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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How can statistical and artificial intelligence approaches predict piping erosion susceptibility?
Hosseinalizadeh, Mohsen ; Kariminejad, Narges ; Rahmati, Omid ; Keesstra, Saskia ; Alinejad, Mohammad ; Mohammadian Behbahani, Ali - \ 2019
Science of the Total Environment 646 (2019). - ISSN 0048-9697 - p. 1554 - 1566.
Loess plateau - Machine learning algorithms - Piping collapse - Susceptibility map - Unmanned aerial vehicle (UAV)

It is of fundamental importance to model the relationship between geo-environmental factors and piping erosion because of the environmental degradation attributed to soil loss. Methods that identify areas prone to piping erosion at the regional scale are limited. The main objective of this research is to develop a novel modeling approach by using three machine learning algorithms—mixture discriminant analysis (MDA), flexible discriminant analysis (FDA), and support vector machine (SVM) in addition to an unmanned aerial vehicle (UAV) images to map susceptibility to piping erosion in the loess-covered hilly region of Golestan Province, Northeast Iran. In this research, we have used 22 geo-environmental indices/factors and 345 identified pipes as predictors and dependent variables. The piping susceptibility maps were assessed by the area under the ROC curve (AUC). Validation of the results showed that the AUC for the three mentioned algorithms varied from 90.32% to 92.45%. We concluded that the proposed approach could efficiently produce a piping susceptibility map.

Flavor Retention and Release from Beverages : A Kinetic and Thermodynamic Perspective
Ammari, Ali ; Schroen, Karin - \ 2018
Journal of Agricultural and Food Chemistry (2018). - ISSN 0021-8561 - p. 9869 - 9881.
aqueous food - experimental method - flavor release - modeling

For the investigation of retention and release of flavor components, various methods are available, which are mostly used on a case-to-case basis depending on the raw material. These effects that originate from kinetics and thermodynamics could be put in a much wider perspective if these fields were taken as a starting point of investigation in combination with rigorous data analysis. In this Review, we give an overview of experimental techniques and data analysis methods, and predictive methods using mass transfer techniques are also discussed in detail. We use this as a foundation to discuss the interactions between volatile flavors and the matrix of liquid foods/beverages. Lipids present in the form of an emulsion are the strongest volatile retainers due to the lipophilic nature of most of the volatile flavors. Proteins also have flavor retention properties, whereas carbohydrates hardly have a retention effect in beverages. Smaller components, such as sugars and salts, can change the water activity, thereby facilitating flavor release. Alternatively, salts can also indirectly affect binding sites of proteins leading to release (e.g., NaCl and Na2SO4) or retention (NaCSN and Cl3CCOONa) of flavors. Furthermore, the effects of temperature and pH are discussed. The Review concludes with a critical section on determination of parameters relevant to flavor release. We highlight the importance of accurate determination of low concentrations when using linearization methods and also show that there is an intrinsic preference for nonlinear regression methods that are much less sensitive to measurement error.

