Browsing by Subject "REGIONS"

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  • Acosta, Nidia Obscura; Mäkinen, Veli; Tomescu, Alexandru I. (2018)
    Background: Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bacterial species present in a sequencing sample. This problem can be naturally formulated as finding a collection of circular walks of a directed graph G that together cover all nodes, or edges, of G. Approach: We address this problem with the "safe and complete" framework of Tomescu and Medvedev (Research in computational Molecular biology-20th annual conference, RECOMB 9649: 152-163, 2016). An algorithm is called safe if it returns only those walks (also called safe) that appear as subwalk in all metagenomic assembly solutions for G. A safe algorithm is called complete if it returns all safe walks of G. Results: We give graph-theoretic characterizations of the safe walks of G, and a safe and complete algorithm finding all safe walks of G. In the node-covering case, our algorithm runs in time O(m(2) + n(3)), and in the edge-covering case it runs in time O(m(2)n); n and m denote the number of nodes and edges, respectively, of G. This algorithm constitutes the first theoretical tight upper bound on what can be safely assembled from metagenomic reads using this problem formulation.
  • Cairo, Massimo; Medvedev, Paul; Acosta, Nidia Obscura; Rizzi, Romeo; Tomescu, Alexandru I. (2019)
    In this article, we consider the following problem. Given a directed graph G, output all walks of G that are sub-walks of all closed edge-covering walks of G. This problem was first considered by Tomescu and Medvedev (RECOMB 2016), who characterized these walks through the notion of omnitig. Omnitigs were shown to be relevant for the genome assembly problem from bioinformatics, where a genome sequence must be assembled from a set of reads from a sequencing experiment. Tomescu and Medvedev (RECOMB 2016) also proposed an algorithm for listing all maximal omnitigs, by launching an exhaustive visit from every edge. In this article, we prove new insights about the structure of omnitigs and solve several open questions about them. We combine these to achieve an O(nm)-time algorithm for outputting all the maximal omnitigs of a graph (with n nodes and m edges). This is also optimal, as we show families of graphs whose total omnitig length is Omega(nm). We implement this algorithm arid show that it is 9-12 times faster in practice than the one of Tomescu and Medvedev (RECOMB 2016).
  • Woolley, Skipton; Bax, Nicolas; Currie, Jock; Dunn, Daniel; Hansen, Cecilie; Hill, Nicole; O'Hara, Timothy; Ovaskainen, Otso; Sayre, Roger; Vanhatalo, Jarno; Dunstan, Piers (2020)
    Bioregions are important tools for understanding and managing natural resources. Bioregions should describe locations of relatively homogenous assemblages of species occur, enabling managers to better regulate activities that might affect these assemblages. Many existing bioregionalization approaches, which rely on expert-derived, Delphic comparisons or environmental surrogates, do not explicitly include observed biological data in such analyses. We highlight that, for bioregionalizations to be useful and reliable for systems scientists and managers, the bioregionalizations need to be based on biological data; to include an easily understood assessment of uncertainty, preferably in a spatial format matching the bioregions; and to be scientifically transparent and reproducible. Statistical models provide a scientifically robust, transparent, and interpretable approach for ensuring that bioregions are formed on the basis of observed biological and physical data. Using statistically derived bioregions provides a repeatable framework for the spatial representation of biodiversity at multiple spatial scales. This results in better-informed management decisions and biodiversity conservation outcomes.
