The association of sigmoidal features and transequatorial interconnecting loops with eruptive solar activity

This thesis examines sigmoidal solar X-ray features and transequatorial-interconnecting loops. Recent studies have suggested that both features exhibit a high probability of eruption to produce a coronal mass ejection (CME). The thesis begins with an introduction to the solar atmosphere and the physics governing its behaviour. The physics involved in flaring and CME onset will then be introduced and difficulties in our understanding of the relationship between these events highlighted. Solar instrumentation and data analysis techniques used throughout this thesis is also introduced together with a discussion of capabilities and limitations. Although many authors have referred to 'sigmoidal' features in the corona, observations have not yet confirmed the nature of such features. Sigmoidal active regions previously observed using Yohkoh/SXT alone form the basis of a multi-wavelength study incorporating SOHO/LASCO, EIT and MDI observations, together with ground-based H-alpha data. Regions previously classified as 'sigmoidal' are frequently found to comprise several shorter loops, the overall projection of which appears to form a single S (or reverse-S) shaped feature. An example of a non-active region sigmoid is studied in terms of its morphology, CME and flaring activity over three solar rotations. This study is the first to consider a sigmoidal feature unconfined by a single active region in detail. The region's flaring and CME activity is studied and the relative timing of eruptive activity and sigmoid appearance is considered. Previous studies have shown transequatorial loop systems (TLS), connecting active regions in opposite hemispheres to disappear in association with CME onset. This thesis describes a number of TLS in terms of their formation, morphology and associated CME and flaring activity. TLS are found to exhibit a variety of responses to CME onset including both brightening and dimming. Loops extending over a wide range in latitude appear more likely to be associated with CME onset

Light availability controls in the benthic nearshore ecosystem of the Elwha River

The Elwha River Restoration Project was the largest US dam removal project to date, both in dam height and sediment released. During dam removal in 2011–2014, ~18 Mt of sediment washed downriver, and macroalgae virtually disappeared from the adjacent nearshore ecosystem. The link between current benthic light availability and sediment delivery and transport has been investigated in order to understand conditions during dam removal. Seven instrument platforms were deployed on the 10-m isobath along a 16 km transect centered on the river mouth for seven fortnightly periods in 2016 and 2017 to monitor near-bed photosynthetically available radiation (PAR), suspended sediment, wave climate, current velocity, temperature, and salinity. Water-column profiles, bed sediment, and water samples were collected during deployments. Seasonally variable chlorophyll-a and colored dissolved organic matter did not contribute substantially to light attenuation compared to suspended sediment. Along the 10-m isobath within 1.5 km of the river mouth, the greatest light attenuation occurred when wave events coincided with or followed periods of high river discharge. However, discharge events lasting attenuation; energetic tidal currents promote rapid sediment export out of the nearshore environment. In the buoyant plume, maximum light attenuation occurred within 1 m of the surface, reducing light through the rest of the water column. Benthic PAR varied more during spring tides when plume location was more variable. Alongshore 1.5 to 8 km from the river mouth, light availability was not directly coupled to river discharge. Light attenuation occurred throughout the water column, influenced by resuspension due to strong currents and wave events. This subsurface attenuation would not be captured by remote sensing. Predicting benthic light availability over event, tidal, and seasonal timescales will improve management strategies designed to limit ecosystem damage during other dam removals or sediment delivery events

