Showing papers by "University of Tokyo published in 2020"

The ATLAS Experiment at the CERN Large Hadron Collider

Abstract: The ATLAS detector as installed in its experimental cavern at point 1 at CERN is described in this paper. A brief overview of the expected performance of the detector when the Large Hadron Collider begins operation is also presented.

Pan-cancer analysis of whole genomes

Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.

Particulate Photocatalysts for Light-Driven Water Splitting: Mechanisms, Challenges, and Design Strategies

Abstract: Solar-driven water splitting provides a leading approach to store the abundant yet intermittent solar energy and produce hydrogen as a clean and sustainable energy carrier. A straightforward route to light-driven water splitting is to apply self-supported particulate photocatalysts, which is expected to allow solar hydrogen to be competitive with fossil-fuel-derived hydrogen on a levelized cost basis. More importantly, the powder-based systems can lend themselves to making functional panels on a large scale while retaining the intrinsic activity of the photocatalyst. However, all attempts to generate hydrogen via powder-based solar water-splitting systems to date have unfortunately fallen short of the efficiency values required for practical applications. Photocatalysis on photocatalyst particles involves three sequential steps: (i) absorption of photons with higher energies than the bandgap of the photocatalysts, leading to the excitation of electron-hole pairs in the particles, (ii) charge separation and migration of these photoexcited carriers, and (iii) surface chemical reactions based on these carriers. In this review, we focus on the challenges of each step and summarize material design strategies to overcome the obstacles and limitations. This review illustrates that it is possible to employ the fundamental principles underlying photosynthesis and the tools of chemical and materials science to design and prepare photocatalysts for overall water splitting.

GW190425: Observation of a Compact Binary Coalescence with Total Mass ∼ 3.4 M O

Abstract: On 2019 April 25, the LIGO Livingston detector observed a compact binary coalescence with signal-to-noise ratio 12.9. The Virgo detector was also taking data that did not contribute to detection due to a low signal-to-noise ratio, but were used for subsequent parameter estimation. The 90% credible intervals for the component masses range from to if we restrict the dimensionless component spin magnitudes to be smaller than 0.05). These mass parameters are consistent with the individual binary components being neutron stars. However, both the source-frame chirp mass and the total mass of this system are significantly larger than those of any other known binary neutron star (BNS) system. The possibility that one or both binary components of the system are black holes cannot be ruled out from gravitational-wave data. We discuss possible origins of the system based on its inconsistency with the known Galactic BNS population. Under the assumption that the signal was produced by a BNS coalescence, the local rate of neutron star mergers is updated to 250-2810.

Photocatalytic water splitting with a quantum efficiency of almost unity

Abstract: Overall water splitting, evolving hydrogen and oxygen in a 2:1 stoichiometric ratio, using particulate photocatalysts is a potential means of achieving scalable and economically viable solar hydrogen production. To obtain high solar energy conversion efficiency, the quantum efficiency of the photocatalytic reaction must be increased over a wide range of wavelengths and semiconductors with narrow bandgaps need to be designed. However, the quantum efficiency associated with overall water splitting using existing photocatalysts is typically lower than ten per cent1,2. Thus, whether a particulate photocatalyst can enable a quantum efficiency of 100 per cent for the greatly endergonic water-splitting reaction remains an open question. Here we demonstrate overall water splitting at an external quantum efficiency of up to 96 per cent at wavelengths between 350 and 360 nanometres, which is equivalent to an internal quantum efficiency of almost unity, using a modified aluminium-doped strontium titanate (SrTiO3:Al) photocatalyst3,4. By selectively photodepositing the cocatalysts Rh/Cr2O3 (ref. 5) and CoOOH (refs. 3,6) for the hydrogen and oxygen evolution reactions, respectively, on different crystal facets of the semiconductor particles using anisotropic charge transport, the hydrogen and oxygen evolution reactions could be promoted separately. This enabled multiple consecutive forward charge transfers without backward charge transfer, reaching the upper limit of quantum efficiency for overall water splitting. Our work demonstrates the feasibility of overall water splitting free from charge recombination losses and introduces an ideal cocatalyst/photocatalyst structure for efficient water splitting. Water splitting with an internal quantum efficiency of almost unity is achieved using a modified semiconductor photocatalyst that selectively promotes the hydrogen and oxygen evolution reactions on separate crystal facets.