  • Guan, Yanlong; Lu, Hongwei; Jiang, Yelin; Tian, Peipei; Qiu, Lihua; Heiskanen, Janne; Pellikka, Petri (2021)
    Variations in climate types are commonly used to describe changes in natural vegetation cover in response to global climate change. However, few attempts have been made to quantify the heterogeneous dynamics of climate types. In this study, based on the Coupled Model Intercomparison Project phase 5 (CMIP5) historical and representative concentration pathway (RCP) runs from 18 global climate models, we used Shannon's Diversity Index (SHDI) and Simpson's Diversity Index (SIDI) to characterise of global climate heterogeneity from a morphological perspective. Our results show that global climate heterogeneity calculated by the SHDI/SIDI indices decreased from 1901 to 2095 at a significance level of 0.01. As radiative forcing intensified from RCP 2.6 to 8.5, the SHDI/SIDI decreased significantly. Furthermore, we observed that the spatial distribution of global climate heterogeneity was significantly reduced, with a pronounced latitudinal trend. Sensitivity analysis indicated that the temperature increase played a more significant role in reducing global climate heterogeneity than precipitation under the three warming scenarios, which is possibly attributed to anthropogenic forcing. Our findings suggest that the dynamics of global climate heterogeneity can be an effective means of quantifying global biodiversity loss.
  • Iqbal, Sumaiya; Perez-Palma, Eduardo; Jespersen, Jakob B.; May, Patrick; Hoksza, David; Heyne, Henrike O.; Ahmed, Shehab S.; Rifat, Zaara T.; Rahman, M. Sohel; Lage, Kasper; Palotie, Aarno; Cottrell, Jeffrey R.; Wagner, Florence F.; Daly, Mark J.; Campbell, Arthur J.; Lal, Dennis (2020)
    Interpretation of the colossal number of genetic variants identified from sequencing applications is one of the major bottlenecks in clinical genetics, with the inference of the effect of amino acid-substituting missense variations on protein structure and function being especially challenging. Here we characterize the three-dimensional (3D) amino acid positions affected in pathogenic and population variants from 1,330 disease-associated genes using over 14,000 experimentally solved human protein structures. By measuring the statistical burden of variations (i.e., point mutations) from all genes on 40 3D protein features, accounting for the structural, chemical, and functional context of the variations' positions, we identify features that are generally associated with pathogenic and population missense variants. We then perform the same amino acid-level analysis individually for 24 protein functional classes, which reveals unique characteristics of the positions of the altered amino acids: We observe up to 46% divergence of the class-specific features from the general characteristics obtained by the analysis on all genes, which is consistent with the structural diversity of essential regions across different protein classes. We demonstrate that the function-specific 3D features of the variants match the readouts of mutagenesis experiments for BRCA1 and PTEN, and positively correlate with an independent set of clinically interpreted pathogenic and benign missense variants. Finally, we make our results available through a web server to foster accessibility and downstream research. Our findings represent a crucial step toward translational genetics, from highlighting the impact of mutations on protein structure to rationalizing the variants' pathogenicity in terms of the perturbed molecular mechanisms.
  • Zöldi, Viktor; Sane, Jussi; Kantele, Anu; Rimhanen-Finne, Ruska; Salmenlinna, Saara; Lyytikäinen, Outi (2018)
    Background: Overnight international travels made by Finns more than doubled during 1995-2015. To estimate risks and observe trends of travel-related notifiable sexually transmitted and food- and water-borne infections (STIs and FWIs) among travellers, we analysed national reports of gonorrhoea, syphilis, hepatitis A, shigellosis, campylobacteriosis and salmonellosis cases and related them to travel statistics. Method: Cases notified as travel-related to the Finnish infectious diseases register were used as numerators and overnight stays of Statistics Finland surveys as denominator. We calculated overall risks (per 100,000 travellers) and assessed trends (using regression model) in various geographic regions. Results: Of all travel-related cases during 1995-2015, 2304 were STIs and 70,929 FWIs. During 2012-2015, Asia-Oceania showed highest risk estimates for gonorrhoea (11.0; 95%CI, 9.5-13), syphilis (1.4; 0.93-2.1), salmonellosis (157; 151-164), and campylobacteriosis (135; 129-141), and Africa for hepatitis A (4.5; 2.5-7.9), and shigellosis (35; 28-43). When evaluating at country level, the highest risks of infections was found in Thailand, except for hepatitis A ranking Hungary the first. During 2000-2011, significantly decreasing trends occurred for most FWIs particularly in the European regions and for STIs in Russia-Baltics. Conclusions: Our findings can be used in targeting pre-travel advice, which should also cover those visiting Thailand or European hepatitis A risk areas.
