Showing papers in "Nature in 2017"
TL;DR: This work demonstrates an artificial intelligence capable of classifying skin cancer with a level of competence comparable to dermatologists, trained end-to-end from images directly, using only pixels and disease labels as inputs.
Abstract: Skin cancer, the most common human malignancy, is primarily diagnosed visually, beginning with an initial clinical screening and followed potentially by dermoscopic analysis, a biopsy and histopathological examination. Automated classification of skin lesions using images is a challenging task owing to the fine-grained variability in the appearance of skin lesions. Deep convolutional neural networks (CNNs) show potential for general and highly variable tasks across many fine-grained object categories. Here we demonstrate classification of skin lesions using a single CNN, trained end-to-end from images directly, using only pixels and disease labels as inputs. We train a CNN using a dataset of 129,450 clinical images-two orders of magnitude larger than previous datasets-consisting of 2,032 different diseases. We test its performance against 21 board-certified dermatologists on biopsy-proven clinical images with two critical binary classification use cases: keratinocyte carcinomas versus benign seborrheic keratoses; and malignant melanomas versus benign nevi. The first case represents the identification of the most common cancers, the second represents the identification of the deadliest skin cancer. The CNN achieves performance on par with all tested experts across both tasks, demonstrating an artificial intelligence capable of classifying skin cancer with a level of competence comparable to dermatologists. Outfitted with deep neural networks, mobile devices can potentially extend the reach of dermatologists outside of the clinic. It is projected that 6.3 billion smartphone subscriptions will exist by the year 2021 (ref. 13) and can therefore potentially provide low-cost universal access to vital diagnostic care.
8,424 citations
TL;DR: An algorithm based solely on reinforcement learning is introduced, without human data, guidance or domain knowledge beyond game rules, that achieves superhuman performance, winning 100–0 against the previously published, champion-defeating AlphaGo.
Abstract: A long-standing goal of artificial intelligence is an algorithm that learns, tabula rasa, superhuman proficiency in challenging domains. Recently, AlphaGo became the first program to defeat a world champion in the game of Go. The tree search in AlphaGo evaluated positions and selected moves using deep neural networks. These neural networks were trained by supervised learning from human expert moves, and by reinforcement learning from self-play. Here we introduce an algorithm based solely on reinforcement learning, without human data, guidance or domain knowledge beyond game rules. AlphaGo becomes its own teacher: a neural network is trained to predict AlphaGo’s own move selections and also the winner of AlphaGo’s games. This neural network improves the strength of the tree search, resulting in higher quality move selection and stronger self-play in the next iteration. Starting tabula rasa, our new program AlphaGo Zero achieved superhuman performance, winning 100–0 against the previously published, champion-defeating AlphaGo. Starting from zero knowledge and without human data, AlphaGo Zero was able to teach itself to play Go and to develop novel strategies that provide new insights into the oldest of games. To beat world champions at the game of Go, the computer program AlphaGo has relied largely on supervised learning from millions of human expert moves. David Silver and colleagues have now produced a system called AlphaGo Zero, which is based purely on reinforcement learning and learns solely from self-play. Starting from random moves, it can reach superhuman level in just a couple of days of training and five million games of self-play, and can now beat all previous versions of AlphaGo. Because the machine independently discovers the same fundamental principles of the game that took humans millennia to conceptualize, the work suggests that such principles have some universal character, beyond human bias.
7,818 citations
TL;DR: It is shown that activated microglia induce A1 astrocytes by secreting Il-1α, TNF and C1q, and that these cytokines together are necessary and sufficient to induce A2 astroCytes, which are abundant in various human neurodegenerative diseases.
Abstract: This work was supported by grants from the National Institutes of Health (R01 AG048814, B.A.B.; RO1 DA15043, B.A.B.; P50 NS38377, V.L.D. and T.M.D.) Christopher and Dana Reeve Foundation (B.A.B.), the Novartis Institute for Biomedical Research (B.A.B.), Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (B.A.B.), the JPB Foundation (B.A.B., T.M.D.), the Cure Alzheimer’s Fund (B.A.B.), the Glenn Foundation (B.A.B.), the Esther B O’Keeffe Charitable Foundation (B.A.B.), the Maryland Stem Cell Research Fund (2013-MSCRFII-0105-00, V.L.D.; 2012-MSCRFII-0268-00, T.M.D.; 2013-MSCRFII-0105-00, T.M.D.; 2014-MSCRFF-0665, M.K.). S.A.L. was supported by a postdoctoral fellowship from the Australian National Health and Medical Research Council (GNT1052961), and the Glenn Foundation Glenn Award. L.E.C. was funded by a Merck Research Laboratories postdoctoral fellowship (administered by the Life Science Research Foundation). W.-S.C. was supported by a career transition grant from NEI (K99EY024690). C.J.B. was supported by a postdoctoral fellowship from Damon Runyon Cancer Research Foundation (DRG-2125-12). L.S. was supported by a postdoctoral fellowship from the German Research Foundation (DFG, SCHI 1330/1-1).
