scispace - formally typeset
Search or ask a question

Showing papers by "University of Stirling published in 2014"



Journal ArticleDOI
David Brawand1, David Brawand2, Catherine E. Wagner3, Catherine E. Wagner4, Yang I. Li2, Milan Malinsky5, Milan Malinsky6, Irene Keller3, Shaohua Fan7, Oleg Simakov7, Alvin Yu Jin Ng8, Zhi Wei Lim8, Etienne Bezault9, Jason Turner-Maier1, Jeremy A. Johnson1, Rosa Alcazar10, Hyun Ji Noh1, Pamela Russell11, Bronwen Aken5, Jessica Alföldi1, Chris T. Amemiya12, Naoual Azzouzi13, Jean-François Baroiller, Frédérique Barloy-Hubler13, Aaron M. Berlin1, Ryan F. Bloomquist14, Karen L. Carleton15, Matthew A. Conte15, Helena D'Cotta, Orly Eshel, Leslie Gaffney1, Francis Galibert13, Hugo F. Gante16, Sante Gnerre1, Lucie Greuter4, Lucie Greuter3, Richard Guyon13, Natalie S. Haddad14, Wilfried Haerty2, Robert M Harris17, Hans A. Hofmann17, Thibaut Hourlier5, Gideon Hulata, David B. Jaffe1, Marcia Lara1, Alison P. Lee8, Iain MacCallum1, Salome Mwaiko4, Masato Nikaido18, Hidenori Nishihara18, Catherine Ozouf-Costaz19, David J. Penman20, Dariusz Przybylski1, Michaelle Rakotomanga13, Suzy C. P. Renn9, Filipe J. Ribeiro1, Micha Ron, Walter Salzburger16, Luis Sanchez-Pulido2, M. Emília Santos16, Steve Searle5, Ted Sharpe1, Ross Swofford1, Frederick J. Tan21, Louise Williams1, Sarah Young1, Shuangye Yin1, Norihiro Okada18, Norihiro Okada22, Thomas D. Kocher15, Eric A. Miska6, Eric S. Lander1, Byrappa Venkatesh8, Russell D. Fernald10, Axel Meyer7, Chris P. Ponting2, J. Todd Streelman14, Kerstin Lindblad-Toh23, Kerstin Lindblad-Toh1, Ole Seehausen3, Ole Seehausen4, Federica Di Palma1, Federica Di Palma24 
18 Sep 2014-Nature
TL;DR: This article found an excess of gene duplications in the East African lineage compared to Nile tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs.
Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

832 citations


David Brawand1, David Brawand2, Catherine E. Wagner3, Catherine E. Wagner4, Yang I. Li2, Milan Malinsky5, Milan Malinsky6, Irene Keller3, Shaohua Fan7, Oleg Simakov7, Alvin Yu Jin Ng8, Zhi Wei Lim8, Etienne Bezault9, Jason Turner-Maier1, Jeremy A. Johnson1, Rosa Alcazar10, Hyun Ji Noh1, Pamela Russell11, Bronwen Aken6, Jessica Alföldi1, Chris T. Amemiya12, Naoual Azzouzi13, Jean-François Baroiller, Frédérique Barloy-Hubler13, Aaron M. Berlin1, Ryan F. Bloomquist14, Karen L. Carleton15, Matthew A. Conte15, Helena D'Cotta, Orly Eshel, Leslie Gaffney1, Francis Galibert13, Hugo F. Gante16, Sante Gnerre1, Lucie Greuter4, Lucie Greuter3, Richard Guyon13, Natalie S. Haddad14, Wilfried Haerty2, Robert M Harris17, Hans A. Hofmann17, Thibaut Hourlier6, Gideon Hulata, David B. Jaffe1, Marcia Lara1, Alison P. Lee8, Iain MacCallum1, Salome Mwaiko4, Masato Nikaido18, Hidenori Nishihara18, Catherine Ozouf-Costaz19, David J. Penman20, Dariusz Przybylski1, Michaelle Rakotomanga13, Suzy C. P. Renn9, Filipe J. Ribeiro1, Micha Ron, Walter Salzburger16, Luis Sanchez-Pulido2, M. Emília Santos16, Steve Searle6, Ted Sharpe1, Ross Swofford1, Frederick J. Tan21, Louise Williams1, Sarah Young1, Shuangye Yin1, Norihiro Okada18, Norihiro Okada22, Thomas D. Kocher15, Eric A. Miska5, Eric S. Lander1, Byrappa Venkatesh8, Russell D. Fernald10, Axel Meyer7, Chris P. Ponting2, J. Todd Streelman14, Kerstin Lindblad-Toh23, Kerstin Lindblad-Toh1, Ole Seehausen3, Ole Seehausen4, Federica Di Palma1, Federica Di Palma24 
01 Sep 2014
TL;DR: It is concluded that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

