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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Influence of synthesis method on molybdenum carbide crystal structure and catalytic performance in stearic acid hydrodeoxygenation
Souza Macedo, Luana ; Oliveira, Ricardo R. ; Haasterecht, Tomas van; Teixeira da Silva, Victor ; Bitter, Harry - \ 2019
Applied Catalysis B-Environmental 241 (2019). - ISSN 0926-3373 - p. 81 - 88.
Crystal structure - Hydrodeoxygenation - Molybdenum carbide - Site density - Synthesis method

The role of the synthesis method of molybdenum carbide nanoparticle catalysts supported on carbon nanofibers on crystal structure and on catalytic performance in hydrodeoxygenation of stearic acid was investigated. We obtained the cubic phase of molybdenum carbide (α-MoC1-x) by impregnating carbon nanofibers with a solution of (NH4)2MoO4, then exposing them to 20% CH4/H2 at 650 °C for 2 h. When increasing the Mo loading from 7.5 wt% to 20 wt% or using the carbothermal reduction method, i.e. using carbon from the support to reduce the (NH4)2MoO4 precursor at 800 °C for 6 h, the hexagonal phase (β-Mo2C) resulted. Experiments with stearic acid hydrodeoxygenation showed that both phases (7.5 wt% Mo) displayed similar intrinsic activities. However, α-MoC1-x/CNF reached 80% stearic acid conversion after 240 min while the β-Mo2C/CNF catalyst attained the same conversion after 360 min. CO chemisorption results showed that α-MoC1-x/CNF and β-Mo2C/CNF have a similar number of potential active sites (66 and 56 μmol g−1, respectively). We attribute the difference in catalytic performance between α-MoC1-x/CNF and β-Mo2C/CNF to differences in the catalyst's crystal structure, more specifically, the associated site density. The face-centered cubic α-MoC1-x/CNF has a lower site density (0.1096 Mo atoms Ų) than the hexagonal close-packed β-Mo2C/CNF (0.1402 Mo atoms Ų), making the Mo atoms at the surface of the α-MoC1-x phase more accessible for large reactant molecules such as stearic acid thus allowing its convertion in shorter times.

Effects of alleles in crossbred pigs estimated for genomic prediction depend on their breed-of-origin
Sevillano, Claudia A. ; Napel, Jan ten; Guimarães, Simone E.F. ; Silva, Fabyano F. ; Calus, Mario P.L. - \ 2018
BMC Genomics 19 (2018)1. - ISSN 1471-2164
Breed-of-origin - Crossbred - Genomic prediction - Pig

Background: This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, and how these are related to estimated effects for purebred performance. Results: SNP-allele substitution effects were estimated for a commonly used SNP panel using a genomic best linear unbiased prediction model with breed-specific partial relationship matrices. Estimated breeding values for purebred and crossbred performance were converted to SNP-allele effects by breed-of-origin. Differences between purebred and crossbred, and between breeds-of-origin were evaluated by comparing percentage of variance explained by genomic regions for back fat thickness (BF), average daily gain (ADG), and residual feed intake (RFI). From ten regions explaining most additive genetic variance for crossbred performance, 1 to 5 regions also appeared in the top ten for purebred performance. The proportion of genetic variance explained by a genomic region and the estimated effect of a haplotype in such a region were different depending upon the breed-of-origin. To illustrate underlying mechanisms, we evaluated the estimated effects across breeds-of-origin for haplotypes associated to the melanocortin 4 receptor (MC4R) gene, and for the MC4Rsnp itself which is a missense mutation with a known effect on BF and ADG. Although estimated allele substitution effects of the MC4Rsnp mutation were very similar across breeds, explained genetic variance of haplotypes associated to the MC4R gene using a SNP panel that does not include the mutation, was considerably lower in one of the breeds where the allele frequency of the mutation was the lowest. Conclusions: Similar regions explaining similar additive genetic variance were observed across purebred and crossbred performance. Moreover, there was some overlap across breeds-of-origin between regions that explained relatively large proportions of genetic variance for crossbred performance; albeit that the actual proportion of variance deviated across breeds-of-origin. Results based on a missense mutation in MC4R confirmed that even if a causal locus has similar effects across breeds-of-origin, estimated effects and explained variance in its region using a commonly used SNP panel can strongly depend on the allele frequency of the underlying causal mutation.