4,326 citations
TL;DR: Xu et al. as mentioned in this paper used magneto-optical Kerr effect microscopy to show that monolayer chromium triiodide (CrI3) is an Ising ferromagnet with out-of-plane spin orientation.
Abstract: Magneto-optical Kerr effect microscopy is used to show that monolayer chromium triiodide is an Ising ferromagnet with out-of-plane spin orientation. The question of what happens to the properties of a material when it is thinned down to atomic-scale thickness has for a long time been a largely hypothetical one. In the past decade, new experimental methods have made it possible to isolate and measure a range of two-dimensional structures, enabling many theoretical predictions to be tested. But it has been a particular challenge to observe intrinsic magnetic effects, which could shed light on the longstanding fundamental question of whether intrinsic long-range magnetic order can robustly exist in two dimensions. In this issue of Nature, two groups address this challenge and report ferromagnetism in atomically thin crystals. Xiang Zhang and colleagues measured atomic layers of Cr2Ge2Te6 and observed ferromagnetic ordering with a transition temperature that, unusually, can be controlled using small magnetic fields. Xiaodong Xu and colleagues measured atomic layers of CrI3 and observed ferromagnetic ordering that, remarkably, was suppressed in double layers of CrI3, but restored in triple layers. The two studies demonstrate a platform with which to test fundamental properties of purely two-dimensional magnets. Since the discovery of graphene1, the family of two-dimensional materials has grown, displaying a broad range of electronic properties. Recent additions include semiconductors with spin–valley coupling2, Ising superconductors3,4,5 that can be tuned into a quantum metal6, possible Mott insulators with tunable charge-density waves7, and topological semimetals with edge transport8,9. However, no two-dimensional crystal with intrinsic magnetism has yet been discovered10,11,12,13,14; such a crystal would be useful in many technologies from sensing to data storage15. Theoretically, magnetic order is prohibited in the two-dimensional isotropic Heisenberg model at finite temperatures by the Mermin–Wagner theorem16. Magnetic anisotropy removes this restriction, however, and enables, for instance, the occurrence of two-dimensional Ising ferromagnetism. Here we use magneto-optical Kerr effect microscopy to demonstrate that monolayer chromium triiodide (CrI3) is an Ising ferromagnet with out-of-plane spin orientation. Its Curie temperature of 45 kelvin is only slightly lower than that of the bulk crystal, 61 kelvin, which is consistent with a weak interlayer coupling. Moreover, our studies suggest a layer-dependent magnetic phase, highlighting thickness-dependent physical properties typical of van der Waals crystals17,18,19. Remarkably, bilayer CrI3 displays suppressed magnetization with a metamagnetic effect20, whereas in trilayer CrI3 the interlayer ferromagnetism observed in the bulk crystal is restored. This work creates opportunities for studying magnetism by harnessing the unusual features of atomically thin materials, such as electrical control for realizing magnetoelectronics12, and van der Waals engineering to produce interface phenomena15.
3,802 citations
TL;DR: It is found that local genetic variation affects gene expression levels for the majority of genes, and inter-chromosomal genetic effects for 93 genes and 112 loci are identified, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
Abstract: Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
3,289 citations
TL;DR: Clinical studies are beginning to define these factors as immune profiles that can predict responses to immunotherapy, suggesting that a broader view of cancer immunity is required.
Abstract: Immunotherapy is proving to be an effective therapeutic approach in a variety of cancers. But despite the clinical success of antibodies against the immune regulators CTLA4 and PD-L1/PD-1, only a subset of people exhibit durable responses, suggesting that a broader view of cancer immunity is required. Immunity is influenced by a complex set of tumour, host and environmental factors that govern the strength and timing of the anticancer response. Clinical studies are beginning to define these factors as immune profiles that can predict responses to immunotherapy. In the context of the cancer-immunity cycle, such factors combine to represent the inherent immunological status - or 'cancer-immune set point' - of an individual.
3,145 citations
TL;DR: Adenine base editors (ABEs) that mediate the conversion of A•T to G•C in genomic DNA are described and a transfer RNA adenosine deaminase is evolved to operate on DNA when fused to a catalytically impaired CRISPR–Cas9 mutant.
Abstract: The spontaneous deamination of cytosine is a major source of transitions from C•G to T•A base pairs, which account for half of known pathogenic point mutations in humans. The ability to efficiently convert targeted A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases. The deamination of adenine yields inosine, which is treated as guanine by polymerases, but no enzymes are known to deaminate adenine in DNA. Here we describe adenine base editors (ABEs) that mediate the conversion of A•T to G•C in genomic DNA. We evolved a transfer RNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9 mutant. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs that convert targeted A•T base pairs efficiently to G•C (approximately 50% efficiency in human cells) with high product purity (typically at least 99.9%) and low rates of indels (typically no more than 0.1%). ABEs introduce point mutations more efficiently and cleanly, and with less off-target genome modification, than a current Cas9 nuclease-based method, and can install disease-correcting or disease-suppressing mutations in human cells. Together with previous base editors, ABEs enable the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.
2,451 citations
IBM1
TL;DR: The experimental optimization of Hamiltonian problems with up to six qubits and more than one hundred Pauli terms is demonstrated, determining the ground-state energy for molecules of increasing size, up to BeH2.
