Browsing by Subject "data analysis"
Now showing items 1-9 of 9
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(Helsingfors universitet, 2011)Metabolomics is a rapidly growing research field that studies the response of biological systems to environmental factors, disease states and genetic modifications. It aims at measuring the complete set of endogenous metabolites, i.e. the metabolome, in a biological sample such as plasma or cells. Because metabolites are the intermediates and end products of biochemical reactions, metabolite compositions and metabolite levels in biological samples can provide a wealth of information on on-going processes in a living system. Due to the complexity of the metabolome, metabolomic analysis poses a challenge to analytical chemistry. Adequate sample preparation is critical to accurate and reproducible analysis, and the analytical techniques must have high resolution and sensitivity to allow detection of as many metabolites as possible. Furthermore, as the information contained in the metabolome is immense, the data set collected from metabolomic studies is very large. In order to extract the relevant information from such large data sets, efficient data processing and multivariate data analysis methods are needed. In the research presented in this thesis, metabolomics was used to study mechanisms of polymeric gene delivery to retinal pigment epithelial (RPE) cells. The aim of the study was to detect differences in metabolomic fingerprints between transfected cells and non-transfected controls, and thereafter to identify metabolites responsible for the discrimination. The plasmid pCMV-β was introduced into RPE cells using the vector polyethyleneimine (PEI). The samples were analyzed using high performance liquid chromatography (HPLC) and ultra performance liquid chromatography (UPLC) coupled to a triple quadrupole (QqQ) mass spectrometer (MS). The software MZmine was used for raw data processing and principal component analysis (PCA) was used in statistical data analysis. The results revealed differences in metabolomic fingerprints between transfected cells and non-transfected controls. However, reliable fingerprinting data could not be obtained because of low analysis repeatability. Therefore, no attempts were made to identify metabolites responsible for discrimination between sample groups. Repeatability and accuracy of analyses can be influenced by protocol optimization. However, in this study, optimization of analytical methods was hindered by the very small number of samples available for analysis. In conclusion, this study demonstrates that obtaining reliable fingerprinting data is technically demanding, and the protocols need to be thoroughly optimized in order to approach the goals of gaining information on mechanisms of gene delivery.
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(2022)Context. Active regions on the photosphere of a star have been the major obstacle for detecting Earth-like exoplanets using the radial velocity (RV) method. A commonly employed solution for addressing stellar activity is to assume a linear relationship between the RV observations and the activity indicators along the entire time series, and then remove the estimated contribution of activity from the variation in RV data (overall correction method). However, since active regions evolve on the photosphere over time, correlations between the RV observations and the activity indicators will correspondingly be anisotropic. Aims. We present an approach that recognizes the RV locations where the correlations between the RV and the activity indicators significantly change in order to better account for variations in RV caused by stellar activity. Methods. The proposed approach uses a general family of statistical breakpoint methods, often referred to as change point detection (CPD) algorithms; several implementations of which are available in R and python. A thorough comparison is made between the breakpoint-based approach and the overall correction method. To ensure wide representativity, we use measurements from real stars that have different levels of stellar activity and whose spectra have different signal-to-noise ratios. Results. When the corrections for stellar activity are applied separately to each temporal segment identified by the breakpoint method, the corresponding residuals in the RV time series are typically much smaller than those obtained by the overall correction method. Consequently, the generalized Lomb-Scargle periodogram contains a smaller number of peaks caused by active regions. The CPD algorithm is particularly effective when focusing on active stars with long time series, such as alpha Cen B. In that case, we demonstrate that the breakpoint method improves the detection limit of exoplanets by 74% on average with respect to the overall correction method. Conclusions. CPD algorithms provide a useful statistical framework for estimating the presence of change points in a time series. Since the process underlying the RV measurements generates anisotropic data by its intrinsic properties, it is natural to use CPD to obtain cleaner signals from RV data. We anticipate that the improved exoplanet detection limit may lead to a widespread adoption of such an approach. Our test on the HD 192310 planetary system is encouraging, as we confirm the presence of the two hosted exoplanets and we determine orbital parameters consistent with the literature, also providing much more precise estimates for HD 192310 c.
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(2018)Data musicalization is the process of automatically composing music based on given data, as an approach to perceptualizing information artistically. The aim of data musicalization is to evoke subjective experiences in relation to the information, rather than merely to convey unemotional information objectively. This paper is written as a tutorial for readers interested in data musicalization. We start by providing a systematic characterization of musicalization approaches, based on their inputs, methods and outputs. We then illustrate data musicalization techniques with examples from several applications: one that perceptualizes physical sleep data as music, several that artistically compose music inspired by the sleep data, one that musicalizes on-line chat conversations to provide a perceptualization of liveliness of a discussion, and one that uses musicalization in a game-like mobile application that allows its users to produce music. We additionally provide a number of electronic samples of music produced by the different musicalization applications.
