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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    Associations between socio-environmental factors and landscape-scale biodiversity recovery in naturally regenerating tropical and subtropical forests
    Crouzeilles, Renato ; Maurenza, Daniel ; Prieto, Pablo V. ; Barros, Felipe S.M. ; Jakovac, Catarina ; Ferreira, Mariana S. ; Chazdon, Robin L. ; Lindenmayer, David B. ; Brancalion, Pedro H.S. ; Ceccon, Eliane ; Adams, Cristina ; Lazos-Chavero, Elena ; Monteiro, Lara ; Junqueira, André B. ; Strassburg, Bernardo B.N. ; Guariguata, Manuel R. - \ 2020
    Conservation Letters (2020). - ISSN 1755-263X
    forest landscape restoration - meta-analysis - natural regeneration - restoration benefits - socioeconomic and biophysical factors
    Natural regeneration is key for large-scale forest restoration, yet it may lead to different biodiversity outcomes depending on socio-environmental context. We combined the results of a global meta-analysis to quantify how biodiversity recovery in naturally regenerating forests deviates from biodiversity values in reference old-growth forests, with structural equation modeling, to identify direct and indirect associations between socioeconomic, biophysical and ecological factors and deviation in biodiversity recovery at a landscape scale. Low deviation within a landscape means higher chances of multiple sites in naturally regenerating forests successfully recovering biodiversity compared to reference forests. Deviation in biodiversity recovery was directly negatively associated with the percentage of cropland, forest cover, and positively associated with the percentage of urban areas in the surrounding landscape. These three factors mediated the indirect associations with rural population size, recent gross deforestation, time since natural regeneration started, mean annual temperature, mean annual water deficit, road density, land opportunity cost, percentage cover of strictly protected forest areas, and human population variation in the surrounding landscape. We suggest that natural forest restoration should be prioritized in landscapes with both low socioeconomic pressures on land use conversion to pasturelands and urban areas, and high percentage of forest cover.
    Antimethanogenic effects of nitrate supplementation in cattle : A meta-analysis
    Feng, X.Y. ; Dijkstra, J. ; Bannink, A. ; Gastelen, S. van; France, J. ; Kebreab, E. - \ 2020
    Journal of Dairy Science 103 (2020)12. - ISSN 0022-0302 - p. 11375 - 11385.
    beef - dairy - meta-analysis - methane - nitrate
    Supplementing a diet with nitrate is regarded as an effective and promising methane (CH4) mitigation strategy by competing with methanogens for available hydrogen through its reduction of ammonia in the rumen. Studies have shown major reductions in CH4 emissions with nitrate supplementation, but with large variation in response. The objective of this study was to quantitatively investigate the effect of dietary nitrate on enteric CH4 production and yield and evaluate the variables with high potential to explain the heterogeneity of between-study variability using meta-analytical models. A data set containing 56 treatments from 24 studies was developed to conduct a meta-analysis. Dry matter (DM) intake, nitrate dose (g/kg of DM), animal body weight, roughage proportion of diet, dietary crude protein and neutral detergent fiber content, CH4 measurement technique, and type of cattle (beef or dairy) were considered as explanatory variables. Average DM intake and CH4 production for dairy cows (16.2 ± 2.93 kg/d; 311 ± 58.8 g/d) were much higher than for beef cattle (8.1 ± 1.57 kg/d; 146 ± 50.9 g/d). Therefore, a relative mean difference was calculated and used to conduct random-effect and mixed-effect model analysis to eliminate the large variations between types of animal due to intake. The final mixed-effect model for CH4 production (g of CH4/d) had 3 explanatory variables and included nitrate dose, type of cattle, and DM intake. The final mixed-effect model for CH4 yield (g of CH4/kg of DM intake) had 2 explanatory variables and included nitrate dose and type of cattle. Nitrate effect sizes on CH4 production (dairy: −20.4 ± 1.89%; beef: −10.1 ± 1.52%) and yield (dairy: −15.5 ± 1.15%; beef: −8.95 ± 1.764%) were significantly different between the 2 types of cattle. When data from slow-release nitrate sources were removed from the analysis, there was no significant difference in type of cattle anymore for CH4 production and yield. Nitrate dose enhanced the mitigating effect of nitrate on CH4 production and yield by 0.911 ± 0.1407% and 0.728 ± 0.2034%, respectively, for every 1 g/kg of DM increase from its mean dietary inclusion (16.7 g/kg of DM). An increase of 1 kg of DM/d in DM intake from its mean dietary intake (11.1 kg of DM/d) decreased the effect of nitrate on CH4 production by 0.691 ± 0.2944%. Overall, this meta-analysis demonstrated that nitrate supplementation reduces CH4 production and yield in a dose-dependent manner, and that elevated DM intake decreases the effect of nitrate supplementation on CH4 production. Furthermore, the stronger antimethanogenic effect on CH4 production and yield in dairy cows than in beef steers could be related to use of slow-release nitrate in beef cattle.
    Influence of nutrients involved in one-carbon metabolism on DNA methylation in adults-a systematic review and meta-analysis
    Amenyah, Sophia D. ; Hughes, Catherine F. ; Ward, Mary ; Rosborough, Samuel ; Deane, Jennifer ; Thursby, Sara Jayne ; Walsh, Colum P. ; Kok, Dieuwertje E. ; Strain, J.J. ; McNulty, Helene ; Lees-Murdock, Diane J. - \ 2020
    Nutrition Reviews 78 (2020)8. - ISSN 0029-6643 - p. 647 - 666.
    B vitamins - DNA methylation - meta-analysis - systematic review