GW190814: Gravitational Waves from the Coalescence of a 23 Solar Mass Black Hole with a 2.6 Solar Mass Compact Object

Abstract: We report the observation of a compact binary coalescence involving a 222–243 M ⊙ black hole and a compact object with a mass of 250–267 M ⊙ (all measurements quoted at the 90% credible level) The gravitational-wave signal, GW190814, was observed during LIGO's and Virgo's third observing run on 2019 August 14 at 21:10:39 UTC and has a signal-to-noise ratio of 25 in the three-detector network The source was localized to 185 deg2 at a distance of ${241}_{-45}^{+41}$ Mpc; no electromagnetic counterpart has been confirmed to date The source has the most unequal mass ratio yet measured with gravitational waves, ${0112}_{-0009}^{+0008}$, and its secondary component is either the lightest black hole or the heaviest neutron star ever discovered in a double compact-object system The dimensionless spin of the primary black hole is tightly constrained to ≤007 Tests of general relativity reveal no measurable deviations from the theory, and its prediction of higher-multipole emission is confirmed at high confidence We estimate a merger rate density of 1–23 Gpc−3 yr−1 for the new class of binary coalescence sources that GW190814 represents Astrophysical models predict that binaries with mass ratios similar to this event can form through several channels, but are unlikely to have formed in globular clusters However, the combination of mass ratio, component masses, and the inferred merger rate for this event challenges all current models of the formation and mass distribution of compact-object binaries

GW190521: A Binary Black Hole Merger with a Total Mass of 150 M

Abstract: On May 21, 2019 at 03:02:29 UTC Advanced LIGO and Advanced Virgo observed a short duration gravitational-wave signal, GW190521, with a three-detector network signal-to-noise ratio of 14.7, and an estimated false-alarm rate of 1 in 4900 yr using a search sensitive to generic transients. If GW190521 is from a quasicircular binary inspiral, then the detected signal is consistent with the merger of two black holes with masses of 85_{-14}^{+21} M_{⊙} and 66_{-18}^{+17} M_{⊙} (90% credible intervals). We infer that the primary black hole mass lies within the gap produced by (pulsational) pair-instability supernova processes, with only a 0.32% probability of being below 65 M_{⊙}. We calculate the mass of the remnant to be 142_{-16}^{+28} M_{⊙}, which can be considered an intermediate mass black hole (IMBH). The luminosity distance of the source is 5.3_{-2.6}^{+2.4} Gpc, corresponding to a redshift of 0.82_{-0.34}^{+0.28}. The inferred rate of mergers similar to GW190521 is 0.13_{-0.11}^{+0.30} Gpc^{-3} yr^{-1}.

H0LiCOW – XIII. A 2.4 per cent measurement of H0 from lensed quasars: 5.3σ tension between early- and late-Universe probes

