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Showing papers by "University of Aberdeen published in 2009"


Journal ArticleDOI
Shaun Purcell1, Shaun Purcell2, Naomi R. Wray3, Jennifer Stone1, Jennifer Stone2, Peter M. Visscher, Michael Conlon O'Donovan4, Patrick F. Sullivan5, Pamela Sklar1, Pamela Sklar2, Douglas M. Ruderfer, Andrew McQuillin, Derek W. Morris6, Colm O'Dushlaine6, Aiden Corvin6, Peter Holmans4, Stuart MacGregor3, Hugh Gurling, Douglas Blackwood7, Nicholas John Craddock5, Michael Gill6, Christina M. Hultman8, Christina M. Hultman9, George Kirov4, Paul Lichtenstein8, Walter J. Muir7, Michael John Owen4, Carlos N. Pato10, Edward M. Scolnick1, Edward M. Scolnick2, David St Clair, Nigel Williams4, Lyudmila Georgieva4, Ivan Nikolov4, Nadine Norton4, Hywel Williams4, Draga Toncheva, Vihra Milanova, Emma Flordal Thelander8, Patrick Sullivan11, Elaine Kenny6, Emma M. Quinn6, Khalid Choudhury12, Susmita Datta12, Jonathan Pimm12, Srinivasa Thirumalai13, Vinay Puri12, Robert Krasucki12, Jacob Lawrence12, Digby Quested14, Nicholas Bass12, Caroline Crombie15, Gillian Fraser15, Soh Leh Kuan, Nicholas Walker, Kevin A. McGhee7, Ben S. Pickard16, P. Malloy7, Alan W Maclean7, Margaret Van Beck7, Michele T. Pato10, Helena Medeiros10, Frank A. Middleton17, Célia Barreto Carvalho10, Christopher P. Morley17, Ayman H. Fanous, David V. Conti10, James A. Knowles10, Carlos Ferreira, António Macedo18, M. Helena Azevedo18, Andrew Kirby1, Andrew Kirby2, Manuel A. R. Ferreira2, Manuel A. R. Ferreira1, Mark J. Daly1, Mark J. Daly2, Kimberly Chambert2, Finny G Kuruvilla2, Stacey Gabriel2, Kristin G. Ardlie2, Jennifer L. Moran2 
06 Aug 2009-Nature
TL;DR: The extent to which common genetic variation underlies the risk of schizophrenia is shown, using two analytic approaches, and the major histocompatibility complex is implicate, which is shown to involve thousands of common alleles of very small effect.
Abstract: Schizophrenia is a severe mental disorder with a lifetime risk of about 1%, characterized by hallucinations, delusions and cognitive deficits, with heritability estimated at up to 80%(1,2). We performed a genome-wide association study of 3,322 European individuals with schizophrenia and 3,587 controls. Here we show, using two analytic approaches, the extent to which common genetic variation underlies the risk of schizophrenia. First, we implicate the major histocompatibility complex. Second, we provide molecular genetic evidence for a substantial polygenic component to the risk of schizophrenia involving thousands of common alleles of very small effect. We show that this component also contributes to the risk of bipolar disorder, but not to several non-psychiatric diseases.

4,573 citations


Journal ArticleDOI
TL;DR: This paper asks how and why stakeholder analysis should be conducted for participatory natural resource management research, and proposes new tools and combinations of methods that can more effectively identify and categorise stakeholders and help understand their inter-relationships.

2,011 citations


Journal ArticleDOI
TL;DR: New definitions for asthma control, severity, and exacerbations are developed, based on current treatment principles and clinical and research relevance, to provide a basis for a multicomponent assessment of asthma by clinicians, researchers, and other relevant groups in the design, conduct, and evaluation of clinical trials, and in clinical practice.
Abstract: Background: The assessment of asthma control is pivotal to the evaluation of treatment response in individuals and in clinical trials. Previously, asthma control, severity, and exacerbations were defined and assessed in many different ways.Purpose: The Task Force was established to provide recommendations about standardization of outcomes relating to asthma control, severity, and exacerbations in clinical trials and clinical practice, for adults and children aged 6 years or older.Methods: A narrative literature review was conducted to evaluate the measurement properties and strengths/weaknesses of outcome measures relevant to asthma control and exacerbations. The review focused on diary variables, physiologic measurements, composite scores, biomarkers, quality of life questionnaires, and indirect measures.Results: The Task Force developed new definitions for asthma control, severity, and exacerbations, based on current treatment principles and clinical and research relevance. In view of current knowledge ...