    CONTEXT: Aberrant DNA methylation is linked to various diseases. The supply of methyl groups for methylation reactions is mediated by S-adenosylmethionine, which depends on the availability of folate and related B vitamins. OBJECTIVES: To investigate the influence of key nutrients involved in 1-carbon metabolism on DNA methylation in adults. DATA SOURCES: Systematic literature searches were conducted in the Cochrane Library, Medline, Embase, Cumulative Index to Nursing and Allied Health Literature Plus, Scopus, and Web of Science databases. Studies that met the inclusion criteria and were published in English were included. DATA EXTRACTION: The first author, study design, sample size, population characteristics, type and duration of intervention, tissue type or cells analyzed, molecular techniques, and DNA methylation outcomes. DATA SYNTHESIS: A meta-analysis of randomized, controlled trials (RCTs) was conducted to investigate the effect of 1-carbon metabolism nutrients on global DNA methylation. Functional analysis and visualization were performed using BioVenn software. RESULTS: From a total of 2620 papers screened by title, 53 studies met the inclusion criteria. Qualitative analysis indicated significant associations between 1-carbon metabolism nutrients and DNA methylation. In meta-analysis of RCTs stratified by method of laboratory analysis, supplementation with folic acid alone or in combination with vitamin B12 significantly increased global DNA methylation in studies using liquid chromatography-mass spectrometry, which had markedly lower heterogeneity (n = 3; Z = 3.31; P = 0.0009; I2 = 0%) in comparison to other methods. Functional analysis highlighted a subset of 12 differentially methylated regions that were significantly related to folate and vitamin B12 biomarkers. CONCLUSION: This study supports significant associations between 1-carbon metabolism nutrients and DNA methylation. However, standardization of DNA methylation techniques is recommended to reduce heterogeneity and facilitate comparison across studies. SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration number: CRD42018091898.

    Selection of indicators for assessing and managing the impacts of bottom trawling on seabed habitats
    Hiddink, Jan Geert ; Kaiser, Michel J. ; Sciberras, Marija ; McConnaughey, Robert A. ; Mazor, Tessa ; Hilborn, Ray ; Collie, Jeremy S. ; Pitcher, C.R. ; Parma, Ana M. ; Suuronen, Petri ; Rijnsdorp, Adriaan D. ; Jennings, Simon - \ 2020
    Journal of Applied Ecology 57 (2020)7. - ISSN 0021-8901 - p. 1199 - 1209.
    beam trawl - ecosystem approach to fisheries management - hydraulic dredge - meta-analysis - otter trawl - scallop dredge - systematic review

