16 research outputs found

    A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction

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    RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods

    The Being of Analogy

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    Similarity has long been excluded from reality in both the analytical and continental traditions. Because it exists in the aesthetic realm, and because aesthetics is thought to be divorced from objective reality, similarity has been confined to the prison of the subject. In The Being of Analogy, Noah Roderick unleashes similarity onto the world of objects. Inspired by object-oriented theories of causality, Roderick argues that similarity is ever present at the birth of new objects. This includes the emergent similarity of new mental objects, such as categories—a phenomenon we recognize as analogy. Analogy, Roderick contends, is at the very heart of cognition and communication, and it is through analogy that we can begin dismantling the impossible wall between knowing and being

    The Marvelous World of tRNAs: From Accurate Mapping to Chemical Modifications

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    Since the discovery of transfer RNAs (tRNAs) as decoders of the genetic code, life science has transformed. Particularly, as soon as the importance of tRNAs in protein synthesis has been established, researchers recognized that the functionality of tRNAs in cellular regulation exceeds beyond this paradigm. A strong impetus for these discoveries came from advances in large-scale RNA sequencing (RNA-seq) and increasingly sophisticated algorithms. Sequencing tRNAs is challenging both experimentally and in terms of the subsequent computational analysis. In RNA-seq data analysis, mapping tRNA reads to a reference genome is an error-prone task. This is in particular true, as chemical modifications introduce systematic reverse transcription errors while at the same time the genomic loci are only approximately identical due to the post-transcriptional maturation of tRNAs. Additionally, their multi-copy nature complicates the precise read assignment to its true genomic origin. In the course of the thesis a computational workflow was established to enable accurate mapping of tRNA reads. The developed method removes most of the mapping artifacts introduced by simpler mapping schemes, as demonstrated by using both simulated and human RNA-seq data. Subsequently, the resulting mapping profiles can be used for reliable identification of specific chemical tRNA modifications with a false discovery rate of only 2%. For that purpose, computational analysis methods were developed that facilitates the sensitive detection and even classification of most tRNA modifications based on their mapping profiles. This comprised both untreated RNA-seq data of various species, as well as treated data of Bacillus subtilis that has been designed to display modifications in a specific read-out in the mapping profile. The discussion focuses on sources of artifacts that complicate the profiling of tRNA modifications and strategies to overcome them. Exemplary studies on the modification pattern of different human tissues and the developmental stages of Dictyostelium discoideum were carried out. These suggested regulatory functions of tRNA modifications in development and during cell differentiation. The main experimental difficulties of tRNA sequencing are caused by extensive, stable secondary structures and the presence of chemical modifications. Current RNA-seq methods do not sample the entire tRNA pool, lose short tRNA fragments, or they lack specificity for tRNAs. Within this thesis, the benchmark and improvement of LOTTE-seq, a method for specific selection of tRNAs for high-throughput sequencing, exhibited that the method solves the experimental challenges and avoids the disadvantages of previous tRNA-seq protocols. Applying the accurate tRNA mapping strategy to LOTTE-seq and other tRNA-specific RNA- seq methods demonstrated that the content of mature tRNAs is highest in LOTTE-seq data, ranging from 90% in Spinacia oleracea to 100% in D. discoideum. Additionally, the thesis addressed the fact that tRNAs are multi-copy genes that undergo concerted evolution which keeps sequences of paralogous genes effectively identical. Therefore, it is impossible to distinguish orthologs from paralogs by sequence similarity alone. Synteny, the maintenance of relative genomic positions, is helpful to disambiguate evolutionary relationships in this situation. During this thesis a workflow was computed for synteny-based orthology identification of tRNA genes. The workflow is based on the use of pre-computed genome-wide multiple sequence alignment blocks as anchors to establish syntenic conservation of sequence intervals. Syntenic clusters of concertedly evolving genes of different tRNA families are then subdivided and processed by cograph editing to recover their duplication histories. A useful outcome of this study is that it highlights the technical problems and difficulties associated with an accurate analysis of the evolution of multi-copy genes. To showcase the method, evolution of tRNAs in primates and fruit flies were reconstructed. In the last decade, a number of reports have described novel aspects of tRNAs in terms of the diversity of their genes. For example, nuclear-encoded mitochondrial-derived tRNAs (nm-tRNAs) have been reported whose presence provokes intriguing questions about their functionality. Within this thesis an annotation strategy was developed that led to the identification of 335 and 43 novel nm-tRNAs in human and mouse, respectively. Interestingly, downstream analyses showed that the localization of several nm-tRNAs in introns and the over-representation of conserved RNA-binding sites of proteins involved in splicing suggest a potential regulatory function of intronic nm-tRNAs in splicing

