Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk
Thomas, Minta ; Sakoda, Lori C. ; Hoffmeister, Michael ; Rosenthal, Elisabeth A. ; Lee, Jeffrey K. ; Duijnhoven, Franzel J.B. van; Platz, Elizabeth A. ; Wu, Anna H. ; Dampier, Christopher H. ; Chapelle, Albert de la; Wolk, Alicja ; Joshi, Amit D. ; Burnett-Hartman, Andrea ; Gsur, Andrea ; Lindblom, Annika ; Castells, Antoni ; Win, Aung Ko ; Namjou, Bahram ; Guelpen, Bethany Van; Tangen, Catherine M. ; He, Qianchuan ; Li, Christopher I. ; Schafmayer, Clemens ; Joshu, Corinne E. ; Ulrich, Cornelia M. ; Bishop, D.T. ; Buchanan, Daniel D. ; Schaid, Daniel ; Drew, David A. ; Muller, David C. ; Duggan, David ; Crosslin, David R. ; Albanes, Demetrius ; Giovannucci, Edward L. ; Larson, Eric ; Qu, Flora ; Mentch, Frank ; Giles, Graham G. ; Hakonarson, Hakon ; Hampel, Heather ; Stanaway, Ian B. ; Figueiredo, Jane C. ; Huyghe, Jeroen R. ; Minnier, Jessica ; Chang-Claude, Jenny ; Hampe, Jochen ; Harley, John B. ; Visvanathan, Kala ; Curtis, Keith R. ; Offit, Kenneth ; Li, Li ; Marchand, Loic Le; Vodickova, Ludmila ; Gunter, Marc J. ; Jenkins, Mark A. ; Slattery, Martha L. ; Lemire, Mathieu ; Woods, Michael O. ; Song, Mingyang ; Murphy, Neil ; Lindor, Noralane M. ; Dikilitas, Ozan ; Pharoah, Paul D.P. ; Campbell, Peter T. ; Newcomb, Polly A. ; Milne, Roger L. ; MacInnis, Robert J. ; Castellví-Bel, Sergi ; Ogino, Shuji ; Berndt, Sonja I. ; Bézieau, Stéphane ; Thibodeau, Stephen N. ; Gallinger, Steven J. ; Zaidi, Syed H. ; Harrison, Tabitha A. ; Keku, Temitope O. ; Hudson, Thomas J. ; Vymetalkova, Veronika ; Moreno, Victor ; Martín, Vicente ; Arndt, Volker ; Wei, Wei Qi ; Chung, Wendy ; Su, Yu Ru ; Hayes, Richard B. ; White, Emily ; Vodicka, Pavel ; Casey, Graham ; Gruber, Stephen B. ; Schoen, Robert E. ; Chan, Andrew T. ; Potter, John D. ; Brenner, Hermann ; Jarvik, Gail P. ; Corley, Douglas A. ; Peters, Ulrike ; Hsu, Li - \ 2020
American Journal of Human Genetics 107 (2020)3. - ISSN 0002-9297 - p. 432 - 444.
cancer risk prediction - colorectal cancer - machine learning - polygenic risk score
Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
Chemical composition, ruminal degradation kinetics, and methane production (in vitro) of winter grass species
Khan, Nazir Ahmad ; Sulaiman, Syed Muhammad ; Hashmi, Majid S. ; Rahman, Sadeeq Ur ; Cone, John W. - \ 2020
Journal of the Science of Food and Agriculture (2020). - ISSN 0022-5142
grass species - in vitro digestibility - in vitro gas production - methane emission - nutritional value
BACKGROUND: Information about the nutritive value, dry matter (DM) digestibility, and methane (CH4) emission potential of grass species is required for their optimal utilization in ruminant rations. The present study was designed: (i) to quantify the nutrient profile, mineral composition and in vitro dry matter digestibility (IVDMD) of winter grass species commonly available in northern Pakistan; and (ii) to measure the in vitro gas production (IVGP) and CH4 emission of the grass species during 72 h in vitro ruminal fermentation. Seven grass species, namely, Cenchrus ciliaris, Setaria anceps, Panicum antidotale, P. maximum, Pennisetum purpureum, Pennisetum orientale, and Atriplex lentiformis were assessed. RESULTS: A high level of variability (P < 0.001) was observed among grass species for the content of all measured nutrients, IVDMD, IVGP, and CH4-production. Notably, the content (g kg−1 DM) of crude protein varied from 59.8 to 143.3, neutral detergent fiber from 560.3 to 717.9, IVDMD from 375.1 to 576.2, and 72 h cumulative IVGP from 97.6 to 227.4 mL g−1 organic matter (OM) and CH4 from 48 to 67 mL g−1 OM. Among the grasses, P. antidotale had greater content (g kg−1 DM) of crude protein (CP) (143.3), IVDMD (576.2), and 72 h cumulative IVGP (227.4 mL g−1 OM), and produced the smallest amount of total CH4 (48 mL g−1 OM) during 72 h fermentation. In contrast, A. lentiformis had the lowest content (g kg−1 DM) of CP (59.8), IVDMD (375.1), 72 h cumulative IVGP (97.6 mL g−1 OM), and produced a greater amount of total CH4 (67 mL g−1 OM) during 72 h fermentation. CONCLUSION: The findings of the current study highlight that it is possible to select and further develop grass species with high nutritional value and lower CH4-production, which can improve livestock productivity, farm profitability, and long-term environment sustainability.
