Browsing by Subject "PATTERNS"

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  • Cannistraci, Carlo Vittorio; Nieminen, Tuomo; Nishi, Masahiro; Khachigian, Levon M.; Viikilä, Juho; Laine, Mika; Cianflone, Domenico; Maseri, Attilio; Yeo, Khung Keong; Bhindi, Ravinay; Ammirati, Enrico (2018)
    Background-ST-elevation acute myocardial infarction (STEMI) represents one of the leading causes of death. The time of STEMI onset has a circadian rhythm with a peak during diurnal hours, and the occurrence of STEMI follows a seasonal pattern with a salient peak of cases in the winter months and a marked reduction of cases in the summer months. Scholars investigated the reason behind the winter peak, suggesting that environmental and climatic factors concur in STEMI pathogenesis, but no studies have investigated whether the circadian rhythm is modified with the seasonal pattern, in particular during the summer reduction in STEMI occurrence. Methods and Results-Here, we provide a multiethnic and multination epidemiological study (from both hemispheres at different latitudes, n= 2270 cases) that investigates whether the circadian variation of STEMI onset is altered in the summer season. The main finding is that the difference between numbers of diurnal (6:00 to 18:00) and nocturnal (18:00 to 6:00) STEMI is markedly decreased in the summer season, and this is a prodrome of a complex mechanism according to which the circadian rhythm of STEMI time onset seems season dependent. Conclusions-The "summer shift" of STEMI to the nocturnal interval is consistent across different populations, and the sunshine duration (a measure related to cloudiness and solar irradiance) underpins this season-dependent circadian perturbation. Vitamin D, which in our results seems correlated with this summer shift, is also primarily regulated by the sunshine duration, and future studies should investigate their joint role in the mechanisms of STEMI etiogenesis.
  • Reichenau, Tim G.; Korres, Wolfgang; Schmidt, Marius; Graf, Alexander; Welp, Gerhard; Meyer, Nele; Stadler, Anja; Brogi, Cosimo; Schneider, Karl (2020)
    The development and validation of hydroecological land-surface models to simulate agricultural areas require extensive data on weather, soil properties, agricultural management, and vegetation states and fluxes. However, these comprehensive data are rarely available since measurement, quality control, documentation, and compilation of the different data types are costly in terms of time and money. Here, we present a comprehensive dataset, which was collected at four agricultural sites within the Rur catchment in western Germany in the framework of the Transregional Collaborative Research Centre 32 (TR32) "Patterns in Soil-Vegetation-Atmosphere Systems: Monitoring, Modeling and Data Assimilation". Vegetation-related data comprise fresh and dry biomass (green and brown, predominantly per organ), plant height, green and brown leaf area index, phenological development state, nitrogen and carbon content (overall > 17 000 entries), and masses of harvest residues and regrowth of vegetation after harvest or before planting of the main crop (> 250 entries). Vegetation data including LAI were collected in frequencies of 1 to 3 weeks in the years 2015 until 2017, mostly during overflights of the Sentinel 1 and Radarsat 2 satellites. In addition, fluxes of carbon, energy, and water (> 180 000 half-hourly records) measured using the eddy covariance technique are included. Three flux time series have simultaneous data from two different heights. Data on agricultural management include sowing and harvest dates as well as information on cultivation, fertilization, and agrochemicals (27 management periods). The dataset also includes gap-filled weather data (> 200 000 hourly records) and soil parameters (particle size distributions, carbon and nitrogen content; > 800 records). These data can also be useful for development and validation of remote-sensing products. The dataset is hosted at the TR32 database (https://www.tr32db.uni-koeln.de/data.php?dataID=1889, last access: 29 September 2020) and has the DOI https://doi.org/10.5880/TR32DB.39 (Reichenau et al., 2020).
  • Kvist, Jouni; Athanasio, Camila Goncalves; Pfrender, Michael E.; Brown, James B.; Colbourne, John K.; Mirbahai, Leda (2020)
    Background Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders. Results In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male Daphnia are dominated with epigenetic modifications that globally promote elevated gene expression, while female Daphnia are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female Daphnia. Furthermore, H3K4me3 modifications are higher in male compared to female Daphnia in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male Daphnia in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes. Conclusions The epigenetic differences between male and female in Daphnia pulex are vast and dominated by changes that promote elevated gene expression in male Daphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.
