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Showing papers by "University of Queensland published in 2013"


Journal ArticleDOI
Ludmil B. Alexandrov1, Serena Nik-Zainal2, Serena Nik-Zainal3, David C. Wedge1, Samuel Aparicio4, Sam Behjati1, Sam Behjati5, Andrew V. Biankin, Graham R. Bignell1, Niccolo Bolli1, Niccolo Bolli5, Åke Borg2, Anne Lise Børresen-Dale6, Anne Lise Børresen-Dale7, Sandrine Boyault8, Birgit Burkhardt8, Adam Butler1, Carlos Caldas9, Helen Davies1, Christine Desmedt, Roland Eils5, Jorunn E. Eyfjord10, John A. Foekens11, Mel Greaves12, Fumie Hosoda13, Barbara Hutter5, Tomislav Ilicic1, Sandrine Imbeaud14, Sandrine Imbeaud15, Marcin Imielinsk14, Natalie Jäger5, David T. W. Jones16, David T. Jones1, Stian Knappskog17, Stian Knappskog11, Marcel Kool11, Sunil R. Lakhani18, Carlos López-Otín18, Sancha Martin1, Nikhil C. Munshi19, Nikhil C. Munshi20, Hiromi Nakamura13, Paul A. Northcott16, Marina Pajic21, Elli Papaemmanuil1, Angelo Paradiso22, John V. Pearson23, Xose S. Puente18, Keiran Raine1, Manasa Ramakrishna1, Andrea L. Richardson19, Andrea L. Richardson22, Julia Richter22, Philip Rosenstiel22, Matthias Schlesner5, Ton N. Schumacher24, Paul N. Span25, Jon W. Teague1, Yasushi Totoki13, Andrew Tutt24, Rafael Valdés-Mas18, Marit M. van Buuren25, Laura van ’t Veer26, Anne Vincent-Salomon27, Nicola Waddell23, Lucy R. Yates1, Icgc PedBrain24, Jessica Zucman-Rossi15, Jessica Zucman-Rossi14, P. Andrew Futreal1, Ultan McDermott1, Peter Lichter24, Matthew Meyerson19, Matthew Meyerson14, Sean M. Grimmond23, Reiner Siebert22, Elias Campo28, Tatsuhiro Shibata13, Stefan M. Pfister11, Stefan M. Pfister16, Peter J. Campbell29, Peter J. Campbell30, Peter J. Campbell3, Michael R. Stratton31, Michael R. Stratton3 
22 Aug 2013-Nature
TL;DR: It is shown that hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types, and this results reveal the diversity of mutational processes underlying the development of cancer.
Abstract: All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.

7,904 citations


Journal ArticleDOI
TL;DR: The Global Burden of Diseases, Injuries, and Risk Factors Study 2010 (GBD 2010) as discussed by the authors was used to estimate the burden of disease attributable to mental and substance use disorders in terms of disability-adjusted life years (DALYs), years of life lost to premature mortality (YLLs), and years lived with disability (YLDs).