(De)coding a technopolity: tethering the civic blockchain to political transformation
Husain, Syed Omer - \ 2020
Wageningen University. Promotor(en): H. Wiskerke, co-promotor(en): D. Roep; A. Franklin. - Wageningen : Wageningen University - ISBN 9789463953092 - 228
This study rests at the intersection of technopolitics, translocal networks and political change. The overall aim of the thesis is to understand, and in turn, influence, the way technology interacts with political transformation. It responds to the fact that social science has thus far neglected to adequately account for and analyze how emerging technologies like blockchain and civic tech influence the way politics is practiced. The main research question guiding the study is how does the design, implementation and use of technopolitical innovations influence the practice of politics. The thesis foregrounds the idea that technopolitical experiments personify a ‘prefigurative politics by design’ i.e. they embody the politics and power structures they want to enable in society.
Conducted as part of the EU-funded SUSPLACE project that explores the transformative capacity of sustainable place-shaping practices, the research was predominantly inspired by a hybrid digital ethnography methodology. The thesis confines its focus to three empirical clusters: technopolitical blockchain projects, government-led blockchain projects and place-based civic engagement technologies. The study delineates how differing politico-social imaginaries play a role in the design and implementation of technopolitical projects; addresses contemporary post-political phenomena such as the depoliticization of agency; and identifies the activation of a place-based geography of political action through digitally-mediated municipal networks. It articulates the language and frameworks necessary to analyze these present-day challenges, while simultaneously developing approaches that can be exported to different domains of political activism.
Technology is not neutral; but neither are its designers and users. The thesis finds that it is through considerable, deliberate efforts, in conjunction with individual and collective choices, that technopolitical innovations can reframe our socio-economic and political realities. The study demonstrates the emphatic and urgent need for researchers, practitioners, politicians and citizens to collaboratively work on redrawing boundaries of access, empowering the citizenry, creating new forms of organization and re-politicizing the economy. It outlines a transdisciplinary research and practice agenda that aims at not only (de)coding the existing technopolitical innovations, but also (re)coding them to create a more equitable system of politics. The thesis concludes that since coding affordances and constraints in a technopolitical system is shown to regulate political agency and even influence the behavior of citizens, we must devise value-driven technology that incentivizes creating a more equitable political system.
Reducing greenhouse gas emissions and grain arsenic and lead levels without compromising yield in organically produced rice
Islam, Syed ; Neergaard, Andreas de; Sander, Bjoern Ole ; Jensen, Lars Stoumann ; Wassmann, Reiner ; Groenigen, Jan Willem van - \ 2020
Agriculture, Ecosystems and Environment 295 (2020). - ISSN 0167-8809
Carbon payment - Dissolved organic carbon - Heavy metals - Methane - Microbial biomass carbon - Nitrous oxide - Organic fertilisers - Please add Global warming potentials - Redox potential - Root biomass - Structural equation modelling
Flooded rice production is crucial to global food security, but there are associated environmental concerns. In particular, it is a significant source of methane (CH4) and nitrous oxide (N2O) emissions and a large consumer of water resources, while arsenic levels in the grain are a serious health concern. There is also a tendency to use more organic fertilisers to close nutrient cycles, posing a threat of even higher GHG emissions and grain arsenic levels. It has been shown that alternate wetting and drying (AWD) water management reduces both water use and GHG emissions, but success at maintaining yields varies. This study tested the effect of early AWD (e-AWD) versus continuous flooding (CF) water management practices on grain yields, GHG emissions and grain arsenic levels in a split-plot field experiment with organic fertilisers under organic management. The treatments included: i) farmyard manure, ii) compost, and iii) biogas digestate, alone or in combination with mineral fertiliser. The e-AWD water regime showed no difference in yield for the organic treatments. Yields significantly increased by 5–16 % in the combination treatments. Root biomass and length increased in the e-AWD treatments up to 72 and 41 %, respectively. The e-AWD water regime reduced seasonal CH4 emissions by 71–85 % for organic treatments and by 51–76 % for combination treatments; this was linked to a 15–47 % reduction in dissolved organic carbon (DOC), thereby reducing methanogenesis. N2O emissions increased by 23–305 % but accounted for <20 % of global warming potential (GWP). Area and yield-scaled GWPs were reduced by 67–83 %. The e–AWD regime altered soil redox potentials, resulting in a reduction in grain arsenic and lead concentrations of up to 66 % and 73 % respectively. Grain cadmium levels were also reduced up to 33 % in organic treatments. Structural equation modelling showed that DOC, redox, ammonium and root biomass were the key traits that regulated emissions and maintained yield. Despite the fact that the experiment was conducted in the dry-season when soil moisture conditions can be relatively well-controlled, our findings should be confirmed in multi-year studies in farmers’ fields. These results suggest that in flooded rice systems receiving organic amendments or organic management, the e-AWD water regime can achieve multiple environmental and food safety objectives without compromising yield.
SUN Business Network Bangladesh workshop on improving nutrition and diets through adopting a food systems lens : Stakeholder engagement and capacity building workshop SUN Business Network Bangladesh
Syed, Ridwam ; Zaman, Tasfia ; Herens, Marion ; Bakker, Sanne ; Vignola, Raffaele - \ 2020
Wageningen : Wageningen Centre for Development Innovation - 18
On the 1st of October 2019 GAIN, jointly with WFP and WCDI, organised a one day workshop for the Sun Business Network in Bangladesh to i) to promote deeper and shared understanding of the pathways for improving nutrition and healthier diets through adopting a food systems lens and to contribute to environmental and social responsibility, and ii) to strengthen the capacity of SBN Bangladesh to understand, strategize and steer action to improve nutrition outcomes through adopting a food systems lens. This report summarizes the results of the presentations provided by GAIN, WFP, Light Castle Partners and WCDI, and the outputs of the group work on food system mapping.
The political imaginaries of blockchain projects: discerning the expressions of an emerging ecosystem
Husain, Syed Omer ; Franklin, Alex ; Roep, Dirk - \ 2020
Sustainability Science 15 (2020). - ISSN 1862-4065 - p. 379 - 394.
