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Dissertations / Theses on the topic 'Life sciences'
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Yu, Jian Qing. "Virtual learning environments and life sciences." Thesis, Nottingham Trent University, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442337.
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Dail, Mathias. "Clustering unstructured life sciences experiments with unsupervised machine learning : Natural language processing for unstructured life sciences texts." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-265549.
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The purpose of this master’s thesis is to analyse different types of document representations in the context of improving, in an unsupervised manner, the searchability of unstructured textual life sciences experiments by clustering similar experiments together. The challenge is to produce, analyse and compare different representations of the life sciences data by using traditional and advanced unsupervised Machine learning models. The text data analysed in this work is noisy and very heterogeneous, as it comes from a real-world Electronic Lab Notebook. Clustering unstructured and unlabeled text experiments is challenging. It requires the creation of representations based only on the relevant information existing in an experiment. This work studies statistical and generative techniques, word embeddings and some of the most recent deep learning models in Natural Language Processing to create the various representation of the studied data. It explores the possibility of combining multiple techniques and using external life-sciences knowledge-bases to create richer representations before applying clustering algorithms. Different types of analysis are performed, including an assessment done by experts, to evaluate and compare the scientific relevance of the cluster of experiments created by the different data representations. The results show that traditional statistical techniques can still produce good baselines. Modern deep learning techniques have been shown to model the studied data well and create rich representations. Combining multiple techniques with external knowledge (biomedical and life-science-related ontologies) have been shown to produce the best results in grouping similar relevant experiments together. The different studied techniques enable to model different, and complementary aspects of a text, therefore combining them is a key to significantly improve the clustering of unstructured data.Syftet med denna uppsats är att analysera olika typer av dokumentrepresentationer för att, på ett oövervakat sätt, förbättra sökbarheten hos ostrukturerade biomedicinska experiment genom att kluster-samla liknande experiment tillsammans. Arbetet innefattar att producera, analysera och jämföra textrepresenta- tioner med hjälp av olika traditionella och moderna maskininlärningsmetoder. Den data som analyserats är brusig och heterogen eftersom den kommer från manuellt skrivna experiment från ett elektroniskt labbokssystem. Att kluster-indela ostrukturerade och oannoterade experiment är en utmaning. Det kräver en representation av texten som enbart baseras på väsentlig information. I denna uppsats har statistiska och generativa tekniker som inbäddade ord samt de senaste framstegen inom djup maskininlärning inom området naturlig textbearbetning använts för att skapa olika textrepresentationer. Genom att kombinera olika tekniker samt att utnyttja externa biomedicinska kunskapskällor har möjligheten att skapa en bättre representation undersökts. Flera analyser har gjorts och dessa har kompletterats med en manuell utvärdering utförd av experter inom det biomedicinska kunskapsfältet. Resultatet visar att traditionella statistiska metoder kan skapa en rimlig basnivå. Moderna djupinlärningsalgoritmer har också visat sig fungera mycket väl och skapat rika representationer av innehållet. Kombinationer av flera tekniker samt användningen av externa biomedicinska kunskapskällor och ontologier har visat sig ge bäst resultat. De olika teknikerna verkar modellera olika och komplementära aspekter av en text, och att kombinera dem kan vara en nyckel till att signifikant förbättra sökbarheten hos ostrukturerad text.
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Booi, Kwanele. "Life Sciences teacher educators’ perspectives of the principle of knowledge integration in the Life Sciences teacher education curriculum." Thesis, Cape Peninsula University of Technology, 2017. http://hdl.handle.net/20.500.11838/2629.
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Thesis (DEd (Education))--Cape Peninsula University of Technology, 2017.This study aimed at examining the Life Sciences teacher educator’s perceptions and perspectives of knowledge integration in the espoused curriculum prescribed by the South African Department of Higher Education and Training through the policy of Minimum Requirements for Teacher Qualifications (MRTEQ). The qualitative research design was adopted for data collection procedures. The selection of the sampling was purposive, in the sense that the Higher Education Institutions (HEIs) who participated were classified into two categories. The first category consisted of three historical or traditional universities and the second category was formed by three higher education institutions that emerged after the merger of Teacher training Colleges, Technikons and universities. The study targeted lecturers, senior lecturers and professors in the field of Life Sciences Education who participated in the development of curriculum for Life Science teacher education and training. The interviews were conducted to elicit data on the experiences and perceptions that influenced the process of designing and developing the curriculum blue print which came out as a product to be adopted by the institution. The results of the empirical study were analysed by using qualitative procedures, which are; coding of data, classification of data into categories and the identification of themes and issues. The contesting views and perceptions were summarised in the results highlighted follows: The school Life Science curriculum requires teachers who are capable of integrating knowledge from various domains of scientific knowledge but the study demonstrates that the Life Science teacher educators who participated in the study had views and perceptions that are not congruent with those of the curriculum as it presently stands. This could imply that the Life Science teachers educated and trained for the school Life Science curriculum could experience problem with its implementation in classrooms. The twenty first century teacher could be expected to demonstrate competences such as; critical thinking, creative thinking, logic and independent thinkers. The study further concluded that there are academics in Science Education departments who still adhere doggedly to the traditional ways teaching their own disciplines. This study confirms the importance of breaking the artificial disciplinary boundaries to facilitate interdisciplinary knowledge construction. This study endorses the emerging trend of knowledge integration in Science Educations.Finally the study suggests that collaborative and collegial deliberations among Science teacher educators and experts in various knowledge domains could be a way of finding common ground on issues highlighted in the study.
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Maherally, Uzma Nooreen. "Development and Validation of the Life Sciences Assessment: A Measure of Preschool Children's Conceptions of Basic Life Sciences." University of Cincinnati / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1396533078.
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Repchevskiy, Dmitry. "Ontology based data integration in life sciences." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/386411.
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The aim of this thesis is to develop standard and practical approaches for the semantic integration of biological data and services. The thesis considers various scenarios where ontologies may benefit bioinformatics web services development, integration and provenance. In spite of the broad use of ontologies in biology, their usage is usually limited to a definition of taxonomic hierarchies. This thesis examines the utility of ontologies for data integration in context of semantic web services development. The biological datatypes ontologies are very valuable for the data integration, especially in a context of continuous standards changes. The thesis evaluates the outdated BioMoby ontology for the generation of modern WS-I and RESTful web services. Another important aspect is the use of ontologies for the web services description. The thesis evaluates the W3C standard WSDL ontology for bioinformatics web services description and provenance. Finally, the integration with modern workflow execution platforms such as Taverna and Galaxy is also considered.
Despite the growing popularity of JSON format, web services vastly depend on XML type system. The OWL2XS tool facilitates semantic web services development providing the automatic XML Schema generation from an appropriate OWL 2 datatype ontology. Web services integration is hardly achievable without a broad standard adoption. The BioNemus application automatically generates standard-based web services from BioMoby ontologies. Semantic representation of web services description simplifies web services search and annotation. Semantic Web Services Registry (BioSWR) is based on W3C WSDL ontology and provides a multifaceted web services view in different formats: OWL 2, WSDL 1.1, WSDL 2.0 and WADL. To demonstrate benefits of ontology-based web services descriptions, BioSWR Taverna OSGI plug-in has been developed. The new, experimental, Taverna WSDL generic library has been used in Galaxy Gears tool which allows integrating web services into the Galaxy workflows.
The thesis explores the scopes of ontologies application for the biological data and services integration, providing a broad set of original tools.El objetivo de la tesis es el desarrollo de una solución práctica y estándar para la integración semántica de los datos y servicios biológicos. La tesis estudia escenarios diferentes en los cuales las ontologías pueden beneficiar el desarrollo de los servicios web, su búsqueda y su visibilidad. A pesar de que las ontologías son ampliamente utilizadas en la biología, su uso habitualmente se limita a la definición de las jerarquías taxonómicas. La tesis examina la utilidad de las ontologías para la integración de los datos en el desarrollo de los servicios web semánticos. Las ontologías que definen los tipos de datos biológicos tienen un gran valor para la integración de los datos, especialmente ante un cambio continuo de los estándares. La tesis evalúa la ontología BioMoby para la generación de los servicios web conforme con las especificaciones WS-I y los servicios REST. Otro aspecto muy importante de la tesis es el uso de las ontologías para la descripción de los servicios web. La tesis evalúa la ontología WSDL promovida por el consorcio W3C para la descripción de los servicios y su búsqueda. Finalmente, se considera la integración con las plataformas modernas de la ejecución de los flujos de trabajo como Taverna y Galaxy. A pesar de la creciente popularidad del formato JSON, los servicios web dependen mucho del XML. La herramienta OWL2XS facilita el desarrollo de los servicios web semánticos generando un esquema XML a partir de una ontología OWL 2. La integración de los servicios web es difícil de conseguir sin una adaptación de los estándares. La aplicación BioNemus genera de manera automática servicios web estándar a partir de las ontologías BioMoby. La representación semántica de los servicios web simplifica su búsqueda y anotación. El Registro Semántico de Servicios Web (BioSWR) está basado en la ontología WSDL del W3C y proporciona una representación en distintos formatos: OWL 2, WSDL 1.1, WSDL 2.0 y WADL. Para demostrar los beneficios de la descripción semántica de los servicios web se ha desarrollado un plugin para Taverna. También se ha implementado una nueva librería experimental que ha sido usada en la aplicación Galaxy Gears, la cual permite la integración de los servicios web en Galaxy. La tesis explora el alcance de la aplicación de las ontologías para la integración de los datos y los servicios biológicos, proporcionando un amplio conjunto de nuevas aplicaciones.