    Bottom trawl fisheries are the most widespread source of anthropogenic physical disturbance to seabed habitats. Development of fisheries-, conservation- and ecosystem-based management strategies requires the selection of indicators of the impact of bottom trawling on the state of benthic biota. Many indicators have been proposed, but no rigorous test of a range of candidate indicators against nine commonly agreed criteria (concreteness, theoretical basis, public awareness, cost, measurement, historical data, sensitivity, responsiveness, specificity) has been performed. Here, we collated data from 41 studies that compared the benthic biota in trawled areas with those in control locations (that were either not trawled or trawled infrequently), examining seven potential indicators (numbers and biomass for individual taxa and whole communities, evenness, Shannon–Wiener diversity and species richness) to assess their performance against the set of nine criteria. The effects of trawling were stronger on whole-community numbers and biomass than for individual taxa. Species richness was also negatively affected by trawling but other measures of diversity were not. Community numbers and biomass met all criteria, taxa numbers and biomass and species richness satisfied most criteria, but evenness and Shannon–Wiener diversity did not respond to trawling and only met few criteria, and hence are not suitable state indicators of the effect of bottom trawling. Synthesis and applications. An evaluation of each candidate indicator against a commonly agreed suite of desirable properties coupled with the outputs of our meta-analysis showed that whole-community numbers of individuals and biomass are the most suitable indicators of bottom trawling impacts as they performed well on all criteria. Strengths of these indicators are that they respond strongly to trawling, relate directly to ecosystem functioning and are straightforward to measure. Evenness and Shannon–Wiener diversity are not responsive to trawling and unsuitable for the monitoring and assessment of bottom trawl impacts.

    Carbohydrate utilisation by tilapia: a meta-analytical approach
    Maas, Roel M. ; Verdegem, Marc C.J. ; Wiegertjes, Geert F. ; Schrama, Johan W. - \ 2020
    Reviews in Aquaculture 12 (2020)3. - ISSN 1753-5123 - p. 1851 - 1866.
    digestibility - meta-analysis - non-starch polysaccharides - Oreochromis niloticus - starch

    Currently, studies reporting the digestibility of carbohydrates, starch and especially non-starch polysaccharides (NSP) in fish are scarce. Carbohydrate digestibility in the diet is largely dependent upon carbohydrate composition (starch vs. NSP). NSP are often considered to be indigestible and thus of no nutritional value. The present study reviews carbohydrates in fish feed, distinguishing between total carbohydrate, starch and NSP. Besides a qualitative approach, a meta-analysis was performed, compiling available data from digestibility studies on tilapia. Our meta-analysis confirms the negative effect of NSP on performance (FCR) and nutrient digestibility (crude protein, fat and energy). However, an average NSP digestibility of 24.3% was calculated in 95 cases. Out of these 95 cases, 88% of them showed a positive NSP digestibility. NSP digestibility was shown to contribute to energy digestibility. The digestion of NSP in fish is associated with fermentation in the gut, producing beneficial volatile fatty acids that are rapidly absorbed by the colonic lumen. Therefore, in diet formulation, digestibility and thus energy originating from NSP should be taken into consideration because NSP contribute to the energy needs of fish, here tilapia. Besides being an energy source, specific types of NSP may have immune-modulating and prebiotic effects and may be increasingly added to fish feed as modulators of fish health. We suggest that NSP is potentially (partly) digested by a wide range of fish species, especially by warm-water species with a long gut adapted to feeding on plant matter, as these factors favour gut fermentation.

    Benefits and trade-offs of replacing synthetic fertilizers by animal manures in crop production in China: A meta-analysis
    Zhang, Xiaoying ; Fang, Qunchao ; Zhang, Tao ; Ma, Wenqi ; Velthof, Gerard L. ; Hou, Yong ; Oenema, Oene ; Zhang, Fusuo - \ 2020
    Global Change Biology 26 (2020)2. - ISSN 1354-1013 - p. 888 - 900.
    ammonia emissions - crop yield - fertilizers - greenhouse gases - livestock manure - meta-analysis - soil type - trade-offs

    Recycling of livestock manure to agricultural land may reduce the use of synthetic fertilizer and thereby enhance the sustainability of food production. However, the effects of substitution of fertilizer by manure on crop yield, nitrogen use efficiency (NUE), and emissions of ammonia (NH3), nitrous oxide (N2O) and methane (CH4) as function of soil and manure properties, experimental duration and application strategies have not been quantified systematically and convincingly yet. Here, we present a meta-analysis of these effects using results of 143 published studies in China. Results indicate that the partial substitution of synthetic fertilizers by manure significantly increased the yield by 6.6% and 3.3% for upland crop and paddy rice, respectively, but full substitution significantly decreased yields (by 9.6% and 4.1%). The response of crop yields to manure substitution varied with soil pH and experimental durations, with relatively large positive responses in acidic soils and long-term experiments. NUE increased significantly at a moderate ratio (<40%) of substitution. NH3 emissions were significantly lower with full substitution (62%–77%), but not with partial substitution. Emissions of CH4 from paddy rice significantly increased with substitution ratio (SR), and varied by application rates and manure types, but N2O emissions decreased. The SR did not significantly influence N2O emissions from upland soils, and a relative scarcity of data on certain manure characteristic was found to hamper identification of the mechanisms. We derived overall mean N2O emission factors (EF) of 0.56% and 0.17%, as well as NH3 EFs of 11.1% and 6.5% for the manure N applied to upland and paddy soils, respectively. Our study shows that partial substitution of fertilizer by manure can increase crop yields, and decrease emissions of NH3 and N2O, but depending on site-specific conditions. Manure addition to paddy rice soils is recommended only if abatement strategies for CH4 emissions are also implemented.

