sources including roads (84%), the ocean (11%), and agricultural soil dust (5%). Using our best estimate of plastic sources and modeled transport pathways, most continents were net importers of plastics from the marine environment, underscoring the cumulative role of legacy pollution in the atmospheric burden of plastic. This effort uses high-resolution spatial and temporal deposition data along with several hypothesized emission sources to constrain atmospheric plastic. Akin to global biogeochemical cycles, plastics now spiral around the globe with distinct atmospheric, oceanic, cryospheric, and terrestrial residence times. Though advancements have been made in the manufacture of biodegradable polymers, our data suggest that extant nonbiodegradable polymers will continue to cycle through the earth’s systems. Due to limited observations and understanding of the source processes, there remain large uncertainties in the transport, deposition, and source attribution of microplastics. Thus, we prioritize future research directions for understanding the plastic cycle.

Indications and Strategy for Active Surveillance of Adult Low-Risk Papillary Thyroid Microcarcinoma: Consensus Statements from the Japan Association of Endocrine Surgery Task Force on Management for Papillary Thyroid Microcarcinoma

Abstract: Background: The question of how to manage patients with low-risk papillary thyroid microcarcinoma (PTMC; T1aN0M0) has recently become an important clinical issue. Two Japanese centers have conducted prospective clinical trials of active surveillance (AS) for low-risk PTMC since the 1990s, reporting favorable outcomes. This policy has thus seen gradual adoption worldwide to avoid overtreatment. Not all PTMCs are suitable for AS, however, and many physicians still hesitate to apply the management policy in daily clinical practice. A task force on management for PTMC created by the Japan Association of Endocrine Surgery collected and analyzed bibliographic evidence and has produced the present consensus statements regarding indications and concrete strategies for AS to facilitate the management of adult patients diagnosed with low-risk PTMC. Summary: These statements provide indications for AS in adult patients with T1aN0M0 low-risk PTMC. PTMCs with clinical lymph node metastasis, distant metastasis, recurrent laryngeal nerve (RLN) paralysis due to carcinoma invasion, or protrusion into the tracheal lumen warrant immediate surgery. Tumors suspected of aggressive subtypes on cytology are recommended for immediate surgery. Immediate surgery is also recommended for tumors adherent to the trachea or located along the course of the RLN. Practical strategies include diagnosis, decision-making, follow-up, and monitoring related to the implementation of AS. The rate of low-risk PTMC progression is lower in older patients. However, we recommend continuing AS as long as circumstances permit. Future tasks in optimizing management for low-risk PTMC are also described, including molecular markers and patient-reported outcomes. Conclusions: An appropriate multidisciplinary team is necessary to accurately evaluate primary tumors and lymph nodes at the beginning of and during AS, and to adequately reach a shared-decision with individual patients. If appropriately applied, AS of low-risk PTMC is a safe management strategy offering favorable outcomes and preserves quality of life at low cost.

