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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    Nitrogen management of vegetable crops
    Tei, Francesco ; Neve, Stefaan De; Haan, Janjo de; Kristensen, Hanne Lakkenborg - \ 2020
    Agricultural Water Management 240 (2020). - ISSN 0378-3774
    Cover crops - Cropping systems - Fertilizers - N balance - N fertilization efficiency - N leaching

    N fertilization is often viewed as a cheap insurance against yield loss in vegetable production because of the generally large added value, resulting in application of fertilizer N often in excess of actual crop demand. In combination with the low fertilizer N recovery by many vegetable crops and the often excessive irrigation, this may lead to both health and environmental risks related to high nitrate concentrations in water leaving the root zone. In this review, we discuss the decisive factors in the overall N balance of field vegetable production systems and the different tools at hand to increase fertilizer use efficiency and consequently reduce N losses to the environment. Based on this, we identify areas of research and technology transfer where further work is required. Only an integration of the different methods and strategies for N management may really mitigate the risk of nitrate leaching and maintain crop yields while enhancing the environmental sustainability of vegetable production systems.

    Liquid flavouring ingredient produced by fermentation
    Mastrigt, Oscar Van; Smid, Eilt Johannes ; Abee, Tjakko ; Lillevang, Søren K. ; Kristensen, Mette Nørtoft - \ 2020
    Octrooinummer: WO2020030811, gepubliceerd: 2020-02-13.

    The present invention relates to a a novel method of preparing a liquid flavouring lingredient by use of fermentation. In particular, the method involves recycling a part of the microorganisms used in the fermentation of flavour and aroma compounds back to the bioreactor for fermentation, while another part of the microorganisms are maintained in the ontained liquid flavouring ingredient. The obtained liquid flavouring ingredient is suitable for use as a tasteenhancer and can be used in food products, such as dairy products, sauces, dressings, seasonings, meat products, bread, and sourkraut.

    Validation of an antimicrobial susceptibility testing protocol for Brachyspira hyodysenteriae and Brachyspira pilosicoli in an international ring trial
    Stubberfield, E. ; Pringle, M. ; Landén, A. ; Veldman, K.T. ; Geurts, Y. ; Jouy, E. ; Devendec, L. Le; Rubin, J.E. ; Kulathunga, D.G.R.S. ; Kristensen, K.A. ; Chanter, J. ; Bollard, A. ; Johnson, P. ; Maycock, J. ; Habighorst-Blome, K. ; Rohde, J. ; Card, R.M. - \ 2020
    Veterinary Microbiology 244 (2020). - ISSN 0378-1135
    Antimicrobial susceptibility testing - Brachyspira - lnu(C) - Ring trial - tva(A) - tva(B)

    Brachyspira hyodysenteriae and Brachyspira pilosicoli cause economically important enteric disease in pigs. Treatment of these infections often includes antimicrobial administration, which can be most effective when therapeutic options are informed by antimicrobial susceptibility testing data. Here we describe a method for broth dilution antimicrobial susceptibility testing of these bacteria, both of which are difficult to culture in vitro. The protocol was evaluated for its fitness for use in an inter-laboratory ring trial involving eight laboratories from seven countries, and employing eleven test strains (5 Brachyspira hyodysenteriae including the type strain B78T and 6 Brachyspira pilosicoli) and six antibiotics. Overall intra- and inter-laboratory reproducibility of this method was very good (>90 % MICs at mode +/- 1 log2). Whole genome sequencing revealed good correspondence between reduced susceptibility and the presence of previously defined antimicrobial resistance determinants. Interestingly, lnu(C) was identified in B. pilosicoli isolates with elevated MICs of lincomycin, whilst tva(B) was associated with elevated MICs of pleuromutilins in this species. We designated two new control strains with MICs lying within currently tested ranges, including for the pleuromutilins, in contrast to the control strain B. hyodysenteriae B78T. These were deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH. The validation of a standard protocol and identification of new control strains facilitates comparisons between studies, establishment of robust interpretative criteria, and ultimately contributes to rational antimicrobial use when treating infected livestock.