  • Kukushkina, Viktorija; Modhukur, Vijayachitra; Suhorutsenko, Marina; Peters, Maire; Magi, Reedik; Rahmioglu, Nilufer; Velthut-Meikas, Agne; Altmae, Signe; Esteban, Francisco J.; Vilo, Jaak; Zondervan, Krina; Salumets, Andres; Laisk-Podar, Triin (2017)
    The inner uterine lining (endometrium) is a unique tissue going through remarkable changes each menstrual cycle. Endometrium has its characteristic DNA methylation profile, although not much is known about the endometrial methylome changes throughout the menstrual cycle. The impact of methylome changes on gene expression and thereby on the function of the tissue, including establishing receptivity to implanting embryo, is also unclear. Therefore, this study used genome-wide technologies to characterize the methylome and the correlation between DNA methylation and gene expression in endometrial biopsies collected from 17 healthy fertile-aged women from pre-receptive and receptive phase within one menstrual cycle. Our study showed that the overall methylome remains relatively stable during this stage of the menstrual cycle, with small-scale changes affecting 5% of the studied CpG sites (22,272 out of studied 437,022 CpGs, FDR <0.05). Of differentially methylated CpG sites with the largest absolute changes in methylation level, approximately 30% correlated with gene expression measured by RNA sequencing, with negative correlations being more common in 5 ' UTR and positive correlations in the gene 'Body' region. According to our results, extracellular matrix organization and immune response are the pathways most affected by methylation changes during the transition from pre-receptive to receptive phase.
  • Long, Kathryn; McGowan, Catherine M.; Hyytiäinen, Heli K. (2020)
    Direct muscular attachment from lumbar vertebrae to the caudal vertebrae of the tail suggests that caudal traction, also described as a tail pull, may affect lumbar vertebral segments and/or associated soft tissues in horses. Traction is a commonly used human manual therapy technique used for pain relief and anecdotally observed to relieve pain in horses. However, research is lacking validating the efficacy of manual caudal traction on the horse. The objective of this study was to determine if caudal traction has an effect on mechanical nociceptive thresholds (MNTs) in a group of horses with clinical signs of back pain. Pressure algometry was used to measure MNTs of five bilateral anatomical sites in the epaxial and pelvic musculature of 11 horses referred to physiotherapy because of clinical signs of back pain. Measurements were recorded both before and immediately after traction. A significant difference (P
  • Morosan, D. E.; Palmerio, E.; Räsänen, J. E.; Kilpua, E. K. J.; Magdalenic, J.; Lynch, B. J.; Kumari, A.; Pomoell, J.; Palmroth, M. (2020)
    Context. Coronal mass ejections (CMEs) are large eruptions of magnetised plasma from the Sun that are often accompanied by solar radio bursts produced by accelerated electrons.Aims. A powerful source for accelerating electron beams are CME-driven shocks, however, there are other mechanisms capable of accelerating electrons during a CME eruption. So far, studies have relied on the traditional classification of solar radio bursts into five groups (Type I-V) based mainly on their shapes and characteristics in dynamic spectra. Here, we aim to determine the origin of moving radio bursts associated with a CME that do not fit into the present classification of the solar radio emission.Methods. By using radio imaging from the Nancay Radioheliograph, combined with observations from the Solar Dynamics Observatory, Solar and Heliospheric Observatory, and Solar Terrestrial Relations Observatory spacecraft, we investigate the moving radio bursts accompanying two subsequent CMEs on 22 May 2013. We use three-dimensional reconstructions of the two associated CME eruptions to show the possible origin of the observed radio emission.Results. We identified three moving radio bursts at unusually high altitudes in the corona that are located at the northern CME flank and move outwards synchronously with the CME. The radio bursts correspond to fine-structured emission in dynamic spectra with durations of similar to 1 s, and they may show forward or reverse frequency drifts. Since the CME expands closely following an earlier CME, a low coronal CME-CME interaction is likely responsible for the observed radio emission.Conclusions. For the first time, we report the existence of new types of short duration bursts, which are signatures of electron beams accelerated at the CME flank. Two subsequent CMEs originating from the same region and propagating in similar directions provide a complex configuration of the ambient magnetic field and favourable conditions for the creation of collapsing magnetic traps. These traps are formed if a CME-driven wave, such as a shock wave, is likely to intersect surrounding magnetic field lines twice. Electrons will thus be further accelerated at the mirror points created at these intersections and eventually escape to produce bursts of plasma emission with forward and reverse drifts.
