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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Assessment of the cross-national validity of an End-anchored 9-point hedonic product liking scale
Beuckelaer, A. de; Zeeman, M. ; Trijp, J.C.M. van - \ 2015
Quality and quantity: international journal of methodology 49 (2015)3. - ISSN 0033-5177 - p. 1267 - 1286.
marketing standardization - response styles - performance - countries - consumers - american - japanese - extreme - bias
Abstract An end-anchored 9-point hedonic product liking (PL) scale is an easy-to-apply instrument to examine consumers’ PL. Because 9-point hedonic PL scales are also popular in cross-national research, strong demands are put on its cross-national equivalence, that is, the absence of cross-national scoring bias. The present study provides a procedure to identify the presence of cross-national scoring bias in the use of the end-anchored 9-point hedonic PL scale or any other rating scale to measure PL. The procedure is illustrated on experimental (illustrative) data from students in four European nations (i.e., Belgium, Germany, the Netherlands, and Spain). It explores cross-national equivalence in terms of (1) mean PL scores, (2) variation in PL scores, and (3) the impact of cross-cultural scoring bias in statistical inference making. Data analyses revealed that cross-national scoring bias only affected the variability in participants’ PL scores, but not the level of their PL scores. However, cross-national scoring bias in variation in PL scores did exert a substantial influence on a statistical inference making of mean PL scores. In sum, this study (1) provides preliminary evidence that cross-national scoring bias may seriously hamper the validity of cross-national comparisons of PL scores; and (2) offers a new methodology allowing food researchers to assess the extent to which the amount of cross-national scoring bias in their PL data will result in invalid cross-national comparisons. Keywords Product liking – Cross-national (cross-cultural)measurement validity/bias – Cross-national scoring bias – End-anchored 9-point hedonic product liking scale
Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]
Khoury, C.K. ; Heider, B. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Miller, R.E. ; Scotland, R.W. ; Wood, J.R.I. ; Rossel, G. ; Eserman, L.A. ; Jarret, R.L. ; Yencho, G.C. ; Bernau, V. ; Juarez, H. ; Sotelo, S. ; Haan, S. de; Struik, P.C. - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 14 p.
species distribution models - phylogenetic-relationships - beta-carotene - convolvulaceae - sequences - diversity - evolution - bias - challenges - tolerance
Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.
Crop wild relatives of pigeonpea [Cajanus cajan (L.) Millsp.]: Distributions, ex situ conservation status, and potential genetic resources for abiotic stress tolerance
Khoury, C.K. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Bernau, V. ; Kassa, M.T. ; Norton, S.L. ; Maesen, L. ; Upadhyaya, H.D. ; Ramirez-Villegas, J. ; Jarvis, A. ; Struik, P.C. - \ 2015
Biological Conservation 184 (2015). - ISSN 0006-3207 - p. 259 - 270.
species distribution models - global food security - male-sterility - climate-change - osmotic adjustment - diversity - bias - biodiversity - adaptation - accessions
Pigeonpea [Cajanus cajan (L.) Millsp.] is a versatile, stress-tolerant, and nutritious grain legume, possessing traits of value for enhancing the sustainability of dry sub-tropical and tropical agricultural systems. The use of crop wild relatives (CWR) in pigeonpea breeding has been successful in providing important resistance, quality, and breeding efficiency traits to the crop. Current breeding objectives for pigeonpea include increasing its tolerance to abiotic stresses, including heat, cold, drought, and waterlogging. Here we assess the potential for pigeonpea CWR to be further employed in crop improvement by compiling wild species occurrence and ex situ conservation information, producing geographic distribution models for the species, identifying gaps in the omprehensiveness of current germplasm collections, and using ecogeographic information to identify CWR populations with the potential to contribute agronomic traits of priority to breeders. The fifteen prioritized relatives of pigeonpea generally occur in South and Southeast Asia to Australia, with the highest concentrations of species in southern India and northern Australia. These taxa differ considerably among themselves and in comparison to the crop in their adaptations to temperature, precipitation and edaphic conditions. We find that these wild genetic resources are broadly under-represented in ex situ conservation systems, with 80% of species assessed as high priority for further collecting, thus their availability to plant breeders is insufficient. We identify species and highlight geographic locations for further collecting in order to improve the completeness of pigeonpea CWR germplasm collections, with particular emphasis on potential traits for abiotic stress tolerance.
