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Showing papers in "Nature in 2008"


Journal ArticleDOI
06 Feb 2008-Nature
TL;DR: Researchers must find a sustainable way of providing the power their modern lifestyles demand to ensure the continued existence of clean energy sources.
Abstract: Researchers must find a sustainable way of providing the power our modern lifestyles demand.

15,980 citations


Journal ArticleDOI
24 Jul 2008-Nature
TL;DR: The molecular pathways of this cancer-related inflammation are now being unravelled, resulting in the identification of new target molecules that could lead to improved diagnosis and treatment.
Abstract: The mediators and cellular effectors of inflammation are important constituents of the local environment of tumours. In some types of cancer, inflammatory conditions are present before a malignant change occurs. Conversely, in other types of cancer, an oncogenic change induces an inflammatory microenvironment that promotes the development of tumours. Regardless of its origin, 'smouldering' inflammation in the tumour microenvironment has many tumour-promoting effects. It aids in the proliferation and survival of malignant cells, promotes angiogenesis and metastasis, subverts adaptive immune responses, and alters responses to hormones and chemotherapeutic agents. The molecular pathways of this cancer-related inflammation are now being unravelled, resulting in the identification of new target molecules that could lead to improved diagnosis and treatment.

9,282 citations


Journal ArticleDOI
01 May 2008-Nature
TL;DR: It is shown, using a simple analytical example, that memristance arises naturally in nanoscale systems in which solid-state electronic and ionic transport are coupled under an external bias voltage.
Abstract: Anyone who ever took an electronics laboratory class will be familiar with the fundamental passive circuit elements: the resistor, the capacitor and the inductor. However, in 1971 Leon Chua reasoned from symmetry arguments that there should be a fourth fundamental element, which he called a memristor (short for memory resistor). Although he showed that such an element has many interesting and valuable circuit properties, until now no one has presented either a useful physical model or an example of a memristor. Here we show, using a simple analytical example, that memristance arises naturally in nanoscale systems in which solid-state electronic and ionic transport are coupled under an external bias voltage. These results serve as the foundation for understanding a wide range of hysteretic current-voltage behaviour observed in many nanoscale electronic devices that involve the motion of charged atomic or molecular species, in particular certain titanium dioxide cross-point switches.

8,971 citations


Journal ArticleDOI
20 Mar 2008-Nature
TL;DR: Some of the science and technology being developed to improve the disinfection and decontamination of water, as well as efforts to increase water supplies through the safe re-use of wastewater and efficient desalination of sea and brackish water are highlighted.
Abstract: One of the most pervasive problems afflicting people throughout the world is inadequate access to clean water and sanitation. Problems with water are expected to grow worse in the coming decades, with water scarcity occurring globally, even in regions currently considered water-rich. Addressing these problems calls out for a tremendous amount of research to be conducted to identify robust new methods of purifying water at lower cost and with less energy, while at the same time minimizing the use of chemicals and impact on the environment. Here we highlight some of the science and technology being developed to improve the disinfection and decontamination of water, as well as efforts to increase water supplies through the safe re-use of wastewater and efficient desalination of sea and brackish water.

6,967 citations


Journal ArticleDOI
23 Oct 2008-Nature
TL;DR: The interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated gliobeasts, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.
Abstract: Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas - the most common type of primary adult brain cancer - and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol- 3- OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.

6,761 citations


Journal ArticleDOI
21 Feb 2008-Nature
TL;DR: It is concluded that global resources to counter disease emergence are poorly allocated, with the majority of the scientific and surveillance effort focused on countries from where the next important EID is least likely to originate.
Abstract: Emerging infectious diseases (EIDs) are a significant burden on global economies and public health. Their emergence is thought to be driven largely by socio-economic, environmental and ecological factors, but no comparative study has explicitly analysed these linkages to understand global temporal and spatial patterns of EIDs. Here we analyse a database of 335 EID 'events' (origins of EIDs) between 1940 and 2004, and demonstrate non-random global patterns. EID events have risen significantly over time after controlling for reporting bias, with their peak incidence (in the 1980s) concomitant with the HIV pandemic. EID events are dominated by zoonoses (60.3% of EIDs): the majority of these (71.8%) originate in wildlife (for example, severe acute respiratory virus, Ebola virus), and are increasing significantly over time. We find that 54.3% of EID events are caused by bacteria or rickettsia, reflecting a large number of drug-resistant microbes in our database. Our results confirm that EID origins are significantly correlated with socio-economic, environmental and ecological factors, and provide a basis for identifying regions where new EIDs are most likely to originate (emerging disease 'hotspots'). They also reveal a substantial risk of wildlife zoonotic and vector-borne EIDs originating at lower latitudes where reporting effort is low. We conclude that global resources to counter disease emergence are poorly allocated, with the majority of the scientific and surveillance effort focused on countries from where the next important EID is least likely to originate.