Abstract: The ground-state energy of small molecules is determined efficiently using six qubits of a superconducting quantum processor. Quantum simulation is currently the most promising application of quantum computers. However, only a few quantum simulations of very small systems have been performed experimentally. Here, researchers from IBM present quantum simulations of larger systems using a variational quantum eigenvalue solver (or eigensolver), a previously suggested method for quantum optimization. They perform quantum chemical calculations of LiH and BeH2 and an energy minimization procedure on a four-qubit Heisenberg model. Their application of the variational quantum eigensolver is hardware-efficient, which means that it is optimized on the given architecture. Noise is a big problem in this implementation, but quantum error correction could eventually help this experimental set-up to yield a quantum simulation of chemically interesting systems on a quantum computer. Quantum computers can be used to address electronic-structure problems and problems in materials science and condensed matter physics that can be formulated as interacting fermionic problems, problems which stretch the limits of existing high-performance computers1. Finding exact solutions to such problems numerically has a computational cost that scales exponentially with the size of the system, and Monte Carlo methods are unsuitable owing to the fermionic sign problem. These limitations of classical computational methods have made solving even few-atom electronic-structure problems interesting for implementation using medium-sized quantum computers. Yet experimental implementations have so far been restricted to molecules involving only hydrogen and helium2,3,4,5,6,7,8. Here we demonstrate the experimental optimization of Hamiltonian problems with up to six qubits and more than one hundred Pauli terms, determining the ground-state energy for molecules of increasing size, up to BeH2. We achieve this result by using a variational quantum eigenvalue solver (eigensolver) with efficiently prepared trial states that are tailored specifically to the interactions that are available in our quantum processor, combined with a compact encoding of fermionic Hamiltonians9 and a robust stochastic optimization routine10. We demonstrate the flexibility of our approach by applying it to a problem of quantum magnetism, an antiferromagnetic Heisenberg model in an external magnetic field. In all cases, we find agreement between our experiments and numerical simulations using a model of the device with noise. Our results help to elucidate the requirements for scaling the method to larger systems and for bridging the gap between key problems in high-performance computing and their implementation on quantum hardware.
2,348 citations
TL;DR: The field of quantum machine learning explores how to devise and implement quantum software that could enable machine learning that is faster than that of classical computers.
Abstract: Recent progress implies that a crossover between machine learning and quantum information processing benefits both fields. Traditional machine learning has dramatically improved the benchmarking an ...
2,162 citations
James Cook University1, University of Leeds2, Queensland Museum3, University of Queensland4, University of Sydney5, Australian Institute of Marine Science6, University of Western Australia7, Griffith University8, National Oceanic and Atmospheric Administration9, Curtin University10, Great Barrier Reef Marine Park Authority11
TL;DR: The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year, suggesting that local protection of reefs affords little or no resistance to extreme heat.
Abstract: During 2015–2016, record temperatures triggered a pan-tropical episode of coral bleaching, the third global-scale event since mass bleaching was first documented in the 1980s. Here we examine how and why the severity of recurrent major bleaching events has varied at multiple scales, using aerial and underwater surveys of Australian reefs combined with satellite-derived sea surface temperatures. The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year. Water quality and fishing pressure had minimal effect on the unprecedented bleaching in 2016, suggesting that local protection of reefs affords little or no resistance to extreme heat. Similarly, past exposure to bleaching in 1998 and 2002 did not lessen the severity of bleaching in 2016. Consequently, immediate global action to curb future warming is essential to secure a future for coral reefs.
2,073 citations
TL;DR: This work demonstrates a method for creating controlled many-body quantum matter that combines deterministically prepared, reconfigurable arrays of individually trapped cold atoms with strong, coherent interactions enabled by excitation to Rydberg states, and realizes a programmable Ising-type quantum spin model with tunable interactions and system sizes of up to 51 qubits.
Abstract: Controllable, coherent many-body systems can provide insights into the fundamental properties of quantum matter, enable the realization of new quantum phases and could ultimately lead to computational systems that outperform existing computers based on classical approaches. Here we demonstrate a method for creating controlled many-body quantum matter that combines deterministically prepared, reconfigurable arrays of individually trapped cold atoms with strong, coherent interactions enabled by excitation to Rydberg states. We realize a programmable Ising-type quantum spin model with tunable interactions and system sizes of up to 51 qubits. Within this model, we observe phase transitions into spatially ordered states that break various discrete symmetries, verify the high-fidelity preparation of these states and investigate the dynamics across the phase transition in large arrays of atoms. In particular, we observe robust many-body dynamics corresponding to persistent oscillations of the order after a rapid quantum quench that results from a sudden transition across the phase boundary. Our method provides a way of exploring many-body phenomena on a programmable quantum simulator and could enable realizations of new quantum algorithms.
TL;DR: The feasibility, safety, and immunogenicity of a vaccine that targets up to 20 predicted personal tumour neoantigens is demonstrated and a strong rationale for further development of this approach, alone and in combination with checkpoint blockade or other immunotherapies is provided.