4,753 citations


Journal ArticleDOI
TL;DR: The authors present severity proportions; burden by country, region, age, sex, and year; as well as burden of depressive disorders as a risk factor for suicide and ischemic heart disease.
Abstract: Background: Depressive disorders were a leading cause of burden in the Global Burden of Disease (GBD) 1990 and 2000 studies. Here, we analyze the burden of depressive disorders in GBD 2010 and present severity proportions, burden by country, region, age, sex, and year, as well as burden of depressive disorders as a risk factor for suicide and ischemic heart disease. Methods and Findings: Burden was calculated for major depressive disorder (MDD) and dysthymia. A systematic review of epidemiological data was conducted. The data were pooled using a Bayesian meta-regression. Disability weights from population survey data quantified the severity of health loss from depressive disorders. These weights were used to calculate years lived with disability (YLDs) and disability adjusted life years (DALYs). Separate DALYs were estimated for suicide and ischemic heart disease attributable to depressive disorders. Depressive disorders were the second leading cause of YLDs in 2010. MDD accounted for 8.2% (5.9%–10.8%) of global YLDs and dysthymia for 1.4% (0.9%–2.0%). Depressive disorders were a leading cause of DALYs even though no mortality was attributed to them as the underlying cause. MDD accounted for 2.5% (1.9%–3.2%) of global DALYs and dysthymia for 0.5% (0.3%–0.6%). There was more regional variation in burden for MDD than for dysthymia; with higher estimates in females, and adults of working age. Whilst burden increased by 37.5% between 1990 and 2010, this was due to population growth and ageing. MDD explained 16 million suicide DALYs and almost 4 million ischemic heart disease DALYs. This attributable burden would increase the overall burden of depressive disorders from 3.0% (2.2%–3.8%) to 3.8% (3.0%–4.7%) of global DALYs. Conclusions: GBD 2010 identified depressive disorders as a leading cause of burden. MDD was also a contributor of burden allocated to suicide and ischemic heart disease. These findings emphasize the importance of including depressive disorders as a public-health priority and implementing cost-effective interventions to reduce its burden. Please see later in the article for the Editors’ Summary.

2,240 citations


Journal ArticleDOI
S. Hong Lee1, Stephan Ripke2, Stephan Ripke3, Benjamin M. Neale3  +402 moreInstitutions (124)
TL;DR: Empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.
Abstract: Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.

2,058 citations


Journal ArticleDOI
29 Mar 2013-Science
TL;DR: Overall, wild insects pollinated crops more effectively; an increase in wild insect visitation enhanced fruit set by twice as much as an equivalent increase in honey bee visitation.
Abstract: The diversity and abundance of wild insect pollinators have declined in many agricultural landscapes. Whether such declines reduce crop yields, or are mitigated by managed pollinators such as honey bees, is unclear. We found universally positive associations of fruit set with flower visitation by wild insects in 41 crop systems worldwide. In contrast, fruit set increased significantly with flower visitation by honey bees in only 14% of the systems surveyed. Overall, wild insects pollinated crops more effectively; an increase in wild insect visitation enhanced fruit set by twice as much as an equivalent increase in honey bee visitation. Visitation by wild insects and honey bees promoted fruit set independently, so pollination by managed honey bees supplemented, rather than substituted for, pollination by wild insects. Our results suggest that new practices for integrated management of both honey bees and diverse wild insect assemblages will enhance global crop yields.

1,881 citations


Journal ArticleDOI
14 Jul 2013-Nature
TL;DR: This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet.
Abstract: Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.

1,856 citations


Journal ArticleDOI
TL;DR: Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.
Abstract: Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE), altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE. DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3' UTR levels of IKZF1 in cis, and chromatin immunoprecipitation and sequencing analysis of the trans-regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.

1,627 citations


Journal ArticleDOI
TL;DR: This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products.

1,560 citations


Journal ArticleDOI
TL;DR: In this article, a route for the controlled synthesis of mesoporous polymer nanospheres, which can be further converted into carbon nanosphere through carbonization, is presented.
Abstract: The controlled synthesis of monodisperse nanospheres faces a number of difficulties, such as extensive crosslinking during hydrothermal processes. Here, the authors show a route for the controlled synthesis of mesoporous polymer nanospheres, which can be further converted into carbon nanospheres through carbonization.

1,542 citations


Journal ArticleDOI
TL;DR: This article synthesized all available studies of the consistency of marine ecological observations with expectations under climate change This yielded a meta-database of 1,735 marine biological responses for which either regional or global climate change was considered as a driver.
Abstract: Research that combines all available studies of biological responses to regional and global climate change shows that 81–83% of all observations were consistent with the expected impacts of climate change These findings were replicated across taxa and oceanic basins Past meta-analyses of the response of marine organisms to climate change have examined a limited range of locations1,2, taxonomic groups2,3,4 and/or biological responses5,6 This has precluded a robust overview of the effect of climate change in the global ocean Here, we synthesized all available studies of the consistency of marine ecological observations with expectations under climate change This yielded a meta-database of 1,735 marine biological responses for which either regional or global climate change was considered as a driver Included were instances of marine taxa responding as expected, in a manner inconsistent with expectations, and taxa demonstrating no response From this database, 81–83% of all observations for distribution, phenology, community composition, abundance, demography and calcification across taxa and ocean basins were consistent with the expected impacts of climate change Of the species responding to climate change, rates of distribution shifts were, on average, consistent with those required to track ocean surface temperature changes Conversely, we did not find a relationship between regional shifts in spring phenology and the seasonality of temperature Rates of observed shifts in species’ distributions and phenology are comparable to, or greater, than those for terrestrial systems