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Rajaram, Lakshminarayan. "Statistical models in environmental and life sciences." [Tampa, Fla] : University of South Florida, 2006. http://purl.fcla.edu/usf/dc/et/SFE0001561.
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Lam, Hoe-chung. "Hong Kong Life Science Museum." Hong Kong : University of Hong Kong, 1997. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25956152.
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Bertthelon, Xavier. "Speckle imaging and image processingapplied to life sciences." Thesis, KTH, Tillämpad fysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-161746.
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Chiu, Eugene 1979. "Characterizing MIT's serial scientist-entrepreneurs in life sciences." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/35552.
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Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006.Includes bibliographical references (leaves 37-40).
Since the Bayh-Dole Act of 1980, the commercialization of ideas generated in academia has driven significant startup activity and expansion in the life sciences. This commercial transformation has been shown by others to be concentrated among a relatively small number of elite academic institutions. However, within these institutions, we find that a small number of prestigious scientists are disproportionately responsible for entrepreneurial and commercial activity. To date, limited research has been conducted which aims to understand the characteristics of such serial scientist-entrepreneurs or their significance in early commercial ventures. This study identifies and characterizes 18 serial scientist-entrepreneurs (defined as faculty who have founded or served on the board of directors of 3 or more startups) on the basis of academic impact, patenting, and social network centrality, as compared to their first-time entrepreneur (i.e., faculty who founded or directed 1-2 companies) and noncommercial peers. These individuals constitute a subset of 66 scientist-entrepreneurs from a population of the 493 scientists who served as faculty in life sciences-related departments at MIT, during the period of 1981 to 2005 (representing the primary commercialization period for biotechnology).
(cont.) The thesis highlights three key findings. First, the subset of 18 serial scientist-entrepreneurs founded or directed two-thirds of all startup ventures associated with the entire population thus underscoring the significant "skew" in commercial activities. Furthermore, empirical analyses revealed that these serial scientist-entrepreneurs had significantly higher academic impact (i.e., "academic prestige"), as measured by citations to their work, as compared to first-time entrepreneurs and noncommercial scientists. Perhaps not surprisingly, they also had significantly higher numbers of issued U.S. patents, compared to first-time entrepreneurs. Second, the serial scientist-entrepreneurs developed robust relationships with a small group of venture capital investors, who have repeatedly funded their companies. Several of these serial scientist-entrepreneurs retained central positions in the social network of faculty entrepreneurs, potentially brokering and accelerating entrepreneurial activity, including scientific advisory board membership, within the community. These findings suggest that serial scientist-entrepreneurs play a vital role in contributing reputation, deep technical insight, access to intellectual property, and relationship networks to startup life sciences ventures.
(cont.) It remains for additional research to determine whether the active involvement of serial scientist-entrepreneurs has resulted in enhanced startup value or performance.
by Eugene Chiu.
S.M.
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Shrestha, Tej Bahadur. "Heterocycles for life-sciences applications and information storage." Diss., Kansas State University, 2010. http://hdl.handle.net/2097/13540.
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Doctor of PhilosophyDepartment of Chemistry
Stefan H. Bossmann
The photochromic spirodihydroindolizine/betaine (DHI/B) system has been reinvestigated applying picosecond, microsecond, stationary absorption measurements, and NMR-kinetics. The first surprise was that the electronic structure of the betaines is quite different than commonly assumed. The photochemical ring-opening of DHIs to betaines is a conrotatory 1,5 electrocyclic reaction, as picosecond absorption spectroscopy confirms. The (disrotatory) thermal ring-closing occurs from the cisoid betaine. The lifetime of the transoid betaine is 60 s at 300 K, whereas the lifetime of the cisoid isomer is of the order of 250 microseconds. According to these results, the electrocyclic back reaction of the betaines to the DHI is NOT rate determining, as previously thought, but the cisoid-transoid-isomerization of the betaine. Although the presence of a second nitrogen atom increases the photostability of the spirodihydroindolizine-pyridazine/betaine-system remarkably, the photochemical reaction mechanism appears to be exactly the same for spirodihydroindolizine-pyridazine/betaine-system. A nondestructive photoswitch or an information recording systems has been explored using styryl-quinolyldihydroindolizines. Both isomers DHI and betaine are fluorescent. When the blue betaine is stabilized in a thin polymethyl methacrylate (PMMA) matrix, it is stable for several hours even in room temperature and very stable at 77K. Although irradiation of visible light = 532 nm allows the photo-induced reaction of the Betaine back to the DHI, a nondestructive read-out can be performed at λ = 645 nm upon excitation with λ = 580 nm. Image recording (write) and read-out, as well as information storage (at 77K) have been demonstrated. Charged and maleimide-functionalized DHI/B systems have beed synthesized for use as photochemical gates of the mycobacterial channel porin MspA. Positively charged and maleimide functionalized DHI groups that were attached to the DHI/B-system permit the binding of the photoswitch to selective positions in the channel proteins due to the presence of a cysteine moiety. An inexpensive new method for the large scale synthesis of coelenterazine is developed. A modified Negishi coupling reaction is used to make pyrazine intermediates from aminopyrazine as an economical starting material. This method permits the use of up to 1g coelenterazine per kg body weight and day, which turns the renilla transfected stem cells into powerful light sources.
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Amaro, Carina Lourenço. "Strategic assessment of Portugal Ventures' life sciences portfolio." Master's thesis, NSBE - UNL, 2013. http://hdl.handle.net/10362/9829.
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A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and EconomicsThis paper intends to present the Management Consulting Lab project developed in partnership with Portugal Ventures. The project has benefits for both students and the client: for students it is an opportunity to gain an innovative learning experience in a reallife setting and apply methodologies learned to solve problems; it also gives companies access to high-quality and cost-effective consulting projects and a young talent pool with new ideas and frameworks. The client’s challenge required thorough analysis to produce several deliverables to the client including a set of recommendations for future implementation based on the team’s main findings.
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Behrisch, Michael. "Stochastical models for networks in the life sciences." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät II, 2008. http://dx.doi.org/10.18452/15716.
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Motiviert durch strukturelle Eigenschaften molekularer Ähnlichkeitsnetzwerke werden die Evolution der größten Komponente eines Netzwerkes in zwei verschiedenen stochastischen Modellen, zufälligen Hypergraphen und zufälligen Schnittgraphen, untersucht. Zuerst wird bewiesen, dass die Anzahl der Knoten in der größten Komponente d-uniformer Hypergraphen einer Normalverteilung folgt. Der Beweis nutzt dabei ausschließlich probabilistische Argumente und keine enumerative Kombinatorik. Diesem grundlegenden Resultat folgen weitere Grenzwertsätze für die gemeinsame Verteilung von Knoten- und Kantenzahl sowie Sätze zur Zusammenhangswahrscheinlichkeit zufälliger Hypergraphen und zur asymptotischen Anzahl zusammenhängender Hypergraphen. Da das Hypergraphenmodell einige Eigenschaften der Realweltdaten nur unzureichend abbildet, wird anschließend die Evolution der größten Komponente in zufälligen Schnittgraphen, die Clustereigenschaften realer Netzwerke widerspiegeln, untersucht. Es wird gezeigt, dass zufällige Schnittgraphen sich von zufälligen (Hyper-)Graphen dadurch unterscheiden, dass (bei einer durchschnittlichen Nachbaranzahl von mehr als eins) weder die größte Komponente linear noch die zweitgrößte Komponente logarithmisch groß in Abhängigkeit von der Knotenzahl ist. Weiterhin wird ein Polynomialzeitalgorithmus zur Überdeckung der Kanten eines Graphen mit möglichst wenigen Cliquen (vollständigen Graphen) beschrieben und seine asymptotische Optimalität im Modell der zufälligen Schnittgraphen bewiesen. Anschließend wird die Entwicklung der chromatischen Zahl untersucht und gezeigt, dass zufällige Schnittgraphen mit hoher Wahrscheinlichkeit mittels verschiedener Greedystrategien optimal gefärbt werden können. Letztendlich zeigen Experimente auf realen Netzen eine Übereinstimmung mit den theoretischen Vorhersagen und legen eine gegenseitige Zertifizierung der Optimalität von Cliquen- und Färbungszahl durch Heuristiken nahe.Motivated by structural properties of molecular similarity networks we study the behaviour of the component evolution in two different stochastic network models, that is random hypergraphs and random intersection graphs. We prove gaussian distribution for the number of vertices in the giant component of a random d-uniform hypergraph. We provide a proof using only probabilistic arguments, avoiding enumerative methods completely. This fundamental result is followed by further limit theorems concerning joint distributions of vertices and edges as well as the connectivity probability of random hypergraphs and the number of connected hypergraphs. Due to deficiencies of the hypergraph model in reflecting properties of the real--world data, we switch the model and study the evolution of the order of the largest component in the random intersection graph model which reflects some clustering properties of real--world networks. We show that for appropriate choice of the parameters random intersection graphs differ from random (hyper-)graphs in that neither the so-called giant component, appearing when the average number of neighbours of a vertex gets larger than one, has linear order nor is the second largest of logarithmic order in the number of vertices. Furthermore we describe a polynomial time algorithm for covering graphs with cliques, prove its asymptotic optimality in a random intersection graph model and study the evolution of the chromatic number in the model showing that, in a certain range of parameters, these random graphs can be coloured optimally with high probability using different greedy algorithms. Experiments on real network data confirm the positive theoretical predictions and suggest that heuristics for the clique and the chromatic number can work hand in hand proving mutual optimality.