  • Morosan, D. E.; Palmerio, E.; Lynch, B. J.; Kilpua, E. K. J. (2020)
    Context. Coronal mass ejections (CMEs) on the Sun are the largest explosions in the Solar System that can drive powerful plasma shocks. The eruptions, shocks, and other processes associated to CMEs are efficient particle accelerators and the accelerated electrons in particular can produce radio bursts through the plasma emission mechanism. Aims. Coronal mass ejections and associated radio bursts have been well studied in cases where the CME originates close to the solar limb or within the frontside disc. Here, we study the radio emission associated with a CME eruption on the back side of the Sun on 22 July 2012. Methods. Using radio imaging from the Nancay Radioheliograph, spectroscopic data from the Nancay Decametric Array, and extreme-ultraviolet observations from the Solar Dynamics Observatory and Solar Terrestrial Relations Observatory spacecraft, we determine the nature of the observed radio emission as well as the location and propagation of the CME. Results. We show that the observed low-intensity radio emission corresponds to a type II radio burst or a short-duration type IV radio burst associated with a CME eruption due to breakout reconnection on the back side of the Sun, as suggested by the pre-eruptive magnetic field configuration. The radio emission consists of a large, extended structure, initially located ahead of the CME, that corresponds to various electron acceleration locations. Conclusions. The observations presented here are consistent with the breakout model of CME eruptions. The extended radio emission coincides with the location of the current sheet and quasi-separatrix boundary of the CME flux and the overlying helmet streamer and also with that of a large shock expected to form ahead of the CME in this configuration.
  • Ukkola-Vuoti, Liisa; Kanduri, Chakravarthi; Oikkonen, Jaana; Buck, Gemma; Blancher, Christine; Raijas, Pirre; Karma, Kai; Lahdesmaki, Harri; Järvelä, Irma (2013)
  • GBD 2017 Diet Collaborators; Afshin, Ashkan; Sur, Patrick John; Lallukka, Tea; Weiderpass, Elisabete; Vasankari, Tommi Juhani (2019)
    Background Suboptimal diet is an important preventable risk factor for non-communicable diseases (NCDs); however, its impact on the burden of NCDs has not been systematically evaluated. This study aimed to evaluate the consumption of major foods and nutrients across 195 countries and to quantify the impact of their suboptimal intake on NCD mortality and morbidity. Methods By use of a comparative risk assessment approach, we estimated the proportion of disease-specific burden attributable to each dietary risk factor (also referred to as population attributable fraction) among adults aged 25 years or older. The main inputs to this analysis included the intake of each dietary factor, the effect size of the dietary factor on disease endpoint, and the level of intake associated with the lowest risk of mortality. Then, by use of diseasespecific population attributable fractions, mortality, and disability-adjusted life-years (DALYs), we calculated the number of deaths and DALYs attributable to diet for each disease outcome. Findings In 2017, 11 million (95% uncertainty interval [UI] 10-12) deaths and 255 million (234-274) DALYs were attributable to dietary risk factors. High intake of sodium (3 million [1-5] deaths and 70 million [34-118] DALYs), low intake of whole grains (3 million [2-4] deaths and 82 million [59-109] DALYs), and low intake of fruits (2 million [1-4] deaths and 65 million [41-92] DALYs) were the leading dietary risk factors for deaths and DALYs globally and in many countries. Dietary data were from mixed sources and were not available for all countries, increasing the statistical uncertainty of our estimates. Interpretation This study provides a comprehensive picture of the potential impact of suboptimal diet on NCD mortality and morbidity, highlighting the need for improving diet across nations. Our findings will inform implementation of evidence-based dietary interventions and provide a platform for evaluation of their impact on human health annually.
