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1
Barkess, Grainne. "Relationship between transgene copy number and variegated expression in mice." Thesis, University of Edinburgh, 2001. http://hdl.handle.net/1842/10735.
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To test the hypothesis that high copy number arrays can be responsible for variegation, site-specific recombination was employed to reduce the copy number at the same genome location, allowing a direct comparison of different copy number arrays at the same integration site. A BLG-loxP transgene was microinjected to produce transgenic mice. High copy founders were used to establish lines and their expression profiles were analysed using in situ hybridisation, Northern blots, and milk protein composition. Two out of five lines showed variegated expression with discreet patches of cells expressing within the mammary gland. The variegating lines and one uniform line were then bred to a line of mice expressing a BLG-Cre recombinase transgene in the mammary gland. The double transgenic animals were analysed for a mammary-specific reduction in copy number and their expression patterns were also studied. In all three lines, after the reduction of copy number there had been a reduction in the number of cells in the mammary gland that expressed the BLG transgene. This was contradictory to the hypothesis that suggested that the variegation should be relieved by a reduction in copy number. The same BLG-loxP lines were then microinjected with a PGK-Cre recombinase construct to produce a reduction of copy number early in development. Microinjected animals were analysed for reduced copy arrays, of which only one line showed evidence. These animals were bred to establish lines with reduced copy number arrays throughout the animal. Their expression profile was analysed as before. Animals that had a reduction to one copy showed no expression, while animals that showed a reduction to two copies showed limited patches of expression. This result mirrored that of the mammary-specific reduction. BLG transgene may require a buffer zone provided by high copy arrays to allow some transgenes within the array to escape genome effects. When the copy number is reduced, the percentage of cells that can escape the silencing is also reduced. It is therefore clear that in some cases, transgenes may only efficiently express as a multicopy array.
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Bich, Hanh Nguyen, and n/a. "The expression of number in English and Vietnamese and its implications for teaching." University of Canberra. Education, 1991. http://erl.canberra.edu.au./public/adt-AUC20060720.122923.
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A cross-sectional study of the performance of groups of Vietnamese
learners is reported with focus on how they deal with the expression of
number in English (singular/plural; definite/indefinite) through a cloze
exercise and a translation excercise. This research investigates the
hypothesis that some NP environments facilitate the distinction between
singular and plural, count and mass, and that the context in which a noun
is used can provide positive clues to the choice of number in nouns. It
has been found that transfer of Vietnamese NP structures into English
occurred where the NP environment was not obviously countable or
uncountable, i.e., it has no conspicuous structural signals for number
determination. Transfer was also found where an NP was taken from its
context. The analysis of learners' errors gives some insight into ways in
which the teaching of the number expression can be made more effective
and beneficial for Vietnamese learners. A number of activities were
suggested, which enable the teacher to exploit the advantages of NP
environments to convey the syntactic-semantic properties of number to
learners. Communicative practice of NP structures (e.g., in a
conversation or a role play activity) can make learners aware of different
aspects of the number expression in English. It is argued that the
pragmatic aspect of the number expression is most important as in use,
the syntactic and semantic properties of the category of number are
unified to achieve communicative purposes.
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Rantanen, Anja. "Regulation of mitochondrial transcription and mtDNA copy number in mammals /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-526-3/.
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Han, Kam-chu Beymier. "DNA copy number and expression analysis of candidate tumour genes in adenocarcinomas of the lung /." View the Table of Contents & Abstract, 2005. http://sunzi.lib.hku.hk/hkuto/record/B3168371X.
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Wilhelm, Martin [Verfasser], and Stefan [Gutachter] Schirra. "Refining expression DAGs in exact-decisions number types / Martin Wilhelm ; Gutachter: Stefan Schirra." Magdeburg : Universitätsbibliothek Otto-von-Guericke-Universität, 2020. http://d-nb.info/1220035319/34.
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Perry, Victoria Kristina. "Integration of copy number aberration and genomic expression data in preinvasive breast cancer." Thesis, Boston University, 2012. https://hdl.handle.net/2144/12588.
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Thesis (Ph.D.)--Boston University
PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.DNA aberration is central to cancer initiation and progression. In particular, DNA copy number changes increase in breast ductal carcinoma in situ (DCIS). This study utilized whole genome single-nucleotide polymorphism (SNP) arrays to determine copy number variation (CNV) in primary breast ductal epithelium. A unique combination of methodologies was employed, including laser-capture microdissection (LCM), a focus on early lesions with matched control samples and integration of multiple large-scale array platforms. To discover regions of variation, automated software and manual curation of copy number boundaries was used. For comparison, normal appearing ducts were obtained from both cancer (HN) and reduction mammoplasty (RM) cases. In these control tissues five common CNV sites were found within 3q, 8p, 13q and 17q, two of which are novel. Complex aberrations seen in DCIS were not found in normal ducts. Within the DCIS samples, 37 common copy number aberrations (CNAs) located over 10 chromosomes were identified. Many of the common CNAs identified provided confirmation of previous aberrations seen in DCIS. However, four locations had not previously been reported in DCIS, including losses at two locations on 1 p (1p31.1 and 1p21.3-p13.2) and a gain (19p13.2) and loss (19 p13.3) on 19p. The losses contain potential tumor suppressor genes (PTGER3, NEGR1, and APC2) while the gain contains PIN1, which is associated with tamoxifen resistance in breast cancer. An integrated approach was used to further elucidate these results by analyzing mRNA expression, miRNA expression together with copy number aberrations in DCIS. Overall, the common CNAs correlated to 15% of expression changes and 17% of miRNA expression changes in DCIS cases. Cell-cell adhesion and extracellular matrix genes are often dysregulated in DCIS. Focusing on these genes, downstream genes that might also be deregulated because of copy number aberrations were examined. Several genes downstream of the RET receptor were found to be aberrant, including DOK4, miR-182, RAP1A, TIAM1 and CDC42. The number of aberrations identified in this pathway highlights its potential role in breast cancer progression. DCIS is highly heterogeneous. This study has demonstrated the utility of integrated analyses in assessing the relative importance of the genetic alterations seen in DCIS.
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Manca, Maurizio. "Role of Variable Number Tandem Repeats (VNTRs) on gene expression in the CNS." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3007520/.
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It is now known that at least 80% of the human genome is composed of non-coding DNA which has a biochemical activity and is involved in a wide range of activities and mechanisms. Among these, epigenetic modifications, cis-trans gene expression regulation, transcription factor binding sequences, are the most studied. Non-coding DNA is often characterised by a polymorphic and repetitive nature and it is composed of a high density of GC nucleotides. These polymorphic and repetitive regions within the population may represent either protective elements or risk factors, based on population studies in various diseases, for several conditions and at the same time have the power to shape our behaviours or wellbeing. The compositions of transcription factor binding sites (BSs) and epigenetic factors at these regions act in concert with external and environmental factors to modify gene function and gene expression. This combined effect of environmental and genetic factors capable of influence people's wellbeing or disease risk is known as Gene - Environment Interaction (GxE) and it is a key feature that allows us to adapt to our surrounding. The data presented in this thesis will try to address some of the well characterised polymorphic variants associated with Central Nervous System (CNS) conditions, such as the Monoamine oxidase A (MAOA) gene, and I will show how they can modify gene expression in response to environmental stimuli. We also report two regulatory regions in the CACNA1C (Calcium Voltage-Gated Channel Subunit Alpha1 C) gene, strongly associated to schizophrenia by GWAS (Genome-Wide Association Study) investigations. Finally I will also report a novel polymorphic microsatellite in the promoter region of the gene that has been defined 'the master regulator' of transcription, the RE1-Silencing Transcription factor (REST) gene, that strongly suggests an association with Alzheimer's disease. Therefore I demonstrate a similarity in mechanisms and in the activity of these repeat elements in the promoter regions of three key genes for CNS behaviour and illustrate the potential power of these elements as transcriptional regulatory DNA regions.
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Mörig, Marc Andreas [Verfasser], and Stefan [Akademischer Betreuer] Schirra. "Algorithm engineering for expression dag based number types / Marc Andreas Mörig. Betreuer: Stefan Schirra." Magdeburg : Universitätsbibliothek, 2015. http://d-nb.info/1072685639/34.
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Chiu, Pui-man. "Molecular genetics of cervical cancer from chromosome number alterations to aberrant gene expressions /." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43085544.
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Han, Kam-chu Beymier, and 韓金柱. "DNA copy number and expression analysis of candidate tumour genes in adenocarcinomas of the lung." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B45010079.
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Johnson, Alexander Arthur Theodore. "Effect of Ploidy Elevation, Copy Number and Parent-Of-Origin on Transgene Expression in Potato." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/28669.
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Recent advances in plant genetic engineering offer substantial benefits to farmers throughout the world. Genetic research has identified many exogenous genes that could considerably decrease production costs through transgene-mediated resistance to insect, viral, fungal and bacterial pathogens. Potato can be produced from true potato seed (TPS) through a sexual polyploidization step, known as 4x-2x hybridization. Little is known regarding the stability of transgenes through sexual polyploidization in potato, although studies have associated ploidy elevation with transgene silencing in plants such as Arabidopsis thaliana. In the present study, potato was transformed with two different transgenes, cry3Aa and PVYo cp, and transgene expression was analyzed through 4x-2x hybridization. Transgene introgression did not affect fertility or agronomic performance (tuber set, average tuber weight, total tuber yield) of the resulting 4x-2x hybrids; however, reduced seed germination was observed for several transgenic lines in an in vitro study. Ploidy elevation did not affect a highly expressed single copy cry3Aa transgene, simplex or duplex, transmitted through pollen to 4x-2x hybrids. By contrast, multiple copies of cry3Aa triggered significant transgene silencing in diploids and silencing was further pronounced upon pollen transmission to 4x-2x hybrids. Crosses between two, single insert plants demonstrated additional evidence that multiple cry3Aa transgenes resulted in reduced expression, as well as provided evidence for maternal effects on expression of the cry3Aa transgene. Finally, Cry3Aa expression levels of progeny derived from low expressing, multiple copy 4x-2x hybrids indicated that reduction of transgene number in progeny, through meiotic segregation, could increase Cry3Aa expression. The results suggest that 4x-2x hybridization using single copy, male parents can result in high expressing, transgenic 4x-2x hybrids while segregating for a low frequency of non-transgenic hybrids that create a "refuge" to inhibit development of resistance to transgenes in pest populations.Ph. D.
