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Showing papers in "Nature in 2015"


Journal ArticleDOI
28 May 2015-Nature
TL;DR: Deep learning is making major advances in solving problems that have resisted the best attempts of the artificial intelligence community for many years, and will have many more successes in the near future because it requires very little engineering by hand and can easily take advantage of increases in the amount of available computation and data.
Abstract: Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.

46,982 citations


Journal ArticleDOI
26 Feb 2015-Nature
TL;DR: This work bridges the divide between high-dimensional sensory inputs and actions, resulting in the first artificial agent that is capable of learning to excel at a diverse array of challenging tasks.
Abstract: The theory of reinforcement learning provides a normative account, deeply rooted in psychological and neuroscientific perspectives on animal behaviour, of how agents may optimize their control of an environment. To use reinforcement learning successfully in situations approaching real-world complexity, however, agents are confronted with a difficult task: they must derive efficient representations of the environment from high-dimensional sensory inputs, and use these to generalize past experience to new situations. Remarkably, humans and other animals seem to solve this problem through a harmonious combination of reinforcement learning and hierarchical sensory processing systems, the former evidenced by a wealth of neural data revealing notable parallels between the phasic signals emitted by dopaminergic neurons and temporal difference reinforcement learning algorithms. While reinforcement learning agents have achieved some successes in a variety of domains, their applicability has previously been limited to domains in which useful features can be handcrafted, or to domains with fully observed, low-dimensional state spaces. Here we use recent advances in training deep neural networks to develop a novel artificial agent, termed a deep Q-network, that can learn successful policies directly from high-dimensional sensory inputs using end-to-end reinforcement learning. We tested this agent on the challenging domain of classic Atari 2600 games. We demonstrate that the deep Q-network agent, receiving only the pixels and the game score as inputs, was able to surpass the performance of all previous algorithms and achieve a level comparable to that of a professional human games tester across a set of 49 games, using the same algorithm, network architecture and hyperparameters. This work bridges the divide between high-dimensional sensory inputs and actions, resulting in the first artificial agent that is capable of learning to excel at a diverse array of challenging tasks.

23,074 citations


Journal ArticleDOI
Adam Auton1, Gonçalo R. Abecasis2, David Altshuler3, Richard Durbin4  +514 moreInstitutions (90)
01 Oct 2015-Nature
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

12,661 citations


Journal ArticleDOI
22 Jan 2015-Nature
TL;DR: This work combines the promising—but relatively unstable formamidinium lead iodide with FAPbI3 with methylammonium lead bromide as the light-harvesting unit in a bilayer solar-cell architecture and improves the power conversion efficiency of the solar cell to more than 18 per cent under a standard illumination.
Abstract: Inorganic–organic lead halide perovskite could be efficient when used as the light-harvesting component of solar cells; here incorporation of methylammonium lead bromide into formamidinium lead iodide stabilizes the perovskite and improves the power conversion efficiency of the solar cell up to 17.9 per cent. Inorganic–organic lead halide perovskites are currently attracting considerable interest for solar-cell applications. Most of the best performing perovskite solar cells to date have made use of methylammonium-based perovskites; formamidinium-based perovskites have also shown promise, but are not as stable. Now Nam Joong Jeon and colleagues show that the formamidinium-based perovskites can be stabilized by the addition of some methylammonium-based perovskite, and that solar cells incorporating the resulting compositionally tuned materials can reach new heights of efficiency. Of the many materials and methodologies aimed at producing low-cost, efficient photovoltaic cells, inorganic–organic lead halide perovskite materials1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17 appear particularly promising for next-generation solar devices owing to their high power conversion efficiency. The highest efficiencies reported for perovskite solar cells so far have been obtained mainly with methylammonium lead halide materials1,2,3,4,5,6,7,8,9,10. Here we combine the promising—owing to its comparatively narrow bandgap—but relatively unstable formamidinium lead iodide (FAPbI3) with methylammonium lead bromide (MAPbBr3) as the light-harvesting unit in a bilayer solar-cell architecture13. We investigated phase stability, morphology of the perovskite layer, hysteresis in current–voltage characteristics, and overall performance as a function of chemical composition. Our results show that incorporation of MAPbBr3 into FAPbI3 stabilizes the perovskite phase of FAPbI3 and improves the power conversion efficiency of the solar cell to more than 18 per cent under a standard illumination of 100 milliwatts per square centimetre. These findings further emphasize the versatility and performance potential of inorganic–organic lead halide perovskite materials for photovoltaic applications.