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Bianchi, Michele <1982>. "Multiscale fabrication of functional materials for life sciences." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2011. http://amsdottorato.unibo.it/3739/1/bianchi_michele_tesi.pdf.
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Regenerative medicine claims for a better understanding of the cause-effect relation between cell behaviour and environment signals. The latter encompasses topographical, chemical and mechanical stimuli, electromagnetic fields, gradients of chemo-attractants and haptotaxis. In this perspective, a spatial control of the structures composing the environment is required.
In this thesis I describe a novel approach for the multiscale patterning of biocompatible functional materials in order to provide systems able to accurately control cell adhesion and proliferation. The behaviour of different neural cell lines in response to several stimuli, specifically chemical, topographical and electrical gradients is presented. For each of the three kind of signals, I chose properly tailored materials and fabrication and characterization techniques.
After a brief introduction on the state of art of nanotechnology, nanofabrication techniques and regenerative medicine in Chapter 1 and a detailed description of the main fabrication and characterization techniques employed in this work in Chapter 2, in Chapter 3 an easy route to obtain accurate control over cell proliferation close to 100% is described (chemical control). In Chapter 4 (topographical control) it is shown how the multiscale patterning of a well-established biocompatible material as titanium dioxide provides a versatile and robust method to study the effect of local topography on cell adhesion and growth. The third signal, viz. electric field, is investigated in Chapter 5 (electrical control), where the very early stages of neural cell adhesion are studied in the presence of modest steady electric fields. In Chapter 6 (appendix) a new patterning technique, called Lithographically Controlled Etching (LCE), is proposed. It is shown how LCE can provide at the same time the micro/nanostructuring and functionalization of a surface with nanosized objects, thus being suitable for applications both in regenerative medicine in biosensing.
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Bianchi, Michele <1982>. "Multiscale fabrication of functional materials for life sciences." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2011. http://amsdottorato.unibo.it/3739/.
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Regenerative medicine claims for a better understanding of the cause-effect relation between cell behaviour and environment signals. The latter encompasses topographical, chemical and mechanical stimuli, electromagnetic fields, gradients of chemo-attractants and haptotaxis. In this perspective, a spatial control of the structures composing the environment is required.
In this thesis I describe a novel approach for the multiscale patterning of biocompatible functional materials in order to provide systems able to accurately control cell adhesion and proliferation. The behaviour of different neural cell lines in response to several stimuli, specifically chemical, topographical and electrical gradients is presented. For each of the three kind of signals, I chose properly tailored materials and fabrication and characterization techniques.
After a brief introduction on the state of art of nanotechnology, nanofabrication techniques and regenerative medicine in Chapter 1 and a detailed description of the main fabrication and characterization techniques employed in this work in Chapter 2, in Chapter 3 an easy route to obtain accurate control over cell proliferation close to 100% is described (chemical control). In Chapter 4 (topographical control) it is shown how the multiscale patterning of a well-established biocompatible material as titanium dioxide provides a versatile and robust method to study the effect of local topography on cell adhesion and growth. The third signal, viz. electric field, is investigated in Chapter 5 (electrical control), where the very early stages of neural cell adhesion are studied in the presence of modest steady electric fields. In Chapter 6 (appendix) a new patterning technique, called Lithographically Controlled Etching (LCE), is proposed. It is shown how LCE can provide at the same time the micro/nanostructuring and functionalization of a surface with nanosized objects, thus being suitable for applications both in regenerative medicine in biosensing.
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LOVINO, MARTA. "Algorithms for complex systems in the life sciences." Doctoral thesis, Politecnico di Torino, 2021. http://hdl.handle.net/11583/2910082.
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Schiavone, G. "DEMOCRATIZING BIOETHICS. ONLINE PARTICIPATION AND THE LIFE SCIENCES." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/257800.
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Bioethics has historically taken up the challenge of creating an arena for the adjudication of permissibility claims for practices in the broad field of the Life Sciences. Long-standing academic arguments have thus managed to percolate into proper political debates and actual policy-making. With the pressing urge to democratize politics overall, the ways in which bioethical issues have been and still are officially discussed have been thoroughly contested. A number of solutions to the alleged lack of transparency, inclusiveness and accountability in bioethical decision-making have been suggested. Some of these solutions resorted to ICTs for their implementation. However it is unclear, so far, exactly to what extent these initiatives have been able to recruit proper participation, foster reasoned deliberation, and, most importantly, cast politically legitimate decisions.
Democratizing Bioethics tackles the unresolved issues of political legitimacy that underlie the current approach to deliberative public engagement initiatives for science policy-making. In doing so, it provides a political framework in which to test political theories supposed to apply to the political management of moral disagreement. Furthermore, it articulates and defends an actual political theory—moderate epistocracy for online deliberation—as a proper political means to deal with disagreement that is essentially moral arising from scientific and technical progress. Finally, the theory is preliminarily empirically tested via a tool for online direct competent participation.
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GIORDANI, ILARIA. "Relational clustering for knowledge discovery in life sciences." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2010. http://hdl.handle.net/10281/7830.
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Clustering is one of the most common machines learning technique, which has been widely applied in genomics, proteomics and more generally in Life Sciences.
In particular, clustering is an unsupervised technique that, based on geometric concepts like distance or similarity, partitions objects into groups, such that objects with similar characteristics are clustered together and dissimilar objects are in different clusters.
In many domains where clustering is applied, some background knowledge is available in different forms: labelled data (specifying the category to which an instance belongs); complementary information about "true" similarity between pairs of objects or about the relationships structure present in the input data; user preferences (for example specifying whether two instances should be in same or different clusters). In particular, in many real-world applications like biological data processing, social network analysis and text mining, data do not exist in isolation, but a rich structure of relationships subsists between them. A simple example can be viewed in biological domain, where there are al lot of relationships between genes and proteins based on many experimental conditions. Another example, maybe common, is the Web search domain where there are relations between documents and words in a text or web pages, search queries and web users.
Our research is focalized on how this background knowledge can be incorporated into traditional clustering algorithms to optimize the process of pattern discovery (clustering) between instances.
In this thesis, we first provide an overview of traditional clustering methods with some important distance measures and then we analyze three particular challenges that we try to overcome with different proposed methods: "feature selection" to reduce high dimensional input space and remove noise from data; "mixed data types" to handle in clustering procedure both numeric and categorical values, typically of life science applications; finally, "knowledge integration" in order to improve the semantic value of clustering incorporating the background knowledge.
Regarding the first challenge we propose a novel approach based on using of genetic programming, an evolutionary algorithm-based methodology, in order to automatically perform feature selection.
Different clustering algorithms are been investigated regarding the second challenge. A modify version of a particular algorithm is proposed and applied to clinical data.
Particularly attention is given to the final challenge, the most important objective of this Thesis: the development of a new relational clustering framework in order to improve the semantic value of clustering taking into account in the clustering algorithm relationships learned from background knowledge.
We investigate and classify existing clustering methods into two principal categories:
- Structure driven approaches: that are bound to data structure.
The data clustering problem is tackled from several dimensions: clustering concurrently columns and rows of a given dataset, like biclustering algorithm or vertical 3-D clustering.
- Knowledge driven approaches: where domain information is used to drive the clustering process and interpret its results: semi-supervised clustering, that using both labelled and unlabeled data, has attracted significant attention. This kind of clustering algorithms represents the first step to implement the proposed general framework that it is classified into this category.
