21 research outputs found

    Multivariat analyse som verktøy til forståelse og reduksjon av kompleksitet av matematiske modeller i systembiologi

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    In the area of systems biology, technologies develop very fast, which allows us to collect massive amounts of various data. The main interest of scientists is to receive an insight into the obtained data sets and discover their inherent properties. Since the data often are rather complex and intimidating equations may be required for modelling, data analysis can be quite challenging for the majority of bio-scientists who do not master advanced mathematics. In this thesis it is proposed to use multivariate statistical methods as a tool for understanding the properties of complex models used for describing biological systems. The methods of multivariate analysis employed in this thesis search for latent variables that form a basis of all processes in a system. This often reduces dimensions of the system and makes it easier to get the whole picture of what is going on. Thus, in this work, methods of multivariate analysis were used with a descriptive purpose in Papers I and IV to discover effects of input variables on a response. Often it is necessary to know a functional form that could have generated the collected data in order to study the behaviour of the system when one or another parameter is tuned. For this purpose, we propose the Direct Look-Up (DLU) approach that is claimed here to be a worthy alternative to the already existing fitting methods due to its high computational speed and ability to avoid many problems such as subjectivity, choice of initial values, local optima and so on (Papers II and III). Another aspect covered in this thesis is an interpretation of function parameters by the custom human language with the use of multivariate analysis. This would enable mathematicians and bio-scientists to understand each other when describing the same object. It was accomplished here by using the concept of a metamodel and sensory analysis in Paper IV. In Paper I, a similar approach was used even though the main focus of the paper was slightly different. The original aim of the article was to show the advantages of the multi-way GEMANOVA analysis over the traditional ANOVA analysis for certain types of data. However, in addition, the relationship between human profiling of data samples and function parameters was discovered. In situations when funds for conducting experiments are limited and it is unrealizable to study all possible parameter combinations, it is necessary to have a smart way of choosing a few but most representative conditions for a particular system. In Paper V Multi-level Binary Replacement design (MBR) was developed as such, which can also be used for searching for a relevant parameter range. This new design method was applied here in Papers II and IV for selection of samples for further analyses.Teknologiutviklingen innenfor systembiologien er nå så rask at det gir mulighet til å samle svært store datamengder på kort tid og til relativ lav pris. Hovedinteressen til forskerne er typisk å få innsikt i dataene og deres iboende egenskaper. Siden data kan være ganske komplekse og ofte beskrives ved kompliserte, gjerne ikke-lineære, funksjoner, kan dataanalyse være ganske utfordrende for mange bioforskere som ikke behersker avansert matematikk. I dette arbeidet er det foreslått å bruke multivariat statistisk analyse for å komme nærmere en forståelse av egenskapene av kompliserte modeller som blir brukt for å beskrive biologiske systemer. De multivariate metodene som er benyttet i denne avhandlingen søker etter latente variabler som utgjør en lineær basis og tilnærming til de komplekse prosessene i et system. Dermed kan man oppnå en forenkling av systemet som er lettere å tolke. I dette arbeidet ble multivariate analysemetoder brukt i denne beskrivende hensikten i Artikler (Papers) I og IV til å oppdage effekter av funksjonsparametre på egenskapene til komplekse matematiske modeller. Ofte er det nødvendig å finne en matematisk funksjon som kunne ha generert de innsamlede dataene for å studere oppførselen av systemet. Med den hensikt foreslår vi en metode for modelltilpasning ved DLU-metoden (the Direct Look-Up) som her påstås å være et verdifullt alternativ til de eksisterende estimeringsmetodene på grunn av høy fart og evne til å unngå typiske problemer som for eksempel subjektivitet, valg av initialverdier, lokale optima, m.m (Artikler II og III). Et annet aspekt dekket i denne avhandlingen er bruken av multivariat analyse til å gi tolking av matematiske funksjonsparametre ved hjelp av et dagligdags vokabular. Dette kan gjøre det enklere for matematikere og bioforskere å forstå hverandre når de beskriver det samme objektet. Det var utført her ved å benytte ideen om en metamodell og sensorisk analyse i Artikkel IV. I Artikkel I var en lignende metode også brukt for å få sensoriske beskrivelser av bilder generert fra differensiallikninger. Hovedfokuset i Artikkel I var imidlertid et annet, nemlig å vise fordelen ved multi-way GEMANOVA-analyse fremfor den tradisjonelle ANOVA-analysen for visse datatyper. I denne artikkelen ble GEMANOVA brukt til å avdekke sammenhengen mellom kompliserte kombinasjoner av funksjonsparametrene og bildedeskriptorer. I situasjoner der ressurser til å utføre eksperimenter er begrenset og det er umulig å prøve ut alle kombinasjoner av parametre, er det behov for metoder som kan bestemme et fåtall av parameterinnstillinger som er mest mulig representative for et bestemt system. I Artikkel V ble derfor Multi-level Binary Replacement (MBR) design utviklet som en sådan, og den kan også brukes for å søke etter et relevant parameterrom for datasimuleringer. Den nye designmetoden ble anvendt i Artikler II og IV for utvelgelse av parameterverdier for videre analyser