Abstract: We present a measurement of the Hubble constant ($H_{0}$) and other cosmological parameters from a joint analysis of six gravitationally lensed quasars with measured time delays. All lenses except the first are analyzed blindly with respect to the cosmological parameters. In a flat $\Lambda$CDM cosmology, we find $H_{0} = 73.3_{-1.8}^{+1.7}$, a 2.4% precision measurement, in agreement with local measurements of $H_{0}$ from type Ia supernovae calibrated by the distance ladder, but in $3.1\sigma$ tension with $Planck$ observations of the cosmic microwave background (CMB). This method is completely independent of both the supernovae and CMB analyses. A combination of time-delay cosmography and the distance ladder results is in $5.3\sigma$ tension with $Planck$ CMB determinations of $H_{0}$ in flat $\Lambda$CDM. We compute Bayes factors to verify that all lenses give statistically consistent results, showing that we are not underestimating our uncertainties and are able to control our systematics. We explore extensions to flat $\Lambda$CDM using constraints from time-delay cosmography alone, as well as combinations with other cosmological probes, including CMB observations from $Planck$, baryon acoustic oscillations, and type Ia supernovae. Time-delay cosmography improves the precision of the other probes, demonstrating the strong complementarity. Allowing for spatial curvature does not resolve the tension with $Planck$. Using the distance constraints from time-delay cosmography to anchor the type Ia supernova distance scale, we reduce the sensitivity of our $H_0$ inference to cosmological model assumptions. For six different cosmological models, our combined inference on $H_{0}$ ranges from $\sim73$-$78~\mathrm{km~s^{-1}~Mpc^{-1}}$, which is consistent with the local distance ladder constraints.

Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development.

Abstract: At the end of 2019, a novel coronavirus (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) was detected in Wuhan, China, that spread rapidly around the world, with severe consequences for human health and the global economy Here, we assessed the replicative ability and pathogenesis of SARS-CoV-2 isolates in Syrian hamsters SARS-CoV-2 isolates replicated efficiently in the lungs of hamsters, causing severe pathological lung lesions following intranasal infection In addition, microcomputed tomographic imaging revealed severe lung injury that shared characteristics with SARS-CoV-2-infected human lung, including severe, bilateral, peripherally distributed, multilobular ground glass opacity, and regions of lung consolidation SARS-CoV-2-infected hamsters mounted neutralizing antibody responses and were protected against subsequent rechallenge with SARS-CoV-2 Moreover, passive transfer of convalescent serum to naive hamsters efficiently suppressed the replication of the virus in the lungs even when the serum was administrated 2 d postinfection of the serum-treated hamsters Collectively, these findings demonstrate that this Syrian hamster model will be useful for understanding SARS-CoV-2 pathogenesis and testing vaccines and antiviral drugs

The 16th Data Release of the Sloan Digital Sky Surveys: First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

Abstract: This paper documents the sixteenth data release (DR16) from the Sloan Digital Sky Surveys; the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the southern hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey (TDSS) and new data from the SPectroscopic IDentification of ERosita Survey (SPIDERS) programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17).

SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo

Abstract: The spike aspartic acid–614 to glycine (D614G) substitution is prevalent in global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, but its effects on viral pathogenesis and transmissibility remain unclear. We engineered a SARS-CoV-2 variant containing this substitution. The variant exhibits more efficient infection, replication, and competitive fitness in primary human airway epithelial cells but maintains similar morphology and in vitro neutralization properties, compared with the ancestral wild-type virus. Infection of human angiotensin-converting enzyme 2 (ACE2) transgenic mice and Syrian hamsters with both viruses resulted in similar viral titers in respiratory tissues and pulmonary disease. However, the D614G variant transmits significantly faster and displayed increased competitive fitness than the wild-type virus in hamsters. These data show that the D614G substitution enhances SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human cells and animal models.

More Diverse Means Better: Multimodal Deep Learning Meets Remote Sensing Imagery Classification

