Portfolio EDEND: 2014-09-15

Publisher name: Oxford University Press PY - 2015/1/1 Y1 - 2015/1/1 N2 - Motivation: MS2-GFP-tagging of RNA is currently the only method to measure intervals between consecutive transcription events in live cells. For this, new transcripts must be accurately detected from intensity time traces. Results: We present a novel method for automatically estimating RNA numbers and production intervals from temporal data of cell fluorescence intensities that reduces uncertainty by exploiting temporal information. We also derive a robust variant, more resistant to outliers caused e.g. by RNAs moving out of focus. Using Monte Carlo simulations, we show that the quantification of RNA numbers and production intervals is generally improved compared with previous methods. Finally, we analyze data from live Escherichia coli and show statistically significant differences to previous methods. The new methods can be used to quantify numbers and production intervals of any fluorescent probes, which are present in low copy numbers, are brighter than the cell background and degrade slowly. Availability: Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7ehakkin22/jumpdet/. Contact: AB - Motivation: MS2-GFP-tagging of RNA is currently the only method to measure intervals between consecutive transcription events in live cells. For this, new transcripts must be accurately detected from intensity time traces. Results: We present a novel method for automatically estimating RNA numbers and production intervals from temporal data of cell fluorescence intensities that reduces uncertainty by exploiting temporal information. We also derive a robust variant, more resistant to outliers caused e.g. by RNAs moving out of focus. Using Monte Carlo simulations, we show that the quantification of RNA numbers and production intervals is generally improved compared with previous methods. Finally, we analyze data from live Escherichia coli and show statistically significant differences to previous methods. The new methods can be used to quantify numbers and production intervals of any fluorescent probes, which are present in low copy numbers, are brighter than the cell background and degrade slowly. Availability: Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7ehakkin22/jumpdet/. Contact: UR - http://www.scopus.com/inward/record.url?scp=84922352843&partnerID=8YFLogxK U2 - 10.1093/bioinformatics/btu592 DO - 10.1093/bioinformatics/btu592 M3 - Article VL - 31 SP - 69 EP - 75 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 1 ER - TY - JOUR T1 - Characterizing rate limiting steps in transcription from RNA production times in live cells AU - Häkkinen, Antti AU - Ribeiro, Andre S. PY - 2016/5/1 Y1 - 2016/5/1 N2 - Motivation: Single-molecule measurements of live Escherichia coli transcription dynamics suggest that this process ranges from sub- to super-Poissonian, depending on the conditions and on the promoter. For its accurate quantification, we propose a model that accommodates all these settings, and statistical methods to estimate the model parameters and to select the relevant components. Results: The new methodology has improved accuracy and avoids overestimating the transcription rate due to finite measurement time, by exploiting unobserved data and by accounting for the effects of discrete sampling. First, we use Monte Carlo simulations of models based on measurements to show that the methods are reliable and offer substantial improvements over previous methods. Next, we apply the methods on measurements of transcription intervals of different promoters in live E. coli, and show that they produce significantly different results, both in low- and high-noise settings, and that, in the latter case, they even lead to qualitatively different results. Finally, we demonstrate that the methods can be generalized for other similar purposes, such as for estimating gene activation kinetics. In this case, the new methods allow quantifying the inducer uptake dynamics as opposed to just comparing them between cases, which was not previously possible. We expect this new methodology to be a valuable tool for functional analysis of cellular processes using single-molecule or single-event microscopy measurements in live cells. AB - Motivation: Single-molecule measurements of live Escherichia coli transcription dynamics suggest that this process ranges from sub- to super-Poissonian, depending on the conditions and on the promoter. For its accurate quantification, we propose a model that accommodates all these settings, and statistical methods to estimate the model parameters and to select the relevant components. Results: The new methodology has improved accuracy and avoids overestimating the transcription rate due to finite measurement time, by exploiting unobserved data and by accounting for the effects of discrete sampling. First, we use Monte Carlo simulations of models based on measurements to show that the