  • Ovaskainen, Otso; Somervuo, Panu; Finkelshtein, Dmitri (2020)
    Agent-based models are used to study complex phenomena in many fields of science. While simulating agent-based models is often straightforward, predicting their behaviour mathematically has remained a key challenge. Recently developed mathematical methods allow the prediction of the emerging spatial patterns for a general class of agent-based models, whereas the prediction of spatio-temporal pattern has been thus far achieved only for special cases. We present a general and mathematically rigorous methodology that allows deriving the spatio-temporal correlation structure for a general class of individual-based models. To do so, we define an auxiliary model, in which each agent type of the primary model expands to three types, called the original, the past and the new agents. In this way, the auxiliary model keeps track of both the initial and current state of the primary model, and hence the spatio-temporal correlations of the primary model can be derived from the spatial correlations of the auxiliary model. We illustrate the agreement between analytical predictions and agent-based simulations using two example models from theoretical ecology. In particular, we show that the methodology is able to correctly predict the dynamical behaviour of a host-parasite model that shows spatially localized oscillations.
  • Khrunin, Andrey V.; Khokhrin, Denis V.; Filippova, Irina N.; Esko, Tonu; Nelis, Mari; Bebyakova, Natalia A.; Bolotova, Natalia L.; Klovins, Janis; Nikitina-Zake, Liene; Rehnström, Karola Hannele; Ripatti, Samuli; Schreiber, Stefan; Franke, Andre; Macek, Milan; Krulisova, Veronika; Lubinski, Jan; Metspalu, Andres; Limborska, Svetlana A. (2013)
  • Oksanen, Otto; Zliobaite, Indre; Saarinen, Juha; Lawing, A. Michelle; Fortelius, Mikael (2019)
    Aim The links between geo- and biodiversity, postulated by Humboldt, can now be made quantitative. Species are adapted to their environments and interact with their environments by having pertinent functional traits. We aim to improve global ecometric models using functional traits for estimating palaeoclimate and apply models to Pleistocene fauna for palaeoclimate interpretation. Location Global at present day, Pleistocene of Europe for fossil data analysis. Taxa Artiodactyla, Perissodactyla, Proboscidea and Primates. Methods We quantify functional traits of large mammal communities and develop statistical models linking trait distributions to local climate at present day. We apply these models to the fossil record, survey functional traits, and quantitatively estimate climates of the past. This approach to analysing functional relationships between faunal communities and their environments is called ecometrics. Results and main conclusions Here, we present new global ecometric models for estimating mean annual and minimum temperature from dental traits of present day mammalian communities. We also present refined models for predicting net primary productivity. Using dental ecometric models, we produce palaeoclimate estimates for 50 Pleistocene fossil localities in Europe and show that the estimates are consistent with trends derived from other proxies, especially for minimum temperatures, which we hypothesize to be ecologically limiting. Our new temperature models allow us to trace the distribution of freezing and non-freezing ecosystems in the recent past, opening new perspectives on the evolution of cold-adaptive biota as the Pleistocene cooling progressed.
  • Lumby, Casper K.; Zhao, Lei; Breuer, Judith; Illingworth, Christopher J. R. (2020)
    Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection N-e for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an N-e of 2.5 x 10(7) (95% confidence range 1.0 x 10(7) to 9.0 x 10(7)) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.
