Modelling rhizomania in sugar beet

With love and gratitude to my parents, for all their advice and encouragement. Acknowledgements I would like to express my sincere gratitude to Dr. Fowler, for his help and guidance as my supervisor for this dissertation. I would also like to thank Dr. Howison for his support as my supervisor during the earlier part of the year, and Dr. Gilligan and Dr. Truscott for the invaluable discussions. I would like to thank the OCIAM Industrial Fund for funding me this year, and Lincoln College for the delicious food and comfortable accom-modation. My thanks go to Keith Gillow, who has always been helpful with queries about LATEX, and all the sta in the Mathematical Institute and Comput-ing Laboratory. I am very grateful to my parents and brother for their continuing guidanc

Rotational Evolution During Type I X-Ray Bursts

The rotation rates of six weakly-magnetic neutron stars accreting in low-mass X-ray binaries have most likely been measured by Type I X-ray burst observations with RXTE. The nearly coherent oscillations detected during the few seconds of thermonuclear burning are most simply understood as rotational modulation of brightness asymmetries on the neutron star surface. We show that, as suggested by Strohmayer and colleagues, the frequency changes of 1-2 Hz observed during bursts are consistent with angular momentum conservation as the burning shell hydrostatically expands and contracts. We calculate how vertical heat propagation through the radiative outer layers of the atmosphere and convection affect the coherence of the oscillation. We show that the evolution of the rotational profile depends strongly on whether the burning layers are composed of pure helium or mixed hydrogen/helium. Our results help explain the absence (presence) of oscillations from hydrogen-burning (helium-rich) bursts that was found by Muno and collaborators. We investigate angular momentum transport within the burning layers and the recoupling of the burning layers with the star. We show that the Kelvin-Helmholtz instability is quenched by the strong stratification, and that mixing between the burning fuel and underlying ashes by the baroclinic instability does not occur. However, the baroclinic instability may have time to operate within the differentially rotating burning layer, potentially bringing it into rigid rotation.Comment: To appear in The Astrophysical Journal; minor corrections made to tables and figure

Essential and checkpoint functions of budding yeast ATM and ATR during meiotic prophase are facilitated by differential phosphorylation of a meiotic adaptor protein, Hop1

A hallmark of the conserved ATM/ATR signalling is its ability to mediate a wide range of functions utilizing only a limited number of adaptors and effector kinases. During meiosis, Tel1 and Mec1, the budding yeast ATM and ATR, respectively, rely on a meiotic adaptor protein Hop1, a 53BP1/Rad9 functional analog, and its associated kinase Mek1, a CHK2/Rad53-paralog, to mediate multiple functions: control of the formation and repair of programmed meiotic DNA double strand breaks, enforcement of inter-homolog bias, regulation of meiotic progression, and implementation of checkpoint responses. Here, we present evidence that the multi-functionality of the Tel1/Mec1-to-Hop1/Mek1 signalling depends on stepwise activation of Mek1 that is mediated by Tel1/Mec1 phosphorylation of two specific residues within Hop1: phosphorylation at the threonine 318 (T318) ensures the transient basal level Mek1 activation required for viable spore formation during unperturbed meiosis. Phosphorylation at the serine 298 (S298) promotes stable Hop1-Mek1 interaction on chromosomes following the initial phospho-T318 mediated Mek1 recruitment. In the absence of Dmc1, the phospho-S298 also promotes Mek1 hyper-activation necessary for implementing meiotic checkpoint arrest. Taking these observations together, we propose that the Hop1 phospho-T318 and phospho-S298 constitute key components of the Tel1/Mec1- based meiotic recombination surveillance (MRS) network and facilitate effective coupling of meiotic recombination and progression during both unperturbed and challenged meiosis

Refining the shallow slip deficit

Geodetic slip inversions for three major (M_w > 7) strike-slip earthquakes (1992 Landers, 1999 Hector Mine and 2010 El Mayor–Cucapah) show a 15–60 per cent reduction in slip near the surface (depth < 2 km) relative to the slip at deeper depths (4–6 km). This significant difference between surface coseismic slip and slip at depth has been termed the shallow slip deficit (SSD). The large magnitude of this deficit has been an enigma since it cannot be explained by shallow creep during the interseismic period or by triggered slip from nearby earthquakes. One potential explanation for the SSD is that the previous geodetic inversions lack data coverage close to surface rupture such that the shallow portions of the slip models are poorly resolved and generally underestimated. In this study, we improve the static coseismic slip inversion for these three earthquakes, especially at shallow depths, by: (1) including data capturing the near-fault deformation from optical imagery and SAR azimuth offsets; (2) refining the interferometric synthetic aperture radar processing with non-boxcar phase filtering, model-dependent range corrections, more complete phase unwrapping by SNAPHU (Statistical Non-linear Approach for Phase Unwrapping) assuming a maximum discontinuity and an on-fault correlation mask; (3) using more detailed, geologically constrained fault geometries and (4) incorporating additional campaign global positioning system (GPS) data. The refined slip models result in much smaller SSDs of 3–19 per cent. We suspect that the remaining minor SSD for these earthquakes likely reflects a combination of our elastic model's inability to fully account for near-surface deformation, which will render our estimates of shallow slip minima, and potentially small amounts of interseismic fault creep or triggered slip, which could ‘make up’ a small percentages of the coseismic SSD during the interseismic period. Our results indicate that it is imperative that slip inversions include accurate measurements of near-fault surface deformation to reliably constrain spatial patterns of slip during major strike-slip earthquakes

