Browsing by Subject "PROJECT"

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  • Schewtschenko, J. A.; Baugh, C. M.; Wilkinson, R. J.; Boehm, C.; Pascoli, S.; Sawala, T. (2016)
    In the thermal dark matter (DM) paradigm, primordial interactions between DM and Standard Model particles are responsible for the observed DM relic density. In Boehm et al., we showed that weak-strength interactions between DM and radiation (photons or neutrinos) can erase small-scale density fluctuations, leading to a suppression of the matter power spectrum compared to the collisionless cold DM (CDM) model. This results in fewer DM subhaloes within Milky Way-like DM haloes, implying a reduction in the abundance of satellite galaxies. Here we use very high-resolution N-body simulations to measure the dynamics of these subhaloes. We find that when interactions are included, the largest subhaloes are less concentrated than their counterparts in the collisionless CDM model and have rotation curves that match observational data, providing a new solution to the 'too big to fail' problem.
  • Jelenkovic, Aline; Sund, Reijo; Yokoyama, Yoshie; Latvala, Antti; Sugawara, Masumi; Tanaka, Mami; Matsumoto, Satoko; Freitas, Duarte L.; Maia, Jose Antonio; Knafo-Noam, Ariel; Mankuta, David; Abramson, Lior; Ji, Fuling; Ning, Feng; Pang, Zengchang; Rebato, Esther; Saudino, Kimberly J.; Cutler, Tessa L.; Hopper, John L.; Ullemar, Vilhelmina; Almqvist, Catarina; Magnusson, Patrik K. E.; Cozen, Wendy; Hwang, Amie E.; Mack, Thomas M.; Nelson, Tracy L.; Whitfield, Keith E.; Sung, Joohon; Kim, Jina; Lee, Jooyeon; Lee, Sooji; Llewellyn, Clare H.; Fisher, Abigail; Medda, Emanuela; Nistico, Lorenza; Toccaceli, Virgilia; Baker, Laura A.; Tuvblad, Catherine; Corley, Robin P.; Huibregtse, Brooke M.; Derom, Catherine A.; Vlietinck, Robert F.; Loos, Ruth J. F.; Burt, S. Alexandra; Klump, Kelly L.; Silberg, Judy L.; Maes, Hermine H.; Krueger, Robert F.; McGue, Matt; Pahlen, Shandell; Gatz, Margaret; Butler, David A.; Harris, Jennifer R.; Brandt, Ingunn; Nilsen, Thomas S.; Harden, K. Paige; Tucker-Drob, Elliot M.; Franz, Carol E.; Kremen, William S.; Lyons, Michael J.; Lichtenstein, Paul; Bartels, Meike; van Beijsterveldt, Catharina E. M.; Willemsen, Gonneke; Oncel, Sevgi Y.; Aliev, Fazil; Jeong, Hoe-Uk; Hur, Yoon-Mi; Turkheimer, Eric; Boomsma, Dorret; Srensen, Thorkild I. A.; Kaprio, Jaakko; Silventoinen, Karri (2020)
    Genetic factors explain a major proportion of human height variation, but differences in mean stature have also been found between socio-economic categories suggesting a possible effect of environment. By utilizing a classical twin design which allows decomposing the variation of height into genetic and environmental components, we tested the hypothesis that environmental variation in height is greater in offspring of lower educated parents. Twin data from 29 cohorts including 65,978 complete twin pairs with information on height at ages 1 to 69 years and on parental education were pooled allowing the analyses at different ages and in three geographic-cultural regions (Europe, North America and Australia, and East Asia). Parental education mostly showed a positive association with offspring height, with significant associations in mid-childhood and from adolescence onwards. In variance decomposition modeling, the genetic and environmental variance components of height did not show a consistent relation to parental education. A random-effects meta-regression analysis of the aggregate-level data showed a trend towards greater shared environmental variation of height in low parental education families. In conclusion, in our very large dataset from twin cohorts around the globe, these results provide only weak evidence for the study hypothesis.
  • Sell, Mila; Vihinen, Hilkka; Gabiso, Galfato; Lindström, Kristina (2018)
    This article describes the process and analyses the results of a project in Ethiopia establishing an innovation platform (IP) as a tool for co-creation from an innovation systems perspective. The results are encouraging, suggesting positive effects both on yields, but more importantly on the capacity and role of participants as communicators and agents of change in the community. The IP seems promising in creating new networks and modes of communication. The importance of good facilitation, commitment by all members from the start, and feedback loops driving the process was found to be essential.