Symposium review: Uncertainties in enteric methane inventories, measurement techniques, and prediction models
Hristov, A.N. ; Kebreab, Ermias ; Niu, Mutian ; Oh, J. ; Bannink, A. ; Bayat, Ali R. ; Boland, Tommy ; Brito, A.F. ; Casper, D.P. ; Crompton, Les A. ; Dijkstra, J. ; Eugène, Maguy A. ; Garnsworthy, Phil C. ; Haque, N. ; Hellwing, Anne L.F. ; Huhtanen, Pekka ; Kreuzer, Michael ; Lund, Peter ; Madsen, Jørgen ; Martin, C. ; Moate, P.J. ; Muetzel, Stefan ; Muñoz, Camila ; Peiren, Nico ; Powell, J.M. ; Reynolds, Chris ; Schwarm, Angela ; Shingfield, Kevin J. ; Storlien, Tonje M. ; Weisbjerg, Martin Riis ; Yáñez-Ruiz, D.R. ; Yu, Z. - \ 2018
Journal of Dairy Science 101 (2018)7. - ISSN 0022-0302 - p. 6655 - 6674.
Ruminant production systems are important contributors to anthropogenic methane (CH4) emissions, but there are large uncertainties in national and global livestock CH4 inventories. Sources of uncertainty in enteric CH4 emissions include animal inventories, feed dry matter intake (DMI), ingredient and chemical composition of the diets, and CH4 emission factors. There is also significant uncertainty associated with enteric CH4 measurements. The most widely used techniques are respiration chambers, the sulfur hexafluoride (SF6) tracer technique, and the automated head-chamber system (GreenFeed; C-Lock Inc., Rapid City, SD). All 3 methods have been successfully used in a large number of experiments with dairy or beef cattle in various environmental conditions, although studies that compare techniques have reported inconsistent results. Although different types of models have been developed to predict enteric CH4 emissions, relatively simple empirical (statistical) models have been commonly used for inventory purposes because of their broad applicability and ease of use compared with more detailed empirical and process-based mechanistic models. However, extant empirical models used to predict enteric CH4 emissions suffer from narrow spatial focus, limited observations, and limitations of the statistical technique used. Therefore, prediction models must be developed from robust data sets that can only be generated through collaboration of scientists across the world. To achieve high prediction accuracy, these data sets should encompass a wide range of diets and production systems within regions and globally. Overall, enteric CH4 prediction models are based on various animal or feed characteristic inputs but are dominated by DMI in one form or another. As a result, accurate prediction of DMI is essential for accurate prediction of livestock CH4 emissions. Analysis of a large data set of individual dairy cattle data showed that simplified enteric CH4 prediction models based on DMI alone or DMI and limited feed- or animal-related inputs can predict average CH4 emission with a similar accuracy to more complex empirical models. These simplified models can be reliably used for emission inventory purposes.
Development of an in vitro protocol to screen Clavibacter michiganensis subsp. michiganensis pathogenicity in different Solanum species.
Mohd Nadzir, M.M. ; Vieira Lelis, Flavia ; Thapa, B. ; Ali, Afrida ; Visser, R.G.F. ; Heusden, A.W. van; Wolf, J.M. van der - \ 2018
Plant Pathology (2018). - ISSN 0032-0862
Clavibacter - Cmm - disease screening - in vitro - PathoScreen - tomato
Clavibacter michiganensis subsp. michiganensis (Cmm) is a quarantine organism in Europe and in many other countries. It is one of the most severe bacterial pathogens affecting tomato. Screening tomato plants for their resistance level
to Cmm requires a large amount of space under quarantine conditions and is therefore costly. This project developed a new inoculation protocol on in vitro tomato plants to facilitate a more economic and higher throughput disease screening. A new method using the PathoScreen system was tested to localize green fluorescent protein-tagged Cmm in planta and to quantify the pathogen based on the percentage of corrected GFP (cGFP%). The system was sensitive in detecting the GFP-tagged Cmm in the shoots, but in the roots a high autofluorescence masked detection and thus sensitivity of the assay. The in vitro protocol was tested on several wild relatives of tomato, which were previously screened in a greenhouse assay. The correlation between wilt symptoms in vitro and wilt symptoms in the greenhouse was overall moderate (r = 0.6462). The protocol worked well in differentiating the two parents that were used in the mapping studies. This study shows that the in vitro protocol can be efficiently used for resistance breeding in many tomato genotypes.
Cyanobacteria dominance drives zooplankton functional dispersion
Josué, Iollanda I.P. ; Cardoso, Simone J. ; Miranda, Marcela ; Mucci, Maíra ; Ger, Kemal Ali ; Roland, Fabio ; Marinho, Marcelo Manzi - \ 2018
Hydrobiologia (2018). - ISSN 0018-8158 - 13 p.
Biodiversity - Eutrophication - Freshwater - Microbial food quality - Plankton

Accelerated eutrophication reduces water quality and shifts plankton communities. However, its effects on the aquatic food web and ecosystem functions remain poorly understood. Within this context, functional ecology can provide valuable links relating community traits to ecosystem functioning. In this study, we assessed the effects of eutrophication and cyanobacteria blooms on zooplankton functional diversity in a tropical hypereutrophic lake. Phytoplankton and zooplankton communities and limnological characteristics of a tropical Brazilian Lake (Southeast, Brazil) were monitored monthly from April 2013 to October 2014. Lake eutrophication indicators were total phosphorus, total chlorophyll-a, and chlorophyll-a per group (blue, green, and brown). The variation of major phytoplankton taxonomic group biomass was calculated and used as a proxy for changes in phytoplankton composition. Zooplankton functional diversity was assessed through functional dispersion and the community-weighted mean trait value. Regressions were performed between the lake eutrophication indicators, the phytoplankton biomass variation, and zooplankton functional dispersion. Our results suggest that eutrophication and cyanobacterial dominance change the composition of zooplankton traits and reduce functional dispersion, leading to zooplankton niche overlap. These findings are important because they provide a meaningful view of phytoplankton-zooplankton trophic interactions and contribute to an improved understanding their functional effects on aquatic ecosystems.

Investigation of Hepatitis A and e viruses in mussels collected from the bosphorus, in Istanbul, Turkey - Short communication
Yilmaz, Huseyin ; Cizmecigil, Utku ; Tarakci, Eda Altan ; Aydin, Ozge ; Yilmaz, Aysun ; Calicioglu, Mehmet ; Ciftcioglu, Gurhan ; Aydin, Ali ; Bostan, Kamil ; Sireli, Tansel ; Guzel, Mine ; Karakullukcu, Asiye ; Kocazeybek, Bekir ; Poel, Wim Van Der; Richt, Juergen ; Turan, Nuri - \ 2018
Czech Journal of Food Science 36 (2018)3. - ISSN 1212-1800 - p. 215 - 220.
Hepatitis - Mussels - Real-time RT-PCR - Turkey - Virus

Hepatitis A and E viruses (HAV and HEV) are recognised as food- and water-borne infections and shellfish are a well-documented source of these viruses. The presence of HAV and HEV in mussels has not previously been investigated in Bosphorus, Istanbul, Turkey, and therefore the aim of this study was to investigate the frequency of HAV and HEV in mussels collected from this location. A total of 92 pooled samples representing 736 mussels originating along the Bosphorus coast were collected from fish distributors. RNA was extracted using the RNeasy Plant Mini Kit and a TaqMan real-time RT-PCR was performed using primers specific to HAV and HEV. Amongst the 92 pooled samples tested, three (3.3%) were found to be positive for HAV by the TaqMan real-time RT-PCR. No HEV was detected in any of the mussels tested. A 174 bp product was observed on gel electrophoresis with HAV positive samples detected by SYBR Green real-time PCR after reverse transcription. This product was sequenced and confirmed to contain HAV sequences by alignment using the data in GenBank. This is the first report describing the presence of HAV in mussels harvested in the Bosphorus, Istanbul, Turkey, indicating the potential contamination of aquatic environment and risk to public health.