Test of Lepton-Flavor Universality in B →k∗ℓ+ℓ- Decays at Belle

Abstract: We acknowledge support from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan, the Japan Society for the Promotion of Science (JSPS), and the Tau-Lepton Physics Research Center of Nagoya University; the Australian Research Council including Grants No. DP180102629, No. DP170102389, No. DP170102204, No. DP150103061, No. FT130100303; Austrian Science Fund (FWF); the National Natural Science Foundation of China under Contracts No. 11435013, No. 11475187, No. 11521505, No. 11575017, No. 11675166, No. 11705209; Key Research Program of Frontier Sciences, Chinese Academy of Sciences (CAS), Grant No. QYZDJ-SSWSLH011; the CAS Center for Excellence in Particle Physics (CCEPP); the Shanghai Pujiang Program under Grant No. 18PJ1401000; the Ministry of Education, Youth and Sports of the Czech Republic under Contract No. LTT17020; the Carl Zeiss Foundation, the Deutsche Forschungsgemeinschaft, the Excellence Cluster Universe, and the VolkswagenStiftung; the Department of Science and Technology of India; the Istituto Nazionale di Fisica Nucleare of Italy; National Research Foundation (NRF) of Korea Grants No. 2016R1D1A1B01010135, No. 2016R1D1A1B02012900, No. 2018R1A2B3003643, No. 2018R1A6A1A06024970, No. 2018R1D1A1B07047294, No. 2019K1A3A7A09033840, No. 2019R1I1A3A01058933; Radiation Science Research Institute, Foreign Large-size Research Facility Application Supporting project, the Global Science Experimental Data Hub Center of the Korea Institute of Science and Technology Information, and KREONET/GLORIAD the Polish Ministry of Science and Higher Education and the National Science Center; the Ministry of Science and Higher Education of the Russian Federation, Agreement No. 14.W03.31.0026; University of Tabuk research Grants No. S-1440-0321, No. S-0256-1438, and No. S-0280-1439 (Saudi Arabia); the Slovenian Research Agency; Ikerbasque, Basque Foundation for Science, Spain; the Swiss National Science Foundation; the Ministry of Education and the Ministry of Science and Technology of Taiwan; and the U.S. Department of Energy and the National Science Foundation.

Upper limits on the isotropic gravitational-wave background from Advanced LIGO and Advanced Virgo’s third observing run

Abstract: We report results of a search for an isotropic gravitational-wave background (GWB) using data from Advanced LIGO’s and Advanced Virgo’s third observing run (O3) combined with upper limits from the earlier O1 and O2 runs. Unlike in previous observing runs in the advanced detector era, we include Virgo in the search for the GWB. The results of the search are consistent with uncorrelated noise, and therefore we place upper limits on the strength of the GWB. We find that the dimensionless energy density Ω GW ≤ 5.8 × 10 − 9 at the 95% credible level for a flat (frequency-independent) GWB, using a prior which is uniform in the log of the strength of the GWB, with 99% of the sensitivity coming from the band 20–76.6 Hz; Ω GW ( f ) ≤ 3.4 × 10 − 9 at 25 Hz for a power-law GWB with a spectral index of 2 / 3 (consistent with expectations for compact binary coalescences), in the band 20–90.6 Hz; and Ω GW ( f ) ≤ 3.9 × 10 − 10 at 25 Hz for a spectral index of 3, in the band 20–291.6 Hz. These upper limits improve over our previous results by a factor of 6.0 for a flat GWB, 8.8 for a spectral index of 2 / 3 , and 13.1 for a spectral index of 3. We also search for a GWB arising from scalar and vector modes, which are predicted by alternative theories of gravity; we do not find evidence of these, and place upper limits on the strength of GWBs with these polarizations. We demonstrate that there is no evidence of correlated noise of magnetic origin by performing a Bayesian analysis that allows for the presence of both a GWB and an effective magnetic background arising from geophysical Schumann resonances. We compare our upper limits to a fiducial model for the GWB from the merger of compact binaries, updating the model to use the most recent data-driven population inference from the systems detected during O3a. Finally, we combine our results with observations of individual mergers and show that, at design sensitivity, this joint approach may yield stronger constraints on the merger rate of binary black holes at z ≳ 2 than can be achieved with individually resolved mergers alone.

Overview of KAGRA: Detector design and construction history

Abstract: KAGRA is a newly built gravitational-wave telescope, a laser interferometer comprising arms with a length of 3\,km, located in Kamioka, Gifu, Japan. KAGRA was constructed under the ground and it is operated using cryogenic mirrors that help in reducing the seismic and thermal noise. Both technologies are expected to provide directions for the future of gravitational-wave telescopes. In 2019, KAGRA finished all installations with the designed configuration, which we call the baseline KAGRA. In this occasion, we present an overview of the baseline KAGRA from various viewpoints in a series of of articles. In this article, we introduce the design configurations of KAGRA with its historical background.