In particular the thesis focuses on the development of a general framework for relational clustering instantiating it for three different life science applications: the first one with the aim of finding groups of gene with similar behaviour respect to their expression and regulatory profile. The second one is a pharmacogenomics application, in which the relational clustering framework is applied on a benchmark dataset (NCI60) to identify a drug treatment to a given cell line based both on drug activity pattern and gene expression profile. Finally, the proposed framework is applied on clinical data: a particular dataset containing different information about patients in anticoagulant therapy has been analyzed to find group of patients with similar behaviour and responses to the therapy.
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Deus, Helena Futscher de. "Improving discovery in the life sciences using semantic Web technologies and linked data: design principles for life sciences knowledge organization systems." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2011. http://hdl.handle.net/10362/5766.
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Dissertation presented to obtain the Ph.D degree in BioinformaticsThe data deluge in biology resulting from wide adoption of highthroughput technologies, coupled with the increasing reliance on web technologies for knowledge organization, sharing and discovery, has created unprecedented opportunities, and challenges, for knowledge engineering in Life Sciences domains. The Semantic Web technologies correspond to a set of standards and best practices for improving data sharing and interoperability on the Web that can greatly advance research in data-driven sciences such as translational medicine and systems biology. Current Semantic Web approaches for addressing those challenges have either relied on automatically formatting biological data sources as RDF (Resource Description Framework), the lingua franca of the Semantic Web, or in the development of bio-{)ntologies. Albeit the significant integrative advances that those represent, wide adoption of Semantic Web technologies by the communities acquiring and modeling experimental biological data has remained suboptimal.(...)
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Lippe, Anka [Verfasser], Jens [Akademischer Betreuer] Christoffers, and Karl-Wilhelm [Akademischer Betreuer] Koch. "Diaminoterephthalsäurederivate: Fluoreszenzfarbstoffe für die Life Sciences und Materials Science / Anka Lippe ; Jens Christoffers, Karl-Wilhelm Koch." Oldenburg : BIS der Universität Oldenburg, 2019. http://d-nb.info/1200547330/34.
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Peiter, Carrie. "Firm co-location and clustering in the life sciences /." free to MU campus, to others for purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p1426094.
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21
Doms, Andreas. "GoPubMed: Ontology-based literature search for the life sciences." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2009. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1232454035091-47450.
Full textAbstract:
Background: Most of our biomedical knowledge is only accessible through texts. The biomedical literature grows exponentially and PubMed comprises over 18.000.000 literature abstracts. Recently much effort has been put into the creation of biomedical ontologies which capture biomedical facts. The exploitation of ontologies to explore the scientific literature is a new area of research. Motivation: When people search, they have questions in mind. Answering questions in a domain requires the knowledge of the terminology of that domain. Classical search engines do not provide background knowledge for the presentation of search results. Ontology annotated structured databases allow for data-mining. The hypothesis is that ontology annotated literature databases allow for text-mining. The central problem is to associate scientific publications with ontological concepts. This is a prerequisite for ontology-based literature search. The question then is how to answer biomedical questions using ontologies and a literature corpus. Finally the task is to automate bibliometric analyses on an corpus of scientific publications. Approach: Recent joint efforts on automatically extracting information from free text showed that the applied methods are complementary. The idea is to employ the rich terminological and relational information stored in biomedical ontologies to markup biomedical text documents. Based on established semantic links between documents and ontology concepts the goal is to answer biomedical question on a corpus of documents. The entirely annotated literature corpus allows for the first time to automatically generate bibliometric analyses for ontological concepts, authors and institutions. Results: This work includes a novel annotation framework for free texts with ontological concepts. The framework allows to generate recognition patterns rules from the terminological and relational information in an ontology. Maximum entropy models can be trained to distinguish the meaning of ambiguous concept labels. The framework was used to develop a annotation pipeline for PubMed abstracts with 27,863 Gene Ontology concepts. The evaluation of the recognition performance yielded a precision of 79.9% and a recall of 72.7% improving the previously used algorithm by 25,7% f-measure. The evaluation was done on a manually created (by the original authors) curation corpus of 689 PubMed abstracts with 18,356 curations of concepts. Methods to reason over large amounts of documents with ontologies were developed. The ability to answer questions with the online system was shown on a set of biomedical question of the TREC Genomics Track 2006 benchmark. This work includes the first ontology-based, large scale, online available, up-to-date bibliometric analysis for topics in molecular biology represented by GO concepts. The automatic bibliometric analysis is in line with existing, but often out-dated, manual analyses. Outlook: A number of promising continuations starting from this work have been spun off. A freely available online search engine has a growing user community. A spin-off company was funded by the High-Tech Gründerfonds which commercializes the new ontology-based search paradigm. Several off-springs of GoPubMed including GoWeb (general web search), Go3R (search in replacement, reduction, refinement methods for animal experiments), GoGene (search in gene/protein databases) are developed.
22
Dietze, Heiko. "GoWeb: Semantic Search and Browsing for the Life Sciences." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-63267.
Full textAbstract:
Searching is a fundamental task to support research. Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing to unstructured text or they assume the existence of structured statements over which they can reason.
This work provides a system for combining the classical keyword-based search engines with semantic annotation. Conventional search results are annotated using a customized annotation algorithm, which takes the textual properties and requirements such as speed and scalability into account. The biomedical background knowledge consists of the GeneOntology and Medical Subject Headings and other related entities, e.g. proteins/gene names and person names. Together they provide the relevant semantic context for a search engine for the life sciences. We develop the system GoWeb for semantic web search and evaluate it using three benchmarks. It is shown that GoWeb is able to aid question answering with success rates up to 79%.
Furthermore, the system also includes semantic hyperlinks that enable semantic browsing of the knowledge space. The semantic hyperlinks facilitate the use of the eScience infrastructure, even complex workflows of composed web services.
To complement the web search of GoWeb, other data source and more specialized information needs are tested in different prototypes. This includes patents and intranet search. Semantic search is applicable for these usage scenarios, but the developed systems also show limits of the semantic approach. That is the size, applicability and completeness of the integrated ontologies, as well as technical issues of text-extraction and meta-data information gathering.
Additionally, semantic indexing as an alternative approach to implement semantic search is implemented and evaluated with a question answering benchmark. A semantic index can help to answer questions and address some limitations of GoWeb. Still the maintenance and optimization of such an index is a challenge, whereas GoWeb provides a straightforward system.
23
Taneri, Pervin Oya. "Implementation Of Constructivist Life Sciences Curriculum: A Case Study." Phd thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612257/index.pdf.
Full textAbstract:
The purpose of this qualitative case study is threefold: (1) to examine the implementation of current Life Sciences curriculum in a selected primary school from the perspectives of teachers, students and administrators(2) to investigate the degree to which teachers&rsquo
, students&rsquo
and administrators&rsquo
perceptions were embedded in the classroom practices
and (3) to identify whether the implementation of the curriculum was conducive to principles of constructivist pedagogy. An elementary school was chosen as a single case in an outer district of Ankara. The participants of the study were the school administrator and 2 co-administrators, 4 classroom teachers and 87 students from different 2nd and 3rd grades classrooms. The data were collected through document analysis, observations in the Life Sciences classes, semi-structured interview with administrators, stimulated recall interview with teachers, and creative drama with students. Content analysis was used to analyze the data. The findings indicated that the suggested Life Sciences Curriculum was conducive to the principles of constructivist pedagogy in terms of its content
teaching and learning processes
instructional methods
assessment methods
and teachers&rsquo
and students&rsquo
roles. However, the acquisitions of the LSC were not conducive to the constructivist approach. The findings on the teachers&rsquo
, students&rsquo
and administrators&rsquo
perceptions about the Life Sciences curriculum indicated that in Life Sciences lessons the teachers seemed to have a role of knowledge transmitter to a group of passive students. According to the findings, the most frequently used teaching methods were lecturing, question-answer and demonstration through using textbooks, workbooks, and white boards. In addition, the most frequently used assessment methods were essay and oral exams, classroom observations and self-assessment. Overall it can be concluded from the findings that although the suggested Life Sciences curriculum was prepared in line with the principles of constructivist pedagogy, the way it was implemented had some deficiencies regarding the actualization of goals suggested by a constructivist curriculum.
24
Nicolau, Daniela E. "Knowledge production and transfer in physical and life sciences /." Access via Murdoch University Digital Theses Project, 2002. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20061122.141122.
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25
Elliott, Victoria Louise. "Novel applications of ICP-MS in the life sciences." Thesis, University of Sheffield, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.427243.
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26
Willis, L. A. "Probabilistic modelling of three phenomena in the Life Sciences." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1318148/.