Abstract: Classification and identification of the materials lying over or beneath the Earth's surface have long been a fundamental but challenging research topic in geoscience and remote sensing (RS) and have garnered a growing concern owing to the recent advancements of deep learning techniques. Although deep networks have been successfully applied in single-modality-dominated classification tasks, yet their performance inevitably meets the bottleneck in complex scenes that need to be finely classified, due to the limitation of information diversity. In this work, we provide a baseline solution to the aforementioned difficulty by developing a general multimodal deep learning (MDL) framework. In particular, we also investigate a special case of multi-modality learning (MML) -- cross-modality learning (CML) that exists widely in RS image classification applications. By focusing on "what", "where", and "how" to fuse, we show different fusion strategies as well as how to train deep networks and build the network architecture. Specifically, five fusion architectures are introduced and developed, further being unified in our MDL framework. More significantly, our framework is not only limited to pixel-wise classification tasks but also applicable to spatial information modeling with convolutional neural networks (CNNs). To validate the effectiveness and superiority of the MDL framework, extensive experiments related to the settings of MML and CML are conducted on two different multimodal RS datasets. Furthermore, the codes and datasets will be available at this https URL, contributing to the RS community.

WILDS: A Benchmark of in-the-Wild Distribution Shifts

Abstract: Distribution shifts -- where the training distribution differs from the test distribution -- can substantially degrade the accuracy of machine learning (ML) systems deployed in the wild. Despite their ubiquity, these real-world distribution shifts are under-represented in the datasets widely used in the ML community today. To address this gap, we present WILDS, a curated collection of 8 benchmark datasets that reflect a diverse range of distribution shifts which naturally arise in real-world applications, such as shifts across hospitals for tumor identification; across camera traps for wildlife monitoring; and across time and location in satellite imaging and poverty mapping. On each dataset, we show that standard training results in substantially lower out-of-distribution than in-distribution performance, and that this gap remains even with models trained by existing methods for handling distribution shifts. This underscores the need for new training methods that produce models which are more robust to the types of distribution shifts that arise in practice. To facilitate method development, we provide an open-source package that automates dataset loading, contains default model architectures and hyperparameters, and standardizes evaluations. Code and leaderboards are available at this https URL.

A connectome and analysis of the adult Drosophila central brain

Abstract: Animal brains of all sizes, from the smallest to the largest, work in broadly similar ways. Studying the brain of any one animal in depth can thus reveal the general principles behind the workings of all brains. The fruit fly Drosophila is a popular choice for such research. With about 100,000 neurons – compared to some 86 billion in humans – the fly brain is small enough to study at the level of individual cells. But it nevertheless supports a range of complex behaviors, including navigation, courtship and learning. Thanks to decades of research, scientists now have a good understanding of which parts of the fruit fly brain support particular behaviors. But exactly how they do this is often unclear. This is because previous studies showing the connections between cells only covered small areas of the brain. This is like trying to understand a novel when all you can see is a few isolated paragraphs. To solve this problem, Scheffer, Xu, Januszewski, Lu, Takemura, Hayworth, Huang, Shinomiya et al. prepared the first complete map of the entire central region of the fruit fly brain. The central brain consists of approximately 25,000 neurons and around 20 million connections. To prepare the map – or connectome – the brain was cut into very thin 8nm slices and photographed with an electron microscope. A three-dimensional map of the neurons and connections in the brain was then reconstructed from these images using machine learning algorithms. Finally, Scheffer et al. used the new connectome to obtain further insights into the circuits that support specific fruit fly behaviors. The central brain connectome is freely available online for anyone to access. When used in combination with existing methods, the map will make it easier to understand how the fly brain works, and how and why it can fail to work correctly. Many of these findings will likely apply to larger brains, including our own. In the long run, studying the fly connectome may therefore lead to a better understanding of the human brain and its disorders. Performing a similar analysis on the brain of a small mammal, by scaling up the methods here, will be a likely next step along this path.

Tropical Cyclones and Climate Change Assessment: Part II: Projected Response to Anthropogenic Warming

Abstract: Model projections of tropical cyclone (TC) activity response to anthropogenic warming in climate models are assessed. Observations, theory, and models, with increasing robustness, indicate ...

Autophagy in Human Diseases

Abstract: Autophagy in Human Diseases Autophagy is a complex process of intracellular degradation of senescent or malfunctioning organelles. Dysregulated autophagy is associated with certain cancers, neurode...

