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Dissertations / Theses on the topic 'Applications in life sciences'

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Published: 10 December 2022
Last updated: 28 January 2023

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1

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 Philosophy
Department 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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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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3

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.

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4

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.

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5

Singh, Gurpreet. "Nanodevices for applications in life sciences and engineering; Fabrication and mechanical characterization." Connect to online resource, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3288721.

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Thesis (Ph.D.)--University of Colorado at Boulder, 2007.
Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7629. Advisers: Roop L. Mahajan; J Richard McIntosh. Includes supplementary digital materials.
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6

Kupferschmidt, Natalia. "Toxicological and Immunomodulatory Properties of Mesoporous Silica Particles : Applications in Life Sciences." Doctoral thesis, Uppsala universitet, Nanoteknologi och funktionella material, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-195904.

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Mesoporous silica particles offer great potential benefits as vehicles for drug delivery and in other biomedical applications. They present a high loading capacity due their ordered and size-tuneable pores that allow molecules to be loaded and released. In addition, they offer the possibility to enhance oral bioavailability of drugs with limited aqueous solubility and to protect pH sensitive drugs from the acidic conditions in the stomach on their way to the intestine. The aim of this thesis was to evaluate the biocompatibility and effects of mesoporous silica particles on immunocompetent cells. Subsequently, two potential life sciences applications were investigated: as adjuvants and as weight reduction agents. Adjuvants are used in vaccines in order to enhance the immunological response towards attenuated and poorly immunogenic antigens. Their function can be mediated through dendritic cells which have a central role in the control of adaptive immunity including immunological memory. Our results show that different types of mesoporous silica particles were able to tune the development of T cells both in human cell cultures and in mice. In contrast to the approved adjuvant alum (aluminium salts) which is a specific inducer of Th2-type immune responses, the particles induced more Th1-like responses, which may be desired in vaccines against allergy and intracellular pathogens such as viruses. Particle exposure to macrophages did not affect their cell function which is crucial for tissue homeostasis, wound repair and in prevention of autoimmune responses. Likewise, the cytokine secretion was not affected, which suggest that macrophages would not modulate the immune response towards the particles. Furthermore, mesoporous silica particles were highly tolerated at daily oral administrations of up to 2000 mg/kg doses for some of the materials prepared. Large pore mesoporous silica particles were shown to act as weight and body fat reduction agents without other observable pathological signs when administered in the diet of obese mice. Together; those results are promising for the development of mesoporous silica as drug delivery systems and adjuvants for oral administration of drugs or vaccines. Additionally, large pore mesoporous silica materials are potential agents for the treatment of obesity.
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7

Lin, Jing [Verfasser]. "Electrochemical microbiosensors and improved immobilization strategies for life sciences applications / Jing Lin." Ulm : Universität Ulm, 2019. http://d-nb.info/1200994477/34.

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8

Nilsson, Roland. "Statistical Feature Selection : With Applications in Life Science." Doctoral thesis, Linköping : Department of Physcis, Chemistry and Biology, Linköping University, 2007. http://www.bibl.liu.se/liupubl/disp/disp2007/tek1090s.pdf.

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9

Sudirman, Azizahalhakim. "Increased Functionality of Optical Fibers for Life-Science Applications." Doctoral thesis, KTH, Kvantelektronik och -optik, QEO, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-145319.

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The objective of this thesis work is to increase the functionality of optical fibers for possible applications in life-sciences. Optical fibers are a promising technology for use in biology and medicine. They are low-costwaveguides, flexible and have a small cross-section. They can guide high-power light with low loss in a micrometer core-size. These features make fibers attractive for minimally-invasive,in-vivostudies. The backwards guidance of the optical signal allows for real-time monitoring of the distance to the scattering targets and to study the environment through Raman scattering and fluorescence excitation. The longitudinal holes introduced in the fibers can be used,for instance,for delivery of medicine to a specific regionof a body. They could even be used for the extractionof species considered interesting for further analysis, for example, studyingcells that may be cancer-related. This thesis deals with four main topics. First, a demonstration is presented of the combination of high-power light guidance for ablation, low-power light reflectometry for positioning, and for liquid retrieval in a single fiber. It was found that in order to exploit the microfluidic possibilities available in optical fibers with holes, one needs to be able to combine fluids and light in a fiber without hindering the low-loss light guidance and the fluid flow. Secondly, one should also be able to couple light into the liquids and backout again. This is the subject of another paper in the present thesis. It was also observed that laser excitation through a fiber for the collection of a low-intensity fluorescence signal was often affected by the luminescence noise createdby the primary-coating of the fiber. This problem makes it difficult to measure low light-levels, for example, from single-cells. Athirdpaper in this thesis then describes a novel approach to reduce the luminescence from the polymer coating of the fiber, with the use of a nanometer-thick carbon layer on the cladding surface. Finally, exploiting some of the results described earlier, an optical fiber with longitudinal holes is used for the excitation, identification and for the collection of particles considered being of interest. The excitation light is guided in the fiber, the identification is performed by choosing the fluorescent particles with the appropriate wavelength, and, when a particle of interest is sufficiently near the fiber-tip, the suction system is activated for collection of the particle with good specificity. It is believed that the work described in this thesis could open the doors for applications in life-sciences and the future use of optical fibers for in-vivo studies.

QC 20140516

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10

Ghosh, Arindam [Verfasser]. "Single Molecule Fluorescence Spectroscopy and Imaging: Advanced Methods and Applications in Life Sciences / Arindam Ghosh." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://d-nb.info/1235222748/34.

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11

Pocheville, Arnaud. "LA NICHE ÉCOLOGIQUE: CONCEPTS, MODÈLES, APPLICATIONS." Phd thesis, Ecole Normale Supérieure de Paris - ENS Paris, 2010. http://tel.archives-ouvertes.fr/tel-00715471.

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Cette thèse est une enquête sur le concept de niche et quelques grands cadres théoriques qui y sont apparentés: la théorie de la niche et la théorie neutraliste en écologie, la théorie de la construction de niche en biologie évolutive, et la niche des cellules souches en écologie intra-organisme. Le premier chapitre retrace l'histoire du concept de niche et confronte la théorie de la niche à une théorie concurrente, la théorie neutraliste. Le concept de niche apparaît comme devant être un explanans de la diversité des espèces et de la structure des écosystèmes. Le deuxième chapitre confronte la théorie évolutive standard à la théorie de la construction de niche, dans laquelle un organisme peut modifier son environnement et ainsi influer sur la sélection à venir. Nous montrons comment caractériser cette confrontation en termes d'échelles temporelles des processus en jeu, ce qui nous permet d'identifier le domaine de validité véritablement propre à la théorie de la construction de niche plus explicitement qu'il ne l'a été par le passé. Le troisième chapitre développe les recherches des deux chapitres précédents dans le cadre de la modélisation d'une thérapie génique comme un processus écologique de compétition et de construction de niche par les cellules. Nous présentons une famille de modèles appliqués à différentes échelles temporelles de la dynamique cellulaire, entre lesquelles le modélisateur précautionneux ne saurait choisir sans résultats expérimentaux spécifiques. Nous concluons sur les conceptions de la relation entre un organisme et son environnement attachées aux diverses facettes du concept.
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12

Hinneburg, Alexander [Verfasser], Stefan [Akademischer Betreuer] Brass, Thomas [Akademischer Betreuer] Seidl, and Myra [Akademischer Betreuer] Spiliopoulou. "Text mining and applications in life sciences / Alexander Hinneburg. Betreuer: Stefan Brass ; Thomas Seidl ; Myra Spiliopoulou." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2011. http://d-nb.info/1025303172/34.

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13

Borghi, Francesco <1984&gt. "Flow Field–Flow Fractionation for size analysis and characterization of nanoparticles for applications in Life Sciences." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6446/.

