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1
Coben, Muhammed Z. "Region-based subband coding of image sequences." Diss., Georgia Institute of Technology, 2003. http://hdl.handle.net/1853/15500.
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Li, Hui. "Dynamic region-based wavelet coding for telemedicine applications." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq24182.pdf.
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Takahashi, Kuniaki 1973. "Edge and region segmentation based video coding method." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/46189.
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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and, Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1998.Includes bibliographical references (p. 61-63).
by Kuniaki Takahashi.
B.S.
M.Eng.
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Gopalan, Ramya. "Exploiting Region Of Interest For Improved Video Coding." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1250622014.
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Rambaruth, Ratna. "Region-based video compression." Thesis, University of Surrey, 1999. http://epubs.surrey.ac.uk/843377/.
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First generation image coding standards are now well-established and coders based on these standards are commercially available. However, for emerging applications, good quality at even lower bitrates is required. Ways of exploiting higher level visual information are currently being explored by the research community in order to achieve high compression. Unfortunately very high level approaches are bound to be restrictive as they are highly dependent on the accuracy of lower-level vision operations. Region-based coding only relies on mid-level image processing and thus is viewed as a promising strategy. In this work, substantial advances to the field of region-based video compression are made by considering the complete scheme. Thus, improvements to the failure regions coding and the motion compensation components have been devised. The failure region coding component was improved by predicting the texture inside the failure region from the neighbourhood of the region. A significant gain over widely used techniques such as the SA-DCT was obtained. The accuracy of the motion compensation component was increased by keeping an accurate internal representation for each region both at the encoder and the decoder side. The proposed region-based coding system is also evaluated against other systems, including the MPEG4 codec which has been recently approved by the MPEG community.
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Parker, Kyle Robert Carl. "Analysis of Mitochondrial DNA Coding Region SNPs by Pyrosequencing." Master's thesis, University of Central Florida, 2007. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2579.
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To date, the use of mitochondrial DNA in forensic analysis has relied on the presence of variations in the control region to differentiate between samples. One problem that this analysis has shown is the occurrence of common Haplogroup H haplotypes or identical sequences. Thus, there is a need to enhance the distinguishing power of this type of analysis. One option has been to investigate the mitochondrial coding region for polymorphisms that could differentiate between samples with identical control region haplotypes. The goal of this study has been to identify polymorphic coding region sites for development in a Pyrosequencing assay that would effectively enhance the discriminatory power of mitochondrial DNA analysis. With this goal in mind, five duplexes have been successfully developed and tested, utilizing the ten polymorphic sites that had been selected, with most sites being specific to Caucasians. Validation studies were performed to test the durability of the assay. The specificity of the assay to primate and non-primate species was determined to be limited to primate species only. Sample variations, including mixtures, dilutions and environmental exposure, were utilized to assess the sensitivity of the Pyrosequencing method. It was found that a minimum initial DNA input of 10fg was necessary for reliable results. The Pyrosequencing assay was able to detect mixtures at a 1:1 ratio and environmental samples exposed to the elements from up to 1 week for blood and 6 weeks for semen. Samples designed to simulate typical casework materials were analyzed and found to provide for consistent results, including trace fingerprints and digested hair shafts. These validation results provide the conclusion that this assay is suitable for use in forensic casework and demonstrate that the mitochondrial coding region provides a viable alternative to hypervariable region analysis.M.S.
Department of Chemistry
Sciences
Forensic Science MS
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Karlsson, Linda S. "Spatio-Temporal Pre-Processing Methods for Region-of-Interest Video Coding." Licentiate thesis, Mid Sweden University, Department of Information Technology and Media, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:miun:diva-51.
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In video transmission at low bit rates the challenge is to compress the video with a minimal reduction of the percieved quality. The compression can be adapted to knowledge of which regions in the video sequence are of most interest to the viewer. Region of interest (ROI) video coding uses this information to control the allocation of bits to the background and the ROI. The aim is to increase the quality in the ROI at the expense of the quality in the background. In order for this to occur the typical content of an ROI for a particular application is firstly determined and the actual detection is performed based on this information. The allocation of bits can then be controlled based on the result of the detection.
In this licenciate thesis existing methods to control bit allocation in ROI video coding are investigated. In particular pre-processing methods that are applied independently of the codec or standard. This makes it possible to apply the method directly to the video sequence without modifications to the codec. Three filters are proposed in this thesis based on previous approaches. The spatial filter that only modifies the background within a single frame and the temporal filter that uses information from the previous frame. These two filters are also combined into a spatio-temporal filter. The abilities of these filters to reduce the number of bits necessary to encode the background and to successfully re-allocate these to the ROI are investigated. In addition the computational compexities of the algorithms are analysed.
The theoretical analysis is verified by quantitative tests. These include measuring the quality using both the PSNR of the ROI and the border of the background, as well as subjective tests with human test subjects and an analysis of motion vector statistics.
The qualitative analysis shows that the spatio-temporal filter has a better coding efficiency than the other filters and it successfully re-allocates the bits from the foreground to the background. The spatio-temporal filter gives an improvement in average PSNR in the ROI of more than 1.32 dB or a reduction in bitrate of 31 % compared to the encoding of the original sequence. This result is similar to or slightly better than the spatial filter. However, the spatio-temporal filter has a better performance, since its computational complexity is lower than that of the spatial filter.
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Johnstone, Pamela. "Cloning and sequence analysis of rubella virus nonstructural protein coding region." Thesis, University of Surrey, 1994. http://epubs.surrey.ac.uk/844437/.
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A reliable working methodology for the reverse transcription (RT) and polymerase chain reaction (PCR) amplification of rubella virus (RV) RNA was established. The effect of magnesium concentration and RNA concentration on the yield and specificity of PCR products was investigated. Factors involved in the design of efficient primers for PCR were also studied. RT primers designed to specifically anneal to the RV genome were shown to increase the yield of PCR product when compared to RT-PCRs in which the RT reaction was primed by random hexamers. Using the RT-PCR technology, nonstructural (NS) protein coding regions of the wild-type strain Thomas and the vaccine strain Cendehill were amplified, cloned and sequenced. In addition a region encompassing part of the 5' NC region and the start NS protein ORF, covering nucleotides 18 to 540, for the wild-type strains Thomas, RB-1 and Machado and vaccine strains Cendehill, RA27/3, HPV77.DE5 and TO-336 was amplified, cloned and sequenced. When the Cendehill and Thomas sequences were compared with the equivalent sequences in the Therien and M33 wild-type strains, three amino acids were found which were unique to the Cendehill vaccine strain. The sequences of part of the 5' NC and 5' end of the NS coding regions of the above strains were compared to the equivalent sequences in the Therien and M33 strains. One amino acid substitution was found which was unique to RA27/3 and a second was identified which was present in both the RA27/3 and TO-336 vaccine strains. Nucleotide substitutions found in an area of the 5' NC region which, it has been suggested, plays a key role in the initiation of translation and positive strand replication were also identified. The importance of all of these substitutions is discussed with particular reference to their possible roles in attenuation. The suitability of the NS RV RT-PCR system developed in the early stages of these studies was examined with regard to its use in the amplification and detection of RV in clinical samples. The results obtained were in total agreement with those obtained using an RT-PCR system which detects the El RV gene and also correlated well with other laboratory results. Possible future applications of the NS RV RT-PCR system were discussed. Results obtained in this thesis were discussed in the context of possible future molecular biology studies in this field.
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Egger, Olivier. "Region representation using nonlinear techniques with applications to image and video coding /." Lausanne : EPFL, 1997. http://library.epfl.ch/theses/?nr=1638.
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Cicconi, Pierangela. "A spatio-temporal region-based video coding scheme for very-low bitrates /." Lausanne : EPFL, 1994. http://library.epfl.ch/theses/?nr=1261.
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Sullivan, Michael A. "Studies on the 5' non-coding region of the genome of poliovirus." Thesis, University of Leicester, 1992. http://hdl.handle.net/2381/34965.
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The last decade has seen widespread application of recombinant DNA technology to the study of picornaviruses. Comparative sequence analysis has revealed that the most highly conserved region amongst many members of this family of viruses is the 5' non-coding region. Using recombinant type 3 polioviruses it has been shown that a single point mutation located in this region dramatically reduces neurovirulence and inhibits the intracellular life-cycle of the virus. Mutation at this nucleotide contributes to the observed reversion to neurovirulence of the Sabin attenuated poliovirus type 3 vaccine strain currently used in vaccination programmes throughout the world. Knowledge concerning the function of the 5' non-coding region remains scant, and as a result, the mechanism whereby a single point mutation within this region results in alteration of the expressed phenotype of the virus remains unknown. Clearly, an understanding of the molecular mechanism(s) involved requires greater knowledge of the function of the 5' non-coding region. This thesis describes the design and construction of vectors that allow analysis of the role of the 5' non-coding region in the control of viral translation, replication, and encapsidation of viral RNA. In the plasmid pRSV-5'polio-CATm2 (N+), the 5' non-coding region of poliovirus was fused to the coding region of the bacterial chloramphenicol acetyltransferase reporter gene. The presence of the 5' non-coding region resulted in the inhibition of CAT expression when this plasmid was introduced into eukaryotic cells in culture. Deletion analysis of the 5' non-coding region in this vector identified two regions that were responsible for the marked inhibition of expression of the reporter gene. It would appear from the results of these experiments that the poliovirus/CAT chimaeric message is translatsed as a normal eukaryotic mRNA and is subject to the rules of the "scanning model". This observation suggests that the 5' non-coding region of poliovirus on its own does not possess features which enable a message containing it to be translated efficiently. It is concluded that a second factor, present in infected cells, is required for the efficient translation of poliovirus. A second plasmid was designed and constructed to investigate the role of the 5' non-coding region in replication and encapsidation of viral RNA. Preliminary data suggest that the product of this vector does undergo replication while its ability to be encapsidated has still to be tested.