Jet energy scale and resolution measured in proton-proton collisions at s =13 TeV with the ATLAS detector

Abstract: Jet energy scale and resolution measurements with their associated uncertainties are reported for jets using 36-81 fb$^{-1}$ of proton-proton collision data with a centre-of-mass energy of $\sqrt{s}=13$ TeV collected by the ATLAS detector at the LHC. Jets are reconstructed using two different input types: topo-clusters formed from energy deposits in calorimeter cells, as well as an algorithmic combination of charged-particle tracks with those topo-clusters, referred to as the ATLAS particle-flow reconstruction method. The anti-$k_t$ jet algorithm with radius parameter $R=0.4$ is the primary jet definition used for both jet types. Jets are initially calibrated using a sequence of simulation-based corrections. Next, several $\textit{in situ}$ techniques are employed to correct for differences between data and simulation and to measure the resolution of jets. The systematic uncertainties in the jet energy scale for central jets ($|\eta| 2.5$ TeV). The relative jet energy resolution is measured and ranges from ($24 \pm 1.5$)% at 20 GeV to ($6 \pm 0.5$)% at 300 GeV.

Projected land ice contributions to twenty-first-century sea level rise

Abstract: The land ice contribution to global mean sea level rise has not yet been predicted1 using ice sheet and glacier models for the latest set of socio-economic scenarios, nor using coordinated exploration of uncertainties arising from the various computer models involved. Two recent international projects generated a large suite of projections using multiple models2,3,4,5,6,7,8, but primarily used previous-generation scenarios9 and climate models10, and could not fully explore known uncertainties. Here we estimate probability distributions for these projections under the new scenarios11,12 using statistical emulation of the ice sheet and glacier models. We find that limiting global warming to 1.5 degrees Celsius would halve the land ice contribution to twenty-first-century sea level rise, relative to current emissions pledges. The median decreases from 25 to 13 centimetres sea level equivalent (SLE) by 2100, with glaciers responsible for half the sea level contribution. The projected Antarctic contribution does not show a clear response to the emissions scenario, owing to uncertainties in the competing processes of increasing ice loss and snowfall accumulation in a warming climate. However, under risk-averse (pessimistic) assumptions, Antarctic ice loss could be five times higher, increasing the median land ice contribution to 42 centimetres SLE under current policies and pledges, with the 95th percentile projection exceeding half a metre even under 1.5 degrees Celsius warming. This would severely limit the possibility of mitigating future coastal flooding. Given this large range (between 13 centimetres SLE using the main projections under 1.5 degrees Celsius warming and 42 centimetres SLE using risk-averse projections under current pledges), adaptation planning for twenty-first-century sea level rise must account for a factor-of-three uncertainty in the land ice contribution until climate policies and the Antarctic response are further constrained.

Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer's disease.

Abstract: Microglia-mediated neuroinflammation has been implicated in the pathogenesis of Alzheimer’s disease (AD). Although microglia in aging and neurodegenerative disease model mice show a loss of homeostatic phenotype and activation of disease-associated microglia (DAM), a correlation between those phenotypes and the degree of neuronal cell loss has not been clarified. In this study, we performed RNA sequencing of microglia isolated from three representative neurodegenerative mouse models, AppNL-G-F/NL-G-F with amyloid pathology, rTg4510 with tauopathy, and SOD1G93A with motor neuron disease by magnetic activated cell sorting. In parallel, gene expression patterns of the human precuneus with early Alzheimer’s change (n = 11) and control brain (n = 14) were also analyzed by RNA sequencing. We found that a substantial reduction of homeostatic microglial genes in rTg4510 and SOD1G93A microglia, whereas DAM genes were uniformly upregulated in all mouse models. The reduction of homeostatic microglial genes was correlated with the degree of neuronal cell loss. In human precuneus with early AD pathology, reduced expression of genes related to microglia- and oligodendrocyte-specific markers was observed, although the expression of DAM genes was not upregulated. Our results implicate a loss of homeostatic microglial function in the progression of AD and other neurodegenerative diseases. Moreover, analyses of human precuneus also suggest loss of microglia and oligodendrocyte functions induced by early amyloid pathology in human.