1,504 citations


Journal ArticleDOI
TL;DR: The collective vision of the future of extracellular enzyme research is offered: one that will depend on imaginative thinking as well as technological advances, and be built upon synergies between diverse disciplines.
Abstract: This review focuses on some important and challenging aspects of soil extracellular enzyme research. We report on recent discoveries, identify key research needs and highlight the many opportunities offered by interactions with other microbial enzymologists. The biggest challenges are to understand how the chemical, physical and biological properties of soil affect enzyme production, diffusion, substrate turnover and the proportion of the product that is made available to the producer cells. Thus, the factors that regulate the synthesis and secretion of extracellular enzymes and their distribution after they are externalized are important topics, not only for soil enzymologists, but also in the broader context of microbial ecology. In addition, there are many uncertainties about the ways in which microbes and their extracellular enzymes overcome the generally destructive, inhibitory and competitive properties of the soil matrix, and the various strategies they adopt for effective substrate detection and utilization. The complexity of extracellular enzyme activities in depolymerising macromolecular organics is exemplified by lignocellulose degradation and how the many enzymes involved respond to structural diversity and changing nutrient availabilities. The impacts of climate change on microbes and their extracellular enzymes, although of profound importance, are not well understood but we suggest how they may be predicted, assessed and managed. We describe recent advances that allow for the manipulation of extracellular enzyme activities to facilitate bioremediation, carbon sequestration and plant growth promotion. We also contribute to the ongoing debate as to how to assay enzyme activities in soil and what the measurements tell us, in the context of both traditional methods and the newer techniques that are being developed and adopted. Finally, we offer our collective vision of the future of extracellular enzyme research: one that will depend on imaginative thinking as well as technological advances, and be built upon synergies between diverse disciplines.

Journal ArticleDOI
TL;DR: This review focuses on the deposition process, the parameters and demands of hydrogels in biofabrication, with special attention to robotic dispensing as an approach that generates constructs of clinically relevant dimensions.
Abstract: With advances in tissue engineering, the possibility of regenerating injured tissue or failing organs has become a realistic prospect for the first time in medical history. Tissue engineering - the combination of bioactive materials with cells to generate engineered constructs that functionally replace lost and/or damaged tissue - is a major strategy to achieve this goal. One facet of tissue engineering is biofabrication, where three-dimensional tissue-like structures composed of biomaterials and cells in a single manufacturing procedure are generated. Cell-laden hydrogels are commonly used in biofabrication and are termed "bioinks". Hydrogels are particularly attractive for biofabrication as they recapitulate several features of the natural extracellular matrix and allow cell encapsulation in a highly hydrated mechanically supportive three-dimensional environment. Additionally, they allow for efficient and homogeneous cell seeding, can provide biologically-relevant chemical and physical signals, and can be formed in various shapes and biomechanical characteristics. However, despite the progress made in modifying hydrogels for enhanced bioactivation, cell survival and tissue formation, little attention has so far been paid to optimize hydrogels for the physico-chemical demands of the biofabrication process. The resulting lack of hydrogel bioinks have been identified as one major hurdle for a more rapid progress of the field. In this review we summarize and focus on the deposition process, the parameters and demands of hydrogels in biofabrication, with special attention to robotic dispensing as an approach that generates constructs of clinically relevant dimensions. We aim to highlight this current lack of effectual hydrogels within biofabrication and initiate new ideas and developments in the design and tailoring of hydrogels. The successful development of a "printable" hydrogel that supports cell adhesion, migration, and differentiation will significantly advance this exciting and promising approach for tissue engineering.