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Nanotechnologies are rapidly expanding because of the opportunities that the new materials offer in many areas such as the manufacturing industry, food production, processing and preservation, and in the pharmaceutical and cosmetic industry. Size distribution of the nanoparticles determines their properties and is a fundamental parameter that needs to be monitored from the small-scale synthesis up to the bulk production and quality control of nanotech products on the market. A consequence of the increasing number of applications of nanomaterial is that the EU regulatory authorities are introducing the obligation for companies that make use of nanomaterials to acquire analytical platforms for the assessment of the size parameters of the nanomaterials. In this work, Asymmetrical Flow Field-Flow Fractionation (AF4) and Hollow Fiber F4 (HF5), hyphenated with Multiangle Light Scattering (MALS) are presented as tools for a deep functional characterization of nanoparticles. In particular, it is demonstrated the applicability of AF4-MALS for the characterization of liposomes in a wide series of mediums. Afterwards the technique is used to explore the functional features of a liposomal drug vector in terms of its biological and physical interaction with blood serum components: a comprehensive approach to understand the behavior of lipid vesicles in terms of drug release and fusion/interaction with other biological species is described, together with weaknesses and strength of the method. Afterwards the size characterization, size stability, and conjugation of azidothymidine drug molecules with a new generation of metastable drug vectors, the Metal Organic Frameworks, is discussed. Lastly, it is shown the applicability of HF5-ICP-MS for the rapid screening of samples of relevant nanorisk: rather than a deep and comprehensive characterization it this time shown a quick and smart methodology that within few steps provides qualitative information on the content of metallic nanoparticles in tattoo ink samples.
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14

Hinneburg, Alexander [Verfasser], Stefan Akademischer Betreuer] Brass, Thomas [Akademischer Betreuer] Seidl, and Myra [Akademischer Betreuer] [Spiliopoulou. "Text mining and applications in life sciences / Alexander Hinneburg. Betreuer: Stefan Brass ; Thomas Seidl ; Myra Spiliopoulou." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2011. http://nbn-resolving.de/urn:nbn:de:gbv:3:4-7603.

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15

Fournier, I. "Développements en Imagerie par Spectrométrie de Masse MALDI et Applications aux Problématiques Biologiques." Habilitation à diriger des recherches, Université des Sciences et Technologie de Lille - Lille I, 2005. http://tel.archives-ouvertes.fr/tel-00167305.

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L'imagerie par spectrométrie de masse MALDI est une technologie actuellement en plein essor. Elle permet d'obtenir rapidement en une seule étape d'acquisition la répartition moléculaire de différents composés (en particulier protéines) présents dans un tissu ; en s'affranchissant des étapes longues et coûteuses en échantillons que sont les extractions et séparations habituellement nécessaires par des techniques plus classiques.
Cependant, afin d'augmenter encore la potentialité de cette technologie, des développements restent encore à effectuer. Les recherches menées ont donc plus particulièrement portées sur ces développements.
En particulier, la recherche et l'étude de nouvelles matrices plus adaptées à l'analyse directe de tissu en MALDI sont particulièrement importantes. Dans ce contexte, certaines matrices ioniques se sont révélées particulièrement adaptées aux tissus en permettant d'obtenir une plus grande intensité du signal, un plus grand nombre de composés détectés, de bonnes performances en mode négatif, une grande homogénéité de cristallisation, une grande stabilité sous vide et une faible ablation de matériel consécutivement à l'irradiation laser. Dans un autre aspect, le traitement préalable des tissus permet également une amélioration de la qualité spectrale et des performances d'études structurales en mode MS/MS. Se sont révélés particulièrement intéressants les traitements des tissus aux solvants organiques et les digestions enzymatiques et en particulier pour les tissus conservés en blocs de paraffine après fixation.
D'autre part l'étude de la répartition des ARNm au sein des tissus est un développement crucial afin d'obtenir des images de colocalisation transcriptome/protéome. Est proposé dans ce travail un nouveau concept permettant de réaliser ces images, basé sur une analyse indirecte des ARNm, au travers de l'utilisation d'un groupement photoclivable relié à un peptide marqueur de séquence connue qui sera détecté.
Enfin, l'ensemble de ces développements trouve de nombreuses applications dans le domaine de la biologie et notamment dans le cadre de pathologies tel que le cancer de l'ovaire.
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16

Dell'Aguzzo, Paolo. "The secret life of software applications." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amslaurea.unibo.it/7405/.

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One of the most undervalued problems by smartphone users is the security of data on their mobile devices. Today smartphones and tablets are used to send messages and photos and especially to stay connected with social networks, forums and other platforms. These devices contain a lot of private information like passwords, phone numbers, private photos, emails, etc. and an attacker may choose to steal or destroy this information. The main topic of this thesis is the security of the applications present on the most popular stores (App Store for iOS and Play Store for Android) and of their mechanisms for the management of security. The analysis is focused on how the architecture of the two systems protects users from threats and highlights the real presence of malware and spyware in their respective application stores. The work described in subsequent chapters explains the study of the behavior of 50 Android applications and 50 iOS applications performed using network analysis software. Furthermore, this thesis presents some statistics about malware and spyware present on the respective stores and the permissions they require. At the end the reader will be able to understand how to recognize malicious applications and which of the two systems is more suitable for him. This is how this thesis is structured. The first chapter introduces the security mechanisms of the Android and iOS platform architectures and the security mechanisms of their respective application stores. The Second chapter explains the work done, what, why and how we have chosen the tools needed to complete our analysis. The third chapter discusses about the execution of tests, the protocol followed and the approach to assess the “level of danger” of each application that has been checked. The fourth chapter explains the results of the tests and introduces some statistics on the presence of malicious applications on Play Store and App Store. The fifth chapter is devoted to the study of the users, what they think about and how they might avoid malicious applications. The sixth chapter seeks to establish, following our methodology, what application store is safer. In the end, the seventh chapter concludes the thesis.
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17

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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18

Smus, Justyna Paulina. "Application of enhanced Raman techniques in life sciences and biomedicine." Thesis, University of Southampton, 2016. https://eprints.soton.ac.uk/409721/.

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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.
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Vestberg, Robert. "Dendron decorated chromophores for optical power limiting applications." Doctoral thesis, Stockholm, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-78.

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20

Bylesjö, Max. "Latent variable based computational methods for applications in life sciences : Analysis and integration of omics data sets." Doctoral thesis, Umeå universitet, Kemi, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1616.

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With the increasing availability of high-throughput systems for parallel monitoring of multiple variables, e.g. levels of large numbers of transcripts in functional genomics experiments, massive amounts of data are being collected even from single experiments. Extracting useful information from such systems is a non-trivial task that requires powerful computational methods to identify common trends and to help detect the underlying biological patterns. This thesis deals with the general computational problems of classifying and integrating high-dimensional empirical data using a latent variable based modeling approach. The underlying principle of this approach is that a complex system can be characterized by a few independent components that characterize the systematic properties of the system. Such a strategy is well suited for handling noisy, multivariate data sets with strong multicollinearity structures, such as those typically encountered in many biological and chemical applications. The main foci of the studies this thesis is based upon are applications and extensions of the orthogonal projections to latent structures (OPLS) method in life science contexts. OPLS is a latent variable based regression method that separately describes systematic sources of variation that are related and unrelated to the modeling aim (for instance, classifying two different categories of samples). This separation of sources of variation can be used to pre-process data, but also has distinct advantages for model interpretation, as exemplified throughout the work. For classification cases, a probabilistic framework for OPLS has been developed that allows the incorporation of both variance and covariance into classification decisions. This can be seen as a unification of two historical classification paradigms based on either variance or covariance. In addition, a non-linear reformulation of the OPLS algorithm is outlined, which is useful for particularly complex regression or classification tasks. The general trend in functional genomics studies in the post-genomics era is to perform increasingly comprehensive characterizations of organisms in order to study the associations between their molecular and cellular components in greater detail. Frequently, abundances of all transcripts, proteins and metabolites are measured simultaneously in an organism at a current state or over time. In this work, a generalization of OPLS is described for the analysis of multiple data sets. It is shown that this method can be used to integrate data in functional genomics experiments by separating the systematic variation that is common to all data sets considered from sources of variation that are specific to each data set.
Funktionsgenomik är ett forskningsområde med det slutgiltiga målet att karakterisera alla gener i ett genom hos en organism. Detta inkluderar studier av hur DNA transkriberas till mRNA, hur det sedan translateras till proteiner och hur dessa proteiner interagerar och påverkar organismens biokemiska processer. Den traditionella ansatsen har varit att studera funktionen, regleringen och translateringen av en gen i taget. Ny teknik inom fältet har dock möjliggjort studier av hur tusentals transkript, proteiner och små molekyler uppträder gemensamt i en organism vid ett givet tillfälle eller över tid. Konkret innebär detta även att stora mängder data genereras även från små, isolerade experiment. Att hitta globala trender och att utvinna användbar information från liknande data-mängder är ett icke-trivialt beräkningsmässigt problem som kräver avancerade och tolkningsbara matematiska modeller. Denna avhandling beskriver utvecklingen och tillämpningen av olika beräkningsmässiga metoder för att klassificera och integrera stora mängder empiriskt (uppmätt) data. Gemensamt för alla metoder är att de baseras på latenta variabler: variabler som inte uppmätts direkt utan som beräknats från andra, observerade variabler. Detta koncept är väl anpassat till studier av komplexa system som kan beskrivas av ett fåtal, oberoende faktorer som karakteriserar de huvudsakliga egenskaperna hos systemet, vilket är kännetecknande för många kemiska och biologiska system. Metoderna som beskrivs i avhandlingen är generella men i huvudsak utvecklade för och tillämpade på data från biologiska experiment. I avhandlingen demonstreras hur dessa metoder kan användas för att hitta komplexa samband mellan uppmätt data och andra faktorer av intresse, utan att förlora de egenskaper hos metoden som är kritiska för att tolka resultaten. Metoderna tillämpas för att hitta gemensamma och unika egenskaper hos regleringen av transkript och hur dessa påverkas av och påverkar små molekyler i trädet poppel. Utöver detta beskrivs ett större experiment i poppel där relationen mellan nivåer av transkript, proteiner och små molekyler undersöks med de utvecklade metoderna.
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Bylesjö, Max. "Latent variable based computational methods for applications in life sciences : Analysis and integration of omics data sets /." Umeå : Chemistry Kemi, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1616.

