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.
  • Cáceres-Jensen, Lizethly; Rodríguez-Becerra, Jorge; Jorquera-Moreno, Bárbara; Escudey, Mauricio; Druker-Ibañez, Sofía; Hernández-Ramos, José; Díaz-Arce, Tatiana; Pernaa, Johannes; Aksela, Maija (2021)
    Teaching the fundamentals of chemical kinetics on the college level is challenging to teachers and students alike due to its abstract nature of concepts and limited connection with real context applications. This study consisted of two phases starting with designing a chemistry education for the sustainable development-based learning environment of reaction kinetics, followed by a case study in which students' perceptions toward learning chemistry by solving a real environmental problem using digital resources, spreadsheets, and an active learning environment, were explored. First, we designed a Socio-Scientific Environmental Chemistry module centered on the sorption kinetic processes of herbicides in volcanic ash derived soils (VADS) and their potential to pollute groundwater. The objective of the learning module was to contribute to the development of sustainability skills, to promote learning of contextualized chemistry knowledge, and to develop scientific skills. This module employs spreadsheets as computational tools in chemistry to model real sorption kinetic data of herbicides in VADS. The learning module was designed for one section of two Analytical Chemistry courses and one Physical Chemistry course of an undergraduate chemistry teacher-training program. After the design phase, the learning module was implemented in each course, and students' perceptions were gathered using the focus group technique. The sample was of 22 students distributed into three focus groups. The data collected were analyzed and categorized through qualitative content analysis using the Technological Pedagogical Science Knowledge (TPASK) framework. On the basis of our findings, the students acquired contextualized chemistry knowledge and develop skills and knowledge related to using digital resources and spreadsheets in a scientific context. Besides, the preservice chemistry teachers' knowledge of pedagogy allowed them to develop some elements of their pedagogical science knowledge and TPASK. This case study shows that the problem-based learning approach offers great potential in supporting a learning environment suitable to working with spreadsheets to solve real-environment problems in chemistry education.
  • 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.
  • Brasseur, Zoe; Castarede, Dimitri; Thomson, Erik S.; Adams, Michael P.; Drossaart van Dusseldorp, Saskia; Heikkilä, Paavo; Korhonen, Kimmo; Lampilahti, Janne; Paramonov, Mikhail; Schneider, Julia; Vogel, Franziska; Wu, Yusheng; Abbatt, Jonathan P. D.; Atanasova, Nina S.; Bamford, Dennis H.; Bertozzi, Barbara; Boyer, Matthew; Brus, David; Daily, Martin I.; Fösig, Romy; Gute, Ellen; Harrison, Alexander D.; Hietala, Paula; Höhler, Kristina; Kanji, Zamin A.; Keskinen, Jorma; Lacher, Larissa; Lampimäki, Markus; Levula, Janne; Manninen, Antti; Nadolny, Jens; Peltola, Maija; Porter, Grace C. E.; Poutanen, Pyry; Proske, Ulrike; Schorr, Tobias; Silas Umo, Nsikanabasi; Stenszky, Janos; Virtanen, Annele; Moisseev, Dmitri; Kulmala, Markku; Murray, Benjamin J.; Petäjä, Tuukka; Möhler, Ottmar; Duplissy, Jonathan (2022)
    The formation of ice particles in Earth's atmosphere strongly influences the dynamics and optical properties of clouds and their impacts on the climate system. Ice formation in clouds is often triggered heterogeneously by ice-nucleating particles (INPs) that represent a very low number of particles in the atmosphere. To date, many sources of INPs, such as mineral and soil dust, have been investigated and identified in the low and mid latitudes. Although less is known about the sources of ice nucleation at high latitudes, efforts have been made to identify the sources of INPs in the Arctic and boreal environments. In this study, we investigate the INP emission potential from high-latitude boreal forests in the mixed-phase cloud regime. We introduce the HyICE-2018 measurement campaign conducted in the boreal forest of Hyytiala, Finland, between February and June 2018. The campaign utilized the infrastructure of the Station for Measuring Ecosystem-Atmosphere Relations (SMEAR) II, with additional INP instruments, including the Portable Ice Nucleation Chamber I and II (PINC and PINCii), the SPectrometer for Ice Nuclei (SPIN), the Portable Ice Nucleation Experiment (PINE), the Ice Nucleation SpEctrometer of the Karlsruhe Institute of Technology (INSEKT) and the Microlitre Nucleation by Immersed Particle Instrument (mu L-NIPI), used to quantify the INP concentrations and sources in the boreal environment. In this contribution, we describe the measurement infrastructure and operating procedures during HyICE-2018, and we report results from specific time periods where INP instruments were run in parallel for inter-comparison purposes. Our results show that the suite of instruments deployed during HyICE-2018 reports consistent results and therefore lays the foundation for forthcoming results to be considered holistically. In addition, we compare measured INP concentrations to INP parameterizations, and we observe good agreement with the Tobo et al. (2013) parameterization developed from measurements conducted in a ponderosa pine forest ecosystem in Colorado, USA.
  • 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.