5,992 citations


Journal ArticleDOI
28 Feb 2008-Nature
TL;DR: Understanding autophagy may ultimately allow scientists and clinicians to harness this process for the purpose of improving human health, and to play a role in cell death.
Abstract: Autophagy, or cellular self-digestion, is a cellular pathway involved in protein and organelle degradation, with an astonishing number of connections to human disease and physiology. For example, autophagic dysfunction is associated with cancer, neurodegeneration, microbial infection and ageing. Paradoxically, although autophagy is primarily a protective process for the cell, it can also play a role in cell death. Understanding autophagy may ultimately allow scientists and clinicians to harness this process for the purpose of improving human health.

5,831 citations


Journal ArticleDOI
10 Mar 2008-Nature
TL;DR: In this article, the authors study the trajectory of 100,000 anonymized mobile phone users whose position is tracked for a six-month period and find that the individual travel patterns collapse into a single spatial probability distribution, indicating that humans follow simple reproducible patterns.
Abstract: The mapping of large-scale human movements is important for urban planning, traffic forecasting and epidemic prevention. Work in animals had suggested that their foraging might be explained in terms of a random walk, a mathematical rendition of a series of random steps, or a Levy flight, a random walk punctuated by occasional larger steps. The role of Levy statistics in animal behaviour is much debated — as explained in an accompanying News Feature — but the idea of extending it to human behaviour was boosted by a report in 2006 of Levy flight-like patterns in human movement tracked via dollar bills. A new human study, based on tracking the trajectory of 100,000 cell-phone users for six months, reveals behaviour close to a Levy pattern, but deviating from it as individual trajectories show a high degree of temporal and spatial regularity: work and other commitments mean we are not as free to roam as a foraging animal. But by correcting the data to accommodate individual variation, simple and predictable patterns in human travel begin to emerge. The cover photo (by Cesar Hidalgo) captures human mobility in New York's Grand Central Station. This study used a sample of 100,000 mobile phone users whose trajectory was tracked for six months to study human mobility patterns. Displacements across all users suggest behaviour close to the Levy-flight-like pattern observed previously based on the motion of marked dollar bills, but with a cutoff in the distribution. The origin of the Levy patterns observed in the aggregate data appears to be population heterogeneity and not Levy patterns at the level of the individual. Despite their importance for urban planning1, traffic forecasting2 and the spread of biological3,4,5 and mobile viruses6, our understanding of the basic laws governing human motion remains limited owing to the lack of tools to monitor the time-resolved location of individuals. Here we study the trajectory of 100,000 anonymized mobile phone users whose position is tracked for a six-month period. We find that, in contrast with the random trajectories predicted by the prevailing Levy flight and random walk models7, human trajectories show a high degree of temporal and spatial regularity, each individual being characterized by a time-independent characteristic travel distance and a significant probability to return to a few highly frequented locations. After correcting for differences in travel distances and the inherent anisotropy of each trajectory, the individual travel patterns collapse into a single spatial probability distribution, indicating that, despite the diversity of their travel history, humans follow simple reproducible patterns. This inherent similarity in travel patterns could impact all phenomena driven by human mobility, from epidemic prevention to emergency response, urban planning and agent-based modelling.

