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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Introductory overview of identifiability analysis: A guide to evaluating whether you have the right type of data for your modeling purpose
Guillaume, Joseph H.A. ; Jakeman, John D. ; Marsili-Libelli, Stefano ; Asher, Michael ; Brunner, Philip ; Croke, B. ; Hill, Mary C. ; Jakeman, Anthony J. ; Keesman, Karel J. ; Razavi, S. ; Stigter, Johannes D. - \ 2019
Environmental Modelling & Software 119 (2019). - ISSN 1364-8152 - p. 418 - 432.
Derivative based methods - Emulation - Hessian - Identifiability - Non-uniqueness - Response surface - Uncertainty

Identifiability is a fundamental concept in parameter estimation, and therefore key to the large majority of environmental modeling applications. Parameter identifiability analysis assesses whether it is theoretically possible to estimate unique parameter values from data, given the quantities measured, conditions present in the forcing data, model structure (and objective function), and properties of errors in the model and observations. In other words, it tackles the problem of whether the right type of data is available to estimate the desired parameter values. Identifiability analysis is therefore an essential technique that should be adopted more routinely in practice, alongside complementary methods such as uncertainty analysis and evaluation of model performance. This article provides an introductory overview to the topic. We recommend that any modeling study should document whether a model is non-identifiable, the source of potential non-identifiability, and how this affects intended project outcomes.

Defining and applying the concept of Favourable Reference Values for species habitats under the EU Birds and Habitats Directives : examples of setting favourable reference values
Bijlsma, R.J. ; Agrillo, E. ; Attorre, F. ; Boitani, L. ; Brunner, A. ; Evans, P. ; Foppen, R. ; Gubbay, S. ; Janssen, J.A.M. ; Kleunen, A. van; Langhout, W. ; Pacifici, M. ; Ramirez, I. ; Rondinini, C. ; Roomen, M. van; Siepel, H. ; Swaaij, C.A.M. van; Winter, H.V. - \ 2019
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2929) - 219
Defining and applying the concept of Favourable Reference Values for species habitats under the EU Birds and Habitats Directives : technical report
Bijlsma, R.J. ; Agrillo, E. ; Attorre, F. ; Boitani, L. ; Brunner, A. ; Evans, P. ; Foppen, R. ; Gubbay, S. ; Janssen, J.A.M. ; Kleunen, A. van; Langhout, W. ; Noordhuis, R. ; Pacifici, M. ; Ramirez, I. ; Rondinini, C. ; Roomen, M. van; Siepel, H. ; Winter, H.V. - \ 2019
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2928) - 93
Exploring urban metabolism—Towards an interdisciplinary perspective
Dijst, M. ; Worrell, E. ; L., Böcker ; P., Brunner ; Davoudi, S. ; Geertman, S. ; Harmsen, R. ; Helbich, M. ; Holtslag, A.A.M. ; Kwan, Mei-Po ; Lenz, B. ; Lyons, G. ; Mokhtarian, P.L. ; Newman, P. ; Perrels, A. ; Ribeiro, A.P. ; Rosales Carreón, J. ; Thomson, G. ; Urge-Vorsatz, D. ; Zeyringer, M. - \ 2018
Resources, Conservation and Recycling 132 (2018). - ISSN 0921-3449 - p. 190 - 203.
The discussion on urban metabolism has been long dominated by natural scientists focussing on natural forces shaping the energy and material flows in urban systems. However, in the anthropocene human forces such as industrialization and urbanization are mobilizing people, goods and information at an increasing pace and as such have a large impact on urban energy and material flows. In this white paper, we develop a combined natural and social science perspective on urban metabolism. More specifically, innovative conceptual and methodological interdisciplinary approaches are identified and discussed to enhance the understanding of the forces that shape urban metabolism, and how these forces affect urban living and the environment. A challenging research agenda on urban metabolism is also presented.
