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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Response to a selection index including environmental costs and risk preferences of producers
Ali, Beshir M. ; Bastiaansen, John W.M. ; Mey, Yann de; Oude Lansink, Alfons G.J.M. - \ 2019
Journal of Animal Science 97 (2019)1. - ISSN 0021-8812 - p. 156 - 171.

Genetic improvement of animals plays an important role in improving the economic and environmental sustainability of livestock production systems. This paper proposes a method to incorporate mitigation of environmental impacts and risk preferences of producers into a breeding objective via economic values (EVs). The paper assesses the effects of using these alternative EVs of breeding goal traits on discounted economic response to selection and on environmental impacts at commercial farm level. The application focuses on a Brazilian pig production system. Separate dam- and sire-line breeding programs that supply parents in a 3-tier production system for producing crossbreds (fattening pigs) at commercial level were assumed. Using EVs that are derived from utility functions by incorporating risk aversion increases the cumulative discounted economic response to selection in sire-line selection (6%) while reducing response in dam-line selection (12%) compared with the use of traditional EVs. The use of EVs that include environmental costs increases the cumulative discounted social response to selection in both dam-line (5%) and sire-line (10%) selections. Emission of greenhouse gases, and excretion of nitrogen and phosphorus can be reduced more with genetic improvements of production traits than reproduction traits for the typical Brazilian farrow-to-finish pig farm. Reductions in environmental impacts do not, however, depend on the use of the different EVs (i.e., with and without taking into account environmental costs and risk). Both environmental costs and risk preferences of producers need to be considered in sire-line selection, and only environmental costs in dam-line selection to improve, at the same time, the economic and environmental sustainability of the Brazilian pig production system.

Biotechnological strategies for the recovery of valuable and critical raw materials from waste electrical and electronic equipment (WEEE) – A review
Işıldar, Arda ; Hullebusch, Eric D. van; Lenz, Markus ; Laing, Gijs Du; Marra, Alessandra ; Cesaro, Alessandra ; Panda, Sandeep ; Akcil, Ata ; Kucuker, Mehmet Ali ; Kuchta, Kerstin - \ 2019
Journal of Hazardous Materials 362 (2019). - ISSN 0304-3894 - p. 467 - 481.
Bioleaching - Bioprecipitation - Biosorption - Biotechnologies - Critical metals - Electronic waste

Critical raw materials (CRMs) are essential in the development of novel high-tech applications. They are essential in sustainable materials and green technologies, including renewable energy, emissionfree electric vehicles and energy-efficient lighting. However, the sustainable supply of CRMs is a major concern. Recycling end-of-life devices is an integral element of the CRMs supply policy of many countries. Waste electrical and electronic equipment (WEEE) is an important secondary source of CRMs. Currently, pyrometallurgical processes are used to recycle metals from WEEE. These processes are deemed imperfect, energy-intensive and non-selective towards CRMs. Biotechnologies are a promising alternative to the current industrial best available technologies (BAT). In this review, we present the current frontiers in CRMs recovery from WEEE using biotechnology, the biochemical fundamentals of these bio-based technologies and discuss recent research and development (R&D) activities. These technologies encompass biologically induced leaching (bioleaching) from various matrices,biomass-induced sorption (biosorption), and bioelectrochemical systems (BES).

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 - \ 2019
Plant Pathology 68 (2019)1. - ISSN 0032-0862 - p. 42 - 48.
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.
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.

