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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Sustainable placeshaping: what, why and how. Findings of the SUSPLACE program
Horlings, L.G. ; Axinte, L. ; Berg, J. van den; Felcis, E. ; Grenni, S. ; Husain, O. ; Nieto Romero, M. ; Papangelou, A. ; Pearson, K. ; Pisters, S. ; Quinn, M. ; Quinney, M. ; Rebelo, C. ; Roep, D. ; Soares da Silva, D. ; Soini, K. ; Šuvajevs, S. ; Taherzadeh, A. ; Vaart, G. van der; Valente, S. ; Vasta, A. ; Vrieze., A. de - \ 2019
Wageningen : SUSPLACE - ISBN 9789463951425 - 84
Creating sustainable places together : A quick start guide for policy-makers and practitioners to place-based working and co-production
Quinn, Matthew ; Vrieze, Anke de; Soares da Silva, D. ; Pearson, K.R. ; Nieto Romero, M. - \ 2019
Wageningen : Wageningen University & Research, SUSPLACE - ISBN 9789463950220 - 11
Variation in foraging strategies over a large spatial scale reduces parent–offspring conflict in Manx shearwaters
Wischnewski, Saskia ; Arneill, Gavin E. ; Bennison, Ashley W. ; Dillane, Eileen ; Poupart, Timothée A. ; Hinde, Camilla A. ; Jessopp, Mark J. ; Quinn, John L. - \ 2019
Animal Behaviour 151 (2019). - ISSN 0003-3472 - p. 165 - 176.
dual foraging - Mid-Altlantic Ridge - parental care - parent–offspring conflict - Procellariiformes - spatial ecology - trade-off - tubenoses

Parental care can lead to a conflict of interest between parents and offspring. For central place foragers, conflict is expected to be particularly intensive in species that feed on relatively inaccessible, distant food resources. Some pelagic seabirds use distinct foraging strategies when provisioning young versus self-feeding: short trips near the colony versus long trips far away. Limited empirical evidence suggests that the strategy used by parents depends on their own state and that of their young, suggesting that dynamic optimization may help reduce conflict. Tests of this hypothesis, however, are scarce. Using a combination of GPS tracking and nest monitoring, we examined whether foraging strategy choice by Manx shearwaters, Puffinus puffinus, is explained by the body condition of parents and offspring before trip departure, and whether choice affects condition upon return. When chick body condition was poor prior to departure, subsequent foraging trips by adults were significantly shorter and faster, and chick condition upon return improved. When chick condition was good prior to departure, the reverse happened. There was no evidence that adult condition affected subsequent trip choice, but adults returning from slow, long-duration trips were in comparatively better condition. Thus, although the trips that were good for offspring were different to those that were favourable for adults, trip choice was only dependent on chick condition, which may explain why there was no evidence for a trade-off between adult and chick condition during individual trips. Our results suggest that spatiotemporal variation in foraging strategies is driven by the conflicting needs of parents and offspring, but that the parents can reduce the conflict, resulting in no detectable trade-off under these conditions. This link between parental care and space use is likely to be widespread in central place foragers but remains largely unexplored in most systems.

D-Trace estimation of a precision matrix with eigenvalue control
Avagyan, Vahe - \ 2019
Communications in statistics: Simulation and computation (2019). - ISSN 0361-0918 - 18 p.
D-trace - Gaussian graphical model - gene expression - Hannan-Quinn information criterion - trace penalization

The estimation of a precision matrix has an important role in several research fields. In high dimensional settings, one of the most prominent approaches to estimate the precision matrix is the Lasso norm penalized convex optimization. This framework guarantees the sparsity of the estimated precision matrix. However, it does not control the eigenspectrum of the obtained estimator. Moreover, Lasso penalization shrinks the largest eigenvalues of the estimated precision matrix. In this article, we focus on D-trace estimation methodology of a precision matrix. We propose imposing a negative trace penalization on the objective function of the D-trace approach, aimed to control the eigenvalues of the estimated precision matrix. Through extensive numerical analysis, using simulated and real datasets, we show the advantageous performance of our proposed methodology.