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Vishwanathan, S. V. N. "Kernel Methods Fast Algorithms and real life applications." Thesis, Indian Institute of Science, 2003. http://hdl.handle.net/2005/49.

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Support Vector Machines (SVM) have recently gained prominence in the field of machine learning and pattern classification (Vapnik, 1995, Herbrich, 2002, Scholkopf and Smola, 2002). Classification is achieved by finding a separating hyperplane in a feature space, which can be mapped back onto a non-linear surface in the input space. However, training an SVM involves solving a quadratic optimization problem, which tends to be computationally intensive. Furthermore, it can be subject to stability problems and is non-trivial to implement. This thesis proposes an fast iterative Support Vector training algorithm which overcomes some of these problems. Our algorithm, which we christen Simple SVM, works mainly for the quadratic soft margin loss (also called the l2 formulation). We also sketch an extension for the linear soft-margin loss (also called the l1 formulation). Simple SVM works by incrementally changing a candidate Support Vector set using a locally greedy approach, until the supporting hyperplane is found within a finite number of iterations. It is derived by a simple (yet computationally crucial) modification of the incremental SVM training algorithms of Cauwenberghs and Poggio (2001) which allows us to perform update operations very efficiently. Constant-time methods for initialization of the algorithm and experimental evidence for the speed of the proposed algorithm, when compared to methods such as Sequential Minimal Optimization and the Nearest Point Algorithm are given. We present results on a variety of real life datasets to validate our claims. In many real life applications, especially for the l2 formulation, the kernel matrix K є R n x n can be written as K = Z T Z + Λ , where, Z є R n x m with m << n and Λ є R n x n is diagonal with nonnegative entries. Hence the matrix K - Λ is rank-degenerate, Extending the work of Fine and Scheinberg (2001) and Gill et al. (1975) we propose an efficient factorization algorithm which can be used to find a L D LT factorization of K in 0(nm2) time. The modified factorization, after a rank one update of K, can be computed in 0(m2) time. We show how the Simple SVM algorithm can be sped up by taking advantage of this new factorization. We also demonstrate applications of our factorization to interior point methods. We show a close relation between the LDV factorization of a rectangular matrix and our LDLT factorization (Gill et al., 1975). An important feature of SVM's is that they can work with data from any input domain as long as a suitable mapping into a Hilbert space can be found, in other words, given the input data we should be able to compute a positive semi definite kernel matrix of the data (Scholkopf and Smola, 2002). In this thesis we propose kernels on a variety of discrete objects, such as strings, trees, Finite State Automata, and Pushdown Automata. We show that our kernels include as special cases the celebrated Pair-HMM kernels (Durbin et al., 1998, Watkins, 2000), the spectrum kernel (Leslie et al., 20024, convolution kernels for NLP (Collins and Duffy, 2001), graph diffusion kernels (Kondor and Lafferty, 2002) and various other string-matching kernels. Because of their widespread applications in bio-informatics and web document based algorithms, string kernels are of special practical importance. By intelligently using the matching statistics algorithm of Chang and Lawler (1994), we propose, perhaps, the first ever algorithm to compute string kernels in linear time. This obviates dynamic programming with quadratic time complexity and makes string kernels a viable alternative for the practitioner. We also propose extensions of our string kernels to compute kernels on trees efficiently. This thesis presents a linear time algorithm for ordered trees and a log-linear time algorithm for unordered trees. In general, SVM's require time proportional to the number of Support Vectors for prediction. In case the dataset is noisy a large fraction of the data points become Support Vectors and thus time required for prediction increases. But, in many applications like search engines or web document retrieval, the dataset is noisy, yet, the speed of prediction is critical. We propose a method for string kernels by which the prediction time can be reduced to linear in the length of the sequence to be classified, regardless of the number of Support Vectors. We achieve this by using a weighted version of our string kernel algorithm. We explore the relationship between dynamic systems and kernels. We define kernels on various kinds of dynamic systems including Markov chains (both discrete and continuous), diffusion processes on graphs and Markov chains, Finite State Automata, various linear time-invariant systems etc Trajectories arc used to define kernels introduced on initial conditions lying underlying dynamic system. The same idea is extended to define Kernels on a. dynamic system with respect to a set of initial conditions. This framework leads to a large number of novel kernels and also generalize many previously proposed kernels. Lack of adequate training data is a problem which plagues classifiers. We propose n new method to generate virtual training samples in the case of handwritten digit data. Our method uses the two dimensional suffix tree representation of a set of matrices to encode an exponential number of virtual samples in linear space thus leading to an increase in classification accuracy. This in turn, leads us naturally to a, compact data dependent representation of a test pattern which we call the description tree. We propose a new kernel for images and demonstrate a quadratic time algorithm for computing it by wing the suffix tree representation of an image. We also describe a method to reduce the prediction time to quadratic in the size of the test image by using techniques similar to those used for string kernels.
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23

Srilatha, Rondla, and Gande Someshwar. "Security Testing for Web Applications in SDLC." Thesis, Blekinge Tekniska Högskola, Sektionen för datavetenskap och kommunikation, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:bth-2903.

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Context: In Web applications, the Software vulnerability can be reduced by applying security testing in all phases of the software development life cycle (SDLC). Lot of vulnerabilities might occur if the security testing is applied in the last phase of SDLC. In order to mitigate these vulnerabilities, a lot of rework is required that involves reverse engineering in the development and design phases. To overcome this situation, organizations are shifting from security testing (performed in last phase) towards security testing in the early phases of SDLC. Objectives: The main objectives of this thesis are to gather the benefits and challenges of security testing in the last phase versus security testing in every phase of the SDLC. After gathering, authors want to compare both implementations because these days most organizations are shifting from last phase to every phase of SDLC. Justification to the reason can be achieved by this comparison. Methods: In order to satisfy the objectives of this thesis, a literature review and interviews were conducted. The literature review was conducted by gathering benefits and challenges of last phase and every phase of SDLC. Authors have applied coding technique to the data gathered from literature review. By using the results from literature review, a set of questions were framed. Based on these questions, interviews in various organizations were performed. To analyze the practitioner’s data we used Sorting and Coding technique. Then, we conducted a comparative analysis to compare both results. Results: Application of security testing in the last phase of the SDLC results in a lot of rework which in turn leads to instability in managing the cost, time and resources in an organisation. In order to overcome this, more and more organisations are introducing security testing at each and every phase of SDLC. Conclusions: It can be concluded that every phase of security testing in SDLC has more benefits than applying in last phase of SDLC. To evaluate this process more research is needed to acquire more knowledge of security testing in all phases of SDLC. Through literature review and interviews conducted, it is evident that security testing at early phases causes a reduction in rework which in turn leads to more efficient management of cost, time and resources of a project.
+91 8977404640
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24

Cox, Tyler L. "Development of ETSU Student Life Android Application." Digital Commons @ East Tennessee State University, 2014. https://dc.etsu.edu/honors/231.