    DataSHIELD:An Ethically Robust Solution to Multiple-Site Individual-Level Data Analysis

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    &lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; DataSHIELD (Data Aggregation Through Anonymous Summary-statistics from Harmonised Individual levEL Databases) has been proposed to facilitate the co-analysis of individual-level data from multiple studies without physically sharing the data. In a previous paper, we investigated whether DataSHIELD could protect participant confidentiality in accordance with UK law. In this follow-up paper, we investigate whether DataSHIELD addresses a broader range of ethics-related data-sharing concerns. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Ethics-related data-sharing concerns of Institutional Review Boards, ethics experts, international research consortia and research participants were identified through a literature search and systematically examined at a multidisciplinary workshop to determine whether DataSHIELD proposes mechanisms which can address these concerns. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; DataSHIELD addresses several ethics-related data-sharing concerns related to privacy, confidentiality, and the protection of the research participant's rights while sharing data and after the data have been shared. The data remain entirely under the direct management of the study that collected them. Data processing commands are strictly supervised, and the data are queried in a protected environment. Issues related to the return of individual research results when data are shared are eliminated; the responsibility for return remains at the study of origin. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; DataSHIELD can provide an innovative and robust solution for addressing commonly encountered ethics-related data-sharing concerns.</jats:p

    DataSHIELD: taking the analysis to the data, not the data to the analysis

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    Research in modern biomedicine and social science requires sample sizes so large that they can often only be achieved through a pooled co-analysis of data from several studies. But the pooling of information from individuals in a central database that may be queried by researchers raises important ethico-legal questions and can be controversial. In the UK this has been highlighted by recent debate and controversy relating to the UK's proposed 'care.data' initiative, and these issues reflect important societal and professional concerns about privacy, confidentiality and intellectual property. DataSHIELD provides a novel technological solution that can circumvent some of the most basic challenges in facilitating the access of researchers and other healthcare professionals to individual-level data. Commands are sent from a central analysis computer (AC) to several data computers (DCs) storing the data to be co-analysed. The data sets are analysed simultaneously but in parallel. The separate parallelized analyses are linked by non-disclosive summary statistics and commands transmitted back and forth between the DCs and the AC. This paper describes the technical implementation of DataSHIELD using a modified R statistical environment linked to an Opal database deployed behind the computer firewall of each DC. Analysis is controlled through a standard R environment at the AC. Based on this Opal/R implementation, DataSHIELD is currently used by the Healthy Obese Project and the Environmental Core Project (BioSHaRE-EU) for the federated analysis of 10 data sets across eight European countries, and this illustrates the opportunities and challenges presented by the DataSHIELD approach. DataSHIELD facilitates important research in settings where: (i) a co-analysis of individual-level data from several studies is scientifically necessary but governance restrictions prohibit the release or sharing of some of the required data, and/or render data access unacceptably slow; (ii) a research group (e.g. in a developing nation) is particularly vulnerable to loss of intellectual property-the researchers want to fully share the information held in their data with national and international collaborators, but do not wish to hand over the physical data themselves; and (iii) a data set is to be included in an individual-level co-analysis but the physical size of the data precludes direct transfer to a new site for analysis