    Dataset: Critically examining the knowledge base required to mechanistically project climate impacts: A case study of Europe's fish and shellfish
    Catalán, Ignacio A. ; Auch, Dominik ; Kamermans, Pauline ; Morales-Nin, Beatriz ; Angelopoulos, Natalie V. ; Reglero, Patricia ; Sandersfeld, Tina ; Peck, Myron A. - \ 2019
    Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB)
    aquaculture - climate change - experiments - fisheries - gap analysis - meta-analysis
    The dataset (Excel) corresponds to the data used to generate the gap analysis of the published paper "Critically examining the knowledge base required to mechanistically project climate impacts: A case study of Europe's fish and shellfish" with DOI: 10.1111/faf.12359 It contains 245 cases and 14 variables. The explanation of the variables is contained in the paper.
    Data from: Virus Shedding of Avian Influenza in Poultry: A Systematic Review and Meta-Analysis
    Germeraad, Evelien ; Sanders, Pim ; Gonzales Rojas, Jose - \ 2019
    Wageningen University & Research
    avian influenza - meta-analysis - poultry - systematic review - virus shedding
    These systematic review and meta-analysis were performed to summarize qualitative and quantitative information on virus shedding levels and duration for different AIV strains in experimentally infected poultry species.
    Combining multi-population datasets for joint genome-wide association and meta-analyses: The case of bovine milk fat composition traits
    Gebreyesus, G. ; Buitenhuis, A.J. ; Poulsen, N.A. ; Visker, M.H.P.W. ; Zhang, Q. ; Valenberg, H.J.F. van; Sun, D. ; Bovenhuis, H. - \ 2019
    Journal of Dairy Science 102 (2019)12. - ISSN 0022-0302 - p. 11124 - 11141.
    mega-analysis - meta-analysis - multi-population GWAS

    In genome-wide association studies (GWAS), sample size is the most important factor affecting statistical power that is under control of the investigator, posing a major challenge in understanding the genetics underlying difficult-to-measure traits. Combining data sets available from different populations for joint or meta-analysis is a promising alternative to increasing sample sizes available for GWAS. Simulation studies indicate statistical advantages from combining raw data or GWAS summaries in enhancing quantitative trait loci (QTL) detection power. However, the complexity of genetics underlying most quantitative traits, which itself is not fully understood, is difficult to fully capture in simulated data sets. In this study, population-specific and combined-population GWAS as well as a meta-analysis of the population-specific GWAS summaries were carried out with the objective of assessing the advantages and challenges of different data-combining strategies in enhancing detection power of GWAS using milk fatty acid (FA) traits as examples. Gas chromatography (GC) quantified milk FA samples and high-density (HD) genotypes were available from 1,566 Dutch, 614 Danish, and 700 Chinese Holstein Friesian cows. Using the joint GWAS, 28 additional genomic regions were detected, with significant associations to at least 1 FA, compared with the population-specific analyses. Some of these additional regions were also detected using the implemented meta-analysis. Furthermore, using the frequently reported variants of the diacylglycerol acyltransferase 1 (DGAT1) and stearoyl-CoA desaturase (SCD1) genes, we show that significant associations were established with more FA traits in the joint GWAS than the remaining scenarios. However, there were few regions detected in the population-specific analyses that were not detected using the joint GWAS or the meta-analyses. Our results show that combining multi-population data set can be a powerful tool to enhance detection power in GWAS for seldom-recorded traits. Detection of a higher number of regions using the meta-analysis, compared with any of the population-specific analyses also emphasizes the utility of these methods in the absence of raw multi-population data sets to undertake joint GWAS.