Abstract: Effective anti-tumour immunity in humans has been associated with the presence of T cells directed at cancer neoantigens, a class of HLA-bound peptides that arise from tumour-specific mutations. They are highly immunogenic because they are not present in normal tissues and hence bypass central thymic tolerance. Although neoantigens were long-envisioned as optimal targets for an anti-tumour immune response, their systematic discovery and evaluation only became feasible with the recent availability of massively parallel sequencing for detection of all coding mutations within tumours, and of machine learning approaches to reliably predict those mutated peptides with high-affinity binding of autologous human leukocyte antigen (HLA) molecules. We hypothesized that vaccination with neoantigens can both expand pre-existing neoantigen-specific T-cell populations and induce a broader repertoire of new T-cell specificities in cancer patients, tipping the intra-tumoural balance in favour of enhanced tumour control. Here we demonstrate the feasibility, safety, and immunogenicity of a vaccine that targets up to 20 predicted personal tumour neoantigens. Vaccine-induced polyfunctional CD4+ and CD8+ T cells targeted 58 (60%) and 15 (16%) of the 97 unique neoantigens used across patients, respectively. These T cells discriminated mutated from wild-type antigens, and in some cases directly recognized autologous tumour. Of six vaccinated patients, four had no recurrence at 25 months after vaccination, while two with recurrent disease were subsequently treated with anti-PD-1 (anti-programmed cell death-1) therapy and experienced complete tumour regression, with expansion of the repertoire of neoantigen-specific T cells. These data provide a strong rationale for further development of this approach, alone and in combination with checkpoint blockade or other immunotherapies.
University of Southern Mississippi1, Atlantic Oceanographic and Meteorological Laboratory2, University of California, San Diego3, University of California, San Francisco4, Indiana University5, IBM6, Broad Institute7, Massachusetts Institute of Technology8, Harvard University9, Northern Arizona University10, Pacific Northwest National Laboratory11, Argonne National Laboratory12, University of Illinois at Chicago13, University of Colorado Boulder14, Cooperative Institute for Research in Environmental Sciences15, University of Southern California16, University of Chicago17, Michigan State University18
TL;DR: A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Abstract: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
TL;DR: The approach to metal-based additive manufacturing is applicable to a wide range of alloys and can be implemented using a range of additive machines, and provides a foundation for broad industrial applicability, including where electron-beam melting or directed-energy-deposition techniques are used instead of selective laser melting.
Abstract: Metal-based additive manufacturing, or three-dimensional (3D) printing, is a potentially disruptive technology across multiple industries, including the aerospace, biomedical and automotive industries. Building up metal components layer by layer increases design freedom and manufacturing flexibility, thereby enabling complex geometries, increased product customization and shorter time to market, while eliminating traditional economy-of-scale constraints. However, currently only a few alloys, the most relevant being AlSi10Mg, TiAl6V4, CoCr and Inconel 718, can be reliably printed; the vast majority of the more than 5,500 alloys in use today cannot be additively manufactured because the melting and solidification dynamics during the printing process lead to intolerable microstructures with large columnar grains and periodic cracks. Here we demonstrate that these issues can be resolved by introducing nanoparticles of nucleants that control solidification during additive manufacturing. We selected the nucleants on the basis of crystallographic information and assembled them onto 7075 and 6061 series aluminium alloy powders. After functionalization with the nucleants, we found that these high-strength aluminium alloys, which were previously incompatible with additive manufacturing, could be processed successfully using selective laser melting. Crack-free, equiaxed (that is, with grains roughly equal in length, width and height), fine-grained microstructures were achieved, resulting in material strengths comparable to that of wrought material. Our approach to metal-based additive manufacturing is applicable to a wide range of alloys and can be implemented using a range of additive machines. It thus provides a foundation for broad industrial applicability, including where electron-beam melting or directed-energy-deposition techniques are used instead of selective laser melting, and will enable additive manufacturing of other alloy systems, such as non-weldable nickel superalloys and intermetallics. Furthermore, this technology could be used in conventional processing such as in joining, casting and injection moulding, in which solidification cracking and hot tearing are also common issues.
TL;DR: The first-in-human application of individualized mutanome vaccines in melanoma is reported, demonstrating that individual mutations can be exploited and opening a path to personalized immunotherapy for patients with cancer.
Abstract: T cells directed against mutant neo-epitopes drive cancer immunity. However, spontaneous immune recognition of mutations is inefficient. We recently introduced the concept of individualized mutanome vaccines and implemented an RNA-based poly-neo-epitope approach to mobilize immunity against a spectrum of cancer mutations. Here we report the first-in-human application of this concept in melanoma. We set up a process comprising comprehensive identification of individual mutations, computational prediction of neo-epitopes, and design and manufacturing of a vaccine unique for each patient. All patients developed T cell responses against multiple vaccine neo-epitopes at up to high single-digit percentages. Vaccine-induced T cell infiltration and neo-epitope-specific killing of autologous tumour cells were shown in post-vaccination resected metastases from two patients. The cumulative rate of metastatic events was highly significantly reduced after the start of vaccination, resulting in a sustained progression-free survival. Two of the five patients with metastatic disease experienced vaccine-related objective responses. One of these patients had a late relapse owing to outgrowth of β2-microglobulin-deficient melanoma cells as an acquired resistance mechanism. A third patient developed a complete response to vaccination in combination with PD-1 blockade therapy. Our study demonstrates that individual mutations can be exploited, thereby opening a path to personalized immunotherapy for patients with cancer.