Journal ArticleDOI
TL;DR: The suite of currently used drugs can be divided into two categories - traditional'small molecule' drugs with typical molecular weights of 5000 Da that are not orally bioavailable and need to be delivered via injection as mentioned in this paper.
Abstract: The suite of currently used drugs can be divided into two categories - traditional 'small molecule' drugs with typical molecular weights of 5000 Da that are not orally bioavailable and need to be delivered via injection. Due to their small size, conventional small molecule drugs may suffer from reduced target selectivity that often ultimately manifests in human side-effects, whereas protein therapeutics tend to be exquisitely specific for their targets due to many more interactions with them, but this comes at a cost of low bioavailability, poor membrane permeability, and metabolic instability. The time has now come to reinvestigate new drug leads that fit between these two molecular weight extremes, with the goal of combining advantages of small molecules (cost, conformational restriction, membrane permeability, metabolic stability, oral bioavailability) with those of proteins (natural components, target specificity, high potency). This article uses selected examples of peptides to highlight the importance of peptide drugs, some potential new opportunities for their exploitation, and some difficult challenges ahead in this field.

Journal ArticleDOI
TL;DR: It is proposed that species distribution modellers should get involved in real decision-making processes that will benefit from their technical input and have the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.
Abstract: Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on-ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision-making contexts when used within a structured and transparent decision-making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of 'translators' between modellers and decision makers. We encourage species distribution modellers to get involved in real decision-making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.

Journal ArticleDOI
Stephan Ripke1, Stephan Ripke2, Colm O'Dushlaine2, Kimberly Chambert2, Jennifer L. Moran2, Anna K. Kähler3, Anna K. Kähler4, Anna K. Kähler5, Susanne Akterin5, Sarah E. Bergen5, Ann L. Collins3, James J. Crowley3, Menachem Fromer1, Menachem Fromer6, Menachem Fromer2, Yunjung Kim3, Sang Hong Lee7, Patrik K. E. Magnusson5, Nicholas E. Sanchez2, Eli A. Stahl6, Stephanie Williams3, Naomi R. Wray7, Kai Xia3, F Bettella8, Anders D. Børglum9, Anders D. Børglum10, Anders D. Børglum11, Brendan Bulik-Sullivan1, Paul Cormican12, Nicholas John Craddock13, Christiaan de Leeuw14, Christiaan de Leeuw15, Naser Durmishi, Michael Gill12, Vera Golimbet16, Marian L. Hamshere13, Peter Holmans13, David M. Hougaard17, Kenneth S. Kendler18, Kuang Fei Lin19, Derek W. Morris12, Ole Mors9, Ole Mors11, Preben Bo Mortensen10, Preben Bo Mortensen9, Benjamin M. Neale2, Benjamin M. Neale1, Francis A. O'Neill20, Michael John Owen13, MilicaPejovic Milovancevic21, Danielle Posthuma22, Danielle Posthuma15, John Powell19, Alexander Richards13, Brien P. Riley18, Douglas M. Ruderfer6, Dan Rujescu23, Dan Rujescu24, Engilbert Sigurdsson25, Teimuraz Silagadze26, August B. Smit15, Hreinn Stefansson8, Stacy Steinberg8, Jaana Suvisaari27, Sarah Tosato28, Matthijs Verhage15, James T.R. Walters13, Elvira Bramon19, Elvira Bramon29, Aiden Corvin12, Michael Conlon O'Donovan13, Kari Stefansson8, Edward M. Scolnick2, Shaun Purcell, Steve McCarroll2, Steve McCarroll1, Pamela Sklar6, Christina M. Hultman5, Patrick F. Sullivan5, Patrick F. Sullivan3 
TL;DR: The authors conducted a multi-stage genome-wide association study (GWAS) for schizophrenia and found that 8,300 independent, mostly common SNPs (95% credible interval of 6,300-10,200 SNPs) contribute to risk for schizophrenia.
Abstract: Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases and 6,243 controls) followed by meta-Analysis with previous schizophrenia GWAS (8,832 cases and 12,067 controls) and finally by replication of SNPs in 168 genomic regions in independent samples (7,413 cases, 19,762 controls and 581 parent-offspring trios). We identified 22 loci associated at genome-wide significance; 13 of these are new, and 1 was previously implicated in bipolar disorder. Examination of candidate genes at these loci suggests the involvement of neuronal calcium signaling. We estimate that 8,300 independent, mostly common SNPs (95% credible interval of 6,300-10,200 SNPs) contribute to risk for schizophrenia and that these collectively account for at least 32% of the variance in liability. Common genetic variation has an important role in the etiology of schizophrenia, and larger studies will allow more detailed understanding of this disorder.