5,291 citations


Journal ArticleDOI
Anshul Kundaje1, Wouter Meuleman1, Wouter Meuleman2, Jason Ernst3, Misha Bilenky4, Angela Yen2, Angela Yen1, Alireza Heravi-Moussavi4, Pouya Kheradpour2, Pouya Kheradpour1, Zhizhuo Zhang2, Zhizhuo Zhang1, Jianrong Wang2, Jianrong Wang1, Michael J. Ziller2, Viren Amin5, John W. Whitaker, Matthew D. Schultz6, Lucas D. Ward2, Lucas D. Ward1, Abhishek Sarkar1, Abhishek Sarkar2, Gerald Quon1, Gerald Quon2, Richard Sandstrom7, Matthew L. Eaton1, Matthew L. Eaton2, Yi-Chieh Wu2, Yi-Chieh Wu1, Andreas R. Pfenning1, Andreas R. Pfenning2, Xinchen Wang2, Xinchen Wang1, Melina Claussnitzer1, Melina Claussnitzer2, Yaping Liu1, Yaping Liu2, Cristian Coarfa5, R. Alan Harris5, Noam Shoresh2, Charles B. Epstein2, Elizabeta Gjoneska2, Elizabeta Gjoneska1, Danny Leung8, Wei Xie8, R. David Hawkins8, Ryan Lister6, Chibo Hong9, Philippe Gascard9, Andrew J. Mungall4, Richard A. Moore4, Eric Chuah4, Angela Tam4, Theresa K. Canfield7, R. Scott Hansen7, Rajinder Kaul7, Peter J. Sabo7, Mukul S. Bansal1, Mukul S. Bansal10, Mukul S. Bansal2, Annaick Carles4, Jesse R. Dixon8, Kai How Farh2, Soheil Feizi2, Soheil Feizi1, Rosa Karlic11, Ah Ram Kim1, Ah Ram Kim2, Ashwinikumar Kulkarni12, Daofeng Li13, Rebecca F. Lowdon13, Ginell Elliott13, Tim R. Mercer14, Shane Neph7, Vitor Onuchic5, Paz Polak15, Paz Polak2, Nisha Rajagopal8, Pradipta R. Ray12, Richard C Sallari1, Richard C Sallari2, Kyle Siebenthall7, Nicholas A Sinnott-Armstrong2, Nicholas A Sinnott-Armstrong1, Michael Stevens13, Robert E. Thurman7, Jie Wu16, Bo Zhang13, Xin Zhou13, Arthur E. Beaudet5, Laurie A. Boyer1, Philip L. De Jager15, Philip L. De Jager2, Peggy J. Farnham17, Susan J. Fisher9, David Haussler18, Steven J.M. Jones4, Steven J.M. Jones19, Wei Li5, Marco A. Marra4, Michael T. McManus9, Shamil R. Sunyaev15, Shamil R. Sunyaev2, James A. Thomson20, Thea D. Tlsty9, Li-Huei Tsai1, Li-Huei Tsai2, Wei Wang, Robert A. Waterland5, Michael Q. Zhang21, Lisa Helbling Chadwick22, Bradley E. Bernstein15, Bradley E. Bernstein6, Bradley E. Bernstein2, Joseph F. Costello9, Joseph R. Ecker11, Martin Hirst4, Alexander Meissner2, Aleksandar Milosavljevic5, Bing Ren8, John A. Stamatoyannopoulos7, Ting Wang13, Manolis Kellis2, Manolis Kellis1 
19 Feb 2015-Nature
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
Abstract: The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

5,037 citations


Journal ArticleDOI
17 Sep 2015-Nature
TL;DR: It is found that emissions from residential energy use such as heating and cooking, prevalent in India and China, have the largest impact on premature mortality globally, being even more dominant if carbonaceous particles are assumed to be most toxic.
Abstract: Assessment of the global burden of disease is based on epidemiological cohort studies that connect premature mortality to a wide range of causes, including the long-term health impacts of ozone and fine particulate matter with a diameter smaller than 2.5 micrometres (PM2.5). It has proved difficult to quantify premature mortality related to air pollution, notably in regions where air quality is not monitored, and also because the toxicity of particles from various sources may vary. Here we use a global atmospheric chemistry model to investigate the link between premature mortality and seven emission source categories in urban and rural environments. In accord with the global burden of disease for 2010 (ref. 5), we calculate that outdoor air pollution, mostly by PM2.5, leads to 3.3 (95 per cent confidence interval 1.61-4.81) million premature deaths per year worldwide, predominantly in Asia. We primarily assume that all particles are equally toxic, but also include a sensitivity study that accounts for differential toxicity. We find that emissions from residential energy use such as heating and cooking, prevalent in India and China, have the largest impact on premature mortality globally, being even more dominant if carbonaceous particles are assumed to be most toxic. Whereas in much of the USA and in a few other countries emissions from traffic and power generation are important, in eastern USA, Europe, Russia and East Asia agricultural emissions make the largest relative contribution to PM2.5, with the estimate of overall health impact depending on assumptions regarding particle toxicity. Model projections based on a business-as-usual emission scenario indicate that the contribution of outdoor air pollution to premature mortality could double by 2050.

3,848 citations


Journal ArticleDOI
28 May 2015-Nature
TL;DR: This Review discusses recent developments in the emerging field of soft robotics, and explores the design and control of soft-bodied robots composed of compliant materials.
Abstract: Conventionally, engineers have employed rigid materials to fabricate precise, predictable robotic systems, which are easily modelled as rigid members connected at discrete joints. Natural systems, however, often match or exceed the performance of robotic systems with deformable bodies. Cephalopods, for example, achieve amazing feats of manipulation and locomotion without a skeleton; even vertebrates such as humans achieve dynamic gaits by storing elastic energy in their compliant bones and soft tissues. Inspired by nature, engineers have begun to explore the design and control of soft-bodied robots composed of compliant materials. This Review discusses recent developments in the emerging field of soft robotics.