1,642 citations


Journal ArticleDOI
TL;DR: This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria and suggests that mechanisms proposed recently in non-gut Clostridium spp.
Abstract: Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

1,529 citations


Journal ArticleDOI
Brian J. Haas1, Sophien Kamoun2, Sophien Kamoun3, Michael C. Zody1, Michael C. Zody4, Rays H. Y. Jiang5, Rays H. Y. Jiang1, Robert E. Handsaker1, Liliana M. Cano3, Manfred Grabherr1, Chinnappa D. Kodira6, Chinnappa D. Kodira1, Sylvain Raffaele3, Trudy Torto-Alalibo6, Trudy Torto-Alalibo2, Tolga O. Bozkurt3, Audrey M. V. Ah-Fong7, Lucia Alvarado1, Vicky L. Anderson8, Miles R. Armstrong9, Anna O. Avrova9, Laura Baxter10, Jim Beynon10, Petra C. Boevink9, Stephanie R. Bollmann11, Jorunn I. B. Bos2, Vincent Bulone12, Guohong Cai13, Cahid Cakir2, James C. Carrington14, Megan Chawner15, Lucio Conti16, Stefano Costanzo11, Richard Ewan16, Noah Fahlgren14, Michael A. Fischbach17, Johanna Fugelstad12, Eleanor M. Gilroy9, Sante Gnerre1, Pamela J. Green18, Laura J. Grenville-Briggs8, John Griffith15, Niklaus J. Grünwald11, Karolyn Horn15, Neil R. Horner8, Chia-Hui Hu19, Edgar Huitema2, Dong-Hoon Jeong18, Alexandra M. E. Jones3, Jonathan D. G. Jones3, Richard W. Jones11, Elinor K. Karlsson1, Sridhara G. Kunjeti20, Kurt Lamour21, Zhenyu Liu2, Li-Jun Ma1, Dan MacLean3, Marcus C. Chibucos22, Hayes McDonald23, Jessica McWalters15, Harold J. G. Meijer5, William Morgan24, Paul Morris25, Carol A. Munro8, Keith O'Neill1, Keith O'Neill6, Manuel D. Ospina-Giraldo15, Andrés Pinzón, Leighton Pritchard9, Bernard H Ramsahoye26, Qinghu Ren27, Silvia Restrepo, Sourav Roy7, Ari Sadanandom16, Alon Savidor28, Sebastian Schornack3, David C. Schwartz29, Ulrike Schumann8, Ben Schwessinger3, Lauren Seyer15, Ted Sharpe1, Cristina Silvar3, Jing Song2, David J. Studholme3, Sean M. Sykes1, Marco Thines30, Marco Thines3, Peter J. I. van de Vondervoort5, Vipaporn Phuntumart25, Stephan Wawra8, R. Weide5, Joe Win3, Carolyn A. Young2, Shiguo Zhou29, William E. Fry13, Blake C. Meyers18, Pieter van West8, Jean B. Ristaino19, Francine Govers5, Paul R. J. Birch31, Stephen C. Whisson9, Howard S. Judelson7, Chad Nusbaum1 
17 Sep 2009-Nature
TL;DR: The sequence of the P. infestans genome is reported, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates and probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Abstract: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

1,341 citations


Journal ArticleDOI
16 Oct 2009-Immunity
TL;DR: Systematic analysis of gnotobiotic mice indicated that colonization by a whole mouse microbiota orchestrated a broad spectrum of proinflammatory T helper 1 (Th1), Th17, and regulatory T cell responses whereas most tested complex microbiota and individual bacteria failed to efficiently stimulate intestinal Tcell responses.

1,307 citations


Journal ArticleDOI
TL;DR: In this paper, the association between systolic or diastolic blood pressure and common variants in eight regions near the CYP17A1 (P = 7 × 10(-24)), CYP1A2(P = 1 × 10-23), FGF5 (P=1 × 10 -21), SH2B3(P= 3 × 10−18), MTHFR(MTHFR), c10orf107(P), ZNF652(ZNF652), PLCD3 (P,P = 5 × 10 −9),
Abstract: Elevated blood pressure is a common, heritable cause of cardiovascular disease worldwide. To date, identification of common genetic variants influencing blood pressure has proven challenging. We tested 2.5 million genotyped and imputed SNPs for association with systolic and diastolic blood pressure in 34,433 subjects of European ancestry from the Global BPgen consortium and followed up findings with direct genotyping (N ≤ 71,225 European ancestry, N ≤ 12,889 Indian Asian ancestry) and in silico comparison (CHARGE consortium, N = 29,136). We identified association between systolic or diastolic blood pressure and common variants in eight regions near the CYP17A1 (P = 7 × 10(-24)), CYP1A2 (P = 1 × 10(-23)), FGF5 (P = 1 × 10(-21)), SH2B3 (P = 3 × 10(-18)), MTHFR (P = 2 × 10(-13)), c10orf107 (P = 1 × 10(-9)), ZNF652 (P = 5 × 10(-9)) and PLCD3 (P = 1 × 10(-8)) genes. All variants associated with continuous blood pressure were associated with dichotomous hypertension. These associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease.

