682 research outputs found

    Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence

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    Botrytis cinerea is a necrotrophic pathogen causing pre- and post-harvest diseases in at least 235 plant species. It manifests extraordinary genotype and phenotype variation. One of the causes of this variation is transposable elements. Two transposable elements have been discovered in this fungus, the retrotransposon (Boty), and the transposon (Flipper). In this work, two complete (Boty-II-76 and Boty-II-103) and two partial (Boty-II-95 and Boty-II-141) long terminal repeat (LTR) retrotransposons were identified by an in silico genomic sequence analysis. Boty-II-76 and Boty-II-103 contain 6439 bp nucleotides with a pair of LTRs at both ends, and an internal deduced pol gene encoding a polyprotein with reverse transcriptase and DDE integrase domains. They are flanked by 5 bp direct repeats (ACCAT, CTTTC). In Boty-II-141, two LTRs at both ends, and a partial internal pol gene encoding a protein with a DDE integrase domain were identified. In Boty-II-95, a right LTR and a partial internal pol gene encoding a protein with no conserved domains were identified. Boty-II uses a self-priming mechanism to initiate synthesis of reverse transcripts. The sequence of the presumed primer binding site for first-strand reverse transcription is 5'-TTGTACCAT-3'. The polypurine-rich sequence for plus-strand DNA synthesis is 5'-GCCTTGAGCGGGGGGTAC-3'. Fourteen Boty-II LTRs that contain 125-158 bp nucleotides and share 69.1 ~ 100% identities with the short inverted terminal repeats of 5 bp (TGTCA\u2026TGACA) were discovered. Analysis of structural features and phylogeny revealed that Boty-II is a novel LTR retrotransposon. It could potentially be used as a novel molecular marker for the investigation of genetic variation in B. cinerea

    A Deficiency Problem of the Least Squares Finite Element Method for Solving Radiative Transfer in Strongly Inhomogeneous Media

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    The accuracy and stability of the least squares finite element method (LSFEM) and the Galerkin finite element method (GFEM) for solving radiative transfer in homogeneous and inhomogeneous media are studied theoretically via a frequency domain technique. The theoretical result confirms the traditional understanding of the superior stability of the LSFEM as compared to the GFEM. However, it is demonstrated numerically and proved theoretically that the LSFEM will suffer a deficiency problem for solving radiative transfer in media with strong inhomogeneity. This deficiency problem of the LSFEM will cause a severe accuracy degradation, which compromises too much of the performance of the LSFEM and makes it not a good choice to solve radiative transfer in strongly inhomogeneous media. It is also theoretically proved that the LSFEM is equivalent to a second order form of radiative transfer equation discretized by the central difference scheme

    On the Derivation of Vector Radiative Transfer Equation for Polarized Radiative Transport in Graded Index Media

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    Light transport in graded index media follows a curved trajectory determined by the Fermat's principle. Besides the effect of variation of the refractive index on the transport of radiative intensity, the curved ray trajectory will induce geometrical effects on the transport of polarization ellipse. This paper presents a complete derivation of vector radiative transfer equation for polarized radiation transport in absorption, emission and scattering graded index media. The derivation is based on the analysis of the conserved quantities for polarized light transport along curved trajectory and a novel approach. The obtained transfer equation can be considered as a generalization of the classic vector radiative transfer equation that is only valid for uniform refractive index media. Several variant forms of the transport equation are also presented, which include the form for Stokes parameters defined with a fixed reference and the Eulerian forms in the ray coordinate and in several common orthogonal coordinate systems.Comment: This paper has been submitted to JQSR

    cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture.

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    Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci. Their enrichment in enhancer-like chromatin signatures, interactions with nearby trait-relevant protein-coding loci, and preferential location at topologically associated domain (TAD) boundaries provide evidence that TR-lincRNAs likely regulate proximal trait-relevant gene expression in cis by modulating local chromosomal architecture. This is consistent with the positive and significant correlation found between TR-lincRNA abundance and intra-TAD DNA-DNA contacts. Our results provide insights into the molecular mode of action by which TR-lincRNAs contribute to complex human traits

    Barriers and facilitators to faecal immunochemical testing in symptomatic populations: a rapid systematic scoping review and gap analysis

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    Aim Faecal immunochemical testing (FIT) is used to triage people with signs or symptoms of a colorectal cancer (CRC). Recent guidelines have recommended further research to improve access, uptake and return of FIT. This systematic scoping review aims to understand the barriers and facilitators to FIT testing in symptomatic patients. Method Qualitative, quantitative and mixed-methods studies published after September 2013 were included. MEDLINE, EMBASE and PsycINFO databases were searched to identify publications examining barriers and facilitators to FIT. Initially, the data underwent thematic analysis, and subsequently, factors were aligned to components of the Capability, Opportunity, Motivation, Behaviour model. All outcomes are presented in adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Results One thousand two hundred thirty-two papers were identified; 11 met the inclusion criteria. Barriers and facilitators were identified at the patient (e.g., knowledge), provider (e.g., general practitioner awareness) and service level (e.g., method of providing FIT kits). Factors were categorised into the subcomponents of the model: psychological capability (e.g., lack of FIT knowledge), reflective motivation (e.g., beliefs regarding FIT sampling and faeces being unhygienic) and automatic motivation (e.g., embarrassment, scary, anxiety provoking). Gaps in knowledge emerged in three domains: (1) patient experience, (2) FIT pathway and (3) healthcare professionals experience of FIT. Conclusion This systematic scoping review provides a summary of the literature on FIT uptake, and identified factors across multiple levels and components. To increase adherence to FIT completion within primary care, a multifaceted theory and evidence-based approach is needed to underpin future behavioural science interventions

    Elastic interactions of active cells with soft materials

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    Anchorage-dependent cells collect information on the mechanical properties of the environment through their contractile machineries and use this information to position and orient themselves. Since the probing process is anisotropic, cellular force patterns during active mechanosensing can be modelled as anisotropic force contraction dipoles. Their build-up depends on the mechanical properties of the environment, including elastic rigidity and prestrain. In a finite sized sample, it also depends on sample geometry and boundary conditions through image strain fields. We discuss the interactions of active cells with an elastic environment and compare it to the case of physical force dipoles. Despite marked differences, both cases can be described in the same theoretical framework. We exactly solve the elastic equations for anisotropic force contraction dipoles in different geometries (full space, halfspace and sphere) and with different boundary conditions. These results are then used to predict optimal position and orientation of mechanosensing cells in soft material.Comment: Revtex, 38 pages, 8 Postscript files included; revised version, accepted for publication in Phys. Rev.

    Spectral Element Method for Vector Radiative Transfer Equation

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    A spectral element method (SEM) is developed to solve polarized radiative transfer in multidimensional participating medium. The angular discretization is based on the discrete-ordinates approach, and the spatial discretization is conducted by spectral element approach. Chebyshev polynomial is used to build basis function on each element. Four various test problems are taken as examples to verify the performance of the SEM. The effectiveness of the SEM is demonstrated. The h and the p convergence characteristics of the SEM are studied. The convergence rate of p-refinement follows the exponential decay trend and is superior to that of h-refinement. The accuracy and efficiency of the higher order approximation in the SEM is well demonstrated for the solution of the VRTE. The predicted angular distribution of brightness temperature and Stokes vector by the SEM agree very well with the benchmark solutions in references. Numerical results show that the SEM is accurate, flexible and effective to solve multidimensional polarized radiative transfer problems.Comment: The paper have bee published in JQSR
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