Use of Repeated Blood Pressure and Cholesterol Measurements to Improve Cardiovascular Disease Risk Prediction : An Individual-Participant-Data Meta-Analysis
Paige, Ellie ; Barrett, Jessica ; Pennells, Lisa ; Sweeting, Michael ; Willeit, Peter ; Angelantonio, Emanuele Di; Gudnason, Vilmundur ; Nordestgaard, Børge G. ; Psaty, Bruce M. ; Goldbourt, Uri ; Best, Lyle G. ; Assmann, Gerd ; Salonen, Jukka T. ; Nietert, Paul J. ; Verschuren, W.M.M. ; Brunner, Eric J. ; Kronmal, Richard A. ; Salomaa, Veikko ; Bakker, Stephan L.J. ; Dagenais, Gilles R. ; Sato, Shinichi ; Jansson, Jan Håkan ; Willeit, Johann ; Onat, Altan ; La Cámara, Agustin Gómez De; Roussel, Ronan ; Völzke, Henry ; Dankner, Rachel ; Tipping, Robert W. ; Meade, Tom W. ; Donfrancesco, Chiara ; Kuller, Lewis H. ; Peters, Annette ; Gallacher, John ; Kromhout, Daan ; Iso, Hiroyasu ; Knuiman, Matthew W. ; Casiglia, Edoardo ; Kavousi, Maryam ; Palmieri, Luigi ; Sundström, Johan ; Davis, Barry R. ; Njølstad, Inger ; Couper, David ; Danesh, John ; Thompson, Simon G. ; Wood, Angela M. - \ 2017
American Journal of Epidemiology 186 (2017)8. - ISSN 0002-9262 - p. 899 - 907.
Cardiovascular disease - Longitudinal measurements - Repeated measurements - Risk factors - Risk prediction
The added value of incorporating information from repeated blood pressure and cholesterol measurements to predict cardiovascular disease (CVD) risk has not been rigorously assessed. We used data on 191,445 adults from the Emerging Risk Factors Collaboration (38 cohorts from 17 countries with data encompassing 1962-2014) with more than 1 million measurements of systolic blood pressure, total cholesterol, and high-density lipoprotein cholesterol. Over a median 12 years of follow-up, 21,170 CVD events occurred. Risk prediction models using cumulative mean values of repeated measurements and summary measures from longitudinal modeling of the repeated measurements were compared with models using measurements from a single time point. Risk discrimination (Cindex) and net reclassification were calculated, and changes in C-indices were meta-analyzed across studies. Compared with the single-time-point model, the cumulative means and longitudinal models increased the C-index by 0.0040 (95% confidence interval (CI): 0.0023, 0.0057) and 0.0023 (95% CI: 0.0005, 0.0042), respectively. Reclassification was also improved in both models; compared with the single-time-point model, overall net reclassification improvements were 0.0369 (95% CI: 0.0303, 0.0436) for the cumulative-means model and 0.0177 (95% CI: 0.0110, 0.0243) for the longitudinal model. In conclusion, incorporating repeated measurements of blood pressure and cholesterol into CVD risk prediction models slightly improves risk prediction.
XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED
Zhao, Chengsong ; Lasses, Theres ; Bako, Laszlo ; Kong, Danyu ; Zhao, Bingyu ; Chanda, Bidisha ; Bombarely, Aureliano ; Cruz-Ramírez, Alfredo ; Scheres, Ben ; Brunner, Amy M. ; Beers, Eric P. - \ 2017
New Phytologist 216 (2017)1. - ISSN 0028-646X - p. 76 - 89.
Arabidopsis thaliana - Angiosperm - Differentiation - LXCXE - NAC domain - Retinoblastoma - Xylem

The Arabidopsis thaliana gene XYLEM NAC DOMAIN1 (XND1) is upregulated in xylem tracheary elements. Yet overexpression of XND1 blocks differentiation of tracheary elements. The molecular mechanism of XND1 action was investigated. Phylogenetic and motif analyses indicated that XND1 and its homologs are present only in angiosperms and possess a highly conserved C-terminal region containing linear motifs (CKII-acidic, LXCXE, E2FTD-like and LXCXE-mimic) predicted to interact with the cell cycle and differentiation regulator RETINOBLASTOMA-RELATED (RBR). Protein-protein interaction and functional analyses of XND1 deletion mutants were used to test the importance of RBR-interaction motifs. Deletion of either the LXCXE or the LXCXE-mimic motif reduced both the XND1-RBR interaction and XND1 efficacy as a repressor of differentiation, with loss of the LXCXE motif having the strongest negative impacts. The function of the XND1 C-terminal domain could be partially replaced by RBR fused to the N-terminal domain of XND1. XND1 also transactivated gene expression in yeast and plants. The properties of XND1, a transactivator that depends on multiple linear RBR-interaction motifs to inhibit differentiation, have not previously been described for a plant protein. XND1 harbors an apparently angiosperm-specific combination of interaction motifs potentially linking the general differentiation regulator RBR with a xylem-specific pathway for inhibition of differentiation.