5,514 citations


Journal ArticleDOI
18 Jun 2008-Nature
TL;DR: In this paper, the authors proposed a method for quantum interconnects, which convert quantum states from one physical system to those of another in a reversible manner, allowing the distribution of entanglement across the network and teleportation of quantum states between nodes.
Abstract: Quantum networks provide opportunities and challenges across a range of intellectual and technical frontiers, including quantum computation, communication and metrology. The realization of quantum networks composed of many nodes and channels requires new scientific capabilities for generating and characterizing quantum coherence and entanglement. Fundamental to this endeavour are quantum interconnects, which convert quantum states from one physical system to those of another in a reversible manner. Such quantum connectivity in networks can be achieved by the optical interactions of single photons and atoms, allowing the distribution of entanglement across the network and the teleportation of quantum states between nodes.

5,003 citations


Journal ArticleDOI
Ruslan Medzhitov1
23 Jul 2008-Nature
TL;DR: This work has shown that tissue stress or malfunction induces an adaptive response that is intermediate between the basal homeostatic state and a classic inflammatory response, which is referred to here as para-inflammation.
Abstract: Inflammation underlies a wide variety of physiological and pathological processes. Although the pathological aspects of many types of inflammation are well appreciated, their physiological functions are mostly unknown. The classic instigators of inflammation - infection and tissue injury - are at one end of a large range of adverse conditions that induce inflammation, and they trigger the recruitment of leukocytes and plasma proteins to the affected tissue site. Tissue stress or malfunction similarly induces an adaptive response, which is referred to here as para-inflammation. This response relies mainly on tissue-resident macrophages and is intermediate between the basal homeostatic state and a classic inflammatory response. Para-inflammation is probably responsible for the chronic inflammatory conditions that are associated with modern human diseases.

4,832 citations


Journal ArticleDOI
27 Nov 2008-Nature
TL;DR: An in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments yielding a digital inventory of gene and mRNA isoform expression suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.
Abstract: Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, 86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or 'switch-like' regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3' untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.

Journal ArticleDOI
06 Nov 2008-Nature
TL;DR: An approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost is reported, effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.
Abstract: DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

Journal ArticleDOI
29 May 2008-Nature
TL;DR: This work synthesized uniform anatase TiO2 single crystals with a high percentage (47 per cent) of {001} facets using hydrofluoric acid as a morphology controlling agent and demonstrates that for fluorine-terminated surfaces this relative stability is reversed.
Abstract: [Yang, Hua Gui; Sun, Cheng Hua; Qiao, Shi Zhang; Liu, Gang; Smith, Sean Campbell; Lu, Gao Qing] Univ Queensland, ARC Ctr Excellence Funct Nanomat, Sch Engn, Brisbane, Qld 4072, Australia. [Yang, Hua Gui; Sun, Cheng Hua; Qiao, Shi Zhang; Liu, Gang; Smith, Sean Campbell; Lu, Gao Qing] Univ Queensland, Australian Inst Bioengn & Nanotechnol, Ctr Computat Mol Sci, Brisbane, Qld 4072, Australia. [Zou, Jin] Univ Queensland, Ctr Microscopy & Microanal, Brisbane, Qld 4072, Australia. [Zou, Jin] Univ Queensland, Sch Engn, Brisbane, Qld 4072, Australia. [Liu, Gang; Cheng, Hui Ming] Chinese Acad Sci, Met Res Inst, Shenyang Natl Lab Mat sci, Shenyang 110016, Peoples R China.;Lu, GQ (reprint author), Univ Queensland, ARC Ctr Excellence Funct Nanomat, Sch Engn, Brisbane, Qld 4072, Australia;s.qiao@uq.edu.au maxlu@uq.edu.au