Biological treatment of produced water coupled with recovery of neutral lipids
Sudmalis, D. ; Silva, P. da; Temmink, H. ; Bijmans, M.M. ; Pereira, M.A. - \ 2018
Water Research 147 (2018). - ISSN 0043-1354 - p. 33 - 42.
Alkane biodegradation - Biological treatment - Neutral lipids production - Produced water

Produced water (PW) is the largest waste stream generated by oil and gas industry. It is commonly treated by physical-chemical processes due to high salt content and poor biodegradability of water insoluble compounds, such as n-alkanes. N-alkanes can represent a major fraction of organic contaminants within PW. In this study the possibility of simultaneous n – alkane biodegradation and production of neutral lipids in a concentrated PW stream with A. borkumenis SK2 as the sole reactor inoculum was investigated. N-alkane removal efficiency up to 99.6%, with influent alkane COD of 7.4 g/L, was achieved in a continuously operated reactor system. Gas chromatography results also showed that the majority of other non-polar compounds present in the PW were biodegraded. Biodegradation of n-alkanes was accompanied by simultaneous production of neutral lipids, mostly wax ester (WE)-alike compounds. We demonstrate, that under nutrient limited conditions and 108.9 ± 3.3 mg/L residual n-alkane concentration the accumulation of extracellular WE-alike compounds can be up to 12 times higher compared to intracellular, reaching 3.08 grams per litre of reactor volume (g/Lreactor) extracellularly and 0.28 g/Lreactor intracellularly. With residual n-alkane concentration of 311.5 ± 34.2 mg/L accumulation of extracellular and intracellular WE-alike compounds can reach up to 6.15 and 0.91 g/Lreactor, respectively. To the best of our knowledge simultaneous PW treatment coupled with production of neutral lipids has never been demonstrated before.

Temporal dominance of sensations, emotions, and temporal liking measured in a bar for two similar wines using a multi-sip approach
Silva, Ana P. ; Voss, Hans Peter ; Zyl, Hannelize van; Hogg, Tim ; Graaf, Cees de; Pintado, Manuela ; Jager, Gerry - \ 2018
Journal of Sensory Studies 33 (2018)5. - ISSN 0887-8250

Eating and drinking are dynamic processes where both sensations and emotions might evolve or change over time during multiple bites/sips. However, most previous studies have measured food-evoked emotions statically, that is, at a fixed time point after consumption and using a single bite/sip approach. This study aimed to explore the sensitivity of temporal dominance of sensations (TDS), of emotions (TDE), and temporal liking (TL), using a multi-sip approach, to differentiate between two comparable tasting wines. A glass of wine, in an appropriate consumption context, a bar, was served to 69 consumers, in two different sessions. It was shown that TDS and TDE captured small differences between equally liked wines. Wines were distinguishable during consumption, based on the dominance of basic sensations such as acid, bitter, and dry, rather than aromatic sensations and based on three emotions pleased, comforted, and relaxed. These emotions were dominant in both wines and in all stages of consumption but differed in the dominance rates. So, the impact of wine consumption on emotions was more uniform during consumption while new sensations became dominant during drinking. Practical implications: The method tested in this study showed a sensitivity level sufficient to capture subtle but significant differences between similar, equally liked wines. Wines tested have a major difference in wine-making process, that is, one of the wines had a particular wood aging processing in new oak barrels conferring specific flavors and associated costs. For the wine industry, the method can be particularly useful to understand to which extent consumers perceive differences in sensations and emotions, in a blind tasting, to investigate if increased costs of production are acceptable and justified. For other food products, the method can be useful to use during product development stage, when the aim is to differentiate prototypes with subtle differences in ingredients composition and associated costs. Knowing when certain sensations and emotions occur during consumption might help to create successful products in the market. Further research using different food or beverages is however necessary to assure its validity.