TL;DR: The results demonstrate an approach for direct and specific targeting of oncogenic KRAS in tumours using iExosomes, and suppressed cancer in multiple mouse models of pancreatic cancer and significantly increased overall survival.
Abstract: The mutant form of the GTPase KRAS is a key driver of pancreatic cancer but remains a challenging therapeutic target. Exosomes are extracellular vesicles generated by all cells, and are naturally present in the blood. Here we show that enhanced retention of exosomes, compared to liposomes, in the circulation of mice is likely due to CD47-mediated protection of exosomes from phagocytosis by monocytes and macrophages. Exosomes derived from normal fibroblast-like mesenchymal cells were engineered to carry short interfering RNA or short hairpin RNA specific to oncogenic KrasG12D, a common mutation in pancreatic cancer. Compared to liposomes, the engineered exosomes (known as iExosomes) target oncogenic KRAS with an enhanced efficacy that is dependent on CD47, and is facilitated by macropinocytosis. Treatment with iExosomes suppressed cancer in multiple mouse models of pancreatic cancer and significantly increased overall survival. Our results demonstrate an approach for direct and specific targeting of oncogenic KRAS in tumours using iExosomes.
University of Liège1, University of Cambridge2, University of Bern3, University of Washington4, California Institute of Technology5, Massachusetts Institute of Technology6, Université de Namur7, Centre national de la recherche scientifique8, University of Paris9, Cadi Ayyad University10, University of California, San Diego11, University of Leicester12, Liverpool John Moores University13, University of Central Lancashire14, King Abdulaziz University15
TL;DR: The observations reveal that at least seven planets with sizes and masses similar to those of Earth revolve around TRAPPIST-1, and the six inner planets form a near-resonant chain, such that their orbital periods are near-ratios of small integers.
Abstract: One aim of modern astronomy is to detect temperate, Earth-like exoplanets that are well suited for atmospheric characterization. Recently, three Earth-sized planets were detected that transit (that is, pass in front of) a star with a mass just eight per cent that of the Sun, located 12 parsecs away. The transiting configuration of these planets, combined with the Jupiter-like size of their host star—named TRAPPIST-1—makes possible in-depth studies of their atmospheric properties with present-day and future astronomical facilities. Here we report the results of a photometric monitoring campaign of that star from the ground and space. Our observations reveal that at least seven planets with sizes and masses similar to those of Earth revolve around TRAPPIST-1. The six inner planets form a near-resonant chain, such that their orbital periods (1.51, 2.42, 4.04, 6.06, 9.1 and 12.35 days) are near-ratios of small integers. This architecture suggests that the planets formed farther from the star and migrated inwards. Moreover, the seven planets have equilibrium temperatures low enough to make possible the presence of liquid water on their surfaces.
TL;DR: It is shown that GSDME, which was originally identified as DFNA5 (deafness, autosomal dominant 5), can switch caspase-3-mediated apoptosis induced by TNF or chemotherapy drugs to pyroptosis, suggesting that casp enzyme activation can trigger necrosis by cleaving G SDME and offer new insights into cancer chemotherapy.
Abstract: Pyroptosis is a form of cell death that is critical for immunity. It can be induced by the canonical caspase-1 inflammasomes or by activation of caspase-4, -5 and -11 by cytosolic lipopolysaccharide. The caspases cleave gasdermin D (GSDMD) in its middle linker to release autoinhibition on its gasdermin-N domain, which executes pyroptosis via its pore-forming activity. GSDMD belongs to a gasdermin family that shares the pore-forming domain. The functions and mechanisms of activation of other gasdermins are unknown. Here we show that GSDME, which was originally identified as DFNA5 (deafness, autosomal dominant 5), can switch caspase-3-mediated apoptosis induced by TNF or chemotherapy drugs to pyroptosis. GSDME was specifically cleaved by caspase-3 in its linker, generating a GSDME-N fragment that perforates membranes and thereby induces pyroptosis. After chemotherapy, cleavage of GSDME by caspase-3 induced pyroptosis in certain GSDME-expressing cancer cells. GSDME was silenced in most cancer cells but expressed in many normal tissues. Human primary cells exhibited GSDME-dependent pyroptosis upon activation of caspase-3 by chemotherapy drugs. Gsdme-/- (also known as Dfna5-/-) mice were protected from chemotherapy-induced tissue damage and weight loss. These findings suggest that caspase-3 activation can trigger necrosis by cleaving GSDME and offer new insights into cancer chemotherapy.
TL;DR: In this article, the authors summarize Watson and Crick's descrip2on of the DNA molecule and conclude that the purpose of this ar2cle was to find out why they wrote it.
