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Showing papers by "University of Aberdeen published in 2011"


Journal ArticleDOI
Jens Kattge1, Sandra Díaz2, Sandra Lavorel3, Iain Colin Prentice4, Paul Leadley5, Gerhard Bönisch1, Eric Garnier3, Mark Westoby4, Peter B. Reich6, Peter B. Reich7, Ian J. Wright4, Johannes H. C. Cornelissen8, Cyrille Violle3, Sandy P. Harrison4, P.M. van Bodegom8, Markus Reichstein1, Brian J. Enquist9, Nadejda A. Soudzilovskaia8, David D. Ackerly10, Madhur Anand11, Owen K. Atkin12, Michael Bahn13, Timothy R. Baker14, Dennis D. Baldocchi10, Renée M. Bekker15, Carolina C. Blanco16, Benjamin Blonder9, William J. Bond17, Ross A. Bradstock18, Daniel E. Bunker19, Fernando Casanoves20, Jeannine Cavender-Bares6, Jeffrey Q. Chambers21, F. S. Chapin22, Jérôme Chave3, David A. Coomes23, William K. Cornwell8, Joseph M. Craine24, B. H. Dobrin9, Leandro da Silva Duarte16, Walter Durka25, James J. Elser26, Gerd Esser27, Marc Estiarte28, William F. Fagan29, Jingyun Fang, Fernando Fernández-Méndez30, Alessandra Fidelis31, Bryan Finegan20, Olivier Flores32, H. Ford33, Dorothea Frank1, Grégoire T. Freschet34, Nikolaos M. Fyllas14, Rachael V. Gallagher4, Walton A. Green35, Alvaro G. Gutiérrez25, Thomas Hickler, Steven I. Higgins36, John G. Hodgson37, Adel Jalili, Steven Jansen38, Carlos Alfredo Joly39, Andrew J. Kerkhoff40, Don Kirkup41, Kaoru Kitajima42, Michael Kleyer43, Stefan Klotz25, Johannes M. H. Knops44, Koen Kramer, Ingolf Kühn16, Hiroko Kurokawa45, Daniel C. Laughlin46, Tali D. Lee47, Michelle R. Leishman4, Frederic Lens48, Tanja Lenz4, Simon L. Lewis14, Jon Lloyd14, Jon Lloyd49, Joan Llusià28, Frédérique Louault50, Siyan Ma10, Miguel D. Mahecha1, Peter Manning51, Tara Joy Massad1, Belinda E. Medlyn4, Julie Messier9, Angela T. Moles52, Sandra Cristina Müller16, Karin Nadrowski53, Shahid Naeem54, Ülo Niinemets55, S. Nöllert1, A. Nüske1, Romà Ogaya28, Jacek Oleksyn56, Vladimir G. Onipchenko57, Yusuke Onoda58, Jenny C. Ordoñez59, Gerhard E. Overbeck16, Wim A. Ozinga59, Sandra Patiño14, Susana Paula60, Juli G. Pausas60, Josep Peñuelas28, Oliver L. Phillips14, Valério D. Pillar16, Hendrik Poorter, Lourens Poorter59, Peter Poschlod61, Andreas Prinzing62, Raphaël Proulx63, Anja Rammig64, Sabine Reinsch65, Björn Reu1, Lawren Sack66, Beatriz Salgado-Negret20, Jordi Sardans28, Satomi Shiodera67, Bill Shipley68, Andrew Siefert69, Enio E. Sosinski70, Jean-François Soussana50, Emily Swaine71, Nathan G. Swenson72, Ken Thompson37, Peter E. Thornton73, Matthew S. Waldram74, Evan Weiher47, Michael T. White75, S. White11, S. J. Wright76, Benjamin Yguel3, Sönke Zaehle1, Amy E. Zanne77, Christian Wirth58 
Max Planck Society1, National University of Cordoba2, Centre national de la recherche scientifique3, Macquarie University4, University of Paris-Sud5, University of Minnesota6, University of Western Sydney7, VU University Amsterdam8, University of Arizona9, University of California, Berkeley10, University of Guelph11, Australian National University12, University of Innsbruck13, University of Leeds14, University of Groningen15, Universidade Federal do Rio Grande do Sul16, University of Cape Town17, University of Wollongong18, New Jersey Institute of Technology19, Centro Agronómico Tropical de Investigación y Enseñanza20, Lawrence Berkeley National Laboratory21, University of Alaska Fairbanks22, University of Cambridge23, Kansas State University24, Helmholtz Centre for Environmental Research - UFZ25, Arizona State University26, University of Giessen27, Autonomous University of Barcelona28, University of Maryland, College Park29, Universidad del Tolima30, University of São Paulo31, University of La Réunion32, University of York33, University of Sydney34, Harvard University35, Goethe University Frankfurt36, University of Sheffield37, University of Ulm38, State University of Campinas39, Kenyon College40, Royal Botanic Gardens41, University of Florida42, University of Oldenburg43, University of Nebraska–Lincoln44, Tohoku University45, Northern Arizona University46, University of Wisconsin–Eau Claire47, Naturalis48, James Cook University49, Institut national de la recherche agronomique50, Newcastle University51, University of New South Wales52, Leipzig University53, Columbia University54, Estonian University of Life Sciences55, Polish Academy of Sciences56, Moscow State University57, Kyushu University58, Wageningen University and Research Centre59, Spanish National Research Council60, University of Regensburg61, University of Rennes62, Université du Québec à Trois-Rivières63, Potsdam Institute for Climate Impact Research64, Technical University of Denmark65, University of California, Los Angeles66, Hokkaido University67, Université de Sherbrooke68, Syracuse University69, Empresa Brasileira de Pesquisa Agropecuária70, University of Aberdeen71, Michigan State University72, Oak Ridge National Laboratory73, University of Leicester74, Utah State University75, Smithsonian Institution76, University of Missouri77
01 Sep 2011
TL;DR: TRY as discussed by the authors is a global database of plant traits, including morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs, which can be used for a wide range of research from evolutionary biology, community and functional ecology to biogeography.
Abstract: Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