1,205 citations


Journal ArticleDOI
11 Sep 2009-Science
TL;DR: These rapid changes in terrestrial, freshwater, and marine systems, presage changes at lower latitudes that will affect natural resources, food production, and future climate buffering, and highlight areas of ecological research that deserve priority as the Arctic continues to warm.
Abstract: At the close of the Fourth International Polar Year, we take stock of the ecological consequences of recent climate change in the Arctic, focusing on effects at population, community, and ecosystem scales. Despite the buffering effect of landscape heterogeneity, Arctic ecosystems and the trophic relationships that structure them have been severely perturbed. These rapid changes may be a bellwether of changes to come at lower latitudes and have the potential to affect ecosystem services related to natural resources, food production, climate regulation, and cultural integrity. We highlight areas of ecological research that deserve priority as the Arctic continues to warm.

1,157 citations


Journal ArticleDOI
TL;DR: Hyperaccumulation appears to involve enhanced arsenate uptake, decreased arsenite-thiol complexation and arsenite efflux to the external medium, greatly enhanced xylem translocation of arsenite, and vacuolar sequestration of arsenites in fronds.
Abstract: Arsenic (As) is an element that is nonessential for and toxic to plants. Arsenic contamination in the environment occurs in many regions, and, depending on environmental factors, its accumulation in food crops may pose a health risk to humans.Recent progress in understanding the mechanisms of As uptake and metabolism in plants is reviewed here. Arsenate is taken up by phosphate transporters. A number of the aquaporin nodulin26-like intrinsic proteins (NIPs) are able to transport arsenite,the predominant form of As in reducing environments. In rice (Oryza sativa), arsenite uptake shares the highly efficient silicon (Si) pathway of entry to root cells and efflux towards the xylem. In root cells arsenate is rapidly reduced to arsenite, which is effluxed to the external medium, complexed by thiol peptides or translocated to shoots. One type of arsenate reductase has been identified, but its in planta functions remain to be investigated. Some fern species in the Pteridaceae family are able to hyperaccumulate As in above-ground tissues. Hyperaccumulation appears to involve enhanced arsenate uptake, decreased arsenite-thiol complexation and arsenite efflux to the external medium, greatly enhanced xylem translocation of arsenite, and vacuolar sequestration of arsenite in fronds. Current knowledge gaps and future research directions are also identified.

1,012 citations


Journal ArticleDOI
04 Jun 2009-Nature
TL;DR: There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence in Candida albicans species.
Abstract: Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.

956 citations


Journal ArticleDOI
19 Feb 2009-Nature
TL;DR: Taxon-specific analyses of African inventory and other data suggest that widespread changes in resource availability, such as increasing atmospheric carbon dioxide concentrations, may be the cause of the increase in carbon stocks, as some theory and models predict.
Abstract: The response of terrestrial vegetation to a globally changing environment is central to predictions of future levels of atmospheric carbon dioxide. The role of tropical forests is critical because they are carbon-dense and highly productive. Inventory plots across Amazonia show that old-growth forests have increased in carbon storage over recent decades, but the response of one-third of the world's tropical forests in Africa is largely unknown owing to an absence of spatially extensive observation networks. Here we report data from a ten-country network of long-term monitoring plots in African tropical forests. We find that across 79 plots (163 ha) above-ground carbon storage in live trees increased by 0.63 Mg C ha(-1) yr(-1) between 1968 and 2007 (95% confidence interval (CI), 0.22-0.94; mean interval, 1987-96). Extrapolation to unmeasured forest components (live roots, small trees, necromass) and scaling to the continent implies a total increase in carbon storage in African tropical forest trees of 0.34 Pg C yr(-1) (CI, 0.15-0.43). These reported changes in carbon storage are similar to those reported for Amazonian forests per unit area, providing evidence that increasing carbon storage in old-growth forests is a pan-tropical phenomenon. Indeed, combining all standardized inventory data from this study and from tropical America and Asia together yields a comparable figure of 0.49 Mg C ha(-1) yr(-1) (n = 156; 562 ha; CI, 0.29-0.66; mean interval, 1987-97). This indicates a carbon sink of 1.3 Pg C yr(-1) (CI, 0.8-1.6) across all tropical forests during recent decades. Taxon-specific analyses of African inventory and other data suggest that widespread changes in resource availability, such as increasing atmospheric carbon dioxide concentrations, may be the cause of the increase in carbon stocks, as some theory and models predict.