An analytical framework for strategic delta planning : negotiating consent for long-term sustainable delta development
Seijger, C. ; Douven, W. ; Halsema, G. van; Hermans, L. ; Evers, J. ; Phi, H.L. ; Khan, M.F. ; Brunner, J. ; Pols, L. ; Ligtvoet, W. ; Koole, S. ; Slager, K. ; Vermoolen, M.S. ; Hasan, S. ; Thi Minh Hoang, Vo - \ 2017
Journal of Environmental Planning and Management 60 (2017)8. - ISSN 0964-0568 - p. 1485 - 1509.
actor coalitions - implementation - innovations - participatory planning tools - Strategic delta planning
Sectoral planning on water, agriculture and urban development has not been able to prevent increased flood risks and environmental degradation in many deltas. Governments conceive strategic delta planning as a promising planning approach and develop strategic delta plans. Such plans are linked to actions and means for implementation in the short-term, in line with long-term strategic choices. This paper introduces an analytical framework that focuses on the role of actors, innovative solutions and participatory planning tools in negotiating consent for the strategic choices in a delta plan and its implementation. Cases of Bangladesh, the Netherlands and Vietnam are discussed as a plausibility probe to explore the framework's potential. The probe reveals that the framework is promising to explain the process and outcomes of strategic delta planning in urbanizing deltas. The paper ends with an initial research agenda to stimulate research and discussion on this new delta planning approach.
Functional characterization of the Phytophthora infestans RXLR effector AVR2
Malec, Marek ; Jäntsch, Christiane ; Wang, Y. ; Breen, Susan ; Gilroy, Eleanor M. ; Govers, F. ; Birch, Paul R.J. ; Brunner, Frédéric - \ 2016
The genome of Phytophthora infestans encodes a large number of RXLR effectors that are aiming to manipulate host cellular functions in order to promote disease. PiAVR2 is an RXLR effector that was shown to interact with potato BSU1-like (BSL) ser/thr phosphatase 1 (Saunders et al., Plant cell 2012), the homolog of Arabidopsis BSL1, a positive regulator of the brassinosteroid (BR) signaling pathway controlling plant growth and development. The exploitation of the large existing -omics, genetic and material resources on BR signaling in Arabidopsis could possibly help to decipher the mechanistic basis of the mode of action of PiAVR2 and guide subsequent work in solanaceous plant species, the natural hosts of P. infestans. Using a cell-based system, we have identified a strong interaction between PiAVR2 and AtBSL1, AtBSL2 and AtBSL3 but not with AtBSU1. In further studies, we show that, although PiAVR2 interacts with BSU1-like phosphatases, it is not affecting typical BR responses such as BR-dependent activation of BES1/BZR2 transcription factor and BR- regulated gene expression. PiAVR2 also does not affect flg22-dependent early immune responses in Arabidopsis such as the oxidative burst, MAP kinase activation, or FRK1 induction. However, PiAVR2 enhances susceptibility to microbe infection in Arabidopsis and PiAVR2 plants are more sensitive to the (hemi)biotrophic pathogen Pseudomonas syringae and Phytophthora capsici but more resistant to the necrotroph Alternaria brassicicola. Future work will aim to determine how PiAVR2 impedes plant immunity through its interaction with the BSLs.