Blockchain - Decentralization - Political imaginaries - Prefigurative politics - Technopolitics
There is a wealth of information, hype around, and research into blockchain’s ‘disruptive’ and ‘transformative’ potential concerning every industry. However, there is an absence of scholarly attention given to identifying and analyzing the political premises and consequences of blockchain projects. Through digital ethnography and participatory action research, this article shows how blockchain experiments personify ‘prefigurative politics’ by design: they embody the politics and power structures which they want to enable in society. By showing how these prefigurative embodiments are informed and determined by the underlying political imaginaries, the article proposes a basic typology of blockchain projects. Furthermore, it outlines a frame to question, cluster, and analyze the expressions of political imaginaries intrinsic to the design and operationalization of blockchain projects on three analytic levels: users, intermediaries, and institutions.
Prefigurative Post-Politics as Strategy: The Case of Government-Led Blockchain Projects
Hussain, Syed Omer ; Roep, D. ; Franklin, Alex - \ 2020
The Journal of The British Blockchain Association 3 (2020)1. - ISSN 2516-3949 - 11 p.
Critically engaging with literature on post-politics, blockchain and algorithmic governance, and drawing also on knowledge gained from undertaking a three-year empirical study, the purpose of this article is to better understand the transformative capacity of government-led blockchain projects. Analysis of a diversity of empirical material, which was guided by a digital ethnography approach, is used to support the furthering of the existing debate on the nature of the post-political as a condition and/or strategy. Through these theoretical and empirical explorations, the article concludes that while the post-political represents a contingent political strategy by governmental actors, it could potentially impose an algorithmically enforced post-political ‘condition’ for the citizen. It is argued that the design, features and mechanisms of government-led projects are deliberately and strategically used to delimit a citizens’ political agency. In order to address this scenario, we argue that there is a need not only to analyse and contribute to the algorithmic design of blockchain projects (i.e. the affordances and constraints they set), but also to the metapolitical narrative underpinning them (i.e. the political imaginaries underlying the various government-led projects).
Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
Küpers, Leanne K. ; Monnereau, Claire ; Sharp, Gemma C. ; Yousefi, Paul ; Salas, Lucas A. ; Ghantous, Akram ; Page, Christian M. ; Reese, Sarah E. ; Wilcox, Allen J. ; Czamara, Darina ; Starling, Anne P. ; Novoloaca, Alexei ; Lent, Samantha ; Roy, Ritu ; Hoyo, Cathrine ; Breton, Carrie V. ; Allard, Catherine ; Just, Allan C. ; Bakulski, Kelly M. ; Holloway, John W. ; Everson, Todd M. ; Xu, Cheng Jian ; Huang, Rae Chi ; Plaat, Diana A. van der; Wielscher, Matthias ; Merid, Simon Kebede ; Ullemar, Vilhelmina ; Rezwan, Faisal I. ; Lahti, Jari ; Dongen, Jenny van; Langie, Sabine A.S. ; Richardson, Tom G. ; Magnus, Maria C. ; Nohr, Ellen A. ; Xu, Zongli ; Duijts, Liesbeth ; Zhao, Shanshan ; Zhang, Weiming ; Plusquin, Michelle ; DeMeo, Dawn L. ; Solomon, Olivia ; Heimovaara, Joosje H. ; Jima, Dereje D. ; Gao, Lu ; Bustamante, Mariona ; Perron, Patrice ; Wright, Robert O. ; Hertz-Picciotto, Irva ; Zhang, Hongmei ; Karagas, Margaret R. ; Gehring, Ulrike ; Marsit, Carmen J. ; Beilin, Lawrence J. ; Vonk, Judith M. ; Jarvelin, Marjo Riitta ; Bergström, Anna ; Örtqvist, Anne K. ; Ewart, Susan ; Villa, Pia M. ; Moore, Sophie E. ; Willemsen, Gonneke ; Standaert, Arnout R.L. ; Håberg, Siri E. ; Sørensen, Thorkild I.A. ; Taylor, Jack A. ; Räikkönen, Katri ; Yang, Ivana V. ; Kechris, Katerina ; Nawrot, Tim S. ; Silver, Matt J. ; Gong, Yun Yun ; Richiardi, Lorenzo ; Kogevinas, Manolis ; Litonjua, Augusto A. ; Eskenazi, Brenda ; Huen, Karen ; Mbarek, Hamdi ; Maguire, Rachel L. ; Dwyer, Terence ; Vrijheid, Martine ; Bouchard, Luigi ; Baccarelli, Andrea A. ; Croen, Lisa A. ; Karmaus, Wilfried ; Anderson, Denise ; Vries, Maaike de; Sebert, Sylvain ; Kere, Juha ; Karlsson, Robert ; Arshad, Syed Hasan ; Hämäläinen, Esa ; Routledge, Michael N. ; Boomsma, Dorret I. ; Feinberg, Andrew P. ; Newschaffer, Craig J. ; Govarts, Eva ; Moisse, Matthieu ; Fallin, M.D. ; Melén, Erik ; Prentice, Andrew M. ; Kajantie, Eero ; Almqvist, Catarina ; Oken, Emily ; Dabelea, Dana ; Boezen, H.M. ; Melton, Phillip E. ; Wright, Rosalind J. ; Koppelman, Gerard H. ; Trevisi, Letizia ; Hivert, Marie France ; Sunyer, Jordi ; Munthe-Kaas, Monica C. ; Murphy, Susan K. ; Corpeleijn, Eva ; Wiemels, Joseph ; Holland, Nina ; Herceg, Zdenko ; Binder, Elisabeth B. ; Davey Smith, George ; Jaddoe, Vincent W.V. ; Lie, Rolv T. ; Nystad, Wenche ; London, Stephanie J. ; Lawlor, Debbie A. ; Relton, Caroline L. ; Snieder, Harold ; Felix, Janine F. - \ 2019
Nature Communications 10 (2019)1. - ISSN 2041-1723
Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (P Bonferroni < 1.06 x 10 −7 ). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10 −74 ) and BMI in pregnancy (3/914, p = 1.13x10 −3 ), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.