GW190412: Observation of a binary-black-hole coalescence with asymmetric masses

Abstract: We report the observation of gravitational waves from a binary-black-hole coalescence during the first two weeks of LIGO’s and Virgo’s third observing run. The signal was recorded on April 12, 2019 at 05∶30∶44 UTC with a network signal-to-noise ratio of 19. The binary is different from observations during the first two observing runs most notably due to its asymmetric masses: a ∼30 M⊙ black hole merged with a ∼8 M⊙ black hole companion. The more massive black hole rotated with a dimensionless spin magnitude between 0.22 and 0.60 (90% probability). Asymmetric systems are predicted to emit gravitational waves with stronger contributions from higher multipoles, and indeed we find strong evidence for gravitational radiation beyond the leading quadrupolar order in the observed signal. A suite of tests performed on GW190412 indicates consistency with Einstein’s general theory of relativity. While the mass ratio of this system differs from all previous detections, we show that it is consistent with the population model of stellar binary black holes inferred from the first two observing runs.

Topological Origin of Non-Hermitian Skin Effects.

Abstract: A unique feature of non-Hermitian systems is the skin effect, which is the extreme sensitivity to the boundary conditions. Here, we reveal that the skin effect originates from intrinsic non-Hermitian topology. Such a topological origin not merely explains the universal feature of the known skin effect, but also leads to new types of the skin effects---symmetry-protected skin effects. In particular, we discover the ${\mathbb{Z}}_{2}$ skin effect protected by time-reversal symmetry. On the basis of topological classification, we also discuss possible other skin effects in arbitrary dimensions. Our work provides a unified understanding about the bulk-boundary correspondence and the skin effects in non-Hermitian systems.

An assessment of Earth's climate sensitivity using multiple lines of evidence

Abstract: We assess evidence relevant to Earth's equilibrium climate sensitivity per doubling of atmospheric CO2, characterized by an effective sensitivity S. This evidence includes feedback process understanding, the historical climate record, and the paleoclimate record. An S value lower than 2 K is difficult to reconcile with any of the three lines of evidence. The amount of cooling during the Last Glacial Maximum provides strong evidence against values of S greater than 4.5 K. Other lines of evidence in combination also show that this is relatively unlikely. We use a Bayesian approach to produce a probability density function (PDF) for S given all the evidence, including tests of robustness to difficult-to-quantify uncertainties and different priors. The 66% range is 2.6-3.9 K for our Baseline calculation and remains within 2.3-4.5 K under the robustness tests; corresponding 5-95% ranges are 2.3-4.7 K, bounded by 2.0-5.7 K (although such high-confidence ranges should be regarded more cautiously). This indicates a stronger constraint on S than reported in past assessments, by lifting the low end of the range. This narrowing occurs because the three lines of evidence agree and are judged to be largely independent and because of greater confidence in understanding feedback processes and in combining evidence. We identify promising avenues for further narrowing the range in S, in particular using comprehensive models and process understanding to address limitations in the traditional forcing-feedback paradigm for interpreting past changes.

Wannier90 as a community code: new features and applications.

Abstract: Wannier90 is an open-source computer program for calculating maximally-localised Wannier functions (MLWFs) from a set of Bloch states. It is interfaced to many widely used electronic-structure codes thanks to its independence from the basis sets representing these Bloch states. In the past few years the development of Wannier90 has transitioned to a community-driven model; this has resulted in a number of new developments that have been recently released in Wannier90 v3.0. In this article we describe these new functionalities, that include the implementation of new features for wannierisation and disentanglement (symmetry-adapted Wannier functions, selectively-localised Wannier functions, selected columns of the density matrix) and the ability to calculate new properties (shift currents and Berry-curvature dipole, and a new interface to many-body perturbation theory); performance improvements, including parallelisation of the core code; enhancements in functionality (support for spinor-valued Wannier functions, more accurate methods to interpolate quantities in the Brillouin zone); improved usability (improved plotting routines, integration with high-throughput automation frameworks), as well as the implementation of modern software engineering practices (unit testing, continuous integration, and automatic source-code documentation). These new features, capabilities, and code development model aim to further sustain and expand the community uptake and range of applicability, that nowadays spans complex and accurate dielectric, electronic, magnetic, optical, topological and transport properties of materials.