The impact of contracts on organic honey producers' incomes in southwestern Ethiopia
Girma, J. ; Gardebroek, C. - \ 2015
Forest Policy and Economics 50 (2015). - ISSN 1389-9341 - p. 259 - 268.
propensity score - countries - schemes - program - africa - bias
In southwestern Ethiopia honey is a non-timber forest product that provides income for many smallholders. Some of these beekeepers supply their honey under contract to a company that markets their organic honey internationally allowing them to access premium markets. Since both production and marketing depend crucially on the forest, both smallholders and the company have an interest in preserving the forest. An important question is whether smallholders also benefit economically from supplying under contract. The objective of this study is to examine the contribution of participation in contract supply of organic honey to beekeepers' income levels in the Sheka zone in southwestern Ethiopia. Results indicate that contract supply improved quality of honey delivered, the prices beekeepers received, and total honey income per household. The findings illustrate the potential of contract supply of forest product for sustainable management of forests.
Natural disasters and economic growth: A meta-analysis
Klomp, J.G. ; Valckx, K. - \ 2014
Global environmental change : human and policy dimensions 26 (2014). - ISSN 0959-3780 - p. 183 - 195.
climate-change - civil conflict - consequences - impacts - matter - bias
Using more than 750 estimates, we perform a meta-regression analysis of studies examining the relationship between economic growth per capita and natural disasters. The studies considered are very different with respect to the type of disasters considered, the sample of countries and time periods covered, model specification, estimators used and publication outlet. After extensive testing of our results, we conclude that there exists a negative genuine effect of natural disasters on economic growth which is increasing over the period of our analysis. Still, the magnitude differs across disasters included and country sample used. In particular, it turns out that climatic disasters in developing countries have the most significant adverse impact on economic growth. However, we also find some evidence that a part of the negative impact of natural disasters found in these studies is caused by a publication bias. (C) 2014 Elsevier Ltd. All rights reserved.
The effect of the solemn oath script in hypothetical choice experiment survey: A pilot study
Magistris, T. de; Pascucci, S. - \ 2014
Economics Letters 123 (2014)2. - ISSN 0165-1765 - p. 252 - 255.
cheap talk - valuation - bias
We test the effect of the solemn oath (HO) in Hypothetical CE Survey (CE). We conducted CE surveys with three treatments: (1) CE without a cognitive task, (2) CE with a CT script, and (3) CE with a HO. Results generally suggest lower WTPs values with the HO, than without the HO script.
The impact of piped water on household welfare: evidence from Vietnam
Viet Cuong, N. ; Vu, T. - \ 2013
Journal of Environmental Planning and Management 56 (2013)9. - ISSN 0964-0568 - p. 1332 - 1358.
reduce diarrhea - bias - adjustment - estimators - india
Clean water is essential for human survival. However, a large proportion of people do not have access to clean water in Vietnam. Approximately only 23% of the population had access to piped water in 2006. This study measures the effect of piped water on household welfare using difference-in-differences estimators and panel data from Vietnam Household Living Standard Surveys. It found that the effect of piped water on household income and working efforts are positive, but are small and not statistically significant. Similarly, the effect of piped water on the sickness of household members is negative, but not statistically significant
Financial Liberalization and Economic Growth
Bumann, S. ; Hermes, N. ; Lensink, B.W. - \ 2013
Journal of International Money and Finance 33 (2013). - ISSN 0261-5606 - p. 255 - 281.
capital account liberalization - meta-regression analysis - developing-countries - aid effectiveness - bias - markets - banking
This study provides a systematic analysis of the empirical literature on the relationship between financial liberalization and economic growth by conducting a meta-analysis, based on 441 t-statistics reported in 60 empirical studies. We focus on explaining the heterogeneity of results in our sample in terms of study-, data- and method-specific characteristics. Although our findings indicate that, on average, there is a positive effect of financial liberalization on growth, the significance of this effect is only weak. Moreover, we find that most of the variables that may help explain the heterogeneity of results are insignificant. There are two exceptions. First, studies carried out based on data from the 1970s on average find a statistically less significant relationship between financial liberalization policies and growth (i.e. they report lower t-statistics) as compared to studies using data from the 1980s. Second, studies controlling for the level of development of the financial system report lower t-statistics for the relationship between liberalization and growth.
