Applications and practical considerations of polarisation structuring by a Fresnel cone

The polarisation property of light has been known about for hundreds of years. Often its use in technology has been limited to uniform states, however, more recently light with structured polarisation has gained interest. This is largely prompted by availability of spatial light modulators for generation, and increased computation speed to model complex focal fields. My PhD research has extended upon work carried out during a master’s project where we investigated the use of a solid glass cone (so-called Fresnel cone) for generating vector vortex beams. The aim of this thesis is to report on the potential use of a Fresnel cone in microscopy and polarimetry applications, and practical implications discovered. Expanding on the previous work, enhanced fidelity polarisation states are measured and a newly developed Fresnel cone coupling technique is shown, allowing high-efficiency annular vector vortex beam generation. We demonstrate through simulations based on vector diffraction theory that azimuthally polarised light with OAM generated using a Fresnel cone can provide sub-diffraction limited focal spots, below those of more well-known radially polarised light. Practical implications were encountered, prompting investigation into the effects of phase aberrations on resulting focal spots, and experimental measurement of cone surface topology. We find the uniformity of the Fresnel cone shape and apex angle is crucial to the focussing properties. For polarimetry application, full details are provided for a single-shot full-Stokes polarimeter technique and proof-of-principle experiment, where broadband operation is demonstrated. I conclude by summarising the findings of my research and suggest potential future work in this area

Thermal and Visual Imaging to Assist with Juvenile Idiopathic Arthritis Examination of the Knees

Juvenile idiopathic arthritis (JIA) causes inflammation of the joints, and it is frequently associated with their pain and stiffness. Its timely diagnosis is important to avoid its progressive damage to the bones and cartilage. Increases in the joint’s temperature and redness could be indicators of active JIA, hence their accurate quantification could assist with diagnosis. Thermal and visual images of the knees in 20 JIA participants (age: mean = 11.2 years, standard deviation = 2.3 years) were studied. The median temperature of knees with active inflammation was 3.198% higher than that of inactive knees. This difference, examined by a Wilcoxon signed-rank test, was statistically significant (p = 0.0078). In six out of the eight participants who had one active inflamed knee, thermal imaging identified the corresponding knee as warmer. In 16 out of 20 participants, the knee identified as warmer by thermal imaging was also identified as having a greater colour change by visual imaging as compared to their respective reference regions. The devised methods could accurately quantify the colour and temperature of the knees. It was concluded that thermal and visual imaging methods can be valuable in examining JIA. Further studies involving a larger number of participants and more detailed explorations would be needed prior to clinical application

Accretion of low angular momentum material onto black holes: 2D magnetohydrodynamical case

We report on the second phase of our study of slightly rotating accretion flows onto black holes. We consider magnetohydrodynamical (MHD) accretion flows with a spherically symmetric density distribution at the outer boundary, but with spherical symmetry broken by the introduction of a small, latitude-dependent angular momentum and a weak radial magnetic field. We study accretion flows by means of numerical 2D, axisymmetric, MHD simulations with and without resistive heating. Our main result is that the properties of the accretion flow depend mostly on an equatorial accretion torus which is made of the material that has too much angular momentum to be accreted directly. The torus accretes, however, because of the transport of angular momentum due to the magnetorotational instability (MRI). Initially, accretion is dominated by the polar funnel, as in the hydrodynamic inviscid case, where material has zero or very low angular momentum. At the later phase of the evolution, the torus thickens towards the poles and develops a corona or an outflow or both. Consequently, the mass accretion through the funnel is stopped. The accretion of rotating gas through the torus is significantly reduced compared to the accretion of non-rotating gas (i.e., the Bondi rate). It is also much smaller than the accretion rate in the inviscid, weakly rotating case.Our results do not change if we switch on or off resistive heating. Overall our simulations are very similar to those presented by Stone, Pringle, Hawley and Balbus despite different initial and outer boundary conditions. Thus, we confirm that MRI is very robust and controls the nature of radiatively inefficient accretion flows.Comment: submitted in Ap

Multivalent Adhesion Molecule 7 Clusters Act as Signaling Platform for Host Cellular GTPase Activation and Facilitate Epithelial Barrier Dysfunction