    Assessment of the value of information of precision livestock farming : A conceptual framework
    Rojo-Gimeno, Cristina ; Voort, Mariska van der; Niemi, Jarkko K. ; Lauwers, Ludwig ; Kristensen, Anders Ringgaard ; Wauters, Erwin - \ 2019
    NJAS Wageningen Journal of Life Sciences 90-91 (2019). - ISSN 1573-5214
    Conceptual framework - Economic analysis - Precision livestock farming - Role of advisors - Value of information

    Although precision livestock farming (PLF) technologies ensure various dimensions of more precise information, the question arises to what extent additional preciseness provides more value. Literature gives insufficient anchor points to estimate the value of information (VOI) obtained with PLF technologies. This study proposes a conceptual framework with building blocks to determine the VOI. Next, the framework is used to describe factors and existing gaps in the VOI assessment. This, finally, leads to reflections and recommendations about how to assess and improve the VOI of PLF. Literature reveals that the VOI surpasses the mere use of more precise information to take decisions, but encompasses a path from data collection to decisions with particular outcomes. The framework interlinks three building blocks: (i) data processing, (ii) decision making and (iii) impact analysis with factors influencing the VOI such as the process to transform data into information, level of precision, decision rules, social influences, the accuracy of information, herd size and prevalence of the condition measured. Besides profitability, outcomes from decisions include the impact on animal welfare, environment, food safety, and food security. The data-to-value framework allows for a better assessment of VOI and its potentials, and provides anchor points to design useful and valuable PLF technologies. The framework also helps to determine the role of advisors in interpreting the more precise information and in formulating farmer-tailored advice to apply the most optimal practices. Both technology design and advisors’ role may enhance the VOI of future PLF developments and applications.

    Enteric methane emission from Jersey cows during the spring transition from indoor feeding to grazing
    Szalanski, Marcin ; Kristensen, Troels ; Difford, Gareth ; Lassen, Jan ; Buitenhuis, Albert J. ; Pszczola, Marcin ; Løvendahl, Peter - \ 2019
    Journal of Dairy Science 102 (2019)7. - ISSN 0022-0302 - p. 6319 - 6329.
    dairy - genotype by environment interaction - grazing - Jersey - methane

    Organic dairy cows in Denmark are often kept indoors during the winter and outside at least part time in the summer. Consequently, their diet changes by the season. We hypothesized that grazing might affect enteric CH 4 emissions due to changes in the nutrition, maintenance, and activity of the cows, and they might differentially respond to these factors. This study assessed the repeatability of enteric CH 4 emission measurements for Jersey cattle in a commercial organic dairy herd in Denmark. It also evaluated the effects of a gradual transition from indoor winter feeding to outdoor spring grazing. Further, it assessed the individual-level correlations between measurements during the consecutive feeding periods (phenotype × environment, P × E) as neither pedigrees nor genotypes were available to estimate a genotype by environment effect. Ninety-six mixed-parity lactating Jersey cows were monitored for 30 d before grazing and for 24 d while grazing. The cows spent 8 to 11 h grazing each day and had free access to an in-barn automatic milking system (AMS). For each visit to the AMS, milk yield was recorded and logged along with date and time. Monitoring equipment installed in the AMS feed bins continuously measured enteric CH 4 and CO 2 concentrations (ppm) using a noninvasive “sniffer” method. Raw enteric CH 4 and CO 2 concentrations and their ratio (CH 4 :CO 2 ) were derived from average concentrations measured during milking and per day for each cow. We used mixed models equations to estimate variance components and adjust for the fixed and random effects influencing the analyzed gas concentrations. Univariate models were used to precorrect the gas measurements for diurnal variation and to estimate the direct effect of grazing on the analyzed concentrations. A bivariate model was used to assess the correlation between the 2 periods (in-barn vs. grazing) for each gas concentration. Grazing had a weak P × E interaction for daily average CH 4 and CO 2 gas concentrations. Bivariate repeatability estimates for average CH 4 and CO 2 concentrations and CH 4 :CO 2 were 0.77 to 0.78, 0.73 to 0.80, and 0.26, respectively. Repeatability for CH 4 :CO 2 was low (0.26) but indicated some between-animal variation. In conclusion, grazing does not create significant shifts compared with indoor feeding in how animals rank for average CH 4 and CO 2 concentrations and CH 4 :CO 2 . We found no evidence that separate evaluation is needed to quantify enteric CH 4 and CO 2 emissions from Jersey cows during in-barn and grazing periods.