Journal ArticleDOI
10 Jan 2008-Nature
TL;DR: In this article, the authors report the electrochemical synthesis of large-area, wafer-scale arrays of rough Si nanowires that are 20-300 nm in diameter.
Abstract: Approximately 90 per cent of the world's power is generated by heat engines that use fossil fuel combustion as a heat source and typically operate at 30-40 per cent efficiency, such that roughly 15 terawatts of heat is lost to the environment. Thermoelectric modules could potentially convert part of this low-grade waste heat to electricity. Their efficiency depends on the thermoelectric figure of merit ZT of their material components, which is a function of the Seebeck coefficient, electrical resistivity, thermal conductivity and absolute temperature. Over the past five decades it has been challenging to increase ZT > 1, since the parameters of ZT are generally interdependent. While nanostructured thermoelectric materials can increase ZT > 1 (refs 2-4), the materials (Bi, Te, Pb, Sb, and Ag) and processes used are not often easy to scale to practically useful dimensions. Here we report the electrochemical synthesis of large-area, wafer-scale arrays of rough Si nanowires that are 20-300 nm in diameter. These nanowires have Seebeck coefficient and electrical resistivity values that are the same as doped bulk Si, but those with diameters of about 50 nm exhibit 100-fold reduction in thermal conductivity, yielding ZT = 0.6 at room temperature. For such nanowires, the lattice contribution to thermal conductivity approaches the amorphous limit for Si, which cannot be explained by current theories. Although bulk Si is a poor thermoelectric material, by greatly reducing thermal conductivity without much affecting the Seebeck coefficient and electrical resistivity, Si nanowire arrays show promise as high-performance, scalable thermoelectric materials.

Journal ArticleDOI
04 Sep 2008-Nature
TL;DR: The impact of micro RNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output.
Abstract: MicroRNAs are endogenous ∼23-nucleotide RNAs that can pair to sites in the messenger RNAs of protein-coding genes to downregulate the expression from these messages. MicroRNAs are known to influence the evolution and stability of many mRNAs, but their global impact on protein output had not been examined. Here we use quantitative mass spectrometry to measure the response of thousands of proteins after introducing microRNAs into cultured cells and after deleting mir-223 in mouse neutrophils. The identities of the responsive proteins indicate that targeting is primarily through seed-matched sites located within favourable predicted contexts in 3′ untranslated regions. Hundreds of genes were directly repressed, albeit each to a modest degree, by individual microRNAs. Although some targets were repressed without detectable changes in mRNA levels, those translationally repressed by more than a third also displayed detectable mRNA destabilization, and, for the more highly repressed targets, mRNA destabilization usually comprised the major component of repression. The impact of microRNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output. MicroRNAs can regulate gene expression by either inhibiting translation of a messenger RNA, or inducing its degradation. While previous studies have measured regulation at the mRNA level, it was unknown how much regulation occurred at the protein level. Now two groups led by David Bartel and Nikolaus Rajewsky have used variants of the technique known as SILAC (stable isotope labelling with amino acids in cell culture) to measure proteome-wide changes in protein level as a function of expression of endogenous and exogenous microRNAs. They find that while microRNAs can directly repress the translation of hundreds of genes, additional indirect effects result in changes in expression of thousands of genes. Many of the changes observed are less than twofold in magnitude, however, indicating either directly or indirectly, microRNAs can act as rheostats to fine-tune protein synthesis to match the needs of the cell at any given time. In one of two studies, a technique known as SILAC is used to measure, on a large scale, changes in protein level as a function of expression of endogenous and exogenous miRNAs. It is found that although miRNAs directly repress the translation of hundreds of genes, additional indirect effects result in changes in expression of thousands of genes.

Journal ArticleDOI
04 Sep 2008-Nature
TL;DR: It is shown that a single miRNA can repress the production of hundreds of proteins, but that this repression is typically relatively mild, and the data suggest that a mi RNA can, by direct or indirect effects, tune protein synthesis from thousands of genes.
Abstract: Animal microRNAs (miRNAs) regulate gene expression by inhibiting translation and/or by inducing degradation of target messenger RNAs. It is unknown how much translational control is exerted by miRNAs on a genome-wide scale. We used a new proteomic approach to measure changes in synthesis of several thousand proteins in response to miRNA transfection or endogenous miRNA knockdown. In parallel, we quantified mRNA levels using microarrays. Here we show that a single miRNA can repress the production of hundreds of proteins, but that this repression is typically relatively mild. A number of known features of the miRNA-binding site such as the seed sequence also govern repression of human protein synthesis, and we report additional target sequence characteristics. We demonstrate that, in addition to downregulating mRNA levels, miRNAs also directly repress translation of hundreds of genes. Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes.