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Pankraz, Alexander. "Analyse der 3' nicht translatierten Region von BVDV CP7." Giessen VVB Laufersweiler, 2007. http://d-nb.info/989047369/34.
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Pankraz, Alexander. "Analyse der 3' nicht translatierten Region von BVDV CP7 /." Gießen : VVB Laufersweiler, 2008. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=016535375&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
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Doudney, Kit William Edwin. "Cosmid contig construction and characterisation of coding sequences in the Friedreich's ataxia region." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314293.
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Hassard, Stuart Richard. "In vitro studies in the 5' non-coding region of human rhinovirus-14." Thesis, University of Essex, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303444.
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Maceira, Duch Marc. "Multi-view depth coding based on a region representation combining color and depth information." Doctoral thesis, Universitat Politècnica de Catalunya, 2017. http://hdl.handle.net/10803/456086.
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Depth map data is used to supplement the color data in multi-view sequences. As depth maps present distinct Characteristics than natural color images, new coding techniques are required to represent their smooth regions and sharp edges. In this thesis, segmentation-based coding techniques are proposed to encode depth maps by exploiting the redundancy between color and depth information. Methods developed combine partitions obtained from color and depth images to find efficient representations. The color image is assumed to be available before the depth map coding process, therefore a color partition can be obtained at the decoder without introducing coding cost.
Two hierarchical image segmentation algorithms are proposed to generate color and depth partitions for coding applications. The color segmentation obtains a super-pixel representation using color information, spatial distribution and shape complexity. The depth segmentation uses a 3D planar model for each region to extract the structure of the scene. Color and depth partitions are combined in depth map coding methods to find the final coding partition.
Different methods for texture representation have been explored in this thesis. Initial approaches used 2D coding methods, while a 3D representation have been proposed to represent depth maps from multiple views with a unique segmentation.
This 3D representation is used to segment depth maps in single-view and multi-view configurations. Final coding partitions are obtained with a rate-distortion optimization over a hierarchy of regions. Segmentation-based coding techniques proposed obtain competitive results with HEVC coding standards.Els mapes de profunditat s'utilitzen per complementar les imatges en color en seqüències de múltiples vistes. Com els mapes de profunditat presenten característiques diferents de les imatges de color natural, es requereixen noves tècniques de codificació per representar les seves característiques regions suaus separades per brusques transicions. En aquesta tesi, es proposen tècniques de codificació basades en segmentació per codificar mapes de profunditat explotant la redundància entre informació de color i profunditat. Els mètodes desenvolupats combinen particions obtingudes d'imatges de color i profunditat per trobar representacions eficients. S'assumeix que la imatge en color està disponible abans del procés de codificació de mapa de profunditat, per tant es pot obtenir una partició de color en el descodificador sense introduir cost de codificació. En primer lloc, es proposen dos algorismes jeràrquics de segmentació d'imatges per generar particions de color i profunditat per a aplicacions de codificació. La segmentació de color obté una representació en forma de superpíxeles usant informació de color, la distribució espacial de les regions i la complexitat de la forma. La segmentació de profunditat utilitza un model de pla 3D per a cada regió, extraient l'estructura de l'escena. Les particions de color i profunditat es combinen en els mètodes de codificació de mapes de profunditat, trobant la partició final de codificació. En aquesta tesi s'han explorat diferents mètodes per a la representació de la textura. Els enfocaments inicials van utilitzar mètodes de codificació 2D. Una representació en 3D s'ha proposat per representar mapes de profunditat a partir de múltiples vistes amb una única segmentació. Aquesta representació 3D s'utilitza per segmentar mapes de profunditat en configuracions de vista únicament i multi-vista. Les particions finals de codificació s'obtenen amb una optimització de "ratedistortion" sobre una jerarquia de regions. Les tècniques de codificació basades en la segmentació propostes obtenen resultats competitius amb les estàndards de codificació HEVC.
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McIlhatton, Michael A. "The sequence of bovine enterovirus strain M4 : studies on the 5' non-coding region." Thesis, Queen's University Belfast, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282257.
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Gutekunst, Karen Ann. "Molecular cloning and characterization of the region of the bacteriophage T4 genome coding for thymidine kinase." Diss., Georgia Institute of Technology, 1987. http://hdl.handle.net/1853/25387.
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Nguyen, Anthony Ngoc. "Importance Prioritised Image Coding in JPEG 2000." Queensland University of Technology, 2005. http://eprints.qut.edu.au/16005/.
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Importance prioritised coding is a principle aimed at improving the interpretability (or image content recognition) versus bit-rate performance of image coding systems. This can be achieved by (1) detecting and tracking image content or regions of interest (ROI) that are crucial to the interpretation of an image, and (2)compressing them in such a manner that enables ROIs to be encoded with higher fidelity and prioritised for dissemination or transmission. Traditional image coding systems prioritise image data according to an objective measure of distortion and this measure does not correlate well with image quality or interpretability. Importance prioritised coding, on the other hand, aims to prioritise image contents according to an 'importance map', which provides a means for modelling and quantifying the relative importance of parts of an image. In such a coding scheme the importance in parts of an image containing ROIs would be higher than other parts of the image. The encoding and prioritisation of ROIs means that the interpretability in these regions would be improved at low bit-rates. An importance prioritised image coder incorporated within the JPEG 2000 international standard for image coding, called IMP-J2K, is proposed to encode and prioritise ROIs according to an 'importance map'. The map can be automatically generated using image processing algorithms that result in a limited number of ROIs, or manually constructed by hand-marking OIs using a priori knowledge. The proposed importance prioritised coder coder provides a user of the encoder with great flexibility in defining single or multiple ROIs with arbitrary degrees of importance and prioritising them using IMP-J2K. Furthermore, IMP-J2K codestreams can be reconstructed by generic JPEG 2000 decoders, which is important for interoperability between imaging systems and processes. The interpretability performance of IMP-J2K was quantitatively assessed using the subjective National Imagery Interpretability Rating Scale (NIIRS). The effect of importance prioritisation on image interpretability was investigated, and a methodology to relate the NIIRS ratings, ROI importance scores and bit-rates was proposed to facilitate NIIRS specifications for importance prioritised coding. In addition, a technique is proposed to construct an importance map by allowing a user of the encoder to use gaze patterns to automatically determine and assign importance to fixated regions (or ROIs) in an image. The importance map can be used by IMP-J2K to bias the encoding of the image to these ROIs, and subsequently to allow a user at the receiver to reconstruct the image as desired by the user of the encoder. Ultimately, with the advancement of automated importance mapping techniques that can reliably predict regions of visual attention, IMP-J2K may play a significant role in matching an image coding scheme to the human visual system.
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Masoudi, Mehrnoush. "Identification of variants within the coding region and 5'-flanking region of the k-casein encoding gene in Holsteins using PCR-RFLP and PCR-SSCP analyses." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=23409.
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Single-strand conformation polymorphism analysis (SSCP) and restriction fragment length polymorphism analysis (RFLP) were used to determine the genotype of Holsteins at the $ kappa$-casein ($ kappa$-CN) locus. A 432-bp fragment within exon IV containing nucleotide substitutions diagnostic of the A- and B-variants of $ kappa$-CN was amplified using the polymerase chain reaction (PCR). The sires from the earliest years of the AI industry had a significantly higher (p $<$ 0.01) frequency of allele than sires in modern usage. These data indicate that selection or milk production parameters may discriminate against the B-allele. SSCP analysis was also used for detecting polymorphisms within the regulatory region of $ kappa$-CN gene. A 640-bp fragment within the 5$ sp prime$-flanking region of bovine $ kappa$-CN gene which contained the TATA box, CAAT box, and exon I was amplified using PCR. The SSCP analysis of this fragment revealed no variation, possibly due to the lower detection efficiency of SSCP with large fragment size. Nested primers were, therefore, designed to amplify fragments of 234- and 486-bp. Polymorphism was detected only in the 486-bp fragment and the two variants were designated M$ sb1$ and M$ sb2.$ The allelic frequencies of M$ sb1$ and M$ sb2$ in bulls used by AI industry before 1970 were 0.67 and 0.33, and in bulls used by AI industry after 1980 the frequencies were 0.68 and 0.32, respectively. The frequency of these alleles were not significantly different in Holsteins used by AI industry before 1970 and after 1980. Unlike the apparent change in frequency of the A- and B-variants noted within exon IV, this polymorphism seems to have not responded to selection. However, a higher frequency of M$ sb1$ allele appeared to be associated with B-variant (exon IV) genotypes. The presence of these variants within the regulatory region may possibly be involved in the quantitative expression of $ kappa$-CN gene. (Abstract shortened by UMI.)