666 citations


Journal ArticleDOI
TL;DR: The routine use of PROMs increases the frequency of discussion of patient outcomes during consultations, and in some studies, PRoms are associated with improved symptom control, increased supportive care measures, and patient satisfaction.
Abstract: Purpose The systematic use of patient-reported outcome measures (PROMs) has been advocated as an effective way to standardize cancer practice. Yet, the question of whether PROMs can lead to actual improvements in the quality of patient care remains under debate. This review examined whether inclusion of PROM in routine clinical practice is associated with improvements in patient outcomes, processes of care, and health service outcomes during active anticancer treatment. Methods A systematic review of five electronic databases (Medline, EMBASE, CINAHL [Cumulative Index to Nursing and Allied Health Literature], PsycINFO, and Psychology and Behavioral Sciences Collection [PBSC]) was conducted from database inception to May 2012 to locate randomized and nonrandomized controlled trials of patients receiving active anticancer treatment or supportive care irrespective of type of cancer. Results Based on prespecified eligibility criteria, we included 26 articles that reported on 24 unique controlled trials. Wide ...

640 citations


Journal ArticleDOI
14 May 2014-BMJ
TL;DR: Behavioural interventions that deal with both diet and physical activity show small but significant benefits on weight loss maintenance.
Abstract: Objective To systematically review and describe currently available approaches to supporting maintenance of weight loss in obese adults and to assess the evidence for the effectiveness of these interventions. Design Systematic review with meta-analysis. Data sources Medline, PsycINFO, Embase, and the Cochrane Central Register of Controlled Trials. Study selection Studies were identified through to January 2014. Randomised trials of interventions to maintain weight loss provided to initially obese adults (aged ≥18) after weight loss of ≥5% body weight with long term (≥12 months) follow-up of weight change (main outcome) were included. Study appraisal and synthesis Potential studies were screened independently and in duplicate; study characteristics and outcomes were extracted. Meta-analyses were conducted to estimate the effects of interventions on weight loss maintenance with the inverse variance method and a random effects model. Results are presented as mean differences in weight change, with 95% confidence intervals. Results 45 trials involving 7788 individuals were included. Behavioural interventions focusing on both food intake and physical activity resulted in an average difference of −1.56 kg (95% confidence interval −2.27 to −0.86 kg; 25 comparisons, 2949 participants) in weight regain compared with controls at 12 months. Orlistat combined with behavioural interventions resulted in a −1.80 kg (−2.54 to −1.06; eight comparisons, 1738 participants) difference compared with placebo at 12 months. All orlistat studies reported higher frequencies of adverse gastrointestinal events in the experimental compared with placebo control groups. A dose-response relation for orlistat treatment was found, with 120 mg doses three times a day leading to greater weight loss maintenance (−2.34 kg, −3.03 to −1.65) compared with 60 mg and 30 mg three times a day (−0.70 kg, 95% confidence interval −1.92 to 0.52), P=0.02. Conclusions Behavioural interventions that deal with both diet and physical activity show small but significant benefits on weight loss maintenance.

600 citations


Journal ArticleDOI
04 Sep 2014-Nature
TL;DR: It is found that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.
Abstract: Soils store about four times as much carbon as plant biomass, and soil microbial respiration releases about 60 petagrams of carbon per year to the atmosphere as carbon dioxide. Short-term experiments have shown that soil microbial respiration increases exponentially with temperature. This information has been incorporated into soil carbon and Earth-system models, which suggest that warming-induced increases in carbon dioxide release from soils represent an important positive feedback loop that could influence twenty-first-century climate change. The magnitude of this feedback remains uncertain, however, not least because the response of soil microbial communities to changing temperatures has the potential to either decrease or increase warming-induced carbon losses substantially. Here we collect soils from different ecosystems along a climate gradient from the Arctic to the Amazon and investigate how microbial community-level responses control the temperature sensitivity of soil respiration. We find that the microbial community-level response more often enhances than reduces the mid- to long-term (90 days) temperature sensitivity of respiration. Furthermore, the strongest enhancing responses were observed in soils with high carbon-to-nitrogen ratios and in soils from cold climatic regions. After 90 days, microbial community responses increased the temperature sensitivity of respiration in high-latitude soils by a factor of 1.4 compared to the instantaneous temperature response. This suggests that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.