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Chiu, Pui-man, and 趙佩文. "Molecular genetics of cervical cancer: from chromosome number alterations to aberrant gene expressions." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43085544.
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Brettner, Leandra M., and Joanna Masel. "Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast." BioMed Central, 2012. http://hdl.handle.net/10150/610103.
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BACKGROUND:A hub protein is one that interacts with many functional partners. The annotation of hub proteins, or more generally the protein-protein interaction "degree" of each gene, requires quality genome-wide data. Data obtained using yeast two-hybrid methods contain many false positive interactions between proteins that rarely encounter each other in living cells, and such data have fallen out of favor.RESULTS:We find that protein "stickiness", measured as network degree in ostensibly low quality yeast two-hybrid data, is a more predictive genomic metric than the number of functional protein-protein interactions, as assessed by supposedly higher quality high throughput affinity capture mass spectrometry data. In the yeast Saccharomyces cerevisiae, a protein's high stickiness, but not its high number of functional interactions, predicts low stochastic noise in gene expression, low plasticity of gene expression across different environments, and high probability of forming a homo-oligomer. Our results are robust to a multiple regression analysis correcting for other known predictors including protein abundance, presence of a TATA box and whether a gene is essential. Once the higher stickiness of homo-oligomers is controlled for, we find that homo-oligomers have noisier and more plastic gene expression than other proteins, consistent with a role for homo-oligomerization in mediating robustness.CONCLUSIONS:Our work validates use of the number of yeast two-hybrid interactions as a metric for protein stickiness. Sticky proteins exhibit low stochastic noise in gene expression, and low plasticity in expression across different environments.
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Jo, Adrienne. "Reduced Expression of Single 16p11.2 CNV Genes Alters Neuronal Morphology." Scholarship @ Claremont, 2019. https://scholarship.claremont.edu/cmc_theses/2091.
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The 16p11.2 copy-number variant (CNV) represents a well-characterized, high-risk factor for autism spectrum disorder that additionally predisposes deletion carriers (16pdel) to increased head circumference, known as macrocephaly. The 16p11.2 CNV consists of 29 known genes, many of which are associated with neurobiological processes relevant for macrocephaly such as cell proliferation and apoptosis, differentiation and cell growth. Our lab’s previous work has demonstrated that induced pluripotent stem cell (iPSC)-derived neurons from 16pdel carriers show altered cellular morphology related to growth, which include increased soma size, total dendritic length and dendritic complexity. However, specific CNV genes responsible for these phenotypes have not been established. Here, we investigate the relationship between three 16p11.2 genes and the observed cellular phenotypes. We differentiated neurons from control iPSC-derived neural progenitor cells (NPCs) and used short hairpin RNA (shRNA) to reduce the expression of these CNV genes: KCTD13, MAPK3 and C16ORF53. We then assessed neuronal morphology by evaluating soma size, total dendritic length and dendritic complexity. We demonstrate that knocking down KCTD13 and C16ORF53 increases soma size and total dendrite length, respectively, similar to that observed in 16pdel iPSC-derived neurons. For this reason, we speculate that these genes may have a role in cell growth and might underlie macrocephaly. Thus, our study investigates genes in the 16p11.2 CNV that contribute to neuronal morphology, which may have a role in influencing brain size.
15
Park, Chrisopher Changsun. "Fine mapping of regulatory loci for mammalian gene expression via induced DNA copy number variation in radiation hybrids." Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1872924251&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Iddawela, Mahesh Yasantha Bandara. "Genome wide copy number and gene expression profiling using archived tissue for molecular marker studies in breast cancer." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609626.
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Taylor, Hannah Louise. "Quantitative detection of low abundance gene expression products in individual E. coli cells." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31258.
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Stochastic fluctuations in mRNA and protein copy number between cells are inevitable during the process gene expression, even when cells carry identical chromosomes. Such fluctuations are able to impact the phenotypic fate of the cell, and are known to have greater impact when the copy number of the molecule involved is low. Additionally, up to 50% of proteins in Escherichia coli are present in the cell at a level of 10 molecules per cell or fewer (Taniguchi et al. 2010). As such, quantification of low copy number gene expression products and their distribution in cellular populations is key in understanding the process of gene expression. Currently, there are few techniques that allow investigation with the single cell and single molecule resolution required to study low copy number gene expression products. This work presents a novel method for protein quantification at the single molecule level, Quantitative HaloTag-TMR labelling, and uses the technique to quantify the absolute numbers of the low copy number RecB, RecC and RecD subunits of the bacterial DNA repair enzyme RecBCD, finding each subunit is present at between two and eight molecules per cell with mean numbers per cell of 4.9, 4.7 and 4.5 respectively. Additionally single molecule mRNA FISH was used to quantify the mRNA levels of recB and recD within cells, with means of 0.21 and 0.31 mRNA per cell being observed respectively. Finally this work presents a new method for use detecting both mRNA and protein simultaneously in individual cells by combining the HaloTag and FISH protocols to give HaloFISH. This work introduces two novel techniques that allow for single cell examination of gene expression, and investigates RecBCD expression at the single molecule level.
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Dillon, Andrew James. "Relationship between EPSPS copy number, expression, and level of resistance to glyphosate in common waterhemp (Amaranthus rudis) from Kansas." Thesis, Kansas State University, 2015. http://hdl.handle.net/2097/19147.
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Master of ScienceAgronomy
Mithila Jugulam
Common waterhemp (Amaranthus rudis) is a problematic weed species of cropping systems throughout the Midwestern states, including Kansas. Recently, waterhemp populations from Kansas were found to have evolved resistance to the widely used herbicide glyphosate as a result of amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), the enzyme target of glyphosate. The objectives of this research were to 1) perform glyphosate dose-response study and determine the relationship between relative EPSPS genomic copies and EPSPS gene expression in glyphosate-resistant waterhemp, and 2) characterize the genomic configuration and distribution of EPSPS copies using florescence in situ hybridization (FISH) in three glyphosate-resistant waterhemp populations. Waterhemp populations from eastern Kansas were screened with 868 g ae haˉ¹ (field used rate) of glyphosate, and genomic DNA and total RNA was isolated from the survivors to determine the EPSPS genomic copies and EPSPS gene expression relative to the acetolactate synthase (ALS) gene using qPCR. Furthermore, waterhemp specific EPSPS probes were synthesized to perform florescence in situ hybridization (FISH) on these glyphosate-resistant plants. Results of these experiments indicate a positive correlation between level of glyphosate resistance, EPSPS copies, and their expression. As expected, a negative correlation was found between shikimate accumulation and EPSPS copies. Sequencing of the EPSPS gene showed no presence of the proline 106 mutation, which is known to be associated with glyphosate resistance suggesting that an insensitive EPSPS enzyme was not involved in the mechanism of glyphosate resistance. FISH analysis of resistant plants illustrated presence of amplified EPSPS copies on two homologous chromosomes, likely near the centromeric region. . This is the first report demonstrating a positive relationship between EPSPS copies and expressions, as well as chromosome configuration of EPSPS copies in glyphosate- resistant waterhemp from Kansas.
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Darna, Mahesh [Verfasser]. "Changing the copy number of transmitter transporters per vesicle - sorting versus expression under regime of day-night cycle / Mahesh Darna." Berlin : Freie Universität Berlin, 2008. http://d-nb.info/1023372118/34.
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Hisham, Ahmed El-Sayed Abou-Taleb. "Comprehensive assessment of the expression of the SWI/SNF complex defines two distinct prognostic subtypes of ovarian clear cell carcinoma." Kyoto University, 2018. http://hdl.handle.net/2433/233839.
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Forsman, M. (Minna). "Histological characteristics and gene expression profiling of Dupuytren’s disease." Doctoral thesis, Oulun yliopisto, 2016. http://urn.fi/urn:isbn:9789526211671.