3,824 citations


Journal ArticleDOI
29 Oct 2015-Nature
TL;DR: Gasdermin D (Gsdmd) is identified by genome-wide clustered regularly interspaced palindromic repeat-Cas9 nuclease screens of caspase-11- and caspasing-1-mediated pyroptosis in mouse bone marrow macrophages to offer insight into inflammasome-mediated immunity/diseases and change the understanding of pyroPTosis and programmed necrosis.
Abstract: Inflammatory caspases (caspase-1, -4, -5 and -11) are critical for innate defences. Caspase-1 is activated by ligands of various canonical inflammasomes, and caspase-4, -5 and -11 directly recognize bacterial lipopolysaccharide, both of which trigger pyroptosis. Despite the crucial role in immunity and endotoxic shock, the mechanism for pyroptosis induction by inflammatory caspases is unknown. Here we identify gasdermin D (Gsdmd) by genome-wide clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 nuclease screens of caspase-11- and caspase-1-mediated pyroptosis in mouse bone marrow macrophages. GSDMD-deficient cells resisted the induction of pyroptosis by cytosolic lipopolysaccharide and known canonical inflammasome ligands. Interleukin-1β release was also diminished in Gsdmd(-/-) cells, despite intact processing by caspase-1. Caspase-1 and caspase-4/5/11 specifically cleaved the linker between the amino-terminal gasdermin-N and carboxy-terminal gasdermin-C domains in GSDMD, which was required and sufficient for pyroptosis. The cleavage released the intramolecular inhibition on the gasdermin-N domain that showed intrinsic pyroptosis-inducing activity. Other gasdermin family members were not cleaved by inflammatory caspases but shared the autoinhibition; gain-of-function mutations in Gsdma3 that cause alopecia and skin defects disrupted the autoinhibition, allowing its gasdermin-N domain to trigger pyroptosis. These findings offer insight into inflammasome-mediated immunity/diseases and also change our understanding of pyroptosis and programmed necrosis.

3,554 citations


Journal ArticleDOI
12 Feb 2015-Nature
TL;DR: A genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals provide strong support for a role of the central nervous system in obesity susceptibility.
Abstract: Obesity is heritable and predisposes to many diseases To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals This analysis identifies 97 BMI-associated loci (P 20% of BMI variation Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis

3,472 citations


Journal ArticleDOI
19 Nov 2015-Nature
TL;DR: It is demonstrated that exosomes from mouse and human lung-, liver- and brain-tropic tumour cells fuse preferentially with resident cells at their predicted destination, namely lung fibroblasts and epithelial cells, liver Kupffer cells and brain endothelial cells.
Abstract: Ever since Stephen Paget's 1889 hypothesis, metastatic organotropism has remained one of cancer's greatest mysteries. Here we demonstrate that exosomes from mouse and human lung-, liver- and brain-tropic tumour cells fuse preferentially with resident cells at their predicted destination, namely lung fibroblasts and epithelial cells, liver Kupffer cells and brain endothelial cells. We show that tumour-derived exosomes uptaken by organ-specific cells prepare the pre-metastatic niche. Treatment with exosomes from lung-tropic models redirected the metastasis of bone-tropic tumour cells. Exosome proteomics revealed distinct integrin expression patterns, in which the exosomal integrins α6β4 and α6β1 were associated with lung metastasis, while exosomal integrin αvβ5 was linked to liver metastasis. Targeting the integrins α6β4 and αvβ5 decreased exosome uptake, as well as lung and liver metastasis, respectively. We demonstrate that exosome integrin uptake by resident cells activates Src phosphorylation and pro-inflammatory S100 gene expression. Finally, our clinical data indicate that exosomal integrins could be used to predict organ-specific metastasis.

3,399 citations


Journal ArticleDOI
29 Jan 2015-Nature
TL;DR: It is shown that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1.
Abstract: The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1 Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22 A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53 Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours Therapeutic candidate alterations were identified in most HNSCCs

Journal ArticleDOI
16 Jul 2015-Nature
TL;DR: In searching for T-cell gateways into and out of the meninges, functional lymphatic vessels lining the dural sinuses are discovered, which may call for a reassessment of basic assumptions in neuroimmunology and sheds new light on the aetiology of neuroinflammatory and neurodegenerative diseases associated with immune system dysfunction.
Abstract: One of the characteristics of the central nervous system is the lack of a classical lymphatic drainage system. Although it is now accepted that the central nervous system undergoes constant immune surveillance that takes place within the meningeal compartment, the mechanisms governing the entrance and exit of immune cells from the central nervous system remain poorly understood. In searching for T-cell gateways into and out of the meninges, we discovered functional lymphatic vessels lining the dural sinuses. These structures express all of the molecular hallmarks of lymphatic endothelial cells, are able to carry both fluid and immune cells from the cerebrospinal fluid, and are connected to the deep cervical lymph nodes. The unique location of these vessels may have impeded their discovery to date, thereby contributing to the long-held concept of the absence of lymphatic vasculature in the central nervous system. The discovery of the central nervous system lymphatic system may call for a reassessment of basic assumptions in neuroimmunology and sheds new light on the aetiology of neuroinflammatory and neurodegenerative diseases associated with immune system dysfunction.

Journal ArticleDOI
02 Apr 2015-Nature
TL;DR: A terrestrial assemblage database of unprecedented geographic and taxonomic coverage is analysed to quantify local biodiversity responses to land use and related changes and shows that in the worst-affected habitats, pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%.
Abstract: Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status.