Association of Cardiometabolic Multimorbidity With Mortality
Angelantonio, Emanuele Di; Kaptoge, Stephen ; Wormser, David ; Willeit, Peter ; Butterworth, Adam S. ; Bansal, Narinder ; O’Keeffe, Linda M. ; Gao, Pei ; Wood, Angela M. ; Burgess, Stephen ; Freitag, Daniel F. ; Pennells, Lisa ; Peters, Sanne A. ; Hart, Carole L. ; Håheim, Lise Lund ; Gillum, Richard F. ; Nordestgaard, Børge G. ; Psaty, Bruce M. ; Yeap, Bu B. ; Knuiman, Matthew W. ; Nietert, Paul J. ; Kauhanen, Jussi ; Salonen, Jukka T. ; Kuller, Lewis H. ; Simons, Leon A. ; Schouw, Yvonne T. van der; Barrett-Connor, Elizabeth ; Selmer, Randi ; Crespo, Carlos J. ; Rodriguez, Beatriz ; Verschuren, Monique W.M. ; Salomaa, Veikko ; Svärdsudd, Kurt ; Harst, Pim Van Der; Björkelund, Cecilia ; Wilhelmsen, Lars ; Wallace, Robert B. ; Brenner, Hermann ; Amouyel, Philippe ; Barr, Elizabeth L.M. ; Iso, Hiroyasu ; Onat, Altan ; Trevisan, Maurizio ; agostino, Ralph B. D'; Cooper, Cyrus ; Kavousi, Maryam ; Welin, Lennart ; Roussel, Ronan ; Hu, Frank B. ; Sato, Shinichi ; Davidson, Karina W. ; Howard, Barbara V. ; Leening, Maarten J.G. ; Rosengren, Annika ; Dörr, Marcus ; Deeg, Dorly J.H. ; Kiechl, Stefan ; Stehouwer, Coen D.A. ; Nissinen, Aulikki ; Giampaoli, Simona ; Donfrancesco, Chiara ; Kromhout, Daan ; Price, Jackie F. ; Peters, Annette ; Meade, Tom W. ; Casiglia, Edoardo ; Lawlor, Debbie A. ; Gallacher, John ; Nagel, Dorothea ; Franco, Oscar H. ; Assmann, Gerd ; Dagenais, Gilles R. ; Jukema, Wouter J. ; Sundström, Johan ; Woodward, Mark ; Brunner, Eric J. ; Khaw, Kay-Tee ; Wareham, Nicholas J. ; Whitsel, Eric A. ; Njølstad, Inger ; Hedblad, Bo ; Wassertheil-Smoller, Sylvia ; Engström, Gunnar ; Rosamond, Wayne D. ; Selvin, Elizabeth ; Sattar, Naveed ; Thompson, Simon G. ; Danesh, John - \ 2015
JAMA: The Journal of the American Medical Association 314 (2015)1. - ISSN 0098-7484 - p. 52 - 60.
Importance The prevalence of cardiometabolic multimorbidity is increasing.

Objective To estimate reductions in life expectancy associated with cardiometabolic multimorbidity.

Design, Setting, and Participants Age- and sex-adjusted mortality rates and hazard ratios (HRs) were calculated using individual participant data from the Emerging Risk Factors Collaboration (689 300 participants; 91 cohorts; years of baseline surveys: 1960-2007; latest mortality follow-up: April 2013; 128 843 deaths). The HRs from the Emerging Risk Factors Collaboration were compared with those from the UK Biobank (499 808 participants; years of baseline surveys: 2006-2010; latest mortality follow-up: November 2013; 7995 deaths). Cumulative survival was estimated by applying calculated age-specific HRs for mortality to contemporary US age-specific death rates.

Exposures A history of 2 or more of the following: diabetes mellitus, stroke, myocardial infarction (MI).

Main Outcomes and Measures All-cause mortality and estimated reductions in life expectancy.
Results In participants in the Emerging Risk Factors Collaboration without a history of diabetes, stroke, or MI at baseline (reference group), the all-cause mortality rate adjusted to the age of 60 years was 6.8 per 1000 person-years. Mortality rates per 1000 person-years were 15.6 in participants with a history of diabetes, 16.1 in those with stroke, 16.8 in those with MI, 32.0 in those with both diabetes and MI, 32.5 in those with both diabetes and stroke, 32.8 in those with both stroke and MI, and 59.5 in those with diabetes, stroke, and MI. Compared with the reference group, the HRs for all-cause mortality were 1.9 (95% CI, 1.8-2.0) in participants with a history of diabetes, 2.1 (95% CI, 2.0-2.2) in those with stroke, 2.0 (95% CI, 1.9-2.2) in those with MI, 3.7 (95% CI, 3.3-4.1) in those with both diabetes and MI, 3.8 (95% CI, 3.5-4.2) in those with both diabetes and stroke, 3.5 (95% CI, 3.1-4.0) in those with both stroke and MI, and 6.9 (95% CI, 5.7-8.3) in those with diabetes, stroke, and MI. The HRs from the Emerging Risk Factors Collaboration were similar to those from the more recently recruited UK Biobank. The HRs were little changed after further adjustment for markers of established intermediate pathways (eg, levels of lipids and blood pressure) and lifestyle factors (eg, smoking, diet). At the age of 60 years, a history of any 2 of these conditions was associated with 12 years of reduced life expectancy and a history of all 3 of these conditions was associated with 15 years of reduced life expectancy.