Data from: A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour
Kim, J.M. ; Santure, Anna W. ; Barton, H.J. ; Quinn, John L. ; Cole, Ella F. ; Visser, M.E. ; Sheldon, B.C. ; Groenen, M. ; Oers, K. van; Slate, J. - \ 2018
adaptation - ecological genetics - genomics/proteomics - natural selection and contemporary evolution - population genetics - empirical - quantitative genetics
High density SNP microarrays (‘SNP chips’) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this paper we describe the development and application of a high density Affymetrix Axiom chip with around 500 000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation (CNVs). The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genome-wide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays, (ii) detecting SNPs by more than one pipeline, and in independent datasets, ensures a high proportion of working assays, (iii) allele frequency ascertainment bias is minimised by performing SNP discovery in individuals from multiple populations and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour
Kim, J.M. ; Santure, A.W. ; Barton, H.J. ; Quinn, J.L. ; Cole, E.F. ; Visser, M.E. ; Sheldon, B.C. ; Groenen, M.A.M. ; Oers, K. van; Slate, J. - \ 2018
Molecular Ecology Resources 18 (2018)4. - ISSN 1755-098X - p. 877 - 891.
Axiom - CNV - Exploration behaviour - GWAS - Personality

High-density SNP microarrays ("SNP chips") are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high-density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.

Personality-dependent differences in problem-solving performance in a social context reflect foraging strategies
Zandberg, Lies ; Quinn, John L. ; Naguib, Marc ; Oers, Kees Van - \ 2016
Behavioural Processes 134 (2016). - ISSN 0376-6357 - p. 95 - 102.
Individuals develop innovative behaviours to solve foraging challenges in the face of changing environmental conditions. Little is known about how individuals differ in their tendency to solve problems and in their subsequent use of this solving behaviour in social contexts. Here we investigated whether individual variation in problem-solving performance could be explained by differences in the likelihood of solving the task, or if they reflect differences in foraging strategy. We tested this by studying the use of a novel foraging skill in groups of great tits (Parus major), consisting of three naive individuals with different personality, and one knowledgeable tutor. We presented them with multiple, identical foraging devices over eight trials. Though birds of different personality type did not differ in solving latency; fast and slow explorers showed a steeper increase over time in their solving rate, compared to intermediate explorers. Despite equal solving potential, personality influenced the subsequent use of the skill, as well as the pay-off received from solving. Thus, variation in the tendency to solve the task reflected differences in foraging strategy among individuals linked to their personality. These results emphasize the importance of considering the social context to fully understand the implications of learning novel skills.
Predicting bee community responses to land-use changes : Effects of geographic and taxonomic biases
Palma, Adriana De; Abrahamczyk, Stefan ; Aizen, Marcelo A. ; Albrecht, Matthias ; Basset, Yves ; Bates, Adam ; Blake, Robin J. ; Boutin, Céline ; Bugter, Rob ; Connop, Stuart ; Cruz-López, Leopoldo ; Cunningham, Saul A. ; Darvill, Ben ; Diekötter, Tim ; Dorn, Silvia ; Downing, Nicola ; Entling, Martin H. ; Farwig, Nina ; Felicioli, Antonio ; Fonte, Steven J. ; Fowler, Robert ; Franzén, Markus ; Goulson, Dave ; Grass, Ingo ; Hanley, Mick E. ; Hendrix, Stephen D. ; Herrmann, Farina ; Herzog, Felix ; Holzschuh, Andrea ; Jauker, Birgit ; Kessler, Michael ; Knight, M.E. ; Kruess, Andreas ; Lavelle, Patrick ; Féon, Violette Le; Lentini, Pia ; Malone, Louise A. ; Marshall, Jon ; Pachón, Eliana Martínez ; McFrederick, Quinn S. ; Morales, Carolina L. ; Mudri-Stojnic, Sonja ; Nates-Parra, Guiomar ; Nilsson, Sven G. ; Öckinger, Erik ; Osgathorpe, Lynne ; Parra-H, Alejandro ; Peres, Carlos A. ; Persson, Anna S. ; Petanidou, Theodora ; Poveda, Katja ; Power, Eileen F. ; Quaranta, Marino ; Quintero, Carolina ; Rader, Romina ; Richards, Miriam H. ; Roulston, Tai ; Rousseau, Laurent ; Sadler, Jonathan P. ; Samnegård, Ulrika ; Schellhorn, Nancy A. ; Schüepp, Christof ; Schweiger, Oliver ; Smith-Pardo, Allan H. ; Steffan-Dewenter, Ingolf ; Stout, Jane C. ; Tonietto, Rebecca K. ; Tscharntke, Teja ; Tylianakis, Jason M. ; Verboven, Hans A.F. ; Vergara, Carlos H. ; Verhulst, Jort ; Westphal, Catrin ; Yoon, Hyung Joo ; Purvis, Andy - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322 - 14 p.