Proceedings ArticleDOI
01 Jan 2013
TL;DR: A versatile, scalable, yet powerful general-purpose robot simulation framework called V-REP, which allows for direct incorporation of various control techniques and renders simulations and simulation models more accessible to a general-public, by reducing the simulation model deployment complexity.
Abstract: From exploring planets to cleaning homes, the reach and versatility of robotics is vast. The integration of actuation, sensing and control makes robotics systems powerful, but complicates their simulation. This paper introduces a versatile, scalable, yet powerful general-purpose robot simulation framework called V-REP. The paper discusses the utility of a portable and flexible simulation framework that allows for direct incorporation of various control techniques. This renders simulations and simulation models more accessible to a general-public, by reducing the simulation model deployment complexity. It also increases productivity by offering built-in and ready-to-use functionalities, as well as a multitude of programming approaches. This allows for a multitude of applications including rapid algorithm development, system verification, rapid prototyping, and deployment for cases such as safety/remote monitoring, training and education, hardware control, and factory automation simulation.

Journal ArticleDOI
TL;DR: It is concluded that the double arcsine transformation is preferred over the logit, and that the MetaXL implementation of multiple category prevalence is an improvement in the methodology of the meta-analysis of prevalence.
Abstract: Meta-analysis is a method to obtain a weighted average of results from various studies. In addition to pooling effect sizes, meta-analysis can also be used to estimate disease frequencies, such as incidence and prevalence. In this article we present methods for the meta-analysis of prevalence. We discuss the logit and double arcsine transformations to stabilise the variance. We note the special situation of multiple category prevalence, and propose solutions to the problems that arise. We describe the implementation of these methods in the MetaXL software, and present a simulation study and the example of multiple sclerosis from the Global Burden of Disease 2010 project. We conclude that the double arcsine transformation is preferred over the logit, and that the MetaXL implementation of multiple category prevalence is an improvement in the methodology of the meta-analysis of prevalence.

Journal ArticleDOI
TL;DR: This work focuses on the well-characterized ability for lncRNAs to function as epigenetic modulators, and suggests that lnc RNAs may be part of a broad epigenetic regulatory network.
Abstract: Genomes of complex organisms encode an abundance and diversity of long noncoding RNAs (lncRNAs) that are expressed throughout the cell and fulfill a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass sensory, guiding, scaffolding and allosteric capacities, derive from folded modular domains in lncRNAs. In this diverse functional repertoire, we focus on the well-characterized ability for lncRNAs to function as epigenetic modulators. Many lncRNAs bind to chromatin-modifying proteins and recruit their catalytic activity to specific sites in the genome, thereby modulating chromatin states and impacting gene expression. Considering this regulatory potential in combination with the abundance of lncRNAs suggests that lncRNAs may be part of a broad epigenetic regulatory network.