  • Haavisto, Anu; Mathiesen, Sidsel; Suominen, Anu; Lähteenmäki, Päivi; Sorensen, Kaspar; Ifversen, Marianne; Juul, Anders; Nielsen, Malene Mejdahl; Müller, Klaus; Jahnukainen, Kirsi (2020)
    There are many known endocrine complications after allogeneic hematopoietic stem cell transplantation (HSCT) in childhood including increased risk of biochemical hypogonadism. However, little is known about sexuality in adulthood following childhood HSCT. In this multicenter study, sexual functions and possible risk factors were assessed comprehensively in two national cohorts (Finland and Denmark) of male adult survivors of childhood HSCT. Compared to a healthy control group (n= 56), HSCT survivors (n= 97) reported less sexual fantasies, poorer orgasms, lower sexual activity with a partner and reduced satisfaction with their sex life, even in the presence of normal erectile functions and a similar frequency of autoerotic acts. Of the HSCT survivors, 35% were cohabitating/married and 66% were sexually active. Risk factors for poorer self-reported sexual functions were partner status (not cohabitating with a partner), depressive symptoms, CNS and testicular irradiation. Sexual dysfunction increased by age in the HSCT group with a pace comparable to that of the control group. However, because of the lower baseline level of sexual functions in the HSCT group, they will reach the level of clinically significant dysfunction at a younger age. Hence, male survivors of childhood HSCT should be interviewed in detail about their sexual health beyond erectile functions.
  • Deschasaux, Melanie; Huybrechts, Inge; Murphy, Neil; Julia, Chantal; Hercberg, Serge; Srour, Bernard; Kesse-Guyot, Emmanuelle; Latino-Martel, Paule; Biessy, Carine; Casagrande, Corinne; Jenab, Mazda; Ward, Heather; Weiderpass, Elisabete; Dahm, Christina C.; Overvad, Kim; Kyro, Cecilie; Olsen, Anja; Affret, Aurelie; Boutron-Ruault, Marie-Christine; Mahamat-Saleh, Yahya; Kaaks, Rudolf; Kuehn, Tilman; Boeing, Heiner; Schwingshackl, Lukas; Bamia, Christina; Peppa, Eleni; Trichopoulou, Antonia; Masala, Giovanna; Krogh, Vittorio; Panico, Salvatore; Tumino, Rosario; Sacerdote, Carlotta; Buen-de-Mesquita, Bas; Peeters, Petra H.; Hjartaker, Anette; Rylander, Charlotta; Skeie, Guri; Ramon Quiros, J.; Jakszyn, Paula; Salamanca-Fernandez, Elena; Maria Huerta, Jose; Ardanaz, Eva; Amiano, Pilar; Ericson, Ulrika; Sonestedt, Emily; Huseinovic, Ena; Johansson, Ingegerd; Khaw, Kay-Tee; Wareham, Nick; Bradbury, Kathryn E.; Perez-Cornago, Aurora; Tsilidis, Konstantinos K.; Ferrari, Pietro; Riboli, Elio; Gunter, Marc J.; Touvier, Mathilde (2018)
    Background Helping consumers make healthier food choices is a key issue for the prevention of cancer and other diseases. In many countries, political authorities are considering the implementation of a simplified labelling system to reflect the nutritional quality of food products. The Nutri-Score, a five-colour nutrition label, is derived from the Nutrient Profiling System of the British Food Standards Agency (modified version) (FSAm-NPS). How the consumption of foods with high/low FSAm-NPS relates to cancer risk has been studied in national/regional cohorts but has not been characterized in diverse European populations. Methods and findings This prospective analysis included 471,495 adults from the European Prospective Investigation into Cancer and Nutrition (EPIC, 1992-2014, median follow-up: 15.3 y), among whom there were 49,794 incident cancer cases (main locations: breast, n = 12,063; prostate, n = 6,745; colon-rectum, n = 5,806). Usual food intakes were assessed with standardized country-specific diet assessment methods. The FSAm-NPS was calculated for each food/beverage using their 100-g content in energy, sugar, saturated fatty acid, sodium, fibres, proteins, and fruits/vegetables/legumes/nuts. The FSAm-NPS scores of all food items usually consumed by a participant were averaged to obtain the individual FSAm-NPS Dietary Index (DI) scores. Multi-adjusted Cox proportional hazards models were computed. A higher FSAm-NPS DI score, reflecting a lower nutritional quality of the food consumed, was associated with a higher risk of total cancer (HRQ5 versus (Q1) = 1.07; 95% CI 1.03-1.10, P-trend <0.001). Absolute cancer rates in those with high and low (quintiles 5 and 1) FSAm-NPS DI scores were 81.4 and 69.5 cases/10,000 person-years, respectively. Higher FSAm-NPS DI scores were specifically associated with higher risks of cancers of the colon-rectum, upper aerodigestive tract and stomach, lung for men, and liver and postmenopausal breast for women (all P <0.05). The main study limitation is that it was based on an observational cohort using self-reported dietary data obtained through a single baseline food frequency questionnaire; thus, exposure misclassification and residual confounding cannot be ruled out. Conclusions In this large multinational European cohort, the consumption of food products with a higher FSAm-NPS score (lower nutritional quality) was associated with a higher risk of cancer. This supports the relevance of the FSAm-NPS as underlying nutrient profiling system for front-of-pack nutrition labels, as well as for other public health nutritional measures.
