Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Adherence and acceptability of community-based distribution of micronutrient powders in Southern Mali
Roschnik, Natalie ; Diarra, Hawa ; Dicko, Yahia ; Diarra, Seybou ; Stanley, Isobel ; Moestue, Helen ; McClean, Judy ; Verhoef, Hans ; Clarke, Sian E. - \ 2019
Maternal and Child Nutrition 15 (2019). - ISSN 1740-8695
cluster randomised controlled trial - community-based - complementary feeding - infant and child nutrition - malaria - Mali - micronutrients - preschool children

Home fortification with micronutrient powders (MNP) has been shown to reduce anaemia, with high overall acceptability and adherence, but there is limited evidence from West Africa. Around 80% of children younger than 5 years are anaemic in Mali, and new interventions are needed. This paper reports on the adherence and acceptability of a community-led MNP intervention targeting children aged 6–59 months in Southern Mali. The MNP were delivered by a multidisciplinary group of community volunteers using community-based preschools, cooking demonstrations, and traditional communication networks to promote MNP, nutrition, hygiene, and child stimulation. The MNP were delivered alongside early childhood development interventions and seasonal malaria chemoprevention. Adherence and acceptability were evaluated through two cross-sectional surveys in 2014 and 2016 and a qualitative evaluation in 2015. Over 80% of parents reported ever having given MNP to their child, with 65% having given MNP for four or more days in the last week. Likely contributors to uptake include: perceived positive changes in the children following MNP use, the selection of a food vehicle that was already commonly given to children (morning porridge or bouillie) and the community driven, decentralized and integrated delivery approach. These findings support recommendations from recent reviews of MNP implementation to use community-based delivery approaches and behaviour change components.

Timing and duration of primary molt in Northern Hemisphere skuas and jaegers
Bemmelen, Rob S.A. van; Clarke, Rohan H. ; Pyle, Peter ; Camphuysen, Kees - \ 2018
The Auk : a quarterly journal of ornithology 135 (2018)4. - ISSN 0004-8038 - p. 1043 - 1054.
annual cycles - molt-migration overlap - primary molt - Stercorariidae
We compared the primary molt of the 4 species of skuas and jaegers (Stercorariidae) that breed in the Northern Hemisphere: Long-tailed Jaeger (Stercorarius longicaudus), Parasitic Jaeger (S. parasiticus), Pomarine Jaeger (S.
pomarinus), and Great Skua (S. skua). We analyzed primary molt data of 1,573 individuals of multiple age classes, mostly collected from photographs taken at sea but also from museum specimens and beached individuals. Whereas molt duration generally increased with species’ size, molt duration in Parasitic and Pomarine jaegers was surprisingly similar given their size difference. Larger species started primary molt earlier and showed more overlap with postbreeding migration, such that there was complete overlap in Great Skua but no overlap in Long-tailed Jaeger. Within jaeger species, the first primary molt cycle took longer than later molt cycles. We suggest that, unlike birds in their first primary molt cycle, birds in their second or subsequent primary molt cycles are time-constrained to complete primary molt before the onset of prebreeding long-distance migration. By contrast, molt duration did not differ between age classes of Great Skuas. Adult Great Skuas may have overcome the time constraint by completely overlapping molt and postbreeding migration. Molt-migration overlap is generally rare in birds but may be feasible for Great Skuas given their shorter migration distance and low migration speed.
Experiencing a water sports holiday as part of a rehabilitation trajectory: identifying the salutogenic mechanisms
Wagenaar, M. ; Vaandrager, L. - \ 2018
In: Tourism, health, wellbeing and protected areas / Azara, Iride, Michopoulou, Eleni, Niccolini, Federico, Derrick Taff, B., Clarke, Alan, CABI - ISBN 9781786391315 - p. 167 - 177.
This chapter presents a case study exploring how people from a rehabilitation centre experienced a water sports holiday. The location was a water sports island in the Loosdrechtse Plassen, a lake district in the Netherlands. The chapter contributes to the existing literature on the benefits of going on nature-based holidays while having a disability. It identifies the salutogenic mechanisms that shaped participants' experiences of the water sports holiday as part of a rehabilitation trajectory and how these experiences influenced their daily life.