Distinct identities of leaf phloem cells revealed by single cell transcriptomics.

Abstract: The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about leaf vascular cells, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading, yet PP has been characterized only microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified at least 19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. We provide evidence that PP development occurs independently from ALTERED PHLOEM DEVELOPMENT, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CCs), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our single-cell RNA-sequencing analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.

Current status of space gravitational wave antenna DECIGO and B-DECIGO

Abstract: The Deci-hertz Interferometer Gravitational Wave Observatory (DECIGO) is a future Japanese space mission with a frequency band of 0.1 Hz to 10 Hz. DECIGO aims at the detection of primordial gravitational waves, which could have been produced during the inflationary period right after the birth of the Universe. There are many other scientific objectives of DECIGO, including the direct measurement of the acceleration of the expansion of the Universe, and reliable and accurate predictions of the timing and locations of neutron star/black hole binary coalescences. DECIGO consists of four clusters of observatories placed in heliocentric orbit. Each cluster consists of three spacecraft, which form three Fabry-Perot Michelson interferometers with an arm length of 1000 km. Three DECIGO clusters will be placed far from each other, and the fourth will be placed in the same position as one of the other three to obtain correlation signals for the detection of primordial gravitational waves. We plan to launch B-DECIGO, which is a scientific pathfinder for DECIGO, before DECIGO in the 2030s to demonstrate the technologies required for DECIGO, as well as to obtain fruitful scientific results to further expand multi-messenger astronomy.

The Atacama cosmology telescope: a catalog of >4000 sunyaev–zel'dovich galaxy clusters

Abstract: We present a catalog of 4195 optically confirmed Sunyaev–Zel’dovich (SZ) selected galaxy clusters detected with signal-to-noise ratio >4 in 13,211 deg2 of sky surveyed by the Atacama Cosmology Telescope (ACT). Cluster candidates were selected by applying a multifrequency matched filter to 98 and 150 GHz maps constructed from ACT observations obtained from 2008 to 2018 and confirmed using deep, wide-area optical surveys. The clusters span the redshift range 0.04 1 clusters, and a total of 868 systems are new discoveries. Assuming an SZ signal versus mass-scaling relation calibrated from X-ray observations, the sample has a 90% completeness mass limit of M500c > 3.8 × 1014 Me, evaluated at z = 0.5, for clusters detected at signal-to-noise ratio >5 in maps filtered at an angular scale of 2 4. The survey has a large overlap with deep optical weak-lensing surveys that are being used to calibrate the SZ signal mass-scaling relation, such as the Dark Energy Survey (4566 deg2), the Hyper Suprime-Cam Subaru Strategic Program (469 deg2), and the Kilo Degree Survey (825 deg2). We highlight some noteworthy objects in the sample, including potentially projected systems, clusters with strong lensing features, clusters with active central galaxies or star formation, and systems of multiple clusters that may be physically associated. The cluster catalog will be a useful resource for future cosmological analyses and studying the evolution of the intracluster medium and galaxies in massive clusters over the past 10 Gyr.

Antitumour immunity regulated by aberrant ERBB family signalling

Abstract: Aberrant signalling of ERBB family members plays an important role in tumorigenesis and in the escape from antitumour immunity in multiple malignancies. Molecular-targeted agents against these signalling pathways exhibit robust clinical efficacy, but patients inevitably experience acquired resistance to these molecular-targeted therapies. Although cancer immunotherapies, including immune checkpoint inhibitors (ICIs), have shown durable antitumour response in a subset of the treated patients in multiple cancer types, clinical efficacy is limited in cancers harbouring activating gene alterations of ERBB family members. In particular, ICI treatment of patients with non-small cell lung cancers with epidermal growth factor receptor (EGFR) alterations and breast cancers with HER2 alterations failed to show clinical benefits, suggesting that EGFR and HER2 signalling may have an essential role in inhibiting antitumour immune responses. Here, we discuss the mechanisms by which the signalling of ERBB family members affects not only autonomous cancer hallmarks, such as uncontrolled cell proliferation, but also antitumour immune responses in the tumour microenvironment and the potential application of immune-genome precision medicine into immunotherapy and molecular-targeted therapy focusing on the signalling of ERBB family members. Aberrant signalling of ERBB family members plays an important role in tumorigenesis and in the escape from antitumour immunity in multiple malignancies. This Review discusses the mechanisms by which this signalling affects antitumour immune responses and the potential application of immune-genome precision medicine in this context.