2,017 citations



Journal ArticleDOI
TL;DR: The authors examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects.
Abstract: We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 x 10(-11)) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 x 10(-9)), ANK3 (rs10994359, P = 2.5 x 10(-8)) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 x 10(-9)).

1,671 citations


Journal ArticleDOI
TL;DR: This taxonomy can be used to improve the specification of interventions in published reports, thus improving replication, implementation and evidence syntheses and will strengthen the scientific study of behaviour change and intervention development.
Abstract: Background: Current reporting of intervention content in published research articles and protocols is generally poor, with great diversity of terminology, resulting in low replicability. This study aimed to extend the scope and improve the reliability of a 26-item taxonomy of behaviour change techniques developed by Abraham and Michie [Abraham, C. and Michie, S. (2008). A taxonomy of behaviour change techniques used in interventions. Health Psychology, 27(3), 379–387.] in order to optimise the reporting and scientific study of behaviour change interventions. Methods: Three UK study centres collaborated in applying this existing taxonomy to two systematic reviews of interventions to increase physical activity and healthy eating. The taxonomy was refined in iterative steps of (1) coding intervention descriptions, and assessing inter-rater reliability, (2) identifying gaps and problems across study centres and (3) refining the labels and definitions based on consensus discussions. Results: Labels and definit...

1,461 citations


Journal ArticleDOI
TL;DR: Time courses obtained by targeted qPCR revealed that ‘blooms’ in specific bacterial groups occurred rapidly after a dietary change, and these were rapidly reversed by the subsequent diet.
Abstract: The populations of dominant species within the human colonic microbiota can potentially be modified by dietary intake with consequences for health. Here we examined the influence of precisely controlled diets in 14 overweight men. Volunteers were provided successively with a control diet, diets high in resistant starch (RS) or non-starch polysaccharides (NSPs) and a reduced carbohydrate weight loss (WL) diet, over 10 weeks. Analysis of 16S rRNA sequences in stool samples of six volunteers detected 320 phylotypes (defined at >98% identity) of which 26, including 19 cultured species, each accounted for >1% of sequences. Although samples clustered more strongly by individual than by diet, time courses obtained by targeted qPCR revealed that 'blooms' in specific bacterial groups occurred rapidly after a dietary change. These were rapidly reversed by the subsequent diet. Relatives of Ruminococcus bromii (R-ruminococci) increased in most volunteers on the RS diet, accounting for a mean of 17% of total bacteria compared with 3.8% on the NSP diet, whereas the uncultured Oscillibacter group increased on the RS and WL diets. Relatives of Eubacterium rectale increased on RS (to mean 10.1%) but decreased, along with Collinsella aerofaciens, on WL. Inter-individual variation was marked, however, with >60% of RS remaining unfermented in two volunteers on the RS diet, compared to <4% in the other 12 volunteers; these two individuals also showed low numbers of R-ruminococci (<1%). Dietary non-digestible carbohydrate can produce marked changes in the gut microbiota, but these depend on the initial composition of an individual's gut microbiota.