  • Tudor-Locke, Catrine; Mire, Emily F.; Dentro, Kara N.; Barreira, Tiago V.; Schuna, John M.; Zhao, Pei; Tremblay, Mark S.; Standage, Martyn; Sarmiento, Olga L.; Onywera, Vincent; Olds, Tim; Matsudo, Victor; Maia, Jose; Maher, Carol; Lambert, Estelle V.; Kurpad, Anura; Kuriyan, Rebecca; Hu, Gang; Fogelholm, Mikael; Chaput, Jean-Philippe; Church, Timothy S.; Katzmarzyk, Peter T.; Grp, I. S. C. O. L. E. Res (2015)
    Background: We present a model for reporting accelerometer paradata (process-related data produced from survey administration) collected in the International Study of Childhood Obesity Lifestyle and the Environment (ISCOLE), a multi-national investigation of >7000 children (averaging 10.5 years of age) sampled from 12 different developed and developing countries and five continents. Methods: ISCOLE employed a 24-hr waist worn 7-day protocol using the ActiGraph GT3X+. Checklists, flow charts, and systematic data queries documented accelerometer paradata from enrollment to data collection and treatment. Paradata included counts of consented and eligible participants, accelerometers distributed for initial and additional monitoring (site specific decisions in the face of initial monitoring failure), inadequate data (e.g., lost/malfunction, insufficient wear time), and averages for waking wear time, valid days of data, participants with valid data (>= 4 valid days of data, including 1 weekend day), and minutes with implausibly high values (>= 20,000 activity counts/min). Results: Of 7806 consented participants, 7372 were deemed eligible to participate, 7314 accelerometers were distributed for initial monitoring and another 106 for additional monitoring. 414 accelerometer data files were inadequate (primarily due to insufficient wear time). Only 29 accelerometers were lost during the implementation of ISCOLE worldwide. The final locked data file consisted of 6553 participant files (90.0% relative to number of participants who completed monitoring) with valid waking wear time, averaging 6.5 valid days and 888.4 minutes/day (14.8 hours). We documented 4762 minutes with implausibly high activity count values from 695 unique participants (9.4% of eligible participants and Conclusions: Detailed accelerometer paradata is useful for standardizing communication, facilitating study management, improving the representative qualities of surveys, tracking study endpoint attainment, comparing studies, and ultimately anticipating and controlling costs.
  • Jääskeläinen, Iiro H.; Hagberg, Lars; Schyman, Tommy; Järvinen, Asko (2018)
    Background: Management practices of complicated skin and skin structure infections (cSSSI) were compared between two areas with similar healthcare structure and low prevalence of antimicrobial resistance.Methods: The high affinity to public health-care in the Nordic countries enabled population-based approach used in this retrospective study. The study population (n=460) consisted of all adult residents from Helsinki (Finland) and Gothenburg (Sweden) treated in hospital due to cSSSI during 2008-2011.Results: The majority of patients in Helsinki (57%) visited more than one ward during their hospital stay while in Gothenburg the majority of patients (85%) were treated in one ward only. Background and disease characteristics were largely similar in both cities but patients in Helsinki were younger [mean(SD) 59(18) versus 63(19) years, p=.0117], and greater proportions had diabetes (50% versus 32%, p
  • Chichorro, Filipe; Juslén, Aino; Cardoso, Pedro (2019)
    Biodiversity is shrinking rapidly, and despite our efforts only a small part of it has been assessed for extinction risk. Identifying the traits that make species vulnerable might help us to predict the status for those less known. We gathered information on the relationships between traits and extinction risk from 173 publications, across all taxa, spatial scales and biogeographical regions, in what we think it is the most comprehensive compilation to date. We aimed to identify (1) taxonomical and spatial biases, and (2) statistically robust and generalizable predictors of extinction risk through the use of meta-analyses. Vertebrates and the Palaearctic are the most studied taxon and region because of higher accumulation of data in these groups. Among the many traits that have been suggested to be predictors, only three had enough data for meta-analyses. Two of them are potentially useful in assessing risk for the lesser-known species: regardless of the taxon, species with small range and narrow habitat breadth are more vulnerable to extinction. Contrastingly, body size (the most studied trait) did not present a consistently positive or negative response. We hypothesize that the relationship between body size and extinction risk is shaped by different aspects, namely the phenomena represented by body size depending on the taxonomic group. To increase our understanding of the drivers of extinction, further studies should focus on understudied groups such as invertebrates and fungi and regions such as the tropics and expand the number of traits in comparative analyses that should avoid current biases.
  • Genome Aggregation Database Prod T; Genome Aggregation Database Consor; Collins, Ryan L.; Brand, Harrison; Karczewski, Konrad J.; Talkowski, Michael E.; Färkkilä, Martti; Groop, Leif; Holi, Matti M.; Kaprio, Jaakko; Palotie, Aarno; Ripatti, Samuli; Tuomi, Tiinamaija; Wessman, Maija; Kallela, Mikko (2020)
    Structural variants (SVs) rearrange large segments of DNA(1) and can have profound consequences in evolution and human disease(2,3). As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD)(4) have become integral in the interpretation of single-nucleotide variants (SNVs)(5). However, there are no reference maps of SVs from high-coverage genome sequencing comparable to those for SNVs. Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54% non-European) in gnomAD. We discovered a rich and complex landscape of 433,371 SVs, from which we estimate that SVs are responsible for 25-29% of all rare protein-truncating events per genome. We found strong correlations between natural selection against damaging SNVs and rare SVs that disrupt or duplicate protein-coding sequence, which suggests that genes that are highly intolerant to loss-of-function are also sensitive to increased dosage(6). We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than all noncoding effects. Finally, we identified very large (over one megabase), rare SVs in 3.9% of samples, and estimate that 0.13% of individuals may carry an SV that meets the existing criteria for clinically important incidental findings(7). This SV resource is freely distributed via the gnomAD browser(8) and will have broad utility in population genetics, disease-association studies, and diagnostic screening.