LocalPork - breeding for local conditions
Bastiaansen, J.W.M. ; Guimarães, S.E.F. ; Ali, B.M. ; Sevillano, C.A. ; Mezencio Godinho, Rodrigo ; Bergsma, Rob ; Lopes, Marcos S. ; Mey, Y. de; Calus, M.P.L. - \ 2018
In: Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. - WCGALP
The LocalPork project aims to improve the efficiency of pork production in Brazil. Pigs in Brazil are usually fed a diet based on corn and soybean. Growing these pigs on a diet that includes local alternative ingredients raises a number of questions related to breeding for such an environment. First, what is the economic and environmental impact of alternative local diets. Second, what are the purebred-crossbred genetic correlations and the extent of genotype by environment interaction. Third, how to accurately predict breeding values based on crossbred performance. Performance of pigs in Brazil that are fed a reference or alternative diets was predicted and alternative diets that include Macaúba or other co-products were found to improve the economic and environmental performance of pork production. Genotype by feed interaction was investigated in crossbred pigs that were fed either a corn and soybean based diet or a diet based on wheat, barley and co-products. Genetic correlations between the diets for growth and residual feed intake were found to be high. The genetic correlation between purebreds and crossbreds for residual feed intake was however found to be only moderate, 0.62. Taking into account the breed origin of haplotypes in crossbreds when predicting breeding values did not substantially increase their accuracies. We speculate that the moderate value of the purebred-crossbred genetic correlation is mainly due to GxE caused by differences in environmental factors, other than diet.
Impact of Soil Water Repellency on Hydrological and Erosion Processes; A Review
Heidary, K. ; Najafi Nejad, A. ; Dekker, L.W. ; Ownegh, M. ; Mohammadian Behbahani, Ali - \ 2018
Ecopersia 6 (2018)4. - ISSN 2322-2700 - p. 269 - 284.
Introduction Soil water repellency was first reported in the first half of the 20th century for peat soils. Depending on the severity of water repellency, a water repellent soil will resist water penetration during seconds to hours or even days. This has detrimental effects on surface and subsurface flow processes such as increased runoff, erosion, and preferential flow. The present study was conducted with the aim of investigating the effects of Soil water repellency
on hydrological and erosion processes in order to identify gaps in the existing investigations. Conclusion Major survey gaps remained, including the dissociation of the symptoms of water repellency on soil erosion such as the existence of a soil crust and little knowledge of the temporal patterns of water repellency and their hydrological outcomes. Understanding the mechanisms
of water repellency is relevant to the separation of different causal chains as well as the adjust runoff coefficients in different water repellency areas. Soil water repellency can be caused by a variety of compounds and processes and generally occurs after a period of drying weather. Under such conditions, the soil can change from a wettable to a water-repellent state when dried below its critical soil water content. Soil water repellency is found to occur in different soils worldwide, ranging from coarse to fine-textured. Water repellency in soils can result in losses of plant-available water, reduced agricultural crop production, and deterioration of turf quality on sports fields.
The minute-scale dynamics of online emotions reveal the effects of affect labeling
Fan, Rui ; Varol, Onur ; Varamesh, Ali ; Barron, Alexander ; Leemput, I.A. van de; Scheffer, M. ; Bollen, J.L.T. - \ 2018
Nature Human Behaviour (2018). - ISSN 2397-3374
Putting one’s feelings into words (also called affect labeling) can attenuate positive and negative emotions. Here, we track the evolution of specific emotions for 74,487 Twitter users by analysing the emotional content of their tweets before and after they explicitly report experiencing a positive or negative emotion. Our results describe the evolution of emotions and their expression at the temporal resolution of one minute. The expression of positive emotions is preceded by a short, steep increase in positive valence and followed by short decay to normal levels. Negative emotions, however, build up more slowly and are followed by a sharp reversal to previous levels, consistent with previous studies demonstrating the attenuating effects of affect labeling. We estimate that positive and negative emotions last approximately 1.25 and 1.5 h, respectively, from onset to evanescence. A separate analysis for male and female individuals suggests the potential for gender-specific differences in emotional dynamics.
Molecular analysis of genetic diversity, population structure, and phylogeny of wild and cultivated tulips (Tulipa L.) by genic microsatellites
Pourkhaloee, Ali ; Khosh-Khui, Morteza ; Arens, Paul ; Salehi, Hassan ; Razi, Hooman ; Niazi, Ali ; Afsharifar, Alireza ; Tuyl, Jaap van - \ 2018
Horticulture Environment and Biotechnology 59 (2018)6. - ISSN 2211-3452 - p. 875 - 888.
Bulb crop - Conservation implications - EST–SSR markers - Population genetics

Tulip (Tulipa L.) is one of the most important ornamental geophytes in the world. Analysis of molecular variability of tulips is of great importance in conservation and parental lines selection in breeding programs. Of the 70 genic microsatellites, 15 highly polymorphic and reproducible markers were used to assess the genetic diversity, structure, and relationships among 280 individuals of 36 wild and cultivated tulip accessions from two countries: Iran and the Netherlands. The mean values of gene diversity and polymorphism information content were 0.69 and 0.66, respectively, which indicated the high discriminatory power of markers. The calculated genetic diversity parameters were found to be the highest in wild T. systola Stapf (Derak region). Bayesian model-based STRUCTURE analysis detected five gene pools for 36 germplasms which corresponded with morphological observations and traditional classifications. Based on analysis of molecular variance, to conserve wild genetic resources in some geographical locations, sampling should be performed from distant locations to achieve high diversity. The unweighted pair group method with arithmetic mean dendrogram and principal component analysis plot indicated that among wild tulips, T. systola and T. micheliana Hoog exhibited the closest relationships with cultivated tulips. Thus, it can be assumed that wild tulips from Iran and perhaps other Middle East countries played a role in the origin of T. gesneriana, which is likely a tulip species hybrid of unclear origin. In conclusion, due to the high genetic variability of wild tulips, they can be used in tulip breeding programs as a source of useful alleles related to resistance against stresses.