Recent advances in pig reproduction : Focus on impact of genetic selection for female fertility
Kemp, Bas ; Silva, Carolina L.A. Da; Soede, Nicoline M. - \ 2018
Reproduction in Domestic Animals 53 (2018)S2. - ISSN 0936-6768 - p. 28 - 36.
genetic selection - litter size - management - sow - weaning-to-oestrus interval

In the past 30 years, sows have been successfully selected for a shorter weaning-to-oestrus interval and increased litter size. This review discusses the consequences of this selection for the reproductive physiology of sows, including the consequences for litter characteristics at birth. It also discusses breeding and management opportunities to deal with this changed genetics.

Genome-wide association studies for tick resistance in Bos taurus × Bos indicus crossbred cattle : A deeper look into this intricate mechanism
Otto, Pamela I. ; Guimarães, Simone E.F. ; Verardo, Lucas L. ; Azevedo, Ana Luísa S. ; Vandenplas, Jeremie ; Soares, Aline C.C. ; Sevillano, Claudia A. ; Veroneze, Renata ; Fatima A. Pires, Maria de; Freitas, Célio de; Prata, Márcia Cristina A. ; Furlong, John ; Verneque, Rui S. ; Martins, Marta Fonseca ; Panetto, João Cláudio C. ; Carvalho, Wanessa A. ; Gobo, Diego O.R. ; Silva, Marcos Vinícius G.B. da; Machado, Marco A. - \ 2018
Journal of Dairy Science (2018). - ISSN 0022-0302
breed of origin - gene network - genetic variance - Gir × Holstein crossbred
Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F2 population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F2 population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.
Short communication: detection and molecular characterization of hepatitis E virus in domestic animals of São Tomé and Príncipe
Mesquita, João Rodrigo ; Istrate, Claudia ; Santos-Ferreira, Nânci L. ; Ferreira, Ana S. ; Abreu-Silva, Joana ; Veiga, José ; Poel, Wim H.M. van der; Nascimento, Maria S.J. - \ 2018
Tropical Animal Health and Production (2018). - ISSN 0049-4747
Domestic animals - Hepatitis E virus - São Tomé e Príncipe - Zoonoses

As in most of the African continent, the status of hepatitis E virus (HEV) infection in domestic animals in São Tomé and Príncipe, an archipelago off the western equatorial coast of Central Africa, is also completely unknown. In the present study, we investigated the presence of HEV among domestic animals in São Tomé and Príncipe. A total of 93 stool samples from different animal species (goat, cow, pig, chicken, duck, and monkey) were tested for HEV RNA using two real-time RT-PCR assays, followed by a nested RT-PCR assay for sequencing and phylogenetic analysis. A total of six samples (1 cow stool and 5 pig stools) were found to be positive for HEV RNA of which one pig stool was positive by broad spectrum nested RT-PCR. Phylogenetic analysis showed that the retrieved sequence clustered within HEV subgenotype 3f, similar to zoonotic strains of European countries and posing interesting questions on past introduction of European HEV into São Tomé and Príncipe archipelago. This is the first report describing the presence and molecular characterization of HEV in São Tomé and Príncipe.

