Browsing by Subject "HISTORY"

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  • Zoonomia Consortium; Genereux, Diane P.; Serres, Aitor; Armstrong, Joel; Kivioja, Teemu; Taipale, Jussi; Karlsson, Elinor K. (2020)
    A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
  • Cockell, Charles S.; Harrison, Jesse P.; Stevens, Adam H.; Payler, Samuel J.; Hughes, Scott S.; Nawotniak, Shannon E. Kobs; Brady, Allyson L.; Elphic, R. C.; Haberle, Christopher W.; Sehlke, Alexander; Beaton, Kara H.; Abercromby, Andrew F. J.; Schwendner, Petra; Wadsworth, Jennifer; Landenmark, Hanna; Cane, Rosie; Dickinson, Andrew W.; Nicholson, Natasha; Perera, Liam; Lim, Darlene S. S. (2019)
    A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.
  • Bodea, Corneliu A.; Neale, Benjamin M.; Ripke, Stephan; Daly, Mark J.; Devlin, Bernie; Roeder, Kathryn; Int IBD Genetics Consortium; Palotie, A. (2016)
    One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.
  • Japan Scoliosis Clinical Res Grp; Texas Scottish Rite Hosp Children (2018)
    Adolescent idiopathic scoliosis (AIS) is a common spinal deformity with the prevalence of approximately 3%. We previously conducted a genome-wide association study (GWAS) using a Japanese cohort and identified a novel locus on chromosome 9p22.2. However, a replication study using multi-population cohorts has not been conducted. To confirm the association of 9p22.2 locus with AIS in multi-ethnic populations, we conducted international meta-analysis using eight cohorts. In total, we analyzed 8,756 cases and 27,822 controls. The analysis showed a convincing evidence of association between rs3904778 and AIS. Seven out of eight cohorts had significant P value, and remaining one cohort also had the same trend as the seven. The combined P was 3.28 x 10(-18) (odds ratio = 1.19, 95% confidence interval = 1.14-1.24). In silico analyses suggested that BNC2 is the AIS susceptibility gene in this locus.
  • Young, Andrew Donovan; Lemmon, Alan R.; Skevington, Jeffrey H.; Mengual, Ximo; Ståhls, Gunilla; Reemer, Menno; Jordaens, Kurt; Kelso, Scott; Lemmon, Emily Moriarty; Hauser, Martin; De Meyer, Marc; Misof, Bernhard; Wiegmann, Brian M. (2016)
    Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
  • Lamnidis, Thiseas C.; Majander, Kerttu; Jeong, Choongwon; Salmela, Elina; Wessman, Anna; Moiseyev, Vyacheslav; Khartanovich, Valery; Balanovsky, Oleg; Ongyerth, Matthias; Weihmann, Antje; Sajantila, Antti; Kelso, Janet; Pääbo, Svante; Onkamo, Päivi; Haak, Wolfgang; Krause, Johannes; Schiffels, Stephan (2018)
    European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.
  • Nagatsu, Michiru (T & T Clark, 2019)
    Advances in Experimental Philosophy
    In this chapter I outline how experimental philosophy can be fruitfully applied to economics as a science, and contribute empirically to debates concerning conceptual and methodological problems in economics. I discuss differences (i) between folk and economic concepts of choice, (ii) between behavioral, psychological and constructive concepts of preferences that figure in methodological debates in economics and psychology. I also discuss how X-phi can shed methodological light on the recent debates on nudges among economists.