Abstract: What is the purpose of this ar2cle? (Why did Watson and Crick write this ar2cle?) _________________________ _________________________ _________________________ _________________________ _________________________ _________________________ _________________________ Summarize Watson and Crick’s descrip2on of the DNA molecule. ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ___________________________________________________
TL;DR: The fully integrated functionality and small size of Neuropixels probes allowed large populations of neurons from several brain structures to be recorded in freely moving animals and opens a path towards recording of brain-wide neural activity during behaviour.
Abstract: New silicon probes known as Neuropixels are shown to record from hundreds of neurons simultaneously in awake and freely moving rodents. Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions. Existing technologies reliably measure activity from a relatively small number of neurons with high spatial and temporal resolution, or from a large volume of neurons with low resolution. Timothy Harris and colleagues describe the design, fabrication and performance of Neuropixels, a silicon probe that can measure well-isolated neural activity from hundreds of neurons. They integrated these probes into a lightweight system that could record activity simultaneously and with high fidelity from hundreds of neurons in awake and freely moving rodents. Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions in both superficial and deep structures1,2. Existing extracellular probes record neural activity with excellent spatial and temporal (sub-millisecond) resolution, but from only a few dozen neurons per shank. Optical Ca2+ imaging3,4,5 offers more coverage but lacks the temporal resolution needed to distinguish individual spikes reliably and does not measure local field potentials. Until now, no technology compatible with use in unrestrained animals has combined high spatiotemporal resolution with large volume coverage. Here we design, fabricate and test a new silicon probe known as Neuropixels to meet this need. Each probe has 384 recording channels that can programmably address 960 complementary metal–oxide–semiconductor (CMOS) processing-compatible low-impedance TiN6 sites that tile a single 10-mm long, 70 × 20-μm cross-section shank. The 6 × 9-mm probe base is fabricated with the shank on a single chip. Voltage signals are filtered, amplified, multiplexed and digitized on the base, allowing the direct transmission of noise-free digital data from the probe. The combination of dense recording sites and high channel count yielded well-isolated spiking activity from hundreds of neurons per probe implanted in mice and rats. Using two probes, more than 700 well-isolated single neurons were recorded simultaneously from five brain structures in an awake mouse. The fully integrated functionality and small size of Neuropixels probes allowed large populations of neurons from several brain structures to be recorded in freely moving animals. This combination of high-performance electrode technology and scalable chip fabrication methods opens a path towards recording of brain-wide neural activity during behaviour.
TL;DR: An alternative sensing scheme is demonstrated, by which the sensitivity of microcavities can be enhanced when operated at non-Hermitian spectral degeneracies known as exceptional points, paves the way for sensors with unprecedented sensitivity.
Abstract: Sensors play an important part in many aspects of daily life such as infrared sensors in home security systems, particle sensors for environmental monitoring and motion sensors in mobile phones. High-quality optical microcavities are prime candidates for sensing applications because of their ability to enhance light-matter interactions in a very confined volume. Examples of such devices include mechanical transducers, magnetometers, single-particle absorption spectrometers, and microcavity sensors for sizing single particles and detecting nanometre-scale objects such as single nanoparticles and atomic ions. Traditionally, a very small perturbation near an optical microcavity introduces either a change in the linewidth or a frequency shift or splitting of a resonance that is proportional to the strength of the perturbation. Here we demonstrate an alternative sensing scheme, by which the sensitivity of microcavities can be enhanced when operated at non-Hermitian spectral degeneracies known as exceptional points. In our experiments, we use two nanoscale scatterers to tune a whispering-gallery-mode micro-toroid cavity, in which light propagates along a concave surface by continuous total internal reflection, in a precise and controlled manner to exceptional points. A target nanoscale object that subsequently enters the evanescent field of the cavity perturbs the system from its exceptional point, leading to frequency splitting. Owing to the complex-square-root topology near an exceptional point, this frequency splitting scales as the square root of the perturbation strength and is therefore larger (for sufficiently small perturbations) than the splitting observed in traditional non-exceptional-point sensing schemes. Our demonstration of exceptional-point-enhanced sensitivity paves the way for sensors with unprecedented sensitivity.
TL;DR: Ab initio calculations of spin dynamics demonstrate that magnetic relaxation at high temperatures is due to local molecular vibrations, indicating that magnetic data storage in single molecules at temperatures above liquid nitrogen should be possible.