Considerations and consequences of allowing DNA sequence data as types of fungal taxa
Zamora, Juan Carlos ; Svensson, Måns ; Kirschner, Roland ; Olariaga, Ibai ; Ryman, Svengunnar ; Parra, Luis Alberto ; Geml, József ; Rosling, Anna ; Adamčík, Slavomír ; Ahti, Teuvo ; Aime, M.C. ; Ainsworth, A.M. ; Albert, László ; Albertó, Edgardo ; García, Alberto Altés ; Ageev, Dmitry ; Agerer, Reinhard ; Aguirre-Hudson, Begoña ; Ammirati, Joe ; Andersson, Harry ; Angelini, Claudio ; Antonín, Vladimír ; Aoki, Takayuki ; Aptroot, André ; Argaud, Didier ; Sosa, Blanca Imelda Arguello ; Aronsen, Arne ; Arup, Ulf ; Asgari, Bita ; Assyov, Boris ; Atienza, Violeta ; Bandini, Ditte ; Baptista-Ferreira, João Luís ; Baral, Hans-Otto ; Baroni, Tim ; Barreto, Robert Weingart ; Beker, Henry ; Bell, Ann ; Bellanger, Jean-Michel ; Bellù, Francesco ; Bemmann, Martin ; Bendiksby, Mika ; Bendiksen, Egil ; Bendiksen, Katriina ; Benedek, Lajos ; Bérešová-Guttová, Anna ; Berger, Franz ; Berndt, Reinhard ; Bernicchia, Annarosa ; Biketova, Alona Yu. ; Bizio, Enrico ; Bjork, Curtis ; Boekhout, Teun ; Boertmann, David ; Böhning, Tanja ; Boittin, Florent ; Boluda, Carlos G. ; Boomsluiter, Menno W. ; Borovička, Jan ; Brandrud, Tor Erik ; Braun, Uwe ; Brodo, Irwin ; Bulyonkova, Tatiana ; Burdsall, Harold H. ; Buyck, Bart ; Burgaz, Ana Rosa ; Calatayud, Vicent ; Callac, Philippe ; Campo, Emanuele ; Candusso, Massimo ; Capoen, Brigitte ; Carbó, Joaquim ; Carbone, Matteo ; Castañeda-ruiz, Rafael F. ; Castellano, Michael A. ; Chen, Jie ; Clerc, Philippe ; Consiglio, Giovanni ; Corriol, Gilles ; Courtecuisse, Régis ; Crespo, Ana ; Cripps, Cathy ; Crous, Pedro W. ; Silva, Gladstone Alves Da ; Silva, Meiriele Da ; Dam, Marjo ; Dam, Nico ; Dämmrich, Frank ; Das, Kanad ; Davies, Linda ; Crop, Eske De; Kesel, Andre De; Kuijper, T.W.M. - \ 2018
IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 167 - 185.
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
Response of the river discharge in the Tocantins River Basin, Brazil, to environmental changes and the associated effects on the energy potential
Cassia Silva Von Randow, Rita de; Rodriguez, Daniel Andrés ; Tomasella, Javier ; Aguiar, Ana Paula Dutra ; Kruijt, Bart ; Kabat, Pavel - \ 2018
Regional Environmental Change (2018). - ISSN 1436-3798 - 12 p.
Climate change - Hydrological modeling - Hydropower potential - Land use and land cover change - Secondary forest

Climate change is expected to impact the hydrological regime worldwide, and land use and land cover change may alter the effects of the former in some cases. Secondary growth in deforested and abandoned areas is one of the main consequences of land use and cover changes in Amazonia. Among land uses, the effects of the secondary growth in water availability in large scale basins are not well understood. This work analyzes the potential effects of secondary growth under climate and land use change on water availability and hydropower in the Tocantins basin, in the Legal Amazon region of Brazil, using the MHD-INPE hydrological model driven by different climate scenarios and two future socioeconomic-based potential land use scenarios. The model projects decrease on discharge under climate change scenarios, which further cause the simulated hydropower energy potential to decrease significantly. When only deforestation scenarios are included, the effects of climate change are weakened, but when secondary growth is also considered, the effects of climate change are enhanced. Results suggest that different aspects of environmental change, such as secondary growth, may affect water production and the sectors depending on it.