methods are reliable and offer substantial improvements over previous methods. Next, we apply the methods on measurements of transcription intervals of different promoters in live E. coli, and show that they produce significantly different results, both in low- and high-noise settings, and that, in the latter case, they even lead to qualitatively different results. Finally, we demonstrate that the methods can be generalized for other similar purposes, such as for estimating gene activation kinetics. In this case, the new methods allow quantifying the inducer uptake dynamics as opposed to just comparing them between cases, which was not previously possible. We expect this new methodology to be a valuable tool for functional analysis of cellular processes using single-molecule or single-event microscopy measurements in live cells. U2 - 10.1093/bioinformatics/btv744 DO - 10.1093/bioinformatics/btv744 M3 - Article VL - 32 SP - 1346 EP - 1352 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 9 ER - TY - JOUR T1 - Satisfiability of modal inclusion logic T2 - Lax and strict semantics AU - Hella, Lauri AU - Kuusisto, Antti AU - Meier, Arne AU - Vollmer, Heribert N1 - DUPL=50949587 PY - 2019/10/1 Y1 - 2019/10/1 N2 - We investigate the computational complexity of the satisfiability problem of modal inclusion logic. We distinguish two variants of the problem: one for the strict and another one for the lax semantics. Both problems turn out to be EXPTIME-complete on general structures. Finally,we showhowfor a specific class of structures NEXPTIME-completeness for these problems under strict semantics can be achieved. AB - We investigate the computational complexity of the satisfiability problem of modal inclusion logic. We distinguish two variants of the problem: one for the strict and another one for the lax semantics. Both problems turn out to be EXPTIME-complete on general structures. Finally,we showhowfor a specific class of structures NEXPTIME-completeness for these problems under strict semantics can be achieved. KW - Computational complexity KW - Modal inclusion logic KW - Satisfiability KW - Team semantics U2 - 10.1145/3356043 DO - 10.1145/3356043 M3 - Article VL - 21 JO - ACM TRANSACTIONS ON COMPUTATIONAL LOGIC JF - ACM TRANSACTIONS ON COMPUTATIONAL LOGIC SN - 1529-3785 IS - 1 M1 - 7 ER - TY - JOUR T1 - Van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads AU - Karilainen, Topi AU - Cramariuc, Oana AU - Kuisma, Mikael AU - Tappura, Kirsi AU - Hukka, Terttu I. N1 - ORG=fys,0.5 ORG=keb,0.5 PY - 2015 Y1 - 2015 N2 - The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin-C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin-C60 dyad using Car-Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long-range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60. In the considered dyad, fullerene's affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close. AB - The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin-C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin-C60 dyad using Car-Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long-range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60. In the considered dyad, fullerene's affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close. KW - Car-Parrinello molecular dynamics KW - Fullerene KW - Porphyrin KW - Time-dependent-density functional theory UR - http://www.scopus.com/inward/record.url?scp=84923259668&partnerID=8YFLogxK U2 - 10.1002/jcc.23834 DO - 10.1002/jcc.23834 M3 - Article VL - 36 SP - 612 EP - 621 JO - Journal of Computational Chemistry JF - Journal of Computational Chemistry SN - 0192-8651 IS - 9 ER - TY - JOUR T1 - Comparative analysis of tissue reconstruction algorithms for 3D histology AU - Kartasalo, Kimmo AU - Latonen, Leena AU - Vihinen, Jorma AU - Visakorpi, Tapio AU - Nykter, Matti AU - Ruusuvuori, Pekka PY - 2018/9/1 Y1 - 2018/9/1 N2 - Motivation: Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking. Results: We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches. AB - Motivation: Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking. Results: We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches. U2 - 10.1093/bioinformatics/bty210 DO - 10.1093/bioinformatics/bty210 M3 - Article VL - 34 SP - 3013 EP - 3021 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 17 ER - TY - GEN T1 - Circularly Polarized Textile Tag Antenna for Wearable Passive UHF RFID Systems AU - Kuang, Ye AU - Ma, Shubin AU - Ukkonen, Leena AU - Virkki, Johanna AU - Björninen, Toni PY - 2019/3/18 Y1 - 2019/3/18 N2 - We present a circularly polarized tag antenna using textile materials for wearable passive ultra high frequency (UHF) radio frequency identification (RFID) system. A corner-truncated square patch with a shorting pin and an inductive feed network are used to achieve circularly polarization and conjugate impedance matching. The antenna has similar best axial ratio values of 2.1 dB and 2.2 dB for