Full textAbstract:
This thesis describes the development and analysis of three probabilistic models of phenomena in the life sciences. Model 1 addresses the phenomenon in breast cancer called ‘dormancy’, where patients relapse suddenly after many years or decades during which they were regarded as cured. Where and by what mechanism the dangerous residual cancer remains hidden for so long is largely a mystery, and this lack of knowledge makes it difficult to design effective preventive treatments. Analysis of our model leads to a number of predictions related to dormancy’s disease course. Models 2 and 3 simulate the formation of high-fidelity, patterned nanoscale ornamentations in the biosilica exoskeletons of diatoms, that today defy synthesis in vitro. Very little is known about this diatom biosilica assembly yet, if the mechanisms are simple or synthetically imitable, then they are potentially of great interest to industry and to the curious scientist. Model 3, which is still presently under study, may lead to predictions about the nature of these mechanisms of biosilica assembly. Notably, Model 3 is a new probabilistic model of a well established pattern formation process that we envisage to have broader application.
27
Brilman, Marina C. "Georges Canguilhem : norms and knowledge in the life sciences." Thesis, London School of Economics and Political Science (University of London), 2009. http://etheses.lse.ac.uk/2994/.
Full textAbstract:
In the second half of the twentieth century, the interest of the social sciences in the life sciences has intensified. This intensification might be explained through the idea that, as Michel Foucault puts it, what defines modem rationality is the entry of 'life' into regimes of knowledge and power. I argue that this 'entry' can be traced back to the work of Immanuel Kant. He established the autonomy of reason by simultaneously including and excluding life from reason. Kant explained the emergence of reason by likening it to a biological process but then excluded such processes from reason through his notion of the 'lawfulness of the contingent'. I argue that this two-pronged approach leads to a recurring negotiation of the relation between life and knowledge in the contemporary life and social sciences. I argue that it was not Foucault who directly engaged with how the life sciences lie at the heart of modern rationality. Rather, it was the French philosopher and historian of science Georges Canguilhem. I argue that he questioned modern rationality by inquiring into some of its most fundamental epistemological or discursive forms. In order to illustrate this, I address his inquiry into the concepts of environment, individuality, knowledge or information, and normativity. The potential of these concepts to migrate across disciplinary boundaries is indicative of the fact that the productivity of Canguilhem's work extends far beyond the life sciences.
28
Kaltenbach, Colin. "College of Agriculture and Life Sciences 2007 Research Awards." College of Agriculture and Life Sciences, University of Arizona (Tucson, AZ), 2007. http://hdl.handle.net/10150/622125.
Full text
29
Doms, Andreas. "GoPubMed: Ontology-based literature search for the life sciences." Doctoral thesis, Technische Universität Dresden, 2008. https://tud.qucosa.de/id/qucosa%3A23835.
Full textAbstract:
Background: Most of our biomedical knowledge is only accessible through texts. The biomedical literature grows exponentially and PubMed comprises over 18.000.000 literature abstracts. Recently much effort has been put into the creation of biomedical ontologies which capture biomedical facts. The exploitation of ontologies to explore the scientific literature is a new area of research. Motivation: When people search, they have questions in mind. Answering questions in a domain requires the knowledge of the terminology of that domain. Classical search engines do not provide background knowledge for the presentation of search results. Ontology annotated structured databases allow for data-mining. The hypothesis is that ontology annotated literature databases allow for text-mining. The central problem is to associate scientific publications with ontological concepts. This is a prerequisite for ontology-based literature search. The question then is how to answer biomedical questions using ontologies and a literature corpus. Finally the task is to automate bibliometric analyses on an corpus of scientific publications. Approach: Recent joint efforts on automatically extracting information from free text showed that the applied methods are complementary. The idea is to employ the rich terminological and relational information stored in biomedical ontologies to markup biomedical text documents. Based on established semantic links between documents and ontology concepts the goal is to answer biomedical question on a corpus of documents. The entirely annotated literature corpus allows for the first time to automatically generate bibliometric analyses for ontological concepts, authors and institutions. Results: This work includes a novel annotation framework for free texts with ontological concepts. The framework allows to generate recognition patterns rules from the terminological and relational information in an ontology. Maximum entropy models can be trained to distinguish the meaning of ambiguous concept labels. The framework was used to develop a annotation pipeline for PubMed abstracts with 27,863 Gene Ontology concepts. The evaluation of the recognition performance yielded a precision of 79.9% and a recall of 72.7% improving the previously used algorithm by 25,7% f-measure. The evaluation was done on a manually created (by the original authors) curation corpus of 689 PubMed abstracts with 18,356 curations of concepts. Methods to reason over large amounts of documents with ontologies were developed. The ability to answer questions with the online system was shown on a set of biomedical question of the TREC Genomics Track 2006 benchmark. This work includes the first ontology-based, large scale, online available, up-to-date bibliometric analysis for topics in molecular biology represented by GO concepts. The automatic bibliometric analysis is in line with existing, but often out-dated, manual analyses. Outlook: A number of promising continuations starting from this work have been spun off. A freely available online search engine has a growing user community. A spin-off company was funded by the High-Tech Gründerfonds which commercializes the new ontology-based search paradigm. Several off-springs of GoPubMed including GoWeb (general web search), Go3R (search in replacement, reduction, refinement methods for animal experiments), GoGene (search in gene/protein databases) are developed.
30
Nicolau, Daniela. "Knowledge production and transfer in physical and life sciences." Thesis, Nicolau, Daniela (2002) Knowledge production and transfer in physical and life sciences. PhD thesis, Murdoch University, 2002. https://researchrepository.murdoch.edu.au/id/eprint/229/.
Full textAbstract:
Questions about knowledge flows between different fields of science are important from a policy perspective. This thesis focuses on knowledge transfer between physical sciences and life sciences. Science and technology are increasingly intertwined in a complex continuum. This complexity of the science and technology today asks for a concerted, articulated and comprehensive understanding of the process of science and technology. The approach that this research has taken is to analyse the process of science and technology. The thesis asks: What is the trade of science and technology? In order to answer this question we developed an anatomy of knowledge and we analysed the internal developments in science via the analysis of the role of the researchers as carriers and producers of knowledge.
Secondly the thesis asks: What are the mechanisms and directions on which scientfic knowledge migrates? This research postulates that the analysis of the process of science and technology translates to the analysis of the production and transfer of scientific and technological knowledge.
What is obvious and essential for science and technology is the difference between the specific mechanisms of knowledge production. This thesis suggests that the modem mode of knowledge production is characterized by an increasing density of communication on three levels: between science and technology - on one hand - and society on the other-; between scientific practitioners; and with the entities of the physical and social world. Central to our research is the concept of 'mode of knowledge production ' with mode 1 and mode 2 being defined by Gibbons.
The four case studies employed emphasise on how collaboration across disciplines is highly important for the production of new knowledge. The main characteristic of newly emerging fields in an increasing synergy between disciplines, which leads to several types of communication between them. With the increasing of the interdisciplinary intensity the border between the production of knowledge and the transfer of knowledge begins to be blurred. The transfer of knowledge occurs today at a more conceptual level. It follows that the production of knowledge has a large component of knowledge transfer. To study it, this thesis proposes a quasiquantitative model. In this unified framework for the knowledge transfer mechanisms, transfer is seen as a process with a number of stages and forms. We tested our framework on four case studies.
The third part of the thesis proposes a taxonomy of interdisciplinarity. and deals with the social engineering of knowledge transfer that is the design of adequate guidelines for policies aiming at maximization of knowledge transfer. In this way the thesis aims to contribute to the understanding of processes of development of new emerging scientific fields.
31
Nicolau, Daniela. "Knowledge production and transfer in physical and life sciences." Murdoch University, 2002. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20061122.141122.
Full textAbstract:
Questions about knowledge flows between different fields of science are important &om
a policy perspective.
This thesis focuses on knowledge transfer between physical sciences and life sciences.
Science and technology are increasingly intemvined in a complex continuum. This
complexity of the science and technology today asks for a concerted, articulated and
comprehensive understanding of the process of science and technology.
The approach that this research has taken is to analyse the process of science and
technology. The thesis asks: What is the trade of science and technologv? In order to
answer this question we developed an anatomy of knowledge and we analysed the
internal developments in science via the analysis of the role of the researchers as carriers
and producers of knowledge.
Secondly the thesis asks: What are the mechanisms and directions on which scientzjic
knowledge migrates? This research postulates that the analysis of the process of science
and technology translates to the analysis of the production and transfer of scientific and
technological knowledge.
What is obvious and essential for science and technology is the difference between the
specific mechanisms of knowledge production. This thesis suggests that the modem
mode of knowledge production is characterized by an increasing density of
communication on three levels: between science and technology - on one hand - and
society on the other-; between scientific practitioners; and with the entities of the physical and social world. Central to our research is the concept of 'mode of knowledge
production ' with mode 1 and mode 2 being defined by Gibbons.
The four case studies employed emphasise on how collaboration across disciplines is
highly important for the production of new knowledge. The main characteristic of newly
emerging fields in an increasing synergy between disciplines, which leads to several
types of communication between them.
With the increasing of the interdisciplinary intensity the border between the production of
knowledge and the transfer of knowledge begins to be blurred. The transfer of knowledge
occurs today at a more conceptual level. It follows that the production of knowledge has a
large .component of knowledge transfer. To study it, ths thesis proposes a quasiquantitative
model. In h s unified &mework for the knowledge tmnsfer mechanisms,
transfer is seen as a process with a number of stages and forms. We tested our framework
on four case studies.
The third part of the thesis proposes a taxonomy of interdsciplinarity. and deals with the
social engineering of knowledge transfer that is the design of adequate guidelines for
policies aiming at maximization of knowledge transfer. In this way the thesis aims to
contribute to the understanding of processes of development of new emerging scientific
fields.
32
Lam, Hoe-chung, and 林浩沖. "Hong Kong Life Science Museum." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1997. http://hub.hku.hk/bib/B3198342X.
Full text
33
Hassanzadah, Ali R. "LIFE EXPECTANCY." CSUSB ScholarWorks, 2016. https://scholarworks.lib.csusb.edu/etd/382.
Full textAbstract:
When someone walks into an insurance company and wants to purchase life insurance, the insurance company has to consider an important question: How long will this client live? His date of death is not exactly predictable, so the insurer does not know exactly when the life insurance benefits will be payable. However, the insurer can use a model that can calculate human mortality. With this mortality model, probabilities of deaths at particular ages can be calculated. Rather than trying to figure out when a client dies, the convention in actuarial science is to phrase things in terms of survival models. There are popular survival functions that enable insurers to perform this calculation. With these functions, insurers are able to efficiently provide this service and ensure that life insurance will continue to be a thriving field of work. After we define basic notation and terms, we look at standard survival models. Then we consider a recently proposed model by Chi Heem Wong and Albert K. Tsui.
34
Spjuth, Ola. "Bioclipse integration of data and software in the life sciences /." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-109305.
Full text
35
Arnold, Darrell. "Nineteenth century life sciences and Hegel's organic view of systems." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=959727175.
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36
Dargatz, Christiane. "Bayesian Inference for Diffusion Processes with Applications in Life Sciences." Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-121361.
Full text
37
Wollweber, Merve [Verfasser]. "Multimodal spectroscopy for application in the life sciences / Merve Wollweber." Hannover : Gottfried Wilhelm Leibniz Universität Hannover, 2018. http://d-nb.info/1192440471/34.
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38
Thorne, David. "A semantic architecture for visualisation applications in the life sciences." Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.705542.
Full text
39
Smus, Justyna Paulina. "Application of enhanced Raman techniques in life sciences and biomedicine." Thesis, University of Southampton, 2016. https://eprints.soton.ac.uk/409721/.
Full textAbstract:
Current understanding of complex biological processes and structures relies entirely on available imaging and sensing techniques. As many of these investigation tools suffer from severe limitations, the need for methods which can provide new insight is growing rapidly. Enhanced Raman techniques are becoming increasingly important research tools in biosciences thanks to their unique non-destructive, non-invasive and label-free nature. This work aimed to demonstrate the capabilities of enhanced Raman techniques in life sciences and biomedicine research. The techniques used in this work were surface-enhanced Raman spectroscopy (SERS) and coherent anti-Stokes Raman scattering (CARS). While SERS uses the enhancement of Raman signals by utilising nanoparticles CARS utilises non-linear optical effects to increase signals. Furthermore, SERS is utilised as an analytical technique using spectral information while CARS is used for chemically selective imaging at a vibrational frequency of molecular bond. The studies in this thesis explore the broad scope of applications of both these enhanced Raman techniques. SERS was used for detection of different bacterial strains, where it was shown that using nanopatterned surfaces resulted in improved distinction compared to use of nanoparticles. SERS was also applied to monitor of intracellular metabolic processes. The effect of different treatments to differentiate SHSY-5Y cells was studied and the changes observed were correlated with biochemical analysis. Additionally, novel SERS nanoparticle probes and their potential in life sciences was also investigated. CARS was used to study stem cell differentiation and food deprivation in nematodes. In both the cases the effect of chemical modulators and treatments was also studied. The results showed that label-free imaging using CARS is a viable and superior alternative to conventional staining used to study these processes in biological sciences. Overall, the work in this thesis establishes the use of SERS and CARS as potent tools in the life sciences.
40
TANGHERLONI, ANDREA. "High-Performance Computing to tackle complex problems in life sciences." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2019. http://hdl.handle.net/10281/241217.
Full textAbstract:
Nuovi ed efficienti metodi computazionali sono attualmente necessari per elaborare la ingente mole di dati generata dalle più recenti tecnologie sviluppate in svariati settori delle scienze della vita, tra cui la biologia computazionale e l’imaging medicale. In altre discipline, come la biologia dei sistemi in cui si modellano matematicamente le reti biochimiche, è necessario affrontare problemi relativi alla mancanza di dati quantitativi, e allo stesso tempo simulare efficacemente le dinamiche emergenti di queste reti.
In questi contesti applicativi, le infrastrutture di calcolo ad elevate prestazioni si stanno rivelando uno strumento fondamentale per affrontare e risolvere i problemi che insorgono, in quanto permettono sia di elaborare in tempo reale ingenti quantità di dati sia di eseguire simulazioni in modo efficace ed efficiente. Durante gli ultimi anni si sta sempre di più radicando l’uso di dispositivi general-purpose caratterizzati da decine, centinaia o migliaia di core di calcolo, come ad esempio i coprocessori Many Integrated Cores e le Graphics Processing Units (GPU). L’uso delle GPU è motivato sia dalla efficienza computazionale che possono raggiungere (nell’ordine dei teraflop) grazie alle migliaia di core a disposizione sia dall’efficienza energetica che le contraddistingue.
Oltre al calcolo ad elevate prestazioni, in questa tesi si sono sfruttate tecniche di intelligenza computazionale per affrontare problemi di ottimizzazione, come ad esempio la stima di parametri nella biologia dei sistemi, l’inferenza degli aplotipi nella bioinformatica, l’enhancement e la segmentazione di immagini medicali caratterizzate da istogrammi bimodali dei livelli di grigio che costituiscono le immagini stesse. La stima di parametri è stata affrontata sfruttando approcci di computazione evolutiva e di swarm intelligence insieme a nuovi simulatori accelerati su GPU - sviluppati appositamente per eseguire in parallelo sia molte simulazioni corrispondenti a diverse parametrizzazione dei modelli matematici che una singola simulazione di reti biochimiche a larga scala - permettendo di ridurre drasticamente il tempo di calcolo richiesto per calcolare le funzioni di fitness di questi approcci. Grazie alla loro efficacia nel risolvere i problemi combinatori, gli Algoritmi Genetici sono stati utilizzati per risolvere i problemi relativi alla ricostruzione degli aplotipi e l’enhancement delle immagini medicali. I due metodi proposti sono stati sviluppati sfruttando il paradigma Master-Slave che permette di distribuire il gravoso carico computazionale richiesto per risolvere questi problemi, riducendo notevolmente i tempi di calcolo.
I risultati ottenuti in questa tesi mostrano come l’utilizzo del calcolo ad elevate prestazioni, unito alle tecniche di intelligenza computazionale, rappresenti una strategia efficace per la risoluzione di questi problemi, permettendo di effettuare analisi computazionali complesse richieste nelle scienze della vita.Recent advances in several research fields of Life Sciences, such as Bioinformatics, Computational Biology and Medical Imaging, are generating huge amounts of data that require effective computational tools to be analyzed, while other disciplines, like Systems Biology, typically deal with mathematical models of biochemical networks, where issues related to the lack of quantitative parameters and the efficient description of the emergent dynamics must be faced. In these contexts, High-Performance Computing (HPC) infrastructures represent a fundamental means to tackle these problems, allowing for both real-time processing of data and fast simulations. In the latest years, the use of general-purpose many-core devices, such as Many Integrated Core coprocessors and Graphics Processing Units (GPUs), gained ground. The second ones, which are pervasive, relatively cheap and extremely efficient parallel many-core coprocessors capable of achieving tera-scale performance on common workstations, have been extensively exploited in the work presented in this thesis. Moreover, some of the problems described here require the application of Computational Intelligence (CI) methods. As a matter fact, the Parameter Estimation problem in Systems Biology, the Haplotype Assembly problem in Genome Analysis as well as the enhancement and segmentation of medical images characterized by a bimodal gray level intensity histogram can be viewed as optimization problems, which can be effectively addressed by relying on CI approaches. In the case of the Parameter Estimation problem, Evolutionary and Swarm Intelligence techniques were exploited and coupled with novel GPU-powered simulators-designed and developed in this thesis to execute both coarse-grained and fine-grained simulations-which were used to perform in a parallel fashion the biochemical simulations underlying the fitness functions required by these population-based approaches. The Haplotype Assembly and the enhancement of medical images problems were both addressed by means of Genetic Algorithms (GAs), which were shown to be very effective in solving combinatorial problems. Since the proposed approaches based on GAs are computationally demanding, a Master-Slave paradigm was exploited to distribute the workload, reducing the required running time. The overall results show that coupling HPC and CI techniques is advantageous to address these problems and speed up the computational analyses in these research fields.