  • Momigliano, Paolo; Florin, Ann-Britt; Merilä, Juha (2021)
    Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (N-e) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) and 16 secondary contact (SC) scenarios, modeling changes in N-e as well as the effects of linked selection and barrier loci. Failure to account for changes in N-e resulted in selecting SC models with long periods of strict isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for N-e changes suggest recent (
  • Ojala, Antti; Saarnisto, Matti; Jungner, Högne; Snowball, Ian; Muscheler, Raimund (2019)
    We present here radiocarbon dating results from two boreal lakes in Finland, which are permanently (meromictic) or seasonally stratified and contain continuous sequences of annually laminated sediments that started to form in the early Holocene. The radiocarbon dating results of different organic components were compared with the varve-based sediment chronologies. The deviation between the Lake Valkiajarvi varve chronology (8400 varve years 2-3% error estimate) and 33 C-14 dates taken from insoluble and soluble organic phases vary inconsistently throughout the Holocene. In extreme cases mean calibrated radiocarbon dates with 95.4% confidence levels (2 sigma) are -2350 and +2040 years offset when compared with the varve chronology. On average, the radiocarbon dates are offset by ca. +550 years. The deviation between the Lake Nautajarvi varve chronology (9898 varve years +/- 1% error estimate) and 26 C-14 dates analyzed with conventional and AMS methods indicates that radiocarbon dates are systematically older by 500-1300 years (about 900 years on average). This significant offset mean that radiocarbon dates obtained from organic bulk sediment of meromictic and seasonally hypoxic lakes must be cautiously interpreted because of the reservoir effect and carbon cycling at the sediment-water interface. Direct evidence was obtained from the dating of soluble fraction and insoluble organic matter from near bottom water in the monimolimnion of Lake Valkiajarvi, which yielded C-14 ages of 560 +/- 80 BP and 2070 +/- 140 BP, respectively. Our study reinforces previous results that age-depth models based on bulk sediment radiocarbon dates obtained on sediments of stratified lakes are of limited value for accurate dating of changes in land use and especially the commence of agriculture.
  • Zheng, GQ; Sundquist, K; Sundquist, J; Forsti, A; Hemminki, O; Hemminki, K (2021)
    Background Previous population-based studies on second primary cancers (SPCs) in urothelial cancers have focused on known risk factors in bladder cancer patients without data on other urothelial sites of the renal pelvis or ureter. Aims To estimate sex-specific risks for any SPCs after urothelial cancers, and in reverse order, for urothelial cancers as SPCs after any cancer. Such two-way analysis may help interpret the results. Methods We employed standardized incidence ratios (SIRs) to estimate bidirectional relative risks of subsequent cancer associated with urothelial cancers. Patient data were obtained from the Swedish Cancer Registry from years 1990 through 2015. Results We identified 46 234 urinary bladder cancers (75% male), 940 ureteral cancers (60% male), and 2410 renal pelvic cancers (57% male). After male bladder cancer, SIRs significantly increased for 9 SPCs, most for ureteral (SIR 41.9) and renal pelvic (17.2) cancers. In the reversed order (bladder cancer as SPC), 10 individual FPCs were associated with an increased risk; highest associations were noted after renal pelvic (21.0) and ureteral (20.9) cancers. After female bladder cancer, SIRs of four SPCs were significantly increased, most for ureteral (87.8) and pelvic (35.7) cancers. Female bladder, ureteral, and pelvic cancers associated are with endometrial cancer. Conclusions The risks of recurrent urothelial cancers were very high, and, at most sites, female risks were twice over the male risks. Risks persisted often to follow-up periods of >5 years, motivating an extended patient follow-up. Lynch syndrome-related cancers were associated with particularly female urothelial cancers, calling for clinical vigilance.
  • Yang, Xin; Leslie, Goska; Doroszuk, Alicja; Aittomäki, Kristiina; Blomqvist, Carl; Heikkinen, Tuomas; Nevanlinna, Heli; Tischkowitz, Marc (2020)
    PURPOSE To estimate age-specific relative and absolute cancer risks of breast cancer and to estimate risks of ovarian, pancreatic, male breast, prostate, and colorectal cancers associated with germline PALB2 pathogenic variants (PVs) because these risks have not been extensively characterized. METHODS We analyzed data from 524 families with PALB2 PVs from 21 countries. Complex segregation analysis was used to estimate relative risks (RRs; relative to country-specific population incidences) and absolute risks of cancers. The models allowed for residual familial aggregation of breast and ovarian cancer and were adjusted for the family-specific ascertainment schemes. RESULTS We found associations between PALB2 PVs and risk of female breast cancer (RR, 7.18; 95% CI, 5.82 to 8.85; P = 6.5 x 10(-76)), ovarian cancer (RR, 2.91; 95% CI, 1.40 to 6.04; P = 4.1 x 10(-3)), pancreatic cancer (RR, 2.37; 95% CI, 1.24 to 4.50; P = 8.7 x 10(-3)), and male breast cancer (RR, 7.34; 95% CI, 1.28 to 42.18; P = 2.6 x 10(-2)). There was no evidence for increased risks of prostate or colorectal cancer. The breast cancer RRs declined with age (P for trend = 2.0 x 10(-3)). After adjusting for family ascertainment, breast cancer risk estimates on the basis of multiple case families were similar to the estimates from families ascertained through population-based studies (P for difference = .41). On the basis of the combined data, the estimated risks to age 80 years were 53% (95% CI, 44% to 63%) for female breast cancer, 5% (95% CI, 2% to 10%) for ovarian cancer, 2%-3% (95% CI females, 1% to 4%; 95% CI males, 2% to 5%) for pancreatic cancer, and 1% (95% CI, 0.2% to 5%) for male breast cancer. CONCLUSION These results confirm PALB2 as a major breast cancer susceptibility gene and establish substantial associations between germline PALB2 PVs and ovarian, pancreatic, and male breast cancers. These findings will facilitate incorporation of PALB2 into risk prediction models and optimize the clinical cancer risk management of PALB2 PV carriers. (C) 2019 by American Society of Clinical Oncology