Regulation of root adaptive anatomical and morphological traits during low soil oxygen.

Abstract: Flooding causes oxygen deprivation in soils. Plants adapt to low soil oxygen availability by changes in root morphology, anatomy, and architecture to maintain root system functioning. Essential traits include aerenchyma formation, a barrier to radial oxygen loss, and outgrowth of adventitious roots into the soil or the floodwater. We highlight recent findings of mechanisms of constitutive aerenchyma formation and of changes in root architecture. Moreover, we use modelling of internal aeration to demonstrate the beneficial effect of increasing cortex-to-stele ratio on sustaining root growth in waterlogged soils. We know the genes for some of the beneficial traits, and the next step is to manipulate these genes in breeding in order to enhance the flood tolerance of our crops.

Ferritinophagy and ferroptosis in the management of metabolic diseases.

Abstract: Ferroptosis is a form of regulated cell death modality associated with disturbed iron-homeostasis and unrestricted lipid peroxidation. Ample evidence has depicted an essential role for ferroptosis as either the cause or consequence for human diseases, denoting the likely therapeutic promises for targeting ferroptosis in the preservation of human health. Ferritinophagy, a selective form of autophagy, contributes to the initiation of ferroptosis through degradation of ferritin, which triggers labile iron overload (IO), lipid peroxidation, membrane damage, and cell death. In this review, we will delineate the role of ferritinophagy in ferroptosis, and its underlying regulatory mechanisms, to unveil the therapeutic value of ferritinophagy as a target in the combat of ferroptosis to manage metabolic diseases.

Muon reconstruction and identification efficiency in ATLAS using the full Run 2 pp collision data set at √ s = 13 TeV

Abstract: This article documents the muon reconstruction and identification efficiency obtained by the ATLAS experiment for 139 $$\hbox {fb}^{-1}$$ fb - 1 of pp collision data at $$\sqrt{s}=13$$ s = 13 TeV collected between 2015 and 2018 during Run 2 of the LHC. The increased instantaneous luminosity delivered by the LHC over this period required a reoptimisation of the criteria for the identification of prompt muons. Improved and newly developed algorithms were deployed to preserve high muon identification efficiency with a low misidentification rate and good momentum resolution. The availability of large samples of $$Z\rightarrow \mu \mu $$ Z → μ μ and $$J/\psi \rightarrow \mu \mu $$ J / ψ → μ μ decays, and the minimisation of systematic uncertainties, allows the efficiencies of criteria for muon identification, primary vertex association, and isolation to be measured with an accuracy at the per-mille level in the bulk of the phase space, and up to the percent level in complex kinematic configurations. Excellent performance is achieved over a range of transverse momenta from 3 GeV to several hundred GeV, and across the full muon detector acceptance of $$|\eta |<2.7$$ | η | < 2.7 .

TMK-based cell-surface auxin signalling activates cell-wall acidification.