490 citations


Journal ArticleDOI
TL;DR: Europe, North America, and the Middle East featured most heavily in trade reports to CITES, whereas trade involving South America and Southeast Asia were given most emphasis in the literature.
Abstract: International trade in exotic pets is an important and increasing driver of biodiversity loss and often compromises the standards required for good animal welfare. We systematically reviewed the scientific and gray literature and used the United Nations Environment Programme - World Conservation Monitoring Centre (UNEP-WCMC) Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) trade database to establish temporal and geographical trade patterns of live exotic birds, mammals, and reptiles and to describe trends in research, taxonomic representation, and level of threat and legal protection of species traded. Birds were the most species-rich and abundant class reported in trade; reptiles were second most abundant but unusually the most studied in this context; and mammals were least abundant in trade. Mammalian and reptilian species traded as pets were more likely to be threatened than expected by random. There have been a substantial number of Appendix I listed captive-bred mammals and birds and wild-caught birds and reptiles reported in trade to CITES. We identified the Middle East's emerging role as a driver of demand for exotic pets of all taxa alongside the well-established and increasing role of South America and Southeast Asia in the market. Europe, North America, and the Middle East featured most heavily in trade reports to CITES, whereas trade involving South America and Southeast Asia were given most emphasis in the literature. For effective monitoring of and appropriate response to the international exotic pet trade, it is imperative that the reliability and detail of CITES trade reports improve and that scientific research be directed toward those taxa and locations that are most vulnerable.

315 citations


Journal ArticleDOI
TL;DR: Probiotics, which are regarded as micro-organisms administered orally leading to health benefits, are used extensively in aquaculture for disease control, notably against bacterial diseases.

274 citations


Journal ArticleDOI
TL;DR: This review focusses on the conversion of hemocyanin into a phenoloxidase-like enzyme and the array of hemOCyanin-derived immune responses documented to date.
Abstract: Substantial evidence gathered recently has revealed the multiple functionalities of hemocyanin. Contrary to previous claims that this ancient protein is involved solely in oxygen transport within the hemolymph of invertebrates, hemocyanin and hemocyanin-derived peptides have been linked to key aspects of innate immunity, in particular, antiviral and phenoloxidase-like activities. Both phenoloxidase and hemocyanin belong to the family of type-3 copper proteins and share a high degree of sequence homology. While the importance of phenoloxidase in immunity and development is well characterised, the contribution of hemocyanin to biological defence systems within invertebrates is not recognised widely. This review focusses on the conversion of hemocyanin into a phenoloxidase-like enzyme and the array of hemocyanin-derived immune responses documented to date.

242 citations


Journal ArticleDOI
01 Feb 2014-Pain
TL;DR: Investigating preoperative sociodemographic and psychological factors, intraoperative clinical factors, and acute postoperative pain in a prospective cohort of 362 women undergoing surgery for primary breast cancer found multiple psychological factors and nerve division was associated with chronic pain at 4 and 9 months.
Abstract: Chronic postsurgical pain (CPSP) is a common postoperative adverse event affecting up to half of women undergoing breast cancer surgery, yet few epidemiological studies have prospectively investigated the role of preoperative, intraoperative, and postoperative risk factors for pain onset and chronicity. We prospectively investigated preoperative sociodemographic and psychological factors, intraoperative clinical factors, and acute postoperative pain in a prospective cohort of 362 women undergoing surgery for primary breast cancer. Intraoperative nerve handling (division or preservation) of the intercostobrachial nerve was recorded. At 4 and 9 months after surgery, incidence of chronic painful symptoms not present preoperatively was 68% and 63%, respectively. Univariate analysis revealed that multiple psychological factors and nerve division was associated with chronic pain at 4 and 9 months. In a multivariate model, independent predictors of CPSP at 4 months included younger age and acute postoperative pain (odds ratio [OR] 1.34, 95% confidence interval [CI] 1.12 to 1.60), whereas preoperative psychological robustness (OR 0.70, 95% CI 0.49 to 0.99), a composite variable comprising high dispositional optimism, high positive affect, and low emotional distress, was protective. At 9 months, younger age, axillary node clearance (OR 2.97, 95% CI 1.09 to 8.06), and severity of acute postoperative pain (OR 1.17, 95% CI 1.00 to 1.37) were predictive of pain persistence. Of those with CPSP, 25% experienced moderate to severe pain and 40% were positive on Douleur Neuropathique 4 and Self-Complete Leeds Assessment of Neuropathic Symptoms and Signs pain scales. Overall, a high proportion of women report painful symptoms, altered sensations, and numbness in the upper body within the first 9 months after resectional breast surgery and cancer treatment.