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Drew, Jeffrey. "Studies on the structure and function of the 5' non-coding region of foot-and-mouth disease virus." Thesis, University of Reading, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.295015.
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BANKS, THERESA ANNE. "IDENTIFICATION AND SEQUENCE OF THE IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION GENE INVOLVED IN CODING FOR AN ANTI-DNA AUTOANTIBODY." Diss., The University of Arizona, 1986. http://hdl.handle.net/10150/183939.
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The major pathologic feature of the human autoimmune disease Systemic Lupus Erythematosus (SLE) and its murine counterpart, murine lupus, is the production of autoantibodies to nucleic acid antigens. In this study, a panel of six murine monoclonal anti-DNA autoantibodies was characterized at both the cellular and molecular levels in order to determine their possible role in the etiology of autoimmune disease. At the cellular level the autoantibodies were found to be highly cross-reactive, binding to three different antigenic forms of DNA as well as to the cell surface of various lymphoid cell lines. Furthermore, the fact that this autoantibody binding could be abrogated by pretreating the cells with either Proteinase K or DNase supports the hypothesis that a DNA binding protein may exist on the cell surface and that DNA bound to this receptor may serve as the target for the anti-DNA autoantibody. At the molecular level, the immunoglobulin (Ig) gene segments (V(H), D, J(H)) used to encode the variable region of the heavy chain of an anti-DNA autoantibody were sequenced. All three gene segments could be identified as members of established Ig gene segment families. In fact, the heavy chain of an antibody directed against the hapten L-glutamine₆₀-L-alanine₃₀-L-tyrosine₁₀ polymer (GAT) was found to utilize the same combination of V(H), D, and J(H) gene segments as the anti-DNA autoantibody. These results clearly indicate that autoantibodies are encoded by gene segments from the same Ig gene families used to encode antibodies to exogenous antigens. However, the discovery that this anti-DNA autoantibody is encoded by the same V(H) gene segment which encodes another anti-DNA autoantibody, derived from a different autoimmune mouse strain, supports the idea that certain V(H) gene segments may, in fact, be preferentially used to encode autoantibodies.
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Khire, Sourabh Mohan. "Enhancing H.26x coding for visual communications - with applications in telemedicine and television." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47577.
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In a wireless and mobile communication paradigm, distribution and sharing of video content often occurs over unfriendly network environments constrained by lack of sufficient bandwidth, and prone to jitter, delay and packet losses. The research presented in this thesis proposed an assortment of application-specific optimizations designed to enable high-quality video communication over bandwidth constrained and unreliable channels. This assortment of solutions, termed herein as the Application Specific Video Coding and Delivery (ASVCD) toolkit, comprises of content and network adaptive approaches such as Region of Interest (ROI) video coding, Multiple Representation Coding (MRC), and Multiple Representation Coding of the Region of Interest (ROI + MRC). Thus, the effectiveness of ROI based video-coding in facilitating diagnostically lossless delivery of surgical videos over very low bandwidth channels was studied in this thesis. Furthermore, to facilitate error resilient video delivery over channels prone to burst losses and signal loss intervals, the MRC scheme was presented in this thesis. Finally, the thesis proposed a scheme for unequal protection of the ROI in the video by using the MRC scheme to effectively enable a distance learning application. To summarize, the ASVCD toolkit contributed in enabling high-quality video communications applications to become seamless and pervasive.
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Bernacki, Lucas Edward. "The Molecular Evolution of Non-Coding DNA and Population Ecology of the Spiny Softshell Turtle (Apalone spinifera) in Lake Champlain." ScholarWorks @ UVM, 2015. http://scholarworks.uvm.edu/graddis/289.
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ABSTRACT
Spiny softshell turtles (Apalone spinifera) occur at the northwest limit of their range in Lake Champlain. This species, although widespread across North America, is listed as threatened in Vermont due to habitat destruction and disturbances of anthropogenic origin. The population of spiny softshell turtles in Lake Champlain is isolated from other North American populations and is considered as an independent management unit. Efforts to obtain information on the biology of spiny softshell turtles in Lake Champlain precede 1936 with conservation measures being initiated in 1987.
Methods of studying spiny softshell turtles in Lake Champlain have included direct observation, mark-recapture, nest beach monitoring, winter diving, and radio telemetry. Each of these approaches has provided some information to the sum of what is known about A. spinifera in Lake Champlain. For example major nesting beaches, hibernacula, and home range size have been determined. Currently spiny softshell turtles primarily inhabit two areas within Lake Champlain, Missisquoi Bay and the mouth of the Lamoille River. However, the population structure and gene flow between spiny softshell turtles inhabiting the Lamoille and Missisquoi regions remained unknown.
A GIS model was created and tested in order to identify additional nesting beaches used by spiny softshell turtles along the Vermont shores of Lake Champlain. Although some additional small potential nesting beaches were found, no additional major nesting sites were found. The GIS model identified the mouth of the Winooski River (the site of a historical population) as potentially suitable nesting habitat; however, no evidence of spiny softshell turtle nesting was found at this site.
A series of methods developed for collecting molecular and population genetic data about spiny softshell turtles in Lake Champlain are described, including techniques for DNA extraction of various tissue types and the design of new primers for PCR amplification and sequencing of the mitochondrial control region (mtD-loop). Techniques for circumventing problems associated with DNA sequence alignment in regions of a variable numbers of tandem repeats (VNTRs) and the presence of heteroplasmy within some individuals are also described. The mtD-loop was found to be a suitable marker to assess the genetic structure of the Lake Champlain population of spiny softshell turtles. No significant genetic sub-structuring was found (FST=0.082, p=0.223) and an indirect estimate of the migration rate between Lamoille and Missisquoi regions of Lake Champlain was high (Nm>5.576).
In addition to consideration of A. spinifera in Lake Champlain, the mtD-loop was modeled across 46 species in 14 families of extant turtles. The primary structure was obtained from DNA sequences accessed from GenBank and secondary structures of the mtD-loop were inferred, (from thermal stabilities) using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order of turtles; however, the inclusion of an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop was common across all turtle families considered. The Cryptodira showed conservation in the primary structure at regular conserved sequence blocks (CSBs), but the Pluerodira displayed little conservation in the primary structure of the mtD-loop. Overall, greater conservation in secondary structure than primary structure was observed in turtle mtD-loop. The AT-rich secondary structural element near the 3' terminus of the mtD-loop may be conserved across turtles due to it serving a functional role during mtDNA transcription.
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Sun, Wei. "Joint Compression and Digital Watermarking: Information-Theoretic Study and Algorithms Development." Thesis, University of Waterloo, 2006. http://hdl.handle.net/10012/2890.
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In digital watermarking, a watermark is embedded into a covertext in such a way that the resulting watermarked signal is robust to certain distortion caused by either standard data processing in a friendly environment or malicious attacks in an unfriendly environment. The watermarked signal can then be used for different purposes ranging from copyright protection, data authentication,fingerprinting, to information hiding. In this thesis, digital watermarking will be investigated from both an information theoretic viewpoint and a numerical computation viewpoint. From the information theoretic viewpoint, we first study a new digital watermarking scenario, in which watermarks and covertexts are generated from a joint memoryless watermark and covertext source. The configuration of this scenario is different from that treated in existing digital watermarking works, where watermarks are assumed independent of covertexts. In the case of public watermarking where the covertext is not accessible to the watermark decoder, a necessary and sufficient condition is determined under which the watermark can be fully recovered with high probability at the end of watermark decoding after the watermarked signal is disturbed by a fixed memoryless attack channel. Moreover, by using similar techniques, a combined source coding and Gel'fand-Pinsker channel coding theorem is established, and an open problem proposed recently by Cox et al is solved. Interestingly, from the sufficient and necessary condition we can show that, in light of the correlation between the watermark and covertext, watermarks still can be fully recovered with high probability even if the entropy of the watermark source is strictly above the standard public watermarking capacity.
We then extend the above watermarking scenario to a case of joint compression and watermarking, where the watermark and covertext are correlated, and the watermarked signal has to be further compressed. Given an additional constraint of the compression rate of the watermarked signals, a necessary and sufficient condition is determined again under which the watermark can be fully recovered with high probability at the end of public watermark decoding after the watermarked signal is disturbed by a fixed memoryless attack channel.
The above two joint compression and watermarking models are further investigated under a less stringent environment where the reproduced watermark at the end of decoding is allowed to be within certain distortion of the original watermark. Sufficient conditions are determined in both cases, under which the original watermark can be reproduced with distortion less than a given distortion level after the watermarked signal is disturbed by a fixed memoryless attack channel and the covertext is not available to the watermark decoder.
Watermarking capacities and joint compression and watermarking rate regions are often characterized and/or presented as optimization problems in information theoretic research. However, it does not mean that they can be calculated easily. In this thesis we first derive closed forms of watermarking capacities of private Laplacian watermarking systems with the magnitude-error distortion measure under a fixed additive Laplacian attack and a fixed arbitrary additive attack, respectively. Then, based on the idea of the Blahut-Arimoto algorithm for computing channel capacities and rate distortion functions, two iterative algorithms are proposed for calculating private watermarking capacities and compression and watermarking rate regions of joint compression and private watermarking systems with finite alphabets. Finally, iterative algorithms are developed for calculating public watermarking capacities and compression and watermarking rate regions of joint compression and public watermarking systems with finite alphabets based on the Blahut-Arimoto algorithm and the Shannon's strategy.