1,443 citations


Journal ArticleDOI
Pamela Sklar1, Pamela Sklar2, Stephan Ripke3, Stephan Ripke2  +189 moreInstitutions (51)
TL;DR: An analysis of all 11,974 bipolar disorder cases and 51,792 controls confirmed genome-wide significant evidence of association for CACNA1C and identified a new intronic variant in ODZ4, and a pathway comprised of subunits of calcium channels enriched in bipolar disorder association intervals was identified.
Abstract: We conducted a combined genome-wide association study (GWAS) of 7,481 individuals with bipolar disorder (cases) and 9,250 controls as part of the Psychiatric GWAS Consortium. Our replication study tested 34 SNPs in 4,496 independent cases with bipolar disorder and 42,422 independent controls and found that 18 of 34 SNPs had P < 0.05, with 31 of 34 SNPs having signals with the same direction of effect (P = 3.8 × 10−7). An analysis of all 11,974 bipolar disorder cases and 51,792 controls confirmed genome-wide significant evidence of association for CACNA1C and identified a new intronic variant in ODZ4. We identified a pathway comprised of subunits of calcium channels enriched in bipolar disorder association intervals. Finally, a combined GWAS analysis of schizophrenia and bipolar disorder yielded strong association evidence for SNPs in CACNA1C and in the region of NEK4-ITIH1-ITIH3-ITIH4. Our replication results imply that increasing sample sizes in bipolar disorder will confirm many additional loci.

1,312 citations


Journal ArticleDOI
TL;DR: This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.
Abstract: Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world ’ s population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identifi ed dozens of common variants infl uencing numerous complex traits. Signifi cant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.

1,170 citations


Journal ArticleDOI
TL;DR: It is demonstrated that Au particles in the size range 3-30 nm on TiO₂ are very active in hydrogen production from ethanol, and the high hydrogen yield observed makes these catalysts promising materials for solar conversion.
Abstract: Catalytic hydrogen production from renewables is a promising method for providing energy carriers in the near future. Photocatalysts capable of promoting this reaction are often composed of noble metal nanoparticles deposited on a semiconductor. The most promising semiconductor at present is TiO₂. The successful design of these catalysts relies on a thorough understanding of the role of the noble metal particle size and the TiO₂ polymorph. Here we demonstrate that Au particles in the size range 3-30 nm on TiO₂ are very active in hydrogen production from ethanol. It was found that Au particles of similar size on anatase nanoparticles delivered a rate two orders of magnitude higher than that recorded for Au on rutile nanoparticles. Surprisingly, it was also found that Au particle size does not affect the photoreaction rate over the 3-12 nm range. The high hydrogen yield observed makes these catalysts promising materials for solar conversion.

1,053 citations


Journal ArticleDOI
01 Jan 2011-Pain
TL;DR: Screening questionnaires are suitable for identifying potential patients with neuropathic pain, but further validation of them is needed for epidemiological purposes and quantitative sensory testing is recommended for selected cases in clinic, including the diagnosis of small fiber neuropathies and for research purposes.
Abstract: This is a revision of guidelines, originally published in 2004, for the assessment of patients with neuropathic pain. Neuropathic pain is defined as pain arising as a direct consequence of a lesion or disease affecting the somatosensory system either at peripheral or central level. Screening questionnaires are suitable for identifying potential patients with neuropathic pain, but further validation of them is needed for epidemiological purposes. Clinical examination, including accurate sensory examination, is the basis of neuropathic pain diagnosis. For more accurate sensory profiling, quantitative sensory testing is recommended for selected cases in clinic, including the diagnosis of small fiber neuropathies and for research purposes. Measurement of trigeminal reflexes mediated by A-beta fibers can be used to differentiate symptomatic trigeminal neuralgia from classical trigeminal neuralgia. Measurement of laser-evoked potentials is useful for assessing function of the A-delta fiber pathways in patients with neuropathic pain. Functional brain imaging is not currently useful for individual patients in clinical practice, but is an interesting research tool. Skin biopsy to measure the intraepidermal nerve fiber density should be performed in patients with clinical signs of small fiber dysfunction. The intensity of pain and treatment effect (both in clinic and trials) should be assessed with numerical rating scale or visual analog scale. For future neuropathic pain trials, pain relief scales, patient and clinician global impression of change, the proportion of responders (50% and 30% pain relief), validated neuropathic pain quality measures and assessment of sleep, mood, functional capacity and quality of life are recommended.