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In this thesis, the author gives a description his journey creating and developing a Student Life Application for East Tennessee State University. This thesis will document his process with development as well as reflect on the struggles and victories in creation of this application.
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25

Araiza, Roberto. "The use of interval-related expert knowledge in processing 2-D and 3-D data with an emphasis on applications to geosciences and biosciences /." To access this resource online via ProQuest Dissertations and Theses @ UTEP, 2007. http://0-proquest.umi.com.lib.utep.edu/login?COPT=REJTPTU0YmImSU5UPTAmVkVSPTI=&clientId=2515.

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26

Ameli, Reza. "An optogenetic headstage for optical stimulation and neural recording in life science applications." Master's thesis, Université Laval, 2015. http://hdl.handle.net/20.500.11794/26055.

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L'optogénétique est une nouvelle méthode de contrôle de l’activité neuronale dans laquelle la lumière est employée pour activer ou arrêter certains neurones. Dans le cadre de ce travail, un dispositif permettant l’acquisition de signaux neuronaux et conduisant à une stimulation optogénétique de façon multicanale et temps-réel a été conçu. Cet outil est muni de deux canaux de stimulation optogénétique et de deux canaux de lecture des signaux neuronaux. La source de lumière est une DEL qui peut consommer jusqu’à 150 milliampères. Les signaux neuronaux acquis sont transmis à un ordinateur par une radio. Les dimensions sont d’environ 20×20×15 mm3 et le poids est de moins de 7 grammes, rendant l’appareil utile pour les expériences sur les petits animaux libres. Selon nos connaissances actuelles, le résultat de ce projet constitue le premier appareil de recherche optogénétique sans-fil, compact offrant la capture de signaux cérébraux et la stimulation optique simultanée.
Optogenetics is a new method for controlling the neural activity where light is used to activate or silence, with high spatial and temporal resolution, genetically light-sensitized neurons. In optogenetics, a light source such as a LED, targets light-sensitized neurons. In this work, a light-weight wireless animal optogenetic headstage has been designed that allows multi-channel simultaneous real-time optical stimulation and neural recording. This system has two optogenetic stimulation channels and two electrophysiological reading channels. The optogenetic stimulation channels benefit from high-power LEDs (sinking 150 milliamps) with flexible stimulation patterns and the recorded neural data is wirelessly sent to a computer. The dimensions of the headstage are almost 20×20×15 mm3 and it weighs less than 7 grams. This headstage is suitable for tests on small freely-moving rodents. To the best of our knowledge, this is the first reported fully wireless headstage to offer simultaneous multichannel optical stimulation along with multichannel neural recording capability.
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Grant, Joshua Ford. "Electrospun Blends of Polydioxanone and Fibrinogen for Urological Applications." VCU Scholars Compass, 2007. http://scholarscompass.vcu.edu/etd/891.

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The need for tissue and organ replacements cannot be satisfied by autograft and allografts alone. The purpose of this study was to investigate the feasibility of electrospinning a blend of polydioxanone and fibrinogen to produce an engineered tissue scaffold. Fiber diameter and pore size of blends were characterized, as well as mechanical strength. Cell proliferation assays for 1 and 7 day cultures were preformed, and a histological evaluation was performed to determine how favorable the various blends were to cell infiltration and proliferation. Some ratios of blends were identified that contained both acceptable mechanical properties and properties that facilitated cell infiltration. These findings pave the way for future refinement and use of these scaffolds for a variety of tissue engineered targets.
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Zhang, Qian [Verfasser], and Wolfgang [Akademischer Betreuer] Parak. "Polymer-Coated Inorganic Nanoparticles: Nanotools for Life Science Applications / Qian Zhang. Betreuer: Wolfgang Parak." Marburg : Philipps-Universität Marburg, 2016. http://d-nb.info/1099594251/34.

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Stankovski, Tomislav. "Tackling the inverse problem for non-autonomous systems : application to the life sciences." Thesis, Lancaster University, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.654941.

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30

Flantua, Elise. "Applications to enhance participation in everyday life for children/adolescents with ID and ASD : A systematic literature review." Thesis, Jönköping University, HLK, CHILD, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:hj:diva-53663.

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31

Derrien, Thomas. "L'analyse comparée des génomes : applications à l'identification de nouveaux gènes canins." Phd thesis, Université Rennes 1, 2007. http://tel.archives-ouvertes.fr/tel-00656330.

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Au cours de ces trois dernières années, le génome du chien a bénéficié d'avancées majeures à sa connaissance. Les projets de cartographie et de séquençage de son génome, motivés par le formidable potentiel qu'offre le chien en tant que modèle génétique, ont généré de grandes quantités de données à analyser. Dans ce contexte, mes travaux de thèse se sont d'abord focalisés sur la conception d'outils bioinformatiques d'intégration de plusieurs ressources afin d'évaluer et de comparer les informations issues des projets de cartographie et de séquence du génome du chien. Avec la disponibilité d'un nombre croissant de génomes séquencés, nous avons développé le programme AutoGRAPH pour formaliser la conservation de l'ordre des gènes orthologues entre les génomes mammifères, automatiser la construction de cartes de synténie entre ces génomes et, enfin, faciliter l'annotation du génome du chien. Un première application de notre méthode a permis de redéfinir la localisation d'une centaine de gènes préalablement assignés au chromosome canin non-assemblé ou "chromosome Unknown". Dans un second projet, nous avons combiné notre approche de conservation de l'ordre des gènes entre deux génomes avec des alignements de séquences ciblés afin d'identifier des nouvelles structures de gènes canins codant pour des protéines. À partir d'un ensemble de 412 gènes orthologues entre quatre génomes de référence (homme - chimpanzé - rat - souris) et présumés absents chez le chien, nous identifions 285 nouveaux gènes canins et/ou nouvelles relations d'orthologie avec les génomes de référence. Enfin, différents mécanismes évolutifs sont suggérés mettant en relation la nature des gènes, la présence de famille de gènes et la composition en séquences pour expliquer la perte de gènes chez le chien.
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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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33

King, Barbara M. "A Software Development Life-Cycle Model for Web-Based Application Development." NSUWorks, 2004. http://nsuworks.nova.edu/gscis_etd/636.

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Software development life cycle models were believed to play a critical role in improving software quality by guiding tasks in the software development processes since being formally introduced and embraced in the 1970s. Many organizations attempted to deploy software development life cycle methodologies with the intent to improve the software development process from conception through implementation to delivery. Numerous established software development models exist, including the classic waterfall life cycle model, Spiral model, Prototyping, Evolutionary, (e.g., Staged, Phased, and Timebox models), object-oriented design (OOD) (e.g., Rational Unified Process), and agile processes (e.g., eXtreme Programming [XP]). The design and development of web-based applications introduced new problems and requirements that did not exist when traditional software development life-cycle models were being put into practice. This research presents empirical software development practice data pertaining to web-based application development. The goal of this project was to answer the question, "What is the general paradigm of an SDLC model for web-based application development?" The focus of the project was to derive an empirical SDLC model for web-based application development. Data from current practices was collected via a web-based application. Study participants used the web-based application to input data concerning the SDLC model of their web-based application development process. The empirical model was derived from the data provided by participants on current professional web-based application development practices. The results of this research showed that although web-based application development life-cycle does parallel traditional SDLCs in some phases, there were enough differences that an exact fit to an existing model does not exist. A modified version of the Classic Waterfall with some repetitiveness of the Spiral model with the addition of optional phases best met the situational requirements of web-based application development.
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Hatt, Mathieu. "Détermination automatique des volumes fonctionnels en imagerie d'émission pour les applications en oncologie." Phd thesis, Université de Bretagne occidentale - Brest, 2008. http://tel.archives-ouvertes.fr/tel-00373581.