Journal ArticleDOI
TL;DR: No evidence of improvement in functional benefit or reduction in length of hospital stay with supplements is found, although Mortality may be reduced in older people who are undernourished.
Abstract: Evidence for the effectiveness of nutritional supplements containing protein and energy, often prescribed for older people, is limited. Malnutrition is more common in this age group and deterioration of nutritional status can occur during illness. It is important to establish whether supplementing the diet is an effective way of improving outcomes for older people at risk from malnutrition. This review examined trials for improvement in nutritional status and clinical outcomes when extra protein and energy were provided, usually as commercial 'sip-feeds'.

Book ChapterDOI
01 Jan 2009
TL;DR: A novel variant of RDF(S), called RDFS-FA, is introduced, which provides a solid semantic foundation for many of the latest Description Logic-based SW ontology languages, such as OWL-DL and OWL2-DL.
Abstract: This chapter introduces Resource Description Framework (RDF), the W3C recommendation for semantic annotations in the Semantic Web It will cover the syntax and semantics of RDF, as well as its relation with the W3C OWL Web Ontology Language To address the mismatch between RDF and OWL-DL, the most expressive decidable fragment of the OWL standard, we introduce a novel variant of RDF(S), called RDFS-FA, which provides a solid semantic foundation for many of the latest Description Logic-based SW ontology languages, such as OWL-DL and OWL2-DL

Journal ArticleDOI
TL;DR: Using country-specific rice consumption data, daily intake of inorganic arsenic was estimated and the associated internal cancer risk was calculated using the U.S. Environmental Protection Agency (EPA) cancer slope.
Abstract: An extensive data set of total arsenic analysis for 901 polished (white) grain samples, originating from 10 countries from 4 continents, was compiled. The samples represented the baseline (i.e., notspecifically collected from arsenic contaminated areas), and all were for market sale in major conurbations. Median total arsenic contents of rice varied 7-fold, with Egypt (0.04 mg/kg) and India (0.07 mg/kg) having the lowest arsenic content while the U.S. (0.25 mg/kg) and France (0.28 mg/kg) had the highest content. Global distribution of total arsenic in rice was modeled by weighting each country's arsenic distribution by that country's contribution to global production. A subset of 63 samples from Bangladesh, China, India, Italy, and the U.S. was analyzed for arsenic species. The relationship between inorganic arsenic contentversus total arsenic contentsignificantly differed among countries, with Bangladesh and India having the steepest slope in linear regression, and the U.S. having the shallowest slope. Using country-specific rice consumption data, daily intake of inorganic arsenic was estimated and the associated internal cancer risk was calculated using the U.S. Environmental Protection Agency (EPA) cancer slope. Median excess internal cancer risks posed by inorganic arsenic ranged 30-fold for the 5 countries examined, being 0.7 per 10,000 for Italians to 22 per 10,000 for Bangladeshis, when a 60 kg person was considered.