Journal ArticleDOI
22 May 2008-Nature
TL;DR: It is shown that extrinsic stimuli are dispensable for the derivation, propagation and pluripotency of ES cells and reveal that ES cells have an innate programme for self-replication that does not require extrinsics instruction.
Abstract: In the three decades since pluripotent mouse embryonic stem (ES) cells were first described they have been derived and maintained by using various empirical combinations of feeder cells, conditioned media, cytokines, growth factors, hormones, fetal calf serum, and serum extracts. Consequently ES-cell self-renewal is generally considered to be dependent on multifactorial stimulation of dedicated transcriptional circuitries, pre-eminent among which is the activation of STAT3 by cytokines (ref. 8). Here we show, however, that extrinsic stimuli are dispensable for the derivation, propagation and pluripotency of ES cells. Self-renewal is enabled by the elimination of differentiation-inducing signalling from mitogen-activated protein kinase. Additional inhibition of glycogen synthase kinase 3 consolidates biosynthetic capacity and suppresses residual differentiation. Complete bypass of cytokine signalling is confirmed by isolating ES cells genetically devoid of STAT3. These findings reveal that ES cells have an innate programme for self-replication that does not require extrinsic instruction. This property may account for their latent tumorigenicity. The delineation of minimal requirements for self-renewal now provides a defined platform for the precise description and dissection of the pluripotent state.

Journal ArticleDOI
12 Jun 2008-Nature
TL;DR: An overview of the current state of fMRI is given, and the current understanding of the haemodynamic signals and the constraints they impose on neuroimaging data interpretation are presented.
Abstract: Functional magnetic resonance imaging (fMRI) is currently the mainstay of neuroimaging in cognitive neuroscience. Advances in scanner technology, image acquisition protocols, experimental design, and analysis methods promise to push forward fMRI from mere cartography to the true study of brain organization. However, fundamental questions concerning the interpretation of fMRI data abound, as the conclusions drawn often ignore the actual limitations of the methodology. Here I give an overview of the current state of fMRI, and draw on neuroimaging and physiological data to present the current understanding of the haemodynamic signals and the constraints they impose on neuroimaging data interpretation.

Journal ArticleDOI
10 Jan 2008-Nature
TL;DR: The data demonstrate that defined factors can reprogramme human cells to pluripotency, and establish a method whereby patient-specific cells might be established in culture.
Abstract: Pluripotency pertains to the cells of early embryos that can generate all of the tissues in the organism. Embryonic stem cells are embryo-derived cell lines that retain pluripotency and represent invaluable tools for research into the mechanisms of tissue formation. Recently, murine fibroblasts have been reprogrammed directly to pluripotency by ectopic expression of four transcription factors (Oct4, Sox2, Klf4 and Myc) to yield induced pluripotent stem (iPS) cells. Using these same factors, we have derived iPS cells from fetal, neonatal and adult human primary cells, including dermal fibroblasts isolated from a skin biopsy of a healthy research subject. Human iPS cells resemble embryonic stem cells in morphology and gene expression and in the capacity to form teratomas in immune-deficient mice. These data demonstrate that defined factors can reprogramme human cells to pluripotency, and establish a method whereby patient-specific cells might be established in culture.

Journal ArticleDOI
17 Jan 2008-Nature
TL;DR: Past episodes of greenhouse warming provide insight into the coupling of climate and the carbon cycle and thus may help to predict the consequences of unabated carbon emissions in the future.
Abstract: Past episodes of greenhouse warming provide insight into the coupling of climate and the carbon cycle and thus may help to predict the consequences of unabated carbon emissions in the future.