Abstract: Magnetic hysteresis is observed in a dysprosocenium complex at temperatures of up to 60 kelvin, the origin of which is the localized metal–ligand vibrational modes unique to dysprosocenium. The discovery of molecules that exhibit magnetic bistability raised hopes for the use of such molecular systems as tiny building blocks for magnetic data storage. Despite a quarter of a century of research, however, the temperatures at which these molecules display their desirable magnetic properties remain frustratingly low. Conrad Goodwin et al. report the synthesis and characterization of a molecular dysprosocenium complex that shows magnetic bistability up to 60 kelvin—tantalizingly close to liquid nitrogen temperatures, the point at which applications would start to become a realistic possibility. Lanthanides have been investigated extensively for potential applications in quantum information processing and high-density data storage at the molecular and atomic scale. Experimental achievements include reading and manipulating single nuclear spins1,2, exploiting atomic clock transitions for robust qubits3 and, most recently, magnetic data storage in single atoms4,5. Single-molecule magnets exhibit magnetic hysteresis of molecular origin6—a magnetic memory effect and a prerequisite of data storage—and so far lanthanide examples have exhibited this phenomenon at the highest temperatures. However, in the nearly 25 years since the discovery of single-molecule magnets7, hysteresis temperatures have increased from 4 kelvin to only about 14 kelvin8,9,10 using a consistent magnetic field sweep rate of about 20 oersted per second, although higher temperatures have been achieved by using very fast sweep rates11,12 (for example, 30 kelvin with 200 oersted per second)12. Here we report a hexa-tert-butyldysprosocenium complex—[Dy(Cpttt)2][B(C6F5)4], with Cpttt = {C5H2tBu3-1,2,4} and tBu = C(CH3)3—which exhibits magnetic hysteresis at temperatures of up to 60 kelvin at a sweep rate of 22 oersted per second. We observe a clear change in the relaxation dynamics at this temperature, which persists in magnetically diluted samples, suggesting that the origin of the hysteresis is the localized metal–ligand vibrational modes that are unique to dysprosocenium. Ab initio calculations of spin dynamics demonstrate that magnetic relaxation at high temperatures is due to local molecular vibrations. These results indicate that, with judicious molecular design, magnetic data storage in single molecules at temperatures above liquid nitrogen should be possible.
TL;DR: Proper regulation and management of energy, substrate diversity and quantity, as well as macromolecular synthesis and breakdown processes, are fundamental to cellular and organismal survival and are paramount to health.
Abstract: Proper regulation and management of energy, substrate diversity and quantity, as well as macromolecular synthesis and breakdown processes, are fundamental to cellular and organismal survival and are paramount to health. Cellular and multicellular organization are defended by the immune response, a robust and critical system through which self is distinguished from non-self, pathogenic signals are recognized and eliminated, and tissue homeostasis is safeguarded. Many layers of evolutionarily conserved interactions occur between immune response and metabolism. Proper maintenance of this delicate balance is crucial for health and has important implications for many pathological states such as obesity, diabetes, and other chronic non-communicable diseases.
TL;DR: It is shown that both mouse and human TAMs express programmed cell death protein 1, and blockade of PD-1–PD-L1 in vivo increases macrophage phagocytosis, reduces tumour growth and lengthens the survival of mice in mouse models of cancer in a macrophages-dependent fashion.
Abstract: Programmed cell death protein 1 (PD-1) is an immune checkpoint receptor that is upregulated on activated T cells for the induction of immune tolerance Tumour cells frequently overexpress the ligand for PD-1, programmed cell death ligand 1 (PD-L1), facilitating their escape from the immune system Monoclonal antibodies that block the interaction between PD-1 and PD-L1, by binding to either the ligand or receptor, have shown notable clinical efficacy in patients with a variety of cancers, including melanoma, colorectal cancer, non-small-cell lung cancer and Hodgkin's lymphoma Although it is well established that PD-1-PD-L1 blockade activates T cells, little is known about the role that this pathway may have in tumour-associated macrophages (TAMs) Here we show that both mouse and human TAMs express PD-1 TAM PD-1 expression increases over time in mouse models of cancer and with increasing disease stage in primary human cancers TAM PD-1 expression correlates negatively with phagocytic potency against tumour cells, and blockade of PD-1-PD-L1 in vivo increases macrophage phagocytosis, reduces tumour growth and lengthens the survival of mice in mouse models of cancer in a macrophage-dependent fashion This suggests that PD-1-PD-L1 therapies may also function through a direct effect on macrophages, with substantial implications for the treatment of cancer with these agents
TL;DR: It is proposed that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.
Abstract: HP1a can nucleate into foci that display liquid properties during the early stages of heterochromatin domain formation in Drosophila embryos, suggesting that the repressive action of heterochromatin may be mediated in part by emergent properties of phase separation. The gene-silencing action of heterochromatin is thought to arise from the spread of proteins such as HP1 that compact the underlying chromatin and recruit repressors. Two papers in this issue demonstrate that HP1α has the ability to form phase-separated droplets. Gary Karpen and colleagues show that HP1α can nucleate into foci that display liquid properties during the early stages of heterochromatin domain formation in Drosophila embryos. Geeta Narlikar and colleagues demonstrate that human HP1α protein also forms phase-separated droplets. Phosphorylation or DNA binding promotes the physical partitioning of HP1α out of the soluble aqueous phase into droplets. These related findings suggest that the repressive action of heterochromatin may be in part mediated by the phase separation of HP1, with the droplets being initiated or dissolved by various ligands depending on nuclear context. Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability1, and silencing of transposon and gene expression2. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA3. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments4. We show that Drosophila HP1a protein undergoes liquid–liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.
TL;DR: The authors' analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus and these data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies.
Abstract: Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies.
TL;DR: It is demonstrated that the class 2 type VI RNA-guided RNA-targeting CRISPR–Cas effector Cas13a (previously known as C2c2) can be engineered for mammalian cell RNA knockdown and binding and is established as a flexible platform for studying RNA in mammalian cells and therapeutic development.