  • Guan, Yanlong; Lu, Hongwei; He, Li; Adhikari, Hari; Pellikka, Petri; Maeda, Eduardo; Heiskanen, Janne (2020)
    Increases and decreases in the areas of climatic types have become one of the most important responses to climate warming. However, few attempts have been made to quantify the complementary relationship between different climate types or to further assess changes in the spatial morphology. In this study, we used different observed datasets to reveal a dispersion phenomenon between major global climate types in 1950-2010, which is significantly consistent with the increasing trend of global temperatures. As the standard deviation of the area of major climate zones strengthened in 1950-2010, the global climatic landscape underwent notable changes. Not only did the area change, but the shape of the overall boundary became regular, the aggregation of climatic patches strengthened, and the climatic diversity declined substantially. However, changes in the global climatic landscapes are not at equilibrium with those on the continental scale. Interpreting these climatic morphological indices can deepen our understanding of the redistribution response mechanisms of species to climate change and help predict how they will be impacted by long-term future climate change.
  • Pereira, Carlos Silva; Teixeira, Joao; Figueiredo, Patricia; Xavier, Joao; Castro, Sao Luis; Brattico, Elvira (2011)
  • Cronemberger, Aurea A.; Aleixo, Alexandre; Mikkelsen, Else K.; Weir, Jason T. (2020)
    How species evolve reproductive isolation in the species-rich Amazon basin is poorly understood in vertebrates. Here, we sequenced a reference genome and used a genome-wide sample of SNPs to analyze a hybrid zone between two highly cryptic species ofHypocnemiswarbling-antbirds-the Rondonia warbling-antbird (H. ochrogyna) and Spix's warbling-antbird (H. striata)-in a headwater region of southern Amazonia. We found that both species commonly hybridize, producing F(1)s and a variety of backcrosses with each species but we detected only one F-2-like hybrid. Patterns of heterozygosity, hybrid index, and interchromosomal linkage disequilibrium in hybrid populations closely match expectations under strong postzygotic isolation. Hybrid zone width (15.4 km) was much narrower than expected (211 km) indicating strong selection against hybrids. A remarkably high degree of concordance in cline centers and widths across loci, and a lack of reduced interspecificF(st)between populations close to versus far from the contact zone, suggest that genetic incompatibilities have rendered most of the genome immune to introgression. These results support intrinsic postzygotic isolation as a driver of speciation in a moderately young cryptic species pair from the Amazon and suggest that species richness of the Amazon may be grossly underestimated.
  • Galbrun, Esther; Tang, Hui; Kaakinen, Anu; Zliobaite, Indre (2021)
    Identifying and understanding limiting conditions is at the centre of ecology and biogeography. Traditionally, associations between climate and occurrences of organisms are inferred from observational data using regression analysis, correlation analysis or clustering. Those methods extract patterns and relationships that hold throughout a dataset. We present a computational methodology called redescription mining, that emphasizes local patterns and associations that hold strongly on subsets of the dataset, instead. We aim to showcase the potential of this methodology for ecological and biogeographical studies, and encourage researchers to try it. Redescription mining can be used to identify associations between different descriptive views of the same system. It produces an ensemble of local models, that provide different perspectives over the system. Each model (redescription) consists of two sets of limiting conditions, over two different views, that hold locally. Limiting conditions, as well as the corresponding subregions, are identified automatically using data analysis algorithms. We explain how this methodology applies to a biogeographic case study focused on China and southern Asia. We consider dental traits of the large herbivorous mammals that occur there and climatic conditions as two aspects of this ecological system, and look for associations between them. Redescription mining can offer more refined inferences on the potential relation between variables describing different aspects of a system than classical methods. Thus, it permits different questions to be posed of the data, and can usefully complement classical methods in ecology and biogeography to uncover novel biogeographic patterns. A python package for carrying out redescription mining analysis is publicly available.