Journal ArticleDOI
24 Apr 2008-Nature
TL;DR: In this article, the authors used incident-photon-energy-modulated angle-resolved photoemission spectroscopy (IPEM-ARPES) to locate the Kramers points at the sample's boundary and provide a comprehensive mapping of the Dirac insulator's gapless surface electron bands.
Abstract: When electrons are subject to a large external magnetic field, the conventional charge quantum Hall effect dictates that an electronic excitation gap is generated in the sample bulk, but metallic conduction is permitted at the boundary. Recent theoretical models suggest that certain bulk insulators with large spin-orbit interactions may also naturally support conducting topological boundary states in the quantum limit, which opens up the possibility for studying unusual quantum Hall-like phenomena in zero external magnetic fields. Bulk Bi(1-x)Sb(x) single crystals are predicted to be prime candidates for one such unusual Hall phase of matter known as the topological insulator. The hallmark of a topological insulator is the existence of metallic surface states that are higher-dimensional analogues of the edge states that characterize a quantum spin Hall insulator. In addition to its interesting boundary states, the bulk of Bi(1-x)Sb(x) is predicted to exhibit three-dimensional Dirac particles, another topic of heightened current interest following the new findings in two-dimensional graphene and charge quantum Hall fractionalization observed in pure bismuth. However, despite numerous transport and magnetic measurements on the Bi(1-x)Sb(x) family since the 1960s, no direct evidence of either topological Hall states or bulk Dirac particles has been found. Here, using incident-photon-energy-modulated angle-resolved photoemission spectroscopy (IPEM-ARPES), we report the direct observation of massive Dirac particles in the bulk of Bi(0.9)Sb(0.1), locate the Kramers points at the sample's boundary and provide a comprehensive mapping of the Dirac insulator's gapless surface electron bands. These findings taken together suggest that the observed surface state on the boundary of the bulk insulator is a realization of the 'topological metal'. They also suggest that this material has potential application in developing next-generation quantum computing devices that may incorporate 'light-like' bulk carriers and spin-textured surface currents.

Journal ArticleDOI
17 Jan 2008-Nature
TL;DR: With humans having an increasing impact on the planet, the interactions between the nitrogen cycle, the carbon cycle and climate are expected to become an increasingly important determinant of the Earth system.
Abstract: With humans having an increasing impact on the planet, the interactions between the nitrogen cycle, the carbon cycle and climate are expected to become an increasingly important determinant of the Earth system.

Journal ArticleDOI
Li Ding1, Gad Getz2, David A. Wheeler3, Elaine R. Mardis1, Michael D. McLellan1, Kristian Cibulskis2, Carrie Sougnez2, Heidi Greulich4, Heidi Greulich2, Donna M. Muzny3, Margaret Morgan3, Lucinda Fulton1, Robert S. Fulton1, Qunyuan Zhang1, Michael C. Wendl1, Michael S. Lawrence2, David E. Larson1, Ken Chen1, David J. Dooling1, Aniko Sabo3, Alicia Hawes3, Hua Shen3, Shalini N. Jhangiani3, Lora Lewis3, Otis Hall3, Yiming Zhu3, Tittu Mathew3, Yanru Ren3, Jiqiang Yao3, Steven E. Scherer3, Kerstin Clerc3, Ginger A. Metcalf3, Brian Ng3, Aleksandar Milosavljevic3, Manuel L. Gonzalez-Garay3, John R. Osborne1, Rick Meyer1, Xiaoqi Shi1, Yuzhu Tang1, Daniel C. Koboldt1, Ling Lin1, Rachel Abbott1, Tracie L. Miner1, Craig Pohl1, Ginger A. Fewell1, Carrie A. Haipek1, Heather Schmidt1, Brian H. Dunford-Shore1, Aldi T. Kraja1, Seth D. Crosby1, Christopher S. Sawyer1, Tammi L. Vickery1, Sacha N. Sander1, Jody S. Robinson1, Wendy Winckler2, Wendy Winckler4, Jennifer Baldwin2, Lucian R. Chirieac4, Amit Dutt2, Amit Dutt4, Timothy Fennell2, Megan Hanna4, Megan Hanna2, Bruce E. Johnson4, Robert C. Onofrio2, Roman K. Thomas5, Giovanni Tonon4, Barbara A. Weir4, Barbara A. Weir2, Xiaojun Zhao2, Xiaojun Zhao4, Liuda Ziaugra2, Michael C. Zody2, Thomas J. Giordano6, Mark B. Orringer6, Jack A. Roth, Margaret R. Spitz7, Ignacio I. Wistuba, Bradley A. Ozenberger8, Peter J. Good8, Andrew C. Chang6, David G. Beer6, Mark A. Watson1, Marc Ladanyi9, Stephen R. Broderick9, Akihiko Yoshizawa9, William D. Travis9, William Pao9, Michael A. Province1, George M. Weinstock1, Harold E. Varmus9, Stacey Gabriel2, Eric S. Lander2, Richard A. Gibbs3, Matthew Meyerson4, Matthew Meyerson2, Richard K. Wilson1 
23 Oct 2008-Nature
TL;DR: Somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B are found.
Abstract: Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.