Journal ArticleDOI
21 Oct 2015-Nature
TL;DR: The data imply statistically significant rejection of the local-realist null hypothesis and could be used for testing less-conventional theories, and for implementing device-independent quantum-secure communication and randomness certification.
Abstract: More than 50 years ago, John Bell proved that no theory of nature that obeys locality and realism can reproduce all the predictions of quantum theory: in any local-realist theory, the correlations between outcomes of measurements on distant particles satisfy an inequality that can be violated if the particles are entangled. Numerous Bell inequality tests have been reported; however, all experiments reported so far required additional assumptions to obtain a contradiction with local realism, resulting in 'loopholes'. Here we report a Bell experiment that is free of any such additional assumption and thus directly tests the principles underlying Bell's inequality. We use an event-ready scheme that enables the generation of robust entanglement between distant electron spins (estimated state fidelity of 0.92 ± 0.03). Efficient spin read-out avoids the fair-sampling assumption (detection loophole), while the use of fast random-basis selection and spin read-out combined with a spatial separation of 1.3 kilometres ensure the required locality conditions. We performed 245 trials that tested the CHSH-Bell inequality S ≤ 2 and found S = 2.42 ± 0.20 (where S quantifies the correlation between measurement outcomes). A null-hypothesis test yields a probability of at most P = 0.039 that a local-realist model for space-like separated sites could produce data with a violation at least as large as we observe, even when allowing for memory in the devices. Our data hence imply statistically significant rejection of the local-realist null hypothesis. This conclusion may be further consolidated in future experiments; for instance, reaching a value of P = 0.001 would require approximately 700 trials for an observed S = 2.4. With improvements, our experiment could be used for testing less-conventional theories, and for implementing device-independent quantum-secure communication and randomness certification.

Journal ArticleDOI
29 Oct 2015-Nature
TL;DR: It is shown that gasdermin D is essential for caspase-11-dependent pyroptosis and interleukin-1β maturation and a key mediator of the host response against Gram-negative bacteria.
Abstract: Intracellular lipopolysaccharide from Gram-negative bacteria including Escherichia coli, Salmonella typhimurium, Shigella flexneri, and Burkholderia thailandensis activates mouse caspase-11, causing pyroptotic cell death, interleukin-1β processing, and lethal septic shock. How caspase-11 executes these downstream signalling events is largely unknown. Here we show that gasdermin D is essential for caspase-11-dependent pyroptosis and interleukin-1β maturation. A forward genetic screen with ethyl-N-nitrosourea-mutagenized mice links Gsdmd to the intracellular lipopolysaccharide response. Macrophages from Gsdmd(-/-) mice generated by gene targeting also exhibit defective pyroptosis and interleukin-1β secretion induced by cytoplasmic lipopolysaccharide or Gram-negative bacteria. In addition, Gsdmd(-/-) mice are protected from a lethal dose of lipopolysaccharide. Mechanistically, caspase-11 cleaves gasdermin D, and the resulting amino-terminal fragment promotes both pyroptosis and NLRP3-dependent activation of caspase-1 in a cell-intrinsic manner. Our data identify gasdermin D as a critical target of caspase-11 and a key mediator of the host response against Gram-negative bacteria.

Journal ArticleDOI
09 Apr 2015-Nature
TL;DR: In this paper, the authors find that current evidence suggests a gradual and prolonged release of greenhouse gas emissions in a warming climate and present a research strategy with which to target poorly understood aspects of permafrost carbon dynamics.
Abstract: Large quantities of organic carbon are stored in frozen soils (permafrost) within Arctic and sub-Arctic regions. A warming climate can induce environmental changes that accelerate the microbial breakdown of organic carbon and the release of the greenhouse gases carbon dioxide and methane. This feedback can accelerate climate change, but the magnitude and timing of greenhouse gas emission from these regions and their impact on climate change remain uncertain. Here we find that current evidence suggests a gradual and prolonged release of greenhouse gas emissions in a warming climate and present a research strategy with which to target poorly understood aspects of permafrost carbon dynamics.

Journal ArticleDOI
07 May 2015-Nature
TL;DR: The experimental implementation of transistor-free metal-oxide memristor crossbars, with device variability sufficiently low to allow operation of integrated neural networks, in a simple network: a single-layer perceptron (an algorithm for linear classification).
Abstract: Despite much progress in semiconductor integrated circuit technology, the extreme complexity of the human cerebral cortex, with its approximately 10(14) synapses, makes the hardware implementation of neuromorphic networks with a comparable number of devices exceptionally challenging. To provide comparable complexity while operating much faster and with manageable power dissipation, networks based on circuits combining complementary metal-oxide-semiconductors (CMOSs) and adjustable two-terminal resistive devices (memristors) have been developed. In such circuits, the usual CMOS stack is augmented with one or several crossbar layers, with memristors at each crosspoint. There have recently been notable improvements in the fabrication of such memristive crossbars and their integration with CMOS circuits, including first demonstrations of their vertical integration. Separately, discrete memristors have been used as artificial synapses in neuromorphic networks. Very recently, such experiments have been extended to crossbar arrays of phase-change memristive devices. The adjustment of such devices, however, requires an additional transistor at each crosspoint, and hence these devices are much harder to scale than metal-oxide memristors, whose nonlinear current-voltage curves enable transistor-free operation. Here we report the experimental implementation of transistor-free metal-oxide memristor crossbars, with device variability sufficiently low to allow operation of integrated neural networks, in a simple network: a single-layer perceptron (an algorithm for linear classification). The network can be taught in situ using a coarse-grain variety of the delta rule algorithm to perform the perfect classification of 3 × 3-pixel black/white images into three classes (representing letters). This demonstration is an important step towards much larger and more complex memristive neuromorphic networks.