MetaIPM: Placing Integral Projection Models Into a Metapopulation Framework

1. Metapopulation models include spatial population dynamics such as dispersion and migration between subpopulations. Integral projection models (IPMs) can include demographic rates as a function of size. Traditionally, metapopulation models do not included detailed populaiton models such as IPMs. In some situations, both local population dynamics (e.g. size-based survival) and spatial dynamics are important. 2. We present a Python package, MetaIPM, which places IPMs into a metapopulation framework, and allow users to readily construct and apply these models that combine local population dynamics within a metapopulation framework. 3. MetaIPM includes an IPM for each subpopulation that is connected to other subpopulations via a metapopulation movement model. These movements can include dispersion, migration or other patterns. The IPM can include for size-specific demographic rates (e.g. survival, recruitment) as well as management actions, such as length-based harvest (e.g. gear specific capture sizes, varying slot limits across political boundaries). The model also allows for changes in metapopulation connectivity between locations, such as a fish passage ladders to enhance movement or deterrents to reduce movement. Thus, resource managers can use MetaIPM to compare different management actions such as the harvest gear type (which can be length-specific) and harvest locations. 4. We demonstrate how MetaIPM may be applied to inform managers seeking to limit the spread of an invasive species in a system with important metapopulation dynamics. Specifically, we compared removal lengths (all length fish versus longer fish only) for an invasive fish population in a fragmented, inland river system. MetaIPM allowed users to compare the importance of harvesting source populations away from the invasion front, as well as species at the invasion front. The model would also allow for future comparisons of different deterrent placement locations in the system. 5. Moving beyond our example system, we describe how MetaIPM can be applied to other species, systems and management approaches. The MetaIPM packages includes Jupyter Notebooks documenting the package as well as a second set of JupyterNotebooks showing the application of the package to our example system

Experiential education and outreach based on nearshore monitoring of the Elwha River restoration project

Nearshore monitoring of benthic habitats and the coastal environment following the Elwha River Restoration project has engaged students and citizens with coastal science and management issues. In the post-dam-removal period, the lessons learned will continue to be disseminated via a UW undergraduate course and an interactive digital map, both designed to engage students and communities in restoration science. The research-focused course developed at the UW Friday Harbor Labs has allowed us to engage diverse undergraduate students (and graduate teaching assistants) in the research process. The course integrates interdisciplinary lectures and workshops on data analysis and laboratory methods, with the research process; from proposal to oceanographic data collection to analysis to publication. The course provides opportunities for student creativity and leadership. Outcome tracking indicates that these undergraduate (and post-bac) students are generally attending graduate school at a high rate, and launching careers in education, coastal management, and other STEM fields. To engage a broader segment of the community and to support decision-making about large-scale coastal restoration projects, we have developed an interactive digital map that will be available on-line, and will also be piloted as a physical interpretive display at the Feiro Marine Life Center in Port Angeles, WA. The interactive digital map is designed to effectively tell the story of the Elwha restoration in the coastal environment through the compilation and display of multiple data sets, some of which have never before been publicly available. Ultimately, the result of long-term monitoring of the Elwha nearshore system will provide a better understanding of the effects of restoration activities, such as dam removal on benthic habitats, and this knowledge will be passed to future managers and citizens through educational and outreach activities that captivate and inspire a broad audience

The deubiquitylase USP31 controls the Chromosomal Passenger Complex and spindle dynamics

We have identified USP31 as a microtubule and centrosome associated deubiquitylase, depletion of which leads to an increase in individual cell mass and defective proliferation. We have examined its dynamics and impact during mitosis. GFP-USP31 associates with the mitotic and central spindles, its levels are increased 2-3-fold in prometaphase compared to asynchronous cells and it is dynamically phosphorylated in a CDK1 dependent manner. We find that USP31 depleted cells display altered spindle morphology and chromosomal segregation errors, whilst stable expression of a catalytically inactive form of USP31 leads to polyploidy. At prometaphase, levels of multiple CPC components are destabilised, most prominently INCENP. Under anaphase conditions, depletion of USP31 impairs the translocation of both endogenous and ectopically expressed INCENP to the spindle mid-zone, whilst expression of catalytically inactive USP31 results in multiple ectopic cleavage furrows. In summary, our data indicate a multifaceted regulatory role for USP31 during mitosis, with a profound impact on chromosomal passenger complex abundance, dynamics and function

LHC sensitivity to the resonance spectrum of a minimal strongly interacting electroweak symmetry breaking sector