Journal ArticleDOI
17 Apr 2008-Nature
TL;DR: It is demonstrated that a generic isolated quantum many-body system does relax to a state well described by the standard statistical-mechanical prescription, and it is shown that time evolution itself plays a merely auxiliary role in relaxation, and that thermalization instead happens at the level of individual eigenstates, as first proposed by Deutsch and Srednicki.
Abstract: It is demonstrated that an isolated generic quantum many-body system does relax to a state well described by the standard statistical mechanical prescription The thermalization happens at the level of individual eigenstates, allowing the computation of thermal averages from knowledge of any eigenstate in the microcanonical energy window An understanding of the temporal evolution of isolated many-body quantum systems has long been elusive Recently, meaningful experimental studies1,2 of the problem have become possible, stimulating theoretical interest3,4,5,6,7 In generic isolated systems, non-equilibrium dynamics is expected8,9 to result in thermalization: a relaxation to states in which the values of macroscopic quantities are stationary, universal with respect to widely differing initial conditions, and predictable using statistical mechanics However, it is not obvious what feature of many-body quantum mechanics makes quantum thermalization possible in a sense analogous to that in which dynamical chaos makes classical thermalization possible10 For example, dynamical chaos itself cannot occur in an isolated quantum system, in which the time evolution is linear and the spectrum is discrete11 Some recent studies4,5 even suggest that statistical mechanics may give incorrect predictions for the outcomes of relaxation in such systems Here we demonstrate that a generic isolated quantum many-body system does relax to a state well described by the standard statistical-mechanical prescription Moreover, we show that time evolution itself plays a merely auxiliary role in relaxation, and that thermalization instead happens at the level of individual eigenstates, as first proposed by Deutsch12 and Srednicki13 A striking consequence of this eigenstate-thermalization scenario, confirmed for our system, is that knowledge of a single many-body eigenstate is sufficient to compute thermal averages—any eigenstate in the microcanonical energy window will do, because they all give the same result

Journal ArticleDOI
10 Jan 2008-Nature
TL;DR: Independent measurements of the Seebeck coefficient, the electrical conductivity and the thermal conductivity, combined with theory, indicate that the improved efficiency originates from phonon effects, and these results are expected to apply to other classes of semiconductor nanomaterials.
Abstract: Thermoelectric materials, capable of converting a thermal gradient to an electric field and vice versa, could be useful in power generation and refrigeration. But the fabrication of the available high-performance thermoelectric materials is not easily scaled up to the volumes needed for large-scale heat energy scavenging applications. Nanostructuring improves thermoelectric capabilities of some materials, but good thermoelectric materials tend not to take readily to nanostructuring. How about silicon? It can be processed on a large scale but has poor thermoelectric properties. Two groups now show that silicon's thermoelectric properties can be vastly improved by structuring it into arrays of nanowires and carefully controlling nanowire morphology and doping. So with more development, silicon may have potential as a thermoelectric material. Thermoelectric materials interconvert thermal gradients and electric fields for power generation or for refrigeration1,2. Thermoelectrics currently find only niche applications because of their limited efficiency, which is measured by the dimensionless parameter ZT—a function of the Seebeck coefficient or thermoelectric power, and of the electrical and thermal conductivities. Maximizing ZT is challenging because optimizing one physical parameter often adversely affects another3. Several groups have achieved significant improvements in ZT through multi-component nanostructured thermoelectrics4,5,6, such as Bi2Te3/Sb2Te3 thin-film superlattices, or embedded PbSeTe quantum dot superlattices. Here we report efficient thermoelectric performance from the single-component system of silicon nanowires for cross-sectional areas of 10 nm × 20 nm and 20 nm × 20 nm. By varying the nanowire size and impurity doping levels, ZT values representing an approximately 100-fold improvement over bulk Si are achieved over a broad temperature range, including ZT ≈ 1 at 200 K. Independent measurements of the Seebeck coefficient, the electrical conductivity and the thermal conductivity, combined with theory, indicate that the improved efficiency originates from phonon effects. These results are expected to apply to other classes of semiconductor nanomaterials.