909 citations


Journal ArticleDOI
TL;DR: In this article, the compatibility relationship between C-A-S-H and N-Aluminum-modified calcium silicate hydrate (C-A,S,H) gels is assessed.

776 citations


Journal ArticleDOI
TL;DR: The relationship between the number of eggs and live birth, across all female age groups, suggests that the numberof eggs in IVF is a robust surrogate outcome for clinical success.
Abstract: methods:Anonymized data on all IVF cycles performed in the UK from April 1991 to June 2008 were obtained from the Human Fertilization and Embryology Authority (HFEA). We analysed data from 400 135 IVF cycles. A logistic model was fitted to predict live birth using fractional polynomials to handle the number of eggs as a continuous independent variable. The prediction model, which was validated on a separate HFEA data set, allowed the estimation of the probability of live birth for a given number of eggs, stratified by age group. We produced a nomogram to predict the live birth rate (LBR) following IVF based on the number of eggs and the age of the female. results:The median number of eggs retrieved per cycle was 9 [inter-quartile range (IQR) 6‐13]. The overall LBR was 21.3% per fresh IVF cycle. There was a strong association between the number of eggs and LBR; LBR rose with an increasing number of eggs up to!15, plateaued between 15 and 20 eggs and steadily declined beyond 20 eggs. During 2006‐2007, the predicted LBR for women with 15 eggs retrieved in age groups 18‐34, 35‐37, 38‐39 and 40 years and over was 40, 36, 27 and 16%, respectively. There was a steady increase in the LBR per egg retrieved over time since 1991. conclusion:The relationship between the number of eggs and live birth, across all female age groups, suggests that the number of eggs in IVF is a robust surrogate outcome for clinical success. The results showed a non-linear relationship between the number of eggs and LBR following IVF treatment. The number of eggs to maximize the LBR is!15.

Journal ArticleDOI
TL;DR: The research relating to these issues highlights flexible, sophisticated systems that support and promote adaptive responses to faces that appear to function to maximize the benefits of both the authors' mate choices and more general decisions about other types of social partners.
Abstract: Face preferences affect a diverse range of critical social outcomes, from mate choices and decisions about platonic relationships to hiring decisions and decisions about social exchange. Firstly, we review the facial characteristics that influence attractiveness judgements of faces (e.g. symmetry, sexually dimorphic shape cues, averageness, skin colour/texture and cues to personality) and then review several important sources of individual differences in face preferences (e.g. hormone levels and fertility, own attractiveness and personality, visual experience, familiarity and imprinting, social learning). The research relating to these issues highlights flexible, sophisticated systems that support and promote adaptive responses to faces that appear to function to maximize the benefits of both our mate choices and more general decisions about other types of social partners.

Journal ArticleDOI
TL;DR: Weight-loss diets that were high in protein but reduced in total carbohydrates and fiber resulted in a significant decrease in fecal cancer-protective metabolites and increased concentrations of hazardous metabolites, which may increase risk of colonic disease.

Journal ArticleDOI
TL;DR: A genome-wide analysis of unrelated adults with data on single nucleotide polymorphisms and detailed phenotypes on cognitive traits unequivocally confirms that a substantial proportion of individual differences in human intelligence is due to genetic variation, and is consistent with many genes of small effects underlying the additive genetic influences on intelligence.
Abstract: General intelligence is an important human quantitative trait that accounts for much of the variation in diverse cognitive abilities. Individual differences in intelligence are strongly associated with many important life outcomes, including educational and occupational attainments, income, health and lifespan. Data from twin and family studies are consistent with a high heritability of intelligence, but this inference has been controversial. We conducted a genome-wide analysis of 3511 unrelated adults with data on 549692 single nucleotide polymorphisms (SNPs) and detailed phenotypes on cognitive traits. We estimate that 40% of the variation in crystallized-type intelligence and 51% of the variation in fluid-type intelligence between individuals is accounted for by linkage disequilibrium between genotyped common SNP markers and unknown causal variants. These estimates provide lower bounds for the narrow-sense heritability of the traits. We partitioned genetic variation on individual chromosomes and found that, on average, longer chromosomes explain more variation. Finally, using just SNP data we predicted B1% of the variance of crystallized and fluid cognitive phenotypes in an independent sample (P=0.009 and 0.028, respectively). Our results unequivocally confirm that a substantial proportion of individual differences in human intelligence is due to genetic variation, and are consistent with many genes of small effects underlying the additive genetic influences on intelligence. Molecular Psychiatry advance online publication, 9 August 2011; doi:10.1038/mp.2011.85