Associations of omega-3 fatty acid supplement use with cardiovascular disease risks meta-analysis of 10 trials involving 77 917 individuals
Aung, Theingi ; Halsey, Jim ; Kromhout, Daan ; Gerstein, Hertzel C. ; Marchioli, Roberto ; Tavazzi, Luigi ; Geleijnse, Johanna M. ; Rauch, Bernhard ; Ness, Andrew ; Galan, Pilar ; Chew, Emily Y. ; Bosch, Jackie ; Collins, Rory ; Lewington, Sarah ; Armitage, Jane ; Clarke, Robert - \ 2018
JAMA Cardiology 3 (2018)3. - ISSN 2380-6583 - p. 225 - 234.
IMPORTANCE Current guidelines advocate the use of marine-derived omega-3 fatty acids supplements for the prevention of coronary heart disease and major vascular events in people with prior coronary heart disease, but large trials of omega-3 fatty acids have produced conflicting results. OBJECTIVE To conduct ameta-analysis of all large trials assessing the associations of omega-3 fatty acid supplements with the risk of fatal and nonfatal coronary heart disease and major vascular events in the full study population and prespecified subgroups. DATA SOURCES AND STUDY SELECTION This meta-analysis included randomized trials that involved at least 500 participants and a treatment duration of at least 1 year and that assessed associations of omega-3 fatty acids with the risk of vascular events. DATA EXTRACTION AND SYNTHESIS Aggregated study-level datawere obtained from 10 large randomized clinical trials. Rate ratios for each trial were synthesized using observed minus expected statistics and variances. Summary rate ratios were estimated by a fixed-effects meta-analysis using 95%confidence intervals for major diseases and 99%confidence intervals for all subgroups. MAIN OUTCOMES AND MEASURES The main outcomes included fatal coronary heart disease, nonfatalmyocardial infarction, stroke, major vascular events, and all-cause mortality, as well as major vascular events in study population subgroups. RESULTS Of the 77 917 high-risk individuals participating in the 10 trials, 47 803 (61.4%) were men, and the mean age at entry was 64.0 years; the trials lasted a mean of 4.4 years. The associations of treatment with outcomes were assessed on 6273 coronary heart disease events (2695 coronary heart disease deaths and 2276 nonfatalmyocardial infarctions) and 12 001 major vascular events. Randomization to omega-3 fatty acid supplementation (eicosapentaenoic acid dose range, 226-1800mg/d) had no significant associations with coronary heart disease death (rate ratio [RR], 0.93; 99%CI, 0.83-1.03; P = .05), nonfatal myocardial infarction (RR, 0.97; 99%CI, 0.87-1.08; P = .43) or any coronary heart disease events (RR, 0.96; 95%CI, 0.90-1.01; P = .12). Neither did randomization to omega-3 fatty acid supplementation have any significant associations with major vascular events (RR, 0.97; 95% CI, 0.93-1.01; P = .10), overall or in any subgroups, including subgroups composed of persons with prior coronary heart disease, diabetes, lipid levels greater than a given cutoff level, or statin use. CONCLUSIONS AND RELEVANCE This meta-analysis demonstrated that omega-3 fatty acids had no significant association with fatal or nonfatal coronary heart disease or any major vascular events. It provides no support for current recommendations for the use of such supplements in people with a history of coronary heart disease.
Response of benthic fauna to experimental bottom fishing : A global meta-analysis
Sciberras, Marija ; Hiddink, Jan Geert ; Jennings, Simon ; Szostek, Claire L. ; Hughes, Kathryn M. ; Kneafsey, Brian ; Clarke, Leo J. ; Ellis, Nick ; Rijnsdorp, Adriaan D. ; Mcconnaughey, Robert A. ; Hilborn, Ray ; Collie, Jeremy S. ; Pitcher, C.R. ; Amoroso, Ricardo O. ; Parma, Ana M. ; Suuronen, Petri ; Kaiser, Michel J. - \ 2018
Fish and Fisheries 19 (2018)4. - ISSN 1467-2960 - p. 698 - 715.
