Дисертації з теми "Sequence analysis methods"
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Park, Jong Hwa. "Genome sequence analysis and methods." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627329.
Повний текст джерелаIsgro, Francesco. "Geometric methods for video sequence analysis and applications." Thesis, Heriot-Watt University, 2001. http://hdl.handle.net/10399/495.
Повний текст джерелаVerzotto, Davide. "Advanced Computational Methods for Massive Biological Sequence Analysis." Doctoral thesis, Università degli studi di Padova, 2011. http://hdl.handle.net/11577/3426282.
Повний текст джерелаCon l'avvento delle moderne tecnologie di sequenziamento, massive quantità di dati biologici, da sequenze proteiche fino a interi genomi, sono disponibili per la ricerca. Questo progresso richiede l'analisi e la classificazione automatica di tali collezioni di dati, al fine di migliorare la conoscenza nel campo delle Scienze della Vita. Nonostante finora siano stati proposti molti approcci per modellare matematicamente le sequenze biologiche, ad esempio cercando pattern e similarità tra sequenze genomiche o proteiche, questi metodi spesso mancano di strutture in grado di indirizzare specifiche questioni biologiche. In questa tesi, presentiamo nuovi metodi computazionali per tre problemi fondamentali della biologia molecolare: la scoperta di relazioni evolutive remote tra sequenze proteiche, l'individuazione di segnali biologici complessi in siti funzionali tra loro correlati, e la ricostruzione della filogenesi di un insieme di organismi, attraverso la comparazione di interi genomi. Il principale contributo è dato dall'analisi sistematica dei pattern che possono interessare questi problemi, portando alla progettazione di nuovi strumenti computazionali efficaci ed efficienti. Vengono introdotti così due paradigmi avanzati per la scoperta e il filtraggio di pattern, basati sull'osservazione che i motivi biologici funzionali, o pattern, sono localizzati in differenti regioni delle sequenze in esame. Questa osservazione consente di realizzare approcci parsimoniosi in grado di evitare un conteggio multiplo degli stessi pattern. Il primo paradigma considerato, ovvero irredundant common motifs, riguarda la scoperta di pattern comuni a coppie di sequenze che hanno occorrenze non coperte da altri pattern, la cui copertura è definita da una maggiore specificità e/o possibile estensione dei pattern. Il secondo paradigma, ovvero underlying motifs, riguarda il filtraggio di pattern che hanno occorrenze non sovrapposte a quelle di altri pattern con maggiore priorità, dove la priorità è definita da proprietà lessicografiche dei pattern al confine tra pattern matching e analisi statistica. Sono stati sviluppati tre metodi computazionali basati su questi paradigmi avanzati. I risultati sperimentali indicano che i nostri metodi sono in grado di identificare le principali similitudini tra sequenze biologiche, utilizzando l'informazione presente in maniera non ridondante. In particolare, impiegando gli irredundant common motifs e le statistiche basate su questi pattern risolviamo il problema della rilevazione di omologie remote tra proteine. I risultati evidenziano che il nostro approccio, chiamato Irredundant Class, ottiene ottime prestazioni su un benchmark impegnativo, e migliora i metodi allo stato dell'arte. Inoltre, per individuare segnali biologici complessi utilizziamo la nozione di underlying motifs, definendo così alcune modalità per il confronto e il filtraggio di motivi degenerati ottenuti tramite moderni strumenti di pattern discovery. Esperimenti su grandi famiglie proteiche dimostrano che il nostro metodo riduce drasticamente il numero di motivi che gli scienziati dovrebbero altrimenti ispezionare manualmente, mettendo in luce inoltre i motivi funzionali identificati in letteratura. Infine, combinando i due paradigmi proposti presentiamo una nuova e pratica funzione di distanza tra interi genomi. Con il nostro metodo, chiamato Unic Subword Approach, relazioniamo tra loro le diverse regioni di due sequenze genomiche, selezionando i motivi conservati durante l'evoluzione. I risultati sperimentali evidenziano che il nostro approccio offre migliori prestazioni rispetto ad altri metodi allo stato dell'arte nella ricostruzione della filogenesi di organismi quali virus, procarioti ed eucarioti unicellulari, identificando inoltre le sottoclassi principali di queste specie.