Conclusions and Relevance Mortality associated with a history of diabetes, stroke, or MI was similar for each condition. Because any combination of these conditions was associated with multiplicative mortality risk, life expectancy was substantially lower in people with multimorbidity.
Sensitivity Analysis of a Land-Use Change Model with and without Agents to Assess Land Abandonment and Long-Term Re-Forestation in a Swiss Mountain Region
Brandle, M. ; Langendijk, G. ; Peter, S. ; Brunner, S.H. - \ 2015
Land 4 (2015)2. - ISSN 2073-445X - p. 475 - 512.
Land abandonment and the subsequent re-forestation are important drivers behind the loss of ecosystem services in mountain regions. Agent-based models can help to identify global change impacts on farmland abandonment and can test policy and management options to counteract this development. Realigning the representation of human decision making with time scales of ecological processes such as reforestation presents a major challenge in this context. Models either focus on the agent-specific behavior anchored in the current generation of farmers at the expense of representing longer scale environmental processes or they emphasize the simulation of long-term economic and forest developments where representation of human behavior is simplified in time and space. In this context, we compare the representation of individual and aggregated decision-making in the same model structure and by doing so address some implications of choosing short or long term time horizons in land-use modeling. Based on survey data, we integrate dynamic agents into a comparative static economic sector supply model in a Swiss mountain region. The results from an extensive sensitivity analysis show that this agent-based land-use change model can reproduce observed data correctly and that both model versions are sensitive to the same model parameters. In particular, in both models the specification of opportunity costs determines the extent of production activities and land-use changes by restricting the output space. Our results point out that the agent-based model can capture short and medium term developments in land abandonment better than the aggregated version without losing its sensitivity to important socio-economic drivers. For comparative static approaches, extensive sensitivity analysis with respect to opportunity costs, i.e., the measure of benefits forgone due to alternative uses of labor is essential for the assessment of the impact of climate change on land abandonment and re-forestation in mountain regions.
Practical identifiability analysis of environmental models
Marsili-Libelli, S. ; Beck, M.B. ; Brunner, P. ; Croke, B. ; Guillaume, J. ; Jakeman, A. ; Jakeman, J. ; Keesman, K.J. ; Stigter, J.D. - \ 2014
Consumption of dairy products and associations with incident diabetes, CHD and mortality in the Whitehall II study
Soedamah-Muthu, S.S. ; Masset, G. ; Verberne, L.D.M. ; Geleijnse, J.M. ; Brunner, E.J. - \ 2013
The British journal of nutrition 109 (2013)4. - ISSN 0007-1145 - p. 718 - 726.
ischemic-heart-disease - postmenopausal women - metabolic syndrome - vascular-disease - life-style - fat intake - vitamin-d - risk - mellitus - milk
Few prospective studies have examined the effects of different types of dairy food on the risks of type 2 diabetes, CHD and mortality. We examined whether intakes of total dairy, high-fat dairy, low-fat dairy, milk and fermented dairy products were related to these outcomes in the Whitehall II prospective cohort study. At baseline, dairy consumption was assessed by FFQ among 4526 subjects (72 % men) with a mean age 56 (sd 6) years. Death certificates and medical records were used to ascertain CHD mortality and non-fatal myocardial infarction. Incident diabetes was detected by the oral glucose tolerance test or self-report. Incidence data were analysed using Cox proportional hazards models, adjusted for lifestyle and dietary factors. During approximately 10 years of follow-up, 273 diabetes, 323 CHD and 237 all-cause mortality cases occurred. In multivariable models, intakes of total dairy and types of dairy products were not significantly associated with incident diabetes or CHD (all P values for trend >0·1). Fermented dairy products was inversely associated with overall mortality (hazard ratios approximately 0·7 in the middle and highest tertiles; P for trend <0·01) but not with incident CHD or diabetes (P>0·3). In conclusion, intakes of total dairy and types of dairy products showed no consistent relationship with incident diabetes, CHD or all-cause mortality.