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Wang, Leyi. "STUDY TOWARD THE DEVELOPMENT OF ADVANCED INFLUENZA VACCINES." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1249332969.
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Haidara, Noûhou El Moctar. "Analyse du rôle de la terminaison de la transcription des ARN non-codants dans la régulation de l’expression des gènes Modulated termination of non-coding transcription partakes in the regulation of gene expression Intrinsic and extrinsic mechanisms cooperate to ensure efficient termination of RNAPIII transcription Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1." Thesis, université Paris-Saclay, 2021. http://www.theses.fr/2021UPASL010.
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La transcription pervasive est un phénomène universel et constitue une source importante d’ARN non-codants. Elle peut s’s’interférer avec l’expression normale des gènes. Cependant,la transcription pervasive peut aussi jouer un rôle dans la régulation de l’expression des gènes en favorisant la répression des gènes spécifiques par un mécanisme d’interférence transcriptionnelle. L’efficacité de la terminaison de la transcription non-codante peut fortement influencer sa capacité de réguler l’expression des gènes voisins. Cependant, à ce jour, il n’est pas clair s’il existe des mécanismes qui modulent l’efficacité de la terminaison non-codante en réponse aux signaux environnementaux afin de réguler l’expression des gènes. Durant ma thèse, j’ai abordé cette question en me focalisant sur la régulation de l’hélicase Sen1, un facteur clé de la terminaison de la transcription non-codante chez S. cerevisiae.Dans un premier temps, nous avons identifié une phosphorylation sur une thréonine conservée située dans le domaine catalytique de Sen1 et nous avons montré que cette phosphorylation réduit la capacité de liaison de Sen1 à l’ARN et par conséquent affecte la terminaison de la transcription non-codante. Par la suite, nous avons réalisé des analyses transcriptomiques à haute résolution et montré que cette phosphorylation conduit à la répression de l’expression de ZAP1 codant pour le régulateur central de la réponse au zinc par interférence transcriptionnelle via un ARN non-codant que nous avons baptisé ZRN1(Zap1 Repressor Non-coding gene 1). En plus, de nombreux gènes supplémentaires présentent un profil d’expression imitant les conditions d’excès de zinc où l’expression de ZAP1 est naturellement réprimée, suggérant que la phosphorylation de Sen1 pourrait participer à la régulation de l’expression des gènes impliqués dans l’homéostasie du zinc. Dans un second temps, en collaboration avec le laboratoire de F. Posas (IRB, Barcelone, Espagne), nous avons identifié des résidus de Sen1 qui peuvent être phosphorylés in vitropar la MAP kinase Hog1, un régulateur clé de la réponse au stress osmotique. Nous avons réalisé des analyses transcriptomiques et montré que certains gènes non-codants cibles de Sen1 sont affectés dans la terminaison de la transcription en condition de stress osmotique. Ces défauts de terminaison sont parfois accompagnés de la répression des gènes en aval ouen antisens et donc, pourraient potentiellement être impliqués dans la régulation de ces gènes en réponse au stress. Nos analyses protéomiques ont indiqué une diminution de l’interaction de Sen1 avec le complexe « Mediator » dans la même condition. Ces résultats nous permettent d’imaginer que les défauts de terminaison en condition de stress osmotique pourraient être provoqués par une diminution de l’efficacité de recrutement de Sen1 par le complexe médiateur. Ces résultats bien que préliminaires, pourraient suggérer l’implication de Sen1 dans la régulation de l’expression des gènes dans la réponse au stress osmotique. Enfin, nous avons analysé le rôle de l’interaction Sen1 avec la phosphatase Glc7, une protéine impliquée dans la terminaison de la transcription de certains gènes non-codants. Nous avons délété le motif d’interaction de Glc7 dans la protéine Sen1 et montré que cette interaction semble être importante pour la terminaison d’un nombre très restreint d’ARN non-codants. Nous avons ensuite montré que la perte de l’interaction de Sen1 avec Glc7 est associée à une augmentation de son interaction avec Nrd1 et Nab3, deux protéines qui interagissent aussi bien avec Sen1 qu’avec les ARN cibles de Sen1. Ces données suggèrent que Glc7 pourrait participer au relâchement de Sen1 de Nrd1 et Nab3 au niveau de certainsPervasive transcription is a universal phenomenon that leads to the production of amultitude of non-coding RNAs. If left uncontrolled, pervasive transcription can bepotentially deleterious for normal gene expression. However, non-coding transcription canalso play important regulatory roles, for instance by promoting the repression of specificgenes by a mechanism of transcriptional interference. The efficiency of transcriptiontermination can strongly influence the regulatory capacity of non-coding transcriptionevents, yet very little is known about the mechanisms modulating the termination of non-coding transcription in response to environmental cues.During my PhD I have addressed this question by investigating the mechanisms thatregulate the activity of the main actor in termination of non-coding transcription in S.cerevisiae, the helicase Sen1. We have identified a phosphorylation at a conservedthreonine of the catalytic domain of Sen1 and we have shown that this phosphorylationreduces the efficiency of Sen1-mediated termination by interfering with Sen1 interactionwith the RNA. Interestingly, we have found that this phosphorylation impairs terminationat an unannotated non-coding gene just upstream of the gene encoding the masterregulator of Zn homeostasis, Zap1, and thus, repression of ZAP1 expression bytranscriptional interference. We have named this non-coding gene ZRN1 for Zap1Repressor Non-coding gene 1. Furthermore, we have found that many additional genesexhibit an expression pattern mimicking conditions of Zn excess, where ZAP1 is naturallyrepressed. Taken together, our results support the idea that Sen1 phosphorylation couldbe involved in the regulation of the expression of genes involved in zinc homeostasis. In parallel, in collaboration with the laboratory of F. Posas (IRB, Barcelona, Spain), wehave identified several residues that can be phosphorylated in vitro by the MPK Hog1, themaster regulator of the osmotic stress response. We have performed high-resolutiontranscriptomic analyses and we have shown that certain Sen1-dependent non-codinggenes exhibit impaired transcription termination under osmotic stress. Interestingly, insome cases these termination defects occur concomitantly with the repression ofdownstream or antisense protein-coding genes, suggesting a possible implication in theregulation of these genes in response to stress. Our proteomic analyses indicated adecrease in the interaction of Sen1 with the mediator complex in the same conditions.These results suggest that the termination defects observed under osmotic stress mightbe due to a decrease in the recruitment of Sen1 by the mediator complex. Thesepreliminary data suggest a possible role for Sen1 in the regulation of gene expression inthe response to osmotic stress. Finally, we analyzed the role of the interaction of Sen1 with the Glc7 phosphatase, an essential protein that has previously been implicated in transcription termination at a subset of non-coding genes. We have deleted the Glc7 interaction motif in Sen1 and we have shown that this interaction is important for transcription termination at a small subset of non-coding genes. In addition, we have shown that the loss of Sen1 interaction with Glc7 is associated with an increase in the interaction with of Sen1 with Nrd1 and Nab3, two proteins that interact with both Sen1 and Sen1 target RNAs. These data suggest that Glc7 may modestly participate in the release of Sen1 from Nrd1 and Nab3 tothe RNA, which might allow more efficient transcription termination by Sen1 in some cases
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Gangadharaiah, Dayananda Sagar. "PATTERNS OF DIPEPTIDE USAGE FOR GENE PREDICTION." Wright State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=wright1279304144.
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Asghar, Naveed. "Ticks and Tick-borne Encephalitis Virus : From Nature to Infection." Doctoral thesis, Södertörns högskola, Miljövetenskap, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-31153.