    The impact of European landscape transitions on the provision of landscape services: an explorative study using six cases of rural land change
    Sluis, T. van der; Pedroli, G.B.M. ; Frederiksen, Pia ; Kristensen, S.B.P. ; Gravsholt Busck, Anne ; Pavlis, V. ; Cosor, G.L. - \ 2019
    Landscape Ecology 34 (2019)2. - ISSN 0921-2973 - p. 307 - 323.
    The reasons for recent landscape change in the European countryside are complex and poorly substantiated. Identification of drivers of landscape
    transition and assessment of the effects on the provision of landscape services are subject of recent debate. Objectives Aims of the paper are to explore what
    implications rural landscape transitions (as identified by land use and land cover changes) have for the provision of landscape services, and whether these
    changes can be related to specific drivers of change. Methods The paper records gross landscape change on the basis of land use and land cover changes in six case study areas in five countries, and assesses the impacts on the provision of landscape services in the past 25 years. Results In the past decades the observed land use and land cover changes in the case studies are relatively small, with a dominance of urbanisation and afforestation processes. However, the impacts of these changes are clearly reflected in a change in landscape services. Conclusions Although the landscape transitions do affect the services, spatial data alone is insufficient to assess cause-effect relationships of landscape transitions, landscape structure and pattern. Circumstantial evidence points to substantial effects of EU and national policies on landscape services through landscape transition. These—often unintentional—effects can substantially affect biodiversity, cultural identity and landscape character. More research is needed on the exact cause-effect relationships between policies and landscape service provision.
    6S rRNA sequence of rumen microbes in dairy cattle
    Difford, Gareth ; Plichta, Damian Rafal ; Løvendahl, Peter ; Lassen, Jan ; Noel, Samantha Joan ; Højberg, Ole ; Wright, André Denis G. ; Zhu, Zhigang ; Kristensen, Lise ; Nielsen, Henrik Bjørn ; Guldbrandtsen, Bernt ; Sahana, Goutam - \ 2018
    Aarhus University
    PRJEB28065 - ERP110230
    The 16S rRNA sequence data was generated in the project entitled "Reduction of methane emissions from dairy cows and concurrent improvement of feed efficiency obtained through host genetics and next generation sequencing of rumen microbiome" using Illumina sequencing technology.
    A comparison of disaggregated nitrogen budgets for Danish agriculture using europe-wide
    Kros, J. ; Hutchings, N.J. ; Kristensen, Inge Toft ; Sillebak Kristensen, Ib ; Børgesen, Christen Duus ; Voogd, J.C.H. ; Dalgaard, T. ; Vries, W. de - \ 2018
    Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows
    Difford, Gareth Frank ; Plichta, Damian Rafal ; Løvendahl, Peter ; Lassen, Jan ; Noel, Samantha Joan ; Højberg, Ole ; Wright, André Denis G. ; Zhu, Zhigang ; Kristensen, Lise ; Nielsen, Henrik Bjørn ; Guldbrandtsen, Bernt ; Sahana, Goutam - \ 2018
    Plos Genetics 14 (2018)10. - ISSN 1553-7404

    Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 production was influenced by individual host (cow) genotype, as well as the host's rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host's genotype and certain taxa were associated with CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH4 emissions in the cattle industry.

    Aroma formation during cheese ripening is best resembled by Lactococcus lactis retentostat cultures
    Mastrigt, Oscar van; Gallegos Tejeda, Diego ; Kristensen, Mette N. ; Abee, Tjakko ; Smid, Eddy J. - \ 2018
    Microbial Cell Factories 17 (2018)1. - ISSN 1475-2859
    Fermentation - Metabolism - VOC - Zero growth