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Une des principales causes d'erreur en analyse semi-quantitative en imagerie par émission de positons (TEP) est la méthode utilisée pour déterminer les volumes d'intérêt sur les images fonctionnelles. Ceci concerne le diagnostic et le suivi thérapeutique en oncologie ainsi que la nouvelle application en plein développement qu'est la radiothérapie guidée par l'image. La faible qualité des images d'émission, liée notamment au bruit et au flou induits par les effets de volume partiels et la variabilité des protocoles d'acquisition et de reconstruction des images, ainsi que le grand nombre de procédures proposées pour définir les volumes, en sont la cause. La plupart des méthodes proposées jusqu'alors sont basées sur des seuillages déterministes, peu robustes au bruit et aux variations de contraste et incapables de gérer les hétérogénéités dans la distribution d'activité des tumeurs. L'objectif de cette thèse est de proposer une approche de segmentation des images 3D, automatique, robuste, précise et reproductible pour déterminer le volume fonctionnel des tumeurs de toutes tailles dont la distribution d'activité peut être très hétérogène. L'approche proposée est fondée sur la segmentation statistique des images, couplée à une modélisation floue, permettant de prendre en compte à la fois l'aspect bruité et l'aspect flou des images de médecine nucléaire. Elle fait appel à une étape d'estimation itérative des paramètres et une modélisation locale du voxel et de son voisinage pour l'estimation et la segmentation. Les méthodes développées ont été évaluées sur de nombreuses données simulées et réelles, tant pour des images de fantômes que pour des images de tumeurs. Les résultats sur fantôme ont permis de valider les performances de l'approche proposée en terme de taille d'objet d'intérêt, jusqu'à 13 mm de diamètre (environ deux fois la résolution spatiale en TEP), ainsi que de confirmer un comportement plus robuste par rapport au bruit, aux variations de contraste ou des paramètres d'acquisition et de reconstruction, que les méthodes de référence basées sur des seuillages. Les résultats obtenus sur différents ensemble de données d'images cliniques de tumeurs, fournies par différents services de médecine nucléaire dans le cadre de multiples collaborations, ont montré la capacité de l'approche à segmenter avec précision des tumeurs complexes, tant en terme de forme que de distribution d'activité, pour lesquelles les méthodes de référence échouent à produire des segmentation cohérentes. La méthode de segmentation développée est également capable de définir des régions d'intérêt au sein même de la tumeur grâce à sa gestion de l'hétérogénéité de l'activité de la tumeur, là où les méthodes de références sont strictement binaires. Les résultats concernant la robustesse et la précision de l'approche sur tumeurs amènent à penser que son utilisation peut être envisagée tant dans le cadre du diagnostic et du suivi thérapeutique, que pour la définition des volumes cibles en radiothérapie, avec le potentiel d'augmenter les doses délivrées aux tumeurs tout en réduisant dans le même temps les doses délivrées aux tissus sains et aux organes à risque environnants, conformément au principe de "dose painting". Des travaux pour évaluer l'impact effectif de la méthodologie dans le contexte de la radiothérapie ont commencé dans le cadre d'un projet ANR, avec un dépôt de brevet associé.
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35

Roach, Necrisha. "The Development of a Novel Multi-dimensional Product for Wound Healing Applications." VCU Scholars Compass, 2010. http://scholarscompass.vcu.edu/etd/2131.

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A characteristic feature of chronic wounds is a prolonged inflammatory response as well as susceptibility to infection. Studies have shown that during the inflammatory response, there is a significant increase in the levels of neutrophil-derived enzymes. The purpose of this work was to determine whether the anionic macromolecule polystyrene sulfonate (PSS) and five of its salt forms, namely PSS-calcium, PSS-chlorhexidine, PSS-doxycycline, PSS-glutathione and PSS-silver are able to inhibit the activity of three of the enzymes whose levels are elevated in chronic wounds: elastase, cathepsin G and myeloperoxidase. In addition to the enzyme inhibition study, the various formulations’ antimicrobial properties were analyzed by evaluating their ability to inhibit the growth of three common clinical isolates: Staphylococcus aureus, Pseudomonas aeruginosa and Acinetobacter baumanii. It is worthy to note that the structure of PSS makes it a very flexible platform to which other molecules can be added in order to address a variety of “targets” as well as tailor quantitative strength. The results from this project showed that purified PSS and the various salt derivatives were able to inhibit elastase and cathepsin G activity. In addition, three of the therapeutic cations attached to PSS: silver, doxycycline and chlorhexidine retained their intrinsic antimicrobial properties without having an adverse effect on healthy tissue. In summary, this study demonstrated that PSS possessed an intrinsic ability to inhibit a number of proteases and that it could also be used as a delivery vehicle for other compounds with potential therapeutic value.
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36

Vom, Braucke Troy S., and tvombraucke@swin edu au. "Establishment of a database for tool life performance." Swinburne University of Technology, 2004. http://adt.lib.swin.edu.au./public/adt-VSWT20050914.085324.

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The cutting tool industry has evolved over the last half century to the point where an increasing range and complexity of cutting tools are available for metal machining. This highlighted a need to provide an intelligent, user-friendly system of tool selection and recommendation that can also provide predictive economic performance data for engineers and end-users alike. Such an 'expert system' was developed for a local manufacturer of cutting tools in the form of a relational database to be accessed over the Internet. A number of performance predictive models were reviewed for various machining processes, however they did not encompass the wide range of variables encountered in metal machining, thus adaptation of these existing models for an expert system was reasoned to be economically prohibitive at this time. Interrogation of published expert systems from cutting tool manufacturers, showed the knowledge-engineered principle to be a common approach to transferring economic and technological information to an end-user. The key advantage being the flexibility to allow further improvements as new knowledge is gained. As such, a relational database was built upon the knowledge-engineered principle, based on skilled craft oriented knowledge to establish an expert system for selection and performance assessment of cutting tools. An investigation into tapping of austenitic stainless steels was undertaken to develop part of a larger expert system. The expert system was then interrogated in this specific area in order to challenge by experiment, the skilled craft oriented knowledge in this area. The experimental results were incorporated into the database where appropriate, providing a user-friendly working expert system for intelligent cutting tool selection, recommendation and performance data.
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37

Bertrand, Samuel. "Les sidérophores de Scedosporium apiospermum : identification, synthèse et applications." Phd thesis, Université d'Angers, 2009. http://tel.archives-ouvertes.fr/tel-00466113.

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Scedosporium apiospermum, pathogène émergent, colonise les voies respiratoires des patients mucoviscidosiques et provoque des infections sévères chez les patients immunodéprimés. Afin d'améliorer notre connaissance sur sa pathogénicité, nous avons étudié sa production en sidérophores. Après une production maximale en milieu de culture liquide déplété en fer et à pH alcalin, les sidérophores ont été récupérés du filtrat de culture par extraction liquide/liquide, et analysés par CLHP en phase inverse. Deux sidérophores, l'acide dimérumique (DMA) et le N-méthyl coprogène B (MCB), ont été identifiés grâce à de la spectrométrie de masse MSn par ionisation par électro-nébulisation. La comparaison des différentes souches fongiques a montré une production importante de MCB pour les isolats cliniques d'origine respiratoire. Après optimisation du protocole d'extraction, de nouveaux sidérophores ont été identifiés à partir d'autres champignons impliqués dans la mucoviscidose. Seul le MCB était présent chez S. apiospermum, constituant ainsi un marqueur de ce champignon. Ainsi, la détection de ce sidérophore dans les expectorations de malades atteints de mucoviscidose pourrait constituer une méthode de diagnostic des infections à S. apiospermum. Dans le but d'étudier plus précisément les mécanismes d'acquisition du fer par S. apiospermum, la synthèse du DMA et du MCB a été entreprise. Ces molécules contiennent respectivement deux à trois monomères de base, la fusarinine. C'est donc la synthèse de la de la fusarinine qui a été effectuée avec un rendement global de 2% en mettant en jeu une synthèse convergente à partir de l'ornithine protégée et du but-3-yn-1-ol.
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38

Dünnbier, Mario [Verfasser]. "Plasma jets for life science applications: characterisation and tuning of the reactive species composition / Mario Dünnbier." Greifswald : Universitätsbibliothek Greifswald, 2015. http://d-nb.info/1080060197/34.