Patterns of outdoor exposure to heat in three South Asian cities
Jacobs, Cor ; Singh, Tanya ; Gorti, Ganesh ; Iftikhar, Usman ; Saeed, Salar ; Syed, Abu ; Abbas, Farhat ; Ahmad, Bashir ; Bhadwal, Suruchi ; Siderius, Christian - \ 2019
Science of the Total Environment 674 (2019). - ISSN 0048-9697 - p. 264 - 278.
Heat exposure - HI - South Asia - Urban heat island - UTCI - WBGT
Low socio-economic status has been widely recognized as a significant factor in enhancing a person's vulnerability to climate change including vulnerability to changes in temperature. Yet, little is known about exposure to heat within cities in developing countries, and even less about exposure within informal neighbourhoods in those countries. This paper presents an assessment of exposure to outdoor heat in the South Asian cities Delhi, Dhaka, and Faisalabad. The temporal evolution of exposure to heat is evaluated, as well as intra-urban differences, using meteorological measurements from mobile and stationary devices (April–September 2016). Exposure to heat is compared between low-income and other neighbourhoods in these cities. Results are expressed in terms of air temperature and in terms of the thermal indices Heat Index (HI), Wet Bulb Globe Temperature (WBGT) and Universal Thermal Climate Index (UTCI) at walking level. Conditions classified as dangerous to very dangerous, and likely to impede productivity, are observed almost every day of the measurement period during daytime, even when air temperature drops after the onset of the monsoon. It is recommended to cast heat warnings in terms of thermal indices instead of just temperature. Our results nuance the idea that people living in informal neighbourhoods are consistently more exposed to heat than people living in more prosperous neighbourhoods. During night-time, exposure does tend to be enhanced in densely-built informal neighbourhoods, but not if the low-income neighbourhoods are more open, or if they are embedded in green/blue areas.
South Asian river basins in a 1.5 °C warmer world
Lutz, Arthur F. ; Maat, Herbert W. ter; Wijngaard, René R. ; Biemans, Hester ; Syed, Abu ; Shrestha, Arun B. ; Wester, Philippus ; Immerzeel, Walter W. - \ 2019
Regional Environmental Change 19 (2019)3. - ISSN 1436-3798 - p. 833 - 847.
1.5 degrees - Brahmaputra - Climate change - Ganges - Indus - Paris agreement - South Asia
In 2015, with the signing of the “Paris Agreement”, 195 countries committed to limiting the increase in global temperature to less than 2 °C with respect to pre-industrial levels and to aim at limiting the increase to 1.5 °C by 2100. The regional ramifications of those thresholds remain however largely unknown and variability in the magnitude of change and the associated impacts are yet to be quantified. We provide a regional quantitative assessment of the impacts of a 1.5 versus a 2 °C global warming for a major global climate change hotspot: the Indus, Ganges, and Brahmaputra river basins (IGB) in South Asia, by analyzing changes in climate change indicators based on 1.5 and 2 °C global warming scenarios. In the analyzed ensemble of general circulation models, a global temperature increase of 1.5 °C implies a temperature increase of 1.4–2.6 (μ = 2.1) °C for the IGB. For the 2.0 °C scenario, the increase would be 2.0–3.4 (μ = 2.7) °C. We show that climate change impacts are more adverse under 2 °C versus 1.5 °C warming and that changes in the indicators’ values are in general linearly correlated to average temperature increase. We also show that for climate projections following Representative Concentration Pathways 4.5 and 8.5, which may be more realistic, the regional temperature increases and changes in climate change indicators are much stronger than for the 1.5 and 2 °C scenarios.
Putative regulatory candidate genes for QTL linked to fruit traits in oil palm (Elaeis guineensis Jacq.)
Ting, Ngoot Chin ; Mayes, Sean ; Massawe, Festo ; Sambanthamurthi, Ravigadevi ; Jansen, Johannes ; Syed Alwee, Sharifah Shahrul Rabiah ; Seng, Tzer Ying ; Ithnin, Maizura ; Singh, Rajinder - \ 2018
Euphytica 214 (2018)11. - ISSN 0014-2336
Deli dura - Marker-assisted selection - Pseudo-chromosome - Yangambi pisifera - Yield components
Palm oil is among the most important vegetable oils, contributing to a quarter of the world’s oils and fats market. The oil palm (Elaeis guineensis Jacq.) fruitlets, which are the source of palm oil, vary from 8 to 20 g in weight. Palm oil content in the fruitlets is approximately 45–50% by weight and an increase in the percentage of mesocarp-to-fruit is likely to have a positive effect on oil yield. In this study, we report a quantitative trait loci (QTL) associated with two yield related components, namely fruit and mesocarp content in a commercial breeding population (Deli dura × Yangambi pisifera). The QTL confidence interval of about 12 cM (~ 6.7 Mbp) was fine-mapped with 31 markers (17 SNPs and 14 SSRs) consisting of 20 nuclear markers derived from the maternal parent, six paternal and five co-segregating markers. Interestingly, inheritance of the paternal alleles leads to a larger difference in both fruit and mesocarp weight, when comparing genotypes in the progeny palms. Candidate genes and transcription factors were mined from the QTL region by positioning markers on the oil palm EG5 genome build. Putative genes and transcription factors involved in various biological processes including flower organ development, flowering, photosynthesis, microtubule formation, nitrogen and lipid metabolism were identified within this QTL interval on pseudo-chromosome 3. This genome-based approach allowed us to identify a number of potential candidate gene markers associated with oil palm fruit and mesocarp weight which can be further evaluated for potential use in marker-assisted breeding.