    Background: Cheese ripening is a complex, time consuming and expensive process, which involves the generation of precursors from carbohydrates, proteins and fats and their subsequent conversion into a wide range of compounds responsible for the flavour and texture of the cheese. This study aims to investigate production of cheese aroma compounds outside the cheese matrix that could be applied for instance as food supplements in dairy or non-dairy products. Results: In this study, aroma formation by a dairy Lactococcus lactis was analysed as a function of the growth medium [milk, hydrolysed micellar casein isolate (MCI) and chemically defined medium (CDM)] and the cultivation conditions (batch culture, retentostat culture and a milli-cheese model system). In the retentostat cultures, the nutrient supply was severely restricted resulting in low growth rates (~ 0.001 h-1), thereby mimicking cheese ripening conditions in which nutrients are scarce and bacteria hardly grow. In total 82 volatile organic compounds were produced by the bacteria. Despite the use of a chemically defined medium, retentostat cultures had the biggest qualitative overlap in aroma production with the milli-cheese model system (36 out of 54 compounds). In the retentostat cultures, 52 known cheese compounds were produced and several important cheese aroma compounds and/or compounds with a buttery or cheese-like aroma increased in retentostat cultures compared to batch cultures and milli-cheeses, such as esters, methyl ketones, diketones and unsaturated ketones. In cultures on CDM and MCI, free fatty acids and their corresponding degradation products were underrepresented compared to what was found in the milli-cheeses. Addition of a mixture of free fatty acids to CDM and MCI could help to enhance flavour formation in these media, thereby even better resembling flavour formation in cheese. Conclusions: This study demonstrates that retentostat cultivation is the preferred method to produce cheese flavours outside the cheese matrix by mimicking the slow growth of bacteria during cheese ripening.

    A comparison of disaggregated nitrogen budgets for Danish agriculture using Europe-wide and national approaches
    Kros, Johannes ; Hutchings, Nicholas J. ; Kristensen, Inge Toft ; Kristensen, Ib Sillebak ; Børgesen, Christen Duus ; Voogd, Jan Cees ; Dalgaard, Tommy ; Vries, Wim de - \ 2018
    Science of the Total Environment 643 (2018). - ISSN 0048-9697 - p. 890 - 901.
    Agricultural soils - Budgets - Disaggregation - Modelling - National - Nitrogen

    Spatially detailed information on agricultural nitrogen (N) budgets is relevant to identify regions where there is a need for a reduction in inputs in view of various forms of N pollution. However, at the scale of the European Union, there is a lack of consistent, reliable, high spatial resolution data necessary for the calculation of regional N losses. To gain insight in the reduction in uncertainty achieved by using higher spatial resolution input data. This was done by comparing spatially disaggregated agricultural N budgets for Denmark for the period 2000–2010, generated by two versions of the European scale model Integrator, a version using high spatial resolution national data for Denmark (Integrator-DK) and a version using available data at the EU scale (Integrator-EU). Results showed that the national N fluxes in the N budgets calculated by the two versions of the model were within 1–5% for N inputs by fertilizer and manure excretion, but inputs by N fixation and N mineralisation differed by 50–100% and N uptake also differed by ca 25%, causing a difference in N leaching and runoff of nearly 50%. Comparison with an independently derived Danish national budget appeared generally to be better with Integrator-EU results in 2000 but with Integrator-DK results in 2010. However, the spatial distribution of manure distribution and N losses from Integrator-DK were closer to observed distributions than those from Integrator-EU. We conclude that close attention to local agronomic practices is needed when using a leaching fraction approach and that for effective support of environmental policymaking, Member States need to collect or submit high spatial resolution agricultural data to Eurostat.