Dredging - Effects of trawling - Fishing impacts - Invertebrate communities - Systematic review - Taxonomic analysis
Bottom-contact fishing gears are globally the most widespread anthropogenic sources of direct disturbance to the seabed and associated biota. Managing these fishing disturbances requires quantification of gear impacts on biota and the rate of recovery following disturbance. We undertook a systematic review and meta-analysis of 122 experiments on the effects-of-bottom fishing to quantify the removal of benthos in the path of the fishing gear and to estimate rates of recovery following disturbance. A gear pass reduced benthic invertebrate abundance by 26% and species richness by 19%. The effect was strongly gear-specific, with gears that penetrate deeper into the sediment having a significantly larger impact than those that penetrate less. Sediment composition (% mud and presence of biogenic habitat) and the history of fishing disturbance prior to an experimental fishing event were also important predictors of depletion, with communities in areas that were not previously fished, predominantly muddy or biogenic habitats being more strongly affected by fishing. Sessile and low mobility biota with longer life-spans such as sponges, soft corals and bivalves took much longer to recover after fishing (>3 year) than mobile biota with shorter life-spans such as polychaetes and malacostracans (<1 year). This meta-analysis provides insights into the dynamics of recovery. Our estimates of depletion along with estimates of recovery rates and large-scale, high-resolution maps of fishing frequency and habitat will support more rigorous assessment of the environmental impacts of bottom-contact gears, thus supporting better informed choices in trade-offs between environmental impacts and fish production.
Analysing intermediary organisations and their influence on upgrading in emerging agricultural clusters
Ramirez, Matias ; Clarke, Ian ; Klerkx, Laurens - \ 2018
Environment and Planning A 50 (2018)6. - ISSN 0308-518X - p. 1314 - 1335.
This paper analyses intermediary organisations in developing economy agricultural clusters. The paper critically engages with a growing narrative in studies of intermediaries that have stressed the ownership structure of intermediaries as a key driver for enabling knowledge transfer, inter-firm learning and upgrading of small producers in clusters. Two case studies of Latin American clusters are presented and discussed. The study suggests that in addition to ownership structure, cluster governance and the embeddedness of intermediaries in clusters are critical factors that need to be taken into account in understanding the influence of intermediaries in the upgrading of small producers in clusters.
Nutrition for the ageing brain: Towards evidence for an optimal diet
Vauzour, David ; Camprubi-Robles, Maria ; Miquel-Kergoat, Sophie ; Andres-Lacueva, Cristina ; Bánáti, Diána ; Barberger-Gateau, Pascale ; Bowman, Gene L. ; Caberlotto, Laura ; Clarke, Robert ; Hogervorst, Eef ; Kiliaan, Amanda J. ; Lucca, Ugo ; Manach, Claudine ; Minihane, Anne-Marie ; Mitchell, Ellen Siobhan ; Perneczky, Robert ; Perry, Hugh ; Roussel, Anne-Marie ; Schuermans, Jeroen ; Sijben, John ; Spencer, Jeremy P.E. ; Thuret, Sandrine ; De Rest, Ondine Van; Vandewoude, Maurits ; Wesnes, Keith ; Williams, Robert J. ; Williams, Robin S.B. ; Ramirez, Maria - \ 2017
Ageing Research Reviews 35 (2017). - ISSN 1568-1637 - p. 222 - 240.
As people age they become increasingly susceptible to chronic and extremely debilitating brain diseases. The precise cause of the neuronal degeneration underlying these disorders, and indeed normal brain ageing remains however elusive. Considering the limits of existing preventive methods, there is a desire to develop effective and safe strategies. Growing preclinical and clinical research in healthy individuals or at the early stage of cognitive decline has demonstrated the beneficial impact of nutrition on cognitive functions. The present review is the most recent in a series produced by the Nutrition and Mental Performance Task Force under the auspice of the International Life Sciences Institute Europe (ILSI Europe). The latest scientific advances specific to how dietary nutrients and non-nutrient may affect cognitive ageing are presented. Furthermore, several key points related to mechanisms contributing to brain ageing, pathological conditions affecting brain function, and brain biomarkers are also discussed. Overall, findings are inconsistent and fragmented and more research is warranted to determine the underlying mechanisms and to establish dose-response relationships for optimal brain maintenance in different population subgroups. Such approaches are likely to provide the necessary evidence to develop research portfolios that will inform about new dietary recommendations on how to prevent cognitive decline.