Journal ArticleDOI
23 Nov 2015-Nature
TL;DR: It is argued that the available evidence does not support the formation of large-molecular-size and persistent ‘humic substances’ in soils, and instead soil organic matter is a continuum of progressively decomposing organic compounds.
Abstract: Instead of containing stable and chemically unique ‘humic substances’, as has been widely accepted, soil organic matter is a mixture of progressively decomposing organic compounds; this has broad implications for soil science and its applications. The exchange of nutrients, energy and carbon between soil organic matter, the soil environment, aquatic systems and the atmosphere is important for agricultural productivity, water quality and climate. Long-standing theory suggests that soil organic matter is composed of inherently stable and chemically unique compounds. Here we argue that the available evidence does not support the formation of large-molecular-size and persistent ‘humic substances’ in soils. Instead, soil organic matter is a continuum of progressively decomposing organic compounds. We discuss implications of this view of the nature of soil organic matter for aquatic health, soil carbon–climate interactions and land management. Soil organic matter contains a large portion of the world's carbon and plays an important role in maintaining productive soils and water quality. Nevertheless, a consensus on the nature of soil organic matter is lacking. Johannes Lehmann and Markus Kleber argue that soil organic matter should no longer be seen as large and persistent, chemically unique substances, but as a continuum of progressively decomposing organic compounds.

Journal ArticleDOI
29 Jan 2015-Nature
TL;DR: Structural-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci is described and the potential of Cas9-based activators as a powerful genetic perturbation technology is demonstrated.
Abstract: Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. Here we describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. We used these engineered Cas9 activation complexes to investigate single-guide RNA (sgRNA) targeting rules for effective transcriptional activation, to demonstrate multiplexed activation of ten genes simultaneously, and to upregulate long intergenic non-coding RNA (lincRNA) transcripts. We also synthesized a library consisting of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes that, upon activation, confer resistance to a BRAF inhibitor. The top hits included genes previously shown to be able to confer resistance, and novel candidates were validated using individual sgRNA and complementary DNA overexpression. A gene expression signature based on the top screening hits correlated with markers of BRAF inhibitor resistance in cell lines and patient-derived samples. These results collectively demonstrate the potential of Cas9-based activators as a powerful genetic perturbation technology.

Journal ArticleDOI
08 Oct 2015-Nature
TL;DR: It is found that Plasmodium falciparum infection prevalence in endemic Africa halved and the incidence of clinical disease fell by 40% between 2000 and 2015, and interventions have averted 663 (542–753 credible interval) million clinical cases since 2000.
Abstract: Since the year 2000, a concerted campaign against malaria has led to unprecedented levels of intervention coverage across sub-Saharan Africa. Understanding the effect of this control effort is vital to inform future control planning. However, the effect of malaria interventions across the varied epidemiological settings of Africa remains poorly understood owing to the absence of reliable surveillance data and the simplistic approaches underlying current disease estimates. Here we link a large database of malaria field surveys with detailed reconstructions of changing intervention coverage to directly evaluate trends from 2000 to 2015, and quantify the attributable effect of malaria disease control efforts. We found that Plasmodium falciparum infection prevalence in endemic Africa halved and the incidence of clinical disease fell by 40% between 2000 and 2015. We estimate that interventions have averted 663 (542-753 credible interval) million clinical cases since 2000. Insecticide-treated nets, the most widespread intervention, were by far the largest contributor (68% of cases averted). Although still below target levels, current malaria interventions have substantially reduced malaria disease incidence across the continent. Increasing access to these interventions, and maintaining their effectiveness in the face of insecticide and drug resistance, should form a cornerstone of post-2015 control strategies.

Journal ArticleDOI
09 Jul 2015-Nature
TL;DR: GPC1+ crExos may serve as a potential non-invasive diagnostic and screening tool to detect early stages of pancreatic cancer to facilitate possible curative surgical therapy.
Abstract: Exosomes are lipid-bilayer-enclosed extracellular vesicles that contain proteins and nucleic acids. They are secreted by all cells and circulate in the blood. Specific detection and isolation of cancer-cell-derived exosomes in the circulation is currently lacking. Using mass spectrometry analyses, we identify a cell surface proteoglycan, glypican-1 (GPC1), specifically enriched on cancer-cell-derived exosomes. GPC1(+) circulating exosomes (crExos) were monitored and isolated using flow cytometry from the serum of patients and mice with cancer. GPC1(+) crExos were detected in the serum of patients with pancreatic cancer with absolute specificity and sensitivity, distinguishing healthy subjects and patients with a benign pancreatic disease from patients with early- and late-stage pancreatic cancer. Levels of GPC1(+) crExos correlate with tumour burden and the survival of pre- and post-surgical patients. GPC1(+) crExos from patients and from mice with spontaneous pancreatic tumours carry specific KRAS mutations, and reliably detect pancreatic intraepithelial lesions in mice despite negative signals by magnetic resonance imaging. GPC1(+) crExos may serve as a potential non-invasive diagnostic and screening tool to detect early stages of pancreatic cancer to facilitate possible curative surgical therapy.