The effective mitigation of greenhouse gas emissions from rice paddies without compromising yield by early-season drainage
Islam, Syed Faiz Ul ; Groenigen, Jan Willem van; Jensen, Lars Stoumann ; Sander, Bjoern Ole ; Neergaard, Andreas de - \ 2018
Science of the Total Environment 612 (2018). - ISSN 0048-9697 - p. 1329 - 1339.
Drainage timing and duration - Global warming potential - Methane - Nitrous oxide - Redox potential - Rice straw management
Global rice production systems face two opposing challenges: the need to increase production to accommodate the world's growing population while simultaneously reducing greenhouse gas (GHG) emissions. Adaptations to drainage regimes are one of the most promising options for methane mitigation in rice production. Whereas several studies have focused on mid-season drainage (MD) to mitigate GHG emissions, early-season drainage (ED) varying in timing and duration has not been extensively studied. However, such ED periods could potentially be very effective since initial available C levels (and thereby the potential for methanogenesis) can be very high in paddy systems with rice straw incorporation. This study tested the effectiveness of seven drainage regimes varying in their timing and duration (combinations of ED and MD) to mitigate CH4 and N2O emissions in a 101-day growth chamber experiment. Emissions were considerably reduced by early-season drainage compared to both conventional continuous flooding (CF) and the MD drainage regime. The results suggest that ED + MD drainage may have the potential to reduce CH4 emissions and yield-scaled GWP by 85–90% compared to CF and by 75–77% compared to MD only. A combination of (short or long) ED drainage and one MD drainage episode was found to be the most effective in mitigating CH4 emissions without negatively affecting yield. In particular, compared with CF, the long early-season drainage treatments LE + SM and LE + LM significantly (p < 0.01) decreased yield-scaled GWP by 85% and 87% respectively. This was associated with carbon being stabilised early in the season, thereby reducing available C for methanogenesis. Overall N2O emissions were small and not significantly affected by ED. It is concluded that ED + MD drainage might be an effective low-tech option for small-scale farmers to reduce GHG emissions and save water while maintaining yield.
Healthcare access and quality index based on mortality from causes amenable to personal health care in 195 countries and territories, 1990-2015: A novel analysis from the global burden of disease study 2015
Barber, Ryan M. ; Fullman, Nancy ; Sorensen, Reed J.D. ; Bollyky, Thomas ; McKee, Martin ; Nolte, Ellen ; Abajobir, Amanuel Alemu ; Abate, Kalkidan Hassen ; Abbafati, Cristiana ; Abbas, Kaja M. ; Abd-Allah, Foad ; Abdulle, Abdishakur M. ; Abdurahman, Ahmed Abdulahi ; Abera, Semaw Ferede ; Abraham, Biju ; Abreha, Girmatsion Fisseha ; Adane, Kelemework ; Adelekan, Ademola Lukman ; Adetifa, Ifedayo Morayo O. ; Afshin, Ashkan ; Agarwal, Arnav ; Agarwal, Sanjay Kumar ; Agarwal, Sunilkumar ; Agrawal, Anurag ; Ahmad Kiadaliri, Aliasghar ; Ahmadi, Alireza ; Ahmed, Kedir Yimam ; Ahmed, Muktar Beshir ; Akinyemi, Rufus Olusola ; Akinyemiju, Tomi F. ; Akseer, Nadia ; Al-Aly, Ziyad ; Alam, Khurshid ; Alam, Noore ; Alam, Sayed Saidul ; Alemu, Zewdie Aderaw ; Alene, Kefyalew Addis ; Alexander, Lily ; Ali, Raghib ; Ali, Syed Danish ; Alizadeh-Navaei, Reza ; Alkerwi, A. ; Alla, François ; Allebeck, Peter ; Beyene, Tariku Jibat ; Geleijnse, Johanna M. ; Hoek, Hans W. ; Liu, Yang ; Vos, Theo ; Wang, Haidong - \ 2017
The Lancet 390 (2017)10091. - ISSN 0140-6736 - p. 231 - 266.
Background National levels of personal health-care access and quality can be approximated by measuring mortality rates from causes that should not be fatal in the presence of effective medical care (ie, amenable mortality). Previous analyses of mortality amenable to health care only focused on high-income countries and faced several methodological challenges. In the present analysis, we use the highly standardised cause of death and risk factor estimates generated through the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) to improve and expand the quantification of personal health-care access and quality for 195 countries and territories from 1990 to 2015. Methods We mapped the most widely used list of causes amenable to personal health care developed by Nolte and McKee to 32 GBD causes. We accounted for variations in cause of death certification and misclassifications through the extensive data standardisation processes and redistribution algorithms developed for GBD. To isolate the effects of personal health-care access and quality, we risk-standardised cause-specific mortality rates for each geography-year by removing the joint effects of local environmental and behavioural risks, and adding back the global levels of risk exposure as estimated for GBD 2015. We employed principal component analysis to create a single, interpretable summary measure-the Healthcare Quality and Access (HAQ) Index-on a scale of 0 to 100. The HAQ Index showed strong convergence validity as compared with other health-system indicators, including health expenditure per capita (r=0·88), an index of 11 universal health coverage interventions (r=0·83), and human resources for health per 1000 (r=0·77). We used free disposal hull analysis with bootstrapping to produce a frontier based on the relationship between the HAQ Index and the Socio-demographic Index (SDI), a measure of overall development consisting of income per capita, average years of education, and total fertility rates. This frontier allowed us to better quantify the maximum levels of personal health-care access and quality achieved across the development spectrum, and pinpoint geographies where gaps between observed and potential levels have narrowed or widened over time. Findings Between 1990 and 2015, nearly all countries and territories saw their HAQ Index values improve; nonetheless, the difference between the highest and lowest observed HAQ Index was larger in 2015 than in 1990, ranging from 28·6 to 94·6. Of 195 geographies, 167 had statistically significant increases in HAQ Index levels since 1990, with South Korea, Turkey, Peru, China, and the Maldives recording among the largest gains by 2015. Performance on the HAQ Index and individual causes showed distinct patterns by region and level of development, yet substantial heterogeneities emerged for several causes, including cancers in highest-SDI countries; chronic kidney disease, diabetes, diarrhoeal diseases, and lower respiratory infections among middle-SDI countries; and measles and tetanus among lowest-SDI countries. While the global HAQ Index average rose from 40·7 (95% uncertainty interval, 39·0-42·8) in 1990 to 53·7 (52·2-55·4) in 2015, far less progress occurred in narrowing the gap between observed HAQ Index values and maximum levels achieved; at the global level, the difference between the observed and frontier HAQ Index only decreased from 21·2 in 1990 to 20·1 in 2015. If every country and territory had achieved the highest observed HAQ Index by their corresponding level of SDI, the global average would have been 73·8 in 2015. Several countries, particularly in eastern and western sub-Saharan Africa, reached HAQ Index values similar to or beyond their development levels, whereas others, namely in southern sub-Saharan Africa, the Middle East, and south Asia, lagged behind what geographies of similar development attained between 1990 and 2015. Interpretation This novel extension of the GBD Study shows the untapped potential for personal health-care access and quality improvement across the development spectrum. Amid substantive advances in personal health care at the national level, heterogeneous patterns for individual causes in given countries or territories suggest that few places have consistently achieved optimal health-care access and quality across health-system functions and therapeutic areas. This is especially evident in middle-SDI countries, many of which have recently undergone or are currently experiencing epidemiological transitions. The HAQ Index, if paired with other measures of health-system characteristics such as intervention coverage, could provide a robust avenue for tracking progress on universal health coverage and identifying local priorities for strengthening personal health-care quality and access throughout the world.