Carbon budgets and energy transition pathways
Vuuren, Detlef P. Van; Soest, Heleen van; Riahi, Keywan ; Clarke, Leon ; Krey, Volker ; Kriegler, Elmar ; Rogelj, Joeri ; Schaeffer, Michiel ; Tavoni, Massimo - \ 2016
Environmental Research Letters 11 (2016)7. - ISSN 1748-9326
Carbon budget - climate policy - integrated assessment - mitigation strategy

Scenarios from integrated assessment models can provide insights into how carbon budgets relate to other policy-relevant indicators by including information on how fast and by how much emissions can be reduced. Such indicators include the peak year of global emissions, the decarbonisation rate and the deployment of low-carbon technology. Here, we show typical values for these indicators for different carbon budgets, using the recently compiled IPCC scenario database, and discuss how these vary as a function of non-CO2 forcing, energy use and policy delay. For carbon budgets of 2000 GtCO2 and less over the 2010-2100 period, supply of low carbon technologies needs to be scaled up massively from today's levels, unless energy use is relatively low. For the subgroup of scenarios with a budget below 1000 GtCO2 (consistent with >66% chance of limiting global warming to below 2 °C relative to preindustrial levels), the 2050 contribution of low-carbon technologies is generally around 50%-75%, compared to less than 20% today (range refers to the 10-90th interval of available data).

Mapping the climate change challenge
Hallegatte, Stephane ; Rogelj, Joeri ; Allen, Myles ; Clarke, Leon ; Edenhofer, Ottmar ; Field, Christopher B. ; Friedlingstein, Pierre ; Kesteren, Line Van; Knutti, Reto ; Mach, Katharine J. ; Mastrandrea, Michael ; Michel, Adrien ; Minx, Jan ; Oppenheimer, Michael ; Plattner, Gian Kasper ; Riahi, Keywan ; Schaeffer, Michiel ; Stocker, Thomas F. ; Vuuren, Detlef P. van - \ 2016
Nature Climate Change 6 (2016)7. - ISSN 1758-678X - p. 663 - 668.

Discussions on a long-term global goal to limit climate change, in the form of an upper limit to warming, were only partially resolved at the United Nations Framework Convention on Climate Change negotiations in Paris, 2015. Such a political agreement must be informed by scientific knowledge. One way to communicate the costs and benefits of policies is through a mapping that systematically explores the consequences of different choices. Such a multi-disciplinary effort based on the analysis of a set of scenarios helped structure the IPCC AR5 Synthesis Report. This Perspective summarizes this approach, reviews its strengths and limitations, and discusses how decision-makers can use its results in practice. It also identifies research needs that can facilitate integrated analysis of climate change and help better inform policy-makers and the public.

GO-FAANG meeting : a Gathering On Functional Annotation of Animal Genomes
Tuggle, Christopher K. ; Giuffra, Elisabetta ; White, Stephen N. ; Clarke, Laura ; Zhou, Huaijun ; Ross, Pablo J. ; Acloque, Hervé ; Reecy, James M. ; Archibald, Alan ; Bellone, Rebecca R. ; Boichard, Michèle ; Chamberlain, Amanda ; Cheng, Hans ; Crooijmans, Richard P.M.A. ; Delany, Mary E. ; Finno, Carrie J. ; Groenen, Martien A.M. ; Hayes, Ben ; Lunney, Joan K. ; Petersen, Jessica L. ; Plastow, Graham S. ; Schmidt, Carl J. ; Song, Jiuzhou ; Watson, Mick - \ 2016
Animal Genetics 47 (2016)5. - ISSN 0268-9146 - p. 528 - 533.
data coordination centre (DCC) - data sharing - Genomics - metanalysis

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.