Journal ArticleDOI
26 Nov 2015-Nature
TL;DR: This work proposes the existence of a previously overlooked type of Weyl fermion that emerges at the boundary between electron and hole pockets in a new phase of matter and discovers a type-II Weyl point, which is still a protected crossing, but appears at the contact of electron and Hole pockets in type- II Weyl semimetals.
Abstract: Fermions--elementary particles such as electrons--are classified as Dirac, Majorana or Weyl. Majorana and Weyl fermions had not been observed experimentally until the recent discovery of condensed matter systems such as topological superconductors and semimetals, in which they arise as low-energy excitations. Here we propose the existence of a previously overlooked type of Weyl fermion that emerges at the boundary between electron and hole pockets in a new phase of matter. This particle was missed by Weyl because it breaks the stringent Lorentz symmetry in high-energy physics. Lorentz invariance, however, is not present in condensed matter physics, and by generalizing the Dirac equation, we find the new type of Weyl fermion. In particular, whereas Weyl semimetals--materials hosting Weyl fermions--were previously thought to have standard Weyl points with a point-like Fermi surface (which we refer to as type-I), we discover a type-II Weyl point, which is still a protected crossing, but appears at the contact of electron and hole pockets in type-II Weyl semimetals. We predict that WTe2 is an example of a topological semimetal hosting the new particle as a low-energy excitation around such a type-II Weyl point. The existence of type-II Weyl points in WTe2 means that many of its physical properties are very different to those of standard Weyl semimetals with point-like Fermi surfaces.

Journal ArticleDOI
Nicola Waddell1, Marina Pajic2, Ann-Marie Patch3, David K. Chang2, Karin S. Kassahn3, Peter Bailey3, Amber L. Johns2, David Miller3, Katia Nones3, Kelly Quek3, Michael C.J. Quinn3, Alan J. Robertson3, Muhammad Zaki Hidayatullah Fadlullah3, Timothy J. C. Bruxner3, Angelika N. Christ3, Ivon Harliwong3, Senel Idrisoglu3, Suzanne Manning3, Craig Nourse3, Ehsan Nourbakhsh3, Shivangi Wani3, Peter J. Wilson3, Emma Markham3, Nicole Cloonan1, Matthew J. Anderson3, J. Lynn Fink3, Oliver Holmes3, Stephen H. Kazakoff3, Conrad Leonard3, Felicity Newell3, Barsha Poudel3, Sarah Song3, Darrin Taylor3, Nick Waddell3, Scott Wood3, Qinying Xu3, Jianmin Wu2, Mark Pinese2, Mark J. Cowley2, Hong C. Lee2, Marc D. Jones2, Adnan Nagrial2, Jeremy L. Humphris2, Lorraine A. Chantrill2, Venessa T. Chin2, Angela Steinmann2, Amanda Mawson2, Emily S. Humphrey2, Emily K. Colvin2, Angela Chou2, Christopher J. Scarlett2, Andreia V. Pinho2, Marc Giry-Laterriere2, Ilse Rooman2, Jaswinder S. Samra4, James G. Kench2, Jessica A. Pettitt2, Neil D. Merrett5, Christopher W. Toon2, Krishna Epari6, Nam Q. Nguyen7, Andrew Barbour8, Nikolajs Zeps9, Nigel B. Jamieson10, Janet Graham11, Simone P. Niclou, Rolf Bjerkvig12, Robert Grützmann13, Daniela Aust13, Ralph H. Hruban14, Anirban Maitra15, Christine A. Iacobuzio-Donahue16, Christopher L. Wolfgang14, Richard A. Morgan14, Rita T. Lawlor17, Vincenzo Corbo, Claudio Bassi, Massimo Falconi, Giuseppe Zamboni17, Giampaolo Tortora, Margaret A. Tempero18, Anthony J. Gill2, James R. Eshleman14, Christian Pilarsky13, Aldo Scarpa17, Elizabeth A. Musgrove19, John V. Pearson1, Andrew V. Biankin2, Sean M. Grimmond3 
26 Feb 2015-Nature
TL;DR: Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency, and 4 of 5 individuals with these measures of defective DNA maintenance responded to platinum therapy.
Abstract: Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.