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

Validating the use of intrinsic markers in body feathers to identify inter-individual differences in non-breeding areas of northern fulmars
Quinn, Lucy R. ; Meharg, Andrew A. ; Franeker, Jan A. van; Graham, Isla M. ; Thompson, Paul M. - \ 2016
Marine Biology 163 (2016). - ISSN 0025-3162 - 12 p.

Many wildlife studies use chemical analyses to explore spatio-temporal variation in diet, migratory patterns and contaminant exposure. Intrinsic markers are particularly valuable for studying non-breeding marine predators, when direct methods of investigation are rarely feasible. However, any inferences regarding foraging ecology are dependent upon the time scale over which tissues such as feathers are formed. In this study, we validate the use of body feathers for studying non-breeding foraging patterns in a pelagic seabird, the northern fulmar. Analysis of carcasses of successfully breeding adult fulmars indicated that body feathers moulted between September and March, whereas analyses of carcasses and activity patterns suggested that wing feather and tail feather moult occurred during more restricted periods (September to October and September to January, respectively). By randomly sampling relevant body feathers, average values for individual birds were shown to be consistent. We also integrated chemical analyses of body feather with geolocation tracking data to demonstrate that analyses of δ13C and δ15N values successfully assigned 88 % of birds to one of two broad wintering regions used by breeding adult fulmars from a Scottish study colony. These data provide strong support for the use of body feathers as a tool for exploring non-breeding foraging patterns and diet in wide-ranging, pelagic seabirds.