Reference EntryDOI
TL;DR: Frail older people confined to institutions may sustain fewer hip and other non-vertebral fractures if given vitamin D with calcium supplements, and there is no evidence of advantage of analogues of vitamin D compared with vitamin D.
Abstract: Background Due to their known effects on bone metabolism, vitamin D and related compounds have been proposed for the prevention of osteoporosis and fractures. Objectives To determine the effects of supplementation with Vitamin D or a Vitamin D analogue in the prevention of fractures of the axial and appendicular skeleton in elderly men or women with involutional or post-menopausal osteoporosis. Search strategy We searched MEDLINE, EMBASE, CINAHL, LILACS, CABNAR, BIOSIS, HEALTHSTAR, Current Contents, The Cochrane Database of Systematic Reviews, the Cochrane Musculoskeletal Injuries Group trials register, and bibliographies of identified trials and reviews. Date of the most recent search: September 2000. Selection criteria Any randomised or quasi-randomised trial which compared vitamin D or a vitamin D analogue, either alone or in combination with calcium supplementation, with a placebo, no intervention, or the administration of calcium supplements, with eligible fracture outcomes, in elderly men or women with involutional or post-menopausal osteoporosis. Data collection and analysis Two reviewers independently assessed trial quality, by use of a nine item scale, and extracted data. Additional information was sought from trialists. Where possible the data were pooled. Pooling of data, where it was admissible, used pooled relative risk and fixed effects model. Main results Almost all estimates of treatment effects are based on single studies. Administration of vitamin D3 alone without calcium co-supplementation was not associated with any reduction in incidence of hip fracture (relative risk (RR) 1.20, 95% confidence interval (CI) 0.83, 1.75) or other non-vertebral fracture. Administration of vitamin D3 with calcium co-supplementation to frail elderly people in sheltered accommodation was associated with a reduction in incidence of hip fracture (RR 0.74, 95% CI 0.60, 0.91). In healthy younger, ambulant participants the effect on hip fracture is unknown (RR 0.36, 95% CI 0.01, 8.78), although there appears to be a significant overall effect on non-vertebral fracture incidence in this group ( RR 0.46, 95% CI 0.23,0.90). Calcitriol (1,25 dihdyroxy vitamin D) was effective in reducing the incidence of vertebral deformity (RR 0.49, 95% CI 0.25, 0.95). Calcitriol was more effective than calcium in reducing the frequency of new vertebral deformities during the third year of treatment (RR 0.28, 95% CI 0.15, 0.52). 1-alpha-hydroxy vitamin D was effective in reducing the incidence of non-vertebral fractures in a single small study of elderly people whose mobility was impaired by neurological disease (RR 0.12, 95% CI 0.02, 0.95). No statistically significant effects were found for other comparisons of vitamin D or its analogues against each other, with and without calcium supplementation. Reviewer's conclusions Uncertainty remains about the efficacy of regimens which include vitamin D or its analogues in fracture prevention. Particularly if co-supplementation of calcium is required, significant cost differences are likely to exist between regimens. Further large randomised trials are currently being conducted to clarify the effectiveness of community fracture prevention programmes employing vitamin D supplementation.

Journal ArticleDOI
TL;DR: Inhibition of the growth of a major group of gram-negative bacteria at mildly acidic pH apparently creates niches that can be exploited by more low pH-tolerant microorganisms.
Abstract: The pH of the colonic lumen varies with anatomical site and microbial fermentation of dietary residue. We have investigated the impact of mildly acidic pH, which occurs in the proximal colon, on the growth of different species of human colonic bacteria in pure culture and in the complete microbial community. Growth was determined for 33 representative human colonic bacteria at three initial pH values (approximately 5.5, 6.2 and 6.7) in anaerobic YCFA medium, which includes a mixture of short-chain fatty acids (SCFA) with 0.2% glucose as energy source. Representatives of all eight Bacteroides species tested grew poorly at pH 5.5, as did Escherichia coli, whereas 19 of the 23 gram-positive anaerobes tested gave growth rates at pH 5.5 that were at least 50% of those at pH 6.7. Growth inhibition of B. thetaiotaomicron at pH 5.5 was increased by the presence of the SCFA mix (33 mM acetate, 9 mM propionate and 1 mM each of iso-valerate, valerate and iso-butyrate). Analysis of amplified 16S rRNA sequences demonstrated a major pH-driven shift within a human faecal bacterial community in a continuous flow fermentor. Bacteroides spp. accounted for 27% of 16S rRNA sequences detected at pH 5.5, but 86% of sequences at pH 6.7. Conversely, butyrate-producing gram-positive bacteria related to Eubacterium rectale represented 50% of all 16S rRNA sequences at pH 5.5, but were not detected at pH 6.7. Inhibition of the growth of a major group of gram-negative bacteria at mildly acidic pH apparently creates niches that can be exploited by more low pH-tolerant microorganisms.

Journal ArticleDOI
TL;DR: The notion of "para-inflammation" as a state between frank, overt destructive inflammation and the non-inflammatory removal of dead or dying cells by apoptosis, to the retinal community is introduced.

Journal ArticleDOI
TL;DR: Together, the data suggest that PARP1 and PARP2 detect disrupted replication forks and attract Mre11 for end processing that is required for subsequent recombination repair and restart of replication forks.
Abstract: If replication forks are perturbed, a multifaceted response including several DNA repair and cell cycle checkpoint pathways is activated to ensure faithful DNA replication. Here, we show that poly(ADP-ribose) polymerase 1 (PARP1) binds to and is activated by stalled replication forks that contain small gaps. PARP1 collaborates with Mre11 to promote replication fork restart after release from replication blocks, most likely by recruiting Mre11 to the replication fork to promote resection of DNA. Both PARP1 and PARP2 are required for hydroxyurea-induced homologous recombination to promote cell survival after replication blocks. Together, our data suggest that PARP1 and PARP2 detect disrupted replication forks and attract Mre11 for end processing that is required for subsequent recombination repair and restart of replication forks.