Low-cost small scale processing technologies for production applications in various environments-Mass produced factories
Bramsiepe, C. ; Sievers, S. ; Seifert, T. ; Stefanidis, G.D. ; Vlachos, D.G. ; Schnitzer, H. ; Muster, B. ; Brunner, C. ; Sanders, J.P.M. ; Bruins, M.E. ; Schembecker, G. - \ 2012
Chemical Engineering and Processing 51 (2012). - ISSN 0255-2701 - p. 32 - 52.
fischer-tropsch synthesis - microwave-assisted pyrolysis - hydrogen-production - bio-oil - oxygenated hydrocarbons - reactive distillation - transportation fuels - microchannel reactor - microreactor stacks - catalytic pyrolysis
The requirements for chemical and food production technologies will change in the future as a result of shorter time to market and increasing market volatility. Especially the rising use of renewable resources will require the implementation of flexible and fast to install small-scale production technologies. The increasing number of necessary apparatuses and their distributed operation, however, will constitute major challenges, both economically and procedurally. The proposed solution to face the economic challenge is modularization and standardization. For food production, dewatering represents a key issue. Thus, biomass processing should first be divided into small-scale water separation steps and then into further large-scale processing steps. As dewatering usually happens thermally and heat exchangers often benefit from the economies of scale, heat supply and energy consumption or heat transfer with little capital investment are further issues. Therefore, temperature levels should be decreased and the use of solar heat increased. For the production of biofuels and chemicals from biomass, process integration and process simplification are proposed to improve the efficacy of production equipment and processes. Choosing raw materials with molecular structures, similar to the desired chemical building block, will lower the need for heat exchange and make small-scale manufacturing of fuels and chemicals possible
Soil Carbon stabilization under increased atmospheric CO2
Hoosbeek, M.R. - \ 2010
In: Proceedings of the COST Action FP0803 Conference on Belowground Carbon Turnover in European Forests – State of the Art, Birmensdorf, Switzerland, 26-28 January 2010. - Birmensdorf, Switzerland : Swiss Federal Institute for Forest, Snow and Landscape Research WSL - p. 35 - 38.
Avr2, an RXLR effector from Phytophthora infestans
Breen, S. ; Gilroy, E.M. ; Armstrong, M.R. ; Morales, J.G. ; Hein, I. ; Douglas, E. ; Boevink, P.C. ; Mc Lellan, H. ; Randall, E. ; Zhendong, T. ; Avrova, A.O. ; Pritchard, L. ; Lokossou, A.A. ; Govers, F. ; Vossen, E.A.G. van der; Vleeshouwers, V. ; Brunner, F. ; Whisson, S.C. ; Birch, P.R.J. - \ 2010
In: Book of Abstracts Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010. - - p. 27 - 27.
Vietnam-Netherlands partnership "water for food & ecosystems"
Long, K.T. ; Halsema, G.E. van; Brunner, J. - \ 2009
[S.l.] : Ministry of Agriculture and Rural Development (MARD) [etc.] - 27
waterbeheer - duurzaamheid (sustainability) - ecosystemen - vennootschappen - vietnam - nederland - water management - sustainability - ecosystems - partnerships - vietnam - netherlands
The EADGENE Microarray Data Analysis Workshop
Koning, D.J. de; Jaffrezic, F. ; Lund, M.S. ; Watson, M. ; Channing, C. ; Hulsegge, B. ; Pool, M.H. ; Buitenhuis, B. ; Hedegaard, J. ; Hornshoj, H. ; Sorensen, P. ; Marot, G. ; Delmas, C. ; Lê Cao, K.A. ; San Cristobal, M. ; Baron, M.D. ; Malinverni, R. ; Stella, A. ; Brunner, R.M. ; Seyfert, H.M. ; Jensen, K. ; Mouzaki, D. ; Waddington, D. ; Jiménez-Marín, A. ; Perez-Alegre, M. ; Perez-Reinado, E. ; Closset, R. ; Detilleux, J.C. ; Dovc, P. ; Lavric, M. ; Nie, H. ; Janss, L. - \ 2007
Genetics, Selection, Evolution 39 (2007)6. - ISSN 0999-193X - p. 621 - 631.
gene-expression - muscle-tissue
Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.