    Privacy protected graphical functionality in DataSHIELD

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    ABSTRACT Objectives In several disciplines such as in biomedicine and social sciences the analysis of individual-level data or the co-analysis of data from different studies requires the pooling and the sharing of those data. However, sharing and combining sensitive individual-level data is often prohibited by ethico-legal constraints and other barriers such as the control maintenance and the huge sample sizes. The graphical illustration of microdata is also often forbidden as can potentially be unsecured on the identification of sensitive information. For example the plot of a standard scatterplot is disclosive as can explicitly specify the exact values of two measurements for each single individual. Approach DataSHIELD (www.datashield.ac.uk) is a novel approach that allows the analysis of sensitive individual-level data and the co-analysis of such data from several studies simultaneously without physically pooling the data. Results DataSHIELD functionality consists of several functions that provide the flexibility of performing data analysis through different statistical techniques. A part of this environment includes a number of graphical-related functions for the graphical illustration of the statistical properties and relationships between different variables. We overview the graphical functions in DataSHIELD (ds.histogram, ds.heatmapPlot, ds.contourPlot) and demonstrate a number of new functions including ds.scatterPlot and ds.boxPlot developed based on the application of different computational approaches like the k-Nearest Neighbours algorithm and ensuring privacy protected analysis. Conclusion DataSHIELD graphical functionality has certain methodological features for the representation of the relationships between different variables preserving their statistical properties and assuring the data privacy protection. These graphical approaches can be used or enhanced for application in various areas where confidentiality and information sensitivity is considered, for example in longitudinal data and survival analysis, in epidemiological studies, in geospatial analysis and several others

    Эффективность использования гетерополисоединений типа (NH4)2[Co(H2O)4]2[Mo8O27]∙6H2O в качестве катализаторов для получения этилена

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    Carrying out heterogeneous acid catalysis with the use of heteropoly compounds has received considerable attention due to the great economic and environmental benefits. In spite of this, its industrial application is limited as there are difficulties in catalyst regeneration (settling) caused by its relatively low thermal stability. The aim of present work was to search and select catalysts related to the class of heteropoly compounds for propane cracking, to test the selectivity of the prosses as well as to discuss possible approaches for solving the problem of catalyst deactivation, that can contribute to achieve stable characteristics of solid heteropoly catalysts. Among these approaches are: the development of new catalysts with high thermal stability, the modification of catalysts to promote coke combustion, the inhibition of coke formation on heteropoly compound catalysts during the process, carrying out the reactions in supercritical media and also the cascade reactions using a multifunctional heteropoly catalyst. The obtained catalyst was also studied by physicochemical methods to get deep knowledge about which features of these compounds influence on the catalytic activity. A highly active and selective catalyst for ammonium octomolybdenocobaltate(II) ammonium (NH4)2[Co(H2O)4]2[Mo8O27]∙6H2O was synthesized for cracking associated petroleum gases. The qualitative, quantitative, and structural composition as well as the specific surface area of the obtained catalyst was established by the methods of X-ray diffraction, X-ray phase and fluorescence analysis. It was revealed that ammonium octomolybdenocobaltate(II) crystallizes in a triclinic syngony with cell parameters: а = 8.6292(9) Å b = 9.4795(10) Å c = 12.2071(13) Å α = 104.326(2)° β = 109.910(2)° γ = 100.820(2)°.Гетерогенный кислотный катализ с помощью гетерополисоединений обладает большой экономической выгодой и экологическими преимуществами. Его применение, однако, было ограничено в некоторой степени из-за относительно низкой термостабильности гетерополисоединений, следовательно, из-за сложности регенерации катализатора (отстаивания). Целью данной работы является поиск и подбор катализаторов из класса гетерополисоединений для крекинга пропана, обсуждение подходов к проблеме дезактивации катализатора, которые могут способствовать достижению устойчивых характеристик твердых катализаторов гетерополисоединений, а так же проверка на селективность в крекинге пропана. Эти подходы включают в себя: разработку новых катализаторов, обладающих высокой термической стабильностью, модификацию катализаторов для улучшения сгорания кокса, ингибирование образования кокса на катализаторах гетерополисоединений во время работы, реакции в сверхкритических средах и каскадные реакции с использованием многофункционального катализатора из гетоерополисоединений. Полученный катализатор так же был исследован физико-химическими методами для более полного понимания какие именно особенности данного класса соединений влияют на каталитическую активность. Был синтезирован высокоактивный и селективный катализатор октомолибденокобальтат(II) аммония (NH4)2[Co(H2O)4]2[Mo8O27]∙6H2O для крекинга попутных нефтяных газов. Установлен качественный, количественный и структурный состав полученного катализатора методами рентгено-структурного, рентгенофазового, рентгенофлюорисцентного анализа, определенна удельная поверхность катализатора, а так же выявлена высокая каталитическая активность. Октомолибденокобальтат(II) аммония кристаллизуется в триклинной сингонии с параметрами ячейки: а = 8.6292(9) Å b = 9.4795(10) Å c = 12.2071(13) Å α = 104.326(2)° β = 109.910(2)° γ = 100.820(2)°
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