Journal ArticleDOI
TL;DR: The global burden of untreated caries, severe periodontitis, and severe tooth loss in 2010 is reported on and the challenge in responding to the diversity of urgent oral health needs worldwide is highlighted, particularly in developing communities.
Abstract: The Global Burden of Disease (GBD) 2010 Study produced comparable estimates of the burden of 291 diseases and injuries in 1990, 2005, and 2010. This article reports on the global burden of untreated caries, severe periodontitis, and severe tooth loss in 2010 and compares those figures with new estimates for 1990. We used disability-adjusted life-years (DALYs) and years lived with disability (YLDs) metrics to quantify burden. Oral conditions affected 3.9 billion people, and untreated caries in permanent teeth was the most prevalent condition evaluated for the entire GBD 2010 Study (global prevalence of 35% for all ages combined). Oral conditions combined accounted for 15 million DALYs globally (1.9% of all YLDs; 0.6% of all DALYs), implying an average health loss of 224 years per 100,000 population. DALYs due to oral conditions increased 20.8% between 1990 and 2010, mainly due to population growth and aging. While DALYs due to severe periodontitis and untreated caries increased, those due to severe tooth loss decreased. DALYs differed by age groups and regions, but not by genders. The findings highlight the challenge in responding to the diversity of urgent oral health needs worldwide, particularly in developing communities.

Journal ArticleDOI
TL;DR: Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition.
Abstract: Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition-independent approach to recover high-quality microbial genomes from deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition. This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms.

Journal ArticleDOI
TL;DR: The authors explore opportunities for an integrated approach in community resilience to inform new research directions and practice, using the productive common ground between two strands of literature on community resilience, one from social-ecological systems and the other from the psychology of development and mental health.
Abstract: We explore opportunities for an integrated approach in community resilience to inform new research directions and practice, using the productive common ground between two strands of literature on community resilience, one from social–ecological systems and the other from the psychology of development and mental health. The first strand treats resilience as a systems concept, dealing with adaptive relationships and learning in social–ecological systems across nested levels, with attention to feedbacks, nonlinearity, unpredictability, scale, renewal cycles, drivers, system memory, disturbance events, and windows of opportunity. The second strand emphasizes identifying and developing community strengths, and building resilience through agency and self-organization, with attention to people–place connections, values and beliefs, knowledge and learning, social networks, collaborative governance, economic diversification, infrastructure, leadership, and outlook. An integrative approach seated in the complex ada...

Journal ArticleDOI
Abstract: Plants that accumulate metal and metalloid trace elements to extraordinarily high concentrations in their living biomass have inspired much research worldwide during the last decades. Hyperaccumulators have been recorded and experimentally confirmed for elements such as nickel, zinc, cadmium, manganese, arsenic and selenium. However, to date, hyperaccumulation of lead, copper, cobalt, chromium and thallium remain largely unconfirmed. Recent uses of the term in relation to rare-earth elements require critical evaluation. Since the mid-1970s the term ‘hyperaccumulator’ has been used millions of times by thousands of people, with varying degrees of precision, aptness and understanding that have not always corresponded with the views of the originators of the terminology and of the present authors. There is therefore a need to clarify the circumstances in which the term ‘hyperaccumulator’ is appropriate and to set out the conditions that should be met when the terms are used. We outline here the main considerations for establishing metal or metalloid hyperaccumulation status of plants, (re)define some of the terminology and note potential pitfalls. Unambiguous communication will require the international scientific community to adopt standard terminology and methods for confirming the reliability of analytical data in relation to metal and metalloid hyperaccumulators.

Journal ArticleDOI
TL;DR: In this paper, the authors review what we know and don't know about Generation Y's use of social media and assess the implications for individuals, firms and society, and develop managerial implications and a research agenda.
Abstract: Purpose – The purpose of this paper is to review what we know – and don't know – about Generation Y's use of social media and to assess the implications for individuals, firms and society.Design/methodology/approach – The paper distinguishes Generation Y from other cohorts in terms of systematic differences in values, preferences and behavior that are stable over time (as opposed to maturational or other differences). It describes their social media use and highlights evidence of intra‐generational variance arising from environmental factors (including economic, cultural, technological and political/legal factors) and individual factors. Individual factors include stable factors (including socio‐economic status, age and lifecycle stage) and dynamic, endogenous factors (including goals, emotions, and social norms).The paper discusses how Generation Y's use of social media influences individuals, firms and society. It develops managerial implications and a research agenda.Findings – Prior research on the so...