In depth investigation of the metabolism of Nectandra megapotamica chemotypes
S. Farias, Katyuce de; Delatte, Thierry ; C. de O. Arruda, Rosani do; Alves, Flavio M. ; Silva, Denise B. ; Beekwilder, Jules ; Carollo, Carlos A. - \ 2018
PLoS One 13 (2018)8. - ISSN 1932-6203

Plants produce a wide range of secondary metabolites. Within a single species, chemotypes can be distinguished by the differences in the composition of the secondary metabolites. Herein, we evaluated Nectandra megapotamica (Spreng.) chemotypes and the balance of different classes of metabolites to verify how significant differences in plant metabolism are regarding chemotypes. We collected N. megapotamica leaves from eight adult plants in two Brazilian states. The essential oils and ethanol/water extracts were analyzed by GC-MS and LC-DAD-MS, respectively. Histochemical tests were performed, as well as chemical analyses of leaves from adaxial and abaxial foliar surfaces of N. megapotamica, and the stereochemistry of α-bisabolol was determined. Two different chemotypes, based on volatile compounds, were identified, distinguished by the presence of isospathulenol, α-bisabolol, β-bisabolene, and (E)-nerolidol for chemotype A, and bicyclogermacrene and elemicin for chemotype B. A stereochemical analysis of chemotype A extract revealed (+)-α-bisabolol enantiomer. Histochemical tests of chemotypes showed similar results and suggested the presence of essential oil in idioblasts stained with the dye NADI. The analyses of chemotype A leaves by GC-MS revealed similar compositions for abaxial and adaxial surfaces, such pattern was also observed for chemotype B. Medium and high polarity metabolites showed high chemical similarities between the chemotypes, highlighting the presence of proanthocyanidins and glycosylated flavonoids (O- and C-glycosides). Thus, N. megapotamica produced distinct volatile chemotypes with highly conserved medium to high polarity compounds. Such results suggest that phenolic derivatives have a basal physiological function, while genetic or environmental differences lead to differentiation in volatile profiles of N. megapotamica.

Crop traits drive soil carbon sequestration under organic farming
García-Palacios, Pablo ; Gattinger, Andreas ; Bracht-Jørgensen, Helene ; Brussaard, Lijbert ; Carvalho, Filipe ; Castro, Helena ; Clément, Jean Christophe ; Deyn, Gerlinde De; Hertefeldt, Tina D'; Foulquier, Arnaud ; Hedlund, Katarina ; Lavorel, Sandra ; Legay, Nicolas ; Lori, Martina ; Mäder, Paul ; Martínez-García, Laura B. ; Martins da Silva, Pedro ; Muller, Adrian ; Nascimento, Eduardo ; Reis, Filipa ; Symanczik, Sarah ; Paulo Sousa, José ; Milla, Rubén - \ 2018
Journal of Applied Ecology 55 (2018)5. - ISSN 0021-8901 - p. 2496 - 2505.
climate change mitigation - crop residue - ecological intensification - leaf nitrogen - meta-analysis - organic farming - resource economics traits - soil carbon stocks

Organic farming (OF) enhances top soil organic carbon (SOC) stocks in croplands compared with conventional farming (CF), which can contribute to sequester C. As farming system differences in the amount of C inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue traits important for soil C losses such as litter decomposition may also play a role. To assess whether crop residue (leaf and root) traits determined SOC sequestration responses to OF, we coupled a global meta-analysis with field measurements across a European-wide network of sites. In the meta-analysis, we related crop species averages of leaf N, leaf-dry matter content, fine-root C and N, with SOC stocks and sequestration responses in OF vs. CF. Across six European sites, we measured the management-induced changes in SOC stocks and leaf litter traits after long-term ecological intensive (e.g. OF) vs. CF comparisons. Our global meta-analysis showed that the positive OF-effects on soil respiration, SOC stocks, and SOC sequestration rates were significant even in organic farms with low manure application rates. Although fertilization intensity was the main driver of OF-effects on SOC, leaf and root N concentrations also played a significant role. Across the six European sites, changes towards higher leaf litter N in CF also promoted lower SOC stocks. Our results highlight that crop species displaying traits indicative of resource-acquisitive strategies (e.g. high leaf and root N) increase the difference in SOC between OF and CF. Indeed, changes towards higher crop residue decomposability was related with decreased SOC stocks under CF across European sites. Synthesis and applications. Our study emphasizes that, with management, changes in crop residue traits contribute to the positive effects of organic farming (OF) on soil carbon sequestration. These results provide a clear message to land managers: the choice of crop species, and more importantly their functional traits (e.g. leave and root nitrogen), should be considered in addition to management practices and climate, when evaluating the potential of OF for climate change mitigation.