    How European Landscape transitions affect the provision of landscape services
    Sluis, T. van der; Brage, Søren ; Kristensen, B. ; Pedroli, G.B.M. - \ 2017
    Toward Reliable Lipoprotein Particle Predictions from NMR Spectra of Human Blood : An Interlaboratory Ring Test
    Monsonis Centelles, Sandra ; Hoefsloot, Huub C.J. ; Khakimov, Bekzod ; Ebrahimi, Parvaneh ; Lind, Mads V. ; Kristensen, Mette ; Roo, Niels De; Jacobs, Doris M. ; Duynhoven, John Van; Cannet, Claire ; Fang, Fang ; Humpfer, Eberhard ; Schäfer, Hartmut ; Spraul, Manfred ; Engelsen, Søren B. ; Smilde, Age K. - \ 2017
    Analytical Chemistry 89 (2017)15. - ISSN 0003-2700 - p. 8004 - 8012.
    Lipoprotein profiling of human blood by 1H nuclear magnetic resonance (NMR) spectroscopy is a rapid and promising approach to monitor health and disease states in medicine and nutrition. However, lack of standardization of measurement protocols has prevented the use of NMR-based lipoprotein profiling in metastudies. In this study, a standardized NMR measurement protocol was applied in a ring test performed across three different laboratories in Europe on plasma and serum samples from 28 individuals. Data was evaluated in terms of (i) spectral differences, (ii) differences in LPD predictions obtained using an existing prediction model, and (iii) agreement of predictions with cholesterol concentrations in high- and low-density lipoproteins (HDL and LDL) particles measured by standardized clinical assays. ANOVA-simultaneous component analysis (ASCA) of the ring test spectral ensemble that contains methylene and methyl peaks (1.4-0.6 ppm) showed that 97.99% of the variance in the data is related to subject, 1.62% to sample type (serum or plasma), and 0.39% to laboratory. This interlaboratory variation is in fact smaller than the maximum acceptable intralaboratory variation on quality control samples. It is also shown that the reproducibility between laboratories is good enough for the LPD predictions to be exchangeable when the standardized NMR measurement protocol is followed. With the successful implementation of this protocol, which results in reproducible prediction of lipoprotein distributions across laboratories, a step is taken toward bringing NMR more into scope of prognostic and diagnostic biomarkers, reducing the need for less efficient methods such as ultracentrifugation or high-performance liquid chromatography (HPLC).
    A comparison of disaggregated nitrogen budgets for Danish agriculture using Europe-wide and national approaches
    Kros, J. ; Hutchings, Nicholas J. ; Toft Kristensen, Inge ; Sillebak Kristensen, Ib ; Borgesen, C.D. ; Voogd, J.C.H. ; Dalgaard, Tommy ; Vries, W. de - \ 2016
    Spatially detailed information on nitrogen (N) budgets is relevant for the identification of regions N pollution needs to be reduced. However, the availability of consistent reliable data is generally lacking. Therefore most models applied in Europe use national or even European scale data as model input. To gain insight in the reduction in uncertainty that could be achieved by using higher resolution input data, spatially disaggregated agricultural N budgets for Denmark for the period 2000-2010 were generated by the European scale model Integrator, being fed with high spatial resolution national data for Denmark (Integrator-DK) and compared with results obtained by using the default data (Integrator-EU). Here we focus on the year 2010, for which the quality of the regional Danish input data was considered best. Results show that clear differences exists for the national budgets calculated by both versions of the model but comparison with an independently derived Danish national budget appeared to be better with Integrator-EU results. However, the spatial distribution of manure distribution and N losses from Integrator-DK are closer to the observed distributions than those from Integrator-EU
    Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
    Henderson, Gemma ; Cox, Faith ; Ganesh, Siva ; Jonker, Arjan ; Young, Wayne ; Abecia, Leticia ; Angarita, Erika ; Aravena, Paula ; Nora Arenas, Graciela ; Ariza, Claudia ; Attwood, Graeme T. ; Mauricio Avila, Jose ; Avila-stagno, Jorge ; Bannink, André ; Barahona, Rolando ; Batistotti, Mariano ; Bertelsen, Mads F. ; Brown-Kav, Aya ; Carvajal, Andres M. ; Cersosimo, Laura ; Vieira Chaves, Alexandre ; Church, John ; Clipson, Nicholas ; Cobos-peralta, Mario A. ; Cookson, Adrian L. ; Cravero, Silvio ; Cristobal Carballo, Omar ; Crosley, Katie ; Cruz, Gustavo ; Cerón Cucchi, María ; Barra, Rodrigo de la; Menezes, Alexandre B. de; Detmann, Edenio ; Dieho, Kasper ; Dijkstra, Jan ; Reis, William L.S. Dos; Dugan, Mike E.R. ; Hadi Ebrahimi, Seyed ; Eythórsdóttir, Emma ; Nde Fon, Fabian ; Fraga, Martín ; Franco, Francisco ; Friedeman, Chris ; Fukuma, Naoki ; Gagić, Dragana ; Gangnat, Isabelle ; Javier Grilli, Diego ; Guan, Le Luo ; Heidarian Miri, Vahideh ; Hernandez-Sanabria, Emma ; Gomez, Alma Ximena Ibarra ; Isah, Olubukola A. ; Ishaq, Suzanne ; Jami, Elie ; Jelincic, Juan ; Kantanen, Juha ; Kelly, William J. ; Kim, Seon-Ho ; Klieve, Athol ; Kobayashi, Yasuo ; Koike, Satoshi ; Kopecny, Jan ; Nygaard Kristensen, Torsten ; Julie Krizsan, Sophie ; Lachance, Hannah ; Lachman, Medora ; Lamberson, William R. ; Lambie, Suzanne ; Lassen, Jan ; Leahy, Sinead C. ; Lee, Sang-Suk ; Leiber, Florian ; Lewis, Eva ; Lin, Bo ; Lira, Raúl ; Lund, Peter ; Macipe, Edgar ; Mamuad, Lovelia L. ; Cuquetto Mantovani, Hilário ; Marcoppido, Gisela Ariana ; Márquez, Cristian ; Martin, Cécile ; Martinez, Gonzalo ; Eugenia Martinez, Maria ; Lucía Mayorga, Olga ; McAllister, Tim A. ; McSweeney, Chris ; Mestre, Lorena ; Minnee, Elena ; Mitsumori, Makoto ; Mizrahi, Itzhak ; Molina, Isabel ; Muenger, Andreas ; Muñoz, Camila ; Murovec, Bostjan ; Newbold, John ; Nsereko, Victor ; O’donovan, Michael ; Okunade, Sunday ; O’neill, Brendan ; Ospina, Sonia ; Ouwerkerk, Diane ; Parra, Diana ; Pereira, Luiz Gustavo Ribeiro ; Pinares-patiño, Cesar ; Pope, Phil B. ; Poulsen, Morten ; Rodehutscord, Markus ; Rodriguez, Tatiana ; Saito, Kunihiko ; Sales, Francisco ; Sauer, Catherine ; Shingfield, Kevin ; Shoji, Noriaki ; Simunek, Jiri ; Stojanović-Radić, Zorica ; Stres, Blaz ; Sun, Xuezhao ; Swartz, Jeffery ; Liang Tan, Zhi ; Tapio, Ilma ; Taxis, Tasia M. ; Tomkins, Nigel ; Ungerfeld, Emilio ; Valizadeh, Reza ; Adrichem, Peter van; Hamme, Jonathan van; Hoven, Woulter van; Waghorn, Garry ; Wallace, John R. ; Wang, Min ; Waters, Sinéad M. ; Keogh, Kate ; Witzig, Maren ; Wright, Andre-Denis G. ; Yamano, Hidehisa ; Yan, Tianhai ; Yáñez-ruiz, David R. ; Yeoman, Carl J. ; Zambrano, Ricardo ; Zeitz, Johanna ; Zhou, Mi ; Wei Zhou, Hua ; Xia Zou, Cai ; Zunino, Pablo ; Janssen, Peter H. - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322 - 2 p.
    The value of pathogen information in treating clinical mastitis
    Cha, Elva ; Smith, Rebecca L. ; Kristensen, Anders R. ; Hertl, Julia A. ; Schukken, Ynte H. ; Tauer, Loren W. ; Welcome, Frank L. ; Gröhn, Yrjö T. - \ 2016
    Journal of Dairy Research 83 (2016)4. - ISSN 0022-0299 - p. 456 - 463.
    dairy - mastitis - Value of information