Oppermann, Madalina. "Chemical and mass spectrometrical methods in protein analysis /." Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4542-x/.
Повний текст джерелаLovmar, Lovisa. "Methods for Analysis of Disease Associated Genomic Sequence Variation." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4525.
Повний текст джерелаReinhardt, Astrid. "Neural network-based methods for large scale protein sequence analysis." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624141.
Повний текст джерелаHenderson, Daniel Adrian. "Modelling and analysis of non-coding DNA sequence data." Thesis, University of Newcastle Upon Tyne, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299427.
Повний текст джерелаTanaka, Emi. "Statistical Methods for Improving Motif Evaluation." Thesis, The University of Sydney, 2014. http://hdl.handle.net/2123/13922.
Повний текст джерелаChen, Zhuo. "Smart Sequence Similarity Search (S⁴) system." CSUSB ScholarWorks, 2004. https://scholarworks.lib.csusb.edu/etd-project/2458.
Повний текст джерелаHolder, Mark Travis. "Using a complex model of sequence evolution to evaluate and improve phylogenetic methods." Access restricted to users with UT Austin EID Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3037500.
Повний текст джерелаRausch, Tobias [Verfasser]. "Dissecting multiple sequence alignment methods : the analysis, design and development of generic multiple sequence alignment components in SeqAn / Tobias Rausch." Berlin : Freie Universität Berlin, 2010. http://d-nb.info/1024541460/34.
Повний текст джерелаWang, Kai. "Novel computational methods for accurate quantitative and qualitative protein function prediction /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/11488.
Повний текст джерелаMiao, Hanjin. "Intelligent system methods for energy management system and sequence-of-events recorder information analysis /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/6133.
Повний текст джерелаRoth, Christian [Verfasser]. "Statistical methods for biological sequence analysis for DNA binding motifs and protein contacts / Christian Roth." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://nbn-resolving.de/urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-5912-0-2.
Повний текст джерелаGelfond, Jonathan A. L. Ibrahim Joseph George. "Bayesian model-based methods for the analysis of DNA microarrays with survival, genetic, and sequence data." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,972.
Повний текст джерелаTitle from electronic title page (viewed Dec. 18, 2007). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biostatistics, School of Public Health." Discipline: Biostatistics; Department/School: Public Health.
De, Groeve Johannes. "A wildlife journey in space and time: methodological advancements in the assessment and analysis of spatio-temporal patterns of animal movement across European landscapes." Doctoral thesis, country:BE, 2018. http://hdl.handle.net/10449/52251.
Повний текст джерелаPratas, Diogo. "Compression and analysis of genomic data." Doctoral thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/16286.
Повний текст джерелаGenomic sequences are large codi ed messages describing most of the structure of all known living organisms. Since the presentation of the rst genomic sequence, a huge amount of genomics data have been generated, with diversi ed characteristics, rendering the data deluge phenomenon a serious problem in most genomics centers. As such, most of the data are discarded (when possible), while other are compressed using general purpose algorithms, often attaining modest data reduction results. Several speci c algorithms have been proposed for the compression of genomic data, but unfortunately only a few of them have been made available as usable and reliable compression tools. From those, most have been developed to some speci c purpose. In this thesis, we propose a compressor for genomic sequences of multiple natures, able to function in a reference or reference-free mode. Besides, it is very exible and can cope with diverse hardware speci cations. It uses a mixture of nite-context models (FCMs) and eXtended FCMs. The results show improvements over state-of-the-art compressors. Since the compressor can be seen as a unsupervised alignment-free method to estimate algorithmic complexity of genomic sequences, it is the ideal candidate to perform analysis of and between sequences. Accordingly, we de ne a way to approximate directly the Normalized Information Distance, aiming to identify evolutionary similarities in intra- and inter-species. Moreover, we introduce a new concept, the Normalized Relative Compression, that is able to quantify and infer new characteristics of the data, previously undetected by other methods. We also investigate local measures, being able to locate speci c events, using complexity pro les. Furthermore, we present and explore a method based on complexity pro les to detect and visualize genomic rearrangements between sequences, identifying several insights of the genomic evolution of humans. Finally, we introduce the concept of relative uniqueness and apply it to the Ebolavirus, identifying three regions that appear in all the virus sequences outbreak but nowhere in the human genome. In fact, we show that these sequences are su cient to classify di erent sub-species. Also, we identify regions in human chromosomes that are absent from close primates DNA, specifying novel traits in human uniqueness.
As sequências genómicas podem ser vistas como grandes mensagens codificadas, descrevendo a maior parte da estrutura de todos os organismos vivos. Desde a apresentação da primeira sequência, um enorme número de dados genómicos tem sido gerado, com diversas características, originando um sério problema de excesso de dados nos principais centros de genómica. Por esta razão, a maioria dos dados é descartada (quando possível), enquanto outros são comprimidos usando algoritmos genéricos, quase sempre obtendo resultados de compressão modestos. Têm também sido propostos alguns algoritmos de compressão para sequências genómicas, mas infelizmente apenas alguns estão disponíveis como ferramentas eficientes e prontas para utilização. Destes, a maioria tem sido utilizada para propósitos específicos. Nesta tese, propomos um compressor para sequências genómicas de natureza múltipla, capaz de funcionar em modo referencial ou sem referência. Além disso, é bastante flexível e pode lidar com diversas especificações de hardware. O compressor usa uma mistura de modelos de contexto-finito (FCMs) e FCMs estendidos. Os resultados mostram melhorias relativamente a compressores estado-dearte. Uma vez que o compressor pode ser visto como um método não supervisionado, que não utiliza alinhamentos para estimar a complexidade algortímica das sequências genómicas, ele é o candidato ideal para realizar análise de e entre sequências. Em conformidade, definimos uma maneira de aproximar directamente a distância de informação normalizada (NID), visando a identificação evolucionária de similaridades em intra e interespécies. Além disso, introduzimos um novo conceito, a compressão relativa normalizada (NRC), que é capaz de quantificar e inferir novas características nos dados, anteriormente indetectados por outros métodos. Investigamos também medidas locais, localizando eventos específicos, usando perfis de complexidade. Propomos e exploramos um novo método baseado em perfis de complexidade para detectar e visualizar rearranjos genómicos entre sequências, identificando algumas características da evolução genómica humana. Por último, introduzimos um novo conceito de singularidade relativa e aplicamo-lo ao Ebolavirus, identificando três regiões presentes em todas as sequências do surto viral, mas ausentes do genoma humano. De facto, mostramos que as três sequências são suficientes para classificar diferentes sub-espécies. Também identificamos regiões nos cromossomas humanos que estão ausentes do ADN de primatas próximos, especificando novas características da singularidade humana.
Bajak, Edyta Zofia. "Genotoxic stress: novel biomarkers and detection methods : uncovering RNAs role in epigenetics of carcinogenesis /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-415-5/.
Повний текст джерелаMarshall, Jean-Claude. "Transcriptional and genetic profiling of human uveal melanoma from an immunosuppressed rabbit model." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103272.
Повний текст джерелаUsing microarrays we identified 314 changes in transcript abundance between the intraocular tumour and metastatic lesions. Principal Components Analysis was used to cluster these transcripts into four distinct groups. A further 61 gene transcripts showed statistically significant changes between re-cultured cells isolated from the model, with the circulating malignant cells representing an intermediate step between cells isolated from intraocular tumours and metastatic lesions. We have produced a detailed analysis of the molecular changes that take place as human uveal melanoma cells evolve from a primary tumour to metastasis in an animal model, including the decrease in expression of specific melanoma markers. These changes were verified using quantitative real time polymerase chain reaction and three different functional assays.
In addition we sought to describe the genetic changes that are present in these cells. Using comparative genomic hybridization arrays we were able to successfully describe the deletions and amplifications that are present in genomic DNA extracted from paraffin embedded sections of the primary tumour. This represents the first time that archival tissue has successfully been used for this sort of analysis in uveal melanoma. We identified several genomic amplifications and deletions including an area of amplification of Wnt2, which is involved in beta-catenin regulation and C-Met, which plays a role in tumour cell homing to the liver in patients.
To the best of our knowledge, this is the first time that a detailed genetic analysis has been carried out on the progression of uveal melanoma from intraocular tumour, to circulation, to the formation of metastases.
Morozov, Vyacheslav. "Computational Methods for Inferring Transcription Factor Binding Sites." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23382.
Повний текст джерелаLu, Yang 1972. "High throughput study of the translational effect of human single nucleotide polymorphisms." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=116089.
Повний текст джерелаMethods: Lymphoblastoid cell lines (LCLs) from 44 HapMap European individuals were used for polyribosomal fractionation and establishing the sample bank for the future study. The fractionated mRNA samples of 10 out of the 44 individuals were run on an Illumina GoldenGate Beadarray to detect allelic imbalance (developed by the group of T.J. Hudson and T.M. Pastinen).
Results: This study established a high-quality RNA bank, including 1,100 RNA fraction samples. By the Illumina chip, translational imbalance was detected in 75 out of 1483 (5.06%) assays, and 63 out of269 (23.4%) genes. The translational effect was well replicable by the resequencing method.
Conclusion: This study found that genetic effect on gene translation is a common mechanism of expression regulation. Our best hit found in the integrin beta 1 binding protein 1 gene (ITGB1BP1 ) highlights the role of mRNA 3'UTR secondary structure in gene translation.
Keywords: Gene translation, High throughput genotyping, Human genetics, Polyribosome, RNA, Single nucleotide polymorphism
Yu, Xuesong. "Statistical methods for analyzing genomic data with consideration of spatial structures /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9553.
Повний текст джерелаWagner, Brandie D. "Permutation based microarray gene selection methods with covarience adjustment applicable to complex diseases /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2007.
Знайти повний текст джерелаTypescript. Includes bibliographical references (leaves 57-60). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;
Buttriss, Gary John Marketing Australian School of Business UNSW. "An analysis of the process of evolution and impact of internet technologies on firm behaviour and performance using narrative sequence methods." Publisher:University of New South Wales. Marketing, 2009. http://handle.unsw.edu.au/1959.4/43561.
Повний текст джерелаRossiny, Vanessa Delphine. "Expression analysis of the 3p25.3-ptelomere genes in epithelial ovarian cancer." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=112355.
Повний текст джерелаFriedrich, Torben. "New statistical Methods of Genome-Scale Data Analysis in Life Science - Applications to enterobacterial Diagnostics, Meta-Analysis of Arabidopsis thaliana Gene Expression and functional Sequence Annotation." kostenfrei, 2009. http://www.opus-bayern.de/uni-wuerzburg/volltexte/2009/3985/.
Повний текст джерелаEllis, Stephen James. "An exploration of James Dreier’s Standard Tune Learning Sequence in a self-directed learning environment : an interpretative phenomenological analysis." Thesis, Rhodes University, 2014. http://hdl.handle.net/10962/d1011312.
Повний текст джерелаWessel, Jennifer. "Human genetic-epidemiologic association analysis via allelic composition and DNA sequence similarity methods applications to blood-based gene expression biomarkers of disease /." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3237548.
Повний текст джерелаTitle from first page of PDF file (viewed December 12, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
Wang, Bo. "Novel statistical methods for evaluation of metabolic biomarkers applied to human cancer cell lines." Miami University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=miami1399046331.
Повний текст джерелаSacan, Ahmet. "Similarity Search And Analysis Of Protein Sequences And Structures: A Residue Contacts Based Approach." Phd thesis, METU, 2008. http://etd.lib.metu.edu.tr/upload/12609754/index.pdf.
Повний текст джерелаCoker, Jeffrey Scott. "The systemic response to fire damage in tomato plants a case study in the development of methods for gene expression analysis using sequence data /." NCSU, 2004. http://www.lib.ncsu.edu/theses/available/etd-05072004-132534/.
Повний текст джерелаThummadi, B. Veeresh. "SOFTWARE DESIGN METHODOLOGIES, ROUTINES AND ITERATIONS: A MULTIPLE-CASE STUDY OF AGILE AND WATERFALL PROCESSES." Case Western Reserve University School of Graduate Studies / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=case1396363465.
Повний текст джерелаChrysostomou, Charalambos. "Characterisation and classification of protein sequences by using enhanced amino acid indices and signal processing-based methods." Thesis, De Montfort University, 2013. http://hdl.handle.net/2086/9895.
Повний текст джерелаLacroix, Céline. "Nrg1p and Rfg1p in Candida albicans yeast-to-hyphae transition." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=112528.
Повний текст джерелаMaskos, Uwe. "A novel method of nucleic acid sequence analysis." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.306792.
Повний текст джерелаMilani, Cintia. "Expressão gênica diferencial das células estromais obtidas de medula óssea na presença ou ausência de célula tumoral oculta em pacientes com câncer de mama." Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/5/5155/tde-19032010-115152/.
Повний текст джерелаStromal cells may influence tumor development in primary and secundary sites, however, molecular characteristics of bone marrow stromal cells from breast cancer patients are almost unknown. Our aim was to evaluate the differential gene expression of bone marrow stromal cells from breast cancer patients in the presence or abscence of occult tumor cells. Bone marrow (BM) aspirates were obtained from 10 breast cancer patients. The presence of occult bone marrow disseminated tumor cells was detected by CK19 expression quantified by reverse transcriptase polymerase chain reaction (RT-PCR). Presence of tumoral cell was detected in four of ten BM samples. Stromal cells primary cultures were established and samples from two patients with positive lymph nodes and presence of occult tumor cells in bone marrow and samples from two patients with negative lymph nodes and abscence of occult tumor cells in bone marrow were selected. All the included patients were postmenopausal with invasive ductal carcinoma and positive estrogen and progesterone receptors detected by immunohistochemical analysis. Gene profile evaluated in cDNA microarray slides containing 4.608 spotted genes revealed 21 differencially expressed genes, nine upregulated (PTHLH, TLOC1, NCOA6, C17orf57, ANAPC11, MAST4, POLR3E, CPNE1 e B4GALT5) and twelve downregulated (MRPL2, NAT10, DAP, RNF2, FLOT2, FKBP10, SLIT3, EBNA1BP2, SLC35B2, MICAL2, GPR3, TSPAN17) in stromal cell derived from bone marrow in the presence of tumor breast cancer cell. Our data suggest that gene expression from bone marrow derived stromall cells in the presence or abscence of occult tumor cells seems similar, however small differences may be identified.
Lamzin, Sergey. "Computational methods for the analysis of next generation viral sequences." Thesis, University of East Anglia, 2016. https://ueaeprints.uea.ac.uk/59666/.
Повний текст джерелаZhu, Jun. "Analysis of transmission system faults in the phase domain." Texas A&M University, 2004. http://hdl.handle.net/1969.1/1061.
Повний текст джерелаAtalar, Deniz. "Functional failure sequences in traffic accidents." Thesis, Loughborough University, 2018. https://dspace.lboro.ac.uk/2134/32727.
Повний текст джерелаQin, Li-Xuan. "The clustering of regression models method with applications in gene expression data /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9591.
Повний текст джерелаTsang, Yee-man Vivien. "Development of a multilocus sequence typing method for analysis of Laribacter hongkongensis." Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31972238.
Повний текст джерелаTsang, Yee-man Vivien, and 曾綺雯. "Development of a multilocus sequence typing method for analysis of Laribacter hongkongensis." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31972238.