Technical note: a mathematical function to predict daily milk yield of dairy cows in relation to the interval between milkings
Klopcic, M. ; Koops, W.J. ; Kuipers, A. - \ 2013
Journal of Dairy Science 96 (2013)9. - ISSN 0022-0302 - p. 6084 - 6090.
testing schemes - single milking - lactation - cattle - protein - model - bias - fat
The milk production of a dairy cow is characterized by lactation production, which is calculated from daily milk yields (DMY) during lactation. The DMY is calculated from one or more milkings a day collected at the farm. Various milking systems are in use today, resulting in one or many recorded milk yields a day, from which different calculations are used to determine DMY. The primary objective of this study was to develop a mathematical function that described milk production of a dairy cow in relation to the interval between 2 milkings. The function was partly based on the biology of the milk production process. This function, called the 3K-function, was able to predict milk production over an interval of 12 h, so DMY was twice this estimate. No external information is needed to incorporate this function in methods to predict DMY. Application of the function on data from different milking systems showed a good fit. This function could be a universal tool to predict DMY for a variety of milking systems, and it seems especially useful for data from robotic milking systems. Further study is needed to evaluate the function under a wide range of circumstances, and to see how it can be incorporated in existing milk recording systems. A secondary objective of using the 3K-function was to compare how much DMY based on different milking systems differed from that based on a twice-a-day milking. Differences were consistent with findings in the literature.
Disaster exposure as a risk factor for mental health problems, eighteen months, four and ten years post-disaster -- a longitudinal study
Berg, B. van den; Wong, A. ; Velden, P.G. ; Boshuizen, H.C. ; Grievink, L. - \ 2012
BMC Psychiatry 12 (2012). - ISSN 1471-244X - 26 p.
posttraumatic-stress-disorder - symptoms - adults - metaanalysis - responses - services - impact - ptsd - bias
BackgroundDisaster experiences have been associated with higher prevalence rates of (mental) health problems. The objective of this study was to examine the independent relation between a series of single disaster experiences versus the independent predictive value of a accumulation of disaster experiences, i.e. a sum score of experiences and symptoms of distress and post-traumatic stress disorder (PTSD). Methods Survivors of a fireworks disaster participated in a longitudinal study and completed a questionnaire three weeks (wave 1), eighteen months (wave 2) and four years post-disaster (wave 3). Ten years post-disaster (wave 4) the respondents consisted of native Dutch survivors only. Main outcome measures were general distress and symptoms of PTSD. Results Degree of disaster exposure (sum score) and some disaster-related experiences (such as house destroyed, injured, confusion) were related to distress at waves 2 and 3. This relation was mediated by distress at an earlier point in time. None of the individual disaster-related experiences was independently related to symptoms of distress. The association between the degree of disaster exposure and symptoms of PTSD at waves 2 and 3 was still statistically significant after controlling for symptoms of distress and PTSD at earlier point in time. The variable ‘house destroyed’ was the only factor that was independently related to symptoms of PTSD at wave 2. Ten years after the disaster, disaster exposure was mediated by symptoms of PTSD at waves 2 and 3. Disaster exposure was not independently related to symptoms of PTSD ten years post-disaster. Conclusions Until 4 years after the disaster, degree of exposure (a sum score) was a risk factor for PTSD symptoms while none of the individual disaster experiences could be identified as an independent risk factor. Ten years post-disaster, disaster exposure was no longer an independent risk factor for symptoms of PTSD. Since symptoms of PTSD and distress at earlier waves perpetuate the symptoms at later waves, health care workers should aim their resources at those who still have symptoms after one and a half year post-disaster, to prevent health problems at medium and long-term.