The burden of cardiovascular diseases among us states, 1990-2016
Roth, Gregory A. ; Johnson, Catherine O. ; Abate, Kalkidan Hassen ; Abd-Allah, Foad ; Ahmed, Muktar ; Alam, Khurshid ; Alam, Tahiya ; Alvis-Guzman, Nelson ; Ansari, Hossein ; Ärnlöv, Johan ; Atey, Tesfay Mehari ; Awasthi, Ashish ; Awoke, Tadesse ; Barac, Aleksandra ; Bärnighausen, Till ; Bedi, Neeraj ; Bennett, Derrick ; Bensenor, Isabela ; Biadgilign, Sibhatu ; Castañeda-Orjuela, Carlos ; Catalá-López, Ferrán ; Davletov, Kairat ; Dharmaratne, Samath ; Ding, Eric L. ; Dubey, Manisha ; Faraon, Emerito Jose Aquino ; Farid, Talha ; Farvid, Maryam S. ; Feigin, Valery ; Fernandes, João ; Frostad, Joseph ; Gebru, Alemseged ; Geleijnse, Johanna M. ; Gona, Philimon Nyakauru ; Griswold, Max ; Hailu, Gessessew Bugssa ; Hankey, Graeme J. ; Hassen, Hamid Yimam ; Havmoeller, Rasmus ; Hay, Simon ; Heckbert, Susan R. ; Irvine, Caleb Mackay Salpeter ; James, Spencer Lewis ; Jara, Dube ; Kasaeian, Amir ; Khan, Abdur Rahman ; Khera, Sahil ; Khoja, Abdullah T. ; Khubchandani, Jagdish ; Kim, Daniel ; Kolte, Dhaval ; Lal, Dharmesh ; Larsson, Anders ; Linn, Shai ; Lotufo, Paulo A. ; Razek, Hassan Magdy Abd El; Mazidi, Mohsen ; Meier, Toni ; Mendoza, Walter ; Mensah, George A. ; Meretoja, Atte ; Mezgebe, Haftay Berhane ; Mirrakhimov, Erkin ; Mohammed, Shafiu ; Moran, Andrew Edward ; Nguyen, Grant ; Nguyen, Minh ; Ong, Kanyin Liane ; Owolabi, Mayowa ; Pletcher, Martin ; Pourmalek, Farshad ; Purcell, Caroline A. ; Qorbani, Mostafa ; Rahman, Mahfuzar ; Rai, Rajesh Kumar ; Ram, Usha ; Reitsma, Marissa Bettay ; Renzaho, Andre M.N. ; Rios-Blancas, Maria Jesus ; Safiri, Saeid ; Salomon, Joshua A. ; Sartorius, Benn ; Sepanlou, Sadaf Ghajarieh ; Shaikh, Masood Ali ; Silva, Diego ; Stranges, Saverio ; Tabarés-Seisdedos, Rafael ; Atnafu, Niguse Tadele ; Thakur, J.S. ; Topor-Madry, Roman ; Truelsen, Thomas ; Tuzcu, E.M. ; Tyrovolas, Stefanos ; Ukwaja, Kingsley Nnanna ; Vasankari, Tommi ; Vlassov, Vasiliy ; Vollset, Stein Emil ; Wakayo, Tolassa ; Weintraub, Robert ; Wolfe, Charles ; Workicho, Abdulhalik ; Xu, Gelin ; Yadgir, Simon ; Yano, Yuichiro ; Yip, Paul ; Yonemoto, Naohiro ; Younis, Mustafa ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Zipkin, Ben ; Afshin, Ashkan ; Gakidou, Emmanuela ; Lim, Stephen S. ; Mokdad, Ali H. ; Naghavi, Mohsen ; Vos, Theo ; Murray, Christopher J.L. - \ 2018
JAMA Cardiology 3 (2018)5. - ISSN 2380-6583 - p. 375 - 389.
Importance: Cardiovascular disease (CVD) is the leading cause of death in the United States, but regional variation within the United States is large. Comparable and consistent state-level measures of total CVD burden and risk factors have not been produced previously. Objective: To quantify and describe levels and trends of lost health due to CVD within the United States from 1990 to 2016 as well as risk factors driving these changes. Design, setting, and participants: Using the Global Burden of Disease methodology, cardiovascular disease mortality, nonfatal health outcomes, and associated risk factors were analyzed by age group, sex, and year from 1990 to 2016 for all residents in the United States using standardized approaches for data processing and statistical modeling. Burden of disease was estimated for 10 groupings of CVD, and comparative risk analysis was performed. Data were analyzed from August 2016 to July 2017. Exposures: Residing in the United States. Main outcomes ans measures: Cardiovascular disease disability-Adjusted life-years (DALYs). Results: Between 1990 and 2016, age-standardized CVD DALYs for all states decreased. Several states had large rises in their relative rank ordering for total CVD DALYs among states, including Arkansas, Oklahoma, Alabama, Kentucky, Missouri, Indiana, Kansas, Alaska, and Iowa. The rate of decline varied widely