  • Guan, Yanlong; Lu, Hongwei; Yin, Chuang; Xue, Yuxuan; Jiang, Yelin; Kang, Yu; He, Li; Heiskanen, Janne (2020)
    Extensive research has focused on the response of vegetation to climate change, including potential mechanisms and resulting impacts. Although many studies have explored the relationship between vegetation and climate change in China, research on spatiotemporal distribution changes of climate regimes using natural vegetation as an indicator is still lacking. Further, limited information is available on the response of vegetation to shifts in China's regional climatic zones. In this study, we applied Mann-Kendall, and correlation analysis to examine the variabilities in temperature, precipitation, surface soil water, normalised difference vegetation index (NDVI), and albedo in China from 1982 to 2012. Our results indicate significant shifts in the distribution of Koppen-Geiger climate classes in China from 12.08% to 18.98% between 1983 and 2012 at a significance level of 0.05 (MK). The percentage areas in the arid and continental zones expanded at a rate of 0.004%/y and 0.12%/y, respectively, while the percentage area in the temperate and alpine zones decreased by -0.05%/y and - 0.07%/y. Sensitivity fitting results between simulated and observed changes identified temperature to be a dominant control on the dynamics of temperate (r(2)= 0.98) and alpine (r(2)= 0.968) zones, while precipitation was the dominant control on the changes of arid (r(2) = 0.856) and continental (r(2) = 0.815) zones. The response of the NDVI to albedo infers a more pronounced radiative response in temperate (r = -0.82, p
  • Sihvonen, Aleksi J.; Leo, Vera; Ripolles, Pablo; Lehtovaara, Terhi; Ylönen, Aki; Rajanaro, Pekka; Laitinen, Sari; Forsblom, Anita; Saunavaara, Jani; Autti, Taina; Laine, Matti; Rodriguez-Fornells, Antoni; Tervaniemi, Mari; Soinila, Seppo; Särkämö, Teppo (2020)
    Objective: Previous studies suggest that daily music listening can aid stroke recovery, but little is known about the stimulus-dependent and neural mechanisms driving this effect. Building on neuroimaging evidence that vocal music engages extensive and bilateral networks in the brain, we sought to determine if it would be more effective for enhancing cognitive and language recovery and neuroplasticity than instrumental music or speech after stroke. Methods: Using data pooled from two single-blind randomized controlled trials in stroke patients (N = 83), we compared the effects of daily listening to self-selected vocal music, instrumental music, and audiobooks during the first 3 poststroke months. Outcome measures comprised neuropsychological tests of verbal memory (primary outcome), language, and attention and a mood questionnaire performed at acute, 3-month, and 6-month stages and structural and functional MRI at acute and 6-month stages. Results: Listening to vocal music enhanced verbal memory recovery more than instrumental music or audiobooks and language recovery more than audiobooks, especially in aphasic patients. Voxel-based morphometry and resting-state and task-based fMRI results showed that vocal music listening selectively increased gray matter volume in left temporal areas and functional connectivity in the default mode network. Interpretation: Vocal music listening is an effective and easily applicable tool to support cognitive recovery after stroke as well as to enhance early language recovery in aphasia. The rehabilitative effects of vocal music are driven by both structural and functional plasticity changes in temporoparietal networks crucial for emotional processing, language, and memory.