224 citations


Journal ArticleDOI
TL;DR: It is demonstrated that field-realistic doses of these pesticides substantially impacts on foraging ability of bumblebee workers when collecting pollen, and it is suggested that this provides a causal mechanism behind reduced queen production in imidacloprid exposed colonies.
Abstract: Bumblebees and other pollinators provide a vital ecosystem service for the agricultural sector. Recent studies however have suggested that exposure to systemic neonicotinoid insecticides in flowering crops has sub-lethal effects on the bumblebee workforce, and hence in reducing queen production. The mechanism behind reduced nest performance, however, remains unclear. Here we use Radio Frequency Identification (RFID) technology to test whether exposure to a low, field realistic dose (0.7 ppb in sugar water and 6 ppb in pollen) of the neonicotinoid imidacloprid, reduces worker foraging efficiency. Whilst the nectar foraging efficiency of bees treated with imidacloprid was not significantly different than that of control bees, treated bees brought back pollen less often than control bees (40 % of trips vs 63 % trips, respectively) and, where pollen was collected, treated bees brought back 31 % less pollen per hour than controls. This study demonstrates that field-realistic doses of these pesticides substantially impacts on foraging ability of bumblebee workers when collecting pollen, and we suggest that this provides a causal mechanism behind reduced queen production in imidacloprid exposed colonies.

Journal ArticleDOI
Alistair W. R. Seddon1, Alistair W. R. Seddon2, Anson W. Mackay3, Ambroise Baker1, H. John B. Birks2, H. John B. Birks4, H. John B. Birks1, Elinor Breman1, Caitlin E. Buck5, Erle C. Ellis6, Cynthia A. Froyd7, Jacquelyn L. Gill8, Lindsey Gillson9, Edward A. Johnson10, Vivienne J. Jones2, Stephen Juggins11, Marc Macias-Fauria1, Keely Mills12, Jesse L. Morris13, David Nogués-Bravo14, Surangi W. Punyasena15, Thomas P. Roland16, Andrew J. Tanentzap17, Katherine J. Willis2, Katherine J. Willis1, Martin Aberhan18, Eline N. van Asperen19, Eline N. van Asperen20, William E. N. Austin21, William E. N. Austin22, Richard W. Battarbee3, Shonil A. Bhagwat1, Christina L. Belanger23, Keith Bennett24, Hilary H. Birks4, Hilary H. Birks2, Christopher Bronk Ramsey1, Stephen J. Brooks25, Mark de Bruyn26, Paul G. Butler27, Frank M. Chambers28, Stewart J. Clarke29, Althea Davies21, John A. Dearing16, Thomas H. G. Ezard16, Angelica Feurdean30, Angelica Feurdean31, Roger J. Flower3, Peter Gell32, Sonja Hausmann33, Erika J. Hogan12, Melanie J. Hopkins34, Melanie J. Hopkins18, Elizabeth S. Jeffers1, Atte Korhola13, Rob Marchant35, Thorsten Kiefer, Mariusz Lamentowicz36, Isabelle Larocque-Tobler, Lourdes López-Merino37, Lee Hsiang Liow38, Suzanne McGowan39, Joshua H. Miller40, Encarni Montoya41, Oliver Morton, Sandra Nogué1, Sandra Nogué2, Chloe Onoufriou42, Lisa P. Boush43, Francisco Rodríguez-Sánchez44, Neil L. Rose3, Carl D. Sayer3, Helen Shaw45, Richard J. Payne46, Gavin Simpson47, Kadri Sohar48, Nicki J. Whitehouse23, Nicki J. Whitehouse49, John W. Williams50, Andrzej Witkowski51 
TL;DR: Using a set of criteria designed to identify realistic and achievable research goals, questions were selected from a pool submitted by the international palaeoecology research community and relevant policy practitioners to highlight its potential for addressing both pure and applied issues related to ecological science and global change.
Abstract: Sediment coring on Lake Baikal, Russia. Palaeoecological information (i.e. the biological and geochemical remains preserved in lake sediments) provide insights into ecological processes and environmental change occurring over decades to millions of years. Our exercise targeted future research areas for palaeoecology by identifying 50 priority questions.