across states, and CVD burden increased for a small number of states in the most recent years. Cardiovascular disease DALYs remained twice as large among men compared with women. Ischemic heart disease was the leading cause of CVD DALYs in all states, but the second most common varied by state. Trends were driven by 12 groups of risk factors, with the largest attributable CVD burden due to dietary risk exposures followed by high systolic blood pressure, high body mass index, high total cholesterol level, high fasting plasma glucose level, tobacco smoking, and low levels of physical activity. Increases in risk-deleted CVD DALY rates between 2006 and 2016 in 16 states suggest additional unmeasured risks beyond these traditional factors. Conclusions and relevance: Large disparities in total burden of CVD persist between US states despite marked improvements in CVD burden. Differences in CVD burden are largely attributable to modifiable risk exposures.
Development and analysis of the Soil Water Infiltration Global database
Rahmati, Mehdi ; Weihermüller, Lutz ; Vanderborght, Jan ; Pachepsky, Yakov A. ; Mao, Lili ; Sadeghi, Seyed Hamidreza ; Moosavi, Niloofar ; Kheirfam, Hossein ; Montzka, Carsten ; Looy, Kris Van; Toth, Brigitta ; Hazbavi, Zeinab ; Yamani, Wafa Al; Albalasmeh, Ammar A. ; Alghzawi, M.Z. ; Angulo-Jaramillo, Rafael ; Antonino, Antônio Celso Dantas ; Arampatzis, George ; Armindo, Robson André ; Asadi, Hossein ; Bamutaze, Yazidhi ; Batlle-Aguilar, Jordi ; Béchet, Béatrice ; Becker, Fabian ; Blöschl, Günter ; Bohne, Klaus ; Braud, Isabelle ; Castellano, Clara ; Cerdà, Artemi ; Chalhoub, Maha ; Cichota, Rogerio ; Císlerová, Milena ; Clothier, Brent ; Coquet, Yves ; Cornelis, Wim ; Corradini, Corrado ; Coutinho, Artur Paiva ; Oliveira, Muriel Bastista De; Macedo, José Ronaldo De; Durães, Matheus Fonseca ; Emami, Hojat ; Eskandari, Iraj ; Farajnia, Asghar ; Flammini, Alessia ; Fodor, Nándor ; Gharaibeh, Mamoun ; Ghavimipanah, Mohamad Hossein ; Ghezzehei, Teamrat A. ; Giertz, Simone ; Hatzigiannakis, Evangelos G. ; Horn, Rainer ; Jiménez, Juan José ; Jacques, Diederik ; Keesstra, Saskia Deborah ; Kelishadi, Hamid ; Kiani-Harchegani, Mahboobeh ; Kouselou, Mehdi ; Jha, Madan Kumar ; Lassabatere, Laurent ; Li, Xiaoyan ; Liebig, Mark A. ; Lichner, Lubomír ; López, María Victoria ; Machiwal, Deepesh ; Mallants, Dirk ; Mallmann, Micael Stolben ; Oliveira Marques, Jean Dalmo De; Marshall, Miles R. ; Mertens, Jan ; Meunier, Félicien ; Mohammadi, Mohammad Hossein ; Mohanty, Binayak P. ; Pulido-Moncada, Mansonia ; Montenegro, Suzana ; Morbidelli, Renato ; Moret-Fernández, David ; Moosavi, Ali Akbar ; Mosaddeghi, Mohammad Reza ; Mousavi, Seyed Bahman ; Mozaffari, Hasan ; Nabiollahi, Kamal ; Neyshabouri, Mohammad Reza ; Ottoni, Marta Vasconcelos ; Ottoni Filho, Theophilo Benedicto ; Pahlavan-Rad, Mohammad Reza ; Panagopoulos, Andreas ; Peth, Stephan ; Peyneau, Pierre Emmanuel ; Picciafuoco, Tommaso ; Poesen, Jean ; Pulido, Manuel ; Reinert, Dalvan José ; Reinsch, Sabine ; Rezaei, Meisam ; Roberts, Francis Parry ; Robinson, David ; Rodrigo-Comino, Jesüs ; Rotunno Filho, Otto Corrêa ; Saito, Tadaomi ; Suganuma, Hideki ; Saltalippi, Carla ; Sándor, Renáta ; Schütt, Brigitta ; Seeger, Manuel ; Sepehrnia, Nasrollah ; Sharifi Moghaddam, Ehsan ; Shukla, Manoj ; Shutaro, Shiraki ; Sorando, Ricardo ; Stanley, Ajayi Asishana ; Strauss, Peter ; Su, Zhongbo ; Taghizadeh-Mehrjardi, Ruhollah ; Taguas, Encarnación ; Teixeira, Wenceslau Geraldes ; Vaezi, Ali Reza ; Vafakhah, Mehdi ; Vogel, Tomas ; Vogeler, Iris ; Votrubova, Jana ; Werner, Steffen ; Winarski, Thierry ; Yilmaz, Deniz ; Young, Michael H. ; Zacharias, Steffen ; Zeng, Yijian ; Zhao, Ying ; Zhao, Hong ; Vereecken, Harry - \ 2018
Earth System Science Data 10 (2018)3. - ISSN 1866-3508 - p. 1237 - 1263.