Generating spatial precipitation ensembles: impact of temporal correlation structure
Rakovec, O. ; Hazenberg, P. ; Torfs, P.J.J.F. ; Weerts, A.H. ; Uijlenhoet, R. - \ 2012
Hydrology and Earth System Sciences 16 (2012)9. - ISSN 1027-5606 - p. 3419 - 3434.
distributed hydrological model - radar rainfall estimation - ourthe catchment - real - bias - assimilation - resolution - region
Sound spatially distributed rainfall fields including a proper spatial and temporal error structure are of key interest for hydrologists to force hydrological models and to identify uncertainties in the simulated and forecasted catchment response. The current paper presents a temporally coherent error identification method based on time-dependent multivariate spatial conditional simulations, which are conditioned on preceding simulations. A sensitivity analysis and real-world experiment are carried out within the hilly region of the Belgian Ardennes. Precipitation fields are simulated for pixels of 10 km x 10 km resolution. Uncertainty analyses in the simulated fields focus on (1) the number of previous simulation hours on which the new simulation is conditioned, (2) the advection speed of the rainfall event, (3) the size of the catchment considered, and (4) the rain gauge density within the catchment. The results for a sensitivity analysis show for typical advection speeds > 20 km h(-1), no uncertainty is added in terms of across ensemble spread when conditioned on more than one or two previous hourly simulations. However, for the real-world experiment, additional uncertainty can still be added when conditioning on a larger number of previous simulations. This is because for actual precipitation fields, the dynamics exhibit a larger spatial and temporal variability. Moreover, by thinning the observation network with 50 %, the added uncertainty increases only slightly and the cross-validation shows that the simulations at the unobserved locations are unbiased. Finally, the first-order autocorrelation coefficients show clear temporal coherence in the time series of the areal precipitation using the time-dependent multivariate conditional simulations, which was not the case using the time-independent univariate conditional simulations. The presented work can be easily implemented within a hydrological calibration and data assimilation framework and can be used as an improvement over currently used simplistic approaches to perturb the interpolated point or spatially distributed precipitation estimates.
The Effects of Demand Characteristics on Research Participant Behaviours in Non-Laboratory Settings: A Systematic Review
McCambridge, J. ; Bruin, M. de; Witton, J. - \ 2012
PLoS ONE 7 (2012)6. - ISSN 1932-6203
self-report - validity - artifact - trial - bias
Background The concept of demand characteristics, which involves research participants being aware of what the researcher is investigating, is well known and widely used within psychology, particularly in laboratory-based studies. Studies of this phenomenon may make a useful contribution to broader consideration of the effects of taking part in research on participant behaviour. This systematic review seeks to summarise data from studies of the effects of demand characteristics on participant behaviours in non-laboratory settings. Methodology/Principal Findings Electronic databases were searched to identify eligible studies. These had to be purposely designed to evaluate possible effects of demand characteristics on at least one behavioural outcome under the autonomous control of the participants and use longitudinal study designs. Only 7 studies were included, 6 providing observational data and 1 experimental study, with 5 studies involving examination of possible effects on health behaviours. Although studies provided some evidence of effects of demand characteristics on participant behaviour, heterogeneous operationalisation of the construct, the limited number of studies and poor quality of study designs made synthesis and interpretation of study findings challenging. Conclusions/Significance Although widely accepted as important in psychology, there have been few dedicated studies of the effects of demand characteristics on research participant behaviours outside laboratory settings. This body of literature does not currently contribute to the wider study of research participation effects. A systematic review of data from laboratory-based studies is needed, as are high-quality primary studies in non-laboratory settings. We suggest that unqualified use of the term demand characteristics should be abandoned
Consumer preferences regarding food-related risk-benefit messages
Dijk, H. van; Kleef, E. van; Owen, H. ; Frewer, L.J. - \ 2012
British Food Journal 114 (2012)3. - ISSN 0007-070X - p. 387 - 400.