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(2020)Objective The aim of this study was to assess the marketing status of the new paediatric medicinal products listed in the 10-year report as initially authorised between 2007 and 2016, reflecting the product availability in four Nordic countries. Design This is a cross-sectional study. Setting Analysis of the national medicine agency's databases in Denmark, Finland, Norway and Sweden. Data source New medicinal products with paediatric indications and new paediatric formulations listed in the Annex of European Medicines Agency's EU Paediatric Regulation 10-year report. Data analysis The products were classified according to national marketing status between January 2019 and March 2019, whether a product was authorised and whether the product was marketed. Main outcome measures The percentages of the new medicinal products with paediatric indications and new paediatric formulations having a valid marketing authorisation and being marketed, both in terms of the sums of all countries and separately for each country. Results Across the four countries, 21%-32% (16/76-24/76) of the new medicinal products were not marketed. Of the new formulations relevant to children, 29%-50% (16/56-28/56) were not marketed, and a significant proportion of these products had never been marketed. Conclusions This study reflects the reality of the implementation of the Paediatric Regulation. The results show that several new paediatric medicines and new formulations are not marketed. This affects the product availability. Similar data from other countries are needed to evaluate the overall European status to find remedies to current situation and increase the availability of the medicines for children. ©
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(2021)Context. The Mutual Impedance Probe (RPC-MIP) carried by the Rosetta spacecraft monitored both the plasma density and the electric field in the close environment of comet 67P/Churyumov-Gerasimenko (67P), as the instrument was operating alternatively in two main modes: active and passive. The active mode is used primarily to perform plasma density measurements, while the passive mode enables the instrument to work as a wave analyzer. Aims. We are reporting electric field emissions at the plasma frequency near comet 67P observed by RPC-MIP passive mode. The electric field emissions are related to Langmuir waves within the cometary ionized environment. In addition, this study gives feedback on the density measurement capability of RPC-MIP in the presence of cold electrons. Methods. We studied the occurrence rate of the electric field emissions as well as their dependence on solar wind structures like stream interaction regions (SIRs) and coronal mass ejections (CMEs). Results. We are showing that strong electric field emissions at the plasma frequency near 67P were present sporadically throughout the period when Rosetta was escorting the comet, without being continuous, as the occurrence rate is reported to be of about 1% of all the measured RPC-MIP passive spectra showing strong electric field emissions. The Langmuir wave activity monitored by RPC-MIP showed measurable enhancements during SIR or CME interactions and near perihelion. Conclusions. According to our results, Langmuir waves are a common feature at 67P during the passage of SIRs. Comparing the plasma frequency given by the RPC-MIP passive mode during Langmuir wave periods with the RPC-MIP active mode observations, we conclude that the measurement accuracy of RPC-MIP depends on the operational submode when the cold electron component dominates the electron density.
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(Helsingin yliopisto, 2019)The Oxford Nanopore MinION is a third generation sequencer utilizing nanopore sequencing technology. The nanopore sequencing method allows sequencing of either DNA or RNA strands as they pass through the membrane-embedded nanopores. By measuring the corresponding fluctuations in the ion flow passing through the nanopore the passing strands can be sequenced directly without additional second-hand reactions or measurements. The MinION sequencing has very distinctly different characteristics compared to the market leaders of the sequencing field. The small form factor of the device further helps it to separate itself from the other alternatives. However, the technology has only been on the market for a very short time and thus very little golden standards regarding its capabilities or usage have been established. This thesis describes our experiences testing the capabilities of the MinION sequencer both before its commercial release as a part of a special early access program, as well as our continued experiments with the device following its commercial launch. The main results of this study include successfully sequencing and aligning E.coli and human gDNA samples to their respective reference genomes. Using our sequencing and analysis pipeline specifically tuned to the MinION we were able to sequence the entire E.coli genome on a single MinION flow cell with an average depth of around 180. Over the course of the thesis project the MinION sequencing protocol was evaluated and optimized in order to determine whether it has the potential to achieve our ultimate goal of reliably sequencing the previously inaccessible genomic regions of the human genome. The possibility of augmenting the sequencing protocol by adding the pre-sequencing target enrichment was also explored. Ultimately we were able to confirm that the MinION sequencer can be used to sequence long DNA fragments from a multitude of sample types. The majority of the produced reads could successfully be aligned against a reference genome. However, the limited yield and sequencing quality of a single experiment does limit the applicability of the method for more complicated genomic studies. These issues can be addressed with various techniques, chiefly target enrichment, but adapting such methods into the sequencing pipeline has its own challenges.