both in air and on-body conditions, and desirable corresponding read range of 9.1 m and 8.4 m. AB - We present a circularly polarized tag antenna using textile materials for wearable passive ultra high frequency (UHF) radio frequency identification (RFID) system. A corner-truncated square patch with a shorting pin and an inductive feed network are used to achieve circularly polarization and conjugate impedance matching. The antenna has similar best axial ratio values of 2.1 dB and 2.2 dB for both in air and on-body conditions, and desirable corresponding read range of 9.1 m and 8.4 m. KW - Circularly polarized antenna KW - Radio frequency identification KW - Wearable antenna U2 - 10.23919/ACESS.2018.8669314 DO - 10.23919/ACESS.2018.8669314 M3 - Conference contribution BT - 2018 International Applied Computational Electromagnetics Society Symposium in China, ACES-China 2018 PB - IEEE ER - TY - JOUR T1 - Modeling mass transfer in fracture flows with the time domain-random walk method AU - Kuva, J. AU - Voutilainen, M. AU - Mattila, K. PY - 2019 Y1 - 2019 N2 - The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous matrix. Simulations with several flow rates, diffusion coefficients, and matrix porosities indicate good agreement between the numerical approximations and analytical solutions. AB - The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous matrix. Simulations with several flow rates, diffusion coefficients, and matrix porosities indicate good agreement between the numerical approximations and analytical solutions. KW - Advection KW - Breakthrough curve KW - Matrix diffusion KW - Porous media KW - Simulation KW - Solute transport U2 - 10.1007/s10596-019-09852-5 DO - 10.1007/s10596-019-09852-5 M3 - Article JO - COMPUTATIONAL GEOSCIENCES JF - COMPUTATIONAL GEOSCIENCES SN - 1420-0597 ER - TY - JOUR T1 - An automated algorithm for reliable equation of state fitting of magnetic systems AU - Levämäki, H. AU - Tian, L.-Y. AU - Vitos, L. AU - Ropo, M. PY - 2019 Y1 - 2019 N2 - In computational physics and materials science ground-state properties are often extracted from an equation of state fit to energy-volume data. Magnetic systems often have multiple magnetic phases present in the energy-volume data, which poses a challenge for the fitting approach because the results are sensitive to the selection of included fitting points. This is because practically all popular equation of state fitting functions, such as Murnaghan and Birch-Murnaghan, assume just one phase and therefore cannot correctly fit magnetic energy-volume data that contains multiple phases. When fitting magnetic energy-volume data it is therefore important to select the range of fitting points in such a way that only points from the one relevant phase are included. We present a simple algorithm that makes the point selection automatically. Selecting fitting points automatically removes human bias and should also be useful for large-scale projects where selecting all fitting points by hand is not feasible. AB - In computational physics and materials science ground-state properties are often extracted from an equation of state fit to energy-volume data. Magnetic systems often have multiple magnetic phases present in the energy-volume data, which poses a challenge for the fitting approach because the results are sensitive to the selection of included fitting points. This is because practically all popular equation of state fitting functions, such as Murnaghan and Birch-Murnaghan, assume just one phase and therefore cannot correctly fit magnetic energy-volume data that contains multiple phases. When fitting magnetic energy-volume data it is therefore important to select the range of fitting points in such a way that only points from the one relevant phase are included. We present a simple algorithm that makes the point selection automatically. Selecting fitting points automatically removes human bias and should also be useful for large-scale projects where selecting all fitting points by hand is not feasible. KW - EOS KW - Equation of state fitting U2 - 10.1016/j.commatsci.2018.09.026 DO - 10.1016/j.commatsci.2018.09.026 M3 - Article VL - 156 SP - 121 EP - 128 JO - Computational Materials Science JF - Computational Materials Science SN - 0927-0256 ER - TY - JOUR T1 - Introducing libeemd T2 - a program package for performing the ensemble empirical mode decomposition AU - Luukko, P. J. J. AU - Helske, J. AU - Räsänen, E. N1 - EXT="Luukko, P. J. J." PY - 2016/6/1 Y1 - 2016/6/1 N2 - The ensemble empirical mode decomposition (EEMD) and its complete variant (CEEMDAN) are adaptive, noise-assisted data analysis methods that improve on the ordinary empirical mode decomposition (EMD). All these methods decompose possibly nonlinear and/or nonstationary time series data into a finite amount of components separated by instantaneous frequencies. This decomposition provides a powerful method to look into the different processes behind a given