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Abstract Dupuytren’s disease is a Caucasian male-dominant disease that affects the palmar fascia. Incidence grows with age, but persons with strong diathesis seem to develop the disease at an earlier age than the majority of the diseased. Myofibroblasts are histopathologically the main cell type in DD tissue. Despite scientific research, the aetiology of the disease is still unrevealed. Only genetic susceptibility is generally accepted as predisposing to DD. Available treatment has thus far been unsatisfactory, because only symptoms can be cured to date.The disease recurs. With genetic susceptibility the recurrence rates are high (even up to 70%) and the time to recurrence is inevitably shorter. This behaviour is considered the aggressive type of DD. To be able to predict the behaviour of DD, whether it is an aggressive or conventional type, twenty-one Dupuytren samples were gathered and compared with five controls by means of immunohistochemical stainings. It was found that cellularity was better expresented in aggressive and recurred samples. Alfa-SMA and Ki-67 showed more activity in the aggressive tissue type of DD. Tenascin was vaguely expressed in aggressive-type samples. To compare the gene and protein expressions and to obtain a more profound understanding of the disease, a microarray technique was used. With a microarray it is possible to compare nucleotide pair hybridisations to resolve the genome of the tissues. In this study RT-PCR was used to examine mRNA levels to determine gene expression changes. Twelve DD palmar fascia samples were compared with three healthy control samples. Both myoglobin and ROR2, which we considered as the most valuable results, were found in the DD samples. ROR2 acts as a receptor or co-receptor for the Wnt system. The Wnt signalling pathway transfers signals from outside of the cell through cell surface receptors, and plays a significant role in proliferation processes such as in fibrotic conditions. To evaluate a possible chromosomal imbalance behind the aetiology of the disease, eighteen DD palmar fascia samples were compared with two reference samples. However, we were not able to detect any chromosomal imbalance in the DD samples. The method used was Oligonucleotide aCGH Agilent’s 60-mer oligonucleotide-based microarray according to the manufacturer’s instructions, which can reveal gains and losses of approximately 35 kilobases in the whole genome. The result does not exclude copy number changes entirely; a small presence of aberrant cells will not be detected if the change is less than 50%. In conclusion, we revealed elements in DD tissue that would enable us to predict the nature of the disease; whether the disease is aggressive with a stronger tendency to recur. Histological differences could be detected, and this can be used to benefit patients. As a new element, ROR2 was discovered in DD tissue.The genome-wide analysis with the 44K oligonucleotide-based array method revealed no changes of DNA number sequencesTiivistelmä Kämmenkalvon kuroumatauti eli Dupuytrenin kontraktuura on valkoihoisen miehen kämmenkalvon sairaus. Sairastumisen todennäköisyys lisääntyy ikääntymiseen liittyen, mutta vahva sukurasitus poikkeuksellisesti altistaa sairaudelle jo tavanomaista nuoremmalla iällä. Myofibroblastit ovat tärkein ja edustetuin solutyyppi Dupuytren kudoksessa. Huolimatta runsaasta tutkimustyöstä ei etiologiaa ole saatu vielä selvitettyä. Sukurasitus näyttää selkeästi altistavan taudille. Toistaiseksi kyetään hoitamaan ainoastaan sairauden aiheuttamat seuraukset, mutta ei perussyytä. Lisäksi tauti uusiutuu. Dupuytrenin sukurasitus lisää uusiutumista suurella todennäköisyydellä. Myös uusiutumisaika on tuolloin tavanomaista nopeampi, ja kyseessä katsotaan olevan ns.aggressiivisempi taudin muoto. Väitöskirjatyössäni pyrittiin löytämään mahdollisia tekijöitä, joiden perusteella voitaisiin ennustaan onko kyseessä aggressiivisempi vai tavanomainen taudin muoto. Tätä varten tutkittiin kaksikymmentä yksi Dupuytren kudosnäytettä ja viisi tervettä kämmenkalvon näytettä immunohistologisilla värjäyksillä, ja voitiin todeta, että soluisuus oli selkeästi koholla aggressiivisten ja taudin uusineiden potilaiden näytteissä. Tulos oli samanlainen myös alfa-SMA ja Ki-67 suhteen. Tenaskiiniä voitiin löytää edellisiä niukemmin aggressiivisista näytteistä. Dupuytrenin taudin luonteen lisäselvittelemiseksi geeni- ja proteiinitasolla tehtiin mikroarray, jossa emäsparien pariutumisen avulla selvitetään taudin genomia ja myös sitten tästä aiheutuvien proteiinien ilmentymistä. Kahtatoista Dupuytren potilaan kämmenkalvon kudosnäyttettä verrattiin kolmeen terveeseen verrokki kudosnäytteeseen ja voitiin todeta myoglobiinin ja ROR2:n selkeät pitoisuuden muutokset terveisiin näytteisiin verrattaessa. ROR2 toimii solujen välisten viestien välityksen reseptorina, eli siirtää signaalin solun ulkopuolelta sen sisäpuolelle solun pinnalla olevan kiinnittymiskohdan avulla. Sillä on selkeä merkitys ja tehtävä proliferatiivisissä tapahtumissa, kuten sidekudoksen lisääntymisessä. Mahdollisia kromosomin määrän muutoksia Dupuytren kudoksessa selviteltiin kahdeksantoista kudosnäytteen tutkimisella ja löydösten tulosta verrattiin sitten kahteen normaaliin verrokki kudosnäytteen tulokseen. Tutkimuksessa ei saatu selville kromosomien määrän muutosta, kun muutosten kokonaismäärä on vähäinen tai ainakin alle 50 % kokonaismäärää alhaisempi. Yhteenvetona voidaan todeta, että löytyi histologisia kudoselementtejä, joiden perusteella voidaan ennustaa, onko Dupuyrenin tauti aggressiivisempi ja todennäköisemmin uusiutuva luonteeltaan. ROR2 ei ole aikaisemmin yhdistetty Dupuytrenin kontraktuuraan. Dupuytren kudoksesta ei voitu 44K oligonukleotide mikroarray tekniikalla paljastaa geenimäärien muutoksia
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Guan, Xiaowei. "Bioinformatics Approaches to Heterogeneous Omic Data Integration." Case Western Reserve University School of Graduate Studies / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=case1340302883.
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Hazlewood, Ralph Jeremiah II. "Molecular genetics of optic nerve disease using patients with cavitary optic disc anomaly." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/1622.
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Glaucoma is the second leading cause of irreversible blindness in the United States and is the leading cause of blindness in African Americans. Cupping or excavation of the optic nerve, which sends the visual signal from the photoreceptors in the eye to the brain, is a chief feature of glaucoma. A similar excavated appearance of the optic nerve is also the primary clinical sign of other congenital malformations of the eye including optic nerve head coloboma, optic pit, and morning glory disc anomaly collectively termed cavitary optic disc anomaly (CODA). Clinical similarities between CODA and glaucoma have suggested that these conditions may have overlapping pathophysiology. Although risk factors are known, such as the elevated intraocular pressure (IOP) observed in some glaucoma subjects, the biological pathways and molecular events that lead to excavation of the optic disc in glaucoma and in CODA are incompletely understood, which has hindered efforts to improve diagnosis and treatment of these diseases. Consequently, there is a critical need to clarify the biological mechanisms that lead to excavation of the optic nerve, which will lead to improvements in our understanding of these important disease processes. Because of their similar clinical phenotypes and the limited therapy geared at lowering IOP in glaucoma patients, our central hypothesis is that genes involved in Mendelian forms of CODA would also be involved in a subset of glaucoma cases and may provide insight into glaucomatous optic neuropathy.
The purpose of my research project has been to identify and functionally characterize the gene that causes congenital autosomal dominant CODA in a multiplex family with 17 affected members. The gene that causes CODA was previously mapped to chromosome 12q14 and following screening of candidate genes within the region that did not yield any plausible coding sequence mutations, a triplication of a 6KB segment of DNA upstream of the matrix metalloproteinase 19 (MMP19) gene was subsequently identified using comparative genomic hybridization arrays and qPCR. This copy number variation (CNV) was present in all affected family members but absent in unaffected family members, a panel of 78 normal control subjects, and the Database of Genomic Variants. In a case-control study of singleton CODA subjects, CNVs were also detected; we detected the same 6KB triplication in 1 of 24 subjects screened. This subject was part of another 3-generation autosomal dominant CODA pedigree where affected members each have the same CNV identified in the larger CODA pedigree. A separate case-control study with 172 glaucoma cases (primary open angle glaucoma = 84, normal tension glaucoma = 88) was evaluated for MMP19 CNVs, however none were detected. Although our cohort of CODA patients is small limiting our ability to accurately determine the proportion of CODA caused by MMP19 mutations, our data indicates that the MMP19 CNV is not an isolated case and additional CODA subjects may have MMP19 defects. Because of the location of the CNV, we evaluated its effect on downstream gene expression with luciferase reporter gene assays. These assays revealed that the 6KB sequence spanned by the CNV in CODA subjects functioned as a transcriptional enhancer; in particular, a 773bp segment had a strong positive influence (8-fold higher) on downstream gene expression. MMP19, a largely understudied gene, was further characterized by expression studies in the optic nerve and retina. Using frozen sections from normal donor eyes, we demonstrated that MMP19 is predominantly localized to the optic nerve head in the lamina cribrosa region with moderate labeling in the postlaminar region, and weak labeling in the prelaminar region and retina. We also evaluated MMP19 expression in relation to the cell types that populate the optic nerve such as astrocytes and retinal ganglion cells. The pattern of expression is consistent with MMP19 being a secreted protein accumulating in the extracellular spaces and basement membranes of the optic nerve. Our studies have identified the first gene associated with CODA and future research is focused on recapitulating CODA phenotypes in animal models and assessing the mechanism of MMP19 involvement during development.
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Nord, Helena. "Application of Genomic and Expression Arrays for Identification of new Cancer Genes." Doctoral thesis, Uppsala universitet, Genomik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121957.
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Copy number variation (CNV) comprises a recently discovered kind of variation involving deletion and duplication of DNA segments of variable size, ranging from a few hundred basepairs to several million. By altering gene dosage levels or disrupting proximal or distant regulatory elements CNVs create human diversity. They represent also an important factor in human evolution and play a role in many disorders including cancer. Array-based comparative genomic hybridization as well as expression arrays are powerful and suitable methods for determination of copy number variations or gene expression changes in the human genome. In paper I we established a 32K clone-based genomic array, covering 99% of the current assembly of the human genome with high resolution and applied it in the profiling of 71 healthy individuals from three ethnic groups. Novel and previously reported CNVs, involving ~3.5% of the genome, were identified. Interestingly, 87% of the detected CNV regions overlapped with known genes indicating that they probably have phenotypic consequences. In papers II through IV we applied this platform to different tumor types, namely two collections of brain tumors, glioblastoma (paper II) and medulloblastoma (paper III), and a set of bladder carcinoma (paper IV) to identify chromosomal alterations at the level of DNA copy number that could be related to tumor initiation/progression. Tumors of the central nervous system represent a heterogeneous group of both benign and malignant neoplasms that affect both children and adults. Glioblastoma and medulloblastoma are two malignant forms. Glioblastoma often affects adults while the embryonal tumor medulloblastoma is the most common malignant brain tumor among children. The detailed profiling of 78 glioblastomas, allowed us to identify a complex pattern of aberrations including frequent and high copy number amplicons (detected in 79% of samples) as well as a number of homozygously deleted loci. These regions encompassed not only previously reported oncogenes and tumor suppressor genes but also numerous novel genes. In paper III, a subset of 26 medulloblastomas was analyzed using the same genomic array. We observed that alterations involving chromosome 17, especially isochromosome 17q, were the most common genomic aberrations in this tumor type, but copy number alterations involving other chromosomes: 1, 7 and 8 were also frequent. Focal amplifications, on chromosome 1 and 3, not previously described, were also detected. These loci may encompass novel genes involved in medulloblastoma development. In paper IV we examined for the presence of DNA copy number alterations and their effect on gene expression in a subset of 21 well-characterized Ta bladder carcinomas, selected for the presence or absence of recurrences. We identified a number of novel genes as well as a significant association between amplifications and high-grade and recurrent tumors which might be clinically useful. The results derived from these studies increase our understanding of the genetic alterations leading to the development of these tumor forms and point out candidate genes that may be used in future as targets for new diagnostic and therapeutic strategies.
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Friedman, Sherry Katherine. "Number of side effects, ambivalence over emotional expression, perceived side effects burden, and psychological distress in women with advanced breast cancer prior to receiving an experimental treatment." Thesis, The University of Arizona, 2000. http://hdl.handle.net/10150/291762.