genetically-modified foods - fish consumption - health - communication - nutrition - attitudes - perception - decisions - industry - bias
Purpose – The aim of this study is to identify and explore consumer preferences and information needs regarding the simultaneous communication of risks and benefits associated with food consumption. The focus is on the net health impact of risks and benefits on life expectancy, quality of life, and disability adjusted life years (DALYs). Design/methodology/approach – Focus groups were conducted in four countries (Iceland, The Netherlands, Portugal, UK). All sessions were audio-taped, transcribed and content analyzed. Findings – Current risk-benefit communication is perceived as “asymmetrical”, confusing, and often distrusted. Participants expressed a preference for more balanced and scientifically derived information. Information about the net health impact on both life expectancy and quality of life was found to be meaningful for food decision making. DALYs were thought too complicated. Research limitations/implications – Findings confirm the importance of incorporating consumers' viewpoints when developing communications about risk and benefits. The results provide insights into potential issues related to the communication of risk and benefit information. The limitations of the qualitative approach adopted in this study suggest that further research utilizing nationally representative samples is needed, which may explore additional metrics to communicate net health effects to consumers. Originality/value – Common measures for assessing both risks and benefits are expected to facilitate the communication of the results of risk-benefit assessment as part of risk analysis. However, research incorporating consumers' perspectives on this issue is scarce. A better understanding of how consumers perceive these measures may promote the development of more effective integrated risk benefit communication.
A gap analysis methodology for collecting crop genepools: a case study with Phaseolus beans
Ramírez-Villegas, J. ; Khoury, C.K. ; Jarvis, A. ; Debouck, D.G. ; Guarino, L. - \ 2010
PLoS ONE 5 (2010)10. - ISSN 1932-6203 - 18 p.
species distribution models - wild relatives - climate-change - sample-size - distributions - conservation - performance - diversity - bias - prediction
Background The wild relatives of crops represent a major source of valuable traits for crop improvement. These resources are threatened by habitat destruction, land use changes, and other factors, requiring their urgent collection and long-term availability for research and breeding from ex situ collections. We propose a method to identify gaps in ex situ collections (i.e. gap analysis) of crop wild relatives as a means to guide efficient and effective collecting activities. Methodology/Principal Findings The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps. We apply the gap analysis methodology to wild taxa of the Phaseolus genepool. Of 85 taxa, 48 (56.5%) are assigned high priority for collecting due to lack of, or under-representation, in genebanks, 17 taxa are given medium priority for collecting, 15 low priority, and 5 species are assessed as adequately represented in ex situ collections. Gap “hotspots”, representing priority target areas for collecting, are concentrated in central Mexico, although the narrow endemic nature of a suite of priority species adds a number of specific additional regions to spatial collecting priorities. Conclusions/Significance Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions. A more detailed prioritization of taxa and geographic areas for collection can be achieved by including in the analysis predictive threat factors, such as climate change or habitat destruction, or by adding additional prioritization filters, such as the degree of relatedness to cultivated species (i.e. ease of use in crop breeding). Furthermore, results for multiple crop genepools may be overlaid, which would allow a global analysis of gaps in ex situ collections of the world's plant genetic resources
Bayesian image restoration models for combining expert knowledge on recording activity with species distribution data
Bierman, S.M. ; Butler, A. ; Marion, G. ; Kuhn, I. - \ 2010
Ecography 33 (2010)3. - ISSN 0906-7590 - p. 451 - 460.