  • FinnGen; Tienari, Pentti (2022)
    Objectives To recontact biobank participants and collect cognitive, behavioural and lifestyle information via a secure online platform. Design Biobank-based recontacting pilot study. Setting Three Finnish biobanks (Helsinki, Auria, Tampere) recruiting participants from February 2021 to July 2021. Participants All eligible invitees were enrolled in FinnGen by their biobanks (Helsinki, Auria, Tampere), had available genetic data and were >18 years old. Individuals with severe neuropsychiatric disease or cognitive or physical disabilities were excluded. Lastly, 5995 participants were selected based on their polygenic score for cognitive abilities and invited to the study. Among invitees, 1115 had successfully participated and completed the study questionnaire(s). Outcome measures The primary outcome was the participation rate among study invitees. Secondary outcomes included questionnaire completion rate, quality of data collected and comparison of participation rate boosting strategies. Results The overall participation rate was 18.6% among all invitees and 23.1% among individuals aged 18-69. A second reminder letter yielded an additional 9.7% participation rate in those who did not respond to the first invitation. Recontacting participants via an online healthcare portal yielded lower participation than recontacting via physical letter. The completion rate of the questionnaire and cognitive tests was high (92% and 85%, respectively), and measurements were overall reliable among participants. For example, the correlation (r) between self-reported body mass index and that collected by the biobanks was 0.92. Conclusion In summary, this pilot suggests that recontacting FinnGen participants with the goal to collect a wide range of cognitive, behavioural and lifestyle information without additional engagement results in a low participation rate, but with reliable data. We suggest that such information be collected at enrolment, if possible, rather than via post hoc recontacting.
  • Koromani, Fjorda; Alonso, Nerea; Alves, Ines; Brandi, Maria Luisa; Foessl, Ines; Formosa, Melissa M.; Morgenstern, Milana Frenkel; Karasik, David; Kolev, Mikhail; Makitie, Outi; Ntzani, Evangelia; Obermayer-Pietsch, Barbara; Ohlsson, Claes; Rauner, Martina; Soe, Kent; Soldatovic, Ivan; Teti, Anna; Valjevac, Amina; Rivadeneira, Fernando (2021)
    Musculoskeletal research has been enriched in the past ten years with a great wealth of new discoveries arising from genome wide association studies (GWAS). In addition to the novel factors identified by GWAS, the advent of whole-genome and whole-exome sequencing efforts in family based studies has also identified new genes and pathways. However, the function and the mechanisms by which such genes influence clinical traits remain largely unknown. There is imperative need to bring multidisciplinary expertise together that will allow translating these genomic discoveries into useful clinical applications with the potential of improving patient care. Therefore "GEnomics of MusculoSkeletal traits TranslatiOnal NEtwork" (GEMSTONE) aims to set the ground for the: 1) functional characterization of discovered genes and pathways; 2) understanding of the correspondence between molecular and clinical assessments; and 3) implementation of novel methodological approaches. This research network is funded by The European Cooperation in Science and Technology (COST). GEMSTONE includes six working groups (WG), each with specific objectives: WG1-Study populations and expertise groups: creating, maintaining and updating an inventory of experts and resources (studies and datasets) participating in the network, helping to assemble focus groups defined by phenotype, functional and methodological expertise. WG2-Phenotyping: describe ways to decompose the phenotypes of the different functional studies into meaningful components that will aid the interpretation of identified biological pathways. WG3 Monogenic conditions - human KO models: makes an inventory of genes underlying musculoskeletal monogenic conditions that aids the assignment of genes to GWAS signals and prioritizing GWAS genes as candidates responsible for monogenic presentations, through biological plausibility. WG4 Functional investigations: creating a roadmap of genes and pathways to be prioritized for functional assessment in cell and organism models of the musculoskeletal system. WG5 Bioinformatics seeks the integration of the knowledge derived from the distinct efforts, with particular emphasis on systems biology and artificial intelligence applications. Finally, WG6 Translational outreach: makes a synopsis of the knowledge derived from the distinct efforts, allowing to prioritize factors within biological pathways, use refined disease trait definitions and/or improve study design of future investigations in a potential therapeutic context (e.g. clinical trials) for musculoskeletal diseases.
  • Baranizadeh, Elham; Arola, Antti; Hamed, Amar; Nieminen, Tuomo; Mikkonen, Santtu; Virtanen, Annele; Kulmala, Markku; Lehtinen, Kari; Laaksonen, Ari (2014)
  • Hernández-Ramos, José; Pernaa, Johannes; Cáceres-Jensen, Lizethly; Rodríguez-Becerra, Jorge (2021)
    Currently, a growing number of learning institutions at all educational levels are including problem-based learning (PBL) in their curricula. PBL scenarios often utilise technology and socio-scientific Issues (SSI), which enables the simultaneous learning of content and creative thinking and working skills needed in generating new knowledge for the future. In this sense, using SSI and technological tools in PBL learning environments can be viewed as a starting point for acquiring and integrating new knowledge. However, there is no comprehensive knowledge regarding the possibilities of this approach. The objective of this systematic review is to produce this knowledge via the PRISMA method. The strategy is used to explore the effects of the described approach through implementations conducted at secondary and undergraduate levels. The data consisted of 33 research articles that were categorised via qualitative content analysis. According to the results, PBL scenarios exploit mainly local SSIs that link scientific knowledge with a meaningful context for students. Technology is principally used in offering technical support for teaching tasks. Lastly, these results are discussed from the technological pedagogical science knowledge (TPASK) framework perspective, which proposes guidelines for achieving the Sustainable Development Goals (SDG).
  • 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: 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.