Browsing by Subject "EXPANSION"

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  • Rajala, Kristiina; Lindroos, Bettina; Hussein, Samer M.; Lappalainen, Riikka S.; Pekkanen-Mattila, Mari; Inzunza, Jose; Rozell, Bjorn; Miettinen, Susanna; Narkilahti, Susanna; Kerkela, Erja; Aalto-Setälä, Katriina; Otonkoski, Timo; Suuronen, Riitta; Hovatta, Outi; Skottman, Heli (2010)
  • Vuoristo, Sanna; Toivonen, Sanna; Weltner, Jere; Mikkola, Milla; Ustinov, Jarkko; Trokovic, Ras; Palgi, Jaan; Lund, Riikka; Tuuri, Timo; Otonkoski, Timo (2013)
  • Van Horebeek, Lies; Hilven, Kelly; Mallants, Klara; Van Nieuwenhuijze, Annemarie; Kelkka, Tiina; Savola, Paula; Mustjoki, Satu; Schlenner, Susan M.; Liston, Adrian; Dubois, Benedicte; Goris, An (2019)
    The role of somatic variants in diseases beyond cancer is increasingly being recognized, with potential roles in autoinflammatory and autoimmune diseases. However, as mutation rates and allele fractions are lower, studies in these diseases are substantially less tolerant of false positives, and bio-informatics algorithms require high replication rates. We developed a pipeline combining two variant callers, MuTect2 and VarScan2, with technical filtering and prioritization. Our pipeline detects somatic variants with allele fractions as low as 0.5% and achieves a replication rate of > 55%. Validation in an independent data set demonstrates excellent performance (sensitivity > 57%, specificity > 98%, replication rate > 80%). We applied this pipeline to the autoimmune disease multiple sclerosis (MS) as a proof-of-principle. We demonstrate that 60% of MS patients carry 2-10 exonic somatic variants in their peripheral blood T and B cells, with the vast majority (80%) occurring in T cells and variants persisting over time. Synonymous variants significantly co-occur with non-synonymous variants. Systematic characterization indicates somatic variants are enriched for being novel or very rare in public databases of germline variants and trend towards being more damaging and conserved, as reflected by higher phred-scaled combined annotation-dependent depletion (CADD) and genomic evolutionary rate profiling (GERP) scores. Our pipeline and proof-of-principle now warrant further investigation of common somatic genetic variation on top of inherited genetic variation in the context of autoimmune disease, where it may offer subtle survival advantages to immune cells and contribute to the capacity of these cells to participate in the autoimmune reaction.
  • Narva, Elisa; Stubb, Aki; Guzman, Camilo; Blomqvist, Matias; Balboa, Diego; Lerche, Martina; Saari, Markku; Otonkoski, Timo; Ivaska, Johanna (2017)
    Cell-type-specific functions and identity are tightly regulated by interactions between the cell cytoskeleton and the extracellular matrix (ECM). Human pluripotent stem cells (hPSCs) have ultimate differentiation capacity and exceptionally low-strength ECM contact, yet the organization and function of adhesion sites and associated actin cytoskeleton remain poorly defined. We imaged hPSCs at the cell-ECM interface with total internal reflection fluorescence microscopy and discovered that adhesions at the colony edge were exceptionally large and connected by thick ventral stress fibers. The actin fence encircling the colony was found to exert extensive Rho-ROCK-myosin-dependent mechanical stress to enforce colony morphology, compaction, and pluripotency and to define mitotic spindle orientation. Remarkably, differentiation altered adhesion organization and signaling characterized by a switch from ventral to dorsal stress fibers, reduced mechanical stress, and increased integrin activity and cell-ECM adhesion strength. Thus, pluripotency appears to be linked to unique colony organization and adhesion structure.