Global, regional, and national age-sex specifc mortality for 264 causes of death, 1980-2016: A systematic analysis for the Global Burden of Disease Study 2016
Naghavi, Mohsen ; Abajobir, Amanuel Alemu ; Abbafati, Cristiana ; Abbas, Kaja M. ; Abd-Allah, Foad ; Abera, Semaw Ferede ; Aboyans, Victor ; Adetokunboh, Olatunji ; Ärnlöv, Johan ; Afshin, Ashkan ; Agrawal, Anurag ; Kiadaliri, Aliasghar Ahmad ; Ahmadi, Alireza ; Ahmed, Muktar Beshir ; Aichour, Amani Nidhal ; Aichour, Ibtihel ; Aichour, Miloud Taki Eddine ; Aiyar, Sneha ; Al-Eyadhy, Ayman ; Alahdab, Fares ; Al-Aly, Ziyad ; Alam, Khurshid ; Alam, Noore ; Alam, Tahiya ; Alene, Kefyalew Addis ; Ali, Syed Danish ; Alizadeh-Navaei, Reza ; Alkaabi, Juma M. ; Alkerwi, A. ; Alla, François ; Allebeck, Peter ; Allen, Christine ; Al-Raddadi, Rajaa ; Alsharif, Ubai ; Altirkawi, Khalid A. ; Alvis-Guzman, Nelson ; Amare, Azmeraw T. ; Amini, Erfan ; Ammar, Walid ; Amoako, Yaw Ampem ; Anber, Nahla ; Andersen, Hjalte H. ; Andrei, Catalina Liliana ; Androudi, Sofa ; Ansari, Hossein ; Hoek, Hans W. ; Liu, Yang ; Nguyen, Cuong Tat ; Nguyen, Quyen Le ; Nguyen, Trang Huyen ; Geleijnse, J.M. - \ 2017
The Lancet 390 (2017)10100. - ISSN 0140-6736 - p. 1151 - 1210.
Background: Monitoring levels and trends in premature mortality is crucial to understanding how societies can address prominent sources of early death. The Global Burden of Disease 2016 Study (GBD 2016) provides a comprehensive assessment of cause-specifc mortality for 264 causes in 195 locations from 1980 to 2016. This assessment includes evaluation of the expected epidemiological transition with changes in development and where local patterns deviate from these trends. Methods: We estimated cause-specifc deaths and years of life lost (YLLs) by age, sex, geography, and year. YLLs were calculated from the sum of each death multiplied by the standard life expectancy at each age. We used the GBD cause of death database composed of: vital registration (VR) data corrected for under-registration and garbage coding; national and subnational verbal autopsy (VA) studies corrected for garbage coding; and other sources including surveys and surveillance systems for specifc causes such as maternal mortality. To facilitate assessment of quality, we reported on the fraction of deaths assigned to GBD Level 1 or Level 2 causes that cannot be underlying causes of death (major garbage codes) by location and year. Based on completeness, garbage coding, cause list detail, and time periods covered, we provided an overall data quality rating for each location with scores ranging from 0 stars (worst) to 5 stars (best). We used robust statistical methods including the Cause of Death Ensemble model (CODEm) to generate estimates for each location, year, age, and sex. We assessed observed and expected levels and trends of cause-specifc deaths in relation to the Socio-demographic Index (SDI), a summary indicator derived from measures of average income per capita, educational attainment, and total fertility, with locations grouped into quintiles by SDI. Relative to GBD 2015, we expanded the GBD cause hierarchy by 18 causes of death for GBD 2016. Findings: The quality of available data varied by location. Data quality in 25 countries rated in the highest category (5 stars), while 48, 30, 21, and 44 countries were rated at each of the succeeding data quality levels. Vital registration or verbal autopsy data were not available in 27 countries, resulting in the assignment of a zero value for data quality. Deaths from non-communicable diseases (NCDs) represented 72·3% (95% uncertainty interval [UI] 71·2-73·2) of deaths in 2016 with 19·3% (18·5-20·4) of deaths in that year occurring from communicable, maternal, neonatal, and nutritional (CMNN) diseases and a further 8·43% (8·00-8·67) from injuries. Although age-standardised rates of death from NCDs decreased globally between 2006 and 2016, total numbers of these deaths increased; both numbers and age-standardised rates of death from CMNN causes decreased in the decade 2006-16 - age-standardised rates of deaths from injuries decreased but total numbers varied little. In 2016, the three leading global causes of death in children under-5 were lower respiratory infections, neonatal preterm birth complications, and neonatal encephalopathy due to birth asphyxia and trauma, combined resulting in 1·80 million deaths (95% UI 1·59 million to 1·89 million). Between 1990 and 2016, a profound shift toward deaths at older ages occurred with a 178% (95% UI 176-181) increase in deaths in ages 90-94 years and a 210% (208-212) increase in deaths older than age 95 years. The ten leading causes by rates of age-standardised YLL signifcantly decreased from 2006 to 2016 (median annualised rate of change was a decrease of 2·89%); the median annualised rate of change for all other causes was lower (a decrease of 1·59%) during the same interval. Globally, the fve leading causes of total YLLs in 2016 were cardiovascular diseases; diarrhoea, lower respiratory infections, and other common infectious diseases; neoplasms; neonatal disorders; and HIV/AIDS and tuberculosis. At a fner level of disaggregation within cause groupings, the ten leading causes of total YLLs in 2016 were ischaemic heart disease, cerebrovascular disease, lower respiratory infections, diarrhoeal diseases, road injuries, malaria, neonatal preterm birth complications, HIV/AIDS, chronic obstructive pulmonary disease, and neonatal encephalopathy due