Journal ArticleDOI
15 Oct 2008-Nature
TL;DR: Recent studies combining behavioural, molecular and electrophysiological techniques reveal that certain aspects of depression result from maladaptive stress-induced neuroplastic changes in specific neural circuits and show that understanding the mechanisms of resilience to stress offers a crucial new dimension for the development of fundamentally novel antidepressant treatments.
Abstract: Unravelling the pathophysiology of depression is a unique challenge. Not only are depressive syndromes heterogeneous and their aetiologies diverse, but symptoms such as guilt and suicidality are impossible to reproduce in animal models. Nevertheless, other symptoms have been accurately modelled, and these, together with clinical data, are providing insight into the neurobiology of depression. Recent studies combining behavioural, molecular and electrophysiological techniques reveal that certain aspects of depression result from maladaptive stress-induced neuroplastic changes in specific neural circuits. They also show that understanding the mechanisms of resilience to stress offers a crucial new dimension for the development of fundamentally novel antidepressant treatments.

Journal ArticleDOI
13 Mar 2008-Nature
TL;DR: It is demonstrated that M2 expression is necessary for aerobic glycolysis and that this metabolic phenotype provides a selective growth advantage for tumour cells in vivo.
Abstract: Many tumour cells express the M2 form of pyruvate kinase rather than the usual M1 form. PKM2 is now shown to promote tumorigenesis and switch the cellular metabolism to increased lactate production and reduced oxygen consumption, recapitulating key aspects of the Warburg effect.

Journal ArticleDOI
14 May 2008-Nature
TL;DR: Knowing how organisms retain the ability to regenerate tissue throughout adult life might help to unlock latent regenerative pathways in humans, which would change medical practice as much as the introduction of antibiotics did in the twentieth century.
Abstract: The repair of wounds is one of the most complex biological processes that occur during human life. After an injury, multiple biological pathways immediately become activated and are synchronized to respond. In human adults, the wound repair process commonly leads to a non-functioning mass of fibrotic tissue known as a scar. By contrast, early in gestation, injured fetal tissues can be completely recreated, without fibrosis, in a process resembling regeneration. Some organisms, however, retain the ability to regenerate tissue throughout adult life. Knowledge gained from studying such organisms might help to unlock latent regenerative pathways in humans, which would change medical practice as much as the introduction of antibiotics did in the twentieth century.

Journal ArticleDOI
21 Feb 2008-Nature
TL;DR: The design and synthesis of molecules that associate together to form both chains and cross-links via hydrogen bonds and the system shows recoverable extensibility up to several hundred per cent and little creep under load are designed and synthesized.
Abstract: Rubbers exhibit enormous extensibility up to several hundred per cent, compared with a few per cent for ordinary solids, and have the ability to recover their original shape and dimensions on release of stress. Rubber elasticity is a property of macromolecules that are either covalently cross-linked or connected in a network by physical associations such as small glassy or crystalline domains, ionic aggregates or multiple hydrogen bonds. Covalent cross-links or strong physical associations prevent flow and creep. Here we design and synthesize molecules that associate together to form both chains and cross-links via hydrogen bonds. The system shows recoverable extensibility up to several hundred per cent and little creep under load. In striking contrast to conventional cross-linked or thermoreversible rubbers made of macromolecules, these systems, when broken or cut, can be simply repaired by bringing together fractured surfaces to self-heal at room temperature. Repaired samples recuperate their enormous extensibility. The process of breaking and healing can be repeated many times. These materials can be easily processed, re-used and recycled. Their unique self-repairing properties, the simplicity of their synthesis, their availability from renewable resources and the low cost of raw ingredients (fatty acids and urea) bode well for future applications.

Journal ArticleDOI
07 Aug 2008-Nature
TL;DR: Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.
Abstract: DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.