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39

Venkatesan, Aravind. "Application of Semantic Web Technology to Establish Knowledge Management and Discovery in the Life Sciences." Doctoral thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for biologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-24074.

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The last three decades has seen the successful development of many high-throughput technologies that have revolutionised and transformed biological research. The application of these technologies has generated large quantities of data allowing new approaches to analyze and integrate these data, which now constitute the field of Systems Biology. Systems Biology aims to enable a holistic understanding of a biological system by mapping interactions between all the biochemical components within the system. This requires integration of interdisciplinary data and knowledge to comprehensively explore the various biological processes of a system. Ontologies in biology (bio-ontologies) and the Semantic Web are playing an increasingly important role in the integration of data and knowledge by offering an explicit, unambiguous and rich representation mechanism. This increased influence led to the proposal of the Semantic Systems Biology paradigm to complement the techniques currently used in Systems Biology. Semantic Systems Biology provides a semantic description of the knowledge about the biological systems on the whole facilitating data integration, knowledge management, reasoning and querying. However, this approach is still a typical product of technology push, offering potential users access to the new technology. This doctoral thesis presents the work performed to bring Semantic Systems Biology closer to biological domain experts. The work covers a variety of aspects of Semantic Systems Biology: The Gene eXpression Knowledge Base is a resource that captures knowledge on gene expression. The knowledge base exploits the power of seamless data integration offered by the semantic web technologies to build large networks of varied datasets, capable of answering complex biological questions. The knowledge base is the result of the active collaboration with the Gastrin Systems Biology group here at the Norwegian University of Science and Technology. This resource was customised by the integration of additional data sets on users’ request. Additionally, the utility of the knowledge base is demonstrated by the conversion of biological questions into computable queries. The joint analysis of the query results has helped in filling knowledge gaps in the biological system of study. Biologists often use different bioinformatics tools to conduct complex biological analysis. However, using these tools frequently poses a steep learning curve for the life science researchers. Therefore, the thesis describes ONTO-ToolKit, a plug-in that allows biologists to exploit bio-ontology based analysis as part of biological workflows in Galaxy. ONTO-ToolKit allows users to perform ontology-based analysis to improve the depth of their overall analysis Visualisation plays a key role in aiding users understand and grasp the knowledge represented in bio-ontologies. To this end, OLSVis, a web application was developed to make ontology browsing intuitive and flexible. Finally, the steps needed to further advance the Semantic Systems Biology approach has been discussed.
Semantic Systems Biology
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40

Seguin, Johanne. "Caractérisation de modèles de tumeurs murines et leurs applications en thérapie anti-angiogénique vectorisée." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2012. http://tel.archives-ouvertes.fr/tel-00836310.

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La première partie de ce travail de thèse a permis de sélectionner parmi un panel de 15 tumeurs murines, les modèles les plus appropriés pour l'étude de molécules à potentiel anti-angiogénique. Deux tumeurs ont été choisies, la tumeur de poumon (Lewis Lung carcinoma, LLC) pour laquelle une forte vascularisation a été observée et la tumeur de côlon (colon tumor 26, C26) pour laquelle l'expression des intégrines αvβ3 et de la sélectine-E a été observée. Les modèles de côlon C26 implantés en sous-cutané (ectopique) et sur le caecum (orthotopique) ont été développés et caractérisés par différentes modalités d'imagerie. L'imagerie optique s'est montrée adaptée uniquement pour la détection précoce des tumeurs, tandis que l'imagerie par résonance magnétique et l'imagerie par ultrason se sont avérées des techniques très adaptées pour le suivi de la croissance des tumeurs implantées en ectopique et en orthotopique. Le développement et la caractérisation de ces modèles se sont révélés très utiles pour la deuxième partie de nos travaux, notamment pour l'évaluation antitumorale d'un flavonoïde la fisétine. La fisétine est un flavonoïde naturel (3,3',4',7-tetrahydroxyflavone) ayant montré une activité anti-angiogénique et des propriétés anticancéreuses.Etant donné sa faible solubilité dans l'eau, une forme liposomale a été développée afin de faciliter son administration systémique.Une efficacité antitumorale plus importante de la fisétine liposomale comparée à la fisétine libre a été obtenue après injection d'une faible dose (21 mg/kg) sur la lignée tumorale LLC. Cette formulation pourrait donc avantageusement être employée pour la formulation de composés de la famille des flavonoïdes
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41

Kennedy, Caroline A. "Learning and Application of Range Management Innovations Among Ranchers in West-Central Colorado." DigitalCommons@USU, 2005. https://digitalcommons.usu.edu/etd/7430.

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Like many ranchers in the West, ranchers in West-Central Colorado are reevaluating their management strategies in the face of forces like drought, rising land prices, and encroaching development. While ranchers seek answers on alternative management strategies, research and Extension personnel search for adequate means of diffusing needed information. Relative to many rural western communities, ranchers in West-Central Colorado show high interest in alternative range management ideas, and many implement changes to their ranch management based on these ideas. This can partially be attributed to a unique support system of Extension and agency personnel with effective, untraditional outreach and land-management approaches. A survey was mailed to all 647 persons on the mailing list for the CSU Tri-River Extension Office, including Forest Service and BLM permittees in Mesa, Delta Montrose, San Miguel, Ouray, Hinsdale, Saguache, and Gunnison counties. The survey was designed to gain insight on how ranchers perceive current Extension efforts, how they learn new management information from peers and Extension/agency personnel, and how they apply these new ideas to their operations. Subsequent qualitative interviews with respondents gathered information on the process of adapting and implementing range management innovations into individual operations. This paper presents the findings of the survey and interviews, and implications for future outreach efforts.
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Toth, Kalman. "Fonctionnalisation d' (endo)fullerène : de la science des matériaux aux applications biomédicales." Phd thesis, Université de Strasbourg, 2012. http://tel.archives-ouvertes.fr/tel-00862768.

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Nous avons synthétisé différentes dyades donneurs-accepteurs (D-A) π-conjuguées à base de fullerène pour des applications photovoltaïques dans lesquelles les unités D étaient soit des oligophenylenevinylenes (OPV) soit des oligophenyleneethynylene (OPE) et les unités A étaient le C60 ou un endofullerène du type Y3N@C80. Il y avait une exigence supplémentaire pour nos matériaux, à savoir qu'ils devaient s'auto-organiser en phases liquides-cristallines. Pour ce faire, toutes les unités D contenaient un promoteur mésogène afin d'induire le mésomorphisme de la dyade D- et donc de contrôler la morphologie des couches minces nécessaires à l'élaboraiton des cellules photovoltaïques grâce à une organisation supramoléculaire. En dehors de cela, nous avons étudié l'influence de la nature chimique du donneur (par exemple lyophile ou amphiphile), de la longueur des oligomères et de la multiaddition sur les propriétés photophysiques et sur l'auto-assemblage. Nous avons synthétisé une dyade OPE-Y3N@C80 qui est le premier dérive mésomorphe et photosensible de ce type de métallofullerène endohédral.
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Vila, Roa Eva Graciela. "Evaluation of Pigments from a Purple Variety of Atriplex hortensis L. for Use in Food Applications." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7436.