Should the Lion Eat Straw Like the Ox? Animal Ethics and the Predation Problem
Keulartz, Jozef - \ 2016
Journal of Agricultural and Environmental Ethics (2016). - ISSN 1187-7863 - 22 p.
Capability approach - Political theory of animal rights - Predation problem - Rights theories - Utilitarianism

Stephen Clark’s article The Rights of Wild Things from 1979 was the starting point for the consideration in the animal ethics literature of the so-called ‘predation problem’. Clark examines the response of David George Ritchie to Henry Stephens Salt, the first writer who has argued explicitly in favor of animal rights. Ritchie attempts to demonstrate—via reductio ad absurdum—that animals cannot have rights, because granting them rights would oblige us to protect prey animals against predators that wrongly violate their rights. This article navigates the reader through the debate sparked off by Clarke’s article, with as final destination what I consider to be the best way to deal with the predation problem. I will successively discuss arguments against the predation reductio from Singer’s utilitarian approach, Regan’s deontological approach, Nussbaum’s capability approach, and Donadson and Kymlicka’s political theory of animal rights.

Enteric Methane Emissions: Mitigation Strategies
Scholten, M.C.T. ; Dijkstra, J. ; Bannink, A. ; Vellinga, Th.V. ; Haas, Y. de; Boer, I.J.M. de; Cone, J.W. ; Middelaar, C.E. van; Clarke, H.J. - \ 2016
Dual thinking for scientists
Scheffer, M. ; Bascompte, J. ; Bjordam, T.K. ; Carpenter, S.R. ; Clarke, L. ; Folke, C. ; Marquet, P.A. ; Mazzeo, N. ; Meerhoff, M. ; Sala, O. ; Westley, F.R. - \ 2015
Ecology and Society 20 (2015)2. - ISSN 1708-3087
Recent studies provide compelling evidence for the idea that creative thinking draws upon two kinds of processes linked to distinct physiological features, and stimulated under different conditions. In short, the fast system-I produces intuition whereas the slow and deliberate system-II produces reasoning. System-I can help see novel solutions and associations instantaneously, but is prone to error. System-II has other biases, but can help checking and modifying the system-I results. Although thinking is the core business of science, the accepted ways of doing our work focus almost entirely on facilitating system-II. We discuss the role of system-I thinking in past scientific breakthroughs, and argue that scientific progress may be catalyzed by creating conditions for such associative intuitive thinking in our academic lives and in education. Unstructured socializing time, education for daring exploration, and cooperation with the arts are among the potential elements. Because such activities may be looked upon as procrastination rather than work, deliberate effort is needed to counteract our systematic bias. © 2015 by the author(s).
Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena?
Rajilic-Stojanovic, M. ; Jonkers, D.M. ; Salonen, A. ; Hanevik, K. ; Raes, J. ; Jalanka, J. ; Vos, W.M. de; Manichanh, C. ; Golic, N. ; Enck, P. ; Philippou, E. ; Iraqi, F.A. ; Clarke, G. ; Spiller, R.C. ; Penders, J. - \ 2015
American Journal of Gastroenterology 110 (2015)2. - ISSN 0002-9270 - p. 278 - 287.