In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements (∼76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76ĝ€% of the experimental sites with agricultural land use as the dominant type (∼40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in ∗.xlsx and ∗.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it.

Prediction of enteric methane production, yield, and intensity in dairy cattle using an intercontinental database
Niu, Mutian ; Kebreab, Ermias ; Hristov, Alexander N. ; Oh, Joonpyo ; Arndt, Claudia ; Bannink, André ; Bayat, Ali R. ; Brito, André F. ; Boland, Tommy ; Casper, David ; Crompton, Les A. ; Dijkstra, Jan ; Eugène, Maguy A. ; Garnsworthy, Phil C. ; Haque, Md Najmul ; Hellwing, Anne L.F. ; Huhtanen, Pekka ; Kreuzer, Michael ; Kuhla, Bjoern ; Lund, Peter ; Madsen, Jørgen ; Martin, Cécile ; Mcclelland, Shelby C. ; Mcgee, Mark ; Moate, Peter J. ; Muetzel, Stefan ; Muñoz, Camila ; O'Kiely, Padraig ; Peiren, Nico ; Reynolds, Christopher K. ; Schwarm, Angela ; Shingfield, Kevin J. ; Storlien, Tonje M. ; Weisbjerg, Martin R. ; Yáñez-Ruiz, David R. ; Yu, Zhongtang - \ 2018
Global Change Biology (2018). - ISSN 1354-1013 - p. 3368 - 3389.
Dairy cows - Dry matter intake - Enteric methane emissions - Methane intensity - Methane yield - Prediction models
Enteric methane (CH4) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CH4 is complex, expensive, and impractical at large scales; therefore, models are commonly used to predict CH4 production. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CH4 production from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CH4 production (g/day per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CH4 prediction accuracy. The intercontinental database covered Europe (EU), the United States (US), and Australia (AU). A sequential approach was taken by incrementally adding key variables to develop models with increasing complexity. Methane emissions were predicted by fitting linear mixed models. Within model categories, an intercontinental model with the most available independent variables performed best with root mean square prediction error (RMSPE) as a percentage of mean observed value of 16.6%, 14.7%, and 19.8% for intercontinental, EU, and United States regions, respectively. Less complex models requiring only DMI had predictive ability comparable to complex models. Enteric CH4 production, yield, and intensity prediction models developed on an intercontinental basis had similar performance across regions, however, intercepts and slopes were different with implications for prediction. Revised CH4 emission conversion factors for specific regions are required to improve CH4 production estimates in national inventories. In conclusion, information on DMI is required for good prediction, and other factors such as dietary neutral detergent fiber (NDF) concentration, improve the prediction. For enteric CH4 yield and intensity prediction, information on milk yield and composition is required for better estimation.
A new drainpipe-envelope concept for subsurface drainage systems in irrigated agriculture
Bahçeci, Idris ; Nacar, Abdullah Suat ; Topalhasan, Lui ; Tari, Ali Fuat ; Ritzema, Henk P. - \ 2018
Irrigation and drainage 67 (2018)S2. - ISSN 1531-0353 - p. 40 - 50.
Drain performance - Entrance resistance - Envelope material - Root growth - Subsurface drainage

On irrigated lands, drainpipe performance is often below standard due to clogging, siltation and root growth inside the pipe. To tackle these problems, an innovative pipe-envelope concept was tested on a 50 ha pilot area in Harran, Turkey, in 2015 and 2016. The new concept, HYDROLUIS, consists of a corrugated inner pipe with three rows of perforations at the top and an unperforated outer pipe that covers about 2/3 of the inner pipe leaving only the unperforated bottom part of the inner pipe in contact with the soil. The main advantages of the new concept are that it works for a wide range of soil textures and there is better protection against root growth inside the pipe. The new concept was compared with a geotextile envelope, a gravel envelope and a control with no envelope. The HYDROLUIS and gravel envelopes had a significantly lower entrance resistance compared to the geotextile, the best drain performance and no signs of sedimentation nor of root growth inside the pipe. The production costs of the HYDROLUIS envelope are comparable to those of pre-wrapped synthetic envelopes and considerably lower than gravel envelopes. It can be concluded that the HYDROLUIS envelope is a promising alternative for sand/gravel or synthetic envelopes in irrigated lands.