We present a unified analysis of the two main production processes of vector boson pairs at the LHC, VV-fusion and qqbar annihilation, in a minimal strongly interacting electroweak symmetry breaking sector. Using a unitarized electroweak chiral Lagrangian formalism and modeling the final V_L V_L strong rescattering effects by a form factor, we describe qqbar annihilation processes in terms of the two chiral parameters that govern elastic V_L V_L scattering. Depending on the values of these two chiral parameters, the unitarized amplitudes may present resonant enhancements in different angular momentum-isospin channels. Scanning this two parameter space, we generate the general resonance spectrum of a minimal strongly interacting electroweak symmetry breaking sector and determine the regions that can be probed at the LHC.Comment: Final version to appear in Phys. Rev. D, including a more detailed exposition and a few more references. Conclusions and results unchanged. 14 pages, 5 figure

Multiomics links global surfactant dysregulation with airflow obstruction and emphysema in COPD

RATIONALE: Pulmonary surfactant is vital for lung homeostasis as it reduces surface tension to prevent alveolar collapse and provides essential immune-regulatory and antipathogenic functions. Previous studies demonstrated dysregulation of some individual surfactant components in COPD. We investigated relationships between COPD disease measures and dysregulation of surfactant components to gain new insights into potential disease mechanisms. METHODS: Bronchoalveolar lavage proteome and lipidome were characterised in ex-smoking mild/moderate COPD subjects (n=26) and healthy ex-smoking (n=20) and never-smoking (n=16) controls using mass spectrometry. Serum surfactant protein analysis was performed. RESULTS: Total phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, surfactant protein (SP)-B, SP-A and SP-D concentrations were lower in COPD versus controls (log2 fold change (log2FC) -2.0, -2.2, -1.5, -0.5, -0.7 and -0.5 (adjusted p<0.02), respectively) and correlated with lung function. Total phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, SP-A, SP-B, SP-D, napsin A and CD44 inversely correlated with computed tomography small airways disease measures (expiratory to inspiratory mean lung density) (r= -0.56, r= -0.58, r= -0.45, r= -0.36, r= -0.44, r= -0.37, r= -0.40 and r= -0.39 (adjusted p<0.05)). Total phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, SP-A, SP-B, SP-D and NAPSA inversely correlated with emphysema (% low-attenuation areas): r= -0.55, r= -0.61, r= -0.48, r= -0.51, r= -0.41, r= -0.31 and r= -0.34, respectively (adjusted p<0.05). Neutrophil elastase, known to degrade SP-A and SP-D, was elevated in COPD versus controls (log2FC 0.40, adjusted p=0.0390), and inversely correlated with SP-A and SP-D. Serum SP-D was increased in COPD versus healthy ex-smoking volunteers, and predicted COPD status (area under the curve 0.85). CONCLUSIONS: Using a multiomics approach, we demonstrate, for the first time, global surfactant dysregulation in COPD that was associated with emphysema, giving new insights into potential mechanisms underlying the cause or consequence of disease

Magnetic Flux Density Sensor Analysis

Undergraduate Basi

PEGylation improves the receptor-mediated transfection efficiency of peptide-targeted, self-assembling, anionic nanocomplexes

Non-viral vector formulations comprise typically complexes of nucleic acids with cationic polymers or lipids. However, for in vivo applications cationic formulations suffer from problems of poor tissue penetration, non-specific binding to cells, interaction with serum proteins and cell adhesion molecules and can lead to inflammatory responses. Anionic formulations may provide a solution to these problems but they have not been developed to the same extent as cationic formulations due to difficulties of nucleic acid packaging and poor transfection efficiency. We have developed novel PEGylated, anionic nanocomplexes containing cationic targeting peptides that act as a bridge between PEGylated anionic liposomes and plasmid DNA. At optimized ratios, the components self-assemble into anionic nanocomplexes with a high packaging efficiency of plasmid DNA. Anionic PEGylated nanocomplexes were resistant to aggregation in serum and transfected cells with a far higher degree of receptor-targeted specificity than their homologous non-PEGylated anionic and cationic counterparts. Gadolinium-labeled, anionic nanoparticles, administered directly to the brain by convection-enhanced delivery displayed improved tissue penetration and dispersal as well as more widespread cellular transfection than cationic formulations. Anionic PEGylated nanocomplexes have widespread potential for in vivo gene therapy due to their targeted transfection efficiency and ability to penetrate tissues