    Virus Shedding of Avian Influenza in Poultry: A Systematic Review and Meta-Analysis
    Germeraad, Evelien A. ; Sanders, Pim ; Hagenaars, Thomas J. ; Jong, Mart C.M. de; Beerens, Nancy ; Gonzales, Jose L. - \ 2019
    Viruses 11 (2019)9. - ISSN 1999-4915
    avian influenza - meta-analysis - poultry - systematic review - virus shedding

    Understanding virus shedding patterns of avian influenza virus (AIV) in poultry is important for understanding host-pathogen interactions and developing effective control strategies. Many AIV strains were studied in challenge experiments in poultry, but no study has combined data from those studies to identify general AIV shedding patterns. These systematic review and meta-analysis were performed to summarize qualitative and quantitative information on virus shedding levels and duration for different AIV strains in experimentally infected poultry species. Methods were designed based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Four electronic databases were used to collect literature. A total of 1155 abstract were screened, with 117 studies selected for the qualitative analysis and 71 studies for the meta-analysis. A large heterogeneity in experimental methods was observed and the quantitative analysis showed that experimental variables such as species, virus origin, age, inoculation route and dose, affect virus shedding (mean, peak and duration) for highly pathogenic AIV (HPAIV), low pathogenic AIV (LPAIV) or both. In conclusion, this study highlights the need to standardize experimental procedures, it provides a comprehensive summary of the shedding patterns of AIV strains by infected poultry and identifies the variables that influence the level and duration of AIV shedding.

    Effectiveness of agri-environmental management on pollinators is moderated more by ecological contrast than by landscape structure or land-use intensity
    Marja, Riho ; Kleijn, David ; Tscharntke, Teja ; Klein, Alexandra Maria ; Frank, Thomas ; Batáry, Péter - \ 2019
    Ecology Letters 22 (2019)9. - ISSN 1461-023X - p. 1493 - 1500.
    Agri-environmental schemes - bees - biodiversity - butterflies - ecosystem services - flower strips - hoverflies - land-use intensity - meta-analysis

    Agri-environment management (AEM) started in the 1980s in Europe to mitigate biodiversity decline, but the effectiveness of AEM has been questioned. We hypothesize that this is caused by a lack of a large enough ecological contrast between AEM and non-treated control sites. The effectiveness of AEM may be moderated by landscape structure and land-use intensity. Here, we examined the influence of local ecological contrast, landscape structure and regional land-use intensity on AEM effectiveness in a meta-analysis of 62 European pollinator studies. We found that ecological contrast was most important in determining the effectiveness of AEM, but landscape structure and regional land-use intensity played also a role. In conclusion, the most successful way to enhance AEM effectiveness for pollinators is to implement measures that result in a large ecological improvement at a local scale, which exhibit a strong contrast to conventional practices in simple landscapes of intensive land-use regions.

    The Mechanisms of Social Norms' Influence on Consumer Decision Making : A Meta-Analysis
    Melnyk, Vladimir ; Herpen, Erica Van; Jak, Suzanne ; Trijp, Hans C.M. Van - \ 2019
    Zeitschrift fur Psychologie / Journal of Psychology 227 (2019)1. - ISSN 2190-8370 - p. 4 - 17.
    decision making Funding: Suzanne Jak was supported by grant NWO-VENI-451-16-001 from the Netherlands Organization for Scientific Research (NWO) Authorship: The first two authors contributed equally. - descriptive norm - injunctive norm - meta-analysis - social norm

    In the past decades, marketing practitioners have embraced social norms as a powerful instrument of influencing consumers' behavior. An important distinction has been made between descriptive norms (what most others do) and injunctive norms (what others approve of), and this meta-analysis across 297 studies examines the effects of these types of social norms on consumer decision-making processes. We argue that descriptive norms directly influence behavior, and consequently that their effect on behavior should be stronger than that of injunctive norms. Injunctive norms, by contrast, should be more strongly related to intentions than descriptive norms. Results of the meta-analysis support these predictions, and furthermore provide new insights into the moderating effects of aspects of the norm (specificity of the norm, norm source) and of the target person (gender, age).