  • Schafstall, Nick; Whitehouse, Nicki; Kuosmanen, Niina; Svobodova-Svitavska, Helena; Saulnier, Melanie; Chiverrell, Richard C.; Fleischer, Peter; Kunes, Petr; Clear, Jennifer L. (2020)
    Montane biomes are niche environments high in biodiversity with a variety of habitats. Often isolated, these non-continuous remnant ecosystems inhabit narrow ecological zones putting them under threat from changing climatic conditions and anthropogenic pressure. Twelve sediment cores were retrieved from a peat bog in Tatra National Park, Slovakia, and correlated to each other by wiggle-matching geochemical signals derived from micro-XRF scanning, to make a reconstruction of past conditions. A fossil beetle (Coleoptera) record, covering the last 1000 years at 50- to 100-year resolution, gives a new insight into changing flora and fauna in this region. Our findings reveal a diverse beetle community with varied ecological groups inhabiting a range of forest, meadow and synanthropic habitats. Changes in the beetle community were related to changes in the landscape, driven by anthropogenic activities. The first clear evidence for human activity in the area occurs c. 1250 CE and coincides with the arrival of beetle species living on the dung of domesticated animals (e.g. Aphodius spp.). From 1500 CE, human (re)settlement, and activities such as pasturing and charcoal burning, appear to have had a pronounced effect on the beetle community. Local beetle diversity declined steadily towards the present day, likely due to an infilling of the forest hollow leading to a decrease in moisture level. We conclude that beetle communities are directly affected by anthropogenic intensity and land-use change. When aiming to preserve or restore natural forest conditions, recording their past changes in diversity can help guide conservation and restoration. In doing so, it is important to look back beyond the time of significant human impact, and for this, information contained in paleoecological records is irreplaceable.
  • Finnish Pediat Diabet Register; Turtinen, Maaret; Härkönen, Taina; Parkkola, Anna; Ilonen, Jorma; Knip, Mikael (2019)
    Aims/hypothesis In previous studies, the risk of developing familial type 1 diabetes has been reported to be more than two times higher in the offspring of affected fathers than in those of affected mothers. We tested the hypothesis that index children with an affected father may have a more aggressive disease process at diagnosis than those with other affected first-degree relatives. Methods A cross-sectional, observational study was performed using the Finnish Pediatric Diabetes Register. Clinical and metabolic characteristics, beta cell autoantibodies and HLA class II genetics were analysed from index children in Finland diagnosed before the age of 15 years between January 2003 and December 2016. Information on the presence of type 1 diabetes in first-degree relatives was collected at diagnosis using a structured questionnaire. Results Out of 4993 newly diagnosed index children, 519 (10.4%) had familial type 1 diabetes. More than 5% (n = 253, 5.1%) had an affected father, 2.8% (n = 141) had an affected mother, 1.9% (n = 95) had an affected sibling and 0.6% (n = 30) had two or more affected family members. All clinical and metabolic variables were markedly poorer in children with sporadic vs familial diabetes. The index children with an affected father or mother were younger than those with an affected sibling (median age 7.59 vs 6.74 vs 10.73 years, respectively; p <0.001). After age- and sex-adjusted analyses, index children with an affected father presented more often with ketoacidosis (9.7% vs 3.6%; p = 0.033) and had greater weight loss before diagnosis (3.2% vs 0%; p = 0.006) than those with an affected mother. Children with familial disease tested negative for all autoantibodies more often (3.5% vs 2.1%; p = 0.041) and had insulin autoantibodies more frequently (49.8% vs 42.2%; p = 0.004) than those with sporadic disease. Both major HLA risk haplotypes (DR3-DQ2 and DR4-DQ8) were more often lacking among children with sporadic vs familial disease (15.9% vs 11.2%; p = 0.006). The DR4-DQ8 haplotype was more frequent in the familial vs the sporadic group (75.7% vs 68.5%; p = 0.001) and especially among children with an affected father when compared with children with sporadic disease (77.5% vs 68.5%; p <0.05). When comparing index children with affected parents diagnosed before or after the birth of the index child, a clear male preponderance was seen among the affected parents diagnosed before the birth of the index child (fathers 66.2% vs mothers 33.8%; p = 0.006), whereas the proportion of fathers and mothers was similar if type 1 diabetes was diagnosed after the birth of the index child. Conclusions/interpretation The more severe metabolic derangement at diagnosis in children with sporadic type 1 diabetes compared with those with familial type 1 diabetes was confirmed. The higher frequency of diabetic ketoacidosis and increased weight loss at diagnosis in index children with an affected father compared with an affected mother support the hypothesis that paternal type 1 diabetes is associated with more severe disease in the offspring than maternal diabetes. The sex difference seen between affected parents diagnosed before and after the birth of the index child supports the hypothesis that maternal insulin treatment protects against type 1 diabetes.