Interrill erodibility in relation to aggregate size class in a semi-arid soil under simulated rainfalls
Vaezi, Ali Reza ; Eslami, Seyedeh Fatemeh ; Keesstra, Saskia - \ 2018
Catena 167 (2018). - ISSN 0341-8162 - p. 385 - 398.
Aggregate stability - Interrill erosion - Rainfall intensity - Saturated hydraulic conductivity - Semi-arid region

Interrill erodibility can be affected by soil aggregates, especially by those aggregate size classes that are dominant in the soil. In the Water erosion Prediction Project (WEPP) model, interrill soil erodibility (Ki) is estimated using very fine sand content. Despite that some studies have indicated an effect of aggregate stability on the Ki, information on the relationship between the aggregate size class and Ki and factors controlling it, particularly in semi-arid region is limited. This study was conducted to determine the variation of Ki for different aggregate size classes under various rainfall intensities and evaluation of the WEPP model in estimating the Ki for different aggregate fractions. Five aggregate size classes (0.25–2, 2–4.75, 4.75–5.6, 5.6–9.75 mm, and 9.75–12.7 mm) were separated from a sandy clay loam soil sampled in an agricultural land and put in laboratory flumes of 100 cm × 50 cm. The flumes were placed on a 9% slope and exposed to ten sequential rainfall simulations varying from 10 to 60 mm h−1 for 30 min. The Ki of each aggregate size classes was determined using the interrill sediment delivery rate and compared this with the values estimated using WEPP. All physicochemical properties were also determined in the aggregate size classes. Organic matter content in the aggregate size classes was very low (0.65–0.73%) and didn't show strong relationships with the aggregate stability and hydraulic conductivity, whereas clay was major factor controlling determining these properties for the different aggregate fractions. Significant differences were found among the aggregate size classes in clay content (P < 0.05), aggregate stability measured using both wet-sieving method (P < 0.05) and water drop test method P < 0.05, saturated hydraulic conductivity (Ks), and measured Ki (P < 0.05). The measured Ki was about 34 and 90 times bigger than the estimated Ki for the fine aggregates and coarse aggregates, respectively. The fine aggregates showed higher susceptibility to interrill detachment with increasing rainfall intensity as compared with the coarse aggregates. Significant decrease was observed in the measured Ki with increasing the aggregate size which was associated with increases in clay content, aggregate stability and Ks. The stability of aggregates against raindrop impact (CND) was an important indicator describing the effect of aggregate size on the interrill erodibility in semi-arid soils. Therefore, this indicator can be taken into account as a soil structure measure to develop a proper equation for estimating interrill erodibility (Ki) for agricultural lands. The minimum use of tillage practices is essential to prevent aggregate breakdown and control interrill erosion in semi-arid regions.

Effects of incorporating environmental cost and risk aversion on economic values of pig breeding goal traits
Ali, B.M. ; Mey, Y. de; Bastiaansen, J.W.M. ; Oude Lansink, A.G.J.M. - \ 2018
Journal of Animal Breeding and Genetics 135 (2018)3. - ISSN 0931-2668 - p. 194 - 207.
Economic values (EVs) of traits, accounting for environmental impacts and risk preferences of farmers, are required to design breeding goals that contribute to both economic and environmental sustainability. The objective of this study was to assess the effects of incorporating environmental costs and the risk preferences of farmers on the EVs of pig breeding goal traits. A breeding goal consisting of both sow efficiency and production traits was defined for a typical Brazilian farrow‐to‐finish pig farm with 1,500 productive sows. A mean‐variance utility function was employed for deriving the EVs at finishing pig level assuming fixed slaughter weight. The inclusion of risk and risk aversion reduces the economic weights of sow efficiency traits (17%) while increasing the importance of production traits (7%). For a risk‐neutral producer, inclusion of environmental cost reduces the economic importance of sow efficiency traits (3%) while increasing the importance of production traits (1%). Genetic changes of breeding goal traits by their genetic standard deviations reduce emissions of greenhouse gases, and excretions of nitrogen and phosphorus per finished pig by up to 6% while increasing farm profit. The estimated EVs could be used to improve selection criteria and thereby contribute to the sustainability of pig production systems.
Geospatial Technologies for All : Selected Papers of the 21st AGILE Conference on Geographic Information Science
Mansourian, Ali ; Pilesjö, Petter ; Harrie, Lars ; Lammeren, R.J.A. van - \ 2018
Springer Publishers (Lecture Notes in Geoinformation and Cartography ) - ISBN 9783319782072 - 382 p.
Forest strata-dependent functional evenness explains whole-community aboveground biomass through opposing mechanisms
Ali, Arshad ; Lohbeck, Madelon ; Yan, En Rong - \ 2018
Forest Ecology and Management 424 (2018). - ISSN 0378-1127 - p. 439 - 447.
Big trees effect - Ecosystem function - Evergreen broadleaf forest - Functional diversity - Niche complementarity - Niche overlap - Overstorey and understorey - Soil nutrients

A positive biodiversity – aboveground biomass relationship is often attributed to the niche complementarity hypothesis. This hypothesis has received much less support when based on functional trait diversity and when tested in complex natural forests. Here, we hypothesized that niche complementarity (high trait diversity) in the understorey and niche overlap (low trait diversity) in the overstorey would drive whole-community aboveground biomass. To test this hypothesis, we used multiple linear regression models to evaluate how functional trait diversity (functional richness, evenness, divergence and dispersion) of overstorey, understorey, and whole-community determine aboveground biomass across 125 plots in a 5-ha subtropical forest of Eastern China. A structural equation model was used to evaluate whether the functional trait diversity of overstorey affects the relationships between understorey functional trait diversity and whole-community aboveground biomass while considering for the effect of environmental factors. We additionally considered the effects of mass ratio (i.e. community-weighted mean of trait values) and stand structural complexity. The strong negative effect of overstorey functional evenness on aboveground biomass provides support to the functional dominance and/or niche overlap rather than niche complementarity effect. The negative effect of overstorey functional evenness on aboveground biomass was also partially mediated by its direct negative effect on understorey functional evenness. The weak positive effect of understorey functional evenness on aboveground biomass provides support to the niche complementarity effect. We conclude that functional evenness of overstorey and understorey strata affect whole-community aboveground biomass differently through opposing mechanisms, regardless of the effects of mass ratio and stand structural complexity.