    The Being of Analogy

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    Similarity has long been excluded from reality in both the analytical and continental traditions. Because it exists in the aesthetic realm, and because aesthetics is thought to be divorced from objective reality, similarity has been confined to the prison of the subject. In The Being of Analogy, Noah Roderick unleashes similarity onto the world of objects. Inspired by object-oriented theories of causality, Roderick argues that similarity is ever present at the birth of new objects. This includes the emergent similarity of new mental objects, such as categories—a phenomenon we recognize as analogy. Analogy, Roderick contends, is at the very heart of cognition and communication, and it is through analogy that we can begin dismantling the impossible wall between knowing and being

    Tartu Ülikooli toimetised. Tööd semiootika alalt. 1964-1992. 0259-4668

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    http://www.ester.ee/record=b1331700*es

    Affording expertise: integrating the biological, cultural and social sites of disciplinary skills and knowledge

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    The coherence of the concept of mental representations is increasingly in question, and hence accounts of expertise based on mental representation. I argue that such mental representational accounts are, at best, inadequate, and propose that turning to ecological psychology and affordance could provide the answer. However, there is no fully agreed understanding of affordance and so the thesis undertakes three main interrelated tasks: First, I review James J. Gibson's writings on affordance before setting out a revised account of affordance using Jacques Derrida's discussion of differance. Differance, as the generation of differences with the deferral of the meanings of those differences is adopted as a model for affordance. Second, affordance - as differance or difference and deferral - is taken as the minimal form of material agency. Drawing upon the process philosophy of Whitehead, agency is understood to be coextensive with material composition, and on this understanding an ontology of agency in medias res, considered as agency that develops within a pre-existing medium or milieu, is developed as an integrating framework within which biological, cultural and social phenomenon are combined in human agency in medias res. Third, human agency in medias res is explored through the process of acquiring expertise. As affordance is the primary ontology of all material reality. All human activity encompassing tools and instruments, representations and language is a concatenation of such constituents, hence expertise as the normative performance of disciplinary activities to disciplinary standards, is founded upon the proper concatenation of constituent affordance. Gaining expertise, meanwhile, precedes through the development of an ecological relation within activity that is founded upon specialised training and practice, and upon the social institution of someone who is socially legitimated as a master of their domain. By ecological relation, I mean to draw attention to the agency that develops and is sustained within the formation and maintenance of ritualised, instrumental, and discursive configurations that come to be identified as a particular domain of knowledge. The closely interrelated themes of affordance and agency in medias res are brought together in a case study of the development of expertise in archaeology by focusing on learning to identify (type) pottery, and on learning to excavate. In learning to type pottery, a novice is inculcated into the language-games of pottery. The formulation of typologies, meanwhile, shows how such language-games form, and how these language-games afford a semantic field that supports archaeologically mundane communications between archaeologists. The event of an excavation is used to focus on social dynamics seen from a perspective of agency in medias res and to demonstrate how wider social, economic and political influences intervene within archaeological discourse and practice to alter the agency of archaeologists in terms of the cognitive authority, and that of archaeology as discipline
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