Journal ArticleDOI
11 May 2015-Nature
TL;DR: The mechanism by which tumour-intrinsic active β-catenin signalling results in T-cell exclusion and resistance to anti-PD-L1/anti-CTLA-4 monoclonal antibody therapy is identified, pointing to new candidate targets for immune potentiation.
Abstract: Melanoma treatment is being revolutionized by the development of effective immunotherapeutic approaches. These strategies include blockade of immune-inhibitory receptors on activated T cells; for example, using monoclonal antibodies against CTLA-4, PD-1, and PD-L1 (refs 3-5). However, only a subset of patients responds to these treatments, and data suggest that therapeutic benefit is preferentially achieved in patients with a pre-existing T-cell response against their tumour, as evidenced by a baseline CD8(+) T-cell infiltration within the tumour microenvironment. Understanding the molecular mechanisms that underlie the presence or absence of a spontaneous anti-tumour T-cell response in subsets of cases, therefore, should enable the development of therapeutic solutions for patients lacking a T-cell infiltrate. Here we identify a melanoma-cell-intrinsic oncogenic pathway that contributes to a lack of T-cell infiltration in melanoma. Molecular analysis of human metastatic melanoma samples revealed a correlation between activation of the WNT/β-catenin signalling pathway and absence of a T-cell gene expression signature. Using autochthonous mouse melanoma models we identified the mechanism by which tumour-intrinsic active β-catenin signalling results in T-cell exclusion and resistance to anti-PD-L1/anti-CTLA-4 monoclonal antibody therapy. Specific oncogenic signals, therefore, can mediate cancer immune evasion and resistance to immunotherapies, pointing to new candidate targets for immune potentiation.

Journal ArticleDOI
Peter H. Sudmant1, Tobias Rausch, Eugene J. Gardner2, Robert E. Handsaker3, Robert E. Handsaker4, Alexej Abyzov5, John Huddleston1, Yan Zhang6, Kai Ye7, Goo Jun8, Goo Jun9, Markus His Yang Fritz, Miriam K. Konkel10, Ankit Malhotra, Adrian M. Stütz, Xinghua Shi11, Francesco Paolo Casale12, Jieming Chen6, Fereydoun Hormozdiari1, Gargi Dayama8, Ken Chen13, Maika Malig1, Mark Chaisson1, Klaudia Walter12, Sascha Meiers, Seva Kashin3, Seva Kashin4, Erik Garrison14, Adam Auton15, Hugo Y. K. Lam, Xinmeng Jasmine Mu6, Xinmeng Jasmine Mu4, Can Alkan16, Danny Antaki17, Taejeong Bae5, Eliza Cerveira, Peter S. Chines18, Zechen Chong13, Laura Clarke12, Elif Dal16, Li Ding7, S. Emery8, Xian Fan13, Madhusudan Gujral17, Fatma Kahveci16, Jeffrey M. Kidd8, Yu Kong15, Eric-Wubbo Lameijer19, Shane A. McCarthy12, Paul Flicek12, Richard A. Gibbs20, Gabor T. Marth14, Christopher E. Mason21, Androniki Menelaou22, Androniki Menelaou23, Donna M. Muzny24, Bradley J. Nelson1, Amina Noor17, Nicholas F. Parrish25, Matthew Pendleton24, Andrew Quitadamo11, Benjamin Raeder, Eric E. Schadt24, Mallory Romanovitch, Andreas Schlattl, Robert Sebra24, Andrey A. Shabalin26, Andreas Untergasser27, Jerilyn A. Walker10, Min Wang20, Fuli Yu20, Chengsheng Zhang, Jing Zhang6, Xiangqun Zheng-Bradley12, Wanding Zhou13, Thomas Zichner, Jonathan Sebat17, Mark A. Batzer10, Steven A. McCarroll3, Steven A. McCarroll4, Ryan E. Mills8, Mark Gerstein6, Ali Bashir24, Oliver Stegle12, Scott E. Devine2, Charles Lee28, Evan E. Eichler1, Jan O. Korbel12 
01 Oct 2015-Nature
TL;DR: In this paper, the authors describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which are constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations.
Abstract: Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Journal ArticleDOI
22 Jan 2015-Nature
TL;DR: The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance, as well as several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors.
Abstract: Antibiotic resistance is spreading faster than the introduction of new compounds into clinical practice, causing a public health crisis. Most antibiotics were produced by screening soil microorganisms, but this limited resource of cultivable bacteria was overmined by the 1960s. Synthetic approaches to produce antibiotics have been unable to replace this platform. Uncultured bacteria make up approximately 99% of all species in external environments, and are an untapped source of new antibiotics. We developed several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors. Here we report a new antibiotic that we term teixobactin, discovered in a screen of uncultured bacteria. Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). We did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin. The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.

Journal ArticleDOI
16 Apr 2015-Nature
TL;DR: Major tumour regressions are reported in a subset of patients with metastatic melanoma treated with an anti-CTLA4 antibody and radiation and reproduced this effect in mouse models, showing that PD-L1 on melanoma cells allows tumours to escape anti- NCTLA4-based therapy, and the combination of radiation, anti- CTLA4 and anti-PD-L 1 promotes response and immunity through distinct mechanisms.
Abstract: Immune checkpoint inhibitors result in impressive clinical responses, but optimal results will require combination with each other and other therapies. This raises fundamental questions about mechanisms of non-redundancy and resistance. Here we report major tumour regressions in a subset of patients with metastatic melanoma treated with an anti-CTLA4 antibody (anti-CTLA4) and radiation, and reproduced this effect in mouse models. Although combined treatment improved responses in irradiated and unirradiated tumours, resistance was common. Unbiased analyses of mice revealed that resistance was due to upregulation of PD-L1 on melanoma cells and associated with T-cell exhaustion. Accordingly, optimal response in melanoma and other cancer types requires radiation, anti-CTLA4 and anti-PD-L1/PD-1. Anti-CTLA4 predominantly inhibits T-regulatory cells (Treg cells), thereby increasing the CD8 T-cell to Treg (CD8/Treg) ratio. Radiation enhances the diversity of the T-cell receptor (TCR) repertoire of intratumoral T cells. Together, anti-CTLA4 promotes expansion of T cells, while radiation shapes the TCR repertoire of the expanded peripheral clones. Addition of PD-L1 blockade reverses T-cell exhaustion to mitigate depression in the CD8/Treg ratio and further encourages oligoclonal T-cell expansion. Similarly to results from mice, patients on our clinical trial with melanoma showing high PD-L1 did not respond to radiation plus anti-CTLA4, demonstrated persistent T-cell exhaustion, and rapidly progressed. Thus, PD-L1 on melanoma cells allows tumours to escape anti-CTLA4-based therapy, and the combination of radiation, anti-CTLA4 and anti-PD-L1 promotes response and immunity through distinct mechanisms.