Aboveground mechanical stimuli affect belowground plant-plant communication
Elhakeem, Ali ; Markovic, Dimitrije ; Broberg, Anders ; Anten, Niels P.R. ; Ninkovic, Velemir - \ 2018
PLoS One 13 (2018)5. - ISSN 1932-6203
Plants can detect the presence of their neighbours and modify their growth behaviour accordingly. But the extent to which this neighbour detection is mediated by abiotic stressors is not well known. In this study we tested the acclimation response of Zea mays L. seedlings through belowground interactions to the presence of their siblings exposed to brief mechano stimuli. Maize seedling simultaneously shared the growth solution of touched plants or they were transferred to the growth solution of previously touched plants. We tested the growth preferences of newly germinated seedlings toward the growth solution of touched (T_solution) or untouched plants (C_solution). The primary root of the newly germinated seedlings grew significantly less towards T_solution than to C_solution. Plants transferred to T_solution allocated more biomass to shoots and less to roots. While plants that simultaneously shared their growth solution with the touched plants produced more biomass. Results show that plant responses to neighbours can be modified by aboveground abiotic stress to those neighbours and suggest that these modifications are mediated by belowground interactions.
Long-term impact of rainfed agricultural land abandonment on soil erosion in the Western Mediterranean basin
Cerdà, Artemi ; Rodrigo-Comino, Jesús ; Novara, Agata ; Brevik, Eric Charles ; Vaezi, Ali Reza ; Pulido, Manuel ; Giménez-Morera, Antonio ; Keesstra, Saskia Deborah - \ 2018
Progress in Physical Geography 42 (2018)2. - ISSN 0309-1333 - p. 202 - 219.
Land use change - plots - rainfall - runoff - scale - sediment - Spain
Land abandonment is widespread in the Mediterranean mountains. The impact of agricultural abandonment results in a shift in ecosystem evolution due to changes in soil erosion, but little is known about long-term soil and water losses. This paper uses 11 years of measurements in two paired plots (abandoned vs control) with four subplots to determine how soil and water losses evolved after abandonment within an agricultural parcel. For two years (2004–2005) both plots were under tillage, and after 2006 one plot was abandoned. The monitored plots measured runoff and sediment concentration after each rainfall event. The results show that during the two years after abandonment there was an increase in sediment yield followed by a decrease. Once the field was abandoned, a sudden increase in runoff (× 2.1 times) and sediment concentration (× 1.2 times) was found due to the lack of vegetation and tillage. After one year, the sediment concentration and, after two years, the runoff rates were lower in the abandoned than in the tilled plots. This short transition period ended in contrasting responses between the control and abandoned plot as the impact of abandonment resulted in 21 times less sediment yield after nine years of abandonment. This occurred despite the fact that the year after the abandonment the abandoned plot had 2.9 times more erosion due to low vegetation recovery and the development of a soil crust. Agriculture land abandonment resulted in lower erosion rates over the long term, but showed an increase in soil and water losses over the short term (two years). Therefore, in the first two years after abandonment there is a particular need to apply nature-based soil and water conservation strategies to prevent soil erosion.
Adjustment of measurement errors to reconcile precipitation distribution in the high-altitude Indus basin
Dahri, Zakir Hussain ; Moors, Eddy ; Ludwig, Fulco ; Ahmad, Shakil ; Khan, Asif ; Ali, Irfan ; Kabat, Pavel - \ 2018
International Journal of Climatology 38 (2018)10. - ISSN 0899-8418 - p. 3842 - 3860.
Bias correction of precipitation - High-altitude Indus basin - Net mass balance contribution to river run-off - Net snow accumulation adjustments - Precipitation distribution - Precipitation measurement errors
Precipitation in the high-altitude Indus basin governs its renewable water resources affecting water, energy and food securities. However, reliable estimates of precipitation climatology and associated hydrological implications are seriously constrained by the quality of observed data. As such, quantitative and spatio-temporal distributions of precipitation estimated by previous studies in the study area are highly contrasting and uncertain. Generally, scarcity and biased distribution of observed data at the higher altitudes and measurement errors in precipitation observations are the primary causes of such uncertainties. In this study, we integrated precipitation data of 307 observatories with the net snow accumulations estimated through mass balance studies at 21 major glacier zones. Precipitation observations are adjusted for measurement errors using the guidelines and standard methods developed under the WMO's international precipitation measurement intercomparisons, while net snow accumulations are adjusted for ablation losses using standard ablation gradients. The results showed more significant increases in precipitation of individual stations located at higher altitudes during winter months, which are consistent with previous studies. Spatial interpolation of unadjusted precipitation observations and net snow accumulations at monthly scale indicated significant improvements in the quantitative and spatio-temporal distribution of precipitation over the unadjusted case and previous studies. Adjustment of river flows revealed only a marginal contribution of net glacier mass balance to river flows. The adjusted precipitation estimates are more consistent with the corresponding adjusted river flows. The study recognized that the higher river flows than the corresponding precipitation estimates by the previous studies are mainly due to underestimated precipitation. The results can be useful for water balance studies and bias correction of gridded precipitation products for the study area.
Biological activity of Pakistani isolate SpltNPV-Pak-BNG in second, third and fourth instar larvae of the leafworm Spodoptera litura
Ali, Ghulam ; Vlak, Just M. ; Werf, Wopke van der - \ 2018
Biocontrol Science and Technology 28 (2018)5. - ISSN 0958-3157 - p. 521 - 527.
biological activity - larval instars - potency - S. litura - Spodoptera litura nucleopolyhedroviruses
Recently, a novel isolate of the baculovirus Spodoptera litura nucleopolyhedrovirus (SpltNPV) has been isolated from Pakistan, which is distinct from the type species SpltNPV-G2 (ICTV). Here, we examined the biological activity of this isolate (SpltNPV-Pak-BNG) in second (L2), third (L3) and fourth instar (L4) larvae of the leafworm S. litura, more specifically to measure biological properties that are relevant for use of this virus for pest control under field conditions. The median lethal dose for L2 and L3 instar larvae was similar, but significantly lower than for L4 larvae. Likewise, the survival time was similar for L2 and L3 larvae (84 h), but was significantly longer for L4 instar larvae (108 h). Thus, in terms of efficacy, S. litura L2 and L3 instar larvae are the preferred targets for S. litura control with SpltNPV-Pak-BNG in field crops in Pakistan. On the basis of our data spray regimes can be designed to control the leafworm in cotton and vegetable crops targeting L2 and L3 larvae.
Preface
Mansourian, Ali ; Pilesjö, Petter ; Harrie, Lars ; Lammeren, Ron van - \ 2018
Lecture Notes in Geoinformation and Cartography part F3 (2018). - ISSN 1863-2351 - p. v - vi.
Diversity and biological activity of nucleopolyhedroviruses of the leafworm Spodoptera litura
Ali, Ghulam - \ 2018
University. Promotor(en): Just Vlak, co-promotor(en): Wopke van der Werf. - Wageningen : Wageningen University - ISBN 9789463432313 - 194

