Host regulation of the replication of the yeast retrotransposon Ty5

The replication of retroelements may have deleterious effects on the hosts. Therefore, elements and their hosts have coevolved mechanisms to regulate retroelement replication. This regulation can occur at the transcriptional, translational, or post-translational levels as well as through targeted integration or cDNA recombination. I have studied host regulation of the Saccharomyces retrotransposon Ty5. I have found that Ty5 transcription is carefully controlled. Transcription of Ty5 is haploid specific and is repressed 10 fold in diploid strains. Ty5 transcription is also regulated by the pheromone response pathway, which is activated during mating. In addition, Ty5 transcription is regulated by flanking sequences. Ty5 preferentially integrates into regions of silent chromatin at the telomeres and the HM loci, which, in turn, represses Ty5 transcription. Although the repressive effects of silent chromatin have been well characterized, I have found that transcription and transposition of Ty5 elements embedded in silent chromatin can be induced by pheromone treatment or during the mating process. Another level of retroelement regulation is the targeting of element cDNA to non-coding regions. cDNA can be targeted by the element-encoded integrase protein or through recombination with pre-existing elements. I found that Ty5 recombines at high frequency with homologous substrates. Two classes of recombinants were identified: tandem elements and elements that arose by marker exchange between the Ty5 cDNA and the substrate. Ty5 cDNA recombination is dependent on the host repair protein Rad52, but not on the host repair protein Rad1 or Ty5 integrase. Using an assay system that allowed me to identify the cis-acting sequences important Ty5 cDNA recombination, I have found that the Ty5 LTR is critical for tandem element formation. Internal Ty5 sequences can facilitate tandem element formation in the presence of an LTR. These data have made it possible for me to propose models for tandem element formation based on recombination between the LTRs of the cDNA and substrate. The LTR was not found to be important for marker exchange events, suggesting that the two classes of recombinants arise by different mechanisms. Targeted integration and recombinational amplification of Ty5 elements at the telomeres suggests that Ty5 may play an important role in telomere structure

Early life mental health and alcohol use behaviours in adulthood: evidence from prospective data in the UK and the US

Evidence on the association between early life mental health and alcohol use behaviours in adulthood is inconsistent. This thesis aims to summarise the available evidence in a systematic way, investigate the association from a developmental perspective and examine the co-development of alcohol use and stressful life events. In the systematic review, positive associations between externalising problems and alcohol outcomes were consistently reported, while associations between the internalising domain and alcohol outcomes varied across subtypes. Internalising problems tended to be negatively associated with alcohol consumption but positively with severe outcomes. Depression tended to be positively associated with alcohol outcomes, while no clear association was evident for anxiety. In two British birth cohorts, early life externalising and internalising problems were associated with problematic drinking in mid-adulthood, with externalising being a risk factor and internalising a protective factor. The strength of these associations did not differ by the developmental timing of externalising or internalising problems and cohort but was stronger in males. Mediation analysis indicated that in the UK context, the association between externalising problems and problematic drinking was not via educational attainment. In Michigan Longitudinal Study, three classes of individuals with heterogeneous dual trajectories of alcohol use and stressful life events over adolescence and young adulthood were identified. Two classes were characterised by consistently low levels of stressful life events with one class having a normative increase in alcohol use, while the other had a rapid escalation from ages 14 to 23. The third class had consistently high levels of alcohol use and stressful life events. Utilising prospective longitudinal data, the current thesis emphasises the interplay between externalising and internalising problems regarding their relationships with alcohol use, highlights potential sex differences in these and reveals the contextual role of stressful life events in the development of alcohol use