Journal ArticleDOI
TL;DR: This work reports the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes, and identifies targets of both breeding-associated genetic sweeps and breeding- associated balancing selection.
Abstract: Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

Journal ArticleDOI
TL;DR: It is found the landscape approach has been refined in response to increasing societal concerns about environment and development tradeoffs and there has been a shift from conservation-orientated perspectives toward increasing integration of poverty alleviation goals.
Abstract: “Landscape approaches” seek to provide tools and concepts for allocating and managing land to achieve social, economic, and environmental objectives in areas where agriculture, mining, and other productive land uses compete with environmental and biodiversity goals. Here we synthesize the current consensus on landscape approaches. This is based on published literature and a consensus-building process to define good practice and is validated by a survey of practitioners. We find the landscape approach has been refined in response to increasing societal concerns about environment and development tradeoffs. Notably, there has been a shift from conservation-orientated perspectives toward increasing integration of poverty alleviation goals. We provide 10 summary principles to support implementation of a landscape approach as it is currently interpreted. These principles emphasize adaptive management, stakeholder involvement, and multiple objectives. Various constraints are recognized, with institutional and governance concerns identified as the most severe obstacles to implementation. We discuss how these principles differ from more traditional sectoral and project-based approaches. Although no panacea, we see few alternatives that are likely to address landscape challenges more effectively than an approach circumscribed by the principles outlined here.

Journal ArticleDOI
TL;DR: Anxiety disorders are common and the substantive and methodological factors identified here explain much of the variability in prevalence estimates, and specific attention should be paid to cultural differences in responses to survey instruments for anxiety disorders.
Abstract: BackgroundThe literature describing the global prevalence of anxiety disorders is highly variable. A systematic review and meta-regression were undertaken to estimate the prevalence of anxiety disorders and to identify factors that may influence these estimates. The findings will inform the new Global Burden of Disease study.MethodA systematic review identified prevalence studies of anxiety disorders published between 1980 and 2009. Electronic databases, reference lists, review articles and monographs were searched and experts then contacted to identify missing studies. Substantive and methodological factors associated with inter-study variability were identified through meta-regression analyses and the global prevalence of anxiety disorders was calculated adjusting for study methodology.ResultsThe prevalence of anxiety disorders was obtained from 87 studies across 44 countries. Estimates of current prevalence ranged between 0.9% and 28.3% and past-year prevalence between 2.4% and 29.8%. Substantive factors including gender, age, culture, conflict and economic status, and urbanicity accounted for the greatest proportion of variability. Methodological factors in the final multivariate model (prevalence period, number of disorders and diagnostic instrument) explained an additional 13% of variance between studies. The global current prevalence of anxiety disorders adjusted for methodological differences was 7.3% (4.8–10.9%) and ranged from 5.3% (3.5–8.1%) in African cultures to 10.4% (7.0–15.5%) in Euro/Anglo cultures.ConclusionsAnxiety disorders are common and the substantive and methodological factors identified here explain much of the variability in prevalence estimates. Specific attention should be paid to cultural differences in responses to survey instruments for anxiety disorders.

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TL;DR: Graphene was doped with both boron and nitrogen at well-defined doping sites to induce a synergistic effect that boosts its catalytic activity for oxygen reduction.
Abstract: Don't be a dope: be a double dope! Graphene was doped with both boron and nitrogen at well-defined doping sites to induce a synergistic effect that boosts its catalytic activity for oxygen reduction (see structure). The excellent catalytic performance of the new metal-free catalyst is comparable to that of commercial Pt/C.