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Vector-borne diseases are an increasing global threat to humans due to climate changes, elevating the risk of infections transmitted by mosquitos, ticks, and other arthropod vectors. Ixodes ricinus, a common tick in Europe, transmits dangerous tick-borne pathogens to humans. Tick-borne encephalitis (TBE) is a vector-borne disease caused by TBE virus (TBEV). Climate change has contributed to increased tick abundance and incidence of tick-borne diseases, and between 10,000 and 15,000 human TBE cases are reported annually in Europe and Asia. TBEV shows a patchy geographical distribution pattern where each patch represents a natural focus. In nature, TBEV is maintained within the tick-rodent enzootic cycle. Co-feeding is the main route for TBEV transmission from infected to uninfected ticks and for maintenance within the natural foci. The increasing number of TBE cases in Scandinavia highlights the importance of characterizing additional TBEV sequences and of identifying novel natural foci, and in this work we sequenced and phylogenetically characterized four TBEV strains: Saringe-2009 (from a blood-fed nymph), JP-296 (from a questing adult male), JP-554 (from a questing adult male), and Mandal-2009 (from a pool of questing nymphs, n = 10). Mandal-2009 represents a TBEV genome from a natural focus in southern Norway. Saringe-2009 is from a natural endemic focus in northern Stockholm, Sweden, and JP-296 and JP-554 originate from a natural focus “Torö” in southern Stockholm. In addition, we have studied the effect of different biotic and abiotic factors on population dynamics of I. ricinus in southern Stockholm and observed significant spatiotemporal variations in tick activity patterns. Seasonal synchrony of immature stages and total tick abundance are important factors for the probability of horizontal transmission of TBEV among co-feeding ticks. We found that the probability of co-occurrence of larvae, nymphs, and female adults was highest during early summer whereas increasing vegetation height and increasing amounts of forest and open water around the study sites had a significant negative effect on co-occurrence of larvae, nymphs, and female adults. The proximal part of the 3 ́non-coding region (3 ́NCR) of TBEV contains an internal poly(A) tract, and genomic analysis of Saringe-2009 revealed variability in the poly(A) tract indicating the existence of different variants within the TBEV pool of Saringe-2009. Like other RNA viruses, TBEV exists as swarms of unique variants called quasispecies. Because Saringe-2009 came from an engorged nymph that had been feeding on blood for >60 h, we propose that Saringe-2009 represents a putative shift in the TBEV pool when the virus switches from ectothermic/tick to endothermic/mammalian environments. We investigated the role of poly(A) tract variability in replication and virulence of TBEV by generating two infectious clones of the TBEV strain Toro-2003, one with a short/wild-type (A)3C(A)6 poly(A) tract and one with a long (A)3C(A)38 poly(A) tract. The infectious clone with the long poly(A) tract showed poor replication in cell culture but was more virulent in C57BL/6 mice than the wild-type clone. RNA folding predictions of the TBEV genomes suggested that insertion of a long poly(A) tract abolishes a stem loop structure at the beginning of the 3 ́NCR. Next generation sequencing (NGS) analysis of the TBEV genomes after passaging in cell culture and/or mouse brain revealed molecular determinants and quasispecies structure that might contribute to the observed differences in virulence. Our findings suggest that the long poly(A) tract imparts instability to the TBEV genome resulting in higher quasispecies diversity that in turn contributes to TBEV virulence. Phylogenetic analysis of Saringe-2009, JP-296, JP-554, and Mandal-2009 predicted a strong evolutionary relationship among the four strains. They clustered with Toro-2003, the first TBEV strain from Torö, demonstrating a Scandinavian clade. Except for the proximal part of the 3 ́NCR, TBEV is highly conserved in its genomic structure. Genomic analysis revealed that Mandal-2009 contains a truncated 3 ́NCR similar to the highly virulent strain Hypr, whereas JP-296 and JP-554 have a genomic organization identical to Toro-2003, the prototypic TBEV strain from the same natural focus. NGS revealed significantly higher quasispecies diversity for JP-296 and JP-554 compared to Mandal-2009. In addition, single nucleotide polymerphism (SNP) analysis showed that 40% of the SNPs were common between quasispecies populations of JP-296 and JP-554, indicating the persistence and maintenance of TBEV quasispecies within the natural focus. Taken together, these findings indicate the importance of environmental factors for the occurrence pattern of the different life-stages of the tick vector, which are important for the persistence of TBEV in nature. Our findings also show that the selection pressure exerted by specific host also affects the population structure of the TBEV quasispecies. In addition, our results further demonstrate that the evolution of quasispecies has effect on TBEV virulence in mice.Vektorburna sjukdomar är ett växande globalt hot mot både människor och djur. De pågående klimatförändringarna kan leda till förhöjda risker för infektioner överförda av myggor, fästingar och andra leddjursvektorer. Ixodes ricinus är en vanlig fästing i Europa som överför fästingburna patogener som är farliga för människor. Fästingburen encefalit (TBE) är en vektorburen sjukdom som orsakas av TBE-virus (TBEV). De pågående klimatförändringarna har bidragit till en ökning både av vektorn och sjukdomsfrekvensen. Mellan 10 000 och 15 000 mänskliga TBE-fall rapporteras årligen i Europa och Asien. Den geografiska fördelningen av TBEV visar ett ojämnt fördelningsmönster där viruset är koncentrerat till vissa fokusområden. TBEV återfinns i naturen i en livscykel där viruset hela tiden överförs mellan fästingar och däggdjur. Spridningen sker dels från en infekterad fästing till ett ryggradsdjur när fästingen äter på värddjuret. Spridning mellan fästingar sker troligen främst genom så kallad “co-feeding”, det vill säga att flera fästingar suger blod samtidigt från samma värddjur. Viruset kan då passera från en infekterad fästing, genom värddjuret till oinfekterade fästingar. Virus kan identifieras och studeras med genetiska metoder. Det ökande antalet TBE-fall i Skandinavien styrker vikten av att hitta och karakterisera ytterligare TBEV-stammar och identifiera nya naturliga fokusområden. Vi har sekvenserat och fylogenetiskt beskrivit fyra TBEV-stammar: Saringe-2009 (blodfylld nymf), JP-296 (födosökande vuxen hane), JP-554 (födosökande vuxen hane) och Mandal-2009 (födosökande nymfer, n = 10). Mandal-2009 är ett TBEV från ett naturligt fokusområde i södra Norge. Saringe-2009 kommer från ett naturligt fokusområde i norra Stockholms län, Sverige. JP-296 och JP-554 härstammar från Torö som är ett naturligt fokusområde i södra Stockholms län, Sverige. Förutom den genetiska sekvenseringen av TBEV har vi också studerat effekten av olika biotiska och abiotiska faktorer på populationsdynamik av I. ricinus i södra Stockholm och observerade variation i fästingsaktivitetsmönster både temporalt och spatialt. Förekomstmönster av fästinglarver, nymfer och vuxna honor, och det totala antalet fästingar är viktiga faktorer för sannolikheten för horisontell överföring av TBEV mellan fästingar. Vi fann att sannolikheten för synkron förekomst av larver, nymfer och honor var högst under försommaren. Vegetationshöjd, mängden skog och mängd öppet vatten runt undersökningsområden hade signifikanta negativa effekter på sannolikheten för att larver, nymfer och honor skulle förekomma samtidigt. Den variabla delen av den icke-kodande 3 ́regionen (3'NCR) av TBEV-genomet innehåller ofta en intern poly(A)-sekvens. Liksom andra RNA-virus, förekommer TBEV som så kallade ”quasispecies” vilka definieras som grupper av olika genetiska varianter av virus. Genom analysen av TBEV-stam Saringe-2009 avslöjades variation i poly(A)-sekvensen vilket indikerar förekomst av ”quasispecies”. Eftersom Saringe-2009 kom från en blodfylld nymf som hade sugit blod i > 60 timmar, föreslår vi att Saringe-2009 visar en förändring i ”quasispecies”-poolen när viruset överförs från exoterm fästingmiljö till endoterm däggdjursmiljö. Vi undersökte poly(A)-ekvensens variabilitet och dess roll vid replikering och för virulens hos TBEV, genom att skapa två infektiösa kloner av Torö-2003 stammen; en med en kort/vild-typ (A)3C(A)6 poly(A)-sekkvens, och en med en lång (A)3C(A)38 poly(A)-sekvens. Den infektiösa klonen med lång poly(A)-sekvens replikerade sämre än vildtypklonen i cellkultur, men (A)3C(A)38 poly(A) var mer virulent i C57BL/6-möss än (A)3C(A)6 poly(A). Datasimulering av TBEV-genomets sekundär-RNA-struktur visade att de längre poly(A)-sekvenserna påverkar veckningen av en specifik sekundärstruktur (SL14) i början av 3 ́NCR. Djupsekvenseringsanalys av TBEV-gnomen avslöjade skillnader för specifika gener och ”quasispecies”-strukturen efter passering i cellkultur och/eller mushjärna. Dessa förändringar föreslås bidra till de observerade skillnaderna i virulens. Våra resultat indikerar att den långa poly(A)-sekvensen ger instabilitet i TBEV-genomet, vilket resulterar i ökad mångfald av ”quasispecies”-populationen som i sin tur kan bidra till TBEV-virulens. Fylogenetisk analys av Saringe-2009, JP-296, JP-554 och Mandal-2009 visade på ett nära släktskap mellan de fyra skandinaviska TBEV-stammarna. De nya stammarna formerade ett kluster med en tidigare TBEV-stam identifierad på Torö (Toro-2003), vilket skapade ett skandinaviskt klad. Genetisk analys visade att Mandal-2009 innehåller en trunkerad 3 ́NCR som liknar den högvirulenta stammen HYPR. JP-296 och JP-554 hade däremot samma genetiska struktur som den längre Torö-2003 stammen från samma fokusområde. Djupsekvensering visade höge mångfald av ”quasispecies”-populationen för JP-296 och JP- 554 jämfört med Mandal-2009. Analys av enkel nukleotid polymorfism (SNP) visade att 40 % av alla SNP var gemensamma mellan ”quasispecies”-populationen för JP-296 och JP-554. Detta indikerar att TBEV-”quasispecies”-strukturen kan vara konserverad för närbesläktade virus vilken kan leda till att den bevaras inom specifika fokusområden. Sammantaget så visar dessa studier att miljöfaktorer påverkar förekomsten av fästingvektorn och dess olika livsstadier, vilket är en bakomliggande faktor för utbredning av TBEV i naturliga fokusområden. Det visar även på att värdmiljön påverkar strukturen för ”quasispecies”-populationen. Dessutom visar våra studier att evolution och utveckling av ”quasispecies”-strukturen kan påverka virulensen för TBEV i möss.