  • Vrieling, Alina; Bueno-De-Mesquita, H. Bas; Ros, Martine M.; Kampman, Ellen; Aben, Katja K.; Buchner, Frederike L.; Jansen, Eugene H.; Roswall, Nina; Tjonneland, Anne; Boutron-Ruault, Marie-Christine; Cadeau, Claire; Chang-Claude, Jenny; Kaaks, Rudolf; Weikert, Steffen; Boeing, Heiner; Trichopoulou, Antonia; Lagiou, Pagona; Trichopoulos, Dimitrios; Sieri, Sabina; Palli, Domenico; Panico, Salvatore; Peeters, Petra H.; Weiderpass, Elisabete; Skeie, Guri; Jakszyn, Paula; Chirlaque, Maria-Dolores; Ardanaz, Eva; Sanchez, Maria-Jose; Ehrnstrom, Roy; Malm, Johan; Ljungberg, Borje; Khaw, Kay-Tee; Wareham, Nick J.; Brennan, Paul; Johansson, Mattias; Riboli, Elio; Kiemeney, Lambertus A. (2019)
    Published associations between dietary folate and bladder cancer risk are inconsistent. Biomarkers may provide more accurate measures of nutrient status. This nested case-control analysis within the European Prospective Investigation into Cancer and Nutrition (EPIC) investigated associations between pre-diagnostic serum folate, homocysteine, vitamins B6 and B12 and the risk of urothelial cell carcinomas of the bladder (UCC). A total of 824 patients with newly diagnosed UCC were matched with 824 cohort members. Serum folate, homocysteine, and vitamins B6 and B12 were measured. Odds ratios (OR) and 95% confidence intervals (CI) for total, aggressive, and non-aggressive UCC were estimated using conditional logistic regression with adjustment for smoking status, smoking duration and intensity, and other potential confounders. Additionally, statistical interaction with smoking status was assessed. A halving in serum folate concentrations was moderately associated with risk of UCC (OR: 1.18; 95% CI: 0.98-1.43), in particular aggressive UCC (OR: 1.34; 95% CI: 1.02-1.75; p-heterogeneity = 0.19). Compared to never smokers in the highest quartile of folate concentrations, this association seemed only apparent among current smokers in the lowest quartile of folate concentrations (OR: 6.26; 95% CI: 3.62-10.81, p-interaction = 0.07). Dietary folate was not associated with aggressive UCC (OR: 1.26; 95% CI: 0.81-1.95; p-heterogeneity = 0.14). No association was observed between serum homocysteine, vitamins B6 and B12 and risk of UCC. This study suggests that lower serum folate concentrations are associated with increased UCC risk, in particular aggressive UCC. Residual confounding by smoking cannot be ruled out and these findings require confirmation in future studies with multiple measurements.
  • Savastano, Stefano; Amendola, Luca; Rubio, Javier; Wetterich, Christof (2019)
    We argue that primordial dark matter halos could be generated during radiation domination by long-range attractive forces stronger than gravity. In this paper, we derive the conditions under which these structures could dominate the dark matter content of the Universe while passing microlensing constraints and cosmic microwave background energy injection bounds. The dark matter particles would be clumped in objects in the solar mass range with typical sizes of the order of the solar system. Consequences for direct dark matter searches are important.