  • Sievänen, Risto; Raumonen, Pasi; Perttunen, Jari; Nikinmaa, Eero Heikki; Kaitaniemi, Pekka Juhani (2018)
    Background and Aims: Functional-structural plant models (FSPMs) allow simulation of tree crown development as the sum of modular (e.g. shoot-level) responses triggered by the local environmental conditions. The actual process of space filling by the crowns can be studied. Although the FSPM simulations are at organ scale, the data for their validation have usually been at more aggregated levels (whole-crown or whole-tree). Measurements made by terrestrial laser scanning (TLS) that have been segmented into elementary units (internodes) offer a phenotyping tool to validate the FSPM predictions at levels comparable with their detail. We demonstrate the testing of different formulations of crown development of Scots pine trees in the LIGNUM model using segmented TLS data. Methods: We made TLS measurements from four sample trees growing in a forest on a relatively poor soil from sapling size to mature stage. The TLS data were segmented into intenodes. The segmentation also produced information on whether needles were present in the internode. We applied different formulations of crown development (flushing of buds and length of growth of new internodes) in LIGNUM. We optimized the parameter values of each formulation using genetic algorithms to observe the best fit of LIGNUM simulations to the measured trees. The fitness function in the estimation combined both tree-level characteristics (e.g. tree height and crown length) and measures of crown shape (e.g. spatial distribution of needle area). Key Results: Comparison of different formulations against the data indicates that the Extended Borchert- Honda model for shoot elongation works best within LIGNUM. Control of growth by local density in the crown was important for all shoot elongation formulations. Modifying the number of lateral buds as a function of local density in the crown was the best way to accomplish density control. Conclusions: It was demonstrated how segmented TLS data can be used in the context of a shoot-based model to select model components.
  • Piirtola, Maarit; Kaprio, Jaakko; Ropponen, Annina (2014)
  • Stegmann, Roelant A.; Zliobaite, Indre; Tolvanen, Tuukka; Hollmén, Jaakko; Read, Jesse (2018)
    Personal mobility data can nowadays be easily collected by personal mobile phones and used for analytical modeling. To assist in such an analysis, a variety of computational approaches have been developed. The goal is to extract mobility patterns in order to provide traveling assistance, information, recommendations or on-demand services. While various computational techniques are being developed, research literature on destination and route prediction lacks consistency in evaluation methods for such approaches. This study presents a review and categorization of evaluation criteria and terminology used in assessing the performance of such methods. The review is complemented by experimental analysis of selected evaluation criteria, to highlight the nuances existing between the evaluation measures. The experimental study uses previously unpublished mobility data of 15 users collected over a period of 6 months in Helsinki metropolitan area in Finland. The article is primarily intended for researchers developing approaches for personalized mobility analysis, as well as a guideline for practitioners to select criteria when assessing and selecting between computational approaches. Our main recommendation is to consider user-specific accuracy measures in addition to averaged aggregates, as well as to take into consideration that for many users accuracy does not saturate fast and the performance keeps evolving over time. Therefore, we recommend using time-weighted measures. (c) 2017 Wiley Periodicals, Inc.