Journal ArticleDOI
TL;DR: Analysis of soil microcosms provides evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.
Abstract: The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH4+-N per gram of soil) and high (200 μg NH4+-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.

Journal ArticleDOI
TL;DR: An overview of new natural products from marine-derived fungi and their biological activities, focusing on the period from 2006 until mid-2010, with a considerable number of which display promising biological and pharmacological properties.

Journal ArticleDOI
TL;DR: In this paper, the authors examine teachers' craft knowledge of their practice of inclusion in terms of what they do, why and how, and identify practical examples of inclusive pedagogy that met the standard of extending what is generally available to everybody, as opposed to providing for all by differentiating for some.
Abstract: This paper reports on a study designed to examine teachers' craft knowledge of their practice of ‘inclusion’ in terms of what they do, why and how. The research approach offers an important alternative to studies of students with ‘additional needs’ and the search to articulate the specialist knowledge and skill required to teach them. Through classroom observations and interviews with 11 teachers of students across the full age range in two Scottish primary schools, we investigated how teachers make meaning of the concept of inclusion in their practice by exploring theoretical assumptions drawn from the literature about inclusive pedagogy. The analysis enabled us to identify practical examples of inclusive pedagogy that met the standard of extending what is generally available to everybody, as opposed to providing for all by differentiating for some. Examples of the inclusive pedagogical approach are provided.

Journal ArticleDOI
TL;DR: The abundance of plastics in stomachs of northern fulmars from the North Sea is used in the OSPAR Ecological Quality Objective (EcoQO) for marine litter and is now also used as an indicator for Good Environmental Status in the European Marine Strategy Framework Directive.

Journal ArticleDOI
TL;DR: There is still little conclusive evidence of any beneficial effect of systemic antioxidant supplementation in patients with sepsis and organ dysfunction, but it has been suggested that antioxidant therapy delivered specifically to mitochondria may be useful.
Abstract: Sepsis-related organ dysfunction remains the most common cause of death in the intensive care unit (ICU), despite advances in healthcare and science. Marked oxidative stress as a result of the inflammatory responses inherent with sepsis initiates changes in mitochondrial function which may result in organ damage. Normally, a complex system of interacting antioxidant defences is able to combat oxidative stress and prevents damage to mitochondria. Despite the accepted role that oxidative stress-mediated injury plays in the development of organ failure, there is still little conclusive evidence of any beneficial effect of systemic antioxidant supplementation in patients with sepsis and organ dysfunction. It has been suggested, however, that antioxidant therapy delivered specifically to mitochondria may be useful.

Journal ArticleDOI
TL;DR: The discovery of Nitrosotalea devanaterra provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling.
Abstract: Nitrification is a fundamental component of the global nitrogen cycle and leads to significant fertilizer loss and atmospheric and groundwater pollution. Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world's soils, equal or exceed those of neutral soils. Paradoxically, autotrophic ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture below pH 6.5, at which ammonia availability is reduced by ionization. Here we report the discovery and cultivation of a chemolithotrophic, obligately acidophilic thaumarchaeal ammonia oxidizer, "Candidatus Nitrosotalea devanaterra," from an acidic agricultural soil. Phylogenetic analysis places the organism within a previously uncultivated thaumarchaeal lineage that has been observed in acidic soils. Growth of the organism is optimal in the pH range 4 to 5 and is restricted to the pH range 4 to 5.5, unlike all previously cultivated ammonia oxidizers. Growth of this organism and associated ammonia oxidation and autotrophy also occur during nitrification in soil at pH 4.5. The discovery of Nitrosotalea devanaterra provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling. Growth at extremely low ammonia concentration (0.18 nM) also challenges accepted views on ammonia uptake and metabolism and indicates novel mechanisms for ammonia oxidation at low pH.