Articles reporting research on Latin American social movements are only rarely transparent
Silva, Sven da; Tamás, Peter A. ; Kampen, Jarl K. - \ 2018
Latin America - methodological transparency - reporting standards - social movements - Systematic review

Social movement scholars often want their research to make a difference beyond the academy. Readers will either read reports directly or they will read reviews that aggregate findings across a number of reports. In either case, readers must find reports to be credible before they will take their findings seriously. While it is not possible to predict the indicators of credibility used by individual, direct readers, formal systems of review do explicate indicators that determine whether a report will be recognized as credible for review. One such indicator, also relevant to pre-publication peer review, is methodological transparency: the extent to which readers are able to detect how research was done and why that made sense. This paper tests published primary research articles on and for social movements in Latin America for compliance with a generous interpretation of methodological transparency. We find that, for the most part, articles are not methodologically transparent. If transparency matters to social movement scholars, the research community may wish to formalize discussions of what aspects of research should be reported and how those reports should be structured.

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.
Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs
Marques, Daniele B.D. ; Bastiaansen, John W.M. ; Broekhuijse, Marleen L.W.J. ; Lopes, Marcos S. ; Knol, Egbert F. ; Harlizius, Barbara ; Guimarães, Simone E.F. ; Silva, Fabyano F. ; Lopes, Paulo S. - \ 2018
Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X

Background: In recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two commercial pig lines (L1: Large White type and L2: Landrace type). Since the number of animals with both phenotypes and genotypes was relatively small in our dataset, we conducted a weighted single-step genome-wide association study, which also allows unequal variances for single nucleotide polymorphisms. In addition, our aim was also to identify candidate genes within QTL regions that explained the highest proportions of genetic variance. Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same semen traits across lines. Results: We identified QTL regions that explained up to 10.8% of the genetic variance of the semen traits on 12 chromosomes in L1 and 11 chromosomes in L2. Sixteen QTL regions in L1 and six QTL regions in L2 were associated with two or more traits within the population. Candidate genes SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG and LOC102167830 were identified in L1 and NME5, AZIN2, SPATA7, METTL3 and HPGDS in L2. No regions overlapped between these two lines. However, the gene network analysis for progressive motility revealed two genes in L1 (PLA2G4A and PTGS2) and one gene in L2 (HPGDS) that were involved in two biological processes i.e. eicosanoid biosynthesis and arachidonic acid metabolism. PTGS2 and HPGDS were also involved in the cyclooxygenase pathway. Conclusions: We identified several QTL regions associated with semen traits in two pig lines, which confirms the assumption of a complex genetic determinism for these traits. A large part of the genetic variance of the semen traits under study was explained by different genes in the two evaluated lines. Nevertheless, the gene network analysis revealed candidate genes that are involved in shared biological pathways that occur in mammalian testes, in both lines.

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity
Schurink, Anouk ; Silva, Vinicius H. da; Velie, Brandon D. ; Dibbits, Bert W. ; Crooijmans, Richard P.M.A. ; François, Liesbeth ; Janssens, Steven ; Stinckens, Anneleen ; Blott, Sarah ; Buys, Nadine ; Lindgren, Gabriella ; Ducro, Bart J. - \ 2018
BMC Genetics 19 (2018)1. - ISSN 1471-2156
Copy number variations - Friesian horse - Genome-wide association study - Insect bite hypersensitivity

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.