41
Reinert, Tilo. "Focussed MeV-Ion Micro- and Nano-Beams in the Life Sciences." Doctoral thesis, Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-197802.
Full textAbstract:
This work presents the development of a sub-micron nuclear microprobe for applications in the life sciences. It includes quantitative trace element analysis with sub-micron spatial resolution, 2D- and 3D-microscopy of density distributions and the targeted irradiation of living cells with counted single ions. The analytical methods base on particle induced X-ray emission spectrometry (PIXE), Rutherford backscattering spectrometry (RBS), scanning transmission ion microscopy (STIM) and STIM-tomography. The specific development of the existing nuclear microprobe LIPSION led to an improved performance of the capabilities for trace element analysis. For sub-micron analysis the spatial resolution could be improved to 300 nm at a sensitivity of about 1 µg/g for metal ions in biological matrices; for a resolution of 1 µm the sensitivity was improved to 200 ng/g (3 µmol/l). This habilitation thesis comprises a short general introduction including the motivation to utilize focussed high energy ion beams, an overview on the applications and actual research fields. The introduction is followed by the basic principles of the equipments and analytical methods. An estimation of the limits of resolution for element analytical and single ion techniques is given for the Leipzig system. Thereafter, selected studies from different research areas are presented. The first presented application is a study from environmental air pollution research. It is demonstrated that the microscopic elemental analysis of single aerosol particles can be used to assess the contributions from different sources. A further example is the analysis of the distribution of nanoparticles in skin cross-sections for a risk assessment of the applications of nanosized physical UV-filters in cosmetic products. The risk assessment is followed by the micro-analysis of trace elements, especially of bound metal ions, in brain sections on the cellular and sub-cellular level. After this the application of focussed MeV ion beams in low dose radiobiological research is presented. Finally, the analysis of 3D-density distributions by proton micro-tomography is demonstrated. A summary concludes on the applications and gives an outlook to further applications and methodological developments. The appendix comprises the relevant publications of the authorDie vorliegende Arbeit etabliert für Anwendungen in den Lebenswissenschaften den Einsatz hochfokussierter MeV-Ionenstrahlen für nuklear-mikroskopische Methoden der quantitativen Spurenelementanalyse, der 2D- und 3D-Dichtemikroskopie sowie für die gezielte Bestrahlung einzelner lebender Zellen für radiobiologische Experimente. Zur Anwendung kamen die Methoden ortsaufgelöste Protonen induzierte Röntgenfluoreszenzanalyse (particle induced X-ray emission - PIXE), Spektrometrie rückgestreuter Ionen (Rutherford backscattering spectrometry - RBS) und Rastertransmissionsionenmikroskopie (scanning transmission ion microscopy - STIM). Durch eine gezielte Weiterentwicklung des bestehenden Ionenstrahlmikroskops, der Hochenergie Ionennanosonde LIPSION, konnte die Ortsauflösung für Spurenelementanalyse auf unter 300 nm verbessert werden, beziehungsweise die Sensitivität für Metallionen in biologischen Proben auf unter 200 ng/g (3 µmol/l) bei einer Ortsauflösung von 1 µm verbessert werden. Die Habilitationsschrift umfasst eine kurze allgemeine Einleitung einschließlich der Motivation für den Einsatz fokussierter MeV-Ionenstrahlen sowie einen Überblick über die Anwendungsgebiete und aktuellen Forschungsschwerpunkte. Danach werden kurz die Grundlagen der Technik und Methoden vorgestellt, gefolgt von einer Abschätzung der Auflösungsgrenzen für Elementanalysen und Einzelionentechniken. Danach werden ausgewählte Anwendungen aus verschiedenen Forschungsgebieten vorgestellt. Das erstes Beispiel ist aus der Umweltforschung. Es wird dargestellt, wie mittels ortsaufgelöster Elementspektroskopie eine Abschätzung der Feinstaubbelastung nach Beiträgen einzelner Verursacherquellen erfolgen kann. Dann folgt als Beispiel eine ortsaufgelöste Analyse der Verteilung von Nanopartikeln aus Sonnencremes in Hautquerschnitten zur Risikoabschätzung der Anwendungen von Nanotechnologie in kosmetischen Produkten. Desweiteren werden Studien der Spurenelementverteilung, speziell der von gebundenen Metallionen, in Hirnschnitten auf zellulärer und subzellulärer Ebene erläutert. Das anschließende Beispiel erläutert die Anwendung niedriger Energiedosen in der Radiobiologie anhand des Beschusses einzelner lebender Zellen mit abgezählten einzelnen Ionen. Als letztes Beispiel wird die Anwendung hochfokussierter Ionenstrahlen für die Mikrotomographie gezeigt. Abschließend folgt eine zusammenfassende Bewertung der vorgestellten Anwendungen mit einem Ausblick auf weitere Anwendungen und methodische Entwicklungen. Der Arbeit sind die relevanten Veröffentlichungen mit Beteiligung des Autors als Anhang beigefügt
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Power, Lucy A. "e-Research in the life sciences : from invisible to virtual colleges." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:de32d659-8908-4ebe-ab50-3ba6330f456a.
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e-Research in the Life Sciences examines the use of online tools in the life sciences and finds that their use has significant impact, namely the formation of a Scientific/Intellectual Movement (SIM) (Frickel & Gross, 2005) complemented by a Computerisation Movement (CM) (Kling & Iacono, 1994) which is mobilising global electronic resources to form visible colleges of life science researchers, who are enrolling others and successfully promoting their open science goals via mainstream scientific literature. Those within this movement are also using these online tools to change their work practices, producing scientific knowledge in a highly networked and distributed group which has less regard for traditional institutional and disciplinary boundaries. This thesis, by combining ideas about SIMs and CMs, fills a gap in research that is typically confined to treating new tools as a part of scientific communication or in specialist areas like distributed collaboration but not in terms of broader changes in science. Case studies have been conducted for three types of online tools: the scientific social networking tool FriendFeed, open laboratory notebooks, and science blogs. Data have been collected from semi-structured interviews, and the online writings of research participants. The case studies of exemplary use by scientists of the web form a baseline for future studies in the area. Boundaries between formal and informal scholarly communication are now blurred. At the formal level, which peer-reviewed print journals continue, many academic publishers now also have online open access, frequently in advance of print publication. At the informal level, what used to be confined to water-cooler chat and the conference circuit is now also discussed on mailing lists, forums and blogs (Borgman, 2007). As these online tools generate new practices they have potential to affect future academic assessment and dissemination practices.
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Taukobong, Tshegofatso Martha. "The visual literacy of Grade 10 Life Sciences learners in cytology." Diss., University of Pretoria, 2017. http://hdl.handle.net/2263/65471.
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In Life Sciences Education, the use of educational external representations (ERs) such as diagrams, models and animations are increasingly appearing in learning and teaching resources. However, their effectiveness is limited if learners experience learning difficulties due to lack of visual literacy and spatial ability skills to work with ERs. The study explored the level of visual literacy of 225 Grade 10 Life Sciences learners in cytology across six secondary schools in Pretoria, Gauteng. It was theorised that ERs need to be integrated in the Life Sciences curricula to develop learners’ visual literacy and spatial ability skills. With this theory, the study aimed to explore the visual literacy of Grade 10 Life Sciences learners and the influence of gender and school location on the visual literacy and spatial ability skills of the learners. Through a quantitative research method a Life Sciences visual literacy questionnaire and a spatial ability test were used to collect data. Collected data was analysed descriptively and inferentially through Statistical Package Social Sciences Version 23. The results showed that most Grade 10 Life Sciences learners lack average visual literacy skills. Furthermore, the results showed that gender doesn’t play a role on the learners’ performance in visual literacy skills as both genders performed equally in both tests, On the other hand, the results showed that the location of the school (urban, rural or township) has an effect on the learners’ performance in visual literacy skills. Teachers need to incorporate different ERs that would stimulate different senses and which will also enhance learners’ visual literacy and spatial ability skills in their lessons. A conclusion and some recommendations for future research are given.Dissertation (MEd)--University of Pretoria, 2017.
Science, Mathematics and Technology Education
MEd
Unrestricted
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Ireland, Carol A. "Adapting to prison life." Thesis, University of Central Lancashire, 2001. http://clok.uclan.ac.uk/6554/.