to birth asphyxia and trauma. Ischaemic heart disease was the leading cause of total YLLs in 113 countries for men and 97 countries for women. Comparisons of observed levels of YLLs by countries, relative to the level of YLLs expected on the basis of SDI alone, highlighted distinct regional patterns including the greater than expected level of YLLs from malaria and from HIV/AIDS across sub-Saharan Africa; diabetes mellitus, especially in Oceania; interpersonal violence, notably within Latin America and the Caribbean; and cardiomyopathy and myocarditis, particularly in eastern and central Europe. The level of YLLs from ischaemic heart disease was less than expected in 117 of 195 locations. Other leading causes of YLLs for which YLLs were notably lower than expected included neonatal preterm birth complications in many locations in both south Asia and southeast Asia, and cerebrovascular disease in western Europe. Interpretation: The past 37 years have featured declining rates of communicable, maternal, neonatal, and nutritional diseases across all quintiles of SDI, with faster than expected gains for many locations relative to their SDI. A global shift towards deaths at older ages suggests success in reducing many causes of early death. YLLs have increased globally for causes such as diabetes mellitus or some neoplasms, and in some locations for causes such as drug use disorders, and confict and terrorism. Increasing levels of YLLs might refect outcomes from conditions that required high levels of care but for which efective treatments remain elusive, potentially increasing costs to health systems.
Geodata To Control Potato Late Blight In Bangladesh
Kessel, G. ; Moene, A.F. ; Valkengoed, E. van; Voet, P. van der; Michielsen, J.M. ; Ahsan, H. ; Schmelzer, T. ; Maroof, M. ; Syed, A. ; Hengsdijk, Huib - \ 2017
In: Proceedings of the sixteenth EuroBlight Workshop. - Wageningen : Wageningen University & Research, Praktijkonderzoek AGV (PAGV-Special Report 18) - p. 59 - 60.
Damage-associated responses of the host contribute to defence against cyst nematodes but not root-knot nematodes
Shah, Syed Jehangir ; Anjam, Muhammad Shahzad ; Mendy, Badou ; Anwer, Muhammad Arslan ; Habash, Samer S. ; Lozano-Torres, Jose L. ; Grundler, Florian M.W. ; Siddique, Shahid - \ 2017
Journal of Experimental Botany 68 (2017)21-22. - ISSN 0022-0957 - p. 5949 - 5960.
When nematodes invade and subsequently migrate within plant roots, they generate cell wall fragments (in the form of oligogalacturonides; OGs) that can act as damage-associated molecular patterns and activate host defence responses. However, the molecular mechanisms mediating damage responses in plant–nematode interactions remain unexplored. Here, we characterized the role of a group of cell wall receptor proteins in Arabidopsis, designated as polygalacturonase-inhibiting proteins (PGIPs), during infection with the cyst nematode Heterodera schachtii and the root-knot nematode Meloidogyne incognita. PGIPs are encoded by a family of two genes in Arabidopsis, and are involved in the formation of active OG elicitors. Our results show that PGIP gene expression is strongly induced in response to cyst nematode invasion of roots. Analyses of loss-of-function mutants and overexpression lines revealed that PGIP1 expression attenuates infection of host roots by cyst nematodes, but not root-knot nematodes. The PGIP1-mediated attenuation of cyst nematode infection involves the activation of plant camalexin and indole-glucosinolate pathways. These combined results provide new insights into the molecular mechanisms underlying plant damage perception and response pathways during infection by cyst and root-knot nematodes, and establishes the function of PGIP in plant resistance to cyst nematodes.
A Tractable Method for Measuring Nanomaterial Risk Using Bayesian Networks
Murphy, Finbarr ; Sheehan, Barry ; Mullins, Martin ; Bouwmeester, Hans ; Marvin, Hans J.P. ; Bouzembrak, Yamine ; Costa, Anna L. ; Das, Rasel ; Stone, Vicki ; Tofail, Syed A.M. - \ 2016
Nanoscale Research Letters 11 (2016)1. - ISSN 1931-7573
Bayesian - Control banding - Risk assessment
While control banding has been identified as a suitable framework for the evaluation and the determination of potential human health risks associated with exposure to nanomaterials (NMs), the approach currently lacks any implementation that enjoys widespread support. Large inconsistencies in characterisation data, toxicological measurements and exposure scenarios make it difficult to map and compare the risk associated with NMs based on physicochemical data, concentration and exposure route. Here we demonstrate the use of Bayesian networks as a reliable tool for NM risk estimation. This tool is tractable, accessible and scalable. Most importantly, it captures a broad span of data types, from complete, high quality data sets through to data sets with missing data and/or values with a relatively high spread of probability distribution. The tool is able to learn iteratively in order to further refine forecasts as the quality of data available improves. We demonstrate how this risk measurement approach works on NMs with varying degrees of risk potential, namely, carbon nanotubes, silver and titanium dioxide. The results afford even non-experts an accurate picture of the occupational risk probabilities associated with these NMs and, in doing so, demonstrated how NM risk can be evaluated into a tractable, quantitative risk comparator.