Abstract: The phytohormone auxin controls many processes in plants, at least in part through its regulation of cell expansion1. The acid growth hypothesis has been proposed to explain auxin-stimulated cell expansion for five decades, but the mechanism that underlies auxin-induced cell-wall acidification is poorly characterized. Auxin induces the phosphorylation and activation of the plasma membrane H+-ATPase that pumps protons into the apoplast2, yet how auxin activates its phosphorylation remains unclear. Here we show that the transmembrane kinase (TMK) auxin-signalling proteins interact with plasma membrane H+-ATPases, inducing their phosphorylation, and thereby promoting cell-wall acidification and hypocotyl cell elongation in Arabidopsis. Auxin induced interactions between TMKs and H+-ATPases in the plasma membrane within seconds, as well as TMK-dependent phosphorylation of the penultimate threonine residue on the H+-ATPases. Our genetic, biochemical and molecular evidence demonstrates that TMKs directly phosphorylate plasma membrane H+-ATPase and are required for auxin-induced H+-ATPase activation, apoplastic acidification and cell expansion. Thus, our findings reveal a crucial connection between auxin and plasma membrane H+-ATPase activation in regulating apoplastic pH changes and cell expansion through TMK-based cell surface auxin signalling. Auxin induces transmembrane-kinase-dependent activation of H+-ATPase in the plasma membrane through phosphorylation of its penultimate threonine residue, promoting apoplastic acidification and hypocotyl cell elongation in Arabidopsis.

Cell surface and intracellular auxin signalling for H+ fluxes in root growth

Abstract: Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments. Auxin rapidly modulates root growth through simultaneous activation of two opposing mechanisms—TMK1-mediated apoplast acidification and TIR1/AFB-mediated apoplast alkalinization.

Social influence and unfollowing accelerate the emergence of echo chambers

Abstract: While social media make it easy to connect with and access information from anyone, they also facilitate basic influence and unfriending mechanisms that may lead to segregated and polarized clusters known as “echo chambers.” Here we study the conditions in which such echo chambers emerge by introducing a simple model of information sharing in online social networks with the two ingredients of influence and unfriending. Users can change both their opinions and social connections based on the information to which they are exposed through sharing. The model dynamics show that even with minimal amounts of influence and unfriending, the social network rapidly devolves into segregated, homogeneous communities. These predictions are consistent with empirical data from Twitter. Although our findings suggest that echo chambers are somewhat inevitable given the mechanisms at play in online social media, they also provide insights into possible mitigation strategies.

Overview of KAGRA: Calibration, detector characterization, physical environmental monitors, and the geophysics interferometer

Abstract: KAGRA is a newly built gravitational wave observatory, a laser interferometer with a 3 km arm length, located at Kamioka, Gifu, Japan. In this series of articles we present an overview of the baseline KAGRA, for which we finished installing the designed configuration in 2019. This article describes the method of calibration (CAL) used for reconstructing gravitational wave signals from the detector outputs, as well as the characterization of the detector (DET). We also review the physical environmental monitoring (PEM) system and the geophysics interferometer (GIF). Both are used for characterizing and evaluating the data quality of the gravitational wave channel. They play important roles in utilizing the detector output for gravitational wave searches. These characterization investigations will be even more important in the near future, once gravitational wave detection has been achieved, and in using KAGRA in the gravitational wave astronomy era.

Construction of Heptagon-Containing Molecular Nanocarbons

Abstract: Molecular nanocarbons containing heptagonal rings have attracted increasing interest due to their dynamic behavior, electronic properties, aromaticity, and solid-state packing. Heptagon incorporation can not only induce negative curvature within nanocarbon scaffolds, but also confer significantly altered properties through interaction with adjacent non-hexagonal rings. Despite the disclosure of several beautiful examples in recent years, synthetic strategies toward heptagon-embedded molecular nanocarbons remain relatively limited due to the intrinsic challenges of heptagon formation and incorporation into polyarene frameworks. In this Review, recent advances in solution-mediated and surface-assisted synthesis of heptagon-containing molecular nanocarbons, as well as the intriguing properties of these frameworks, will be discussed.