Modelling the impact of vector control on lymphatic filariasis programmes: current approaches and limitations

Vector control is widely considered an important tool for lymphatic filariasis (LF) elimination but is not usually included in programme budgets and has often been secondary to other policy questions in modelling studies. Evidence from the field demonstrates that vector control can have a large impact on programme outcomes and even halt transmission entirely, but implementation is expensive. Models of LF have the potential to inform where and when resources should be focused, but often simplify vector dynamics and focus on capturing human prevalence trends, making them comparatively ill-designed for direct analysis of vector control measures. We review the recent modelling literature and present additional results using a well-established model, highlighting areas of agreement between model predictions and field evidence, and discussing the possible determinants of existing disagreements. We conclude that there are likely to be long-term benefits of vector control, both on accelerating programmes and preventing resurgence. Key words: lymphatic filariasis; vector control; modelling; elimination; resurgence

Seven challenges in modeling vaccine preventable diseasesC

Vaccination has been one of the most successful public health measures since the introduction of basic sanitation. Substantial mortality and morbidity reductions have been achieved via vaccination against many infections, and the list of diseases that are potentially controllable by vaccines is growing steadily. We introduce key challenges for modelling in shaping our understanding and guiding policy decisions related to vaccine preventable diseases

Multiexcitons confined within a sub-excitonic volume: Spectroscopic and dynamical signatures of neutral and charged biexcitons in ultrasmall semiconductor nanocrystals

The use of ultrafast gating techniques allows us to resolve both spectrally and temporally the emission from short-lived neutral and negatively charged biexcitons in ultrasmall (sub-10 nm) CdSe nanocrystals (nanocrystal quantum dots). Because of forced overlap of electronic wave functions and reduced dielectric screening, these states are characterized by giant interaction energies of tens (neutral biexcitons) to hundreds (charged biexcitons) of meV. Both types of biexcitons show extremely short lifetimes (from sub-100 picoseconds to sub-picosecond time scales) that rapidly shorten with decreasing nanocrystal size. These ultrafast relaxation dynamics are explained in terms of highly efficient nonradiative Auger recombination.Comment: 5 pages, 4 figures, to be published in Phys. Rev.

Plasmonic Band-Pass Microfilters for LWIR Absorption Spectroscopy

Absorption spectroscopy in the long wave infrared provides an effective method for identification of various hazardous chemicals. We present a theoretical design for plasmonic band-pass filters that can be used to provide wavelength selectivity for uncooled microbolometer sensors. The microfilters consist of a pair of input reflection gratings that couple light into a plasmonic waveguide with a central resonant waveguide cavity. An output transmission grating on the other side of the structure pulls light out of the waveguide where it is detected by a closely spaced sensor. Fabrication of the filters can be performed using standard photolithography procedures. A spectral bandpass with a full-width at half-maximum (FWHM) of 100 nm can be obtained with a center wavelength spanning the entire 8–12 μm atmospheric transmission window by simple geometric scaling of only the lateral dimensions. This allows the simultaneous fabrication of all the wavelength filters needed for a full spectrometer on a chip

Responsible modelling : unit testing for infectious disease epidemiology

Infectious disease epidemiology is increasingly reliant on large-scale computation and inference. Models have guided health policy for epidemics including COVID-19 and Ebola and endemic diseases including malaria and tuberculosis. Yet a coding bug may bias results, yielding incorrect conclusions and actions causing avoidable harm. We are ethically obliged to make our code as free of error as possible. Unit testing is a coding method to avoid such bugs, but it is rarely used in epidemiology. We demonstrate how unit testing can handle the particular quirks of infectious disease models and aim to increase uptake of this methodology in our field

Is ongoing testosterone required after pubertal induction in Duchenne muscular dystrophy?

Glucocorticoids (GCs) reduce inflammation and preserve muscle function in boys with Duchenne muscular dystrophy (DMD) but cause pubertal delay. Pubertal induction with testosterone is recommended but longer-term outcome is unknown. Objective: To assess hypothalamic–pituitary–gonadal axis, muscle volume and function 5 years after pubertal induction. Methods: A prospective observational follow-up of a clinical study was conducted. 15 GC-treated males with DMD were treated with incremental testosterone for 2 years (end of regimen +2 years) then evaluated at +2.5 years and +5 y ears (final follow-up ~3 years after last injection). Data collected included testicular volume (TV), gonadotrophin, testosterone, inhibin B, muscle function, and limb muscle MRI. Results: Participants were 18.7 years (s.d. 1.6) at the final follow-up and had been on GC for 11.2 years (s.d. 2.2). Testosterone levels were similar at +2.5 years (8.6 nmol /L (s.d. 3.4) and 5 years (11.0 nmol/L (s.d. 6.1). TV increased from 2.8 mL ( s.d. 0.9) at +2 years to 7.1 mL (s.d. 1.8) then 10.6 mL (s.d. 3.5) at +2.5 years and +5.0 years (P < 0.001). Inhibin B levels increased from 55.6 pg/mL (s.d. 47.0) at baseline to 158.2 pg/mL ( s.d. 87.6), P =0.004 at 5 years but remained lower than reference values (mean 305 pg/mL). Muscle contractile bulk decreased. Interpretation: Pubertal induction with testosterone in DMD is associated with HPG axis activation and ongoing increases in inhibin B, TV, and testosterone concentrations. Some patients have normal levels which is promising regarding future fertility. Given the beneficial impact of testosterone on bone health, muscle, and well-being, monitoring testosterone levels in this population and supplementation of sub-optimal levels is important