Journal ArticleDOI
Lawrence N. Hudson1, Tim Newbold2, Tim Newbold3, Sara Contu1  +270 moreInstitutions (167)
TL;DR: A new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world is described and assessed.
Abstract: Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species Existing global databases of species’ threat status or population time series are dominated by charismatic species The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines We describe and assess a new database of more than 16 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – wwwpredictsorguk) We make site-level summary data available alongside this article The full database will be publicly available in 2015

Journal ArticleDOI
TL;DR: The European guidelines for the management of basal cell carcinoma (BCC) published by the former BCC subcommittee of the Guidelines Committee of the European Dermatology Forum (EDF) were published in 2006.
Abstract: Background European guidelines for the management of basal cell carcinoma (BCC) prepared by the former BCC subcommittee of the Guidelines Committee of the European Dermatology Forum (EDF) were published in 2006. ObjectivesTo present updated guidelines that include consensual expert definitions on various BCC types, prognosis and risk factors for BCC as well as review recommendations for diagnosis and treatment reflecting current published evidence. MethodsThese guidelines (S1 type) were prepared by the new BCC subgroup of the European Dermatology Forum (EDF)’s Guidelines Committee through extensive literature review (up to 2012) and expert experience; they were extensively discussed within the EDF subcommittee and approved by peer reviewers of the EDF.ResultsBCC is a common tumour with an incidence rising worldwide. Three major clinical types of BCC are recognized: nodular, superficial and morpheaform. Four histological subtypes are defined: superficial, nodular, infiltrative and morpheaform. On the basis of the risk of relapse, three prognosis groups have been identified: high, intermediate and low risk. According to these classifications and evidence-based evaluation of the therapeutic strategies available, a decision tree is proposed for the management of BCCs. Conclusions. The guidelines offer a useful tool that will help dermatologists to select the most appropriate treatment for individual patients.

Journal ArticleDOI
TL;DR: While theNumber of deceased donors is higher than the number of living donors, opt-out consent leads to a relative increase in the total number of livers and kidneys transplanted.
Abstract: Policy decisions about opt-in and opt-out consent for organ donation are based on limited evidence. To fill this gap we investigated the difference between deceased and living organ donation rates in opt-in and opt-out consent systems across a 13 year period. We controlled for extensive covariates and estimated the causal effect of consent with instrumental variables analysis. This panel study used secondary data analysis to compare organ donor and transplant rates in 48 countries that had either opt-in or opt-out consent. Organ donation data were obtained over a 13-year period between 2000 and 2012. The main outcome measures were the number of donors, number of transplants per organ and total number (deceased plus living) of kidneys and livers transplanted. The role of consent on donor and transplant rates was assessed using multilevel modeling and the causal effect estimated with instrumental variables analysis. Deceased donor rates (per-million population) were higher in opt-out (M = 14.24) than opt-in consent countries (M = 9.98; χ = -4.27, 95% confidence interval (CI) = -8.08, -0.45, P = .029). However, the number of living donors was higher in opt-in (M = 9.36) than opt-out countries (M = 5.49; B = 3.86, 95% CI = 1.16, 6.56, P = .006). Importantly, the total number of kidneys transplanted (deceased plus living) was higher in opt-out (M = 28.32) than opt-in countries (M = 22.43; B = -5.89, 95% CI = -11.60, -0.17, P = .044). Similarly, the total number of livers transplanted was higher in opt-out (M = 11.26) than opt-in countries (M = 7.53; B = -3.73, 95% CI = -7.47, 0.01, P = .051). Instrumental variables analysis suggested that the effect of opt-in versus opt-out consent on the difference between deceased and living donor rates is causal. While the number of deceased donors is higher than the number of living donors, opt-out consent leads to a relative increase in the total number of livers and kidneys transplanted.

Journal ArticleDOI
TL;DR: This manuscript describes the first high-density SNP genotyping array for Atlantic salmon, likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.
Abstract: Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.

Journal ArticleDOI
TL;DR: The ecological and genetic data suggest a major invasion event that is currently unfolding in southern South America with disastrous consequences for the native bumblebee species.
Abstract: Summary: The Palaearctic Bombus ruderatus (in 1982/1983) and Bombus terrestris (1998) have both been introduced into South America (Chile) for pollination purposes. We here report on the results of sampling campaigns in 2004, and 2010-2012 showing that both species have established and massively expanded their range. Bombus terrestris, in particular, has spread by some 200 km year-1 and had reached the Atlantic coast in Argentina by the end of 2011. Both species, and especially B. terrestris, are infected by protozoan parasites that seem to spread along with the imported hosts and spillover to native species. Genetic analyses by polymorphic microsatellite loci suggest that the host population of B. terrestris is genetically diverse, as expected from a large invading founder population, and structured through isolation by distance. Genetically, the populations of the trypanosomatid parasite, Crithidia bombi, sampled in 2004 are less diverse, and distinct from the ones sampled later. Current C. bombi populations are highly heterozygous and also structured through isolation by distance correlating with the genetic distances of B. terrestris, suggesting the latter's expansion to be a main structuring factor for the parasite. Remarkably, wherever B. terrestris spreads, the native Bombus dahlbomii disappears although the reasons remain unclear. Our ecological and genetic data suggest a major invasion event that is currently unfolding in southern South America with disastrous consequences for the native bumblebee species. © 2013 British Ecological Society.