Journal ArticleDOI
TL;DR: Ongoing obstacles related to the study design of randomised controlled trials and non-randomised studies assessing surgical interventions are discussed.

Journal ArticleDOI
TL;DR: Overall, these data identify fibrillar Aβ as a pathogenic entity powerfully altering neuronal membrane properties such that hyperexcitability of pyramidal cells culminates in epileptiform activity.
Abstract: Alzheimer's disease is associated with an increased risk of unprovoked seizures. However, the underlying mechanisms of seizure induction remain elusive. Here, we performed video-EEG recordings in mice carrying mutant human APPswe and PS1dE9 genes (APdE9 mice) and their wild-type littermates to determine the prevalence of unprovoked seizures. In two recording episodes at the onset of amyloid beta (Abeta) pathogenesis (3 and 4.5 months of age), at least one unprovoked seizure was detected in 65% of APdE9 mice, of which 46% had multiple seizures and 38% had a generalized seizure. None of the wild-type mice had seizures. In a subset of APdE9 mice, seizure phenotype was associated with a loss of calbindin-D28k immunoreactivity in dentate granular cells and ectopic expression of neuropeptide Y in mossy fibers. In APdE9 mice, persistently decreased resting membrane potential in neocortical layer 2/3 pyramidal cells and dentate granule cells underpinned increased network excitability as identified by patch-clamp electrophysiology. At stimulus strengths evoking single-component EPSPs in wild-type littermates, APdE9 mice exhibited decreased action potential threshold and burst firing of pyramidal cells. Bath application (1 h) of Abeta1-42 or Abeta25-35 (proto-)fibrils but not oligomers induced significant membrane depolarization of pyramidal cells and increased the activity of excitatory cell populations as measured by extracellular field recordings in the juvenile rodent brain, confirming the pathogenic significance of bath-applied Abeta (proto-)fibrils. Overall, these data identify fibrillar Abeta as a pathogenic entity powerfully altering neuronal membrane properties such that hyperexcitability of pyramidal cells culminates in epileptiform activity.

Journal ArticleDOI
TL;DR: A broader overview of the role of antibiotics and antibiotic resistance in nature from the evolutionary and ecological prospective suggests that antibiotics have evolved as another way of intra- and inter-domain communication in various ecosystems.
Abstract: Investigations of antibiotic resistance from an environmental prospective shed new light on a problem that was traditionally confined to a subset of clinically relevant antibiotic-resistant bacterial pathogens. It is clear that the environmental microbiota, even in apparently antibiotic-free environments, possess an enormous number and diversity of antibiotic resistance genes, some of which are very similar to the genes circulating in pathogenic microbiota. It is difficult to explain the role of antibiotics and antibiotic resistance in natural environments from an anthropocentric point of view, which is focused on clinical aspects such as the efficiency of antibiotics in clearing infections and pathogens that are resistant to antibiotic treatment. A broader overview of the role of antibiotics and antibiotic resistance in nature from the evolutionary and ecological prospective suggests that antibiotics have evolved as another way of intra- and inter-domain communication in various ecosystems. This signalling by non-clinical concentrations of antibiotics in the environment results in adaptive phenotypic and genotypic responses of microbiota and other members of the community. Understanding the complex picture of evolution and ecology of antibiotics and antibiotic resistance may help to understand the processes leading to the emergence and dissemination of antibiotic resistance and also help to control it, at least in relation to the newer antibiotics now entering clinical practice.