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The purpose of this descriptive-exploratory, secondary analysis study was to explore the relationships between number of side effects, ambivalence over emotional expression, perceived side effects burden, and psychological distress in women with advanced breast cancer six days prior to receiving an experimental procedure; namely, an autologous bone marrow transplant. The sample consisted of 21 middle aged (M = 46.24), mostly married (n = 14) Caucasian (n = 20) women who had recently completed induction therapy and were found eligible to participate in a highly experimental treatment for their advanced breast cancer (Stage III or IV). Spearman's correlation analysis was used to identify relationships among the variables. The significance value was set at ≤ .10. This study supported a strong significant positive relationship (r = .589) between ambivalence over emotional expression and psychological distress and a moderate significant positive relationship between number of side effects and psychological distress (r = .38). Implications and limitations are discussed.
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Sandgren, Johanna. "Array-based Genomic and Epigenomic Studies in Healthy Individuals and Endocrine Tumours." Doctoral thesis, Uppsala universitet, Institutionen för kirurgiska vetenskaper, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129533.
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The human genome is a dynamic structure, recently recognized to present with significant large-scale structural variation. DNA-copy number changes represent one common type of such variation and is found both between individuals and within the somatic cells of the same individual, especially in disease states like cancer. Apart from DNA-rearrangements, epigenomic changes are increasingly acknowledged as important events in the maintenance of genomic integrity. In this thesis, different array-based methods have been applied for global genomic and epigenomic profiling of both normal and cancer cells. In paper I, a genomic microarray was established and used to determine DNA-copy number variants (CNVs) in a cohort of 76 healthy individuals from three ethnic populations. We identified 315 CNV regions that in total encompassed ~3,5% of the genome. In paper II, the array was utilized to discover CNVs within several differentiated tissues from the same subject. Six variants were identified providing evidence for somatic mosaicism. In paper III and IV we studied pheochromocytomas and paragangliomas, rare endocrine tumours that most often present as benign and sporadic with unclear genetic/epigenetic cause. Genome-wide DNA-copy number analysis of 53 benign and malignant samples in paper III revealed numerous common and novel chromosomal regions of losses and gains. High frequencies of relatively small overlapping regions of deletions were detected on chromosome 1p arm, encompassing several candidate tumour suppressor genes. In paper IV, an epigenomic map for two histone modifications associated with silent (H3K27me3) or active (H3K4me3) gene transcription, was generated for one malignant pheochromocytoma. Integrated analysis of global histone methylation, copy number alterations and gene expression data aided in the identification of candidate tumour genes. In conclusion, the performed studies have contributed to gain knowledge of CNVs in healthy individuals, and identified regions and genes which are likely associated with the development and progression of pheochromocytoma/paraganglioma.
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Fida, Mariam. "Roles of EEF1A2 & PTK6 in breast cancer." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5544.
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Eukaryotic Translation Elongation Factor 1 Alpha (EEF1A) exists as two forms with different tissue specificities and encoded by separate loci: eEF1A1 on 6q13 and eEF1A2 on 20q13.3. eEF1A1 is ubiquitously expressed whereas eEF1A2 expression is normally limited to the heart, brain and skeletal muscles. eEF1A proteins are GTP-binding proteins that recruit an amino-acylated tRNA to the ribosome during the elongation phase of protein translation. eEF1A2 mRNA and protein are highly expressed in 50–60% of primary human breast tumors and metastases but not in normal breast epithelium. Since it is also overexpressed in 30% of primary human ovarian tumors, transforms rodent fibroblasts and increases their tumorigenicity in nude mice, eEF1A2 is considered to be a potential human oncogene. The mechanism of eEF1A2 expression is yet to be determined. Studies showed no gene mutation and no correlation between locus amplification or methylation and gene expression. Phosphate Tyrosine Kinase-6 (PTK6) is also located on 20q13.3. It is 48kb upstream of EEF1A2. PTK6 is a non-receptor tyrosine-kinase that is normally expressed in epithelial linings, prostate, skin and oral epithelium but it is not detected in the normal human mammary epithelium. PTK6 has been found to be expressed in many breast cancer cell lines and in approximately 60% of primary human breast tumors but it has not been detected in normal human breast tissue nor in fibroadenomas. Like other tyrosine kinases, PTK6 phosphorylates and activates downstream substrates that would be predicted to lead to increased transcriptional activity and therefore mediates proliferation of breast cancer cells. PTK6 is considered a prognostic marker of metastasis-free survival in breast cancer independent of the classical markers of tumor size, lymph node involvement and HER2 status. The aim of this project was to characterize for the first time the genomic region containing the two mentioned breast cancer oncogenes and understand their various roleswhether they act in tandem or independently in breast tumorigenesis. Immunohistochemistry was performed on tissue microarrays from 300 breast cancer patients to detect the expression levels of eEF1A2 and PTK6. Tumors that showed a high co-expression were analyzed for the genes’ copy number. An increased copy number of PTK6 was detected but not of eEF1A2 nor of adjacent genes on the 20q13.3 amplicon. To understand the effect of EEF1A2 expression on other genes, microarray analysis was performed on NIH-3T3 cells stably transfected with EEF1A2. Many upregulated genes were associated with different types of cancers. This was further confirmed by real-time PCR. However, when the NIH-3T3 cells were transiently transfected with EEF1A2, the genes that were upregulated in the microarray study showed no change in expression. In conclusion, EEF1A2 and PTK6 act independently and each acts through a different mechanism in breast tumorigenesis.
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Guennel, Tobias. "Statistical Methods for Normalization and Analysis of High-Throughput Genomic Data." VCU Scholars Compass, 2012. http://scholarscompass.vcu.edu/etd/2647.
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High-throughput genomic datasets obtained from microarray or sequencing studies have revolutionized the field of molecular biology over the last decade. The complexity of these new technologies also poses new challenges to statisticians to separate biological relevant information from technical noise. Two methods are introduced that address important issues with normalization of array comparative genomic hybridization (aCGH) microarrays and the analysis of RNA sequencing (RNA-Seq) studies. Many studies investigating copy number aberrations at the DNA level for cancer and genetic studies use comparative genomic hybridization (CGH) on oligo arrays. However, aCGH data often suffer from low signal to noise ratios resulting in poor resolution of fine features. Bilke et al. showed that the commonly used running average noise reduction strategy performs poorly when errors are dominated by systematic components. A method called pcaCGH is proposed that significantly reduces noise using a non-parametric regression on technical covariates of probes to estimate systematic bias. Then a robust principal components analysis (PCA) estimates any remaining systematic bias not explained by technical covariates used in the preceding regression. The proposed algorithm is demonstrated on two CGH datasets measuring the NCI-60 cell lines utilizing NimbleGen and Agilent microarrays. The method achieves a nominal error variance reduction of 60%-65% as well as an 2-fold increase in signal to noise ratio on average, resulting in more detailed copy number estimates. Furthermore, correlations of signal intensity ratios of NimbleGen and Agilent arrays are increased by 40% on average, indicating a significant improvement in agreement between the technologies. A second algorithm called gamSeq is introduced to test for differential gene expression in RNA sequencing studies. Limitations of existing methods are outlined and the proposed algorithm is compared to these existing algorithms. Simulation studies and real data are used to show that gamSeq improves upon existing methods with regards to type I error control while maintaining similar or better power for a range of sample sizes for RNA-Seq studies. Furthermore, the proposed method is applied to detect differential 3' UTR usage.
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Hessler, Theresa L. "The effects of an extended prompt versus a typical prompt on the length and quality of first draft essays written by secondary students with mild disabilities." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1124204799.
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Thesis (Ph. D.)--Ohio State University, 2005.Title from first page of PDF file. Document formatted into pages; contains xv, 210 p.; also includes graphics. Includes bibliographical references (p. 132-138). Available online via OhioLINK's ETD Center
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Meneguin, Christian Reis. "Seleção de características a partir da integração de dados por meio de análise de variação de número de cópias (CNV) para associação genótipo-fenótipo de doenças complexas." reponame:Repositório Institucional da UFABC, 2018.
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Orientador: Prof. Dr. David Corrêa Martins JúniorDissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Ciência da Computação, Santo André, 2018.
As pesquisas em biologia sistêmica caracterizam-se pela interdisciplinaridade, a compreensão com visão ampla sobre as interações ocorridas internamente em organismos biológicos, hereditariedade e a influência de fatores ambientais. Neste cenário, é constituída uma rede complexa de interações na qual seus componentes são de diferentes tipos, como as variações do número de cópias (Copy Number Variation - CNVs), genes, entre outros. As doenças complexas que ocorrem neste contexto normalmente são consequências de perturbações intracelulares e intercelulares em tecidos e órgãos, sendo desenvolvidas de forma multifatorial, ou seja, a causa e o desenvolvimento dessas doenças são fruto de diversos fatores genéticos e ambientais. Nos últimos anos, tem sido produzido um volume bastante elevado de dados biológicos gerados por técnicas de sequenciamento de alto desempenho, requerendo pesquisas que envolvam para uma análise integrada desses dados. As variações do número de cópias (Copy Number Variation - CNVs), ou seja, a variação no número de repetições de subsequências de DNA entre indivíduos, se mostram úteis visto que estão relacionadas com outros tipos de dados como genes e dados de expressão gênica (abundâncias de mRNAs transcritos pelos genes em diferentes contextos). Devido a natureza heterogênea e a imensa quantidade de dados, a análise integrativa é um desafio computacional para o qual abordagens vêm sendo propostas. Neste sentido, nesta dissertação foi proposto um método que realiza a integração de dados (CNVs, dados de expressão gênica, haploinsuficiência, imprint, entre outros) por meio de um processo que permite identificar trechos comuns de CNVs entre amostras de diferentes indivíduos, sejam estas amostras de caso ou de controle e que possuem informações obtidas a partir das integrações feitas. Com este processo, o método aqui proposto diferencia-se dos métodos que realizam integração de dados por meio da análise de sobreposição dos dados biológicos, mas não geram novos dados contendo intervalos de CNVs existentes entre as amostras. O método proposto foi analisado com base no estudo de caso do autismo (Transtornos do Espectro Autista - TEA). O autismo, além de ser considerado uma doença complexa, possui algumas particularidades que dificultam o seu estudo quando comparado a outros tipos de doenças complexas como o câncer, por exemplo. Foram realizados dois experimentos que envolveram dados dos CNVs de indivíduos com TEA (caso) e indivíduos sem este transtorno (controle). Também foi feito um experimento utilizando amostras de CNVs de TEA e amostras de CNVs relacionados a outras doenças do neurodesenvolvimento. Os experimentos envolveram a integração dos tipos de dados propostos. Foi possível identificar trechos de CNVs que estão presentes somente em amostras associadas aos casos e não em controles, ou cenários de trechos de CNVs presentes em amostras de TEA e ausentes nas amostras de outras doenças do neurodesenvolvimento, e vice-versa. Os resultados também refletiram a tendência de indivíduos do gênero masculino serem mais afetados por TEA em relação ao feminino. Foi possível também identificar genes associados e informações como o biotipo e se estão presentes em dados de haploinsuficiência, imprint ou ainda dados de expressão agrupados em regiões e períodos. Finalmente, análises de enriquecimento das listas de genes dos CNVs resultantes do método apontam para diversas vias relacionadas com o TEA, tais como as vias de sinalização do receptor toll-like dependente de TRIF, do ácido gama-aminobutírico (GABA), de transmissão sináptica e secreção neurotransmissora, de recepção da insulina, de percepção sensorial olfativa, e de adesão celular independente de cálcio.
Researches in systems biology are characterized by interdisciplinarity, wide-ranging understanding of interactions within biological organisms, heredity, and the influence of environmental factors. In this scenario, a complex network of interactions is constituted of different types of components, such as CNVs (Copy Number Variations), genes, and others. Complex diseases that occur in this context are usually consequences of intracellular, intercellular, tissue, organ, and multifactorial disorders, i.e., the cause and development of these diseases are the result of various genetic and environmental factors. In recent years, a very large volume of biological data generated by high performance sequencing techniques has been produced, requiring researches involving an integrated analysis of these data. CNVs, i.e., the variation in the number of DNA subsequences between individuals, are useful because they are related to other types of data such as genes and gene expression data (abundances of mRNAs transcribed by genes in different contexts). Due to the heterogeneous nature and the immense amount of data, integrative analysis is a computational challenge for which approaches have been proposed. In this sense, in this dissertation a method was proposed that performs a data integration (CNVs, gene expression data, haploinsufficiency, imprint, among others) through a process that allows to identify common portions of CNVs between samples of different individuals, being these case or control samples and that have information obtained from the integration performed. In this context, the method proposed here differs from the methods that carry out data integration through the analysis of the overlay of the biological data, but does not generate new data containing ranges of CNVs existing between the samples. The proposed method was analyzed on the basis of the case study of Autistic Spectrum Disorder (ASD). Besides being considered a complex disease, TEA has some peculiarities that hinder its study when compared to other types of complex diseases such as cancer, for example. As a case study, two experiments were carried out that involved data from the CNVs of individuals with ASD (case) and individuals without this disorder (control). An experiment was also done using samples of ASD CNVs and CNVs samples related to other neurodevelopmental diseases. The experiments involved the integration of the proposed data types. Among the results, the method identified excerpts of CNVs that are present only in samples associated with the cases and not in controls, or scenarios of CNVs snippets present in TEA samples and not present in other neurodevelopmental disease samples, and vice-versa. The results also reflected the tendency for males to be more affected by TEA compared to the females. In the excerpts of CNVs in certain results, it was possible to identify associated gene informations such as the biotype and whether they are present in Haploinsufficiency, imprint or even expression data grouped in regions and periods. Finally, enrichment analyses involving lists of genes from the resulting CNVs point to several signaling pathways related to TEA, such as TRIF-dependent toll-like receptor signaling, gamma aminobutyric acid (GABA), synaptic transmission and neurotransmitter secretion, insulin reception, olfactory sensorial perception, and calcium independent cell-cell adhesion.
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Albiges-Sauvin, Laurence. "Caractérisation des Carcinomes Papillaires du Rein." Thesis, Paris 11, 2013. http://www.theses.fr/2013PA11T070.
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Les Carcinomes Papillaires du Rein (pRCC) représentent la seconde forme histologique de cancers du rein . Ils correspondent à une entité hétérogène de tumeurs subdivisées en type I et type II sur leurs caractéristiques anatomopathologiques. Leur pronostic au stade métastatique est inferieur à celui des carcinomes à cellules claires. Les caractéristiques biologiques des pRCC sont mal connues et n’ont pas permis de développer jusqu'à ce jour de thérapeutiques spécifiques.Ce travail propose, en première partie, une synthèse des données disponibles biologiques, anatomo-pathologiques, thérapeutiques et pronostiques des pRCC. Cette synthèse a fait l’objet d’une publication. ( Albiges et al. The Oncologist 2012)Le second volet est dédié à l’analyse de la place du proto-oncogène MET au sein des pRCC de type I et II et plus particulièrement les différentes modalités d’activation de ce gène. Cette analyse (i) caractérise les anomalies quantitatives de l’ADN du gène MET (CGH array pour les pRCC de type II et CGMA pour les pRCC de type I) et leur corrélation au niveau d’expression génique; (ii) recherche l’existence de mutations activatrices du domaine tyrosine kinase par séquençage du gène MET chez les pRCC de type I; et (iii) analyse également les niveaux d’expression du ligand et des co-activateurs de ce récepteur MET. Ces résultats sont en cours de publication (Albiges et al. Clinical Cancer Research)Le troisième et dernier volet de ce travail vise à identifier des pistes biologiques propres aux pRCC par l’analyses de sous groupes distinguable en termes de profils d’expression génique et surtout par l’analyses des anomalies de l’ADN identifiées par CGH array des pRCC de type II, couplées aux données de transcriptomePapillary renal cell carcinomas (pRCC) are the second most common form of Renal Carcinomas and belongs to the non clear cell carcinomas family. This tumour type is an heterogeneous group of tumours usually subdivided in type I and type II according to pathological features. The prognosis of pRCC in the metastatic setting is worse to clear cell carcinoma’s prognosis. Biological characteristics of pRCC are poorly known and did not allow the development of specific targeted therapies.This work first presents a synthesis of published data regarding biology, pathology, therapeutics and prognosis of pRCC. This review has been published. (Albiges et al. The Oncologist 2012)Second part is dedicated to the analysis of MET proto-oncogene across pRCC. The main focus is to assess MET activation drivers. This analysis (i) characterises MET gene DNA copy number alterations (CGH array for type II pRCC and CGMA approach for Type I pRCC) and their correlation with gene expression profiling; (ii) assess activating mutations within the tyrosine kinase of MET gene in the type I pRCC; and (iii) investigate expression level of ligand and co-activators of MET receptor. This analysis is under publication. (Albiges et al. Clinical Cancer Research)Third and last part of this work aims at identifing new biological pathway specific to pRCC using clustering of gene expression profiling and DNA abnormalities assessed by CGHarray inthe type II pRCC subtypes with matching gene expression data
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Cooper, Jennifer L. "Gene expression analysis of Sucrose synthase1 and Shrunken1 in euploid and aneuploid maize /." free to MU campus, to others for purchase, 2001. http://wwwlib.umi.com/cr/mo/fullcit?p3025614.
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Preuten, Tobias. "Organellar gene expression." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2010. http://dx.doi.org/10.18452/16142.
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Zusätzlich zu der eubakteriellen RNA-Polymerase (RNAP) der Plastiden sind im Zellkern von Arabidopsis thaliana drei weitere, phagentypische RNAP kodiert, die jeweils aus nur einer Einheit aufgebaut sind. Die Enzyme RpoTp und RpoTm werden in die Plastiden, bzw. die Mitochondrien transportiert, während RpoTmp in beiden Organellen zu finden ist. Um die Lichtabhängigkeit der RpoT-Gene zu untersuchen, wurde die lichtinduzierte Akkumulation ihrer Transkripte in 7-Tage alten Keimlingen, sowie 3- bzw. 9-Wochen alten Rosettenblättern mittels quantitativer real-time PCR ermittelt. Die entwicklungsabhängige Regulation der RpoT-Transkript-Akkumulation wurde außerdem während der Blattentwicklung analysiert. Zusätzlich wurde der Einfluss des circadianen Rhythmus untersucht. Es stellte sich heraus, dass die Transkriptakkumulation aller drei RpoT-Gene stark lichtinduziert war und nur marginalen circadianen Schwankungen unterlag. In weiteren Versuchen mit verschiedenen Lichtrezeptor-Mutanten und unterschiedlichen Lichtqualitäten wurde der Einfluss multipler Rezeptoren auf den Prozess der Lichtinduktion gezeigt. In den Zellen höherer Pflanzen finden sich drei Genome. Die Biogenese von Chloroplasten und Mitochondrien, sowie lebenswichtige Prozesse, wie Atmung und Photosynthese setzen oftmals die Aktivität von Genen auf mindestens zwei dieser Genome voraus. Eine intrazelluläre Kommunikation zwischen den verschiedenen Genomen ist daher unumgänglich für einen funktionierenden Stoffwechsel der Pflanze. In dieser Arbeit wurde herausgestellt, dass die Zahl mitochondrialer Genkopien in photosynthetisch inaktiven Arabidopsis-Keimlingen drastisch erhöht ist. Bei der Untersuchung des DNA-Gehaltes in Proben, die Altersstufen von 2-Tage alten Keimblättern bis hin zu 37-Tage alten, seneszenten Rosettenblättern umfassten, fand sich ein deutlicher Anstieg der Kopienzahlen in älteren Rosettenblättern. Außerdem unterschieden sich die Kopienzahlen der untersuchten Gene zum Teil erheblich voneinander.In addition to eubacterial-like multi-subunit RNA polymerases (RNAP) localized in plastids and the nucleus, Arabidopsis thaliana contains three phage-like single-unit, nuclear-encoded, organellar RNAPs. The enzymes RpoTp and RpoTm are imported into plastids and mitochondria, respectively, whereas RpoTmp shows dual targeting properties into both organelles. To investigate if expression of the RpoT genes is light-dependent, light-induced transcript accumulation of RpoTm, RpoTp and RpoTmp was analyzed using quantitative real-time-PCR in 7-day-old seedlings as well as in 3- and 9-week-old rosette leaves. To address the question whether RpoT transcript accumulation is regulated differentially during plant development transcript abundance was measured during leaf development. Additionally, effects of the plants circadian rhythm on RpoT transcript accumulation were analyzed. Transcripts of all three RpoT genes were found to be strongly light-induced even in senescent leaves and only marginally influenced by the circadian clock. Further analyses employing different photoreceptor mutants and light qualities revealed the involvement of multiple receptors in the light-induction process. The biogenesis of mitochondria and chloroplasts as well as processes like respiration and photosynthesis require the activity of genes residing in at least two distinct genomes. There have to be ways of intracellular communication between different genomes to control gene activities in response to developmental and metabolic needs of the plant. In this study, it was shown that gene copy numbers drastically increased in photosynthetically inactive Arabidopsis seedlings. Mitochondrial DNA contents in cotyledons and leaves ranging in age from 2-day-old cotyledons to 37-day-old senescent rosette leaves were examined. A common increase in senescing rosette leaves and drastic differences between individual genes were found, revealing the importance of an integrative chondriome in higher plant cells.
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Prunier, Stephen G. "Individual Differences in the Mental Representation of Verbal Probability Expressions: The Role of Numeracy." University of Toledo / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501800053986437.
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Feng, Yuanjian. "Detection and Characterization of Multilevel Genomic Patterns." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/38577.
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DNA microarray has become a powerful tool in genetics, molecular biology, and biomedical research. DNA microarray can be used for measuring the genotypes, structural changes, and gene expressions of human genomes. Detection and characterization of multilevel, high-throughput microarray genomic data pose new challenges to statistical pattern recognition and machine learning research. In this dissertation, we propose novel computational methods for analyzing DNA copy number changes and learning the trees of phenotypes using DNA microarray data.
DNA copy number change is an important form of structural variations in human genomes. The copy number signals measured by high-density DNA microarrays usually have low signal-to-noise ratios and complex patterns due to inhomogeneous composition of tissue samples. We propose a robust detection method for extracting copy number changes in a single signal profile and consensus copy number changes in the signal profiles of a population. We adapt a solution-path algorithm to efficiently solve the optimization problems associated with the proposed method. We tested the proposed method on both simulation and real CGH and SNP microarray datasets, and observed competitively improved performance as compared to several widely-adopted copy number change detection methods. We also propose a chromosome instability measure to summarize the extracted copy number changes for assessing chromosomal instabilities of tumor genomes. The proposed measure demonstrates distinct patterns between different subtypes of ovarian serous carcinomas and normal samples.
Among active research on complex human diseases using genomic data, little effort and progress have been made in discovering the relational structural information embedded in the molecular data. We propose two stability analysis based methods to learn stable and highly resolved trees of phenotypes using microarray gene expression data of heterogeneous diseases. In the first method, we use a hierarchical, divisive visualization approach to explore the tree of phenotypes and a leave-one-out cross validation to select stable tree structures. In the second method, we propose a node bandwidth constraint to construct stable trees that can balance the descriptive power and reproducibility of tree structures. Using a top-down merging procedure, we modify the binary tree structures learned by hierarchical group clustering methods to achieve a given node bandwidth. We use a bootstrap based stability analysis to select stable tree structures under different node bandwidth constraints. The experimental results on two microarray gene expression datasets of human diseases show that the proposed methods can discover stable trees of phenotypes that reveal the relationships between multiple diseases with biological plausibility.Ph. D.
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Michal, Joshua Paul. "The Expressive Phrasing Concepts of Marcel Tabuteau Applied to Concerto in Eb Major for Horn and Orchestra, K. 417 by W.A. Mozart." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1406050637.
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Gonçalves, Jaciane Coelho. "Influência do número de repetições na identificação de genes diferencialmente expressos em experimentos de RNA-Seq." Universidade Federal de Viçosa, 2013. http://locus.ufv.br/handle/123456789/4066.
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Previous issue date: 2013-01-16One of the current objectives of molecular biology is to measure and assess the gene expression profiles in different types of biological tissues, to understand the mechanisms of molecular transformation under certain conditions. Next-generation sequencing (NGS) technologies promote DNA sequencing in platforms capable of generating information about millions of base pairs in a single step. However these technologies still have high cost, making it difficult to obtain large number of repetitions of sample data. Therefore, it becomes necessary the discovery and the improvement of efficient statistical methodologies for optimizing analysis of data generated in genome sequencing platforms. The overall objective of this work was to evaluate the effect of the number of repetitions in the identification of differentially expressed genes, in RNA-Seq experiments, contributing to the clarification of the statistic that researchers will assist in data analysis in RNA-Seq experiments. Specifically, we evaluate empirically the effect of the number of repetitions in the statistical analysis of gene expression in RNA-Seq experiments. To carry out the analyses we used a dataset defined in Li et al. (2008), which compared treated and non-treated cancer cells. That work had four biological replications for the control group (non-treated) and three replications for biological treatment group (cells that have received the treatment). The data was analyzed using the package DESeq from the statistical environment R. A total of 2566 genes were considered differentially expressed (DE) when we evaluate the original and complete dataset. When we analyzed three replications of the control and treatment, we found, on average, 2153 genes DE. From the moment in which only two reps for both treatments were used, were identified, on average, 1241 genes DE. The major change in the number of genes DE was observed when replications were not used. In this case we identified around 44 differentially expressed genes. According to the results generated in the analysis, it was possible to verify that the number of repetitions is an essential factor in order to obtain a significant number of differentially expressed genes.
Um dos objetivos atuais da biologia molecular é medir e avaliar os perfis de expressão gênica em diferentes tipos de tecidos biológicos, para entender os mecanismos de transformação molecular sob determinadas condições. Tecnologias de sequenciamento de Nova Geração (NGS) promovem o sequenciamento de DNA em plataformas capazes de gerar informações sobre milhões de pares de bases em uma única etapa. Porém essas tecnologias ainda apresentam custo elevado, dificultando a obtenção de elevado número de repetições de dados amostrais. Assim, torna-se necessária a descoberta e o aprimoramento de metodologias estatísticas eficientes para a otimização das análises de dados gerados em plataformas de sequenciamento de genomas. O objetivo geral desse trabalho consistiu em avaliar o efeito do número de repetições na identificação de genes diferencialmente expressos, em experimentos de RNA-Seq, contribuindo para o esclarecimento de pesquisadores que venham a auxiliar nas análises de dados em experimentos de RNA-Seq. De forma específica, avaliamos empiricamente o efeito do número de repetições na análise estatística da expressão gênica em experimentos de RNA-Seq. Para a realização das análises foi utilizado um conjunto de dados definido em Li et al. (2008), o qual comparou células cancerígenas tratadas e não tratadas. Naquele estudo havia quatro repetições biológicas para o grupo controle (células não tratadas) e três repetições biológicas para grupo de tratamento (células que receberam o tratamento). Os dados foram analisados utilizando o pacote DESeq do Programa computacional R. Um total de 2566 genes foram considerados diferencialmente expressos (DE) quando avaliamos o conjunto de dados original completo. Quando analisamos três repetições do controle e do tratamento, nós encontramos, em média, 2153 genes DE. A partir do momento em que apenas duas repetições para ambos os tratamentos foram utilizadas, foram identificadas, em média, 1241 genes DE. A grande alteração no número de genes DE foi observada quando repetições não foram utilizadas. Nesse caso identificamos em torno de 44 genes diferencialmente expressos. De acordo com os resultados gerados nas análises, foi possível verificar que o número de repetições é um fator essencial para se obter um número significativo de genes diferencialmente expressos.
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SANTOS, Ana Cláudia Guedes dos. "Uma contribuição ao ensino de números irracionais e de incomensurabilidade para o ensino médio." Universidade Federal de Campina Grande, 2013. http://dspace.sti.ufcg.edu.br:8080/jspui/handle/riufcg/2161.
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Capes
Este trabalho tem como proposta pedagógica apresentar aos alunos o conceito de segmentos comensuráveis e de segmentos incomensuráveis, mostrando a importância desses conceitos para o estudo dos números racionais e irracionais. Veremos um processo de verificação da comensurabilidade de dois segmentos, doravante P.V.C.D.S, que é um processo geométrico de verificação de comensurabilidade de dois segmentos. A partir do P.V.C.D.S, apresentamos a demonstração clássica de que p2 é irracional, com uma abordagem geométrica, mostrando que o segmento do lado de um quadrado de medida 1 e o segmento de sua diagonal são incomensuráveis. Ainda apresentamos um estudo sobre expressões decimais, no qual será apresentado um teorema que nos permite verificar se uma fração irredutível possui representação decimal finita ou infinita e periódica. Também apresentamos outro teorema que nos permite transformar expressões decimais finitas e infinitas e periódicas na sua forma de fração. Por fim, apresentaremos algumas sugestões de atividades, que englobam todo conteúdo do presente TCC. Essas atividades foram aplicadas a uma turma de 1 ano do Ensino Médio de uma escola pública, e as respostas dos alunos estão anexadas ao trabalho.
This work have pedagogical proposed to introduce the concept of commensurable segments and incommensurable segments, showing the importance of these concepts for the study of rational and irrational numbers. We will stabelish a verification process to detect the mensurability of two segments, which is a geometric process. We present the classic demonstration that root of 2 is irrational with a geometric approach, showing that the segment of the side of a square measuring its diagonal are immeasurable. We still will present a study on decimal expressions, and prove a theorem that allows to check that an irreducible fraction has decimal representation finite or infinite and periodic. We also present another theorem that allows us to turn decimal expressions finite or infinite and periodic on its fraction form. Finally we present some suggestions for activities that include all content of the TCC. These activities have been applied to a class of 1st year of high school at a public school, and the students’ answers are attached to the work.
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Stander, Barend Andre. "Differential effects of Sutherlandia frutescens subs. microphylla on cell numbers, morphology, gene and protein expression in a breast adenocarcinoma and a normal breast epithelial cell line." Diss., Access to E-Thesis, 2007. http://upetd.up.ac.za/thesis/available/etd-08052008-093345/.
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Susini, Laurent. "Implication de Siah-1 dans la dégradation des protéines et dans l' expression des gènes durant la réversion tumorale." Paris 7, 2003. http://www.theses.fr/2003PA077115.
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Benevides, Kristina, Oscar Broström, Kalman Grim Elison, Hugo Swenson, Andrei Vlassov, and Josefin Ågren. "Stabil och antibiotikafri läkemedelsproduktion i rekombinant Escherichia coli." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-323719.
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Den här rapporten presenterar ett antibiotikafritt, stabilt och kromosombaserat expressionssystem för läkemedelsproduktion i Escherichia coli på beställning av företaget Affibody AB. E. coli-stammen BL21(DE3) valdes som värdorganism för expressionssystemet. Systemet består av en genkassett som innehåller en T7-promotor, en 5′-UTR från genen ompA och en terminatorsekvens från RNA-operonet rrnB. Fyra kopior av genkassetten ska integreras i pseudogenerna caiB, yjjM, hsdS och yjiV. En datormodell som modellerar det egentliga kopietalet i cellerna har skapats i mjukvaran MATLAB, vilket visar att det uppskattas vara maximalt 32 kopior av genkassetten per cell på grund av replikation av kromosomen. Ett högt pH i fermentorn; att använda fed-batch och blandade kolhydratkällor; och att använda stammen BL21(DE3) minskar acetatproduktionen i cellen. En lägre acetatproduktion kan leda till en högre produkthalt. En proteinutbytesmodell för mjukvaran MATLAB har konstruerats för att uppskatta koncentrationen av Affibody®-molekylen i en E. coli cell.
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Silva, Emerson José da. "As construções geométricas via geometria dinâmica do software régua e compasso." Universidade Federal de Goiás, 2014. http://repositorio.bc.ufg.br/tede/handle/tede/3982.
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Dissertação - Emerson José da Silva - 2014.pdf: 7690015 bytes, checksum: 913769b0dd5913e4688da0ec1491b760 (MD5)Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-01-28T12:58:40Z (GMT) No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Emerson José da Silva - 2014.pdf: 7690015 bytes, checksum: 913769b0dd5913e4688da0ec1491b760 (MD5)
Made available in DSpace on 2015-01-28T12:58:40Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Emerson José da Silva - 2014.pdf: 7690015 bytes, checksum: 913769b0dd5913e4688da0ec1491b760 (MD5) Previous issue date: 2014-08-21
In this work we revisit the subject Geometric Constructions into ruler and compass, using the dynamic geometry software 'Ruler and Compass' as an auxiliary tool in the teaching and learning of geometry, building examples and suggestions for activities with the software. Brought to the fore the possibility of building into ruler and compass, solutions to several problems that can be presented as algebraic expressions. Yet addressed the possibility of constructing a number, using only ruler and compass and discuss the famous and historical problems of geometrical construction: doubling the cube, squaring the circle and the trisection of the angle. We add appendices which present other possible constructions and also bring suggestions for activities with ruler and compass software. Keywords
Neste trabalho revisitamos o assunto Construções Geométricas via régua e compasso, utilizando o software de Geometria Dinâmica ‘Régua e Compasso’ como uma ferramenta auxiliar no ensino e aprendizagem de Geometria, construindo exemplos e sugestões de atividades com o software. Trouxemos à tona a possibilidade da construção, via régua e compasso, de soluções para vários problemas que podem ser apresentados por expressões algébricas. Abordamos ainda a possibilidade da construção de um número, utilizando-se apenas a régua e o compasso e discutimos os célebres e históricos problemas de construção geométrica: duplicação do cubo, quadratura do círculo e trissecção do ângulo. Acrescemos ainda apêndices onde apresentamos outros tipos de construções possíveis e também trazemos sugestões de atividades com o software ‘Régua e Compasso’.
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Houg, Morgan. "Les recherches arithmétiques de Leibniz à Paris : sur certaines questions de nombres dans la seconde moitié du XVIIe siècle." Thesis, Université de Paris (2019-....), 2019. http://www.theses.fr/2019UNIP7172.
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À son arrivée à Paris, Leibniz rencontre de nombreux acteurs du paysage scientifique. À leur contact, il va se former a la pratique des mathématiques. Nous nous intéressons ici a la facette arithmétique de son travail, largement dominée dès 1672 par un problème diophantien tentaculaire appelant de solides notions d'algèbre. Alors que des études sérieuses ont été réalisées sur le problème, nous proposons une approche qui tente de dépasser la seule description des essais de résolution tous infructueux de ce problème dit des six carres. Nous avons cherché à montrer que Leibniz s'était véritablement approprié le résultat. En nous fondant sur une étude au plus près des textes mathématiques édités par l'Académie de Berlin, nous avons tracé la ligne d'une recherche parallèle sur les nombres conduite par Leibniz à partir de ces essais de résolution du problème des six carres. L'étude des correspondances savantes de la seconde moitié du XVIIe siècle a été convoquée pour venir illustrer les investigations autour du problème. Nous les avons utilisées aussi pour animer le détachement progressif du problème à mesure que Leibniz a gagné en aisance dans l'arithmétique et a découvert de nouvelles façons de travailler. Nous suggérons dans cette étude une relecture de la manière dont le problème des six carrés a été construit par son créateur, Jacques Ozanam. Nous argumentons notamment le fait que sa résolution était intimement liée à deux éléments, l'un mathématique et l'autre historique, sur lesquels Leibniz manquait de maîtrise : les techniques de quadrature algébrique et la rédaction du Diophante d'Ozanam. Dérouté par les deux à la fois, nous présentons par la suite Leibniz comme un ≪ errant à but ≫ dès le moment ou il parvient à voir dans les méthodes de factorisations et développements parfois lourdes qu'il a mises au point dans le cadre du problème, des applications aux propriétés de divisibilité dans les entiers. Nous nous sommes alors proposé de tirer le fil de l'étude sur les entiers qui en découle pour finir par montrer un Leibniz arithméticien, devisant sur les nombres premiers et leur distribution. Nous montrons donc que l'histoire de la pratique arithmétique de Leibniz a Paris est étroitement liée à sa propre histoire de mathématicien et qu'elle est un témoin de sa capacité à acquérir puis dépasser les fondamentaux de son époque, de sa capacité à devenir un chercheurUpon his arrival in Paris, G. W. Leibniz met many scientists. Through discussions and debates with them, he acquired knowledge of mathematics. We have focused here on his work in arithmetic, which in 1672 is dominated to a large extent, by a branched Diophantine problem that requires a significant use of algebra to be solved. While some credible studies have been published on this problem we’ve aimed at trying to go further than a mere description of failed attempts at solving this problem, known as the “sixsquare problem”. We have sought to show that Leibniz engaged in depth with this subject. Based on mathematical studies published by the Berlin Academy of Sciences, we have conducted parallel research on numbers by Leibniz, stemming from these attempts. By studying the correspondences of scholars from the late 17th century, we have been able to illustrate advances in the resolution of the problem, and we have also used them to show the way Leibniz gradually came to neglect the problem as found new ways to work in arithmetic. As a result, this study proposes a reinterpretation of the way the six-square problem was constructed by its creator, Jacques Ozanam. We’ve also insisted on the fact that the resolution was closely linked to two elements, one mathematical, the other historical, which Leibniz did not master: algebraic squaring methods and the preparation of a book by Ozanam, Diophante. These two factors set Leibniz back, and sharpened his dedication to his goal as soon as he succeeded in finding, in the burdensome factorization and development theories he had developed for the six-square problem, some properties of the divisibility of numbers. Finally, we have endeavored to examine these works to portray Leibniz as an arithmetician who, in particular, wrote original texts on prime numbers and even on their repartition. Thus we show that the history of Leibniz’s arithmetical practice in Paris is closely linked to his own history as a mathematician, and that it bears witness to his ability to gain knowledge, and then to go further than the expertise of his time, thereby contributing to his own development as a researcher
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Arias, Badia Blanca. "Television dialogue and subtitling: a corpus-driven study of police procedurals." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/404733.
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The specialised literature has suggested the intermediate position of television dialogue and subtitling along the continuum from spoken to written language (e.g. Díaz-Cintas 2003; Quaglio 2009; Forchini 2012). This dissertation adopts a corpus-driven methodology to tackle this issue from a descriptive, contrastive point of view. It reports on results of the analysis of the Corpus of Police Procedurals (CoPP), a corpus containing the transcribed dialogue (EN) and the DVD subtitling (ES) of fifteen episodes of three contemporary police procedurals, namely Dexter (Showtime, 2006), The Mentalist (Warner Bros, 2008), and Castle (ABC, 2009). A selection of syntactic and lexical features typically attributed to either poles of the continuum have been scrutinized from a quantitative and a qualitative approach. The statistical basis of the quantitative study allows identification of patterns of behaviour (i.e. norms) on the dialogue creators’ and the subtitlers’ part. Qualitative lexical analysis adapts the corpus pattern analysis (CPA) methodology proposed by Hanks (esp. 2004, 2013a), to date used for lexicographic purposes only, for the study of lexical exploitation, i.e. creativity, in this type of texts.La bibliografía especializada ha sugerido la posición del diálogo televisivo y del subtitulado como géneros intermedios en el continuo oralidad-escritura (p. ej. Díaz-Cintas 2003, Quaglio 2009; Forchini 2012). Esta tesis adopta la metodología corpus-driven (‘dirigida por el corpus’) para abordar esta cuestión desde un punto de vista descriptivo y contrastivo, a partir del análisis del Corpus of Police Procedurals (CoPP), un corpus compilado para los propósitos de esta investigación que contiene, alineados, el diálogo (EN) y el subtitulado para DVD (ES) de quince capítulos de tres series de ficción policíaca procesal contemporáneas: Dexter (Showtime, 2006), El mentalista (Warner Bros, 2008) y Castle (ABC, 2009). Una selección de rasgos sintácticos y léxicos prototípicamente atribuidos a ambos polos del continuo han sido examinados tanto cuantitativa como cualitativamente. La base estadística de los análisis cuantitativos llevados a cabo revela patrones de comportamiento (normas) en los creadores del diálogo ficcional y en sus traductores. El análisis cualitativo del léxico adapta la metodología lexicográfica de análisis de patrones de corpus (CPA) propuesta por Hanks (esp. 2004, 2013a) para el estudio de la explotación léxica (creatividad) en este tipo de textos.
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Hsu, Fang-Han. "Copy Number and Gene Expression: Stochastic Modeling and Therapeutic Application." Thesis, 2013. http://hdl.handle.net/1969.1/149298.
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The advances of high-throughput technologies, such as next-generation sequencing and microarrays, have rapidly improved the accessibility of molecular profiles in tumor samples. However, due to the immaturity of relevant theories, analyzing these data and systematically understanding the underlying mechanisms causing diseases, which are essential in the development of therapeutic applications, remain challenging.