AeroCom phase III multi-model evaluation of the aerosol life cycle and optical properties using ground- and space-based remote sensing as well as surface in situ observations

Abstract: . Within the framework of the AeroCom (Aerosol Comparisons between Observations and Models) initiative, the state-of-the-art modelling of aerosol optical properties is assessed from 14 global models participating in the phase III control experiment (AP3). The models are similar to CMIP6/AerChemMIP Earth System Models (ESMs) and provide a robust multi-model ensemble. Inter-model spread of aerosol species lifetimes and emissions appears to be similar to that of mass extinction coefficients (MECs), suggesting that aerosol optical depth (AOD) uncertainties are associated with a broad spectrum of parameterised aerosol processes. Total AOD is approximately the same as in AeroCom phase I (AP1) simulations. However, we find a 50 % decrease in the optical depth (OD) of black carbon (BC), attributable to a combination of decreased emissions and lifetimes. Relative contributions from sea salt (SS) and dust (DU) have shifted from being approximately equal in AP1 to SS contributing about 2∕3 of the natural AOD in AP3. This shift is linked with a decrease in DU mass burden, a lower DU MEC, and a slight decrease in DU lifetime, suggesting coarser DU particle sizes in AP3 compared to AP1. Relative to observations, the AP3 ensemble median and most of the participating models underestimate all aerosol optical properties investigated, that is, total AOD as well as fine and coarse AOD (AOD f , AOD c ), Angstrom exponent (AE), dry surface scattering (SC dry ), and absorption (AC dry ) coefficients. Compared to AERONET, the models underestimate total AOD by ca. 21 % ± 20 % (as inferred from the ensemble median and interquartile range). Against satellite data, the ensemble AOD biases range from − 37 % (MODIS-Terra) to − 16 % (MERGED-FMI, a multi-satellite AOD product), which we explain by differences between individual satellites and AERONET measurements themselves. Correlation coefficients ( R ) between model and observation AOD records are generally high ( R>0 .75), suggesting that the models are capable of capturing spatio-temporal variations in AOD. We find a much larger underestimate in coarse AOD c ( ∼ − 45 % ± 25 %) than in fine AOD f ( ∼ − 15 % ± 25 %) with slightly increased inter-model spread compared to total AOD. These results indicate problems in the modelling of DU and SS. The AOD c bias is likely due to missing DU over continental land masses (particularly over the United States, SE Asia, and S. America), while marine AERONET sites and the AATSR SU satellite data suggest more moderate oceanic biases in AOD c . Column AEs are underestimated by about 10 % ± 16 %. For situations in which measurements show AE > 2, models underestimate AERONET AE by ca. 35 %. In contrast, all models (but one) exhibit large overestimates in AE when coarse aerosol dominates (bias ca. + 140 % if observed AE 0.5). Simulated AE does not span the observed AE variability. These results indicate that models overestimate particle size (or underestimate the fine-mode fraction) for fine-dominated aerosol and underestimate size (or overestimate the fine-mode fraction) for coarse-dominated aerosol. This must have implications for lifetime, water uptake, scattering enhancement, and the aerosol radiative effect, which we can not quantify at this moment. Comparison against Global Atmosphere Watch (GAW) in situ data results in mean bias and inter-model variations of − 35 % ± 25 % and − 20 % ± 18 % for SC dry and AC dry , respectively. The larger underestimate of SC dry than AC dry suggests the models will simulate an aerosol single scattering albedo that is too low. The larger underestimate of SC dry than ambient air AOD is consistent with recent findings that models overestimate scattering enhancement due to hygroscopic growth. The broadly consistent negative bias in AOD and surface scattering suggests an underestimate of aerosol radiative effects in current global aerosol models. Considerable inter-model diversity in the simulated optical properties is often found in regions that are, unfortunately, not or only sparsely covered by ground-based observations. This includes, for instance, the Sahara, Amazonia, central Australia, and the South Pacific. This highlights the need for a better site coverage in the observations, which would enable us to better assess the models, but also the performance of satellite products in these regions. Using fine-mode AOD as a proxy for present-day aerosol forcing estimates, our results suggest that models underestimate aerosol forcing by ca. − 15 %, however, with a considerably large interquartile range, suggesting a spread between − 35 % and + 10 %.