Journal ArticleDOI
12 Feb 2015-Nature
TL;DR: The discovery of high-temperature superconductivity in the copper oxides in 1986 triggered a huge amount of innovative scientific inquiry but unresolved issues include the astonishing complexity of the phase diagram, the unprecedented prominence of various forms of collective fluctuations, and the simplicity and insensitivity to material details of the ‘normal’ state at elevated temperatures.
Abstract: The discovery of high-temperature superconductivity in the copper oxides in 1986 triggered a huge amount of innovative scientific inquiry. In the almost three decades since, much has been learned about the novel forms of quantum matter that are exhibited in these strongly correlated electron systems. A qualitative understanding of the nature of the superconducting state itself has been achieved. However, unresolved issues include the astonishing complexity of the phase diagram, the unprecedented prominence of various forms of collective fluctuations, and the simplicity and insensitivity to material details of the 'normal' state at elevated temperatures.

Journal ArticleDOI
20 Aug 2015-Nature
TL;DR: Using genome editing to knockout five autophagy receptors in HeLa cells, this work shows that two receptors previously linked to xenophagy, NDP52 and optineurin, are the primary receptors for PINK1- and parkin-mediated mitophagy.
Abstract: Protein aggregates and damaged organelles are tagged with ubiquitin chains to trigger selective autophagy. To initiate mitophagy, the ubiquitin kinase PINK1 phosphorylates ubiquitin to activate the ubiquitin ligase parkin, which builds ubiquitin chains on mitochondrial outer membrane proteins, where they act to recruit autophagy receptors. Using genome editing to knockout five autophagy receptors in HeLa cells, here we show that two receptors previously linked to xenophagy, NDP52 and optineurin, are the primary receptors for PINK1- and parkin-mediated mitophagy. PINK1 recruits NDP52 and optineurin, but not p62, to mitochondria to activate mitophagy directly, independently of parkin. Once recruited to mitochondria, NDP52 and optineurin recruit the autophagy factors ULK1, DFCP1 and WIPI1 to focal spots proximal to mitochondria, revealing a function for these autophagy receptors upstream of LC3. This supports a new model in which PINK1-generated phospho-ubiquitin serves as the autophagy signal on mitochondria, and parkin then acts to amplify this signal. This work also suggests direct and broader roles for ubiquitin phosphorylation in other autophagy pathways.

Journal ArticleDOI
03 Sep 2015-Nature
TL;DR: S sulfur hydride is investigated, and it is argued that the phase responsible for high-Tc superconductivity in this system is likely to be H3S, formed from H2S by decomposition under pressure, which raises hope for the prospects for achieving room-temperature super conductivity in other hydrogen-based materials.
Abstract: A superconductor is a material that can conduct electricity without resistance below a superconducting transition temperature, Tc. The highest Tc that has been achieved to date is in the copper oxide system: 133 kelvin at ambient pressure and 164 kelvin at high pressures. As the nature of superconductivity in these materials is still not fully understood (they are not conventional superconductors), the prospects for achieving still higher transition temperatures by this route are not clear. In contrast, the Bardeen-Cooper-Schrieffer theory of conventional superconductivity gives a guide for achieving high Tc with no theoretical upper bound--all that is needed is a favourable combination of high-frequency phonons, strong electron-phonon coupling, and a high density of states. These conditions can in principle be fulfilled for metallic hydrogen and covalent compounds dominated by hydrogen, as hydrogen atoms provide the necessary high-frequency phonon modes as well as the strong electron-phonon coupling. Numerous calculations support this idea and have predicted transition temperatures in the range 50-235 kelvin for many hydrides, but only a moderate Tc of 17 kelvin has been observed experimentally. Here we investigate sulfur hydride, where a Tc of 80 kelvin has been predicted. We find that this system transforms to a metal at a pressure of approximately 90 gigapascals. On cooling, we see signatures of superconductivity: a sharp drop of the resistivity to zero and a decrease of the transition temperature with magnetic field, with magnetic susceptibility measurements confirming a Tc of 203 kelvin. Moreover, a pronounced isotope shift of Tc in sulfur deuteride is suggestive of an electron-phonon mechanism of superconductivity that is consistent with the Bardeen-Cooper-Schrieffer scenario. We argue that the phase responsible for high-Tc superconductivity in this system is likely to be H3S, formed from H2S by decomposition under pressure. These findings raise hope for the prospects for achieving room-temperature superconductivity in other hydrogen-based materials.