Повний текст джерелаFigueiredo, Dulce Sachiko Yamamoto de. "Identificação fenotípica e molecular, perfil de suscetibilidade aos antifúngicos e detecção de glucuronoxilomanana em isolados clínicos de Trichosporon." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/5/5133/tde-24022014-161059/.
Повний текст джерелаInvasive Trichosporon spp. infections occur more frequently in neutropenic patients, especially those with hematologic malignancies, and are associated with high mortality rates due to difficulties in identifying the pathogen and treating patients with drugs most currently employed in antifungal therapy. Trichosporon species identification is important for epidemiological studies and to better define eventual species-specific clinical association. Additionally, antifungal susceptibility may vary according to the species. Furthermore, glucuronoxylomannan (GXM) is a cell wall-associated polysaccharide produced by genus Trichosporon, which may be involved in virulence mechanisms of this pathogen. This study aimed (i) to identify Trichosporon species isolated from hospitalized patients by both phenotypic and molecular methods, comparing results; (ii) to verify the distribution of these species in invasive and non-invasive infection episodes; (iii) to determine the in vitro activities of various antifungals agents against the Trichosporon spp. isolates, employing a reference micro-dilution method and a commercial system; (iv) and to analyze the surface expression of GXM. Seventy-four Trichosporon spp. isolates obtained from clinical specimens of patients admitted to the Hospital das Clínicas-FMUSP and to other hospitals in the state of São Paulo, from 2003 to 2011, were included in the study. Nineteen samples were isolated from sterile deep sites (invasive infections) and 55 were isolated from catheter and urine samples (non-invasive isolates). All isolates were submitted to phenotypic analysis, which consisted in morphological features observation, physiological tests and determination of the biochemical profile by VITEK 2 system. Molecular identification was performed by sequencing of IGS1 and D1/D2 regions from the ribosomal DNA. The susceptibility antifungal profiles of the 74 isolates were analyzed by both the EUCAST micro-dilution method (reference) employing fluconazole (FCZ), itraconazole (ITZ), voriconazole (VCZ), ketoconazole (CTZ), amphotericin B (AMB) and 5 - flucytosine (5FC), and the commercial micro-dilution test Sensititre YeastOne, with the same drugs employed in EUCAST plus posaconazole (POS) and caspofungin (CAS). The minimum inhibitory concentration values (MIC), categorical and essential errors as well as other susceptibility parameters were compared between both methods. The cell wall expression of GXM of all isolates was measured by flow cytometry employing an anti-GXM monoclonal antibody. The morphological and physiological features of the Trichosporon spp. isolates were insufficientto define species. The carbohydrate assimilation analysis, performed by VITEK 2 system, has resulted in 71 isolates identified as T. asahii (17 from invasive infections and 54 non-invasive isolates) and one isolate as T. mucoides (invasive). The species identification for the two remaining isolates (one invasive and one non-invasive) was inconclusive. For this reason, a manual auxanogram was performed with these isolates, resulting again in non-conclusive species identification. By the automated sequencing method, 62 of the 74 isolates were identified as T. asahii, showing 82.4% of agreement with the VITEK 2 identification. Eleven isolates were identified by sequencing as T. inkin (8), T. faecale (2) and T. dermatis (1), showing disagreement identification with the VITEK 2 system. Regarding the two isolates with inconclusive results by the carbohydrate assimilation, the molecular technique identified one as T. asahii, whereas for the other isolate the sequencing was also unable to define species. Therefore, among the 74 studied isolates, 62 were identified as T. asahii, eight as T. inkin, two as T. faecale and one as T. dermatis; and two isolates remained with unconclusive identification. Almost all Trichosporon spp. isolates displayed susceptibility to VCZ with both methods. By the EUCAST method, high values of MIC were observed for AMB, while by the commercial test especially the invasive isolates showed susceptibility to this drug. Additionally, the Sensititre kit provided elevated MIC values for FCZ, POS and CAS. In regards to 5FC, the MIC 90% values were consistently high (16 mg/L) in both methodologies. The MIC values obtained by both EUCAST and commercial methods were compared, resulting