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This thesis examines longitudinally how young offenders cope with prison life, in particular the relationship between early coping styles and later levels of psychological health' and homesickness. The research was conducted in two parts. The first was a preliminary study to modify a homesickness questionnaire (Archer et al, 1998) for use within a prison population. The modified questionnaire (HQ-P) demonstrated good reliability. The second part consisted of the longitudinal study. This comprised three phases where individuals were assessed within two weeks of arriving into the prison system (phase one, N = 261), six weeks later (phase two, N = 133) and four to six months after phase one (phase three, N = 55). At each phase, individuals were asked to complete a coping styles questionnaire, psychological health and homesickness measures. A small number of the sample at phase one also took part in a semi-structured interview. This was to explore qualitatively their methods of coping, management of relationships and levels of support experienced within the first two weeks of arrival into the prison system. The results demonstrated that the use of emotional and avoidance coping within two weeks of arrival into prison was related to better levels of psychological health and lower levels of homesickness some six weeks and four to six months later. Individuals also demonstrated preferences for particular coping strategies that remained consistent across each phase. There are many implications of these findings. The first of these is the demonstration that levels of homesickness remain consistently high as time continues in prison. The study also reflects the importance of not labelling coping strategies as universally effective or ineffective, and allowing a more realistic exploration of their significance as a result. The effective early use of avoidance and emotional coping upon later levels of psychological health and homesickness would contrast against coping theory, that has previously regarded emotional and avoidance coping as hindering effective management of the stressor (Zeinder and Endler, 1996 and Menaghan, 1982). ___________________ 'Psychological health refers to symptoms expressed in the Middlesex Hospital Questionnaire (Crown and Crisp, 1966). These include depression, free-floating anxiety, obsessional and hysteric symptoms, also somatic symptoms which has a physical base. When discussing the findings throughout this thesis, references to psychological health are a combination of the above symptoms.
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Stinson, Alicia M. "Spiritual Life Review with Older Adults| Finding Meaning in Late Life Development." Thesis, University of South Florida, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3568765.
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Spirituality has been recognized as a positive factor in the lives of older adults, especially as it influences their emotional, mental, and physical well-being. This convenience sample study included 17 older adults residing at a faith based continuing care retirement community in Florida. The sample was represented by Caucasian older adults with an average age of 84 years, highly educated, majority Protestant and mostly female. Spiritual life reviews were conducted using spiritual life maps (Hodge, 2005) and semi-structured interview questions. Erikson's epigenetic stage of ego-integrity was used along with Butler's life review process and Tornstam's gerotranscendence as a conceptual framework for understanding late life development and spirituality in older adults. This mostly qualitative study used a hermeneutic phenomenological approach to analyze the responses to the open-ended interview questions about spirituality across the life-time. Ego-integrity was measured at the beginning and end of the spiritual life review study.
Paired t-tests found that participation in the spiritual life review did not influence the ego integrity scores of participants. Specifically, there were no statistically significant difference between the pre ego integrity score (M=82.94, SD= 8.235) and the post ego integrity score (M=84.47, SD= 7.551); t (16) = -.769 p= .453. However, in comparison, the qualitative analysis revealed that the spiritual life review does influence ego-integrity in some participants. Additionally, the spiritual life review confirms gerotranscendence and contributes to information about spiritual development in the lives of older adults. The conclusion offers a discussion about the study's limitations, strengths, implications for future research, and suggestions for clinical practice.
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O'Brien, Carrie J. "Terrestrial Small Mammals from the Gamba Complex in Gabon: Distribution Patterns and Landscape Influences." DigitalCommons@USU, 2009. https://digitalcommons.usu.edu/etd/353.
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The small mammal communities of central Africa are not well understood, and the southwestern section of Gabon has not been previously surveyed except for some recent work in Monts Doudou. At five sites within the Gamba Complex we set out to 1) document the species of terrestrial rodents (Muridae) and shrews (Soricidae) weighing less than 100 g, 2) compare the community composition between inland and coastal sites, and 3) evaluate our sampling protocols. Using a combination of pitfall lines, Sherman live traps, and snap traps we captured 721 individuals of 12 rodent and 10 shrew species in 15,792 trap-nights. The rodent community was dominated by Hylomyscus stella and the shrew community by Sylvisorex johnstoni, in agreement with nearby studies. The coastal sites were less diverse with 3 rodent species and 1 shrew species only found at inland sites. The inland Rabi site had the most diverse small mammal community due to 2 species captured in secondary forests and fields near the oil facility. Our use of pitfalls was essential to our capture of shrews, and our protocol of switching from live to snap traps midway through the trapping period resulted in more species than expected.
The ecological factors influencing distribution patterns of small mammals in central Africa is not well understood. We evaluated the role of disturbance at paired inland and coastal sites using landscape variables generated from satellite imagery. Regression analyses revealed that while the amount of forest present at a site was strongly correlated with rodent richness (F = 16.437; df = 1; p = 0.001), shrew richness was negatively correlated with the amount of roads (partial F = 12.232; df = 1; p = 0.007) and rainfall (partial F = 6.035; df = 1; p = 0.036) and positively with elevation (partial F = 6.832; df = 1; p = 0.028). Our results suggest that while disturbance at Rabi has created additional habitats for rodents, the loss of specialist rodents from coastal sites reflects their inability to tolerate the edge-affected, fragmented, and less diverse forests in that region.
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Gagnon, Bruno. "End-of-life : insight from administrative data." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=29436.
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The purpose of this study is to develop and test the validity of an algorithm allowing the classification of the decedents as were dying of, died of and died with BC, using administrative data, for the study of service delivery to the terminally ill.Validation was carried out through a chart review of a sample of BC decedents extracted from a tumor registry. The algorithm was then applied to the decedents of a cohort of women with BC. The three groups were compared for their distributions of age and place of death.
The validation showed an excellent crude agreement (0.96). Of the 3334 deaths, 2293 were classified as were dying of, 142 as died of, and 949 as died with. The comparison of age showed that women who died with were older than women who were dying of. These two groups differed in their distributions of place of death.
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Wiik, Marianne, and Mikaela Sahlin. "Life Cycle Assessment : Life cycle assessment of a high speed centrifugal separator." Thesis, KTH, Industriell ekologi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-32798.
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The main objective is to perform a life cycle assessment (LCA) on a hot milk high-speed centrifugal separator (HMRPX 918-HGV-74C, product number 881275 01 01. The purpose of a life cycle assessment (LCA) is to provide a picture of a product’s total environmental impact during its lifecycle. The study is carried out according to ISO 14 040, i.e. all methods, data and assumptions are accounted for in order to make an external review possible. An LCA could provide the basis for an Environmental Product Declaration (EPD). The LCA clearly shows that the main environmental impact of the separator is caused by CIP and electricity used during operation. The major part of the impact from the CIP chemicals is due to the energy needed for their manufacture. Fossil fuels account for most of the impact for both operation and manufacture of chemicals. Therefore customers should be encouraged to use environmentally friendly electricity and chemicals, such as renewable energy sources and sodium hydroxide made with membrane technology. It is also important to use as little as possible of cleaning agents and make sure that waste is treated properly.www.ima.kth.se
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Nadrowski, Karin, Daniel Seifarth, Sophia Ratcliffe, Christian Wirth, and Lutz Maicher. "Identifiers in e-Science platforms for the ecological sciences." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-101319.
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In the emerging Web of Data, publishing stable and unique identifiers promises great potential in using the web as common platform to discover and enrich data in the ecologic sciences. With our collaborative e-Science platform “BEFdata”, we generated and published unique identifiers for the data repository of the Biodiversity – Ecosystem Functioning Research Unit of the German Research Foundation (BEF-China; DFG: FOR 891). We linked part of the identifiers to two external data providers, thus creating a virtual common platform including several ecological repositories. We used the Global Biodiversity Facility (GBIF) as well the International Plant Name Index (IPNI) to enrich the data from our own field observations. We conclude in discussing other potential providers for identifiers for the ecological research domain. We demonstrate the ease of making use of existing decentralized and unsupervised identifiers for a data repository, which opens new avenues to collaborative data discovery for learning, teaching, and research in ecology.
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Susanto, Steffenie. "Pediatric venipuncture| Child Life specialists' perspectives." Thesis, Mills College, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=1538411.
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During procedures like venipuncture, Child Life Specialists are able to incorporate non-pharmacological measures when most medical staff focused on pharmacological measures. There is little research about what types of interventions Child Life Specialists believe are effective at minimizing children's pain and increasing coping skills during venipuncture. The purpose of the current study was to examine Child Life Specialists' perspectives on the different techniques available in the hospital setting. An online survey of 75 Certified Child Life Specialists asked about the types of techniques that Child Life Specialists use during venipuncture. Further, questions asked how Child Life Specialists felt about the efficacy of pharmacological and non-pharmacological techniques with a variety of different ages. Results revealed that Child Life Specialists felt that combining two techniques helps to minimize pain during venipuncture for pediatric patients more than the use of a single technique. These results applied to preschoolers, school-aged children and adolescents.
Keywords: child life specialist, venipuncture, pain, distress