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Fatani, Imade Fahd Eddine. "Contribution à l’étude de l’optimisation conjointe source-canal d’une transmission vidéo dans un contexte MIMO sans fil : application à la vidéosurveillance embarquée pour les transports publics." Valenciennes, 2010. http://ged.univ-valenciennes.fr/nuxeo/site/esupversions/f1e3d785-7cbb-4d39-86d8-eec5433f62a0.
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Les applications de vidéosurveillance pour les transports publics s’appuient sur des systèmes de communication sans fil qui requièrent des débits élevés entre les véhicules et le sol et des critères de qualité de service élevés. Afin de répondre à ces contraintes, dans ce travail nous avons proposé de tenir compte à la fois des paramètres de transmission et de d’encodage vidéo en combinant les techniques de codage MDC (Multiple Description Coding) et de codage par zone d'intérêt (ROI, Region Of Interest) avec différentes schémas MIMO (Mulitple Input Multiple Output) sur la base de la couche PHY du standard Wifi IEEE802. 11n dans un environnement de type métro (tunnel). Dans un premier temps, nous avons montré qu'il est possible d'améliorer les performances d'un système MIMO en optimisant l'allocation des bits et des puissances indépendamment de l'information à transmettre. Nous proposons deux approches aboutissant à la répartition optimale des ressources qui permettent d'atteindre un ordre de diversité maximal et offrent de meilleures performances que le précodeur max-SNR dans le cas d’un canal corrélé ou non. Nous montrons ensuite que l’association d’un codage MDC avec des schémas MIMO constitue une stratégie intéressante afin d’adapter le contenu vidéo à la structure multi-antennes, en particulier lorsqu’aucune connaissance de l’état du canal n’est pas disponible en émission. En outre, il est possible d'améliorer les performances en utilisant un lien retour à faible débit grâce aux techniques OSM (Orthogonalized Spatial Multiplexing) et à l’OSM précodé. Enfin, dans le cas où la connaissance du canal à l’émission est parfaite, pour un lien retour offrant un débit suffisant, nous avons associé les techniques MIMO et un mécanisme de codage vidéo hiérarchique qui consiste en la séparation de la scène en régions d'intérêt. Le flux correspondant à la zone d’intérêt maximal est transmis sur le canal propre de plus grand gain. Ceci permet d'assurer une meilleure robustesse de transmission et garantit ainsi un niveau acceptable pour la QoS perçue par le centre de contrôle. La création des différentes régions d’intérêt s’appuie sur l’outil FMO (Flexible Macroblock Ordering) introduit dans le nouveau standard de compression H. 264/AVC. Ainsi, les différents schémas de transmission proposés permettent d’accroître la qualité de service d’un flux vidéo sans augmenter la puissance émise ni multiplier le nombre de points d’accès radio de l’infrastructureVideo monitoring applications in the Public Transport field rely on wireless telecommunication systems which require high data rate between vehicles and the ground and high Quality of Service (QoS). In order to satisfy these constraints we have proposed to take into account both transmission parameters and video coding by combining Multiple Description Coding (MDC) and Region Of Interest coding with different MIMO (Mulitple Input Multiple Output) schemes on the basis of the PHY layer of IEEE802. 11n Wifi standard in a metro environment (tunnel). First, we have shown that it is possible to increase the performance of a MIMO system by optimizing bits and power allocation independently of the type of information to be transmitted. Two approaches are proposed. They lead to an optimal repartition of resources, reach maximal diversity order and they outperform the max-SNR precoder performances. Secondly, the association of MDC with MIMO schemes is introduced to adapt the video content to the multi antenna structure particularly when the channel knowledge is not available at transmitter side. Furthermore, the performances can be enhanced using a low data rate return link and considering the Orthogonalized Spatial Multiplexing (OSM) and the precoded OSM. When perfect channel information is available at transmitter side thanks to a high data rate return link, MIMO schemes are associated with hierarchic video coding consisting in the separation of regions of interest in the scene. The stream associated to the area with the maximal interest is transmitted on the eigen channel with the higher gain. This strategy allows to guaranty better robustness and acceptable QoS of the video streams observed in the control-center. The creation of the different regions of interest is based on the Flexible Macroblock Ordering (FMO) technique introduced in the new compression standard H. 264/AVC. We have shown the interest of the different transmission schemes proposed in order to enhance the QoS of a video stream with no increase of the transmitted power and of the number of radio access points along the infrastructure
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Beka, Sylvia Enobong. "The genomics of Type 1 Diabetes susceptibility regions and effect of regulatory SNPs." Thesis, University of Hertfordshire, 2016. http://hdl.handle.net/2299/17200.
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Human complex diseases, like Diabetes and Cancer, affect many people worldwide today. Despite existing knowledge, many of these diseases are still not preventable. Complex diseases are known to be caused by a combination of genetic factors, as well as environmental and life style factors. The scope of this investigation covered the genomics of Type 1 Diabetes (T1D). There are 49 human genomic regions that are known to carry markers (disease-associated single nucleotide mutations) for T1D, and these were extensively studied in this research. The aim was to find out in how far this disease may be caused by problems in gene regulation rather than in gene coding. For this, the genetic factors associated with T1D, including the single point mutations and susceptibility regions, were characterised on the basis of their genomic attributes. Furthermore, mutations that occur in binding sites for transcription factors were analysed for change in the conspicuousness of their binding region, caused by allele substitution. This is called SNP (Single nucleotide polymorphism) sensitivity. From this study, it was found that the markers for T1D are mostly non-coding SNPs that occur in introns and non-coding gene transcripts, these are structures known to be involved in gene regulatory activity. It was also discovered that the T1D susceptibility regions contain an abundance of intronic, non-coding transcript and regulatory nucleotides, and that they can be split into three distinct groups on the basis of their structural and functional genomic contents. Finally, using an algorithm designed for this study, thirty-seven SNPs that change the representation of their surrounding region were identified. These regulatory mutations are non-associated T1D-SNPs that are mostly characterised by Cytosine to Thymine (C-T) transition mutations. They were found to be closer in average distance to the disease-associated SNPs than other SNPs in binding sites, and also to occur frequently in the binding motifs for the USF (Upstream stimulatory factor) protein family which is linked to problems in Type 2 diabetes.
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Mayhew, Michael. "Coding regions under non-coding selection: implications for transcriptional and post-transcriptional gene regulation." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=21995.
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The signals that facilitate transcriptional and post-transcriptional gene expression regulation are still being understood. Comparative genomics approaches based on the premise that sequence or structure conservation implies functionality have successfully distinguished true regulatory sequences and structures from prediction noise. Protein-coding regions of genes have often been overlooked as potential regulatory sequence regions. A set of 8785 coding region sequences were previously found to be conserved significantly above a baseline protein-coding conservation level. We call these sequences coding regions under non-coding selection or CRUNCS. Analysis of the sequences, the primary contribution of this work, revealed that CRUNCS bases are more often found in coding exon edges and in middle coding exons. CRUNCS-containing genes are more significantly enriched for regulation of transcription and translation, protein ubiquitination, and mRNA processing. CRUNCS are significantly enriched for RNA secondary structure elements. We also uncovered statistical evidence linking CRUNCS to gene splicing regulation.Les méthodes de génomique comparatives qui sont tirées de la prémisse que la conservation de la séquence ou de la structure implique la conservation de la fonctionnalité, sont parvenues à identifier de vrais signaux régulateurs. Les régions codantes ont souvent été négligées comme des régions potentiellement régulatrices. Un ensemble de 8785 séquences de ces régions plus conservées que prévues a été précédement identifié. L'analyse de ces séquences appelées CRUNCS a révélé que les acides nucléiques des CRUNCS sont plus nombreux aux extrémités des exons et dans les exons centraux. Les gènes contenants des CRUNCS sont enrichis des catégories fonctionnelles comprenant : la régulation de la transcription et la traduction, l'ubiquitination des protéines et le traitement des ARNm. Les CRUNCS sont enrichis d'éléments de structure secondaire de l'ARN. Nous avons aussi découvert des preuves statistiques démontrant que les CRUNCS jouent un rôle dans la régulation de l'épissage des gènes.
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USUI, Shin'ichi, Masayuki TANIMOTO, Toshiaki FUJII, Tadahiko KIMOTO, and Hiroshi OHYAMA. "Fractal Image Coding Based on Classified Range Regions." Institute of Electronics, Information and Communication Engineers, 1998. http://hdl.handle.net/2237/14996.
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Leung, Raymond Electrical Engineering & Telecommunications Faculty of Engineering UNSW. "Scalable video compression with optimized visual performance and random accessibility." Awarded by:University of New South Wales. Electrical Engineering and Telecommunications, 2006. http://handle.unsw.edu.au/1959.4/24192.