in significant differences of MIC values for all tested antifungal drugs; major categorical errors occurred at relatively high percentage with the commercial method. No statistically significant differences in MIC values were verified when invasive and non-invasive isolates were compared. Around 30% of both invasive and non-invasive isolates showed cross-resistance to FCZ and VCZ, while a small number of isolates was multiresistant. The GXM analysis by cytometry demonstrated no significant differences between invasive and non- invasive isolates. This study demonstrated that T. asahii was the most frequently isolated species from both deep and non-sterile sites of the patients. The classical phenotypic methodology was not able to define Trichosporon species, and the VITEK 2 system identification showed disagreement with the sequencing technique for the non-T. asahii species. Regarding the in vitro susceptibility tests, VCZ was the most effective drug against the isolates, whereas most of them appear to be less susceptible to AMB, FCZ and POS. The discrepancies in the Trichosporon spp. susceptibility results between the reference and commercial methods suggest that the latter requires further evaluation tests before it can be used in routine laboratory. Although the GXM expression seemed to be equal in both invasive and non-invasive Trichosporon spp. isolates, phagocytic assays should be performed in order to determine the protective effect of the polysaccharide against phagocytosis
Khouri, Raoul-Emil Roger. "Two-photon calcium imaging sequence Analysis Pipeline : a method for analyzing neuronal network activity." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/119748.
Повний текст джерелаThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (page 73).
Investigating the development of neuronal networks can help us to identify new therapies and treatments for conditions that affect the brain, such as autism and Alzheimer's disease. Two-photon calcium imaging has been a powerful tool for the investigation of the development of neuronal networks. However, one of the major challenges of working with two-photon calcium images is processing the large data sets, which often requires manual analysis by a skilled researcher. Here, we introduce a machine learning (ML) pipeline for the analysis of two-photon calcium image sequences. This semi-autonomous ML pipeline includes proposed methods for automatically identifying neurons, signal extraction, signal processing, event detection, feature extraction, and analysis. We run our ML pipeline on a dataset of two-photon calcium image sequences extracted by our team. This dataset includes two-photon calcium image sequences of spontaneous network activity from primary cortical cultures of Mecp2-deficient and wild-type mice. Loss-of-function mutation in the MECP2 gene, causes 95% of Rett syndrome cases and some cases of autism. We evaluate our ML pipeline using this dataset. Our ML pipeline reduces the time required to analyze two-photon calcium images from over 10 minutes to about 30 seconds per sample. Our goal is to accelerate the analysis of neuronal network function to aid in our understanding of neurological disorders and the identification of novel therapeutic targets.
by Raoul-Emil Roger Khouri.
M. Eng.
Stebbing, Richard. "Model-based segmentation methods for analysis of 2D and 3D ultrasound images and sequences." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:f0e855ca-5ed9-4e40-994c-9b470d5594bf.
Повний текст джерелаTan, Angela Y. C. "The development of an efficient method of mitochondrial DNA analysis." Monash University, Dept. of Forensic Medicine, 2003. http://arrow.monash.edu.au/hdl/1959.1/9525.
Повний текст джерелаLan, Yang. "Computational Approaches for Time Series Analysis and Prediction. Data-Driven Methods for Pseudo-Periodical Sequences." Thesis, University of Bradford, 2009. http://hdl.handle.net/10454/4317.
Повний текст джерелаCarls, Stefan. "Optimization of pyrosequencing method for copy number analysis of CYP2D6." Thesis, Uppsala universitet, Institutionen för kvinnors och barns hälsa, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-324758.
Повний текст джерелаLiu, Kwong Ip. "Digital net experimental designs, function interpolations using low discrepancy sequence and goodness of fit tests by discrepancy." HKBU Institutional Repository, 2007. http://repository.hkbu.edu.hk/etd_ra/807.
Повний текст джерелаPaci, Giulia. "Statistical methods for the analysis of DNA sequences: application to dinucleotide distribution in the human genome." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amslaurea.unibo.it/7615/.
Повний текст джерела