time series data, and provides a way to separate short time-scale events from a general trend. We present a free software implementation of EMD, EEMD and CEEMDAN and give an overview of the EMD methodology and the algorithms used in the decomposition. We release our implementation, libeemd, with the aim of providing a user-friendly, fast, stable, well-documented and easily extensible EEMD library for anyone interested in using (E)EMD in the analysis of time series data. While written in C for numerical efficiency, our implementation includes interfaces to the Python and R languages, and interfaces to other languages are straightforward. AB - The ensemble empirical mode decomposition (EEMD) and its complete variant (CEEMDAN) are adaptive, noise-assisted data analysis methods that improve on the ordinary empirical mode decomposition (EMD). All these methods decompose possibly nonlinear and/or nonstationary time series data into a finite amount of components separated by instantaneous frequencies. This decomposition provides a powerful method to look into the different processes behind a given time series data, and provides a way to separate short time-scale events from a general trend. We present a free software implementation of EMD, EEMD and CEEMDAN and give an overview of the EMD methodology and the algorithms used in the decomposition. We release our implementation, libeemd, with the aim of providing a user-friendly, fast, stable, well-documented and easily extensible EEMD library for anyone interested in using (E)EMD in the analysis of time series data. While written in C for numerical efficiency, our implementation includes interfaces to the Python and R languages, and interfaces to other languages are straightforward. KW - Adaptive data analysis KW - Detrending KW - Hilbert–Huang transform KW - Intrinsic mode function KW - Noise-assisted data analysis KW - Time series analysis U2 - 10.1007/s00180-015-0603-9 DO - 10.1007/s00180-015-0603-9 M3 - Article VL - 31 SP - 545 EP - 557 JO - Computational Statistics JF - Computational Statistics SN - 0943-4062 IS - 2 ER - TY - JOUR T1 - Growth behavior and magnetic properties of spherical uranium oxide nanoclusters AU - Ma, Li AU - Ray, Asok K. PY - 2013/2 Y1 - 2013/2 N2 - The growth behavior and magnetic properties of spherical uranium oxide nanoclusters have been investigated using the generalized gradient approximation (GGA) to density functional theory (DFT). The geometries of UnO m clusters remain the Oh symmetry after DFT relaxation. The largest binding energy corresponds to the cluster with the smallest deviation from the bulk (UO2) ratio. The electronic structures and magnetic properties of these nanoclusters are presented. We find the chemical bonding between the U and O atoms has a significant ionic character. The reduction of magnetism in the inner positions can be understood by the charge transfer and the hybridization between U atoms and the neighboring O atoms. AB - The growth behavior and magnetic properties of spherical uranium oxide nanoclusters have been investigated using the generalized gradient approximation (GGA) to density functional theory (DFT). The geometries of UnO m clusters remain the Oh symmetry after DFT relaxation. The largest binding energy corresponds to the cluster with the smallest deviation from the bulk (UO2) ratio. The electronic structures and magnetic properties of these nanoclusters are presented. We find the chemical bonding between the U and O atoms has a significant ionic character. The reduction of magnetism in the inner positions can be understood by the charge transfer and the hybridization between U atoms and the neighboring O atoms. KW - Growth behavior KW - Magnetism KW - Nanoclusters KW - Uranium oxide UR - http://www.scopus.com/inward/record.url?scp=84876525693&partnerID=8YFLogxK U2 - 10.1166/jctn.2013.2701 DO - 10.1166/jctn.2013.2701 M3 - Article VL - 10 SP - 334 EP - 340 JO - Journal of Computational and Theoretical Nanoscience JF - Journal of Computational and Theoretical Nanoscience SN - 1546-1955 IS - 2 ER - TY - JOUR T1 - Density functional theory study of FePdn (n = 2-14) clusters and interactions with small molecules AU - Ma, Li AU - Wang, Jianguang AU - Hao, Yuanyuan AU - Wang, Guanghou PY - 2013/2 Y1 - 2013/2 N2 - First-principles calculations have been conducted to investigate the properties of FePdn (n = 2-14) clusters. In the lowest energy structures of FePdn clusters, the Fe atom gradually moves from the convex to the surface, and then to the interior site with the number of Pd atoms increasing from 2 to 14. The magnetic moments of Pdn clusters have been enhanced by the doping of Fe impurity. Furthermore, the adsorption of small molecules, including NH3, H2O, CO, H2, and O2, on the higher stability of FePdn (n = 5, 7, 10, and 12) clusters were studied. The lowest energy adsorption structures are obtained for each molecule. On the whole, the adsorption energies vary as the order of Ea(H2O)