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This thesis is concerned with maximizing the coding efficiency, random accessibility and visual performance of scalable compressed video. The unifying theme behind this work is the use of finely embedded localized coding structures, which govern the extent to which these goals may be jointly achieved. The first part focuses on scalable volumetric image compression. We investigate 3D transform and coding techniques which exploit inter-slice statistical redundancies without compromising slice accessibility. Our study shows that the motion-compensated temporal discrete wavelet transform (MC-TDWT) practically achieves an upper bound to the compression efficiency of slice transforms. From a video coding perspective, we find that most of the coding gain is attributed to offsetting the learning penalty in adaptive arithmetic coding through 3D code-block extension, rather than inter-frame context modelling. The second aspect of this thesis examines random accessibility. Accessibility refers to the ease with which a region of interest is accessed (subband samples needed for reconstruction are retrieved) from a compressed video bitstream, subject to spatiotemporal code-block constraints. We investigate the fundamental implications of motion compensation for random access efficiency and the compression performance of scalable interactive video. We demonstrate that inclusion of motion compensation operators within the lifting steps of a temporal subband transform incurs a random access penalty which depends on the characteristics of the motion field. The final aspect of this thesis aims to minimize the perceptual impact of visible distortion in scalable reconstructed video. We present a visual optimization strategy based on distortion scaling which raises the distortion-length slope of perceptually significant samples. This alters the codestream embedding order during post-compression rate-distortion optimization, thus allowing visually sensitive sites to be encoded with higher fidelity at a given bit-rate. For visual sensitivity analysis, we propose a contrast perception model that incorporates an adaptive masking slope. This versatile feature provides a context which models perceptual significance. It enables scene structures that otherwise suffer significant degradation to be preserved at lower bit-rates. The novelty in our approach derives from a set of "perceptual mappings" which account for quantization noise shaping effects induced by motion-compensated temporal synthesis. The proposed technique reduces wavelet compression artefacts and improves the perceptual quality of video.
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Nordholm, Johan. "NA transmembrane domain : Amphiphilic drift to accommodate two functions." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-142051.
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Neuraminidase (NA) is one of two major antigens on the surface of influenza A viruses. It is comprised of a single N-terminal transmembrane domain (TMD), a stalk domain, and a C-terminal enzymatic head domain that cleaves sialic acid, most notably to release new particles from the host cell surface. NA is only enzymatically active as a homo-tetramer. However, it is not known which properties facilitate the oligomerization of NA during assembly. Our results show that, apart from anchoring the protein to the membrane, the NA TMD also contributes to the assembly process by keeping the stalk in a tetrameric conformation. The ability of the TMD to oligomerize is shown to be dependent on its amphiphilic characteristics that was largely conserved across the nine NA subtypes (N1-N9). Over time the NA TMDs in human H1N1 viruses were found to have become more amphiphilic, which correlated with stronger oligomerization. An old H1N1 virus with a more recent N1 TMD had impaired growth, but readily acquired compensatory mutations in the TMD to restore growth, by reverting the TMD oligomerization strength back to that of the old TMD, demonstrating a biological role of the TMD in folding and assembly. NA and the other viral proteins are spatially and temporally coordinated to achieve optimal viral production. By using a co-transfection analysis, the high AU-content in the NA and HA ER-targeting sequence coding regions (for NA TMD as well as the HA signal sequence) were found to inhibit their expression. The inhibition was alleviated by the early expressed influenza RNA-binding protein NS1, which promoted translation and showed enriched foci at the endoplasmic reticulum (ER). NS1, which expresses early during infection, is therefore likely the regulator of NA and HA to prevent premature expression. These results show that the NA TMD is under substantial selection pressure at both the nucleotide and amino acid level to accommodate its roles in ER-targeting, protein folding, and post-transcriptional regulation.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Accepted.
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Kim, Anthony Eli. "On network coding capacity : matroidal networks and network capacity regions." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/62657.
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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 68-70).
One fundamental problem in the field of network coding is to determine the network coding capacity of networks under various network coding schemes. In this thesis, we address the problem with two approaches: matroidal networks and capacity regions. In our matroidal approach, we prove the converse of the theorem which states that, if a network is scalar-linearly solvable then it is a matroidal network associated with a representable matroid over a finite field. As a consequence, we obtain a correspondence between scalar-linearly solvable networks and representable matroids over finite fields in the framework of matroidal networks. We prove a theorem about the scalar-linear solvability of networks and field characteristics. We provide a method for generating scalar-linearly solvable networks that are potentially different from the networks that we already know are scalar-linearly solvable. In our capacity region approach, we define a multi-dimensional object, called the network capacity region, associated with networks that is analogous to the rate regions in information theory. For the network routing capacity region, we show that the region is a computable rational polytope and provide exact algorithms and approximation heuristics for computing the region. For the network linear coding capacity region, we construct a computable rational polytope, with respect to a given finite field, that inner bounds the linear coding capacity region and provide exact algorithms and approximation heuristics for computing the polytope. The exact algorithms and approximation heuristics we present are not polynomial time schemes and may depend on the output size.
by Anthony Eli Kim.
M.Eng.
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Silva, Cauane Blumenberg. "Adaptive tiling algorithm based on highly correlated picture regions for the HEVC standard." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2014. http://hdl.handle.net/10183/96040.
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Esta dissertação de mestrado propõe um algoritmo adaptativo que é capaz de dinamicamente definir partições tile para quadros intra- e inter-preditos com o objetivo de reduzir o impacto na eficiência de codificação. Tiles são novas ferramentas orientadas ao paralelismo que integram o padrão de codificação de vídeos de alta eficiência (HEVC – High Efficiency Video Coding standard), as quais dividem o quadro em regiões retangulares independentes que podem ser processadas paralelamente. Para viabilizar o paralelismo, os tiles quebram as dependências de codificação através de suas bordas, gerando impactos na eficiência de codificação. Este impacto pode ser ainda maior caso os limites dos tiles dividam regiões altamente correlacionadas do quadro, porque a maior parte das ferramentas de codificação usam informações de contexto durante o processo de codificação. Assim, o algoritmo proposto agrupa as regiões do quadro que são altamente correlacionadas dentro de um mesmo tile para reduzir o impacto na eficiência de codificação que é inerente ao uso de tiles. Para localizar as regiões altamente correlacionadas do quadro de uma maneira inteligente, as características da imagem e também as informações de codificação são analisadas, gerando mapas de particionamento que servem como parâmetro de entrada para o algoritmo. Baseado nesses mapas, o algoritmo localiza as quebras naturais de contexto presentes nos quadros do vídeo e define os limites dos tiles nessas regiões. Dessa maneira, as quebras de dependência causadas pelas bordas dos tiles coincidem com as quebras de contexto naturais do quadro, minimizando as perdas na eficiência de codificação causadas pelo uso dos tiles. O algoritmo proposto é capaz de reduzir mais de 0.4% e mais de 0.5% o impacto na eficiência de codificação causado pelos tiles em quadros intra-preditos e inter-preditos, respectivamente, quando comparado com tiles uniformes.This Master Thesis proposes an adaptive algorithm that is able to dynamically choose suitable tile partitions for intra- and inter-predicted frames in order to reduce the impact on coding efficiency arising from such partitioning. Tiles are novel parallelismoriented tools that integrate the High Efficiency Video Coding (HEVC) standard, which divide the frame into independent rectangular regions that can be processed in parallel. To enable the parallelism, tiles break the coding dependencies across their boundaries leading to coding efficiency impacts. These impacts can be even higher if tile boundaries split highly correlated picture regions, because most of the coding tools use context information during the encoding process. Hence, the proposed algorithm clusters the highly correlated picture regions inside the same tile to reduce the inherent coding efficiency impact of using tiles. To wisely locate the highly correlated picture regions, image characteristics and encoding information are analyzed, generating partitioning maps that serve as the algorithm input. Based on these maps, the algorithm locates the natural context break of the picture and defines the tile boundaries on these key regions. This way, the dependency breaks caused by the tile boundaries match the natural context breaks of a picture, then minimizing the coding efficiency losses caused by the use of tiles. The proposed adaptive tiling algorithm, in some cases, provides over 0.4% and over 0.5% of BD-rate savings for intra- and inter-predicted frames respectively, when compared to uniform-spaced tiles, an approach which does not consider the picture context to define the tile partitions.
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Casas, Pla Josep Ramon. "Image Compression based on Perceptual Coding Techniques." Doctoral thesis, Universitat Politècnica de Catalunya, 1996. http://hdl.handle.net/10803/6920.
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En aquesta tesi s'estudien els mètodes de codificació d'imatges i seqüències de vídeo des del punt de vista de la forma en què el sistema visual humà percep i entén la informació visual. La rellevància d'aquest estudi ve donada pel paper tan important que tenen els senyals d'imatge en la civilització actual i pel gran volum de dades que representen les fonts d'informació visual pels sistemes que les han de processar. S'han estudiat tres aproximacions per a la codificació de textures en un esquema avançat de compressió fonamentat en aspectes de percepció visual. La primera aproximació es basa en les transicions de la imatge i estudia la interpolació d'àrees suaus a partir de les esmentades transicions. La segona contempla l'extracció, selecció i codificació de detalls significatius per al sistema visual humà.
Finalment, la tercera aproximació estudia la representació eficient de les textures fines i homogènies, que donen una aparença natural a les imatges sintetitzades aconseguint elevades tasses de compressió. Per a l'aplicació d'aquestes tècniques a la codificació d'imatge i vídeo, es proposa un model d'imatge de tres components adaptat a les característiques perceptuals de la visió humana.
Les aproximacions de codificació objecte de l'estudi han portat al disseny de tècniques noves d'anàlisi i codificació d'imatge. A partir d'eines no lineals de tractament obtingudes de l'entorn de la Morfologia Matemàtica, s'han desenvolupat tres tècniques de codificació de textures. En concret,
- Un mètode d'interpolació "morfològica" orientat a la resolució del problema d'interpolació de senyals bidimensionals a partir de conjunts arbitraris de punts dispersos.