Journal ArticleDOI
01 Jul 2011-Bone
TL;DR: These discoveries are also giving insights into some of the adverse effects of bisphosphonates, such as the acute phase reaction that is triggered by inhibition of FPP synthase in peripheral blood monocytes.

Journal ArticleDOI
TL;DR: It is shown that photographs are not consistent indicators of facial appearance because they are blind to within-person variability, which has important practical implications, and suggests that face photographs are unsuitable as proof of identity.

Journal ArticleDOI
TL;DR: The bone remodelling cycle maintains the integrity of the skeleton through the balanced activities of its constituent cell types, including the bone-forming osteoblast, a cell that produces the organic bone matrix and aids its mineralisation during remodelling.
Abstract: The bone remodelling cycle (see Poster panel “The bone remodelling cycle”) maintains the integrity of the skeleton through the balanced activities of its constituent cell types. These are the bone-forming osteoblast, a cell that produces the organic bone matrix and aids its mineralisation ([


Journal ArticleDOI
01 Jun 2011-Brain
TL;DR: The findings support the suggestion that a disruption in the encoding of prediction error signals contributes to anhedonia symptoms in depression and support proposals that psychiatric syndromes reflect different disorders of neural valuation and incentive salience formation.
Abstract: The dopamine system has been linked to anhedonia in depression and both the positive and negative symptoms of schizophrenia, but it remains unclear how dopamine dysfunction could mechanistically relate to observed symptoms. There is considerable evidence that phasic dopamine signals encode prediction error (differences between expected and actual outcomes), with reinforcement learning theories being based on prediction error-mediated learning of associations. It has been hypothesized that abnormal encoding of neural prediction error signals could underlie anhedonia in depression and negative symptoms in schizophrenia by disrupting learning and blunting the salience of rewarding events, and contribute to psychotic symptoms by promoting aberrant perceptions and the formation of delusions. To test this, we used model based functional magnetic resonance imaging and an instrumental reward-learning task to investigate the neural correlates of prediction errors and expected-reward values in patients with depression (n=15), patients with schizophrenia (n=14) and healthy controls (n=17). Both patient groups exhibited abnormalities in neural prediction errors, but the spatial pattern of abnormality differed, with the degree of abnormality correlating with syndrome severity. Specifically, reduced prediction errors in the striatum and midbrain were found in depression, with the extent of signal reduction in the bilateral caudate, nucleus accumbens and midbrain correlating with increased anhedonia severity. In schizophrenia, reduced prediction error signals were observed in the caudate, thalamus, insula and amygdala-hippocampal complex, with a trend for reduced prediction errors in the midbrain, and the degree of blunting in the encoding of prediction errors in the insula, amygdala-hippocampal complex and midbrain correlating with increased severity of psychotic symptoms. Schizophrenia was also associated with disruption in the encoding of expected-reward values in the bilateral amygdala-hippocampal complex and parahippocampal gyrus, with the degree of disruption correlating with psychotic symptom severity. Neural signal abnormalities did not correlate with negative symptom severity in schizophrenia. These findings support the suggestion that a disruption in the encoding of prediction error signals contributes to anhedonia symptoms in depression. In schizophrenia, the findings support the postulate of an abnormality in error-dependent updating of inferences and beliefs driving psychotic symptoms. Phasic dopamine abnormalities in depression and schizophrenia are suggested by our observation of prediction error abnormalities in dopamine-rich brain areas, given the evidence for dopamine encoding prediction errors. The findings are consistent with proposals that psychiatric syndromes reflect different disorders of neural valuation and incentive salience formation, which helps bridge the gap between biological and phenomenological levels of understanding.