pseudo-absence data - biodiversity databases - plant diversity - habitat - abundance - patterns - wildlife - europe - rates - bias
Biological atlases are, for many species, the only source of information on their distribution over large geographical areas, and are widely used to inform models of the environmental distribution of species. Such data are not collected using standardized survey techniques, however, and spatial variations in coverage (the relative extent or completeness of records) may lead to variations in the probability that the species will be recorded at locations where it is present (the "recording probability"). If spatial patterns in recording probabilities are correlated with key environmental variables, then biased estimates of the relationships between environmental variables and species distributions may be obtained. We outline a general statistical framework for modelling the environmental distribution of species using, known as Bayesian Image Restoration (BIR). BIR can be used in combination with any species distribution model, but in addition allows us to account for spatial heterogeneity in recording probabilities by utilizing expert knowledge on spatial patterns in coverage. We illustrate the methodology by applying it to maps of the recorded distribution of two plant species in Germany, taken from the German atlas of vascular plants. We find that estimated spatial patterns in recording probabilities for both species are correlated with key environmental variables. Consequently, different relationships between the probability of presence of a species and environmental variables were obtained when the species distribution models were parameterised within a BIR framework. Care must be taken in the application of BIR, since the resulting inferences can depend strongly upon the modelling assumptions that are adopted. Nevertheless, we conclude that BIR has the potential to make better use of uncertain information on species distributions than conventional methods, and can be used to formally investigate the robustness of inferences on the environmental distribution of species to assumptions concerning spatial patterns in recording probabilities
Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance
Hickey, J.M. ; Veerkamp, R.F. ; Calus, M.P.L. ; Mulder, H.A. ; Thompson, R. - \ 2009
Genetics, Selection, Evolution 41 (2009). - ISSN 0999-193X - 9 p.
genetic evaluations - breeding values - model - algorithms - selection - accuracy - trait - bias
Calculation of the exact prediction error variance covariance matrix is often computationally too demanding, which limits its application in REML algorithms, the calculation of accuracies of estimated breeding values and the control of variance of response to selection. Alternatively Monte Carlo sampling can be used to calculate approximations of the prediction error variance, which converge to the true values if enough samples are used. However, in practical situations the number of samples, which are computationally feasible, is limited. The objective of this study was to compare the convergence rate of different formulations of the prediction error variance calculated using Monte Carlo sampling. Four of these formulations were published, four were corresponding alternative versions, and two were derived as part of this study. The different formulations had different convergence rates and these were shown to depend on the number of samples and on the level of prediction error variance. Four formulations were competitive and these made use of information on either the variance of the estimated breeding value and on the variance of the true breeding value minus the estimated breeding value or on the covariance between the true and estimated breeding values
Developing a discrimination rule between breast cancer patients and controls using proteomics mass spectrometric data: A three-step approach
Heidema, A.G. ; Nagelkerke, N. - \ 2008
Statistical Applications in Genetics and Molecular Biology 7 (2008)2. - ISSN 1544-6115 - 9 p.
random forest - classification - selection - bias
To discriminate between breast cancer patients and controls, we used a three-step approach to obtain our decision rule. First, we ranked the mass/charge values using random forests, because it generates importance indices that take possible interactions into account. We observed that the top ranked variables consisted of highly correlated contiguous mass/charge values, which were grouped in the second step into new variables. Finally, these newly created variables were used as predictors to find a suitable discrimination rule. In this last step, we compared three different methods, namely Classification and Regression Tree ( CART), logistic regression and penalized logistic regression. Logistic regression and penalized logistic regression performed equally well and both had a higher classification accuracy than CART. The model obtained with penalized logistic regression was chosen as we hypothesized that this model would provide a better classification accuracy in the validation set. The solution had a good performance on the training set with a classification accuracy of 86.3%, and a sensitivity and specificity of 86.8% and 85.7%, respectively.
Eight-fold increased risk for congenital heart defects in children carrying the nicotinamide N-methyltransferase polymorphism and exposed to medicines and low nicotinamide
Driel, L.M.J.W. van; Smedts, H.P.M. ; Helbing, W.A. ; Isaacs, A. ; Lindemans, J. ; Uitterlinden, A.G. ; Duijn, C.M. van; Vries, J.H.M. de; Steegers, E.A.P. ; Steegers-Theunissen, R.P.M. - \ 2008
European Heart Journal 29 (2008)11. - ISSN 0195-668X - p. 1424 - 1431.