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Atriplex hortensis L., also known as orach, is a leafy vegetable from the Amaranthaceae family, which has historically been consumed as a potherb, like spinach. The brightly colored leaves are a source of high quality protein, but may also be of interest as a potential source of natural food pigments. An aqueous extraction was obtained from the freshly harvested leaves of the'Triple Purple' variety of A. hortensis. The extract was spray-dried into a powder, and individual pigments were analyzed using HPLC and LC-MS. The powder was also included as a color additive in a typical stabilizer/sweetener preparation and mixed into plain yogurt. Two batches of colored yogurt were held under light and dark conditions and tested for pH and color (L*a*b*) every 15 days. A visual sensory panel was performed on days 0, 45, and 90 to evaluate the color acceptance.A total of three types of betacyanins and six types of anthocyanins were tentatively identified by HPLC and/or LC-MS. Orach pigments in yogurt were not stable under full light exposure. The color of samples exposed to light degraded within days. There were statistically significant differences found in L*a*b* scores in the dark treatment, beyond 30 days; but these modest changes in dark-stored samples were not found to be statistically significant in the consumer sensory panel. The tentative identification of both anthocyanins and betacyanins in orach is a novel finding in botanical research, as the literature indicates that these two pigment classes are mutually exclusive. The application of heat during pigment extraction, spray drying, and yogurt color additive preparation, did not appear to appreciably affect stability of orach pigments, indicating that orach extract could be used as a color in different process applications, if protected from light.
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BARRA, Vincent. "Fusion d'images 3D du cerveau - Etude de modèles et applications." Phd thesis, Université d'Auvergne - Clermont-Ferrand I, 2000. http://tel.archives-ouvertes.fr/tel-00005976.

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Le recueil de données diverses issues de l'imagerie, de compétences expertes ou de signaux physiologiques est devenu courant pour l'étude d'une pathologie donnée. Leur exploitation est effectuée par le clinicien qui les analyse et les agrège en fonction de ses connaissances. La motivation de ce travail est de modéliser ce processus d'agrégation à l'aide de techniques empruntées à la fusion de données, dans le cadre d'études portant sur le cerveau. Le processus de fusion est décomposé en trois phases fondamentales. Nous modélisons tout d'abord les informations dans un cadre théorique commun. Le formalisme retenu est celui de la logique possibiliste, permettant de prendre en compte les ambiguïtés inhérentes aux données médicales. Nous proposons de modéliser d'une part la distribution des tissus cérébraux dans les images IRM, TEM et TEP par un algorithme de classification flou sur des vecteurs forme appropriés et d'autre part des informations issues de connaissances expertes. Nous agrégeons ensuite ces différentes informations par un opérateur de fusion. Celui-ci doit affirmer les redondances, gérer les complémentarités et prendre en compte les conflits soulignant souvent la présence d'une pathologie. Nous proposons alors trois modèles d'agrégation : la fusion d'images IRM, la fusion d'images anatomiques et fonctionnelles, et la fusion d'une image IRM et d'informations symboliques. Nous construisons enfin une information synthétique permettant d'exploiter les résultats de la fusion . Nous définissons pour chaque modèle une image permettant par exemple de proposer un diagnostic, d'établir un pronostic ou d'élaborer une aide thérapeutique. Quatre applications cliniques sont proposées en illustration : la quantification de volumes de tissus cérébraux, l'étude de la démence de type Alzheimer, l'étude de l'épilepsie et la localisation du noyau sous-thalamique pour le traitement de la maladie de Parkinson. Pour chacun de ces cas, outre les développements décrits auparavant, des modèles spécifiques à la pathologie étudiée sont proposés et une validation clinique des résultats est effectuée. Enfin, une application réalisée en collaboration avec la société SEGAMI, concrétisant et valorisant de façon industrielle ce travail, est présentée.
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Ortiz, Cano Hector Genaro. "Pre-Columbian Cultivation of Agave Species Through Rock Mulching: Potential for Modern Applications." BYU ScholarsArchive, 2021. https://scholarsarchive.byu.edu/etd/9174.

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As global temperatures rise, cultivation of C3 and C4 crops in arid and semi-arid regions will face major challenges in producing biomass for billions of people. Conventional agricultural techniques that require copious irrigation will need to be complemented with dryland-farming techniques and drought-tolerant crops, such as those from the Agave genus, which use CAM photosynthesis. In the past and present, humans from arid and semi-arid regions of America have maintained a symbiotic relationship using and cultivating Agave (Agavoideae, Asparagaceae). In pre-Columbian times, Native Americans from arid regions relied on Agave cultivation as a subsistence crop to produce food, medicine, and fiber. The Hohokam in the Sonoran Desert cultivated Agave plants using rock mulching, also known as rock piles. This technique enabled the Hohokam to extensively cultivate Agave despite the limited rainwater available in the harsh Sonoran Desert. Although there are several decades of archaeological research for documenting the history of rock piles and Agave in the region beginning in the late 1970s, few studies have addressed the modern application of rock piles to cultivate Agave. Our research employed a multidisciplinary approach to bridge the historic use of rock piles to cultivate Agave with the potential application of rock piles for modern cultivation. In addition to summarizing what is known about the archaeology of Hohokam rock piles, we compiled an extensive review of the literature available on the agroecology, physiology, and natural history of Agave. We described key aspects associated with the hydrology and physical properties of Hohokam rock piles that can bolster Agave CAM photosynthesis in dry regions. We found that the use of rock piles is a feasible means of cultivating Agave under hot and dry conditions in arid regions. In addition, we used an ecological niche modeling approach and field data from Hohokam rock-pile sites and current Agave fields to assess the potential environments where rock piles could be used to cultivate Agave plants in Arizona, USA and Sonora, Mexico. We also combined an experimental archaeology approach with experimental plant physiology where we surveyed Hohokam rock-pile fields at archaeological sites to collect information about the composition of rock piles. We then created a rock-pile field where we evaluated and observed the effects of rock piles on Agave CAM utilization, mainly nocturnal CO2 uptake of Agave. Our results indicated that rock piles provide direct insulation to root systems, which indirectly benefited Agave carbon uptake and reduced temperature and drought stress. Although more agronomic research about rock pile use is needed, our research suggests that rock piles can be applied to cultivate Agave because of the physiological benefits provided such as increasing nocturnal total CO2 uptake. In addition, the suitability of rock piles in the U.S borderlands indicates that rock piles can be applied beyond the regions where they were used by the Hohokam in pre-historic times.
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46

Blum, Michael G. B. "Statistique bayésienne et applications en génétique des populations." Habilitation à diriger des recherches, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00766196.

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Les approches statistiques en génétique des populations visent deux objectifs distincts qui sont la description des données et la possibilité d'inférer les processus évolutifs qui ont généré les patrons observés. Le premier chapitre de ce manuscrit décrit nos apports théoriques et méthodologiques concernant le calcul bayésien approché (Approximate Bayesian Computation) qui permet de réaliser l'objectif d'inférence des processus évolutifs. Je décris des résultats asymptotiques qui permettent de décrire des propriétés statistiques du calcul bayésien approché. Ces résultats mettent en évidence à la fois l'intérêt des méthodes dites avec ajustement qui reposent sur des équations de régression et aussi l'intérêt de réduire la dimension des descripteurs statistiques utilisés dans le calcul bayésien approché. Je présente ensuite une méthode originale de calcul bayésien approché qui permet de manière conjointe d'effectuer des ajustements et de réduire la dimension des descripteurs statistiques. Une comparaison des différentes méthodes de réduction de dimension clos le premier chapitre. Le deuxième chapitre est consacré à l'objectif de description des données et se place plus particulièrement dans un cadre spatial. Les méthodes statistiques proposées reposent sur le concept d'isolement par la distance qui est une forme particulière de l'autocorrélation spatiale où la corrélation entre individus décroit avec la distance. Une approche originale de krigeage nous permet de caractériser des patrons d'isolement par la distance non-stationnaire où la manière avec laquelle la corrélation entre individus décroit avec la distance dépend de l'espace. Une deuxième extension que nous proposons est celle d'isolement par la distance anisotrope que nous caractérisons et testons à partir d'une équation de régression. La conclusion de ce manuscrit met l'accent sur les problèmes d'interprétation des résultats statistiques, l'importance de l'échantillonnage et la nécessité de tester l'adéquation des modèles aux données. Je conclus par des perspectives qui se proposent de faire passer l'analyse statistique bayésienne à l'échelle des données massives produites en génétique.
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47

Vanee, Niti. "HIGH THROUGHPUT DATA FRAMEWORK BASED CHARACTERIZATION AND EVALUATIONS OF THERMOBIFIDA FUSCA FOR INDUSTRIAL APPLICATIONS." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3274.