Electronic structures of [111]-oriented free-standing InAs and InP nanowires

We report on a theoretical study of the electronic structures of the [111]-oriented, free-standing, zincblende InAs and InP nanowires with hexagonal cross sections by means of an atomistic $sp^{3}s^{*}$, spin-orbit interaction included, nearest-neighbor, tight-binding method. The band structures and the band state wave functions of these nanowires are calculated and the symmetry properties of the bands and band states are analyzed based on the $C_{3v}$ double point group. It is shown that all bands of these nanowires are doubly degenerate at the $\Gamma$-point and some of these bands will split into non-degenerate bands when the wave vector $k$ moves away from the $\Gamma$-point as a manifestation of spin-splitting due to spin-orbit interaction. It is also shown that the lower conduction bands of these nanowires all show simple parabolic dispersion relations, while the top valence bands show complex dispersion relations and band crossings. The band state wave functions are presented by the spatial probability distributions and it is found that all the band states show $2\pi/3$-rotation symmetric probability distributions. The effects of quantum confinement on the band structures of the [111]-oriented InAs and InP nanowires are also examined and an empirical formula for the description of quantization energies of the lowest conduction band and the highest valence band is presented. The formula can simply be used to estimate the enhancement of the band gaps of the nanowires at different sizes as a result of quantum confinement.Comment: 9 pages, 8 figures. arXiv admin note: substantial text overlap with arXiv:1502.0756

Controlled Porosity in Thermochromic Coatings

Vanadium dioxide is a promising thermochromic material, seemed as the great candidate for smart window applications. The real application of VO2 requires high visible transmission (Tlum) as well as large solar modulating abilities (∆Tsol), which could not be achieved by pristine VO2 materials due to the trade-off between Tlum and ∆Tsol. Here in, the porosity design is thoroughly reviewed from the effect on modulating the thermochromic performance to the porous control and preparation. To begin with, the history, advantages, challenges and approaches to tackle the issues comprised of antireflection multilayer structure, nanothermochromism, patterning and porous design is introduced in detail. Then, the effect of porosity on improving the thermochromic performance of VO2 thin films is demonstrated using the newest experimental and simulation results. In the following, the porous control and structural synthesis, including the polymer-assisted deposition (PAD), freeze-drying, colloidal lithography as well as the dual phase transformation is summarized. Fourthly, the characterization methods, composed of scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM), X-ray diffraction (XRD), Raman spectroscopy as well as UV-Vis-NIR spectroscopy are demonstrated. Finally, the challenges that the porous design faces and possible approaches to optimize the performance are presented

Nonlocal Means-Based Denoising for Medical Images

Medical images often consist of low-contrast objects corrupted by random noise arising in the image acquisition process. Thus, image denoising is one of the fundamental tasks required by medical imaging analysis. Nonlocal means (NL-means) method provides a powerful framework for denoising. In this work, we investigate an adaptive denoising scheme based on the patch NL-means algorithm for medical imaging denoising. In contrast with the traditional NL-means algorithm, the proposed adaptive NL-means denoising scheme has three unique features. First, we use a restricted local neighbourhood where the true intensity for each noisy pixel is estimated from a set of selected neighbouring pixels to perform the denoising process. Second, the weights used are calculated thanks to the similarity between the patch to denoise and the other patches candidates. Finally, we apply the steering kernel to preserve the details of the images. The proposed method has been compared with similar state-of-art methods over synthetic and real clinical medical images showing an improved performance in all cases analyzed

Diverse variability of surface chlorophyll during the evolution of Gulf Stream rings

Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 48(5), (2021): e2020GL091461, https://doi.org/10.1029/2020GL091461.We investigate how the near-surface chlorophyll (CHL)-a evolves in Gulf Stream (GS) warm-core rings (WCRs) and cold-core rings (CCRs) using multi-platform satellite observations. Averaged CHL anomaly (CHLA) within the rings exhibits both positive and negative linear trends during the evolution of the WCRs while negative trends dominate in CCRs. This difference is associated with a variety of physical processes occurring during the evolution process. Meanwhile, eddy-centric analysis reveals four spatial patterns of CHLA long-term trends, some of which highlights the importance of rings in shaping surface CHL. Short-term fluctuations of CHLA in WCRs and CCRs are closely correlated with mixed layer depth and sea surface temperature anomaly and highlight the complex interplay between multiple mechanisms. In addition, we find higher concentration CHL in some WCRs than that in CCRs during the same season, providing an alternative view of the characteristics of the surface ecosystem in Gulf Stream rings.This work was supported by the National Science Foundation Ocean Science Division under grant OCE-1558960. JN was supported by the Fundamental Research Funds for the Central Universities (Hohai University) under grant B200203005 and the China Scholarship Council.2021-08-1