  • Kaivola, Karri; Kiviharju, Anna; Jansson, Lilja; Rantalainen, Ville; Eriksson, Johan G.; Strandberg, Timo E.; Laaksovirta, Hannu; Renton, Alan E; Traynor, Bryan J.; Myllykangas, Liisa; Tienari, Pentti (2019)
    The hexanucleotide repeat expansion in C9orf72 is a common cause of amyotrophic lateral sclerosis/frontotemporal dementia and also rarely found in other psychiatric and neurodegenerative conditions. Alleles with >30 repeats are often considered an expansion, but the pathogenic repeat length threshold is still unclear. It is also unclear whether intermediate repeat length alleles (often defined either as 7-30 or 20-30 repeats) have clinically significant effects. We determined the C9orf72 repeat length distribution in 3142 older Finns (aged 60-104 years). The longest nonexpanded allele was 45 repeats. We found 7-45 repeats in 1036/3142 (33%) individuals, 20-45 repeats in 56/3142 (1.8%), 30-45 repeats in 12/3142 (0.38%), and expansion (>45 repeats) in 6/3142 (0.19%). There was no apparent clustering of neurodegenerative or psychiatric diseases in individuals with 30-45 repeats indicating that 30-45 repeats are not pathogenic. None of the 6 expansion carriers had a diagnosis of amyotrophic lateral sclerosis/frontotemporal dementia but 4 had a diagnosis of a neurodegenerative or psychiatric disease. Intermediate length alleles (categorized as 7-45 and 20-45 repeats) did not associate with Alzheimer's disease or cognitive impairment. (C) 2019 The Author(s). Published by Elsevier Inc.
  • Lehikoinen, Elina; Parviainen, Tuure Ossian; Helenius, Juha Pekka; Jalava, Mika; Salonen, Arto O.; Kummu, Matti (2019)
    Water scarcity is a severe global threat, and it will only become more critical with a growing and wealthier population. Annually, considerable volumes of water are transferred virtually through the global food system to secure nations’ food supply and to diversify diets. Our objective is to assess, whether specializing water-intensive production for exports in areas with an abundance of natural resources, would contribute to globally resource-efficient food production. We calculated Finland’s virtual water net export potential (four scenarios) by reallocating the present underutilized agricultural land and combining that with a domestic diet change (three scenarios) to maximize the exports of cattle products. Assessed scenarios indicate that the greatest potential to net export Assessed scenarios indicate that the greatest potential to net export virtual water (3.7 billion m3 year−1, 25-time increase to current) was achieved when local production was maximized with domestic and exported feed, and bovine meat consumption in Finland wasreplaced with a vegetarian substitute. This corresponds to annual virtual water consumption for food of about 3.6 million global citizens (assuming 1032 m3 cap−1 year−1). Therefore our results suggest, that optimizing water-intensive production to water-rich areas, has a significant impact on global water savings. In addition, increasing exports from such areas by decreasing the domestic demand for water-intensive products to meet the nutrition recommendation levels, saves water resources.
  • Forrest, M.; Eronen, J. T.; Utescher, T.; Knorr, G.; Stepanek, C.; Lohmann, G.; Hickler, T. (2015)
    There is an increasing need to understand the pre-Quaternary warm climates, how climate-vegetation interactions functioned in the past, and how we can use this information to understand the present. Here we report vegetation modelling results for the Late Miocene (11-7 Ma) to study the mechanisms of vegetation dynamics and the role of different forcing factors that influence the spatial patterns of vegetation coverage. One of the key uncertainties is the atmospheric concentration of CO2 during past climates. Estimates for the last 20 million years range from 280 to 500 ppm. We simulated Late Miocene vegetation using two plausible CO2 concentrations, 280 ppm CO2 and 450 ppm CO2, with a dynamic global vegetation model (LPJ-GUESS) driven by climate input from a coupled AOGCM (Atmosphere-Ocean General Circulation Model). The simulated vegetation was compared to existing plant fossil data for the whole Northern Hemisphere. For the comparison we developed a novel approach that uses information of the relative dominance of different plant functional types (PFTs) in the palaeobotanical data to provide a quantitative estimate of the agreement between the simulated and reconstructed vegetation. Based on this quantitative assessment we find that pre-industrial CO2 levels are largely consistent with the presence of seasonal temperate forests in Europe (suggested by fossil data) and open vegetation in North America (suggested by multiple lines of evidence). This suggests that during the Late Miocene the CO2 levels have been relatively low, or that other factors that are not included in the models maintained the seasonal temperate forests and open vegetation.
  • Kullberg, Peter; Toivonen, Tuuli; Pouzols, Federico Montesino; Lehtomäki, Joona; Di Minin, Enrico; Moilanen, Atte (2015)
    Complementarity and cost-efficiency are widely used principles for protected area network design. Despite the wide use and robust theoretical underpinnings, their effects on the performance and patterns of priority areas are rarely studied in detail. Here we compare two approaches for identifying the management priority areas inside the global protected area network: 1) a scoring-based approach, used in recently published analysis and 2) a spatial prioritization method, which accounts for complementarity and area-efficiency. Using the same IUCN species distribution data the complementarity method found an equal-area set of priority areas with double the mean species ranges covered compared to the scoringbased approach. The complementarity set also had 72% more species with full ranges covered, and lacked any coverage only for half of the species compared to the scoring approach. Protected areas in our complementarity-based solution were on average smaller and geographically more scattered. The large difference between the two solutions highlights the need for critical thinking about the selected prioritization method. According to our analysis, accounting for complementarity and area-efficiency can lead to considerable improvements when setting management priorities for the global protected area network.
  • Carvalho, Jose C.; Cardoso, Pedro (2020)
    Hutchinson's n-dimensional hypervolume concept holds a central role across different fields of ecology and evolution. The question of the amount of hypervolume overlap and differentiation between species is of great interest to understand the processes that drive niche dynamics, competitive interactions and, ultimately, community assembly. A framework is proposed to decompose overall differentiation among hypervolumes into two distinct components: niche shifts and niche contraction/expansion processes. Niche shift corresponds to the replacement of space between the hypervolumes occupied by two species, whereas niche contraction/expansion processes correspond to net differences between the amount of space enclosed by each hypervolume. A procedure to implement non-continuous trait data in the estimation ofn-dimensional hypervolumes is proposed. Hypervolumes were constructed for three Darwin' finches,Geospiza conirostris,Geospiza magnirostris, andGeospiza difficilisusing intraspecific trait data. Results showed that significant niche shifts, not niche contraction, occurred betweenG. conirostrisandG. magnirostrisin Genovesa island, where they live in sympatry. This means thatG. conirostrisoccupied a different niche space and not a reduced space on Genovesa.G. difficiliswas well differentiated from the other two species. The proposed framework allows disentangling different processes underlying niche partitioning between coexisting species. This framework offers novel insights to understand the drivers of niche partitioning strategies among coexisting species.
  • Gasbarra, Dario; Pajevic, Sinisa; Basser, Peter J. (2017)
    Tensor-valued and matrix-valued measurements of different physical properties are increasingly available in material sciences and medical imaging applications. The eigenvalues and eigenvectors of such multivariate data provide novel and unique information, but at the cost of requiring a more complex statistical analysis. In this work we derive the distributions of eigenvalues and eigenvectors in the special but important case of m x m symmetric random matrices, D, observed with isotropic matrix-variate Gaussian noise. The properties of these distributions depend strongly on the symmetries of the mean tensor/matrix, (D) over bar. When (D) over bar has repeated eigenvalues, the eigenvalues of D are not asymptotically Gaussian, and repulsion is observed between the eigenvalues corresponding to the same (D) over bar eigenspaces. We apply these results to diffusion tensor imaging (DTI), with m = 3, addressing an important problem of detecting the symmetries of the diffusion tensor, and seeking an experimental design that could potentially yield an isotropic Gaussian distribution. In the 3-dimensional case, when the mean tensor is spherically symmetric and the noise is Gaussian and isotropic, the asymptotic distribution of the first three eigenvalue central moment statistics is simple and can be used to test for isotropy. In order to apply such tests, we use quadrature rules of order t >= 4 with constant weights on the unit sphere to design a DTI-experiment with the property that isotropy of the underlying true tensor implies isotropy of the Fisher information. We also explain the potential implications of the methods using simulated DTI data with a Rician noise model.
  • Martinelli, M.; Martins, C. J. A. P.; Nesseris, S.; Sapone, D.; Tutusaus, I.; Avgoustidis, A.; Camera, S.; Carbone, C.; Casas, S.; Ilic, S.; Sakr, Z.; Yankelevich, V.; Auricchio, N.; Balestra, A.; Bodendorf, C.; Bonino, D.; Branchini, E.; Brescia, M.; Brinchmann, J.; Capobianco, V.; Carretero, J.; Castellano, M.; Cavuoti, S.; Cledassou, R.; Congedo, G.; Conversi, L.; Corcione, L.; Dubath, F.; Ealet, A.; Frailis, M.; Franceschi, E.; Fumana, M.; Garilli, B.; Gillis, B.; Giocoli, C.; Grupp, F.; Haugan, S. V. H.; Holmes, W.; Hormuth, F.; Jahnke, K.; Kermiche, S.; Kilbinger, M.; Kitching, T. D.; Kubik, B.; Kunz, M.; Kurki-Suonio, H.; Ligori, S.; Lilje, P. B.; Lloro, I.; Marggraf, O.; Markovic, K.; Massey, R.; Mei, S.; Meneghetti, M.; Meylan, G.; Moscardini, L.; Niemi, S.; Padilla, C.; Paltani, S.; Pasian, F.; Pettorino, V.; Pires, S.; Polenta, G.; Poncet, M.; Popa, L.; Pozzetti, L.; Raison, F.; Rhodes, J.; Roncarelli, M.; Saglia, R.; Schneider, P.; Secroun, A.; Serrano, S.; Sirignano, C.; Sirri, G.; Sureau, F.; Taylor, A. N.; Tereno, I.; Toledo-Moreo, R.; Valenziano, L.; Vassallo, T.; Wang, Y.; Welikala, N.; Weller, J.; Zacchei, A. (2020)
    Context. In metric theories of gravity with photon number conservation, the luminosity and angular diameter distances are related via the Etherington relation, also known as the distance duality relation (DDR). A violation of this relation would rule out the standard cosmological paradigm and point to the presence of new physics.Aims. We quantify the ability of Euclid, in combination with contemporary surveys, to improve the current constraints on deviations from the DDR in the redshift range 0<z<1.6.Methods. We start with an analysis of the latest available data, improving previously reported constraints by a factor of 2.5. We then present a detailed analysis of simulated Euclid and external data products, using both standard parametric methods (relying on phenomenological descriptions of possible DDR violations) and a machine learning reconstruction using genetic algorithms.Results. We find that for parametric methods Euclid can (in combination with external probes) improve current constraints by approximately a factor of six, while for non-parametric methods Euclid can improve current constraints by a factor of three.Conclusions. Our results highlight the importance of surveys like Euclid in accurately testing the pillars of the current cosmological paradigm and constraining physics beyond the standard cosmological model.
  • Aints, Alar; Mölder, Signe; Salumets, Andres (2019)
    Endometriosis is a benign chronic condition characterized by the existence of endometrial-like stroma and glandular tissue in extrauterine locations. The molecular mechanisms of its pathogenesis have not been elucidated. We have studied the role of EXTL3 (exostosin-like 3) in endometriosis and found that it is expressed in endometrial tissue as well as endometriosis lesions. We have found that serum from endometriosis patients contains a factor or factors, which interact with EXTL3 resulting in strongly increased colony formation in regenerating cell culture. We also found increased anti-EXTL3 antibodies in endometriosis patients' sera. EXTL3 is an N-acetyl glucosamine (GlcNAc) transferase, performing a key step in heparan sulfate (HS) glucosaminoglycan synthesis. Many viruses replicate in regenerating epithelial cells and use HS as a receptor for cell entry. We measured antibody titres to viruses, which use HS as a receptor for cell entry, and found rarely increased titres for these viruses in endometriosis sera, whereas titres to viruses using other receptors were equally distributed in study groups. The data indicate that perturbation of HS metabolism is associated with endometriosis.
  • Owall, Louise; Darvann, Tron A.; Hove, Hanne B.; Heliövaara, Arja; Duno, Morten; Kreiborg, Sven; Hermann, Nuno (2021)
    Objective: To quantify soft tissue facial asymmetry (FA) in children with nonsyndromic and Muenke syndrome-associated unicoronal synostosis (NS-UCS and MS-UCS), hypothesizing that MS-UCS presents with significantly larger FA than NS-UCS. Design: Retrospective cohort study. Patients and Methods: Twenty-one children (mean age: 0.6 years; range: 0.1-1.4 years) were included in the study (NS-UCS = 14; MS-UCS = 7). From presurgical computed tomography scans, facial surfaces were constructed for analysis. A landmark guided atlas was deformed to match each patient's surface, obtaining spatially detailed left-right point correspondence. Facial asymmetry was calculated in each surface point across the face, as the length (mm) of an asymmetry vector, with its Cartesian components providing 3 directions. Mean FA was calculated for the full face, and the forehead, eye, nose, cheek, mouth, and chin regions. Results: For the full face, a significant difference of 2.4 mm (P = .001) was calculated between the 2 groups, predominately in the transverse direction (1.5 mm; P < .001). The forehead and chin regions presented with the largest significant difference, 3.5 mm (P = .002) and 3.2 mm (P < .001), respectively; followed by the eye (2.4 mm; P = .004), cheek (2.2 mm; P = .004), nose (1.7 mm; P = .001), and mouth (1.4 mm; P = .009) regions. The transverse direction presented with the largest significant difference in the forehead, chin, mouth, and nose regions, the sagittal direction in the cheek region, and the vertical direction in the eye region. Conclusions: Muenke syndrome-associated unicoronal synostosis presented with significantly larger FA in all regions compared to NS-UCS. The largest significant differences were found in the forehead and chin regions, predominantly in the transverse direction.
  • Sizov, Oleg; Ezhova, Ekaterina; Tsymbarovich, Petr; Soromotin, A; Prihod'ko, Nikolay; Petäjä, Tuukka; Zilitinkevich, Sergej; Kulmala, Markku; Bäck, Jaana; Köster, Kajar (2021)
    The rapidly warming Arctic undergoes transitions that can influence global carbon balance. One of the key processes is the shift towards vegetation types with higher biomass underlining a stronger carbon sink. The shift is predicted by bioclimatic models based on abiotic climatic factors, but it is not always confirmed with observations. Recent studies highlight the role of disturbances in the shift. Here we use high-resolution remote sensing to study the process of transition from tundra to forest and its connection to wildfires in the 20 000 km(2) area in northwest Siberia. Overall, 40 % of the study area was burned during a 60-year period. Three quarters of the burned areas were dry tundra. About 10 % of the study area experienced two-three fires with an interval of 15-60 years suggesting a shorter fire return interval than that reported earlier for the northern areas of central Siberia (130-350 years). Based on our results, the shift in vegetation (within the 60-year period) occurred in 40 %-85 % of the burned territories. All fire-affected territories were flat; therefore no effect of topography was detected. Oppositely, in the undisturbed areas, a transition of vegetation was observed only in 6 %-15 % of the territories, characterized by steeper topographic slopes. Our results suggest a strong role of disturbances in the tree advance in northwest Siberia.
  • Duru, Ilhan Cem; Andreevskaya, Margarita; Laine, Pia; Rode, Tone Mari; Ylinen, Anne; Lovdal, Trond; Bar, Nadav; Crauwels, Peter; Riedel, Christian U.; Bucur, Florentina Ionela; Nicolau, Anca Ioana; Auvinen, Petri (2020)
    BackgroundHigh pressure processing (HPP; i.e. 100-600MPa pressure depending on product) is a non-thermal preservation technique adopted by the food industry to decrease significantly foodborne pathogens, including Listeria monocytogenes, from food. However, susceptibility towards pressure differs among diverse strains of L. monocytogenes and it is unclear if this is due to their intrinsic characteristics related to genomic content. Here, we tested the barotolerance of 10 different L. monocytogenes strains, from food and food processing environments and widely used reference strains including clinical isolate, to pressure treatments with 400 and 600MPa. Genome sequencing and genome comparison of the tested L. monocytogenes strains were performed to investigate the relation between genomic profile and pressure tolerance.ResultsNone of the tested strains were tolerant to 600MPa. A reduction of more than 5 log(10) was observed for all strains after 1min 600MPa pressure treatment. L. monocytogenes strain RO15 showed no significant reduction in viable cell counts after 400MPa for 1min and was therefore defined as barotolerant. Genome analysis of so far unsequenced L. monocytogenes strain RO15, 2HF33, MB5, AB199, AB120, C7, and RO4 allowed us to compare the gene content of all strains tested. This revealed that the three most pressure tolerant strains had more than one CRISPR system with self-targeting spacers. Furthermore, several anti-CRISPR genes were detected in these strains. Pan-genome analysis showed that 10 prophage genes were significantly associated with the three most barotolerant strains.ConclusionsL. monocytogenes strain RO15 was the most pressure tolerant among the selected strains. Genome comparison suggests that there might be a relationship between prophages and pressure tolerance in L. monocytogenes.
  • Di Minin, Enrico; Soutullo, Alvaro; Bartesaghi, Lucia; Rios, Mariana; Szephegyi, Maria Nube; Moilanen, Atte (2017)
    Gaps in research exist for country-wide analyses to identify areas of particular importance for biodiversity and ecosystem services to help reach Aichi Target 11 in developing countries. Here we provide a spatial conservation prioritization approach that ranks landowners for maximizing the representation of biodiversity features and ecosystem services, while exploring the trade-offs with agricultural and commercial forestry production and land cost, using Uruguay as a case study. Specifically, we explored four policy scenarios, ranging from a business as usual scenario where only biodiversity and ecosystem services were included in the analysis to a potentially unsustainable scenario where expansion of alternative land uses and economic development would be given higher priority over biodiversity and ecosystem services. At the 17% land target proposed for conservation, the representation levels for biodiversity and ecosystem services were, on average, higher under the business as usual scenario. However, a small addition to the proposed target (from 17 to 20%) allowed to meet same representation levels for biodiversity and ecosystem services, while decreasing conflict with agricultural and commercial forestry production and opportunity costs to local landowners. Under the unsustainable scenario, a striking 41% addition to the conservation target (from 17 to 58%) was needed to meet same representation levels for threatened ecosystems and ecosystem services, which are crucial to sustain human well-being. Our results highlight that more realistic and potentially higher conservation targets, than politically set targets, can be achieved at the country level when sustainable development needs are also accounted for. (C) 2016 The Authors. Published by Elsevier Ltd.
  • Paloniemi, Riikka; Hujala, Teppo; Rantala, Salla; Harlio, Kirsi Annika; Salomaa, Anna Alina; Primmer, Eeva; Pynnönen, Sari; Arponen, Anni Katri Ilona (2018)
    Improving the effectiveness of voluntary biodiversity policies requires developing trans-disciplinary conservation plans that consider social constraints to achieving ecological objectives. We integrated data on landowners' willingness to participate in voluntary conservation efforts with ecological data on conservation values in a spatial prioritization, and found that doing so considerably reduced the loss in conservation value caused by landowners' reluctance to participate. We learned that conducting prioritization with stakeholder input gained through dialogue during field visits could be beneficial for increasing the legitimacy of conservation plans with stakeholders. Thus, in addition to developing a methodology for using data on stakeholder perceptions of conservation in spatial prioritization, our study suggests that engaging landowners and other stakeholders in the conservation prioritization process will improve the success of conservation plans.
  • Moschou, Sofia-Paraskevi; Pierrard, Viviane; Keppens, Rony; Pomoell, Jens (2017)
    An exospheric kinetic solar wind model is interfaced with an observation-driven single-fluid magnetohydrodynamic (MHD) model. Initially, a photospheric magnetogram serves as observational input in the fluid approach to extrapolate the heliospheric magnetic field. Then semi-empirical coronal models are used for estimating the plasma characteristics up to a heliocentric distance of 0.1 AU. From there on, a full MHD model that computes the three-dimensional time-dependent evolution of the solar wind macroscopic variables up to the orbit of Earth is used. After interfacing the density and velocity at the inner MHD boundary, we compare our results with those of a kinetic exospheric solar wind model based on the assumption of Maxwell and Kappa velocity distribution functions for protons and electrons, respectively, as well as with in situ observations at 1 AU. This provides insight into more physically detailed processes, such as coronal heating and solar wind acceleration, which naturally arise from including suprathermal electrons in the model. We are interested in the profile of the solar wind speed and density at 1 AU, in characterizing the slow and fast source regions of the wind, and in comparing MHD with exospheric models in similar conditions. We calculate the energetics of both models from low to high heliocentric distances.
  • Tokariev, Anton; Roberts, James A.; Zalesky, Andrew; Zhao, Xuelong; Vanhatalo, Sampsa; Breakspear, Michael; Cocchi, Luca (2019)
    Sleep architecture carries vital information about brain health across the lifespan. In particular, the ability to express distinct vigilance states is a key physiological marker of neurological wellbeing in the newborn infant although systems-level mechanisms remain elusive. Here, we demonstrate that the transition from quiet to active sleep in newborn infants is marked by a substantial reorganization of large-scale cortical activity and functional brain networks. This reorganization is attenuated in preterm infants and predicts visual performance at two years. We find a striking match between these empirical effects and a computational model of large-scale brain states which uncovers fundamental biophysical mechanisms not evident from inspection of the data. Active sleep is defined by reduced energy in a uniform mode of neural activity and increased energy in two more complex anteroposterior modes. Preterm-born infants show a deficit in this sleep-related reorganization of modal energy that carries novel prognostic information.
  • Acharya, S.; Brucken, E. J.; Chang, B.; Kim, D. J.; Litichevskyi, V.; Mieskolainen, M. M.; Orava, R.; Rak, J.; Räsänen, S. S.; Snellman, T. W.; Trzaska, W. H.; Viinikainen, J.; The ALICE collaboration (2017)
    The transverse momentum (p(T)) spectra and elliptic flow coefficient (v(2)) of deuterons and anti-deuterons at mid-rapidity (|y| <0.5) are measured with the ALICE detector at the LHC in Pb-Pb collisions at root s(NN) = 2.76 TeV. The measurement of the p(T) spectra of (anti-)deuterons is done up to 8 GeV/c in 0-10% centrality class and up to 6 GeV/c in 10-20% and 20-40% centrality classes. The v(2) is measured in the 0.8 <p(T) <5 GeV/c interval and in six different centrality intervals (0-5, 5-10, 10-20, 20-30, 30-40 and 40-50%) using the scalar product technique. Measured pi(+/-), K-+/- and p+(p) over bar transverse-momentum spectra and v(2) are used to predict the deuteron p(T) spectra and v(2) within the Blast-Wave model. The predictions are able to reproduce the v(2) coefficient in the measured p(T) range and the transverse-momentum spectra for p(T) > 1.8 GeV/c within the experimental uncertainties. The measurement of the coalescence parameter B-2 is performed, showing a p(T) dependence in contrast with the simplest coalescence model, which fails to reproduce also the measured v(2) coefficient. In addition, the coalescence parameter B-2 and the elliptic flow coefficient in the 20-40% centrality interval are compared with the AMPT model which is able, in its version without string melting, to reproduce the measured v(2)(p(T)) and the B-2(p(T)) trend.