Specific root length as an indicator of environmental change
Ostonen, I. ; Püttsepp, Ü. ; Biel, C. ; Alberton, O. ; Bakker, M.R. ; Löhmus, K. ; Majdi, H. ; Metcalfe, J.D. ; Olsthoorn, A.F.M. ; Pronk, A.A. ; Vanguelova, E. ; Weih, M. ; Brunner, I. - \ 2007
Plant Biosystems 141 (2007)3. - ISSN 1126-3504 - p. 426 - 442.
spruce picea-abies - elevated atmospheric co2 - pine pinus-sylvestris - soil solution chemistry - potential growth-rate - fine-root - norway spruce - l. karst. - nutrient availability - silver birch
Specific root length (SRL, m g-1) is probably the most frequently measured morphological parameter of fine roots. It is believed to characterize economic aspects of the root system and to be indicative of environmental changes. The main objectives of this paper were to review and summarize the published SRL data for different tree species throughout Europe and to assess SRL under varying environmental conditions. Meta-analysis was used to summarize the response of SRL to the following manipulated environmental conditions: fertilization, irrigation, elevated temperature, elevated CO2, Al-stress, reduced light, heavy metal stress and physical disturbance of soil. SRL was found to be strongly dependent on the fine root classes, i.e. on the ectomycorrhizal short roots (ECM), and on the roots
A text-mining analysis of the human phenome
Driel, M.A. van; Bruggeman, J. ; Vriend, G. ; Brunner, H.G. ; Leunissen, J.A.M. - \ 2006
European Journal of Human Genetics 14 (2006)5. - ISSN 1018-4813 - p. 535 - 542.
saccharomyces-cerevisiae - protein families - gene ontology - genome - identification - biology - knowledgebase - products - database - disease
A number of large-scale efforts are underway to define the relationships between genes and proteins in various species. But, few attempts have been made to systematically classify all such relationships at the phenotype level. Also, it is unknown whether such a phenotype map would carry biologically meaningful information. We have used text mining to classify over 5000 human phenotypes contained in the Online Mendelian Inheritance in Man database. We find that similarity between phenotypes reflects biological modules of interacting functionally related genes. These similarities are positively correlated with a number of measures of gene function, including relatedness at the level of protein sequence, protein motifs, functional annotation, and direct protein¿protein interaction. Phenotype grouping reflects the modular nature of human disease genetics. Thus, phenotype mapping may be used to predict candidate genes for diseases as well as functional relations between genes and proteins. Such predictions will further improve if a unified system of phenotype descriptors is developed. The phenotype similarity data are accessible through a web interface at http://www.cmbi.ru.nl/MimMiner/
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases
Driel, M.A. van; Cuelenaere, K. ; Kemmeren, P.P.C.W. ; Leunissen, J.A.M. ; Brunner, H.G. ; Vriend, G. - \ 2005
Nucleic acids research 33 (2005)SUPP/2. - ISSN 0305-1048 - p. w758 - w761.
candidate genes - expression database - genome database - disorders - identification - malformations - knowledgebase - map
The identification of genes underlying human genetic disorders requires the combination of data related to cytogenetic localization, phenotypes and expression patterns, to generate a list of candidate genes. In the field of human genetics, it is normal to perform this combination analysis by hand. We report on GeneSeeker (http://www.cmbi.ru.nl/GeneSeeker/), a web server that gathers and combines data from a series of databases. All database searches are performed via the web interfaces provided with the original databases, guaranteeing that the most recent data are queried, and obviating data warehousing. GeneSeeker makes the same selection of candidate genes as the human geneticists would have performed, and thus reducing the time-consuming process to a few minutes. GeneSeeker is particularly well suited for syndromes in which the disease gene displays altered expression patterns in the affected tissue(s).
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