  • Vanhatalo, Jarno; Hartmann, Marcelo; Veneranta, Lari (2020)
    Species distribution models (SDM) are a key tool in ecology, conservation and management of natural resources. Two key components of the state-of-the-art SDMs are the description for species distribution response along environmental covariates and the spatial random effect that captures deviations from the distribution patterns explained by environmental covariates. Joint species distribution models (JSDMs) additionally include interspecific correlations which have been shown to improve their descriptive and predictive performance compared to single species models. However, current JSDMs are restricted to hierarchical generalized linear modeling framework. Their limitation is that parametric models have trouble in explaining changes in abundance due, for example, highly non-linear physical tolerance limits which is particularly important when predicting species distribution in new areas or under scenarios of environmental change. On the other hand, semi-parametric response functions have been shown to improve the predictive performance of SDMs in these tasks in single species models. Here, we propose JSDMs where the responses to environmental covariates are modeled with additive multivariate Gaussian processes coded as linear models of coregionalization. These allow inference for wide range of functional forms and interspecific correlations between the responses. We propose also an efficient approach for inference with Laplace approximation and parameterization of the interspecific covariance matrices on the euclidean space. We demonstrate the benefits of our model with two small scale examples and one real world case study. We use cross-validation to compare the proposed model to analogous semi-parametric single species models and parametric single and joint species models in interpolation and extrapolation tasks. The proposed model outperforms the alternative models in all cases. We also show that the proposed model can be seen as an extension of the current state-of-the-art JSDMs to semi-parametric models.
  • Danielsson, Maria; Lammi, Anelma; Siitonen, Simo; Ollgren, Jukka; Pylkkanen, Liisa; Vasankari, Tuula (2019)
    Background The consumption of tobacco products has evolved to include more complex combinations of different products. We investigated the tobacco habits of a representative population of young Finnish male conscripts in order to evaluate the prevalence of dual use of cigarettes and snus as well as the transition from one tobacco product to another. In addition, we evaluated the correlation between the level of education and the use of cigarettes and snus. Methods A questionnaire-based survey was carried out in three out of 17 garrisons among conscripts during their first week of service in 2014. A total of 1971 male conscripts were selected by simple random sampling of the 9013 males in the selected garrisons. Of them 1916 participated and filled in the questionnaire. The response rate was 97.2%. The questionnaire consisted of 25 questions including age, gender, basic education, use of tobacco products as well as questions assessing nicotine dependency. Results The amount of dual users of cigarettes and snus was 21%. There was a higher probability of dual use of cigarettes and snus among smokers compared to snus users (p <0.001). One third (35%) of former smokers reported daily snus use and over 40% of the former snus users smoked daily. One third (34%) of the participants reported snus usage and 14% of the study subjects used snus daily. 40% of the study population were smokers and over 25% smoked daily. Of the participants with basic educational background 57% smoked daily (p <0.001), however, no association between snus and level of education was found (p = 0.69). Conclusions This study provides better understanding of the complex tobacco habits of young adult males. The simultaneous usage of multiple tobacco products as well as the high tendency to transition from one tobacco product to another should be taken into consideration when planning cessation interventions in health care settings and tobacco control policies at societal levels.
  • Kolehmainen, Anne Maarit; Pasanen, Annukka; Tuomi, Taru; Koivisto-Korander, Riitta; Butzow, Ralf; Loukovaara, Mikko (2019)
    Objective To study the association of the American Society of Anesthesiologists (ASA) physical status score with long-term outcome in endometrial cancer. Methods Overall, disease-specific and non-cancer-related survival were estimated using simple and multivariable Cox regression analyses and the Kaplan-Meier method. Results A total of 1166 patients were included in the study. Median follow-up time was 76 (range 1-136) months. All-cause and non-cancer-related mortality were increased in patients whose ASA physical status score was III (HRs 2.5 and 8.0, respectively) or IV (HRs 5.7 and 25, respectively), and cancer-related mortality was increased in patients whose score was IV (HR 2.7). Kaplan-Meier analyses demonstrated a worse overall, disease-specific and non-cancer-related survival for patients whose score was >= III (p= III in both subgroups of stages (p=0.003 and p=0.017 for stage I and stages II-IV, respectively). ASA physical status score remained an independent predictor of all-cause mortality (HR 2.2 for scores >= III), cancer-related mortality (HRs 1.7 and 2.2 for scores >= III and IV, respectively) and non-cancer related mortality (HR 3.1 for scores >= III) after adjustment for prognostically relevant clinicopathologic and blood-based covariates. ASA physical status score also remained an independent predictor of cancer-related mortality after exclusion of patients who were at risk for nodal involvement based on features of the primary tumor but who did not undergo lymphadenectomy, and patients with advanced disease who received suboptimal chemotherapy (HRs 1.6 and 2.5 for scores >= III and IV, respectively). Conclusions ASA physical status score independently predicts overall survival, disease-specific survival, and non-cancer-related survival in endometrial cancer.
  • Seppala, Otto; Karvonen, Anssi; Kuosa, Marja; Haataja, Maarit; Jokela, Jukka (2013)