  • Mehlig, Kirsten; Bogl, Leonie H.; Hunsberger, Monica; Ahrens, Wolfgang; De Henauw, Stefaan; Iguacel, Isabel; Jilani, Hannah; Molnar, Denes; Pala, Valeria; Russo, Paola; Tornaritis, Michael; Veidebaum, Toomas; Kaprio, Jaakko; Lissner, Lauren (2018)
    Objective: The present study investigated the association between sugar and fat intake in childhood in relation to alcohol use in adolescence. We hypothesized that early exposure to diets high in fat and sugar may affect ingestive behaviours later in life, including alcohol use. Design/Setting/Subjects: Children from the European IDEFICS/I.Family cohort study were examined at ages 5-9 years and followed up at ages 11-16 years. FFQ were completed by parents on behalf of children, and later by adolescents themselves. Complete data were available in 2263 participants. Children's propensities to consume foods high in fat and sugar were calculated and dichotomized at median values. Adolescents' use of alcohol was classified as at least weekly v. less frequent use. Log-binomial regression linked sugar and fat consumption in childhood to risk of alcohol use in adolescence, adjusted for relevant covariates. Results: Five per cent of adolescents reported weekly alcohol consumption. Children with high propensity to consume sugar and fat were at greater risk of later alcohol use, compared with children with low fat and low sugar propensity (relative risk = 2.46; 95% CI 1.47, 4.12), independent of age, sex and survey country. The association was not explained by parental income and education, strict parenting style or child's health-related quality of life and was only partly mediated by sustained consumption of sugar and fat into adolescence. Conclusions: Frequent consumption of foods high in fat and sugar in childhood predicted regular use of alcohol in adolescence.
  • Ovaskainen, Otso; Meyke, Evgeniy; Lo, Coong; Tikhonov, Gleb; Delgado, Maria del Mar; Roslin, Tomas; Gurarie, Eliezer; Abadonova, Marina; Abduraimov, Ozodbek; Adrianova, Olga; Akimova, Tatiana; Akkiev, Muzhigit; Ananin, Aleksandr; Andreeva, Elena; Andriychuk, Natalia; Antipin, Maxim; Arzamascev, Konstantin; Babina, Svetlana; Babushkin, Miroslav; Bakin, Oleg; Barabancova, Anna; Basilskaja, Inna; Belova, Nina; Belyaeva, Natalia; Bespalova, Tatjana; Bisikalova, Evgeniya; Bobretsov, Anatoly; Bobrov, Vladimir; Bobrovskyi, Vadim; Bochkareva, Elena; Bogdanov, Gennady; Bolshakov, Vladimir; Bondarchuk, Svetlana; Bukharova, Evgeniya; Butunina, Alena; Buyvolov, Yuri; Buyvolova, Anna; Bykov, Yuri; Chakhireva, Elena; Chashchina, Olga; Cherenkova, Nadezhda; Chistjakov, Sergej; Chuhontseva, Svetlana; Davydov, Evgeniy A.; Demchenko, Viktor; Diadicheva, Elena; Dobrolyubov, Aleksandr; Dostoyevskaya, Ludmila; Drovnina, Svetlana; Drozdova, Zoya; Dubanaev, Akynaly; Dubrovsky, Yuriy; Elsukov, Sergey; Epova, Lidia; Ermakova, Olga; Ermakova, Olga; Esengeldenova, Aleksandra; Evstigneev, Oleg; Fedchenko, Irina; Fedotova, Violetta; Filatova, Tatiana; Gashev, Sergey; Gavrilov, Anatoliy; Gaydysh, Irina; Golovcov, Dmitrij; Goncharova, Nadezhda; Gorbunova, Elena; Gordeeva, Tatyana; Grishchenko, Vitaly; Gromyko, Ludmila; Hohryakov, Vladimir; Hritankov, Alexander; Ignatenko, Elena; Igosheva, Svetlana; Ivanova, Uliya; Ivanova, Natalya; Kalinkin, Yury; Kaygorodova, Evgeniya; Kazansky, Fedor; Kiseleva, Darya; Knorre, Anastasia; Kolpashikov, Leonid; Korobov, Evgenii; Korolyova, Helen; Korotkikh, Natalia; Kosenkov, Gennadiy; Kossenko, Sergey; Kotlugalyamova, Elvira; Kozlovsky, Evgeny; Kozsheechkin, Vladimir; Kozurak, Alla; Kozyr, Irina; Krasnopevtseva, Aleksandra; Kruglikov, Sergey; Kuberskaya, Olga; Kudryavtsev, Aleksey; Kulebyakina, Elena; Kulsha, Yuliia; Kupriyanova, Margarita; Kurbanbagamaev, Murad; Kutenkov, Anatoliy; Kutenkova, Nadezhda; Kuyantseva, Nadezhda; Kuznetsov, Andrey; Larin, Evgeniy; Lebedev, Pavel; Litvinov, Kirill; Luzhkova, Natalia; Mahmudov, Azizbek; Makovkina, Lidiya; Mamontov, Viktor; Mayorova, Svetlana; Megalinskaja, Irina; Meydus, Artur; Minin, Aleksandr; Mitrofanov, Oleg; Motruk, Mykhailo; Myslenkov, Aleksandr; Nasonova, Nina; Nemtseva, Natalia; Nesterova, Irina; Nezdoliy, Tamara; Niroda, Tatyana; Novikova, Tatiana; Panicheva, Darya; Pavlov, Alexey; Pavlova, Klara; Petrenko, Polina; Podolski, Sergei; Polikarpova, Natalja; Polyanskaya, Tatiana; Pospelov, Igor; Pospelova, Elena; Prokhorov, Ilya; Prokosheva, Irina; Puchnina, Lyudmila; Putrashyk, Ivan; Raiskaya, Julia; Rozhkov, Yuri; Rozhkova, Olga; Rudenko, Marina; Rybnikova, Irina; Rykova, Svetlana; Sahnevich, Miroslava; Samoylov, Alexander; Sanko, Valeri; Sapelnikova, Inna; Sazonov, Sergei; Selyunina, Zoya; Shalaeva, Ksenia; Shashkov, Maksim; Shcherbakov, Anatoliy; Shevchyk, Vasyl; Shubin, Sergej; Shujskaja, Elena; Sibgatullin, Rustam; Sikkila, Natalia; Sitnikova, Elena; Sivkov, Andrei; Skok, Nataliya; Skorokhodova, Svetlana; Smirnova, Elena; Sokolova, Galina; Sopin, Vladimir; Spasovski, Yurii; Stepanov, Sergei; Stratiy, Vitaliy; Strekalovskaya, Violetta; Sukhov, Alexander; Suleymanova, Guzalya; Sultangareeva, Lilija; Teleganova, Viktorija; Teplov, Viktor; Teplova, Valentina; Tertitsa, Tatiana; Timoshkin, Vladislav; Tirski, Dmitry; Tolmachev, Andrej; Tomilin, Aleksey; Tselishcheva, Ludmila; Turgunov, Mirabdulla; Tyukh, Yurij; Vladimir, Van; Vargot, Elena; Vasin, Aleksander; Vasina, Aleksandra; Vekliuk, Anatoliy; Vetchinnikova, Lidia; Vinogradov, Vladislav; Volodchenkov, Nikolay; Voloshina, Inna; Xoliqov, Tura; Yablonovska-Grishchenko, Eugenia; Yakovlev, Vladimir; Yakovleva, Marina; Yantser, Oksana; Yarema, Yurij; Zahvatov, Andrey; Zakharov, Valery; Zelenetskiy, Nicolay; Zheltukhin, Anatolii; Zubina, Tatyana; Kurhinen, Juri (2020)
    We present an extensive, large-scale, long-term and multitaxon database on phenological and climatic variation, involving 506,186 observation dates acquired in 471 localities in Russian Federation, Ukraine, Uzbekistan, Belarus and Kyrgyzstan. The data cover the period 1890-2018, with 96% of the data being from 1960 onwards. The database is rich in plants, birds and climatic events, but also includes insects, amphibians, reptiles and fungi. The database includes multiple events per species, such as the onset days of leaf unfolding and leaf fall for plants, and the days for first spring and last autumn occurrences for birds. The data were acquired using standardized methods by permanent staff of national parks and nature reserves (87% of the data) and members of a phenological observation network (13% of the data). The database is valuable for exploring how species respond in their phenology to climate change. Large-scale analyses of spatial variation in phenological response can help to better predict the consequences of species and community responses to climate change.