Enhancing the environmental and economic sustainability of pig farming: the case of Brazil
Ali, Beshir Melkaw - \ 2018
Wageningen University. Promotor(en): Alfons Oude Lansink, co-promotor(en): Yann de Mey; John Bastiaansen. - Wageningen : Wageningen University - ISBN 9789463435284 - 233
Input Selection of Wavelet-Coupled Neural Network Models for Rainfall-Runoff Modelling
Shoaib, Muhammad ; Shamseldin, Asaad Y. ; Khan, Sher ; Sultan, Muhammad ; Ahmad, Fiaz ; Sultan, Tahir ; Dahri, Zakir Hussain ; Ali, Irfan - \ 2018
Water Resources Management (2018). - ISSN 0920-4741 - 19 p.
Artificial neural network - Discrete wavelet transformation - Rainfall-runoff modelling - Wavelet sub-series

The use of wavelet-coupled data-driven models is increasing in the field of hydrological modelling. However, wavelet-coupled artificial neural network (ANN) models inherit the disadvantages of containing more complex structure and enhanced simulation time as a result of use of increased multiple input sub-series obtained by the wavelet transformation (WT). So, the identification of dominant wavelet sub-series containing significant information regarding the hydrological system and subsequent use of those dominant sub-series only as input is crucial for the development of wavelet-coupled ANN models. This study is therefore conducted to evaluate various approaches for selection of dominant wavelet sub-series and their effect on other critical issues of suitable wavelet function, decomposition level and input vector for the development of wavelet-coupled rainfall-runoff models. Four different approaches to identify dominant wavelet sub-series, ten different wavelet functions, nine decomposition levels, and five different input vectors are considered in the present study. Out of four tested approaches, the study advocates the use of relative weight analysis (RWA) for the selection of dominant input wavelet sub-series in the development of wavelet-coupled models. The db8 and the dmey (Discrete approximation of Meyer) wavelet functions at level nine were found to provide the best performance with the RWA approach.

Phosphopantetheinyl transferase (Ppt)-mediated biosynthesis of lysine, but not siderophores or DHN melanin, is required for virulence of Zymoseptoria tritici on wheat
Derbyshire, Mark C. ; Gohari, Amir Mirzadi ; Mehrabi, Rahim ; Kilaru, Sreedhar ; Steinberg, Gero ; Ali, Solaf ; Bailey, Andy ; Hammond-Kosack, Kim ; Kema, Gert H.J. ; Rudd, Jason J. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB) disease of wheat. Z. tritici is an apoplastic fungal pathogen, which does not penetrate plant cells at any stage of infection, and has a long initial period of symptomless leaf colonisation. During this phase it is unclear to what extent the fungus can access host plant nutrients or communicate with plant cells. Several important primary and secondary metabolite pathways in fungi are regulated by the post-translational activator phosphopantetheinyl transferase (Ppt) which provides an essential co-factor for lysine biosynthesis and the activities of non-ribosomal peptide synthases (NRPS) and polyketide synthases (PKS). To investigate the relative importance of lysine biosynthesis, NRPS-based siderophore production and PKS-based DHN melanin biosynthesis, we generated deletion mutants of ZtPpt. The ∆ZtPpt strains were auxotrophic for lysine and iron, non-melanised and non-pathogenic on wheat. Deletion of the three target genes likely affected by ZtPpt loss of function (Aar- lysine; Nrps1-siderophore and Pks1- melanin), highlighted that lysine auxotrophy was the main contributing factor for loss of virulence, with no reduction caused by loss of siderophore production or melanisation. This reveals Ppt, and the lysine biosynthesis pathway, as potential targets for fungicides effective against Z. tritici.

Analysis of drought and vulnerability in the North Darfur region of Sudan
Mohmmed, Alnail ; Zhang, Ke ; Kabenge, Martin ; Keesstra, Saskia ; Cerdà, Artemi ; Reuben, Makomere ; Elbashier, Mohammed M.A. ; Dalson, Twecan ; Ali, Albashir A.S. - \ 2018
Land Degradation and Development 29 (2018)12. - ISSN 1085-3278
drought - meteorology - North Darfur region - remote sensing - vulnerability index

North Darfur of Sudan is located on the edge of the Sahara Desert and endures frequent droughts due to water shortages and high summer temperatures. Monitoring and understanding drought characteristics are essential for integrated drought risk mitigation and prevetion of land degradation. This study evaluates drought conditions in North Darfur by analyzing the spatiotemporal distribution of drought using three drought indices (Standardized Precipitation Index, Vegetation Condition Index, and Soil Moisture Content Index) and their combined drought index (CDI) from 2004 to 2013. Biophysical and socioeconomic indicators are further used to measure vulnerability to drought risk and its three components (exposure, sensitivity, and adaptive capacity) through a comprehensive risk assessment framework. The results show that most of North Darfur has experienced prolonged droughts during the study period, especially from 2007 to 2011. There is also a significant correlation between the monsoon season CDI and annual crop yield anomaly. The results confirm the validity of the CDI index, which provides a comprehensive description of the drought situation by combing four drought indices quantifying different drought aspects. The vulnerability results show that the majority of this region is highly exposed and sensitive to drought risks. In particular, the northern zone of the region is highly vulnerable, which is categorized by less-crop diversity, higher land degradation, frequent droughts, and high-poverty levels. This study provides valuable information for coping with climate change-induced drought risk in this region and demonstrates that there is still a large room for enhancing the adaptation capacity in this region.

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.
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.

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