Effect of a school-based oral health education in preventing untreated dental caries and increasing knowledge, attitude, and practices among adolescents in Bangladesh
Haque, Syed Emdadul ; Rahman, Mosiur ; Itsuko, Kawashima ; Mutahara, Muhmuda ; Kayako, Sakisaka ; Tsutsumi, Atsuro ; Islam, Md Jahirul ; Mostofa, Md Golam - \ 2016
BMC Oral Health 16 (2016)1. - ISSN 1472-6831
Adolescents - Bangladesh - Dental caries - School-based health education
Background: There is a dearth of published literature that demonstrates the impact and effectiveness of school-based oral health education (OHE) program in Bangladesh and it is one of the most neglected activities in the field of public health. Keeping this in mind, the objectives of this study were to assess the effectiveness of OHE program in: 1) increasing oral health knowledge, attitude, and practices and 2) decreasing the prevalence of untreated dental caries among 6-8 grade school students in Bangladesh. Methods: This intervention study was conducted in Araihazar Thana, Narayanganj district, Bangladesh during April 2012 to March 2013. The total participants were 944 students from three local schools. At baseline, students were assessed for oral health knowledge, attitude and practices using a self-administered structured questionnaire and untreated dental caries was assessed using clinical examination. Follow up study was done after 6 months from baseline. McNemar's chi-square analysis was used to evaluate the impact of OHE program on four recurrent themes of oral health between the baseline and follow-up. Multiple logistic regression analyses were used to determine the impact of the intervention group on our outcome variables. Results: Significant improvement was observed regarding school aged adolescents' self-reported higher knowledge, attitude and practices scores (p <0.001) at follow-up compared with baseline. The prevalence of untreated dental caries of the study population after the OHE program was significantly (p <0.01) reduced to 42.5 %. Multiple logistic regression analyses showed that the OHE intervention remained a significant predictor in reducing the risk of untreated dental caries (adjusted odds ratio [AOR] =0.51; 95 % confidence interval [CI] = 0.37, 0.81). In the follow-up period participants were 2.21 times (95 % CI = 1.87, 3.45) more likely to have higher level of knowledge regarding oral health compared to baseline. Compared with baseline participants in the follow-up were 1.89 times (95 % CI = 1.44-2.87) more likely to have higher attitude towards oral health. In addition, OHE intervention was found to be significantly associated with higher level of practices toward oral health (AOR = 1.64; 95 % CI = 1.12, 3.38). Conclusions: This study indicated that OHE intervention was effective in increasing i) knowledge, ii) attitude, and iii) practices towards oral health; it also significantly reduced the prevalence of untreated dental caries among school aged adolescents from grade 6-8 in a deprived rural area of Bangladesh.
Trends in flood risk management in deltas around the world: Are we going ‘soft’?
Wesselink, A. ; Warner, J.F. ; Syed, M.A. ; Chan, F. ; Tran, D.D. ; Huq, H. ; Huthoff, F. ; Thuy, N. Le; Pinter, N. ; Staveren, M.F. van; Wester, P. ; Zegwaard, A. - \ 2015
International Journal of Water Governance 3 (2015)4. - ISSN 2211-4491 - p. 25 - 46.
Flood-risk management (FRM) is shaped by context: a society’s cultural background; physical possibilities and constraints; and the historical development of that society’s economy, politi- cal system, education, etc. These provide different drivers for change, in interaction with more global developments. We compare historical and current FRM in six delta areas and their con- texts: Rhine/Meuse/Scheldt (The Netherlands), Pearl River (China), Mekong (Vietnam), Ganges/ Brahmaputra/Meghna (Bangladesh) Zambezi/Limpopo (Mozambique), and Mississippi (USA). We show that in many countries the emphasis is shifting from ‘hard’ engineering, such as dikes, towards non-structural ‘soft’ measures, such as planning restrictions or early warning systems, while the ‘hard’ responses are softened in some by a ‘building with nature’ approach. However, this is by no means a universal development. One consistent feature of the application of ‘hard’ FRM technology to deltas is that it pushes them towards a technological ‘lock-in’ in which fewer and fewer ‘soft’ FRM alternatives are feasible due to increased ood risks. By contrast, ‘soft’ FRM is typically exible, allowing a range of future options, including future hard elements if needed and appropriate. These experiences should lead to serious re ection on whether ‘hard’ FRM should be recommended when ‘soft’ FRM options are still open.
Locus-dependent selection in crop-wild hybrids of lettuce under field conditions and its implication for GM crop development
Hooftman, D.A.P. ; Flavell, A.J. ; Jansen, J. ; Nijs, J.C.M. den; Syed, N.H. ; Sorensen, A.P. ; Wengel, P.O. ter; Wiel, C.C.M. van de - \ 2011
Evolutionary Applications 4 (2011)5. - ISSN 1752-4563 - p. 648 - 659.
sunflower helianthus-annuus - genetically-modified crops - linkage disequilibrium - gene flow - cultivated sunflower - artificial selection - disease resistance - lactuca-serriola - risk-assessment - transgene flow
Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter’s ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent’s habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence.