Browsing by Subject "MAPS"

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  • Euclid Collaboration; Guglielmo, Christopher G.; Gozaliasl, G.; Keihanen, E.; Kurki-Suonio, H.; Kirkpatrick IV, C.C. (2020)
    The Complete Calibration of the Colour-Redshift Relation survey (C3R2) is a spectroscopic e ffort involving ESO and Keck facilities designed specifically to empirically calibrate the galaxy colour-redshift relation - P(z jC) to the Euclid depth (iAB = 24 :5) and is intimately linked to the success of upcoming Stage IV dark energy missions based on weak lensing cosmology. The aim is to build a spectroscopic calibration sample that is as representative as possible of the galaxies of the Euclid weak lensing sample. In order to minimise the number of spectroscopic observations necessary to fill the gaps in current knowledge of the P(z jC), self-organising map (SOM) representations of the galaxy colour space have been constructed. Here we present the first results of an ESO@VLT Large Programme approved in the context of C3R2, which makes use of the two VLT optical and near-infrared multi-object spectrographs, FORS2 and KMOS. This data release paper focuses on high-quality spectroscopic redshifts of high-redshift galaxies observed with the KMOS spectrograph in the near-infrared H- and K-bands. A total of 424 highly-reliable redshifts are measured in the 1:3 2 galaxies.
  • Girardello, Marco; Chapman, Anna; Dennis, Roger; Kaila, Lauri; Borges, Paulo; Santangeli, Andrea (2019)
    Species distribution data are crucial for assessing the conservation status of species (red listing, IUCN) and implementing international conservation targets, such as those set by the International Convention on Biological Diversity. Although there have been a number of efforts aimed at aggregating biodiversity data, information on the distribution of many taxa is still scanty (i.e. the Wallacean Shortfall). In this study, we use a large database, including over 19 million species occurrence records, to identify knowledge gaps in biodiversity inventories for butterfly records at a global level. Bayesian hierarchical spatial models were used to quantify the relationship between gaps in inventory completeness and the density of roads, protected areas and elevational range, the former variable being a proxy for accessibility, the latter two for attractiveness to recorders. Our results show that despite > 100 years of butterfly sampling, knowledge of the distribution of butterflies is still limited in tropical areas. The results revealed that gaps in butterfly inventories are largely concentrated in areas of low elevational range, low density of protected areas and low road density. We conclude that the Wallacean Shortfall is a problem even for one of the best studied insect groups. In the light of these data limitations, we discuss prospects for filling gaps in butterfly inventories at the global scale within relatively short time frames. We argue that a combination of citizen science and quantitative tools may help to fill knowledge gaps and inform conservation decisions.
  • Hannula-Jouppi, Katariina; Massinen, Satu; Siljander, Tuula; Mäkelä, Siru Päivikki; Kivinen, Katja; Leinonen, Rasko; Jiao, Hong; Aitos, Paivi; Karppelin, Matti; Vuopio, Jaana; Syrjanen, Jaana; Kere, Juha (2013)
  • Juvela, Mika; He, Jinhua; Pattle, Katherine; Liu, Tie; Bendo, George; Eden, David J.; Feher, Orsolya; Fich, Michel; Fuller, Gary; Hirano, Naomi; Kim, Kee-Tae; Li, Di; Liu, Sheng-Yuan; Malinen, Johanna; Marshall, Douglas J.; Paradis, Deborah; Parsons, Harriet; Pelkonen, Veli-Matti; Rawlings, Mark G.; Ristorcelli, Isabelle; Samal, Manash R.; Tatematsu, Ken'ichi; Thompson, Mark; Traficante, Alessio; Wang, Ke; Ward-Thompson, Derek; Wu, Yuefang; Yi, Hee-Weon; Yoo, Hyunju (2018)
    Context. Analysis of all-sky Planck submillimetre observations and the IRAS 100 mu m data has led to the detection of a population of Galactic cold clumps. The clumps can be used to study star formation and dust properties in a wide range of Galactic environments. Aims. Our aim is to measure dust spectral energy distribution ( SED) variations as a function of the spatial scale and the wavelength. Methods. We examined the SEDs at large scales using IRAS, Planck, and Herschel data. At smaller scales, we compared JCMT/SCUBA-2 850 mu m maps with Herschel data that were filtered using the SCUBA-2 pipeline. Clumps were extracted using the Fellwalker method, and their spectra were modelled as modified blackbody functions. Results. According to IRAS and Planck data, most fields have dust colour temperatures T-C similar to 14-18K and opacity spectral index values of beta = 1.5-1.9. The clumps and cores identified in SCUBA-2 maps have T similar to 13K and similar beta values. There are some indications of the dust emission spectrum becoming flatter at wavelengths longer than 500 mu m. In fits involving Planck data, the significance is limited by the uncertainty of the corrections for CO line contamination. The fits to the SPIRE data give a median beta value that is slightly above 1.8. In the joint SPIRE and SCUBA-2 850 mu m fits, the value decreases to beta similar to 1.6. Most of the observed T-beta anticorrelation can be explained by noise. Conclusions. The typical submillimetre opacity spectral index fi of cold clumps is found to be similar to 1.7. This is above the values of diffuse clouds, but lower than in some previous studies of dense clumps. There is only tentative evidence of a T-beta anticorrelation and beta decreasing at millimetre wavelengths.
  • Benkyi, Isaac; Staszewska-Krajewska, Olga; Gryko, Daniel T.; Jaszuński, Michał; Stanger, Amnon; Sundholm, Dage (2020)
    The aromaticity of three nonplanar, fully conjugated aza-nanographenes built around a pyrrolo[3,2-b]pyrrole core is assessed through the application of two different computational procedures—GIMIC and NICS. We examine the calculated magnetically induced current densities (GIMIC) and nucleus-independent chemical shifts (NICS). The structural differences between these three apparently similar molecules lead to significantly different aromatic properties. GIMIC analysis indicates that the peripheral diatropic ring current of 3.9 nA/T for the studied bowl-shaped diaza-nanographene is the strongest, followed by the double [6]helicene which lacks seven-membered rings, and is practically nonexistent for the double [5]helicene possessing seven-membered rings. The biggest difference however is that in the two not-fully-fused molecules, the central pyrrole rings possess a significant diatropic current of about 4.1 nA/T, whereas there is no such current in the diaza-nanographene. Moreover, the antiaromaticity of the seven-membered rings is increasing while moving from double [5]helicene to diaza-nanographene (from −2.4 to −6.0 nA/T). The induced currents derived from NICSπ,zz-XY-scan analysis for all of the studied systems are in qualitative agreement with the GIMIC results. Subtle differences may originate from σ-electron currents in GIMIC or inaccuracy of NICSπ,zz values due to the nonplanarity of the systems, but the general picture is similar.
  • Huong Thi Thanh Nguyen; Trung Minh Doan; Tomppo, Erkki; McRoberts, Ronald E. (2020)
    Information on land use and land cover (LULC) including forest cover is important for the development of strategies for land planning and management. Satellite remotely sensed data of varying resolutions have been an unmatched source of such information that can be used to produce estimates with a greater degree of confidence than traditional inventory estimates. However, use of these data has always been a challenge in tropical regions owing to the complexity of the biophysical environment, clouds, and haze, and atmospheric moisture content, all of which impede accurate LULC classification. We tested a parametric classifier (logistic regression) and three non-parametric machine learning classifiers (improved k-nearest neighbors, random forests, and support vector machine) for classification of multi-temporal Sentinel 2 satellite imagery into LULC categories in Dak Nong province, Vietnam. A total of 446 images, 235 from the year 2017 and 211 from the year 2018, were pre-processed to gain high quality images for mapping LULC in the 6516 km(2) study area. The Sentinel 2 images were tested and classified separately for four temporal periods: (i) dry season, (ii) rainy season, (iii) the entirety of the year 2017, and (iv) the combination of dry and rainy seasons. Eleven different LULC classes were discriminated of which five were forest classes. For each combination of temporal image set and classifier, a confusion matrix was constructed using independent reference data and pixel classifications, and the area on the ground of each class was estimated. For overall temporal periods and classifiers, overall accuracy ranged from 63.9% to 80.3%, and the Kappa coefficient ranged from 0.611 to 0.813. Area estimates for individual classes ranged from 70 km(2) (1% of the study area) to 2200 km(2) (34% of the study area) with greater uncertainties for smaller classes.
  • Rastas, Pasi (2017)
    Motivation: Accurate and dense linkage maps are useful in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other genomic data analyses. Moreover, linkage mapping is one of the best ways to detect errors in de novo genome assemblies, as well as to orient and place assembly contigs within chromosomes. A small mapping cross of tens of individuals will detect many errors where distant parts of the genome are erroneously joined together. With more individuals and markers, even more local errors can be detected and more contigs can be oriented. However, the tools that are currently available for constructing linkage maps are not well suited for large, possible low-coverage, whole genome sequencing datasets. Results: Here we present a linkage mapping software Lep-MAP3, capable of mapping high-throughput whole genome sequencing datasets. Such data allows cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for thousands of individual samples, enabling, among other analyses, comprehensive validation and refinement of de novo genome assemblies. The algorithms of Lep-MAP3 can analyse low-coverage datasets and reduce data filtering and curation on any data. This yields more markers in the final maps with less manual work even on problematic datasets. We demonstrate that Lep-MAP3 obtains very good performance already on 5x sequencing coverage and outperforms the fastest available software on simulated data on accuracy and often on speed. We also construct de novo linkage maps on 7-12x whole-genome data on the Red postman butterfly (Heliconius erato) with almost 3 million markers.
  • Pankka, Pekka; Soultanis, Elefterios (2020)
    We construct, for a locally compact metric space X, a space of polylipschitz forms Gamma over bar c*(X), which is a pre-dual for the space of metric currents D*(X) of Ambrosio and Kirchheim. These polylipschitz forms may be seen as an analog of differential forms in the metric setting.
  • Koponen, Ismo T.; Nousiainen, Maija (2018)
    Learning scientific knowledge is largely based on understanding what are its key concepts and how they are related. The relational structure of concepts also affects how concepts are introduced in teaching scientific knowledge. We model here how students organise their knowledge when they represent their understanding of how physics concepts are related. The model is based on assumptions that students use simple basic linking-motifs in introducing new concepts and mostly relate them to concepts that were introduced a few steps earlier, i.e. following a genealogical ordering. The resulting genealogical networks have relatively high local clustering coefficients of nodes but otherwise resemble networks obtained with an identical degree distribution of nodes but with random linking between them (i.e. the configuration-model). However, a few key nodes having a special structural role emerge and these nodes have a higher than average communicability betweenness centralities. These features agree with the empirically found properties of students' concept networks. (C) 2017 Elsevier B.V. All rights reserved.
  • Kauranen, Aapo; Luisto, Rami; Tengvall, Ville (2022)
    We study global injectivity of proper branched coverings from the open Euclidean n$n$-ball onto an open subset of the Euclidean n$n$-space in the case where the branch set is compact. In particular, we show that such mappings are homeomorphisms when n=3$n=3$ or when the branch set is empty. This gives a positive answer to the corresponding cases of a question of Vuorinen.
  • Aghanim, N.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kiiveri, Kimmo; Kurki-Suonio, H.; Lähteenmäki, Anne; Lindholm, V.; Poutanen, T.; Suur-Uski, Anna-Stiina; Tuovinen, J.; Väliviita, Jussi; Planck Collaboration (2014)
  • Aghanim, N.; Juvela, M.; Kangaslahti, P.; Keihanen, E.; Keskitalo, R.; Kiiveri, K.; Kurki-Suonio, H.; Lähteenmäki, Anne; Lindholm, V.; Poutanen, T.; Suur-Uski, A. -S.; Tuovinen, J.; Väliviita, Jussi; Varis, J.; Planck Collaboration (2014)
  • Ade, P. A. R.; Juvela, M.; Keihanen, E.; Kurki-Suonio, H.; Poutanen, T.; Suur-Uski, A. -S.; Tuovinen, J.; Valiviita, J.; Planck Collaboration (2014)
  • Ade, P. A. R.; Kurki-Suonio, H.; Suur-Uski, A. -S.; Valiviita, J.; Planck Collaboration (2014)
  • Planck Collaboration; Akrami, Y.; Keihänen, E.; Kiiveri, K.; Kurki-Suonio, H.; Lindholm, V.; Savelainen, M.; Suur-Uski, A-S.; Väliviita, J. (2020)
    We present the NPIPE processing pipeline, which produces calibrated frequency maps in temperature and polarization from data from the Planck Low Frequency Instrument (LFI) and High Frequency Instrument (HFI) using high-performance computers. NPIPE represents a natural evolution of previous Planck analysis efforts, and combines some of the most powerful features of the separate LFI and HFI analysis pipelines. For example, following the LFI 2018 processing procedure, NPIPE uses foreground polarization priors during the calibration stage in order to break scanning-induced degeneracies. Similarly, NPIPE employs the HFI 2018 time-domain processing methodology to correct for bandpass mismatch at all frequencies. In addition, NPIPE introduces several improvements, including, but not limited to: inclusion of the 8% of data collected during repointing manoeuvres; smoothing of the LFI reference load data streams; in-flight estimation of detector polarization parameters; and construction of maximally independent detector-set split maps. For component-separation purposes, important improvements include: maps that retain the CMB Solar dipole, allowing for high-precision relative calibration in higher-level analyses; well-defined single-detector maps, allowing for robust CO extraction; and HFI temperature maps between 217 and 857 GHz that are binned into 0 ' .9 pixels (N-side = 4096), ensuring that the full angular information in the data is represented in the maps even at the highest Planck resolutions. The net effect of these improvements is lower levels of noise and systematics in both frequency and component maps at essentially all angular scales, as well as notably improved internal consistency between the various frequency channels. Based on the NPIPE maps, we present the first estimate of the Solar dipole determined through component separation across all nine Planck frequencies. The amplitude is (3366.6 +/- 2.7) mu K, consistent with, albeit slightly higher than, earlier estimates. From the large-scale polarization data, we derive an updated estimate of the optical depth of reionization of tau =0.051 +/- 0.006, which appears robust with respect to data and sky cuts. There are 600 complete signal, noise and systematics simulations of the full-frequency and detector-set maps. As a Planck first, these simulations include full time-domain processing of the beam-convolved CMB anisotropies. The release of NPIPE maps and simulations is accompanied with a complete suite of raw and processed time-ordered data and the software, scripts, auxiliary data, and parameter files needed to improve further on the analysis and to run matching simulations.
  • Aghanim, N.; Keihänen, E.; Kiiveri, K.; Kurki-Suonio, H.; Lindholm, V.; Savelainen, M.; Suur-Uski, A. -S.; Väliviita, J.; Planck Collaboration (2017)
    The six parameters of the standard Lambda CDM model have best-fit values derived from the Planck temperature power spectrum that are shifted somewhat from the best-fit values derived from WMAP data. These shifts are driven by features in the Planck temperature power spectrum at angular scales that had never before been measured to cosmic-variance level precision. We have investigated these shifts to determine whether they are within the range of expectation and to understand their origin in the data. Taking our parameter set to be the optical depth of the reionized intergalactic medium tau, the baryon density omega(b), the matter density omega(m), the angular size of the sound horizon theta(*), the spectral index of the primordial power spectrum, n(s), and A(s)e(-2 pi) (where As is the amplitude of the primordial power spectrum), we have examined the change in best-fit values between a WMAP-like large angular-scale data set (with multipole moment l <800 in the Planck temperature power spectrum) and an all angular-scale data set (l <2500 Planck temperature power spectrum), each with a prior on tau of 0.07 +/- 0.02. We find that the shifts, in units of the 1 sigma expected dispersion for each parameter, are {Delta tau, Delta A(s)e(-2 tau), Delta n(s), Delta omega(m), Delta omega(b), Delta theta(*)} = {-1.7, -2.2, 1.2, 2.0, 1.1, 0.9}, with a chi(2) value of 8.0. We find that this chi(2) value is exceeded in 15% of our simulated data sets, and that a parameter deviates by more than 2.2 sigma in 9% of simulated data sets, meaning that the shifts are not unusually large. Comparing l <800 instead to l > 800, or splitting at a different multipole, yields similar results. We examined the l <800 model residuals in the l > 800 power spectrum data and find that the features there that drive these shifts are a set of oscillations across a broad range of angular scales. Although they partly appear similar to the effects of enhanced gravitational lensing, the shifts in Lambda CDM parameters that arise in response to these features correspond to model spectrum changes that are predominantly due to non-lensing effects; the only exception is tau, which, at fixed A(s)e(-2 tau), affects the l > 800 temperature power spectrum solely through the associated change in As and the impact of that on the lensing potential power spectrum. We also ask, "what is it about the power spectrum at l <800 that leads to somewhat different best-fit parameters than come from the full l range?" We find that if we discard the data at l <30, where there is a roughly 2 sigma downward fluctuation in power relative to the model that best fits the full l range, the l <800 best-fit parameters shift significantly towards the l <2500 best-fit parameters. In contrast, including l <30, this previously noted "low-l deficit" drives ns up and impacts parameters correlated with ns, such as omega(m) and H-0. As expected, the l <30 data have a much greater impact on the l <800 best fit than on the l <2500 best fit. So although the shifts are not very significant, we find that they can be understood through the combined effects of an oscillatory-like set of high-l residuals and the deficit in low-l power, excursions consistent with sample variance that happen to map onto changes in cosmological parameters. Finally, we examine agreement between Planck TT data and two other CMB data sets, namely the Planck lensing reconstruction and the TT power spectrum measured by the South Pole Telescope, again finding a lack of convincing evidence of any significant deviations in parameters, suggesting that current CMB data sets give an internally consistent picture of the Lambda CDM model.
  • Gumenyuk, Pavel; Prause, Istvan (2018)
    Becker (J Reine Angew Math 255: 23-43, 1972) discovered a sufficient condition for quasiconformal extendibility of Loewner chains. Many known conditions for quasiconformal extendibility of holomorphic functions in the unit disk can be deduced from his result. We give a new proof of (a generalization of) Becker's result based on Slodkowski's Extended.-Lemma. Moreover, we characterize all quasiconformal extensions produced by Becker's (classical) construction and use that to obtain examples in which Becker's extension is extremal (i. e. optimal in the sense of maximal dilatation) or, on the contrary, fails to be extremal.
  • Korhonen, Tellervo; Loukola, Anu; Wedenoja, Juho; Nyman, Emma; Latvala, Antti; Broms, Ulla; Happola, Anja; Paunio, Tiina; Schrage, Andrew J.; Vink, Jaqueline M.; Mbarek, Hamdi; Boomsma, Dorret I.; Penninx, Brenda W. J. H.; Pergadia, Michele L.; Madden, Pamela A. F.; Kaprio, Jaakko (2014)
  • Sahu, Biswajyoti; Hartonen, Tuomo; Pihlajamaa, Päivi; Wei, Bei; Dave, Kashyap; Zhu, Fangjie; Kaasinen, Eevi; Lidschreiber, Katja; Lidschreiber, Michael; Daub, Carsten O.; Cramer, Patrick; Kivioja, Teemu; Taipale, Jussi (2022)
    Analysis of massively parallel reporter assays measuring the transcriptional activity of DNA sequences indicates that most transcription factor (TF) activity is additive and does not rely on specific TF-TF interactions. Individual TFs can have different gene regulatory activities. DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an similar to 100 times larger sequence space than the human genome using massively parallel reporter assays (MPRAs). Machine learning models revealed that transcription factors (TFs) generally act in an additive manner with weak grammar and that most enhancers increase expression from a promoter by a mechanism that does not appear to involve specific TF-TF interactions. The enhancers themselves can be classified into three types: classical, closed chromatin and chromatin dependent. We also show that few TFs are strongly active in a cell, with most activities being similar between cell types. Individual TFs can have multiple gene regulatory activities, including chromatin opening and enhancing, promoting and determining transcription start site (TSS) activity, consistent with the view that the TF binding motif is the key atomic unit of gene expression.
  • Koponen, Ismo (2021)
    Associative knowledge networks are often explored by using the so-called spreading activation model to find their key items and their rankings. The spreading activation model is based on the idea of diffusion- or random walk -like spreading of activation in the network. Here, we propose a generalisation, which relaxes an assumption of simple Brownian-like random walk (or equally, ordinary diffusion process) and takes into account nonlocal jump processes, typical for superdiffusive processes, by using fractional graph Laplacian. In addition, the model allows a nonlinearity of the diffusion process. These generalizations provide a dynamic equation that is analogous to fractional porous medium diffusion equation in a continuum case. A solution of the generalized equation is obtained in the form of a recently proposed q-generalized matrix transformation, the so-called q-adjacency kernel, which can be adopted as a systemic state describing spreading activation. Based on the systemic state, a new centrality measure called activity centrality is introduced for ranking the importance of items (nodes) in spreading activation. To demonstrate the viability of analysis based on systemic states, we use empirical data from a recently reported case of a university students' associative knowledge network about the history of science. It is shown that, while a choice of model does not alter rankings of the items with the highest rank, rankings of nodes with lower ranks depend essentially on the diffusion model.