Journal ArticleDOI
T. Batey1
TL;DR: Soil compaction is an important component of the land degradation syndrome which is an issue for soil management throughout the world as discussed by the authors, and it is a long standing phenomenon not only associated with agriculture but also with forest harvesting, amenity land use, pipeline installation, land restoration and wildlife trampling.
Abstract: Soil compaction is an important component of the land degradation syndrome which is an issue for soil management throughout the world. It is a long standing phenomenon not only associated with agriculture but also with forest harvesting, amenity land use, pipeline installation, land restoration and wildlife trampling. This review concentrates on the impact of soil compaction on practical soil management issues, an area not previously reviewed. It discusses in the context of the current situation, the causes, identification, effects and alleviation of compaction. The principal causes are when compressive forces derived from wheels, tillage machinery and from the trampling of animals, act on compressible soil. Compact soils can also be found under natural conditions without human or animal involvement. Compaction alters many soil properties and adverse effects are mostly linked to a reduction in permeability to air, water and roots. Many methods can be used to measure the changes. In practical situations, the use of visual and tactile methods directly in the field is recommended. The worst problems tend to occur when root crops and vegetables are harvested from soils at or wetter than field capacity. As discussed by a farmer, the effects on crop uniformity and quality (as well as a reduction in yield) can be marked. By contrast, rendzinas and other calcareous soils growing mainly cereals are comparatively free of compaction problems. The effect of a given level of compaction is related to both weather and climate; where soil moisture deficits are large, a restriction in root depth may have severe effects but the same level of compaction may have a negligible effect where moisture deficits are small. Topsoil compaction in sloping landscapes enhances runoff and may induce erosion particularly along wheeltracks, with consequent off-farm environmental impacts. Indirect effects of compaction include denitrification which is likely to lead to nitrogen deficiency in crops. The effects of heavy tractors and harvesters can to some extent be compensated for by a reduction in tyre pressures although there is concern that deep-seated compaction may occur. Techniques for loosening compaction up to depths of 45 cm are well established but to correct deeper problems presents difficulties. Several authors recommend that monitoring of soil physical conditions, including compaction, should be part of routine soil management.

Journal ArticleDOI
TL;DR: Key developments in the current understanding of Se in higher plants are reviewed and recent advances in the genetic engineering of Se metabolism are discussed, particularly for biofortification and phytoremediation of Se-contaminated environments.

Journal ArticleDOI
TL;DR: Examples of application of the approach to phenotyping in the field and the steps in data analysis are outlined, demonstrating that clear genotypic variation may be detected despite substantial variation in soil moisture status or incident radiation by the use of appropriate normalisation techniques.
Abstract: Thermal imaging using infrared (IR) is now an established technology for the study of stomatal responses and for phenotyping plants for differences in stomatal behaviour. This paper outlines the potential applications of IR sensing in drought phenotyping, with particular emphasis on a description of the problems with extrapolation of the technique from the study of single leaves in controlled environments to the study of plant canopies is field plots, with examples taken from studies on grapevine (Vitis vinifera L.) and rice (Oryza sativa L.). Particular problems include the sensitivity of leaf temperature (and potentially the temperature of reference surfaces) to both temporal and spatial variation in absorbed radiation, with leaf temperature varying by as much as 15°C between full sun and deep shade. Examples of application of the approach to phenotyping in the field and the steps in data analysis are outlined, demonstrating that clear genotypic variation may be detected despite substantial variation in soil moisture status or incident radiation by the use of appropriate normalisation techniques.

Journal ArticleDOI
TL;DR: In this paper, the effect of different concentrations of Na2O on the structure of a composition of fresh C-S-H gels was addressed. And the results showed that the addition of various concentrations of sodium leads to C−S−H gel modification even in the very short term.

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TL;DR: It is concluded that NRXN1 deletions affecting exons confer risk of schizophrenia.
Abstract: Deletions within the neurexin 1 gene (NRXN1; 2p16.3) are associated with autism and have also been reported in two families with schizophrenia. We examined NRXN1, and the closely related NRXN2 and NRXN3 genes, for copy number variants (CNVs) in 2977 schizophrenia patients and 33 746 controls from seven European populations (Iceland, Finland, Norway, Germany, The Netherlands, Italy and UK) using microarray data. We found 66 deletions and 5 duplications in NRXN1, including a de novo deletion: 12 deletions and 2 duplications occurred in schizophrenia cases (0.47%) compared to 49 and 3 (0.15%) in controls. There was no common breakpoint and the CNVs varied from 18 to 420 kb. No CNVs were found in NRXN2 or NRXN3. We performed a Cochran-Mantel-Haenszel exact test to estimate association between all CNVs and schizophrenia (P = 0.13; OR = 1.73; 95% CI 0.81-3.50). Because the penetrance of NRXN1 CNVs may vary according to the level of functional impact on the gene, we next restricted the association analysis to CNVs that disrupt exons (0.24% of cases and 0.015% of controls). These were significantly associated with a high odds ratio (P = 0.0027; OR 8.97, 95% CI 1.8-51.9). We conclude that NRXN1 deletions affecting exons confer risk of schizophrenia.

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TL;DR: The current understanding of the process by which N(2)O is produced and destroyed is reviewed and the potential for feeding this into new approaches for combating N( 2)O release is discussed.