    Critically examining the knowledge base required to mechanistically project climate impacts: A case study of Europe's fish and shellfish
    Catalán, Ignacio A. ; Auch, Dominik ; Kamermans, Pauline ; Morales-nin, Beatriz ; Angelopoulos, Natalie V. ; Reglero, Patricia ; Sandersfeld, Tina ; Peck, Myron A. - \ 2019
    Fish and Fisheries 20 (2019)3. - ISSN 1467-2960 - p. 501 - 517.
    aquaculture - climate change - experiments - fisheries - gap analysis - meta-analysis
    An amalgam of empirical data from laboratory and field studies is needed to build robust, theoretical models of climate impacts that can provide science-based advice for sustainable management of fish and shellfish resources. Using a semi-systematic literature review, Gap Analysis and multilevel meta-analysis,we assessed the status of empirical knowledge on the direct effects of climate change on 37 high-value species targeted by European fisheries and aquaculture sectors operating in marine and freshwater regions. Knowledge on potential climate change-related drivers (single or combined) on several responses (vital rates) across four categories (exploitation sector, region, life stage, species), was considerably unbalanced as well as biased, including a low number of studies (a) examining the interaction of abiotic factors, (b) offering opportunities to assess local adaptation, (c) targeting lower-value species. The meta-analysisrevealed that projected warming would increase mean growth rates in fishand mollusks and significantly elevate metabolic rates in fish. Decreased levels ofdissolved oxygen depressed rates of growth and metabolism across coherent species groups (e.g., small pelagics, etc.) while expected declines in pH reduced growth in most species groups and increased mortality in bivalves. The meta-analytical results were influenced by the study design and moderators (e.g., life stage, season). Although meta-analytic tools have become increasingly popular, when performed on the limited available data, these analyses cannot grasp relevant population effects, even in species with a long history of study. We recommend actions to overcome these shortcomings and improve mechanistic (cause-and-effect) projections of climate impacts on fish and shellfish.
    Plant-derived polyunsaturated fatty acids and markers of glucose metabolism and insulin resistance : A meta-analysis of randomized controlled feeding trials
    Wanders, Anne J. ; Blom, Wendy A.M. ; Zock, Peter L. ; Geleijnse, Johanna M. ; Brouwer, Ingeborg A. ; Alssema, Marjan - \ 2019
    BMJ Open Diabetes Research and Care 7 (2019)1. - ISSN 2052-4897
    dietary fat - glucose metabolism - insulin resistance - Linoleic acid - meta-analysis

    The objective of this meta-analysis was to investigate the effects of plant-derived polyunsaturated fatty acids (PUFAs) on glucose metabolism and insulin resistance. Scopus and PubMed databases were searched until January 2018. Eligible studies were randomized controlled feeding trials that investigated the effects of a diet high in plant-derived PUFA as compared with saturated fatty acids (SFA) or carbohydrates and measured markers of glucose metabolism and insulin resistance as outcomes. Data from 13 relevant studies (19 comparisons of plant-derived PUFA with control) were retrieved. Plant-derived PUFA did not significantly affect fasting glucose (-0.01 mmol/L (95 % CI - 0.06 to 0.03 mmol/L)), but lowered fasting insulin by 2.6 pmol/L (-4.9 to -0.2 pmol/L) and homeostatic model assessment-insulin resistance (HOMA-IR) by 0.12 units (-0.23 to - 0.01 units). In dose-response analyses, a 5% increase in energy (En%) from PUFA significantly reduced insulin by 5.8 pmol/L (95% CI -10.2 to -1.3 pmol/L), but not glucose (change -0.07, 95% CI -0.17 to 0.04 mmol/L) and HOMA-IR (change - 0.24, 95% CI -0.56 to 0.07 units). In subgroup analyses, studies with higher PUFA dose (upper tertiles) reduced insulin (-6.7, -10.5 to -2.9 pmol/L) and HOMA-IR (-0.28, -0.45 to -0.12 units), but not glucose (-0.09, 95% CI -0.18 to 0.01 mmol/L), as compared with an isocaloric control. Subgroup analyses showed no differences in effects between SFA and carbohydrates as replacement nutrients (p interaction ≥0.05). Evidence from randomized controlled trials indicated that plant-derived PUFA as an isocaloric replacement for SFA or carbohydrates probably reduces fasting insulin and HOMA-IR in populations without diabetes.