plasma homocysteine - gene - pregnancy - malformations - multivitamin - association - methylation - supplements - folate - bias
Aims: Congenital heart defects (CHDs) have a multifactorial origin, in which subtle genetic factors and peri-conception exposures interact. We hypothesize that derangements in the homocysteine and detoxification pathways, due to a polymorphism in the nicotinamide N-methyltransferase (NNMT) gene, low maternal dietary nicotinamide intake, and medicine use in the peri-conception period, affect CHD risk. Methods and results: In 292 case and 316 control families, maternal peri-conception medicine use and low dietary intake of nicotinamide (13.8 mg/day) were independently associated with CHD risk [odds ratio (95% confidence interval) 1.6 (1.1¿2.3) and 1.5 (1.03¿2.3), respectively]. No significant association was found for the NNMT AG/AA genotype in mothers [0.9 (0.7¿1.3)], fathers [1.1 (0.8¿1.6)], or children [1.1 (0.8¿1.6)]. However, the combination of peri-conception medicine use, low dietary nicotinamide intake, and the NNMT AG/AA genotype in mothers or children showed risk of 2.7 (1.02¿8.1) and 8.8 (2.4¿32.5), respectively. Conclusion: Children carrying the NNMT A allele face additional CHD risk in combination with peri-conception exposure to medicines and/or a low dietary nicotinamide intake. These findings provide a first set of data against which future studies with larger sample sizes can be compared with.
Identification of glucose-fermenting bacteria present in an in-vitro model of the human inetstine by RNA-stable isotope probing
Egert, M.G.G. ; Graaf, A.A. de; Maathuis, A. ; Waard, P. de; Plugge, C.M. ; Smidt, H. ; Deutz, N.E.P. ; Dijkema, C. ; Vos, W.M. de; Venema, K. - \ 2007
FEMS microbiology ecology 60 (2007)1. - ISSN 0168-6496 - p. 126 - 135.
microbial community structure - fragment-length-polymorphism - chain fatty-acids - propionate oxidation - diversity - pcr - microorganisms - tract - colon - bias
16S rRNA-based stable isotope probing (SIP) and nuclear magnetic resonance (NMR) spectroscopy-based metabolic profiling were used to identify bacteria fermenting glucose under conditions simulating the human intestine. The TIM-2 in vitro model of the human intestine was inoculated with a GI tract microbiota resembling that of the small intestine, to which subsequently 4, 20 or 40 mM of [U-13C]-glucose were added. RNA was extracted from lumen samples after 0 (control), 1, 2 and 4 h and subjected to density-gradient ultracentrifugation. Phylogenetic analysis of unlabeled 16S rRNA revealed a microbial community dominated by lactic acid bacteria and Clostridium perfringens. Distinct 13C-incorporation into bacterial RNA was only observed for the 40-mM addition. 16S rRNA fingerprinting showed an activity drop of Lactobacillus fermentum after glucose addition, while Streptococcus bovis and C. perfringens were identified as the most active glucose-fermenters. Accordingly, NMR analysis identified lactate, acetate, butyrate and formate as the principal fermentation products, constituting up to 91% of the 13C-carbon balance. RNA-SIP combined with metabolic profiling allowed us to detect differential utilization of a general model carbohydrate, indicating that this approach holds great potential to identify bacteria involved in the fermentation of dietary relevant oligo- and polymeric carbohydrates in the human intestine.
Interpreting the change detection error matrix
Oort, P.A.J. van - \ 2007
Remote Sensing of Environment 108 (2007)1. - ISSN 0034-4257 - p. 1 - 8.
remotely-sensed data - land-cover change - classification accuracy - thematic maps - impacts - database - imagery - model - bias
Two different matrices are commonly reported in assessment of change detection accuracy: (1) single date error matrices and (2) binary change/no change error matrices. The third, less common form of reporting, is the transition error matrix. This paper discuses the relation between these matrices. First, it is shown that the transition error matrix implicitly measures temporal correlation in classification errors. Based on two assumptions (no correlation, maximum correlation), the single date error matrices can be used to obtain a most pessimistic and most optimistic estimate of the transition accuracy. Next, it is shown that the change/no change error matrix does not quantify certain classification errors. It is shown that change/no change error matrix can be used complementary to the full transition error matrix in efforts to improve transition detection accuracy. Despite its advantages, the transition error matrix is only very rarely reported, while it is of interest to all those interested in the accuracy of transitions (from¿to) in change detection.
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