Data from: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations
Santure, Anna W. ; Poissant, Jocelyn ; Cauwer, Isabelle De; Oers, K. van; Robinson, Matthew R. ; Quinn, John L. ; Groenen, Martien ; Visser, Marcel ; Sheldon, Ben C. ; Slate, Jon - \ 2015
University of Auckland
quantitative genetics - GWAS - chromosome partitioning - genomics - Parus major - genome wide association - QTL mapping
Currently there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe, and consequently are considered an ecological 'model organism'. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long-term study populations of great tit - one in the Netherlands, and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population-specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population-specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations, and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free-living populations.
Can small still be beautiful? Moving local sweetpotato seed systems to scale in sub-Saharan Africa.
McEwan, M. ; Almekinders, C.J.M. ; Abidin, C. - \ 2015
In: Potato and Sweetpotato in Africa / Low, J., Nyongesa, M., Quinn, S., Parker, M., CABI - ISBN 9781780644202 - p. 289 - 310.
In sub-Saharan Africa (SSA), a range of farmer-based practices for the conservation and multiplication of sweetpotato planting material has evolved. In bimodal rainfall areas, sequential planting ensures that a ware crop is in the ground for most of the year, and vines are harvested from one crop to plant the next one. In unimodal areas with a long dry season, practices include the use of 'volunteer' planting material from sprouting roots which have been left in the ground from the previous crop. The predominant sources of planting material are from the farmer's own field or from friends or neighbours. However, these practices result in limited amounts of planting material being available at the start of the rains and contribute to the build-up of pests and diseases contributing to suboptimal root crop production. Sweetpotato breeding efforts are leading to the development of new varieties that are preferred by farmers and consumers. However, without strong linkages to seed multiplication and dissemination efforts these varieties may not quickly benefit large numbers of smallholder farmers and consumers. Increasingly there are specialized vine multipliers who have been supported by 'project' interventions. Yet, it is not clear whether and how these interventions have built on the successful elements of existing practices. Our chapter examines the literature on local seed system functioning, and the implications for crops such as sweetpotato. The chapter reviews recent efforts to multiply and disseminate sweetpotato planting material in Mozambique, Uganda, Tanzania, Malawi, Ethiopia and West Africa. New varieties and technologies have been promoted together with interventions to 'engineer' changes in the organization and coordination of the seed system. We review the country cases to gauge the extent to which successful elements of farmer-based practices for managing sweetpotato planting material have been identified and built into the process of redesigning the seed system. A number of issues are identified for discussion. These include: (i) What are the critical points for interaction between the traditional farmer-based practices and the formal seed system?; (ii) What are the trade-offs between remaining local, and yet achieving scale?; and (iii) How can the quality of planting material be assured as we go to scale? We also assess the different drivers for the seed system, and the implications for the functions of various stakeholders and patterns of communication and coordination. The chapter concludes by highlighting gaps in our current understanding for getting sweetpotato seed systems not only moving, but working at scale.
Educating and training a workforce for nutrition in a post-2015 world
Fanzo, Jessica C. ; Graziose, Matthew M. ; Kraemer, Klaus ; Gillespie, Stuart ; Johnston, Jessica L. ; Pee, Saskia de; Monterrosa, Eva ; Badham, Jane ; Bloem, Martin W. ; Dangour, Alan D. ; Deckelbaum, Richard ; Dobermann, Achim ; Fracassi, Patrizia ; Hossain, S.M.M. ; Ingram, John ; Jerling, Johann C. ; Jones, C.J. ; Jap, Stefanus Indrayana ; Kiess, Lynnda ; Marshall, Quinn ; Martin, Keith ; Narayan, Anuradha ; Amuyunzu-Nayamongo, Mary ; Pepping, Fré ; West, Keith P. - \ 2015
Advances in Nutrition 6 (2015). - ISSN 2161-8313 - p. 639 - 647.
Capacity development - Malnutrition - Sustainable development goals - Training - Workforce

Nearly all countries in the world today are burdened with malnutrition, manifesting as undernutrition, micronutrient deficiencies, and/or overweight and obesity. Despite some progress, efforts to alleviate malnutrition are hampered by a shortage in number, skills, and geographic coverage, of a workforce for nutrition. Here, we report the findings of the Castel Gandolfo workshop, a convening of experts from diverse fields in March 2014 to consider how to develop the capacity of a global cadre of nutrition professionals for the post-2015 development era. Workshop participants identified several requirements for developing a workforce for nutrition, including an ability to work as part of a multisectoral team; communication, advocacy, and leadership skills to engage decision makers; and a set of technical skills to address future challenges for nutrition. Other opportunities were highlighted that could immediately contribute to capacity development, including the creation of a consortium to link global North and South universities, online training modules for middle managers, and practical, hands-on experiences for frontline nutrition workers. Institutional and organizational support is needed to enable workshop recommendations on education and training to be effectively implemented and sustained. The findings from the Castel Gandolfo workshop can contribute to the delivery of successful nutrition-relevant actions in the face of mounting external pressures and informing and attaining the forthcoming Sustainable Development Goals.

Durable cisgenic resistance to Phytophthora infestans in potato and perspectives for applications in Africa
Gheysen, G. ; Heremans, B. ; Droogenbroeck, B. van; Custers, R. ; Vossen, J.H. ; Visser, R.G.F. ; Jacobsen, E. ; Hutten, R.C.B. ; Haverkort, A.J. - \ 2015
In: Potato and sweetpotato in Africa: transforming the value chains for food and nutrition security / Low, J., Nyongesa, M., Quinn, S., Parker, M., Nairobi, Kenya : CABI - ISBN 9781780644202 - p. 122 - 127.
Late blight caused by Phytophthora infestans is a major constraint in potato production. A promising strategy to combat late blight in potato is to combine different resistance genes to achieve durable resistance. Resistance genes from wild relatives can be introduced by breeding or by transformation. Single resistance genes are not durable because mutant pathogens that avoid recognition will easily be selected. Genetic engineering is a straightforward method allowing introduction of a combination of natural resistance genes into a potato cultivar without altering other agronomic characteristics. Since these genes can also be introduced by conventional breeding methods, the resulting potato plants are called cisgenic, in contrast to transgenic potatoes that have received DNA from non-crossable species. Three R genes conferring resistance to P. infestans (Rpi), Rpi-sto1 (Solanum stoloniferum), Rpi-vnt1.1 (Solanum venturii) and Rpi-blb3 (Solanum bulbocastanum), were cloned and transformed separately or as a combination into the susceptible cultivar Désirée. The transformed clones were screened for late blight resistance using a detached leaf assay, and they were also evaluated for true-to-type performance under greenhouse conditions. To evaluate the performance of the resistance genes or combinations in realistic conditions, selected clones were tested in field trials in The Netherlands and Belgium in 2011 and 2012. This was done in comparison with the susceptible parent Désirée, and other susceptible and resistant cultivars. In both years plots were not treated with fungicides against P. infestans. In contrast to 2011, the summer of 2012 was humid resulting in high natural disease pressure. Nevertheless the two seasons showed similar results with clear differences between the susceptible reference clones and the genetically modified resistant clones. About 20 resistance genes against P. infestans have currently been mapped or cloned and more will follow. Therefore a collection can be generated of double or triple R gene-containing resistant cultivars that have the potential to make potato cultivation more sustainable. Based on the current potato cultivation area in East Africa, the effect of using cultivars with durable resistance on increasing potato yield in East Africa can be predicted.
Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations
Santure, Anna W. ; Poissant, Jocelyn ; Cauwer, Isabelle De; Oers, Kees van; Robinson, Matthew R. ; Quinn, John L. ; Groenen, M.A.M. ; Visser, M.E. ; Sheldon, Ben C. ; Slate, Jon - \ 2015
Molecular Ecology 24 (2015)24. - ISSN 0962-1083 - p. 6148 - 6162.
chromosome partitioning - genome-wide association - genomics - GWAS - QTL mapping - quantitative genetics

Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe and consequently are considered an ecological 'model organism'. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long-term study populations of great tits - one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population-specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population-specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free-living populations.

The farming systems of potential potato production areas of Chencha, southern Ethiopia
Mazengia, W. ; Schulte, R.P.O. ; Tadese, Y. ; Griffin, D. ; Schulz, S. ; Struik, P.C. - \ 2015
In: Potato and sweetpotato in Africa : Transforming the value chains for food and nutrition security / Low, J., Nyongesa, M., Quinn, S., Parker, M., Cambridge : CABI - ISBN 9781780644202 - p. 382 - 396.
Improving seed health and seed performance by positive selection in three Kenyan potato varieties
Schulte-Geldermann, E. ; Gildemacher, P.R. ; Struik, P.C. - \ 2015
In: Potato and sweet potato in Africa. Transforming the value chains for food and nutrition security / Low, J., Nyongesa, M., Quinn, S., Parker, M., Cambridge : CABI - ISBN 9781780644202 - p. 254 - 260.
Towards a low-cost, full-service air quality data archival system
Samourkasidis, Argyris ; Athanasiadis, Ioannis N. - \ 2014
In: Proceedings - 7th International Congress on Environmental Modelling and Software: Bold Visions for Environmental Modeling, iEMSs 2014. - International Environmental Modelling and Software Society - ISBN 9788890357442 - p. 1192 - 1199.
Environmental data archive - Low-cost sensors - Metadata harvesting - Open archives - Semantic web - Sensor observations - Sharing and reuse - SOS
We present our explorations towards a low-cost solution for creating an autonomous environmental data archival system. AiRCHIVE is a software platform for providing open access to sensor data with different ways, that account for machine interoperability. It is built with Raspberry Pi, a low-cost, pocket-size computer, and Air Pi a low-cost amateur sensory kit for air quality monitoring. Raspberry Pi with AirPi allowed us to easily capture raw sensor data and store them in a local database, and with AiRCHIVE we deployed "on sensor" a web server that provides with a set of services for data preprocessing and dissemination, including an implementation of OGC/SOS services and the OAI/PMH harvesting protocol.
Metadata extraction using semantic and Natural Language Processing techniques
Knapen, M.J.R. ; Hüsing, T. ; Jacob, K. ; Randen, Y. van; Reis, S. ; Roosenschoon, O.R. ; Janssen, S.J.C. - \ 2014
In: Proceedings of the International Environmental Modelling and Software Society (iEMSs) 7th Intl. Congress on Env. Modelling and Software. - San Diego : - ISBN 9788890357442 - p. 385 - 391.
RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs
Widmann, J. ; Stombaugh, J. ; Mcdonald, D. ; Chocholousova, J. ; Gardner, P. ; Iyer, M.K. ; Liu, Z.Z. ; Lozupone, C.A. ; Quinn, J. ; Smit, S. ; Wikman, S. ; Zaneveld, J.R.R. ; Knight, R. - \ 2012
RNA-A Publication of the RNA Society 18 (2012)7. - ISSN 1355-8382 - p. 1319 - 1327.
multiple sequence alignment - in-vitro selection - base-pairs - aminoglycoside antibiotics - molecular discrimination - nucleotide composition - aptamer complex - binding rna - recognition - motifs
Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in the refinement of these algorithms, we manually curated a set of 148 alignments with a total of 9600 unique sequences, in which each alignment was backed by at least one crystal or NMR structure. These alignments included both naturally and artificially selected molecules. We used principles of isostericity to improve the alignments from an average of 83%-94% isosteric base pairs. We expect that this alignment collection will assist in a wide range of benchmarking efforts and provide new insight into evolutionary principles governing change in RNA structural motifs. The improved alignments have been contributed to the Rfam database.
Environmental decision support systems (EDSS) development - Challenges and best practices
McIntosh, B.S. ; Ascough, J.C. ; Twery, M. ; Chew, J. ; Elmahdi, A. ; Haase, D. ; Harou, J.J. ; Hepting, D. ; Cuddy, S. ; Jakeman, A.J. ; Chen, S. ; Kassahun, A. ; Lautenbach, S. ; Matthews, K. ; Merritt, W. ; Quinn, N.W.T. ; Rodriguez-Roda, I. ; Sieber, S. ; Stavenga, M. ; Sulis, A. ; Ticehurst, J. ; Volk, M. ; Wrobel, M. ; Delden, H. ; El-Sawah, S. ; Rizzoli, A. ; Voinov, A. - \ 2011
Environmental Modelling & Software 26 (2011)12. - ISSN 1364-8152 - p. 1389 - 1402.
river-basin management - ecosystem management - resource management - united-states - integration - models - tools - information - policy - dss
Despite the perceived value of DSS in informing environmental and natural resource management, DSS tools often fail to be adopted by intended end users. By drawing together the experience of a global group of EDSS developers, we have identified and assessed key challenges in EDSS development and offer recommendations to resolve them. Challenges related to engaging end users in EDSS development emphasise the need for a participatory process that embraces end users and stakeholders throughout the design and development process. Adoption challenges concerned with individual and organisational capacities to use EDSS and the match between EDSS and organisational goals can be overcome through the use of an internal champion to promote the EDSS at different levels of a target organisation; coordinate and build capacity within the organisation, and; ensure that developers maintain focus on developing EDSS which are relatively easy and inexpensive to use and update (and which are perceived as such by the target users). Significant challenges exist in relation to ensuring EDSS longevity and financial sustainability. Such business challenges may be met through planning and design that considers the long-term costs of training, support, and maintenance; revenue generation and licensing by instituting processes which support communication and interactions; and by employing software technology which enables easy model expansion and re use to gain an economy of scale and reduce development costs. A final group of perhaps more problematic challenges relate to how the success of EDSS ought to be evaluated. Whilst success can be framed relatively easily in terms of interactions with end users, difficulties of definition and measurability emerge in relation to the extent to which EDSS achieve intended outcomes. To tackle the challenges described, the authors provide a set of best practice recommendations concerned with promoting design for ease of use, design for usefulness, establishing trust and credibility, promoting EDSS acceptance, and starting simple and small in functionality terms. Following these recommendations should enhance the achievement of successful EDSS adoption, but more importantly, help facilitate the achievement of desirable social and environmental outcomes.
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