  • Baranizadeh, Elham; Arola, Antti; Hamed, Amar; Nieminen, Tuomo; Mikkonen, Santtu; Virtanen, Annele; Kulmala, Markku; Lehtinen, Kari; Laaksonen, Ari (2014)
  • Xu, Cheng-Jian; Bonder, Marc Jan; Soderhall, Cilla; Bustamante, Mariona; Baiz, Nour; Gehring, Ulrike; Jankipersadsing, Soesma A.; van der Vlies, Pieter; van Diemen, Cleo C.; van Rijkom, Bianca; Just, Jocelyne; Kull, Inger; Kere, Juha; Anto, Josep Maria; Bousquet, Jean; Zhernakova, Alexandra; Wijmenga, Cisca; Annesi-Maesano, Isabella; Sunyer, Jordi; Melen, Erik; Li, Yang; Postma, Dirkje S.; Koppelman, Gerard H. (2017)
    Background: DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood. Results: By analysing 538 paired DNA blood samples from children at birth and at 4-5 years old and 726 paired samples from children at 4 and 8 years old from four European birth cohorts using the Illumina Infinium Human Methylation 450 k chip, we have identified 14,150 consistent age-differential methylation sites (a-DMSs) at epigenome-wide significance of rho <1.14x10(-7). Genes with an increase in age-differential methylation were enriched in pathways related to 'development', and were more often located in bivalent transcription start site (TSS) regions, which can silence or activate expression of developmental genes. Genes with a decrease in age-differential methylation were involved in cell signalling, and enriched on H3K27ac, which can predict developmental state. Maternal smoking tended to decrease methylation levels at the identified da-DMSs. We also found 101 a-DMSs (0.71%) that were regulated by genetic variants using cis-differential Methylation Quantitative Trait Locus (cis-dMeQTL) mapping. Moreover, a-DMS-associated genes during early development were significantly more likely to be linked with disease. Conclusion: Our study provides new insights into the dynamic epigenetic landscape of the first 8 years of life.
  • Schaller, Matthieu; Frenk, Carlos S.; Fattahi, Azadeh; Navarro, Julio F.; Oman, Kyle A.; Sawala, Till (2016)
    We investigate the presence and importance of dark matter discs in a sample of 24 simulated Milky Way galaxies in the APOSTLE project, part of the EAGLE programme of hydrodynamic simulations in Lambda CDM cosmology. It has been suggested that a dark disc in the Milky Way may boost the dark matter density and modify the velocity modulus relative to a smooth halo at the position of the Sun, with ramifications for direct detection experiments. From a kinematic decomposition of the dark matter and a real space analysis of all 24 haloes, we find that only one of the simulated Milky Way analogues has a detectable dark disc component. This unique event was caused by a merger at late time with an LMC-mass satellite at very low grazing angle. Considering that even this rare scenario only enhances the dark matter density at the solar radius by 35 per cent and affects the high-energy tail of the dark matter velocity distribution by less than 1 per cent, we conclude that the presence of a dark disc in the Milky Way is unlikely, and is very unlikely to have a significant effect on direct detection experiments.
  • Titeux, Nicolas; Maes, Dirk; Van Daele, Toon; Onkelinx, Thierry; Heikkinen, Risto K.; Romo, Helena; Garcia-Barros, Enrique; Munguira, Miguel L.; Thuiller, Wilfried; van Swaay, Chris A. M.; Schweiger, Oliver; Settele, Josef; Harpke, Alexander; Wiemers, Martin; Brotons, Lluis; Luoto, Miska (2017)
    Aim: Species distribution models built with geographically restricted data often fail to capture the full range of conditions experienced by species across their entire distribution area. Using such models to predict distribution shifts under future environmental change may, therefore, produce biased projections. However, restricted-scale models have the potential to include a larger sample of taxa for which distribution data are available and to provide finer-resolution projections that are better applied to conservation planning than the forecasts of broad-scale models. We examine the circumstances under which the projected shifts in species richness patterns derived from restricted-scale and broad-scale models are most likely to be similar. Location: Europe. Methods: The distribution of butterflies in Finland, Belgium/Netherlands and Spain was modelled based on restricted-scale (local) and broad-scale (continental) distribution and climate data. Both types of models were projected under future climate change scenarios to assess potential changes in species richness. Results: In Finland, species richness was projected to increase strongly based on restricted-scale models and to decrease slightly with broad-scale models. In Belgium/Netherlands, restricted-scale models projected a larger decrease in richness than broad-scale models. In Spain, both models projected a slight decrease in richness. We obtained similar projections based on restricted-scale and broad-scale models only in Spain because the climatic conditions available here covered the warm part of the distributions of butterflies better than in Finland and Belgium/Netherlands. Main conclusions: Restricted-scale models that fail to capture the warm part of species distributions produce biased estimates of future changes in species richness when projected under climatic conditions with no modern analogue in the study area. We recommend the use of distribution data beyond the boundaries of the study area to capture the part of the species response curves reflecting the climatic conditions that will prevail within that area in the future.
  • Valenzuela, Daniel; Norri, Tuukka; Välimäki, Niko; Pitkänen, Esa; Mäkinen, Veli (2018)
    Background: Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation. Results: We propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation - a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: https://gitlab.com/dvalenzu/PanVC. Conclusions: Our experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.