Journal ArticleDOI
TL;DR: In this paper, the authors evaluate two contrasting paradigms for the assessment of social values in non-monetary terms: an instrumental paradigm involving an objective assessment of the distribution, type and intensity of values that individuals assign to the current state of ecosystems and a deliberative paradigm involving the exploration of desired end states through group discussion.

Journal ArticleDOI
Victoria K. Alogna1, M. K. Attaya2, P. Aucoin3, Štěpán Bahník4, S. Birch5, Angie R. Birt3, Brian H. Bornstein6, Samantha Bouwmeester7, Maria A. Brandimonte8, Charity Brown9, K. Buswell10, Curt A. Carlson11, Maria A. Carlson11, Simon Chu, Aleksandra Cislak12, M. Colarusso13, Melissa F. Colloff14, Kimberly S. Dellapaolera6, Jean-Francois Delvenne9, A. Di Domenico, Aaron Drummond15, Gerald Echterhoff16, John E. Edlund17, Casey Eggleston18, Beth Fairfield, Gregory Franco19, Fiona Gabbert20, Bradlee W. Gamblin21, Maryanne Garry19, R. Gentry10, Elizabeth Gilbert18, D. L. Greenberg22, Jamin Halberstadt1, Lauren C. Hall15, Peter J. B. Hancock23, D. Hirsch24, Glenys A. Holt25, Joshua Conrad Jackson1, Jonathan Jong26, Andre Kehn21, C. Koch10, René Kopietz16, U. Körner27, Melina A. Kunar14, Calvin K. Lai18, Stephen R. H. Langton23, Fábio Pitombo Leite28, Nicola Mammarella, John E. Marsh29, K. A. McConnaughy2, S. McCoy30, Alex H. McIntyre23, Christian A. Meissner31, Robert B. Michael19, A. A. Mitchell32, M. Mugayar-Baldocchi22, R. Musselman13, C. Ng1, Austin Lee Nichols33, Narina Nunez34, Matthew A. Palmer25, J. E. Pappagianopoulos2, Marilyn S. Petro32, Christopher R. Poirier2, Emma Portch9, M. Rainsford25, A. Rancourt30, C. Romig24, Eva Rubínová35, Mevagh Sanson19, Liam Satchell36, James D. Sauer36, Kimberly Schweitzer34, J. Shaheed10, Faye Collette Skelton29, G. A. Sullivan2, Kyle J. Susa37, Jessica K. Swanner31, W. B. Thompson38, R. Todaro24, Joanna Ulatowska, Tim Valentine20, Peter P. J. L. Verkoeijen7, Marek A. Vranka39, Kimberley A. Wade14, Christopher A. Was24, Dawn R. Weatherford40, K. Wiseman34, Tara Zaksaite9, Daniel V. Zuj25, Rolf A. Zwaan7 
TL;DR: This article found that participants who described the robber were 25% worse at identifying the robber in a lineup than were participants who instead listed U.S. states and capitals, which has been termed the verbal overshadowing effect.
Abstract: Trying to remember something now typically improves your ability to remember it later. However, after watching a video of a simulated bank robbery, participants who verbally described the robber were 25% worse at identifying the robber in a lineup than were participants who instead listed U.S. states and capitals—this has been termed the “verbal overshadowing” effect (Schooler & Engstler-Schooler, 1990). More recent studies suggested that this effect might be substantially smaller than first reported. Given uncertainty about the effect size, the influence of this finding in the memory literature, and its practical importance for police procedures, we conducted two collections of preregistered direct replications (RRR1 and RRR2) that differed only in the order of the description task and a filler task. In RRR1, when the description task immediately followed the robbery, participants who provided a description were 4% less likely to select the robber than were those in the control condition. In RRR2, when the description was delayed by 20 min, they were 16% less likely to select the robber. These findings reveal a robust verbal overshadowing effect that is strongly influenced by the relative timing of the tasks. The discussion considers further implications of these replications for our understanding of verbal overshadowing.

Journal ArticleDOI
TL;DR: In this article, the authors examine the characteristics and attributes of the effective professional learning community as identified in the literature, drawing out the tensions and contradictions embodied in the terms professional, learning and community.
Abstract: The concept of the professional learning community (PLC) has been embraced widely in schools as a means for teachers to engage in professional development leading to enhanced pupil learning. However, the term has become so ubiquitous it is in danger of losing all meaning, or worse, of reifying ‘teacher learning’ within a narrowly defined ambit which loses sight of the essentially contestable concepts which underpin it. The primary aim of this paper is therefore to (re-)examine the assumptions underpinning the PLC as a vehicle for teacher led change in schools in order to confront and unsettle a complacent and potentially damaging empirical consensus around teacher learning. This paper examines the characteristics and attributes of the ‘effective’ professional learning community as identified in the literature, drawing out the tensions and contradictions embodied in the terms professional, learning and community. The paper considers the implications of this analysis for practice, and concludes by offering some insights into the nature of ‘school improvement’, and the role of PLCs in realizing this.

Journal ArticleDOI
TL;DR: In this article, sustainable performance differences within the Greek food supply chain and numerous statistical comparisons of its key members (growers, manufacturers, wholesalers and retailers) with respect to firm size were analyzed using ANOVA.

Journal ArticleDOI
TL;DR: The hibernating squirrel has been identified as an innovative model to study resistance to atrophy and how nutrient supplementation may further enhance recovery and reduce atrophy despite unloading or ageing is currently of great interest.
Abstract: Maintenance of skeletal muscle is essential for health and survival. There are marked losses of skeletal muscle mass as well as strength and physiological function under conditions of low mechanical load, such as space flight, as well as ground based models such as bed rest, immobilization, disuse, and various animal models. Disuse atrophy is caused by mechanical unloading of muscle and this leads to reduced muscle mass without fiber attrition. Skeletal muscle stem cells (satellite cells) and myonuclei are integrally involved in skeletal muscle responses to environmental changes that induce atrophy. Myonuclear domain size is influenced differently in fast and slow twitch muscle, but also by different models of muscle wasting, a factor that is not yet understood. Although the myonuclear domain is 3-dimensional this is rarely considered. Apoptosis as a mechanism for myonuclear loss with atrophy is controversial, whereas cell death of satellite cells has not been considered. Molecular signals such as myostatin/SMAD pathway, MAFbx, and MuRF1 E3 ligases of the ubiquitin proteasome pathway and IGF1-AKT-mTOR pathway are 3 distinctly different contributors to skeletal muscle protein adaptation to disuse. Molecular signaling pathways activated in muscle fibers by disuse are rarely considered within satellite cells themselves despite similar exposure to unloading or low mechanical load. These molecular pathways interact with each other during atrophy and also when various interventions are applied that could alleviate atrophy. Re-applying mechanical load is an obvious method to restore muscle mass, however how nutrient supplementation (e.g., amino acids) may further enhance recovery (or reduce atrophy despite unloading or ageing) is currently of great interest. Satellite cells are particularly responsive to myostatin and to growth factors. Recently, the hibernating squirrel has been identified as an innovative model to study resistance to atrophy.

Journal ArticleDOI
TL;DR: The authors examined the role of decision-making and consumption contexts on the efficacy of advertising appeals for environmentally friendly products and policies and found that consumers are more responsive to other-benefit appeals and in more private settings they favor self-benefit appeal.
Abstract: There are two forms of advertising appeals for environmentally friendly products and policies: those that provide consumer benefit (e.g., cost savings) and those that provide societal benefit (e.g., lower emissions). This research examines the role of decision-making and consumption contexts on the efficacy of each appeal. The results of three studies indicate that in contexts where consumers experience heightened public accountability they are more responsive to other-benefit appeals, and in more private settings they favor self-benefit appeals. We replicate this finding across multiple samples, product categories, and consumption and decision-making contexts. Our findings reconcile previously conflicting research on the efficacy of either appeal type and provide guidance for marketers seeking to promote environmentally friendly consumption.

Journal ArticleDOI
TL;DR: In this paper, the authors investigated the effect of single doses of biochar and repeat-applications (two years later) on heavy metal content and distribution in soil, together with metal concentrations in plants (barley, beans) over repeated cropping cycles.

Journal ArticleDOI
TL;DR: In this paper, the authors explore the roles of professional and hierarchical differentiation, and how there were organisational and managerial limitations to the practical application of the "new museology" that has shaped museum functions and roles.

Journal ArticleDOI
TL;DR: In this article, the authors provide a controlled evaluation of a peer mentoring scheme within UK universities, focusing on direct, mediating and moderating effects of mentoring on levels of wellbeing, integration and retention.
Abstract: Peer mentoring is becoming increasingly popular in UK higher education, however, there remains little good quality, theoretically driven and evaluative research. The current study aims to bridge the gap between theory, practice and evaluation by providing a controlled evaluation of a peer mentoring scheme within UK universities. 109 first year undergraduates from two matched universities completed questionnaires at two time points: during the first week of university and again 10 weeks later. Results focused on direct, mediating and moderating effects of mentoring on levels of wellbeing, integration and retention. Peer mentored individuals showed higher levels of integration to university. Four times as many non-peer mentored students had seriously considered leaving university compared to peer mentored students. Integration partially mediated the relationship between mentoring and intention to stay at university. Moderating effects analyses indicate that mentoring may buffer the effect of the transition to University. Results are discussed in relation to Tinto’s theory of student retention, the benefits and practicalities of peer mentoring within UK universities and the methodological limitations within this study.

Journal ArticleDOI
TL;DR: EmoSenticSpace, a new framework for affective common-sense reasoning that extends WordNet-Affect and SenticNet by providing both emotion labels and polarity scores for a large set of natural language concepts, is proposed.
Abstract: Emotions play a key role in natural language understanding and sensemaking. Pure machine learning usually fails to recognize and interpret emotions in text accurately. The need for knowledge bases that give access to semantics and sentics (the conceptual and affective information) associated with natural language is growing exponentially in the context of big social data analysis. To this end, this paper proposes EmoSenticSpace, a new framework for affective common-sense reasoning that extends WordNet-Affect and SenticNet by providing both emotion labels and polarity scores for a large set of natural language concepts. The framework is built by means of fuzzy c-means clustering and support-vector-machine classification, and takes into account a number of similarity measures, including point-wise mutual information and emotional affinity. EmoSenticSpace was tested on three emotion-related natural language processing tasks, namely sentiment analysis, emotion recognition, and personality detection. In all cases, the proposed framework outperforms the state-of-the-art. In particular, the direct evaluation of EmoSenticSpace against psychological features provided in the benchmark ISEAR dataset shows a 92.15% agreement.

Journal ArticleDOI
TL;DR: This work states that C.A.M.M., A.J.B. and D.E.E are members of the guideline development group and have participated in the advisory boards of Almirall, Astellas and LEO Pharma (nonspecific).
Abstract: Conflicts of interest C.A.M. has acted as an invited speaker for Galderma (specific), Astellas (nonspecific), Almirall (nonspecific) and LEO Pharma (nonspecific); has received sponsorship to attend conferences from LEO Pharma (nonspecific); and has participated in the advisory boards of Almirall, Astellas and LEO Pharma (nonspecific). D.J.E. has participated in the advisory board of, and received travel expenses from LEO Pharma (nonspecific). C.A.M., A.J.B. and D.J.E. are members of the guideline development group.

Journal ArticleDOI
TL;DR: In this paper, a choice experiment survey asked Scottish households for their willingness to pay for additional marine protected areas in the Scottish deep-sea and the experiment focused on the elicitation of economic values for two aspects of marine biodiversity: (i) the existence value for deep sea species and (ii) the option value of deep sea organisms as a source for future medicinal products.

Journal ArticleDOI
TL;DR: In current debates about professional practice and education, increasing emphasis is placed on understanding learning as a process of ongoing participation rather than one of acquiring knowledge and skills.
Abstract: Context In current debates about professional practice and education, increasing emphasis is placed on understanding learning as a process of ongoing participation rather than one of acquiring knowledge and skills. However, although this socio-cultural view is important and useful, issues have emerged in studies of practice-based learning that point to certain oversights. Methods Three issues are described here: (i) the limited attention paid to the importance of materiality – objects, technologies, nature, etc. – in questions of learning; (ii) the human-centric view of practice that fails to note the relations among social and material forces, and (iii) the conflicts between ideals of evidence-based standardised models and the sociomaterial contingencies of clinical practice. Discussion It is argued here that a socio-material approach to practice and learning offers important insights for medical education. This view is in line with a growing field of research in the materiality of everyday life, which embraces wide-ranging families of theory that can be only briefly mentioned in this short paper. The main premise they share is that social and material forces, culture, nature and technology, are enmeshed in everyday practice. Objects and humans act upon one another in ways that mutually transform their characteristics and activity. Examples from research in medical practice show how materials actively influence clinical practice, how learning itself is a material matter, how protocols are in fact temporary sociomaterial achievements, and how practices form unique and sometimes conflicting sociomaterial worlds, with diverse diagnostic and treatment approaches for the same thing. Conclusions This discussion concludes with implications for learning in practice. What is required is a shift from an emphasis on acquiring knowledge to participating more wisely in particular situations. This focus is on learning how to attune to minor material fluctuations and surprises, how to track one's own and others’ effects on ‘intra-actions’ and emerging effects, and how to improvise solutions.