Irritable bowel syndrome (IBS) is a heterogeneous functional disorder with a multifactorial etiology that involves the interplay of both host and environmental factors. Among environmental factors relevant for IBS etiology, the diet stands out given that the majority of IBS patients report their symptoms to be triggered by meals or specific foods. The diet provides substrates for microbial fermentation, and, as the composition of the intestinal microbiota is disturbed in IBS patients, the link between diet, microbiota composition, and microbial fermentation products might have an essential role in IBS etiology. In this review, we summarize current evidence regarding the impact of diet and the intestinal microbiota on IBS symptoms, as well as the reported interactions between diet and the microbiota composition. On the basis of the existing data, we suggest pathways (mechanisms) by which diet components, via the microbial fermentation, could trigger IBS symptoms. Finally, this review provides recommendations for future studies that would enable elucidation of the role of diet and microbiota and how these factors may be (inter)related in the pathophysiology of IBS
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter
Archibald, A.L. ; Bottema, C.D. ; Brauning, R. ; Burgess, S.C. ; Burt, D.W. ; Casas, E. ; Cheng, H.H. ; Clarke, L. ; Couldrey, C. ; Dalrymple, B.P. ; Elsik, C.G. ; Foissac, S. ; Giuffra, E. ; Groenen, M.A.M. ; Hayes, B.J. ; Huang, L.S. ; Khatib, H. ; Kijas, J.W. ; Kim, H. ; Lunney, J.K. ; McCarthy, F.M. ; McEwan, J. ; Moore, S. ; Nanduri, B. ; Notredame, C. ; Palti, Y. ; Plastow, G.S. ; Reecy, J.M. ; Rohrer, G. ; Sarropoulou, E. ; Schmidt, C.J. ; Silverstein, J. ; Tellam, R.L. ; Tixier-Boichard, M. ; Tosser-klopp, G. ; Tuggle, C.K. ; Vilkki, J. ; White, S.N. ; Zhao, S. ; Zhou, H. - \ 2015
Genome Biology 16 (2015). - ISSN 1474-7596 - 6 p.
We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.
Identification of QTL markers contributing to plant growth, oil yield and fatty acid composition in the oilseed crop Jatropha curcas L.
King, A.J. ; Montes, L.R. ; Clarke, J.G. ; Itzep, J. ; Perez, C.A.A. ; Jongschaap, R.E.E. ; Visser, R.G.F. ; Loo, E.N. van; Graham, I.A. - \ 2015
Biotechnology for Biofuels 8 (2015). - ISSN 1754-6834 - 17 p.
Background: Economical cultivation of the oilseed crop Jatropha curcas is currently hampered in part due to the non-availability of purpose-bred cultivars. Although genetic maps and genome sequence data exist for this crop, marker-assisted breeding has not yet been implemented due to a lack of available marker–trait association studies. To identify the location of beneficial alleles for use in plant breeding, we performed quantitative trait loci (QTL) analysis for a number of agronomic traits in two biparental mapping populations. Results: The mapping populations segregated for a range of traits contributing to oil yield, including plant height, stem diameter, number of branches, total seeds per plant, 100-seed weight, seed oil content and fatty acid composition. QTL were detected for each of these traits and often over multiple years, with some variation in the phenotypic variance explained between different years. In one of the mapping populations where we recorded vegetative traits, we also observed co-localization of QTL for stem diameter and plant height, which were both overdominant, suggesting a possible locus conferring a pleotropic heterosis effect. By using a candidate gene approach and integrating physical mapping data from a recent high-quality release of the Jatropha genome, we were also able to position a large number of genes involved in the biosynthesis of storage lipids onto the genetic map. By comparing the position of these genes with QTL, we were able to detect a number of genes potentially underlying seed traits, including phosphatidate phosphatase genes. Conclusions: The QTL we have identified will serve as a useful starting point in the creation of new varieties of J. curcas with improved agronomic performance for seed and oil productivity. Our ability to physically map a significant proportion of the Jatropha genome sequence onto our genetic map could also prove useful in identifying the genes underlying particular traits, allowing more controlled and precise introgression of desirable alleles and permitting the pyramiding or stacking of multiple QTL. Keywords: Jatropha curcas, Linkage mapping, QTL analysis, Oil content, Seed weight, Seed yield
Managing a complex population strucutre exploring the importance of information from fisheries-independent sources
Hintzen, N.T. ; Roel, B.A. ; Benden, D.P.L.D. ; Clarke, M. ; Egan, A. ; Nash, R.D.M. ; Rohlf, N. ; Hatfield, E.M.C. - \ 2015
ICES Journal of Marine Science 72 (2015)2. - ISSN 1054-3139 - p. 528 - 542.