Vibrio parahaemolyticus is an emerging bacterial pathogen which colonizes the gastrointestinal tract and can cause severe enteritis and bacteraemia. During infection, V. parahaemolyticus primarily attaches to the small intestine, where it causes extensive tissue damage and compromises epithelial barrier integrity. We have previously described that Multivalent Adhesion Molecule (MAM) 7 contributes to initial attachment of V. parahaemolyticus to epithelial cells. Here we show that the bacterial adhesin, through multivalent interactions between surface-induced adhesin clusters and phosphatidic acid lipids in the host cell membrane, induces activation of the small GTPase RhoA and actin rearrangements in host cells. In infection studies with V. parahaemolyticus we further demonstrate that adhesin-triggered activation of the ROCK/LIMK signaling axis is sufficient to redistribute tight junction proteins, leading to a loss of epithelial barrier function. Taken together, these findings show an unprecedented mechanism by which an adhesin acts as assembly platform for a host cellular signaling pathway, which ultimately facilitates breaching of the epithelial barrier by a bacterial pathogen. © 2014 Lim et al

On MHD jet production in the collapsing and rotating envelope

We present results from axisymmetric, time-dependent hydrodynamical (HD) and magnetohydrodynamical (MHD) simulations of a gaseous envelope collapsing onto a black hole (BH). We consider gas with so small angular momentum that after an initial transient, the flow in the HD case, accretes directly onto a BH without forming a rotationally support torus. However, in the MHD case even with a very weak initial magnetic field, the flow settles into a configuration with four components: (i) an equatorial inflow, (ii) a bipolar outflow, (iii) polar funnel outflow, and (iv) polar funnel inflow. We focus our analysis on the second flow component of the MHD flow which represents a simple yet robust example of a well-organized inflow/outflow solution to the problem of MHD jet formation. The jet is heavy, highly magnetized, and driven by magnetic and centrifugal forces. A significant fraction of the total energy in the jet is carried out by a large scale magnetic field. We review previous simulations, where specific angular momentum was higher than that assumed here, and conclude that our bipolar outflow develops for a wide range of the properties of the flow near the equator and near the poles. Future work on such a simple inflow/outflow solution will help to pinpoint the key elements of real jets/outflows as well as help to interpret much more complex simulations aimed at studying jet formation and collapse of magnetized envelopes.Comment: to appear in ApJ, revised version with new HD result

Zip4/Spo22 Is Required for Class I CO Formation but Not for Synapsis Completion in Arabidopsis thaliana

In budding yeast meiosis, the formation of class I interference-sensitive crossovers requires the ZMM proteins. These ZMM proteins are essential in forming a mature synaptonemal complex, and a subset of these (Zip2, Zip3, and Zip4) has been proposed to compose the core of synapsis initiation complexes (SICs). Zip4/Spo22 functions with Zip2 to promote polymerization of Zip1 along chromosomes, making it a crucial SIC component. In higher eukaryotes, synapsis and recombination have often been correlated, but it is totally unknown how these two processes are linked. In this study, we present the characterization of a higher eukaryote SIC component homologue: Arabidopsis AtZIP4. We show that mutations in AtZIP4 belong to the same epistasis group as Atmsh4 and eliminate approximately 85% of crossovers (COs). Furthermore, genetic analyses on two adjacent intervals of Chromosome I established that the remaining COs in Atzip4 do not show interference. Lastly, immunolocalization studies showed that polymerization of the central element of the synaptonemal complex is not affected in Atzip4 background, even if it may proceed from fewer sites compared to wild type. These results reveal that Zip4 function in class I CO formation is conserved from budding yeast to Arabidopsis. On the other hand, and contrary to the situation in yeast, mutation in AtZIP4 does not prevent synapsis, showing that both aspects of the Zip4 function (i.e., class I CO maturation and synapsis) can be uncoupled

Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale

Background: Batch effects in DNA methylation microarray experiments can lead to spurious results if not properly handled during the plating of samples. Methods: Two pilot studies examining the association of DNA methylation patterns across the genome with obesity in Samoan men were investigated for chip- and row-specific batch effects. For each study, the DNA of 46 obese men and 46 lean men were assayed using Illumina's Infinium HumanMethylation450 BeadChip. In the first study (Sample One), samples from obese and lean subjects were examined on separate chips. In the second study (Sample Two), the samples were balanced on the chips by lean/obese status, age group, and census region. We used methylumi, watermelon, and limma R packages, as well as ComBat, to analyze the data. Principal component analysis and linear regression were respectively employed to identify the top principal components and to test for their association with the batches and lean/obese status. To identify differentially methylated positions (DMPs) between obese and lean males at each locus, we used a moderated t-test.Results: Chip effects were effectively removed from Sample Two but not Sample One. In addition, dramatic differences were observed between the two sets of DMP results. After removing'' batch effects with ComBat, Sample One had 94,191 probes differentially methylated at a q-value threshold of 0.05 while Sample Two had zero differentially methylated probes. The disparate results from Sample One and Sample Two likely arise due to the confounding of lean/obese status with chip and row batch effects.Conclusion: Even the best possible statistical adjustments for batch effects may not completely remove them. Proper study design is vital for guarding against spurious findings due to such effects