Increased resistance of emerging cotton leafworm Spodoptera litura in Pakistan and elsewhere to chemical insecticides calls for an alternative method of control. Isolates of nucleopolyhedrovirus (NPVs) of S. litura (SpltNPV) were collected from infected larvae in different ecological and geographic regions of Pakistan. The genotypic diversity of these SpltNPV isolates, their relation to geographical (spatial) distribution and cropping system, and their biological activity, in particular dose response, speed of kill and effects on feeding, were explored. The first Pakistani isolate, SpltNPV-Pak-BNG, was studied and compared to a presumable SpltNPV reference isolate, SpltNPV-G1. SpltNPV-Pak-BNG killed S. litura larvae significantly faster than SpltNPV-G1. Genetic analysis revealed that SpltNPV-Pak-BNG and SpltNPV-G1 are variants of different virus species, SpltNPV and SpliNPV, respectively. The biological activity of SpltNPV-Pak-BNG was determined in different instars larvae of S. litura showing that S. litura second or third instar larvae are preferred targets for S. litura control with SpltNPV-Pak-BNG in field crops. SpltNPV-Pak-BNG infected S. litura larvae with final polyhedrosis showed reduced food intake and weight gain. Interestingly, the mock-infected- larvae and the larvae that survived viral exposure, exhibited the same food consumption and weight gain.

Twenty-two SpltNPV isolates were finally collected from S. litura from different agro-ecological regions and cropping systems in Pakistan to explore the genetic diversity of the virus on a spatial scale and explore its possible adaptation to region and crop systems. Among the SpltNPV-Pak isolates tested, isolates TAX1, SFD1, SFD2 and GRW1 were faster killing than other Pakistani isolates. All isolates were genotypic variants of a single SpltNPV ‘regiotype’, suggesting common recent ancestry, and distinct from the virus species type SpltNPV-G2. There was a strong correlation between geographic location and a SpltNPV genogroup, and less so between the latter and the cropping system. Sequence analysis of SpltNPV-Pak isolates BNG (slow virus) and TAX1 (fast virus) showed major differences, notably the absence of homologous repeat region 17 in TAX1 and gene 125 in BNG. There is strong purifying selection on gene 122, encoding a putative viral fibroblast growth factor known to be involved in baculovirus virulence.

The results presented in this thesis considerably enhanced our understanding of the genetic and biological diversity of SpltNPVs in conjunction with their spatial distribution and the crop system involved. In addition, the results may be used to the develop SpltNPV as an eco-rational control agent of the leafworm S. litura in Pakistan.

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