1,720,965 research outputs found
Algorithms for computational mass spectrometry based on the optimal transport theory
No full textIn this dissertation, we present a novel approach to developing computational methods for the analysis of mass and nuclear magnetic resonance spectra. We start with
the discussion of the state-of-the-art approaches, illustrated by a study of nuclear
magnetic resonance spectra of St John’s wort extracts. We describe the need for
mathematical theory for comparison of spectra of different molecules and with different resolutions. We then describe how to use the notion of optimal transport of
signal and the Wasserstein distance to develop algorithms for fitting a linear combination of reference spectra to a spectrum of a mixture of chemical compounds. The
algorithm makes it possible to accurately estimate the amounts of compounds with
overlapping spectra. We finish the dissertation with an application of our methods
to the problem of segmentation of mass spectrometric images, where we show that
they allow for obtaining biologically accurate and meaningful results when other
common approaches fail. Our results are applicable for various types of spectrometry and spectroscopy, including NMR spectroscopy and mass spectrometry. The
algorithms developed as a part of this thesis are available in an open-source Python
3 package masserstein available at https://github.com/mciach/masserstein.W niniejszej rozprawie przedstawiamy nowe podejscie do projektowania metod obliczeniowych do analizy widm masowych oraz widm magnetycznego rezonansu jadrowego (NMR). Rozprawe rozpoczynamy omówieniem obecnie stosowanych metod na przykładzie analizy widm NMR wyciagów z dziurawca. Uzasadniamy potrzebe opracowania aparatu matematycznego do porównywania widm róznych czasteczek oraz o róznej rozdzielczosci. Nastepnie opisujemy, w jaki sposób wykorzystac koncepcje optymalnego transportu sygnału i odległosci Wassersteina do opracowania algorytmu dopasowujacego kombinacje liniowa widm referencyjnych do widma mieszaniny zwiazków chemicznych. Metoda ta
pozwala na dokładna estymacje zawartosci zwiazków o nakładajacych sie widmach. Rozprawe konczymy zastosowaniem opracowanych metod do analizy obrazów spektrometrycznych, gdzie pokazujemy, ze pozwalaja one na otrzymanie biologicznie znaczacych wyników nawet gdy inne metody zawodza. Podejscie do analizy widm zaprezentowane w niniejszej pracy ma zastosowanie do róznych typów spektrometrii i spektroskopii, wliczajac w to spektroskopie magnetycznego rezonansu jadrowego oraz spektrometrie mas. Algorytmy opracowane w ramach ninejszej pracy zostały zaimplementowane
w pakiecie masserstein jezyka programowania Python 3, dostepnym pod adresem https://github.com/mciach/masserstein
Masserstein: Linear regression of mass spectra by optimal transport
No full textRationale The linear regression of mass spectra is a computational problem defined as fitting a linear combination of reference spectra to an experimental one. It is typically used to estimate the relative quantities of selected ions. In this work, we study this problem in an abstract setting to develop new approaches applicable to a diverse range of experiments. Methods To overcome the sensitivity of the ordinary least-squares regression to measurement inaccuracies, we base our methods on a non-conventional spectral dissimilarity measure, known as the Wasserstein or the Earth Mover's distance. This distance is based on the notion of the cost of transporting signal between mass spectra, which renders it naturally robust to measurement inaccuracies in the mass domain. Results Using a data set of 200 mass spectra, we show that our approach is capable of estimating ion proportions accurately without extensive preprocessing of spectra required by other methods. The conclusions are further substantiated using data sets simulated in a way that mimics most of the measurement inaccuracies occurring in real experiments. Conclusions We have developed a linear regression algorithm based on the notion of the cost of transporting signal between spectra. Our implementation is available in a Python 3 package called masserstein, which is freely available at .Fonds Wetenschappelijk Onderzoek, Grant/Award Number: VS.028.19N; Narodowe Centrum Nauki, Grant/Award Numbers: 2017/26/D/ST6/00304, 2018/29/B/ST6/00681
This work was funded by the Special Research Fund (BOF) of the Hasselt University BOF18BL09, the FWO-PAS grant VS.028.19N, and the Polish National Science Centre grants #2018/29/ B/ST6/00681 and #2017/26/D/ST6/00304.Ciach, MA (corresponding author), Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
[email protected]
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry
No full textElectron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several concurrent reactions triggered by the transfer of an electron from its anion source to sample cations. Transferring an electron causes peptide backbone cleavage while leaving labile post-translational modifications intact. The obtained fragmentation spectra provide valuable information for sequence and structure analyses. In this study, we propose a formal mathematical model of the ETD fragmentation process in the form of a system of stochastic differential equations describing its joint dynamics. Parameters of the model correspond to the rates of occurring reactions. Their estimates for various experimental settings give insight into the dynamics of the ETD process. We estimate the model parameters from the relative quantities of fragmentation products in a given mass spectrum by solving a nonlinear optimization problem. The cost function penalizes for the differences between the analytically derived average number of reaction products and their experimental counterparts. The presented method proves highly robust to noise in silico. Moreover, the model can explain a considerable amount of experimental results for a wide range of instrumentation settings. The implementation of the presented workflow, code-named ETDetective, is freely available under the two-clause BSD license.This work was partially supported by the National Science Centre grant numbers 2013/09/B/ST6/01575, 2014/12/W/ST5/00592, and 2015/17/N/ST6/03565 and the SBO grant InSPECtor (120025) of the Flemish Agency for Innovation by Science and Technology (IWT). The authors thank the Research Foundation-Flanders (FWO) for funding a PhD fellowship (F.L.). The Synapt G2 mass spectrometer is funded by a grant from the Hercules Foundation-Flanders
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