Excess electronic recoil events in XENON1T

Abstract: We report results from searches for new physics with low-energy electronic recoil data recorded with the XENON1T detector. With an exposure of 0.65 tonne-years and an unprecedentedly low background rate of 76±2stat events/(tonne×year×keV) between 1 and 30 keV, the data enable one of the most sensitive searches for solar axions, an enhanced neutrino magnetic moment using solar neutrinos, and bosonic dark matter. An excess over known backgrounds is observed at low energies and most prominent between 2 and 3 keV. The solar axion model has a 3.4σ significance, and a three-dimensional 90% confidence surface is reported for axion couplings to electrons, photons, and nucleons. This surface is inscribed in the cuboid defined by gae<3.8×10-12, gaeganeff<4.8×10-18, and gaegaγ<7.7×10-22 GeV-1, and excludes either gae=0 or gaegaγ=gaeganeff=0. The neutrino magnetic moment signal is similarly favored over background at 3.2σ, and a confidence interval of μν∈(1.4,2.9)×10-11 μB (90% C.L.) is reported. Both results are in strong tension with stellar constraints. The excess can also be explained by β decays of tritium at 3.2σ significance with a corresponding tritium concentration in xenon of (6.2±2.0)×10-25 mol/mol. Such a trace amount can neither be confirmed nor excluded with current knowledge of its production and reduction mechanisms. The significances of the solar axion and neutrino magnetic moment hypotheses are decreased to 2.0σ and 0.9σ, respectively, if an unconstrained tritium component is included in the fitting. With respect to bosonic dark matter, the excess favors a monoenergetic peak at (2.3±0.2) keV (68% C.L.) with a 3.0σ global (4.0σ local) significance over background. This analysis sets the most restrictive direct constraints to date on pseudoscalar and vector bosonic dark matter for most masses between 1 and 210 keV/c2. We also consider the possibility that Ar37 may be present in the detector, yielding a 2.82 keV peak from electron capture. Contrary to tritium, the Ar37 concentration can be tightly constrained and is found to be negligible.

Non-Hermitian Physics

Abstract: A review is given on the foundations and applications of non-Hermitian classical and quantum physics. First, key theorems and central concepts in non-Hermitian linear algebra, including Jordan normal form, biorthogonality, exceptional points, pseudo-Hermiticity and parity-time symmetry, are delineated in a pedagogical and mathematically coherent manner. Building on these, we provide an overview of how diverse classical systems, ranging from photonics, mechanics, electrical circuits, acoustics to active matter, can be used to simulate non-Hermitian wave physics. In particular, we discuss rich and unique phenomena found therein, such as unidirectional invisibility, enhanced sensitivity, topological energy transfer, coherent perfect absorption, single-mode lasing, and robust biological transport. We then explain in detail how non-Hermitian operators emerge as an effective description of open quantum systems on the basis of the Feshbach projection approach and the quantum trajectory approach. We discuss their applications to physical systems relevant to a variety of fields, including atomic, molecular and optical physics, mesoscopic physics, and nuclear physics with emphasis on prominent phenomena/subjects in quantum regimes, such as quantum resonances, superradiance, continuous quantum Zeno effect, quantum critical phenomena, Dirac spectra in quantum chromodynamics, and nonunitary conformal field theories. Finally, we introduce the notion of band topology in complex spectra of non-Hermitian systems and present their classifications by providing the proof, firstly given by this review in a complete manner, as well as a number of instructive examples. Other topics related to non-Hermitian physics, including nonreciprocal transport, speed limits, nonunitary quantum walk, are also reviewed.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Abstract: The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

Combating COVID-19-The role of robotics in managing public health and infectious diseases.