- S'ha introduït de manera experimental un criteri subjectiu empíric per a la ordenació i selecció de detalls en les imatges, segons un criteri perceptual.
- Finalment, s'ha investigat l'aplicació d'una tècnica clàssica, la codificació "subbanda", a l'interior de regions de forma arbitrària, resultant en un nou mètode de codificació de textures anomenat "Region-based subband coding".
Aquestes tècniques han estat innovadores en el camp de codificació d'imatge entre les anomenades tècniques orientades a objectes o de Segona Generació. Tanmateix, el model d'imatge estudiat, es troba en la línia de les últimes propostes en l'entorn de l'MPEG4, el futur estàndard per a comunicació d'imatge a baixa velocitat, que contempla la possibilitat de la manipulació de continguts.
This thesis studies image and video sequence coding methods from the point of view of the way the human visual system perceives and understands visual information. The relevance of such study is due, on the one hand, to the important role that visual signals have in our civilization and, on the other hand, to the problem of representing the large amount of data that image and video processing systems have to deal with.
Three different approaches have been investigated for the coding of image textures in an advanced compression scheme relying in aspects of visual perception. The first approach is based on image transitions and the interpolation of smooth areas from such transitions. The second one, considers the extraction, selection and coding of meaningful image details.
Finally, the third approach studies the efficient representation of homogeneous fine textures that give a natural appearance to the reconstructed images at high compression levels. In order to apply these techniques for still image and video coding, a three component model of the image, that matches the perceptual properties of the human vision, is put forward.
The coding approaches subject of research have leaded to the design of three new image analysis and coding techniques. Using non-linear tools from the framework of Mathematical Morphology, three texture coding techniques are developed. In particular,
- A "morphological" image interpolation method aimed at the problem of scattered data interpolation.
- An empirical subjective criterion for the ranking and selection of image details according to visual perception.
- The application of a conventional image coding technique, subband coding, to the coding of arbitrarily shaped image regions (region-based subband coding).
These are new texture coding techniques in the field of object-oriented and Second Generation image and video coding schemes. Furthermore, the model of the image that has been investigated follows the line of the last proposals in the framework of MPEG4, the forthcoming coding standard for low bit-rate visual communications, which considers the possibility of content-based manipulation and coding of visual information.
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Konda, Jayashree. "Identification of protein coding regions in microbial genomes using unsupervised clustering." abstract and full text PDF (UNR users only), 2009. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1472961.
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Hector, Ralph David. "Investigation of non-protein-coding regions in the human cytomegalovirus genome." Thesis, University of Glasgow, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.425168.
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Chen, Hui 1974. "Algorithms and statistics for the detection of binding sites in coding regions." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=97926.
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This thesis deals with the problem of detecting binding sites in coding regions. A new comparative analysis method is developed by improving an existing method called COSMO.The inter-species sequence conservation observed in coding regions may be the result of two types of selective pressure: the selective pressure on the protein encoded and, sometimes, the selective pressure on the binding sites. To predict some region in coding regions as a binding site, one needs to make sure that the conservation observed in this region is not due to the selective pressure on the protein encoded. To achieve this, COSMO built a null model with only the selective pressure on the protein encoded and computed p-values for the observed conservation scores, conditional on the fixed set of amino acids observed at the leaves.
It is believed, however, that the selective pressure on the protein assumed in COSMO is overly strong. Consequently, some interesting regions may be left undetected. In this thesis, a new method, COSMO-2, is developed to relax this assumption.
The amino acids are first classified into a fixed number of overlapping functional classes by applying an expectation maximization algorithm on a protein database. Two probabilities for each gene position are then calculated: (i) the probability of observing a certain degree of conservation in the orthologous sequences generated under each class in the null model (i.e. the p-value of the observed conservation under each class); and (ii) the probability that the codon column associated with that gene position belongs to each class. The p-value of the observed conservation for each gene position is the sum of the products of the two probabilities for all classes. Regions with low p-values are identified as potential binding sites.
Five sets of orthologous genes are analyzed using COSMO-2. The results show that COSMO-2 can detect the interesting regions identified by COSMO and can detect more interesting regions than COSMO in some cases.
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Schotsch, Birgit [Verfasser]. "Rateless coding in the finite length regime / Birgit Elke Schotsch." Aachen : Hochschulbibliothek der Rheinisch-Westfälischen Technischen Hochschule Aachen, 2014. http://d-nb.info/1059647885/34.
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Lomelin, David. "Using human genetic variation to predict functional elements in non-coding genomic regions." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2010. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3390057.
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Wiseman, J. "Relocalisation of β-globin coding sequences by myosin heavy chain and vimentin 3' untranslated regions." Thesis, University of Aberdeen, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318982.
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The presence of a localisation signal within the 3' untranslated regions of myosin heavy chain and vimentin messenger RNAs was investigated by studying mRNA distribution in myoblasts and fibroblasts which were transfected with β-globin and chimaeric β-globin-myosin and β-globin-vimentin gene constructs. In cells transfected with constructs containing either a fragment of the β-globin gene containing both coding and 3' untranslated sequences or the β-globin coding sequences alone, in situ hybridisation revealed that the mRNAs transcribed from these constructs were distributed throughout the cytoplasm without any evident localisation. In contrast, within cells transfected with constructs containing β-globin coding sequences linked to the myosin heavy chain or vimentin 3' untranslated sequences there was a strong perinuclear localisation of the chimaeric mRNAs. This indicated that loss of its 3' untranslated region does not affect distribution of β-globin mRNA whereas the 3' untranslated sequences of both myosin heavy chain and vimentin cause a relocalisation of β-globin mRNA. The ability of the myosin heavy chain 3' untranslated region to relocalise β-globin coding sequences was investigated in the more complex cellular environment of skeletal muscle by intra-muscular injection of β-globin and chimaeric β-globin-myosin constructs. In muscle injected with β-globin constructs in situ hybridisation revealed that mRNAs transcribed from these constructs were distributed throughout the muscle section with no apparent localisation.
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Riley, Alura. "Regulation of the X-linked Inhibitor of Apoptosis Protein (XIAP) expression through alternative non-coding regions." Thesis, University of Ottawa (Canada), 2009. http://hdl.handle.net/10393/28172.
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The X-linked Inhibitor of Apoptosis Protein (XIAP) counters diverse apoptotic pathways through inhibition of caspases. The levels of XIAP protein can be increased translationally in response to pathophysiological stress, elevating the apoptotic threshold of cells. Here, I have characterized two XIAP mRNA isoforms, which differ only in their 5' untranslated regions. When global translation is attenuated during pathophysiological stress, the translation of one XIAP mRNA isoform is dramatically increased through the action of an Internal Ribosome Entry Site (IRES). In contrast, the second XIAP mRNA isoform supports cap-dependent translation of Xiap, but does not contain a functional IRES element. The physiological relevance and contribution of the XIAP mRNA variants to XIAP protein levels have been examined using RNA Interference, in conjunction with a cellular stress model. The distinct translational activities of these two transcripts under cellular stress suggest a model for a dual mode of XIAP regulation, which may be a common mechanism.
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Strugnell, Tod Dwayne. "Effects of cyclin A2 non-coding regions on reporter gene translation during early development in Xenopus laevis." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq20855.pdf.
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Vural, Mehmet. "Achievable Coding Rates For Awgn And Block Fading Channels In The Finite Blocklength Regime." Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612348/index.pdf.
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In practice, a communication system works with finite blocklength codes because of the delay constraints and the information-theoretic bounds which are proposed for finite blocklength systems can be exploited to determine the performance of a designed system. In this thesis, achievable rates for given average error probabilities are considered for finite blocklength systems. Although classical bounds can be used to upper bound the error probability, these bounds require the optimization of auxiliary variables. In this work, a bound which is called the dependence testing (DT) bound that is free of any auxiliary variables is exploited. The DT bound is evaluated by introducing a normal approximation to the information density. Simulations carried out both for the Gaussian and discrete input alphabets show the proposed approximation enables very good prediction of the achievable rates. The proposed approximation is also used to calculate the average error probability for block fading channels. Simulations performed for Rayleigh block fading channels demonstrate that the total blocklength of the system in addition to the number of fading blocks should be accounted for especially when the number of fading blocks is large. A power allocation problem in block fading channels when the channel state information is available to the transmitting side is investigated in the final part of this work. The DT bound is optimized for a given channel state vector by allocating different power levels to each fading block by exploiting short-term power allocation. A simple power allocation algorithm is proposed which comes out with very similar results compared with the analytically computed values.
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Nilsson, Martina. "Mitochondrial DNA in Sensitive Forensic Analysis." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7458.
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McIninch, James David. "Prediction of protein coding regions in unannotated DNA sequences using an inhomogeneous Markov model of genetic information encoding." Diss., Georgia Institute of Technology, 1997. http://hdl.handle.net/1853/25224.
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Uslu, Veli Vural [Verfasser], and Joachim [Akademischer Betreuer] Wittbrodt. "Functions of the Distant Non-Coding Regions in Controlling c-Myc Expression / Veli Vural Uslu ; Betreuer: Joachim Wittbrodt." Heidelberg : Universitätsbibliothek Heidelberg, 2014. http://d-nb.info/1180299841/34.
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