herring clupea-harengus - state-space model - north-sea - stock assessment - spawning components - management advice - british-isles - celtic sea - dynamics - atlantic
Natural resource managers aim to manage fish stocks at sustainable levels. Often, management of these stocks is based on the results of analytical stock assessments. Accurate catch data, which can be attributed to a specific population unit and reflects the population structure, are needed for these approaches. Often though, the quality of the catch data is compromised when dealing with a complex population structure where fish of different population units mix in a fishery. The herring population units west of the British Isles are prone to mixing. Here, the inability to perfectly allocate the fish caught to the population unit they originate from, due to classification problems, poses problems for management. These mixing proportions are often unknown; therefore, we use simulation modelling combined with management strategy evaluation to evaluate the role fisheries-independent surveys can play in an assessment to provide unbiased results, irrespective of population unit mixing and classification success. We show that failure to account for mixing is one of the major drivers of biased estimates of population abundance, affecting biomass reference points and MSY targets. When mixing of population units occurs, the role a survey can play to provide unbiased assessment results is limited. Either different assessment models should be employed or stock status should be considered from the survey data alone. In addition, correctly classifying the origin of fish is especially important for those population units that are markedly smaller in size than other units in the population complex. Without high classification success rates, smaller population units are extremely vulnerable to overexploitation.
Effects of homocysteine lowering with B vitamins on cognitive aging; meta-analysis of 11 trials with cognitive data on 22,000 individuals
Clarke, R. ; Bennett, D. ; Parish, S. ; Eussen, S.J.P.M. ; Groot, C.P.G.M. de - \ 2014
American Journal of Clinical Nutrition 100 (2014)2. - ISSN 0002-9165 - p. 657 - 666.
randomized controlled-trial - folic-acid supplementation - placebo-controlled trial - alzheimers-disease - older-adults - cardiovascular-disease - plasma homocysteine - stroke prevention - vascular-disease - double-blind
Background: Elevated plasma homocysteine is a risk factor for Alzheimer disease, but the relevance of homocysteine lowering to slow the rate of cognitive aging is uncertain. Objective: The aim was to assess the effects of treatment with B vitamins compared with placebo, when administered for several years, on composite domains of cognitive function, global cognitive function, and cognitive aging. Design: A meta-analysis was conducted by using data combined from 11 large trials in 22,000 participants. Domain-based z scores (for memory, speed, and executive function and a domain-composite score for global cognitive function) were available before and after treatment (mean duration: 2.3 y) in the 4 cognitive-domain trials (1340 individuals); Mini-Mental State Examination (MMSE)–type tests were available at the end of treatment (mean duration: 5 y) in the 7 global cognition trials (20,431 individuals). Results: The domain-composite and MMSE-type global cognitive function z scores both decreased with age (mean ± SE: -0.054 ± 0.004 and -0.036 ± 0.001/y, respectively). Allocation to B vitamins lowered homocysteine concentrations by 28% in the cognitive-domain trials but had no significant effects on the z score differences from baseline for individual domains or for global cognitive function (z score difference: 0.00; 95% CI: -0.05, 0.06). Likewise, allocation to B vitamins lowered homocysteine by 26% in the global cognition trials but also had no significant effect on end-treatment MMSE-type global cognitive function (z score difference: -0.01; 95% CI: -0.03, 0.02). Overall, the effect of a 25% reduction in homocysteine equated to 0.02 y (95% CI: -0.10, 0.13 y) of cognitive aging per year and excluded reductions of >1 mo per year of treatment. Conclusion: Homocysteine lowering by using B vitamins had no significant effect on individual cognitive domains or global cognitive function or on cognitive aging.
Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease
Meurs, J.B.J. van; Pare, G. ; Schwartz, S.M. ; Hazra, A. ; Tanaka, T. ; Vermeulen, S.H. ; Cotlarciuc, I. ; Yuan, X. ; Malarstig, A. ; Bandinelli, S. ; Bis, J.C. ; Morn, H. ; Brown, M.J. ; Chen, C. ; Chen, Y.D. ; Clarke, R.J. ; Dehghan, A. ; Erdmann, J. ; Ferrucci, L. ; Hamsten, A. ; Hofman, A. ; Hunten, D.J. ; Goel, A. ; Johnson, A.D. ; Kathiresan, S. ; Kampman, E. ; Kiel, D.P. ; Kiemeney, L.A. ; Chambers, J.C. ; Kraft, P. ; Lindemans, J. ; McKnight, B. ; Nelson, C.P. ; O'Donnell, C.J. ; Psaty, B.M. ; Ridken, P.M. ; Rivadeneira, F. ; Rose, L.M. ; Seedoif, U. ; Siscovick, D.S. ; Schunkert, H. ; Selhub, J. ; Ueland, P.M. ; Vollenweiden, P. ; Waeben, G. ; Waterworth, D.M. ; Watkins, H. ; Witteman, J.C.M. ; Heijen, M. den; Jacques, P. ; Uitterlinden, A.G. ; Koonet, J.S. ; Rader, D.J. ; Reilly, M.P. ; Moose, V. ; Chasman, D.I. ; Samani, N.J. ; Ahmadi, K.R. - \ 2013
American Journal of Clinical Nutrition 98 (2013)3. - ISSN 0002-9165 - p. 668 - 676.
genome-wide association - cardiovascular-disease - mendelian randomization - heart-disease - expression - metaanalysis - mthfr - polymorphism - women - identification
Background: The strong observational association between total homocysteine (tHcy) concentrations and risk of coronary artery disease (CAD) and the null associations in the homocysteinelowering trials have prompted the need to identify genetic variants associated with homocysteine concentrations and risk of CAD. Objective: We tested whether common genetic polymorphisms associated with variation in tlicy are also associated with CAD. Design: We conducted a meta-analysis of genome-wide association studies (GWAS) on tHcy concentrations in 44,147 individuals of European descent. Polymolphisms associated with tHcy (P <10(-8)) were tested for association with CAD in 31,400 cases and 92,927 controls. Results: Common variants at 13 loci, explaining 5.9% of the variation in tHcy, were associated with tHcy concentrations, including 6 novel loci in or near MMACHC (2.1 X 10(-9)), SLC17A3 (1.0 x 10(-8)), GTPB10 (1.7 X 10(-8)), CUBN (7.5 X 10(-1)), HNFlA (1.2 x 10(-12)), and FUT2 (6.6 x 10(-9)), and variants previously reported at or near the MTHFR, MTR, CPS1, MUT, NOX4, DPEP1, and CBS genes. Individuals within the highest 10% of the genotype risk score (GRS) had 3-gmol/L higher mean tHcy concentrations than did those within the lowest 10% of the GRS (P = 1 X 10(-36)). The GRS was not associated with risk of CAD (OR: 1.01; 95% CI: 0.98, 1.04; P = 0.49). Conclusions: We identified several novel loci that influence plasma tHcy concentrations. Overall, common genetic variants that influence plasma tHcy concentrations are not associated with risk of CAD in white populations, which further refutes the causal relevance of moderately elevated tHey concentrations and tHcy-related pathways for CAD.
Benefits, Costs, and Consumer Perceptions of the Potential Introduction of a Fungus-Resistant Banana in Uganda and Policy Implications
Kikulwe, E.M. ; Birol, E. ; Wesseler, J.H.H. ; Falck-Zepeda, J. - \ 2013
In: Genetically modified crops in Africa: Economic and policy lessons froms countries south of the Sahara / Falck-Zepeda, J., Gruère, G., Sithole-Niang, I., Washington DC, USA : IFPRI - ISBN 9780896297951 - p. 99 - 141.
Banana is a staple crop in Uganda. Ugandans have the highest per capita consumption of cooking bananas in the world (Clarke 2003). However, banana production in Uganda is limited by several productivity constraints, such as insects, diseases, soil depletion, and poor agronomic practices. To address these constraints, the country has invested significant resources in research and development (R&D) and other publicly funded programs, pursuing approaches over both the short and long term. Uganda formally initiated its short-term approach in the early 1990s; it involves the collection of both local and foreign germplasms for the evaluation and selection of cultivars tolerant to the productivity constraints. The long-term approach, launched in 1995, includes breeding for resistance to the productivity constraints using conventional breeding methods and genetic engineering. Genetic engineering projects in Uganda target the most popular and infertile cultivars that cannot be improved through conventional (cross) breeding.
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