Abstract: COVID-19 may drive sustained research in robotics to address risks of infectious diseases. COVID-19 may drive sustained research in robotics to address risks of infectious diseases.

Constraints on Primordial Black Holes

Abstract: We update the constraints on the fraction of the Universe going into primordial black holes (PBHs) over the mass range $10^{-5}$--$10^{50}$ g. Those smaller than $\sim 10^{15}$ g would have evaporated by now due to Hawking radiation, so their abundance at formation is constrained by the effects of evaporated particles on big bang nucleosynthesis, the cosmic microwave background (CMB), the Galactic and extragalactic $\gamma$-ray and cosmic ray backgrounds and the possible generation of stable Planck mass relics. PBHs larger than $\sim 10^{15}$ g are subject to a variety of constraints associated with gravitational lensing, dynamical effects, influence on large-scale structure, accretion and gravitational waves. We discuss the constraints on both the initial collapse fraction and the current fraction of the cold dark matter in PBHs at each mass scale but stress that many of the constraints are associated with observational or theoretical uncertainties and some are no longer applicable. We also consider indirect constraints associated with the amplitude of the primordial density fluctuations, such as second-order tensor perturbations and $\mu$-distortions arising from the effect of acoustic reheating on the CMB, but these only apply if PBHs are created from the high-$\sigma$ peaks of nearly Gaussian fluctuations. Finally we discuss how the constraints are modified if the PBHs have an extended mass function, this being relevant if PBHs provide some combination of the dark matter, the LIGO/Virgo coalescences and the seeds for cosmic structure.

Transmission of SARS-CoV-2 in Domestic Cats.

Abstract: Coronavirus in Cats SARS-CoV-2 was detected in three cats after they were cohoused with cats that had been experimentally inoculated with the virus. Cats may be a silent intermediate host of SARS-C...

Structures of α-synuclein filaments from multiple system atrophy

Abstract: Synucleinopathies, which include multiple system atrophy (MSA), Parkinson’s disease, Parkinson’s disease with dementia and dementia with Lewy bodies (DLB), are human neurodegenerative diseases1. Existing treatments are at best symptomatic. These diseases are characterized by the presence of, and believed to be caused by the formation of, filamentous inclusions of α-synuclein in brain cells2,3. However, the structures of α-synuclein filaments from the human brain are unknown. Here, using cryo-electron microscopy, we show that α-synuclein inclusions from the brains of individuals with MSA are made of two types of filament, each of which consists of two different protofilaments. In each type of filament, non-proteinaceous molecules are present at the interface of the two protofilaments. Using two-dimensional class averaging, we show that α-synuclein filaments from the brains of individuals with MSA differ from those of individuals with DLB, which suggests that distinct conformers or strains characterize specific synucleinopathies. As is the case with tau assemblies4–9, the structures of α-synuclein filaments extracted from the brains of individuals with MSA differ from those formed in vitro using recombinant proteins, which has implications for understanding the mechanisms of aggregate propagation and neurodegeneration in the human brain. These findings have diagnostic and potential therapeutic relevance, especially because of the unmet clinical need to be able to image filamentous α-synuclein inclusions in the human brain. Cryo-electron microscopy reveals the structures of α-synuclein filaments from the brains of individuals with multiple system atrophy.

Rethinking drug design in the artificial intelligence era

Abstract: Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some protagonists point to vast opportunities potentially offered by such tools, others remain sceptical, waiting for a clear impact to be shown in drug discovery projects. The reality is probably somewhere in-between these extremes, yet it is clear that AI is providing new challenges not only for the scientists involved but also for the biopharma industry and its established processes for discovering and developing new medicines. This article presents the views of a diverse group of international experts on the 'grand challenges' in small-molecule drug discovery with AI and the approaches to address them.