Journal ArticleDOI
TL;DR: In this article, the authors investigated the evidence that nutrient and food intake modifies the risk of children developing allergy and found that serum vitamin A was lower in children with asthma compared with controls (odds ratio [OR], 0.25; 95% CI, 0.10-0.40).
Abstract: Background Epidemiologic studies suggest that deficiencies of the nutrients selenium; zinc; vitamins A, C, D, and E; and low fruit and vegetable intake may be associated with the development of asthma and allergic disorders. Objectives To investigate the evidence that nutrient and food intake modifies the risk of children developing allergy. Methods We systematically searched 11 databases. Studies were critically appraised, and meta-analyses were undertaken. Results We identified 62 eligible reports. There were no randomized controlled trials. Studies used cohort (n = 21), case-control (n = 15), or cross-sectional (n = 26) designs. All studies were judged to be at moderate to substantial risk of bias. Meta-analysis revealed that serum vitamin A was lower in children with asthma compared with controls (odds ratio [OR], 0.25; 95% CI, 0.10-0.40). Meta-analyses also showed that high maternal dietary vitamin D and E intakes during pregnancy were protective for the development of wheezing outcomes (OR, 0.56, 95% CI, 0.42-0.73; and OR, 0.68, 95% CI, 0.52-0.88, respectively). Adherence to a Mediterranean diet was protective for persistent wheeze (OR, 0.22; 95% CI, 0.08-0.58) and atopy (OR, 0.55; 95% CI, 0.31-0.97). Seventeen of 22 fruit and vegetable studies reported beneficial associations with asthma and allergic outcomes. Results were not supportive for other allergic outcomes for these vitamins or nutrients, or for any outcomes in relation to vitamin C and selenium. Conclusion: The available epidemiologic evidence is weak but nonetheless supportive with respect to vitamins A, D, and E; zinc; fruits and vegetables; and a Mediterranean diet for the prevention of asthma. Experimental studies of these exposures are now warranted.

Journal ArticleDOI
TL;DR: The authors' ecological understanding of wildlife infectious diseases from the individual host to the ecosystem scale is reviewed, highlighting where conceptual thinking lacks verification, discussing difficulties and challenges, and offering potential future research directions.
Abstract: 1. We review our ecological understanding of wildlife infectious diseases from the individual host to the ecosystem scale, highlighting where conceptual thinking lacks verification, discussing difficulties and challenges, and offering potential future research directions. 2. New molecular approaches hold potential to increase our understanding of parasite interactions within hosts. Also, advances in our knowledge of immune systems makes immunological parameters viable measures of parasite exposure, and useful tools for improving our understanding of causal mechanisms. 3. Studies of transmission dynamics have revealed the importance of heterogeneity in host behaviour and physiology, and of contact processes operating at different spatial and temporal scales. An important future challenge is to determine the key transmission mechanisms maintaining the persistence of different types of diseases in the wild. 4. Regulation of host populations is too complex to consider parasite effects in isolation from other factors. One solution is to seek a unified understanding of the conditions under which (and the ecological rules determining when) population scale impacts of parasites can occur. 5. Good evidence now shows that both direct effects of parasites, and trait mediated indirect effects, frequently mediate the success of invasive species and their impacts on recipient communities. A wider exploration of these effects is now needed. 6. At the ecosystem scale, research is needed to characterize the circumstances and conditions under which both fluxes in parasite biomass, and trait mediated effects, are significant in ecosystem processes, and to demonstrate that parasites do indeed increase 'ecosystem health'. 7. There is a general need for more empirical testing of predictions and subsequent development of theory in the classic research cycle. Experimental field studies, meta-analyses, the collection and analysis of long-term data sets, and data constrained modelling, will all be key to advancing our understanding. 8. Finally, we are only now beginning to understand the importance of cross-scale interactions associated with parasitism. Such interactions may offer key insights into bigger picture questions such as when and how different regulatory factors are important, when disease can cause species extinctions, and what characteristics are indicative of functionally resilient ecosystems.

Journal ArticleDOI
TL;DR: Evolution based on specific adaptations to soil pH and niche specialization are suggested, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.
Abstract: Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5≤ pH <7), or alkalinophilic (pH ≥7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5–8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5–7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.

Book ChapterDOI
01 Jan 2011
TL;DR: This chapter shows how a system can recommend to a group of users by aggregating information from individual user models and modelling the users affective state.
Abstract: This chapter shows how a system can recommend to a group of users by aggregating information from individual user models and modelling the users affective state. It summarizes results from previous research in this area. It also shows how group recommendation techniques can be applied when recommending to individuals, in particular for solving the cold-start problem and dealing with multiple criteria.

Journal ArticleDOI
TL;DR: This article provided percentile norms for a series of self-report mood scales, including self-reported mood scales with very limited normative data, and used them to improve the quality of the data.
Abstract: Despite their widespread use, many self‐report mood scales have very limited normative data. To rectify this, Crawford et al. have recently provided percentile norms for a series of self‐report sca...