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(2019)We study interplanetary coronal mass ejections (ICMEs) measured by probes at different heliocentric distances (0.3-1 AU) to investigate the propagation of ICMEs in the inner heliosphere and determine how the generic features of ICMEs change with heliospheric distance. Using data from the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER), Venus Express and ACE spacecraft, we analyze with the superposed epoch technique the profiles of ICME substructures, namely, the sheath and the magnetic ejecta. We determine that the median magnetic field magnitude in the sheath correlates well with ICME speeds at 1 AU, and we use this proxy to order the ICMEs at all spacecraft. We then investigate the typical ICME profiles for three categories equivalent to slow, intermediate, and fast ICMEs. Contrary to fast ICMEs, slow ICMEs have a weaker solar wind field at the front and a more symmetric magnetic field profile. We find the asymmetry to be less pronounced at Earth than at Mercury, indicating a relaxation taking place as ICMEs propagate. We also find that the magnetic field intensities in the wake region of the ICMEs do not go back to the pre-ICME solar wind intensities, suggesting that the effects of ICMEs on the ambient solar wind last longer than the duration of the transient event. Such results provide an indication of physical processes that need to be reproduced by numerical simulations of ICME propagation. The samples studied here will be greatly improved by future missions dedicated to the exploration of the inner heliosphere, such as Parker Solar Probe and Solar Orbiter.
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(2022)Context. Airless planetary bodies are studied mainly by remote sensing methods. Reflectance spectroscopy is often used to derive their compositions. One of the main complications for the interpretation of reflectance spectra is surface alteration by space weathering caused by irradiation by solar wind and micrometeoroid particles. Aims. We aim to evaluate the damage to the samples from H+ and laser irradiation and relate it to the observed alteration in the spectra. Methods. We used olivine (OL) and pyroxene (OPX) pellets irradiated by 5 keV H+ ions and individual femtosecond laser pulses and measured their visible (VIS) and near-infrared (NIR) spectra. We observed the pellets with scanning and transmission electron microscopy. We studied structural, mineralogical, and chemical modifications in the samples. Finally, we connected the material observations to changes in the reflectance spectra. Results. In both minerals, H+ irradiation induces partially amorphous sub-surface layers containing small vesicles. In OL pellets, these vesicles are more tightly packed than in OPX ones. Any related spectral change is mainly in the VIS spectral slope. Changes due to laser irradiation are mostly dependent on the material's melting temperature. Of all the samples, only the laser-irradiated OL contains nanophase Fe particles, which induce detectable spectral slope change throughout the measured spectral range. Our results suggest that spectral changes at VIS-NIR wavelengths are mainly dependent on the thickness of (partially) amorphous sub-surface layers. Furthermore, amorphisation smooths micro-roughness, increasing the contribution of volume scattering and absorption over surface scattering. Conclusions. Soon after exposure to the space environment, the appearance of partially amorphous sub-surface layers results in rapid changes in the VIS spectral slope. In later stages (onset of micrometeoroid bombardment), we expect an emergence of nanoparticles to also mildly affect the NIR spectral slope. An increase in the dimensions of amorphous layers and vesicles in the more space-weathered material will only cause band-depth variation and darkening.
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(2022)Context. The direct imaging of potentially habitable exoplanets is one prime science case for the next generation of high contrast imaging instruments on ground-based, extremely large telescopes. To reach this demanding science goal, the instruments are equipped with eXtreme Adaptive Optics (XAO) systems which will control thousands of actuators at a framerate of kilohertz to several kilohertz. Most of the habitable exoplanets are located at small angular separations from their host stars, where the current control laws of XAO systems leave strong residuals. Aims. Current AO control strategies such as static matrix-based wavefront reconstruction and integrator control suffer from a temporal delay error and are sensitive to mis-registration, that is, to dynamic variations of the control system geometry. We aim to produce control methods that cope with these limitations, provide a significantly improved AO correction, and, therefore, reduce the residual flux in the coronagraphic point spread function (PSF). Methods. We extend previous work in reinforcement learning for AO. The improved method, called the Policy Optimization for Adaptive Optics (PO4AO), learns a dynamics model and optimizes a control neural network, called a policy. We introduce the method and study it through numerical simulations of XAO with Pyramid wavefront sensor (PWFS) for the 8-m and 40-m telescope aperture cases. We further implemented PO4AO and carried out experiments in a laboratory environment using Magellan Adaptive Optics eXtreme system (MagAO-X) at the Steward laboratory. Results. PO4AO provides the desired performance by improving the coronagraphic contrast in numerical simulations by factors of 3-5 within the control region of deformable mirror and PWFS, both in simulation and in the laboratory. The presented method is also quick to train, that is, on timescales of typically 5-10 s, and the inference time is sufficiently small (