Abstract: RNA has important and diverse roles in biology, but molecular tools to manipulate and measure it are limited. For example, RNA interference can efficiently knockdown RNAs, but it is prone to off-target effects, and visualizing RNAs typically relies on the introduction of exogenous tags. Here we demonstrate that the class 2 type VI RNA-guided RNA-targeting CRISPR-Cas effector Cas13a (previously known as C2c2) can be engineered for mammalian cell RNA knockdown and binding. After initial screening of 15 orthologues, we identified Cas13a from Leptotrichia wadei (LwaCas13a) as the most effective in an interference assay in Escherichia coli. LwaCas13a can be heterologously expressed in mammalian and plant cells for targeted knockdown of either reporter or endogenous transcripts with comparable levels of knockdown as RNA interference and improved specificity. Catalytically inactive LwaCas13a maintains targeted RNA binding activity, which we leveraged for programmable tracking of transcripts in live cells. Our results establish CRISPR-Cas13a as a flexible platform for studying RNA in mammalian cells and therapeutic development.
TL;DR: Higher-order exceptional points are observed in a coupled cavity arrangement—specifically, a ternary, parity–time-symmetric photonic laser molecule—with a carefully tailored gain–loss distribution and it is found that the frequency response follows a cube-root dependence on induced perturbations in the refractive index.
Abstract: Non-Hermitian degeneracies, also known as exceptional points, have recently emerged as a new way to engineer the response of open physical systems, that is, those that interact with the environment. They correspond to points in parameter space at which the eigenvalues of the underlying system and the corresponding eigenvectors simultaneously coalesce. In optics, the abrupt nature of the phase transitions that are encountered around exceptional points has been shown to lead to many intriguing phenomena, such as loss-induced transparency, unidirectional invisibility, band merging, topological chirality and laser mode selectivity. Recently, it has been shown that the bifurcation properties of second-order non-Hermitian degeneracies can provide a means of enhancing the sensitivity (frequency shifts) of resonant optical structures to external perturbations. Of particular interest is the use of even higher-order exceptional points (greater than second order), which in principle could further amplify the effect of perturbations, leading to even greater sensitivity. Although a growing number of theoretical studies have been devoted to such higher-order degeneracies, their experimental demonstration in the optical domain has so far remained elusive. Here we report the observation of higher-order exceptional points in a coupled cavity arrangement-specifically, a ternary, parity-time-symmetric photonic laser molecule-with a carefully tailored gain-loss distribution. We study the system in the spectral domain and find that the frequency response associated with this system follows a cube-root dependence on induced perturbations in the refractive index. Our work paves the way for utilizing non-Hermitian degeneracies in fields including photonics, optomechanics, microwaves and atomic physics.
TL;DR: Scheres et al. as mentioned in this paper presented a 3.4-3.5-resolution image of the brain of an individual with Alzheimer's disease and showed that the protein cores are made of two identical protofilaments comprising residues 306-378 of tau protein.
Abstract: Alzheimer’s disease is the most common neurodegenerative disease, and there are no mechanism-based therapies. The disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex. Neurofibrillary lesions comprise paired helical and straight tau filaments, whereas tau filaments with different morphologies characterize other neurodegenerative diseases. No high-resolution structures of tau filaments are available. Here we present cryo-electron microscopy (cryo-EM) maps at 3.4–3.5 A resolution and corresponding atomic models of paired helical and straight filaments from the brain of an individual with Alzheimer’s disease. Filament cores are made of two identical protofilaments comprising residues 306–378 of tau protein, which adopt a combined cross-β/β-helix structure and define the seed for tau aggregation. Paired helical and straight filaments differ in their inter-protofilament packing, showing that they are ultrastructural polymorphs. These findings demonstrate that cryo-EM allows atomic characterization of amyloid filaments from patient-derived material, and pave the way for investigation of a range of neurodegenerative diseases. High-resolution structures of tau filaments shed light on the ultrastructure of neurofibrillary lesions in Alzheimer’s disease. Alzheimer's disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex. The lesions are made of paired helical and straight tau filaments (PHFs and SFs, respectively). Different tau filaments characterize other neurodegenerative diseases, suggesting that molecular conformers of aggregated tau underlie human tauopathies. No high-resolution structures of tau filaments are currently available. Here, Sjors Scheres and colleagues present cryo-electron microscopy (cryo-EM) maps at 3.5 A resolution and corresponding atomic models of PHFs and SFs from the brain of an individual with Alzheimer's disease. Their results show that cryo-EM enables atomic characterization of amyloid filaments from patient-derived material and could be used to study a range of neurodegenerative diseases.
TL;DR: It is shown by direct protein delivery into mammalian cells that an HP1 α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α, suggesting that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context.
Abstract: Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands. Known components of heterochromatin such as nucleosomes and DNA preferentially partition into the HP1α droplets, but molecules such as the transcription factor TFIIB show no preference. Using a single-molecule DNA curtain assay, we find that both unmodified and phosphorylated HP1α induce rapid compaction of DNA strands into puncta, although with different characteristics. We show by direct protein delivery into mammalian cells that an HP1α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α. These findings suggest that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context.