Journal ArticleDOI
29 Aug 2013-Nature
TL;DR: Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and 13C- and 15N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor and Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME -2d.
Abstract: An anaerobic methanotroph (ANME-2d) can perform nitrate-driven anaerobic oxidation of methane through reverse methanogenesis, using nitrate as the terminal electron acceptor, and nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium. Microbes capable of the anaerobic oxidation of methane (AOM) are important for controlling the flux of methane from anoxic marine sediments. Recent work has demonstrated AOM coupled to sulphate reduction in a consortium of ANME (anaerobic methanotrophic archaea) and sulphate-reducing bacteria, and coupled to nitrite reduction in consortia enriched with the bacterium Candidatus Methylomirabilis oxyfera and the novel ANME-2d lineage. Here Gene Tyson and colleagues show that a novel ANME-2d archaeon, which they name Candidatus Methanoperedens nitroreducens, is able to performing nitrate-driven AOM without a partner organism via reverse methanogenesis with nitrate as the terminal electron acceptor, using genes for nitrate reduction that have been laterally transferred from a bacterial donor. The authors speculate that ANME- 2d or Methanoperedenaceae lineage may have a pivotal role in linking the global carbon and nitrogen cycles in anoxic environments. Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron1, manganese1 and sulphate2 reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus ‘Methylomirabilis oxyfera’ can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway3. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of ‘M. oxyfera’ and a novel ANME lineage, ANME-2d4,5. However, as ‘M. oxyfera’ can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and 13C- and 15N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting ‘M. oxyfera’ in the system. We propose the name Candidatus ‘Methanoperedens nitroreducens’ for the ANME-2d population and the family Candidatus ‘Methanoperedenaceae’ for the ANME-2d lineage. We predict that ‘M. nitroreducens’ and other members of the ‘Methanoperedenaceae’ have an important role in linking the global carbon and nitrogen cycles in anoxic environments.

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TL;DR: This synthesis reveals that pollinator persistence will depend on both the maintenance of high-quality habitats around farms and on local management practices that may offset impacts of intensive monoculture agriculture.
Abstract: Bees provide essential pollination services that are potentially affected both by local farm management and the surrounding landscape. To better understand these different factors, we modelled the relative effects of landscape composition (nesting and floral resources within foraging distances), landscape configuration (patch shape, interpatch connectivity and habitat aggregation) and farm management (organic vs. conventional and local-scale field diversity), and their interactions, on wild bee abundance and richness for 39 crop systems globally. Bee abundance and richness were higher in diversified and organic fields and in landscapes comprising more high-quality habitats; bee richness on conventional fields with low diversity benefited most from high-quality surrounding land cover. Landscape configuration effects were weak. Bee responses varied slightly by biome. Our synthesis reveals that pollinator persistence will depend on both the maintenance of high-quality habitats around farms and on local management practices that may offset impacts of intensive monoculture agriculture.

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TL;DR: The risk of death from cigarette smoking continues to increase among women and the increased risks are now nearly identical for men and women, as compared with persons who have never smoked.
Abstract: Background The disease risks from cigarette smoking increased in the United States over most of the 20th century, first among male smokers and later among female smokers. Whether these risks have continued to increase during the past 20 years is unclear. Methods We measured temporal trends in mortality across three time periods (1959-1965, 1982-1988, and 2000-2010), comparing absolute and relative risks according to sex and self-reported smoking status in two historical cohort studies and in five pooled contemporary cohort studies, among participants who became 55 years of age or older during follow-up. Results For women who were current smokers, as compared with women who had never smoked, the relative risks of death from lung cancer were 2.73, 12.65, and 25.66 in the 1960s, 1980s, and contemporary cohorts, respectively; corresponding relative risks for male current smokers, as compared with men who had never smoked, were 12.22, 23.81, and 24.97. In the contemporary cohorts, male and female current smokers also had similar relative risks for death from chronic obstructive pulmonary disease (COPD) (25.61 for men and 22.35 for women), ischemic heart disease (2.50 for men and 2.86 for women), any type of stroke (1.92 for men and 2.10 for women), and all causes combined (2.80 for men and 2.76 for women). Mortality from COPD among male smokers continued to increase in the contemporary cohorts in nearly all the age groups represented in the study and within each stratum of duration and intensity of smoking. Among men 55 to 74 years of age and women 60 to 74 years of age, all-cause mortality was at least three times as high among current smokers as among those who had never smoked. Smoking cessation at any age dramatically reduced death rates. Conclusions The risk of death from cigarette smoking continues to increase among women and the increased risks are now nearly identical for men and women, as compared with persons who have never smoked. Among men, the risks associated with smoking have plateaued at the high levels seen in the 1980s, except for a continuing, unexplained increase in mortality from COPD.