816 research outputs found
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Modelling and valuation of guarantees in with-profit and unitised with-profit life insurance contracts
Insights into protein-RNA complexes from computational analyses of iCLIP experiments
RNA-binding proteins (RBPs) are the primary regulators of all aspects of posttranscriptional gene regulation. In order to understand how RBPs perform their function, it is important to identify their binding sites. Recently, new techniques have been developed to employ high-throughput sequencing to study protein-RNA interactions in vivo, including the individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP). iCLIP identiļ¬es sites of protein-RNA crosslinking with nucleotide resolution in a transcriptome-wide manner. It is composed of over60steps,whichcanbemodiļ¬ed,butitisnotclearhowvariationsinthemethod affect the assignment of RNA binding sites. This is even more pertinent given that several variants of iCLIP have been developed. A central question of my research is how to correctly assign binding sites to RBPs using the data produced by iCLIP and similar techniques. I ļ¬rst focused on the technical analyses and solutions for the iCLIP method. I examinedcDNAdeletionsandcrosslink-associatedmotifstoshowthatthestartsof cDNAs are appropriate to assign the crosslink sites in all variants of CLIP, including iCLIP, eCLIP and irCLIP. I also showed that the non-coinciding cDNA-starts are caused by technical conditions in the iCLIP protocol that may lead to sequence constraintsatcDNA-endsintheļ¬nalcDNAlibrary. Ialsodemonstratedtheimportance of fully optimizing the RNase and puriļ¬cation conditions in iCLIP to avoid thesecDNA-endconstraints. Next,IdevelopedCLIPo,acomputationalframework that assesses various features of iCLIP data to provide quality control standards which reveals how technical variations between experiments affect the speciļ¬city of assigned binding sites. I used CLIPo to compare multiple PTBP1 experiments produced by iCLIP, eCLIP and irCLIP, to reveal major effects of sequence constraintsatcDNA-endsorstarts,cDNAlengthdistributionandnon-speciļ¬ccontaminants. Moreover, I assessed how the variations between these methods inļ¬uence themechanisticconclusions. Thus,CLIPopresentsthequalitycontrolstandardsfor transcriptome-wide assignment of protein-RNA binding sites. I continued with analyses of RBP complexes by using data from spliceosomeiCLIP. This method simultaneously detects crosslink sites of small nuclear ribonucleoproteins (snRNPs) and auxiliary splicing factors on pre-mRNAs. I demonstratedthatthehighresolutionofspliceosome-iCLIPallowsfordistinctionbetween multiple proximal RNA binding sites, which can be valuable for transcriptomewide studies of large ribonucleoprotein complexes. Moreover, I showed that spliceosome-iCLIP can experimentally identify over 50,000 human branch points. In summary, I detected technical biases from iCLIP data, and demonstrated how such biases can be avoided, so that cDNA-starts appropriately assign the RNA binding sites. CLIPo analysis proved a useful quality control tool that evaluates data speciļ¬city across different methods, and I applied it to iCLIP, irCLIP and ENCODE eCLIP datasets. I presented how spliceosome-iCLIP data can be used to study the splicing machinery on pre-mRNAs and how to use constrained cDNAs from spliceosome-iCLIP data to identify branch points on a genome-wide scale. Taken together, these studies provide new insights into the ļ¬eld of RNA biology and can be used for future studies of iCLIP and related methods
Existence and Uniqueness of Tri-tronqu\'ee Solutions of the second Painlev\'e hierarchy
The first five classical Painlev\'e equations are known to have solutions
described by divergent asymptotic power series near infinity. Here we prove
that such solutions also exist for the infinite hierarchy of equations
associated with the second Painlev\'e equation. Moreover we prove that these
are unique in certain sectors near infinity.Comment: 13 pages, Late
Autoresonance in a Dissipative System
We study the autoresonant solution of Duffing's equation in the presence of
dissipation. This solution is proved to be an attracting set. We evaluate the
maximal amplitude of the autoresonant solution and the time of transition from
autoresonant growth of the amplitude to the mode of fast oscillations.
Analytical results are illustrated by numerical simulations.Comment: 22 pages, 3 figure
Data Science Issues in Understanding Protein-RNA Interactions
An interplay of experimental and computational methods is required to achieve a comprehensive understanding of proteināRNA interactions. UV crosslinking and immunoprecipitation (CLIP) identifies endogenous interactions by sequencing RNA fragments that copurify with a selected RNA-binding protein under stringent conditions. Here we focus on approaches for the analysis of the resulting data and appraise the methods for peak calling, visualization, analysis, and computational modeling of proteināRNA binding sites. We advocate that the sensitivity and specificity of data be assessed in combination for computational quality control. Moreover, we demonstrate the value of analyzing sequence motif enrichment in peaks assigned from CLIP data and of visualizing RNA maps, which examine the positional distribution of peaks around regulated landmarks in transcripts. We use these to assess how variations in CLIP data quality and in different peak calling methods affect the insights into regulatory mechanisms. We conclude by discussing future opportunities for the computational analysis of proteināRNA interaction experiments
Psoriasis Vulgaris: A Genetic Approach
Evidence for a genetic contribution in psoriasis comes from direct examination of a large segment of the population in an isolated island environment, epidemiologic and questionnaire studies presented to psoriatic patients, twin studies collected from the literature and from twin registries, and splitsibship analysis. The concordance of psoriasis in monozygotic twins was 65ā72%, whereas psoriasis in dizygotic twins was 15ā30%. Determination of concordance in older twin pairs from a national twin registry in Denmark revealed nearly 90ā100% heritability. In order to link psoriasis with known markers within the human genome, serologic studies have been carried out with a variety of blood group and polymorphic protein antigens. A weak association with the MNS and Lewis Blood Groups Systems (relative risk, 3.5) has been identified. Stronger associations with class I B locus and class II D locus genes (relative risk, 8ā12) have also been determined by studies of the human lymphocyte-antigen system. Finally, a strong association with HLA Cw6 has been determined; this marker is thought to be in linkage disequilibrium with B and D locus genes previously associated with psoriasis. The relative risk of developing psoriasis in HLA Cw6 positive individuals is about 24. A few large kindred have been reported in the dermatology literature. These support the hypothesis of autosomal dominant inheritance with penetrance of approximately 60%. In cooperation with The National Psoriasis Foundation, we have now identified over 90 families with psoriasis in three generations. We have begun the process of ascertainment, the construction of family trees, and the collection of leukocyte DNA for linkage analysis with established restriction fragment polymorphisms (RFLP). Our initial assessment is being directed to four RFLP that span approximately 30 centiMorgans of the short arm of human chromosome 6. Although karyotyping is uncommoly done in patients because of psoriasis, we now seek evidence of translocation of chromosome 6 in association with psoriasis
Hard loss of stability in Painlev\'e-2 equation
A special asymptotic solution of the Painlev\'e-2 equation with small
parameter is studied. This solution has a critical point corresponding to
a bifurcation phenomenon. When the constructed solution varies slowly
and when the solution oscillates very fast. We investigate the
transitional layer in detail and obtain a smooth asymptotic solution, using a
sequence of scaling and matching procedures
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