Corrigendum : Factors affecting quality and health promoting compounds during growth and postharvest life of sweet cherry (Prunus avium L.) (Front. Plant Sci (2017) 8, (2166), 10.3389/fpls.2017.02166)
Correia, Sofia ; Schouten, Rob ; Silva, Ana P. ; Gonçalves, Berta - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X

There is an error in the Funding statement. The correct Name for the Funder is INTERACT project—Integrative Research in Environment, Agro-Chains and Technology, no. NORTE-01-0145-FEDER-000017, in its line of research entitled ISAC-P2, co-financed by the European Regional Development Fund (ERDF) through NORTE 2020 (North Regional Operational Program 2014/2020). The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. Authors acknowledge the support provided by European Investment Funds by FEDER/COMPETE/POCI-Operational Competitiveness and Internationalization Programme, under the Project POCI-01-0145-FEDER-006958 and National Funds by FCT-Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013. SC acknowledge the support provided by the FCT-Portuguese Foundation for Science and Technology (SFRH/BD/52541/2014), under the Doctoral Programme Agricultural Production Chains—from fork to farm (PD/00122/2012).

Breed-specific genome-wide association study for purebred and crossbred performance
Sevillano Del Aguila, C.A. ; Guimaraes, S.E.F. ; Silva, F. ; Calus, M.P.L. - \ 2018
In: Proceedings 11th World Congress of Genetics Applied to Livestock Production. -
Insight into the Role of Facultative Bacteria Stimulated by Microaeration in Continuous Bioreactors Converting LCFA to Methane
Duarte, M.S. ; Silva, Sérgio A. ; Salvador, Andreia F. ; Cavaleiro, Ana J. ; Stams, Alfons J.M. ; Alves, M.M. ; Pereira, M.A. - \ 2018
Environmental Science and Technology 52 (2018)11. - ISSN 0013-936X - p. 6497 - 6507.

Conversion of unsaturated long chain fatty acids (LCFA) to methane in continuous bioreactors is not fully understood. Palmitate (C16:0) often accumulates during oleate (C18:1) biodegradation in methanogenic bioreactors, and the reason why this happens and which microorganisms catalyze this reaction remains unknown. Facultative anaerobic bacteria are frequently found in continuous reactors operated at high LCFA loads, but their function is unclear. To get more insight on the role of these bacteria, LCFA conversion was studied under microaerophilic conditions. For that, we compared bioreactors treating oleate-based wastewater (organic loading rates of 1 and 3 kg COD m-3 d-1), operated under different redox conditions (strictly anaerobic-AnR, -350 mV; microaerophilic-MaR, -250 mV). At the higher load, palmitate accumulated 7 times more in the MaR, where facultative anaerobes were more abundant, and only the biomass from this reactor could recover the methanogenic activity after a transient inhibition. In a second experiment, the abundance of facultative anaerobic bacteria, particularly Pseudomonas spp. (from which two strains were isolated), was strongly correlated (p < 0.05) with palmitate-to-total LCFA percentage in the biofilm formed in a continuous plug flow reactor fed with very high loads of oleate. This work strongly suggests that microaeration stimulates the development of facultative bacteria that are critical for achieving LCFA conversion to methane in continuous bioreactors. Microbial networks and interactions of facultative and strict anaerobes in microbial communities should be considered in future studies.

Theorizing Slum Politics in Recife, Brazil : Community leaders symbolize the inconsistency of the urban situation
Silva, Sven da; Vries, P.A. de - \ 2018
In: Cities and Citizenship in Latin America & the Carribean. - Delft : TU Delft - ISBN 9789463660501 - p. 64 - 71.
Cities and Citizenship in Contemporary Latin America and the Caribbean : conference proceedings NALACS Conference 16-17 June 2016, TU Delft
Rocco, Roberto ; Silva, Sven da - \ 2018
Delft : TU Delft - ISBN 9789463660501 - 184 p.
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