    The mechanism of the social norms' influence on consumer decision making: A Meta-analysis
    Melnyk, Vladimir ; Herpen, Erica Van; Jak, Suzanne ; Trijp, Hans C.M. Van - \ 2018
    Wageningen University & Research
    social norm - injunctive norm - descriptive norm - meta-analysis - behavior - intention
    Digital supplements for: Melnyk, V., van Herpen, E., Jak, S., & van Trijp, H. C. M. (2019). The mechanisms of social norms’ influence on consumer decision making: A meta-analysis. Zeitschrift für Psychologie, 227(1), 4-17.
    Supplemental Material for Vandenplas, Calus, and Gorjanc, 2018
    Vandenplas, Jeremie ; Calus, Mario ; Gorjanc, Gregor - \ 2018
    Wageningen University & Research
    meta-analysis - quantitative trait - statistical method - genomic prediction - multi-population - summary statistics
    This study presents a method for genomic prediction that uses individual-level data and summary statistics from multiple populations. Genome-wide markers are nowadays widely used to predict complex traits, and genomic prediction using multi-population data are an appealing approach to achieve higher prediction accuracies. However, sharing of individual-level data across populations is not always possible. We present a method that enables integration of summary statistics from separate analyses with the available individual-level data. The data can either consist of individuals with single or multiple (weighted) phenotype records per individual. We developed a method based on a hypothetical joint analysis model and absorption of population-specific information. We show that population-specific information is fully captured by estimated allele substitution effects and the accuracy of those estimates, i.e., the summary statistics. The method gives identical result as the joint analysis of all individual-level data when complete summary statistics are available. We provide a series of easy-to-use approximations that can be used when complete summary statistics are not available or impractical to share. Simulations show that approximations enable integration of different sources of information across a wide range of settings, yielding accurate predictions. The method can be readily extended to multiple-traits. In summary, the developed method enables integration of genome-wide data in the individual-level or summary statistics from multiple populations to obtain more accurate estimates of allele substitution effects and genomic predictions.
    Data from: Assessing bottom-trawling impacts based on the longevity of benthic invertebrates
    Hiddink, Jan Geert ; Jennings, Simon ; Sciberras, Marija ; Bolam, Stefan G. ; Cambiè, Giulia ; Mcconnaughey, Robert A. ; Mazor, Tessa ; Hilborn, Ray ; Collie, Jeremy S. ; Pitcher, C.R. ; Parma, Ana M. ; Suuronen, Petri ; Kaiser, Michel J. ; Rijnsdorp, A.D. - \ 2018
    Bangor University
    fisheries management - bottom trawl - benthic invertebrates - impact assessment - meta-analysis - systematic review - life history - seabed disturbance
    Bottom trawling is the most widespread human activity directly affecting seabed habitats. Assessment and effective management of the effects of bottom trawling at the scale of fisheries requires an understanding of differences in sensitivity of biota to trawling. Responses to disturbance are expected to depend on the intrinsic rate of increase of populations (r), which is expected to be linearly related to the reciprocal of longevity. 2. We examine the relationship between the longevity of benthic invertebrates and their response to bottom trawling; both in terms of the immediate mortality following a trawl pass and their subsequent rates of recovery. We collate all available data from experimental and comparative trawling studies, and test how longevity influences these aspects of sensitivity. 3. The shortest-lived organisms (<1yr) increased in abundance shortly after experimental trawling, but showed no response to trawling in longer-term comparative studies. Conversely, the abundance of biota with a life-span >1yr decreased by ~9% immediately following a trawl pass. The effect of bottom trawling in comparative studies increased with longevity, with a 2-3× larger effect on biota living >10yr than on biota living 1-3yr. We attribute this difference to the slower recovery rates of the longer-lived biota. 4. The observed relationship between the intrinsic rate of population increase (r, our metric of recovery rate) and the reciprocal of longevity matches theoretical expectation and predicts that the sensitivity of habitats to bottom trawling is higher in habitats with higher proportions of long-lived organisms. 5. Synthesis and Applications. Where the longevity of a species or the longevity distribution of a community is known or can be inferred, our estimates of depletion and intrinsic rate of increase can be combined with high-resolution maps of trawling intensity to assess trawling impacts at the scale of the fishery or other defined unit of assessment. Our estimates of r may also be used to estimate recovery times following other forms of seabed disturbance.
    Quantitative analysis of the dose–response of white spot syndrome virus in shrimp
    Ngo, Thuy T.N. ; Senior, Alistair M. ; Culina, Antica ; Santos, Eduardo S.A. ; Vlak, Just M. ; Zwart, Mark P. - \ 2018
    Journal of Fish Diseases 41 (2018)11. - ISSN 0140-7775 - p. 1733 - 1744.
    dose–response - infection - meta-analysis - modelling - shrimp - white spot syndrome virus