    The objective of this study was to determine the economic value of obtaining timely and more accurate clinical mastitis (CM) test results for optimal treatment of cows. Typically CM is first identified when the farmer observes recognisable outward signs. Further information of whether the pathogen causing CM is Gram-positive, Gram-negative or other (including no growth) can be determined by using on-farm culture methods. The most detailed level of information for mastitis diagnostics is obtainable by sending milk samples for culture to an external laboratory. Knowing the exact pathogen permits the treatment method to be specifically targeted to the causation pathogen, resulting in less discarded milk. The disadvantages are the additional waiting time to receive test results, which delays treating cows, and the cost of the culture test. Net returns per year (NR) for various levels of information were estimated using a dynamic programming model. The Value of Information (VOI) was then calculated as the difference in NR using a specific level of information as compared to more detailed information on the CM causative agent. The highest VOI was observed where the farmer assumed the pathogen causing CM was the one with the highest incidence in the herd and no pathogen specific CM information was obtained. The VOI of pathogen specific information, compared with non-optimal treatment of Staphylococcus aureus where recurrence and spread occurred due to lack of treatment efficacy, was $20.43 when the same incorrect treatment was applied to recurrent cases, and $30.52 when recurrent cases were assumed to be the next highest incidence pathogen and treated accordingly. This indicates that negative consequences associated with choosing the wrong CM treatment can make additional information cost-effective if pathogen identification is assessed at the generic information level and if the pathogen can spread to other cows if not treated appropriately.

    New technologies for DNA analysis – a review of the READNA Project
    McGinn, Steven ; Bauer, David ; Brefort, Thomas ; Dong, Liqin ; El-Sagheer, Afaf ; Elsharawy, Abdou ; Evans, Geraint ; Falk-Sörqvist, Elin ; Forster, Michael ; Fredriksson, Simon ; Freeman, Peter ; Freitag, Camilla ; Fritzsche, Joachim ; Gibson, Spencer ; Gullberg, Mats ; Gut, Marta ; Heath, Simon ; Heath-Brun, Isabelle ; Heron, Andrew J. ; Hohlbein, Johannes ; Ke, Rongqin ; Lancaster, Owen ; Reste, Ludovic Le; Maglia, Giovanni ; Marie, Rodolphe ; Mauger, Florence ; Mertes, Florian ; Mignardi, Marco ; Moens, Lotte ; Oostmeijer, Jelle ; Out, Ruud ; Pedersen, Jonas Nyvold ; Persson, Fredrik ; Picaud, Vincent ; Rotem, Dvir ; Schracke, Nadine ; Sengenes, Jennifer ; Stähler, Peer F. ; Stade, Björn ; Stoddart, David ; Teng, Xia ; Veal, Colin D. ; Zahra, Nathalie ; Bayley, Hagan ; Beier, Markus ; Brown, Tom ; Dekker, Cees ; Ekström, Björn ; Flyvbjerg, Henrik ; Franke, Andre ; Guenther, Simone ; Kapanidis, Achillefs N. ; Kaye, Jane ; Kristensen, Anders ; Lehrach, Hans ; Mangion, Jonathan ; Sauer, Sascha ; Schyns, Emile ; Tost, Jörg ; Helvoort, Joop M.L.M. van; Zaag, Pieter J. van der; Tegenfeldt, Jonas O. ; Brookes, Anthony J. ; Mir, Kalim ; Nilsson, Mats ; Willcocks, James P. ; Gut, Ivo G. - \ 2016
    New Biotechnology 33 (2016)3. - ISSN 1871-6784 - p. 311 - 330.
    The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3rd and 4th generation of sequencing methods with nanopores and in situ sequencing, respectively.
    Patterns and rivers of land use change in selected European rural landscapes.
    Pilgaard Kristensen, Søren Bech ; Gravsholt Busck, Anne ; Sluis, T. van der; Gaube, V. - \ 2016
    Land Use Policy 57 (2016). - ISSN 0264-8377 - p. 786 - 799.
    Many of the semi-natural landscape elements found in rural areas, such as woodlots, hedgerows and grasslands, were originally maintained as part of the agricultural system. During the 20th century, they lost most of their functions and were often removed or transformed. Presently, production concerns are less dominant and many landscape and land use changes are undertaken to improve public goods or fulfil personal and family ambitions and values. This paper investigates the patterns of farm-level land use changes that occurred between 2002 and 2012 in three different landscape regions of Europe (peri-urban landscapes, areas with marginal potential for agriculture, post-socialist landscapes) and the drivers behind, based on a questionnaire survey in six study areas. A second objective is to analyse landowners’ decision-making and endogenous factors that are correlated with their engagement in land use changes. Common to all areas is that agricultural production is under pressure due to physical or socio-economic challenges. The results indicate that relatively more nature or landscape features have been added by landowners than removed by them in the six study areas. Furthermore, the analysis revealed that full-time landowners were responsible for the largest proportion of landscape change and that the areas involved differed greatly. The analysis also underlined the variety of European landscapes, as many landscape activities exhibited strong geographical patterns. A multivariate analysis of the relationship between ten farm and landowner characteristics confirmed the geographical diversity, as only a dummy variable representing the geographical location was statistically significant. When location was omitted from the analysis, two factors were significant: farm size and ownership of livestock. In addition, the results suggest that landowners in peri-urban locations were more engaged in landscape activities than landowners in other locations.
    Dynamics in national agri-environmental policy implementation under changing EU policy priorities: Does one size fit all?
    Vesterager, J.P. ; Frederiksen, P. ; Kristensen, S.B.P. ; Vadineanu, A. ; Gaube, V. ; Geamana, N.A. ; Pavlis, V. ; Terkenli, T.S. ; Bucur, M.M. ; Sluis, T. van der; Busck, A.G. - \ 2016
    Land Use Policy 57 (2016). - ISSN 0264-8377 - p. 764 - 776.
    Over the past 30 years, Agri-Environmental Policies (AEP) in the EU have developed with relative national autonomy and according to the subsidiarity principle. The environmental directives represent an increase in EU-level environmental ambitions and challenge the current implementation of EU AEP by creating an increasingly demanding set of regulations with which each member state must comply. National AEP implementation may, however, maintain original characteristics and fail to adopt or transform as EU policy implementation proceeds or when EU policies develop. This creates a potential gap between EU policies and national policy implementation resulting in the ensuing national policy dynamics and adaptations becoming issues of interest. This raises a central question regarding the extent to which national AEP implementation can help us predict whether AEP will be suitable to achieve environmental directive objectives nationally in the future. In this paper, we first investigate the dynamics in the implementation of national Agri-Environmental Schemes (AES) through changes in (i) AES policy objectives over time, (ii) administrative implementation structures, and (iii) administrative policy decision structures in the Netherlands, Denmark, Greece, Austria and Romania. Second, we examine the extent to which various factors have influenced the development of national policies over time. The study identifies development based on the theory of ‘process of institutional change’, i.e. we qualitatively estimate the costs of change based on proposed factors including economic conditions in relation to AES implementation, political institutional capacity, policy legacy, policy preferences, and current discourse. On this background, we identify differences in implementation strategies or outcomes in terms of inertia, absorption and transformation, which are characteristic of the national responses to changing AEP at the EU level. We discuss AES dynamics; whether policy content or structures should be in focus for future policy design and the implications of these findings for the future role of AEP in fulfilling environmental directives and argue why a one size fits all rule does not adequately cover current AES development.
    Impacts of underwater noise on marine vertebrates : Project introduction and first results
    Liebschner, Alexander ; Seibel, Henrike ; Teilmann, Jonas ; Wittekind, Dietrich ; Parmentier, Eric ; Dähne, Michael ; Dietz, Rune ; Driver, Jörg ; Elk, Cornelis van; Everaarts, Eligius ; Findeisen, Henning ; Kristensen, Jacob ; Lehnert, Kristina ; Lucke, Klaus ; Merck, Thomas ; Müller, Sabine ; Pawliczka, Iwona ; Ronnenberg, Katrin ; Rosenberger, Tanja ; Ruser, Andreas ; Tougaard, Jakob ; Schuster, Max ; Sundermeyer, Janne ; Sveegaard, Signe ; Siebert, Ursula - \ 2016
    In: The Effects of Noise on Aquatic Life II Springer New York LLC (Advances in Experimental Medicine and Biology ) - ISBN 9781493929801 - p. 631 - 636.
    Auditory evoked potential - Noise logger - Stress - Tagging - Temporary threshold

    The project conducts application-oriented research on impacts of underwater noise on marine vertebrates in the North and Baltic Seas. In distinct subprojects, the hearing sensitivity of harbor porpoises and gray seals as well as the acoustic tolerance limit of harbor porpoises to impulsive noise from pile driving and stress reactions caused by anthropogenic noise is investigated. Animals are equipped with DTAGs capable of recording the actual surrounding noise field of free-swimming harbor porpoises and seals. Acoustic noise mapping including porpoise detectors in the Natura 2000 sites of the North and Baltic Seas will help to fully understand current noise impacts.

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