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TL;DR: A minority of interventions showed larger effects, but no specific reminder or contextual features were significantly associated with effect magnitude, and further research must identify design features and contextual factors consistently associated with larger improvements in provider behaviour.
Abstract: Background The opportunity to improve care by delivering decision support to clinicians at the point of care represents one of the main incentives for implementing sophisticated clinical information systems. Previous reviews of computer reminder and decision support systems have reported mixed effects, possibly because they did not distinguish point of care computer reminders from e-mail alerts, computer-generated paper reminders, and other modes of delivering ‘computer reminders’. Objectives To evaluate the effects on processes and outcomes of care attributable to on-screen computer reminders delivered to clinicians at the point of care. Search methods We searched the Cochrane EPOC Group Trials register, MEDLINE, EMBASE and CINAHL and CENTRAL to July 2008, and scanned bibliographies from key articles. Selection criteria Studies of a reminder delivered via a computer system routinely used by clinicians, with a randomised or quasi-randomised design and reporting at least one outcome involving a clinical endpoint or adherence to a recommended process of care. Data collection and analysis Two authors independently screened studies for eligibility and abstracted data. For each study, we calculated the median improvement in adherence to target processes of care and also identified the outcome with the largest such improvement. We then calculated the median absolute improvement in process adherence across all studies using both the median outcome from each study and the best outcome. Main results Twenty-eight studies (reporting a total of thirty-two comparisons) were included. Computer reminders achieved a median improvement in process adherence of 4.2% (interquartile range (IQR): 0.8% to 18.8%) across all reported process outcomes, 3.3% (IQR: 0.5% to 10.6%) for medication ordering, 3.8% (IQR: 0.5% to 6.6%) for vaccinations, and 3.8% (IQR: 0.4% to 16.3%) for test ordering. In a sensitivity analysis using the best outcome from each study, the median improvement was 5.6% (IQR: 2.0% to 19.2%) across all process measures and 6.2% (IQR: 3.0% to 28.0%) across measures of medication ordering. In the eight comparisons that reported dichotomous clinical endpoints, intervention patients experienced a median absolute improvement of 2.5% (IQR: 1.3% to 4.2%). Blood pressure was the most commonly reported clinical endpoint, with intervention patients experiencing a median reduction in their systolic blood pressure of 1.0 mmHg (IQR: 2.3 mmHg reduction to 2.0 mmHg increase). Authors' conclusions Point of care computer reminders generally achieve small to modest improvements in provider behaviour. A minority of interventions showed larger effects, but no specific reminder or contextual features were significantly associated with effect magnitude. Further research must identify design features and contextual factors consistently associated with larger improvements in provider behaviour if computer reminders are to succeed on more than a trial and error basis.

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TL;DR: These data suggest that very few schizophrenia patients share identical genomic causation, potentially complicating efforts to personalize treatment regimens and support the emerging view that rare deleterious variants may be more important in schizophrenia predisposition than common polymorphisms.
Abstract: We report a genome-wide assessment of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) in schizophrenia. We investigated SNPs using 871 patients and 863 controls, following up the top hits in four independent cohorts comprising 1,460 patients and 12,995 controls, all of European origin. We found no genome-wide significant associations, nor could we provide support for any previously reported candidate gene or genome-wide associations. We went on to examine CNVs using a subset of 1,013 cases and 1,084 controls of European ancestry, and a further set of 60 cases and 64 controls of African ancestry. We found that eight cases and zero controls carried deletions greater than 2 Mb, of which two, at 8p22 and 16p13.11-p12.4, are newly reported here. A further evaluation of 1,378 controls identified no deletions greater than 2 Mb, suggesting a high prior probability of disease involvement when such deletions are observed in cases. We also provide further evidence for some smaller, previously reported, schizophrenia-associated CNVs, such as those in NRXN1 and APBA2. We could not provide strong support for the hypothesis that schizophrenia patients have a significantly greater “load” of large (>100 kb), rare CNVs, nor could we find common CNVs that associate with schizophrenia. Finally, we did not provide support for the suggestion that schizophrenia-associated CNVs may preferentially disrupt genes in neurodevelopmental pathways. Collectively, these analyses provide the first integrated study of SNPs and CNVs in schizophrenia and support the emerging view that rare deleterious variants may be more important in schizophrenia predisposition than common polymorphisms. While our analyses do not suggest that implicated CNVs impinge on particular key pathways, we do support the contribution of specific genomic regions in schizophrenia, presumably due to recurrent mutation. On balance, these data suggest that very few schizophrenia patients share identical genomic causation, potentially complicating efforts to personalize treatment regimens.