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Cellulolytic organisms are being heavily studied for the production of biofuels, given that lignocellulosic biomass would be a cheap, abundant, and renewable starting material for chemical production. A challenge with cellulolytic microorganisms is that they are typically poorly characterized and often difficult to genetically manipulate. Our group focuses characterization and engineering of a thermophilic aerobic, cellulolytic actinobacterium, Thermobifida fusca. The wider range of optimal temperature and pH for the growth condition, besides the secretion of several group of cellulases, have made this microbe a potentially efficient host system for industrially application. After the development of first ever successful genetic manipulation protocol by for T. fusca in 2011 in our group the quest continues to better understand and further explore this microbe with such remarkable capabilities. Available genome annotation of the bacteria gives a preliminary clue towards the exploration of its biological system. Genome-scale metabolic reconstruction provides one such framework to populate all the available piece of information to mimic the biological systems to the closest functional state. Further, this skeletal base network can be made more realistic by applying the constraint that controls the flux through various reactions in the pathway network thereby providing the optimal solution space for operation. For the purpose of curation of this in silico model, we aim to integrate the experimental datasets (proteomic and metabolomics) and optimize the agreement between the in silico and in vivo conditions at a steady state condition. Once the model considerably imitates the original biological network, it will be used for the fundamental understanding of the microbial system for the application towards production biofuel and high yields of compound of pharmaceutical interest. The ultimate objective of this project is to design the candidate strain for the cellulolytic production of Natural products. Natural products play an important role in manufacturing of several active pharmaceutical ingredients (APIs). APIs or precursors of APIs can be produced in living organisms with the major challenge of designing and optimizing metabolic pathways to obtain the compounds of interest. In this capacity, living organisms can act as renewable catalysts with high product specificity to produce APIs with potential cost savings over purely synthetic chemistry synthesis routes. This is an effort to understand and design industrially usable microorganism T. fusca to act as a host system for the purpose of production of these compounds. The present project focuses on, in silico characterization and experimental validation of T. fusca, with particular focus on the terpenoids backbone biosynthesis (TBB) pathways using a genome-scale metabolic model, transcriptomics, proteomics and metabolite analysis. The DXP pathway leads to the production of terpenoids precursors that have applications in nutraceutics and pharmaceutics. This study generates the metabolic model, iTFU975 for T. fusca based on the proteomics dataset as the starting point. Further the model and the experimental dataset together helps to characterize the secondary metabolites pathways and compounds in the network associated with the production of terpenoids. In conclusion, this is an effort to characterize the natural products biosynthesis in T. fusca by establishing a bridge between the analytical methodologies and computational efficiencies on “-omics” knowledge to prove the diverse applicability of Systems Biology.
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Ramraj, Varun. "Exploiting whole-PDB analysis in novel bioinformatics applications." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6c59c813-2a4c-440c-940b-d334c02dd075.

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The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. Approximately 200 new structures are added weekly to the PDB, and at the time of writing, it contains approximately 97,000 structures. This represents an expanding wealth of high-quality information but there seem to be few bioinformatics tools that consider and analyse these data as an ensemble. This thesis explores the development of three efficient, fast algorithms and software implementations to study protein structure using the entire PDB. The first project is a crystal-form matching tool that takes a unit cell and quickly (< 1 second) retrieves the most related matches from the PDB. The unit cell matches are combined with sequence alignments using a novel Family Clustering Algorithm to display the results in a user-friendly way. The software tool, Nearest-cell, has been incorporated into the X-ray data collection pipeline at the Diamond Light Source, and is also available as a public web service. The bulk of the thesis is devoted to the study and prediction of protein disorder. Initially, trying to update and extend an existing predictor, RONN, the limitations of the method were exposed and a novel predictor (called MoreRONN) was developed that incorporates a novel sequence-based clustering approach to disorder data inferred from the PDB and DisProt. MoreRONN is now clearly the best-in-class disorder predictor and will soon be offered as a public web service. The third project explores the development of a clustering algorithm for protein structural fragments that can work on the scale of the whole PDB. While protein structures have long been clustered into loose families, there has to date been no comprehensive analytical clustering of short (~6 residue) fragments. A novel fragment clustering tool was built that is now leading to a public database of fragment families and representative structural fragments that should prove extremely helpful for both basic understanding and experimentation. Together, these three projects exemplify how cutting-edge computational approaches applied to extensive protein structure libraries can provide user-friendly tools that address critical everyday issues for structural biologists.
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EL, Berbari Racha. "Segmentation d'images de contraction et de rehaussement tardif en IRM cardiaque. Application a l'étude de la fonction contractile et de la viabilité myocardique." Phd thesis, Télécom ParisTech, 2009. http://pastel.archives-ouvertes.fr/pastel-00006081.

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L'IRM cardiovasculaire, malgré son émergence récente, occupe une place de plus en plus importante en routine clinique. Elle se distingue des autres modalités d'imagerie par son innocuité, son excellente résolution spatiale, son bon contraste et par sa capacité d'imager des données anatomiques et fonctionnelles (contractilité et viabilité) en un seul examen. L'interprétation des examens cliniques est fortement dominée par l'analyse visuelle qui est fonction de l'acuité et de l'expertise de l'operateur. La majorité des analyses quantitatives ou semi-quantitatives nécessite une segmentation des structures cardiaques, essentiellement du ventricule gauche ; cette segmentation est réalisée le plus souvent manuellement ou semi-automatiquement. Ainsi cette analyse reste sujette µa une variabilité inter et intra-observateur et est difficilement applicable dans la pratique quotidienne. L'objectif de cette thèse est de contribuer µa la réduction de cette variabilité et du temps passé par l'expert via le développement d'une méthode de segmentation automatique du ventricule gauche pour apporter une aide au diagnostic. Nos applications concernent à la fois les études dynamiques de la fonction contractile (Ciné) et les images statiques de rehaussement tardif (RT). La méthode de segmentation automatique du ventricule gauche a été développée en utilisant une approche fondée sur les contours actifs. L'apport innovant proposé dans ce travail porte sur une étape de filtrage utilisant les filtres morphologiques, qui a permis de résoudre les problèmes dus a la présence des muscles papillaires dans la cavité et aux inhomogénéités de niveau de gris dans la cavité dues au aux sanguin. Cette méthode, qui a fait l'objet d'une validation en comparant les résultats au tracé réalise par un expert est robuste et simple µa utiliser en clinique. Deux applications cliniques requérant l'utilisation de cette méthode ont été mises en place. Tout d'abord, la combinaison de la méthode automatisée de segmentation a une méthode quantitative d'imagerie paramétrique, a permis l'estimation des paramètres segmentaires de temps moyen de contraction et de vitesse de l'endocarde évaluant la cinétique pariétale du ventricule gauche sur des images Ciné. Cette approche a été mise en œuvre sur une base de trente-six témoins ainsi que sur une base de dix patients ayant subi un infarctus du myocarde. Une seconde application a permis de quantifier l'extension transmurale de l'infarctus du myocarde de façon automatique, en segmentant les images Ciné puis en superposant les contours obtenus sur les images de RT après un recalage des deux acquisitions. La quantification de la transmuralité a été réalisée par un algorithme des k-moyennes floues appliqué aux images de RT segmentées. Cette approche a été appliquée à une série de neuf patients confrontée a l'interprétation visuelle des examens. Dans un dernier temps, dans le but d'améliorer la qualité des images de RT3D, une approche de restauration d'images avec préservation des discontinuités a été proposée pour reconstruire un volume de RT hyper-résolu et isotrope µa partir de l'acquisition de trois volumes anisotropes suivant les directions classiques : petit axe, grand axe 2-cavités et grand axe 4-cavités. Les résultats obtenus lors de ce travail de thèse sont encourageants et ouvrent des pistes sur des perspectives cliniques.
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Reinert, Tilo [Verfasser], Tilman [Akademischer Betreuer] Butz, Josef [Gutachter] Käs, Philippe [Gutachter] Moretto, and Günter [Gutachter] Schmahl. "Focussed MeV-Ion Micro- and Nano-Beams in the Life Sciences : Selected Applications / Tilo Reinert ; Gutachter: Josef Käs, Philippe Moretto, Günter Schmahl ; Betreuer: Tilman Butz." Leipzig : Universitätsbibliothek Leipzig, 2016. http://d-nb.info/1240396120/34.

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