  • Paajanen, Juuso; Laaksonen, Sanna; Ilonen, Ilkka; Vehmas, Tapio; Mäyränpää, Mikko I.; Sutinen, Eva; Kettunen, Eeva; Salo, Jarmo A.; Räsänen, Jari; Wolff, Henrik; Myllärniemi, Marjukka (2020)
    Within a larger national malignant pleural mesothelioma cohort, we identified 43 patients with unusually long survival times. This study aimed to evaluate the diagnostic accuracy in this subgroup, and the diagnosis was confirmed to be correct in most cases. In addition, we searched for clinical factors related to the prolonged survival time. Introduction: Malignant pleural mesothelioma (MPM) is a fatal malignancy strongly associated with previous asbestos exposure. Overall survival remains dismal, partly owing to poor response to available treatment. The aims of this study were to evaluate diagnostic accuracy in a group of patients with MPM with an unusually long survival time and to assess the factors related to this prolonged survival. Materials and Methods: Forty-three patients with overall survival exceeding 5 years were accepted to the long-term survivor (LTS) group, and these patients were compared with 84 patients with epithelial MPM. Data were collected from various national registries and electronic medical records. In addition, all available histopathologic diagnostic samples and computed tomography studies were re-evaluated by experienced specialists. Results: Our study showed a good diagnostic accuracy, with only 1 (0.5%) patient having an incorrect MPM diagnosis. Two (0.9%) localized malignant mesotheliomas and 2 (0.9%) well-differentiated papillary mesotheliomas were also found. LTS patients were younger, more frequently female, had a better performance status at time of diagnosis, and had less evidence of prior asbestos exposure. In multivariate analysis, we showed tumor size, Eastern Cooperative Oncology Group performance status, and first-line treatment (both surgery and chemotherapy) to be associated with survival time. Conclusion: We confirmed the diagnosis of MPM in an overwhelming majority of patients in the LTS group. An epithelial subtype of MPM behaving clinically more indolently seems to exist, but further tumor and genetic characterization is needed. The prolonged survival time is most likely explained by a combination of tumor-, patient-, and treatment-related factors. (C) 2020 Elsevier Inc. All rights reserved.
  • Žliobaite, Indrė (2019)
    Fossils are the remains organisms from earlier geological periods preserved in sedimentary rock. The global fossil record documents and characterizes the evidence about organisms that existed at different times and places during the Earth's history. One of the major directions in computational analysis of such data is to reconstruct environmental conditions and track climate changes over millions of years. Distribution of fossil animals in space and time make informative features for such modeling, yet concept drift presents one of the main computational challenges. As species continuously go extinct and new species originate, animal communities today are different from the communities of the past, and the communities at different times in the past are different from each other. The fossil record is continuously increasing as new fossils and localities are being discovered, but it is not possible to observe or measure their environmental contexts directly, because the time is gone. Labeled data linking organisms to climate is available only for the present day, where climatic conditions can be measured. The approach is to train models on the present day and use them to predict climatic conditions over the past. But since species representation is continuously changing, transfer learning approaches are needed to make models applicable and climate estimates to be comparable across geological times. Here we discuss predictive modeling settings for such paleoclimate reconstruction from the fossil record. We compare and experimentally analyze three baseline approaches for predictive paleoclimate reconstruction: (1) averaging over habitats of species, (2) using presence-absence of species as features, and (3) using functional characteristics of species communities as features. Our experiments on the present day African data and a case study on the fossil data from the Turkana Basin over the last 7 million of years suggest that presence-absence approaches are the most accurate over short time horizons, while species community approaches, also known as ecometrics, are the most informative over longer time horizons when, due to ongoing evolution, taxonomic relations between the present day and fossil species become more and more uncertain.