This dissertation attempts to clarify the effects of DNA copy number alterations (CNAs), which are known to be common mutations in genetic diseases, on steady- state gene expression values, time-course expression activities, and the effectiveness of targeted therapy. Assuming DNA copies operate as independent subsystems producing gene transcripts, queueing theory is applied to model the stochastic processes representing the arrival of transcription factors (TFs) and the departure of mRNA. The copy-number-gene-expression relationships are shown to be generally nonlinear. Based on the mRNA production rates of two transcription models, one corresponding to an unlimited state with prolific production and one corresponding to a restrictive state with limited production, the dynamic effects of CNAs on gene expression are analyzed. Simulations reveal that CNAs can alter the amplitudes of transcriptional bursting and transcriptional oscillation, suggesting the capability of CNAs to interfere with the regulatory signaling mechanism. With this finding, a string-structured Bayesian network that models a signaling pathway and incorporates the interference due to CNAs is proposed. Using mathematical induction, the upstream and downstream CNAs are found to have equal influence on drug effectiveness. Scoring functions for the detection of unfavorable CNAs in targeted therapy are consequently proposed.
Rigorous experiments are keys to unraveling the etiology of genetic diseases such as cancer, and the proposed models can be applied to provide theory-supporting hypotheses for experimental design.
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LI, JIA-LING, and 李佳玲. ""Happy" or "Sad"? Impacts of Victim Number and Identification on Donation Intention of Different Facial Expression." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/ufy3vt.
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碩士國立高雄科技大學
國際企業系
107
In daily life, we can always see many charity organization′s print advertisements which are often presented by different facial expression of children. Previous research has demonstrated different results about facial expression. Based on this foundation, this research proposed two moderators of victim number and identification to explore whether they changed the influence of facial expression on donors’ attention and the intention of donation, and empathy is proposed as the underlying mechanism behind intention of donation. This research used three experimented designs to collect data. The first experiment is a 2 (facial expression: happy face vs. sad face) x2 (victim number: single person vs. group) between-factor design, and data were collected by eye tracking and questionnaire. Experiment 2 is a 2 (facial expression: happy face vs. sad face) x3 (victim number : single person vs. tight group vs. loose group) between-factor design. The last experiment 3 is a 2 (facial expression: happy face vs. sad face) x2 (victim number: single person vs. group) x2 (identification: identifiable vs. unidentifiable) between-factor design. Results indicate that based on results of eye tracking, the time and frequency of looking at the happy face were more than sad face.When single child was presented in the ad, donation effect of sad face was better than happy face. When group were presented in the ad, the donation effect of happy faces were better than sad faces. Further, when group was subdivided into tight or loose, happy faces were better than sad faces in the condition of tight group, however, there was no difference between happy faces and sad faces in the condition of loose group. Regarding three-way interactions for single identifiable victim, there was no difference between happy face and sad face. However, for single unidentifiable victim, sad face was better than happy face. When identifiable group were presented, sad faces were better than happy. But when unidentifiable group were presented, happy faces were better than sad faces. Finally, this research further showed that empathy explains the interactive effects above.
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Huang, Chun-Feng, and 黃駿豐. "Electrical Activity and Channel Expression in Pulmonary Vein and Left Atrium Cardiomyocytes of Various Nucleus Number." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/77622600888281460097.
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碩士臺北醫學大學
臨床醫學研究所
97
Introduction Atrial fibrillation (AF) is the most important clinical arrhythmia which induces cardiac dysfunction and increases mortality and morbidity. Pulmonary veins (PVs) were known to be important sources of ectopic beats with the initiation of paroxysmal atrial fibrillation and the foci of ectopic atrial tachycardia. However, the characteristics of arrhythmogenic cardiomyocytes in left atrium (LA) and pulmonary vein have not been identified. Aim The purposes of this study were to evaluate the electrophysiological difference and ion channel properties between mononucleated and binucleated cardiomyocytes in LA and PV. Material and Methods Male rabbits of 3months old (n=18; 1.5-2 kg) were sacrificed. Isolated LA-PV cardiomyocytes were obtaied by enzyme. Whole-cell patch clamp and immunostaining were used to study the electroactivity and ion channel of DAPI-identified mononucleated and binucleated cardiomyocytes in LA and PV. Results Compared to binucleated cardiomyocytes, mononucleated cardiomyocytes (n=10) have more positive resting membrane potential than binucleated myocytes (n=17) in LA (-57.9±1.0 mV versus -62.2±1.2 mV, P<0.05). Similarly, mononucleated cardiomyocytes (n=10) have more positive resting membrane potential than binucleated cardiomyocytes (n=10) in PV (-56.5±1.1 mV versus -64.0±1.6 mV, P<0.05). In pacemaker PV cardiomyocytes, mononucleated myocytes (n=34) have higher frequency of beating rates than binucleated myocytes (n=34) (2.1±0.2 Hz versus 1.3±0.2 Hz, P<0.05). Mononucleated cardiomyocytes (n=19) have smaller IK1 current density than binucleated cardiomyocytes (n=12) in PV (-2.6±0.2 pA/pF versus -3.5±0.4 pA/pF, P<0.05). Besides, the ICa,L is larger in mononucleated myocytes (n=16) than in binucleated myocytes (n=15) of LA (-14.2±1.3 pA/pF versus -10.9±0.9 pA/pF, P< 0.05). The ICa,L is also larger in mononucleated cardiomyocytes (n=18) than in binucleated cardiomyocytes (n=18) of LA (-9.3±0.7 pA/pF versus -7.0±0.8 pA/pF, P<0.05). In PV,. the RyR2 density of mononucleated myocytes (n=27) is higher than that of binucleated myocytes (n=17) of LA (100.3±4.2 IU/μm2 versus 85.1±3.3 IU/μm2, P<0.05). The RyR2 density of mononucleated cardiomyocytes (n=16) is also higher than that of binucleated cardiomyocytes (n=18) of PV (139.8±5.0 IU/μm2 versus 124.1±5.4 IU/μm2, P<0.05). Moreover, the mononucleated myocytes (n=20) had a larger [Ca2+]i transient than the binucleated myocytes (n=10) in LA (F-F0/F0, 0.52±0.06 IU versus 0.19±0.05 IU, P<0.05). Similarly, the amplitude of the [Ca2+]i transient of mononucleated cardioimyocytes (n=15) was also larger than that of binucleated cardiomyocytes (n=10) in PV (F-F0/F0, 0.64±0.09 IU versus 0.20±0.03 IU, P<0.05). In addition, the duration of [Ca2+]i transients of mononucleated myocytes (n=20) was longer than that of binucleated myocytes (n=10) in LA (67.9±6.9 ms versus 40.2±3.7 ms, P<0.05). In PV, as compared with binucleated cardiomyocytes (n=10), the mononucleated cardiomyocytes (n=15) also had a longer duration of [Ca2+]i transients (69.2±5.3 ms versus 45.3±5.9 ms, P<0.05) Conclusions The study first demonstrate the different electrophysiology characteristics between mononucleated and binucleated cardiomyocytes in LA and PV. Moreover, this study demonstrated the feasibility to examine the response of mononucleated and binucleated cardiomyocytes to drugs that were shown to induce AF.
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Chang, Jung-Chih, and 張榕芝. "Concurrent Analysis between Copy Number Variation and Gene Expression of Female Non-Smoking Lung Cancer in Taiwan." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/15323915492732477296.
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碩士國立臺灣大學
生醫電子與資訊學研究所
99
To identify genes with genomic alterations and/or transcriptional dysregulation, a concurrent analyzing method was developed to integrate data form copy number (CN) and gene expression (GE). This study contains three major parts: determine the correlation between CN and GE, perform pathway analysis by Gene Set Enrichment Analysis (GSEA), and to summarize all the pathways enriched by CN, GE, and correlation between CN and GE using a scoring method. Two datasets were analyzed to evaluate the performance of the method. The first dataset was from 44 female non-smoking lung cancer patients, which contain both paired normal and tumor tissues. The other dataset was retrieved from the Gene Expression Omnibus: GSE19539 ovarian cancer samples with two subtypes, endometrioid and serous. Both the datasets have CN and GE microarray data from the same individual. Copy number was analyzed by Affymetrix SNP 6.0 array in the both datasets. Gene expression profiles were analyzed by Affymetrix U133plus 2.0 array in the first dataset and Affymetrix 1.0 ST array in the second one. To further explore those identified pathways, Support Vector Machine (SVM) was used for classification. The classification results had higher prediction sensitivity and specificity compared with traditional analysis methods. In addition, using integration of data from both DNA and RNA levels is much biological meaningful, and may reveal much information about disease-causing genes and their regulation mechanisms. In summary, the results indicated that concurrent analyses may help to identify potential biomarkers with lower false positive rates.
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Costa, Catarina Pedrosa Martins da. "Emerging genetic alterations linked to male infertility: X-chromosome Copy Number Variation and Spermatogenesis regulatory genes' expression." Dissertação, 2017. https://repositorio-aberto.up.pt/handle/10216/104309.
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Liu, Yao-Wen, and 劉耀文. "Study on the Effect of SIRT3 Expression on Mitochondrial DNA Copy Number in Human Cancer Cell Lines." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/61810526492028912928.
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碩士國立陽明大學
藥理學研究所
101
The mutations in mitochondrial DNA (mtDNA) have been found in many human cancers. The phenomena could lead cancer cells to change their way of energy metabolism, increase the production of reactive oxygen species (ROS) and reduce their sensitivity to drugs. However, the mechanism for maintaining mitochondrial genetic stability and mtDNA copy number is still unknown. Sirtuins (SIRT1–7) are the mammalian homologues of the Sir2 gene in Saccharomyces cerevisiae. Besides, SIRT3 plays an important role in regulation of maintaining mitochondrial integrity and function. Previous studies found that SIRT3 can interact with p53, which can abolish the p53 signaling in apoptosis, growth arrest and aging. The other studies also showed that there is reduced mtDNA copy number in SIRT3 knockout mice with aging. Thus, the aim of this study is to investigate the effect of SIRT3 expression on mtDNA copy number in human cancer cell lines. The results showed that SIRT3 can be overexpressed via pcDNA™3.1 / myc-His vector and the transfected SIRT3 is functional. In addition, I also used the SIRT3 based on pcDNA vector to investigate mtDNA copy number. The results showed that mtDNA copy number was not up-regulated. Then I used SIRT3 shRNA based on pLKO.1 vector to knockdown SIRT3. The results showed that it can actually reduce the expression of SIRT3 in cancer cells. However, mtDNA copy number was not down-regulated in most of these cells except for HeLa cells. Based on these findings, SIRT3 can regulate mtDNA copy number in HeLa cells, but the mechanism needs to be further studied.