    White spot syndrome virus (WSSV) is an important cause of mortality and economic losses in shrimp farming. Although WSSV-induced mortality is virus dose dependent and WSSV infection does not necessarily lead to mortality, the relationships between virus-particle dose, infection and mortality have not been analysed quantitatively. Here, we explored WSSV dose–response by a combination of experiments, modelling and meta-analysis. We performed dose–response experiments in Penaeus vannamei postlarvae, recorded host mortality and detected WSSV infection. When we fitted infection models to these data, two models—differing in whether they incorporated heterogeneous host susceptibility to the virus or not—were supported for two independent experiments. To determine the generality of these results, we reanalysed published data sets and then performed a meta-analysis. We found that WSSV dose–response kinetics is indeed variable over experiments. We could not clearly identify which specific infection model has the most support by meta-analysis, but we argue that these results also are most concordant with a model incorporating varying levels of heterogeneous host susceptibility to WSSV. We have identified suitable models for analysing WSSV dose–response, which can elucidate the most basic virus–host interactions and help to avoid underestimating WSSV infection at low virus doses.

    Crop traits drive soil carbon sequestration under organic farming
    García-Palacios, Pablo ; Gattinger, Andreas ; Bracht-Jørgensen, Helene ; Brussaard, Lijbert ; Carvalho, Filipe ; Castro, Helena ; Clément, Jean Christophe ; Deyn, Gerlinde De; Hertefeldt, Tina D'; Foulquier, Arnaud ; Hedlund, Katarina ; Lavorel, Sandra ; Legay, Nicolas ; Lori, Martina ; Mäder, Paul ; Martínez-García, Laura B. ; Martins da Silva, Pedro ; Muller, Adrian ; Nascimento, Eduardo ; Reis, Filipa ; Symanczik, Sarah ; Paulo Sousa, José ; Milla, Rubén - \ 2018
    Journal of Applied Ecology 55 (2018)5. - ISSN 0021-8901 - p. 2496 - 2505.
    climate change mitigation - crop residue - ecological intensification - leaf nitrogen - meta-analysis - organic farming - resource economics traits - soil carbon stocks

    Organic farming (OF) enhances top soil organic carbon (SOC) stocks in croplands compared with conventional farming (CF), which can contribute to sequester C. As farming system differences in the amount of C inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue traits important for soil C losses such as litter decomposition may also play a role. To assess whether crop residue (leaf and root) traits determined SOC sequestration responses to OF, we coupled a global meta-analysis with field measurements across a European-wide network of sites. In the meta-analysis, we related crop species averages of leaf N, leaf-dry matter content, fine-root C and N, with SOC stocks and sequestration responses in OF vs. CF. Across six European sites, we measured the management-induced changes in SOC stocks and leaf litter traits after long-term ecological intensive (e.g. OF) vs. CF comparisons. Our global meta-analysis showed that the positive OF-effects on soil respiration, SOC stocks, and SOC sequestration rates were significant even in organic farms with low manure application rates. Although fertilization intensity was the main driver of OF-effects on SOC, leaf and root N concentrations also played a significant role. Across the six European sites, changes towards higher leaf litter N in CF also promoted lower SOC stocks. Our results highlight that crop species displaying traits indicative of resource-acquisitive strategies (e.g. high leaf and root N) increase the difference in SOC between OF and CF. Indeed, changes towards higher crop residue decomposability was related with decreased SOC stocks under CF across European sites. Synthesis and applications. Our study emphasizes that, with management, changes in crop residue traits contribute to the positive effects of organic farming (OF) on soil carbon sequestration. These results provide a clear message to land managers: the choice of crop species, and more importantly their functional traits (e.g. leave and root nitrogen), should be considered in addition to management practices and climate, when evaluating the potential of OF for climate change mitigation.

    Relative importance of competition and plant–soil feedback, their synergy, context dependency and implications for coexistence
    Lekberg, Ylva ; Bever, James D. ; Bunn, Rebecca A. ; Callaway, Ragan M. ; Hart, Miranda M. ; Kivlin, Stephanie N. ; Klironomos, John ; Larkin, Beau G. ; Maron, John L. ; Reinhart, Kurt O. ; Remke, Michael ; Putten, Wim H. van der - \ 2018
    Ecology Letters 21 (2018)8. - ISSN 1461-023X - p. 1268 - 1281.
    Additive interaction - coexistence - competition - facilitation - meta-analysis - mutualist - pathogen - plant–soil feedback - resource gradient - soil biota

    Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition vs. plant–soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter- to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbour identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low-resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure.

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