  • Frank, Christoph; Sundquist, Jan; Yu, Hongyao; Hemminki, Akseli; Hemminki, Kari (2017)
    Relatives of cancer patients are at an increased risk of the same (concordant) cancer but whether they are at a risk for different (discordant) cancers is largely unknown - beyond well characterized hereditary cancer syndromes - but would be of major scientific and clinical interest. We therefore decided to resolve the issue by analyzing familial risks when family members were diagnosed with any discordant cancers. We compared the population impact of concordant to discordant familial cancer. The Swedish Family-Cancer Database (FCD) was used to calculate familial relative risks (RRs) for family members of cancer patients, for the 27 most common cancers. Population attributable fractions (PAFs) were estimated for concordant and discordant family histories. Discordant cancers in the family were detected as significant risk factors for the majority of cancers, although the corresponding RRs were modest compared to RRs for concordant cancers. Risks increased with the number of affected family members with the highest RRs for pancreatic (2.31), lung (1.69), kidney (1.98), nervous system (1.79) and thyroid cancers (3.28), when 5 or more family members were diagnosed with discordant cancers. For most cancers, the PAF for discordant family history exceeded that for concordant family history. Our findings suggest that there is an unspecific genetic predisposition to cancer with clinical consequences. We consider it unlikely that shared environmental risk factors could essentially contribute to the risks for diverse discordant cancers, which are likely driven by genetic predisposition. The identification of genes that moderately increase the risk for many cancers will be a challenge.
  • Hirvonen, Eveliina; Stepanov, Mikhael; Kilpeläinen, Maritta; Lindqvist, Ari; Laitinen, Tarja (2019)
    Introduction: Smoking has a significant impact on the development and progression of asthma and chronic obstructive pulmonary disease (COPD). Self-reported questionnaires and structured interviews are usually the only way to study patients' smoking history. In this study, we aim to examine the consistency of the responses of asthma and COPD patients to repeated standardised questions on their smoking habits over the period of 10 years. Methods: The study population consisted of 1329 asthma and 959 COPD patients, who enrolled in the study during years 2005-2007. A follow-up questionnaire was mailed to the participants 1, 2, 4, 6, 8, and 10 years after the recruitment. Results: Among the participants who returned three or more questionnaires (N = 1454), 78.5 % of the patients reported unchanged smoking status (never smoker, ex-smoker or current smoker) across the time. In 4.5% of the answers, the reported smoking statuses were considered unreliable/conflicting (first never smoker and, later, smoker or ex-smoker). The remainder of the patients changed their status from current smoker to ex-smoker and vice versa at least once, most likely due to struggling with quitting. COPD patients were more frequently heavy ex- or current smokers compared to the asthma group. The intraclass coefficient correlations between self-reported starting (0.85) and stopping (0.94) years as well as the consumption of cigarettes (0.74) over time showed good reliability among both asthma and COPD patients. Conclusion: Self-reported smoking data among elderly asthma and COPD patients over a 10-year follow-up is reliable. Pack years can be considered a rough estimate for their comprehensive consumption of tobacco products over time. We also observed that the questionnaire we used was not designed for dynamic changes in smoking which are rather common among heavy smokers especially when the follow-up time is several years, as in our study.
  • Luoma, Emilia; Nevalainen, Lauri; Altarriba, Elias; Helle, Inari; Lehikoinen, Annukka (2021)
    Ship hulls create a vector for the transportation of harmful non-indigenous species (NIS) all over the world. To sustainably prevent NIS introductions, the joint consideration of environmental, economic and social aspects in the search of optimal biofouling management strategies is needed. This article presents a multi-perspective soft systems analysis of the biofouling management problem, based on an extensive literature review and expert knowledge collected in the Baltic Sea area during 2018-2020. The resulting conceptual influence diagram (CID) reveals the multidimensionality of the problem by visualizing the causal relations between the key elements and demonstrating the entanglement of social, ecological and technical aspects. Seen as a boundary object, we suggest the CID can support open dialogue and better risk communication among stakeholders by providing an illustrative and directly applicable starting point for the discussions. It also provides a basis for quantitative management optimization in the future.